bioRxiv Channel: University of Hong Kong https://biorxiv.org This feed contains articles for bioRxiv Channel "University of Hong Kong" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ From peer-reviewed to peer-reproduced: a role for data standards, models and computational workflows in scholarly publishing ]]> https://biorxiv.org/content/10.1101/011973v1?rss=1 Alejandra Gonzalez-Beltran Peter Li Jun Zhao Maria Susana Avila-Garcia Marco Roos Mark Thompson Eelke van der Horst Rajaram Kaliyaperumal Ruibang Luo Tin-Lap Lee Tak-wah Lam Scott C. Edmunds Susanna-Assunta Sansone Philippe Rocca-Serra 2014-12-08 doi:10.1101/011973 Cold Spring Harbor Laboratory Press 2014-12-08 <![CDATA[ Exploring functional variation affecting ceRNA regulation in humans ]]> https://biorxiv.org/content/10.1101/016865v1?rss=1 Mulin Jun Li Jiexing Wu Peng Jiang Wei Li Yun Zhu Daniel Fernandez Russell J. H. Ryan Yiwen Chen Junwen Wang Jun S. Liu X. Shirley Liu 2015-03-22 doi:10.1101/016865 Cold Spring Harbor Laboratory Press 2015-03-22 <![CDATA[ Polygenic scores using summary statistics via penalized regression ]]> https://biorxiv.org/content/10.1101/058214v1?rss=1 Timothy Mak Robert Milan Porsch Shing Wan Choi Xueya Zhou Pak Chung Sham 2016-06-10 doi:10.1101/058214 Cold Spring Harbor Laboratory Press 2016-06-10 <![CDATA[ Sacral agenesis: A whole exome sequencing and copy number study ]]> https://biorxiv.org/content/10.1101/058578v1?rss=1 Robert Milan Porsch Elisa Merello Patrizia De Marco Guo Cheng Laura Rodriguez Paul Tam Stacey Cherny Pak Sham Valeria Carpa Maria-Mercè Garcia-Barcelo Desmond Campbell 2016-06-13 doi:10.1101/058578 Cold Spring Harbor Laboratory Press 2016-06-13 <![CDATA[ An RNA editing/binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer ]]> https://biorxiv.org/content/10.1101/062778v1?rss=1 Lihua Qi Yangyang Song Tim Hon Man Chan Henry Yang Chi Ho Lin Daryl Jin Tai Tay HuiQi Hong Jaymie Siqi Lin Vanessa Hui En Ng Julien Jean Pierre Maury Daniel G Tenen Leilei (Polly) Chen 2016-07-08 doi:10.1101/062778 Cold Spring Harbor Laboratory Press 2016-07-08 <![CDATA[ Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model ]]> https://biorxiv.org/content/10.1101/073239v1?rss=1 0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained by only non-membrane proteins, our deep learning method works very well on membrane protein contact prediction. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 4 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one {beta} protein of 182 residues, one +{beta} protein of 125 residues, one protein of 140 residues and one protein of 217 residues.nnAvailability: http://raptorx.uchicago.edu/ContactMap/nnAuthor SummaryProtein contact prediction from sequence alone is an important problem. Recently exciting progress has been made on this problem due to the development of direct evolutionary coupling analysis (DCA). However, DCA is effective on only some proteins with a very large number (>1000) of sequence homologs. To further improve contact prediction, we borrow ideas from the latest breakthrough of deep learning, a powerful machine learning technique that has recently revolutionized object recognition, speech recognition and the GO game. We have developed a new deep learning method that predicts contacts by integrating both sequence conservation and co-variation information through an ultra-deep neural network, which can model very complex relationship between sequence and contact map as well as high-order correlation among residues.nnOur test results suggest that deep learning can revolutionize protein contact prediction. Tested on 398 membrane proteins, the L/10 long-range accuracy obtained by our method is 77.6% while that by the state-of-the-art methods CCMpred and MetaPSICOV is 51.8% and 61.2%, respectively. Ab initio folding using our predicted contacts as restraints can generate much better 3D structural models than the other contact prediction methods. In particular, without using any force fields our predicted contacts yield correct folds for 203 of the 579 test proteins, while MetaPSICOV- and CCMpred can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have much better quality than template-based models (TBM) built from the training proteins. For example, our contact-assisted models have TMscore>0.5 for 208 of the 398 membrane proteins while TBMs have TMscore >0.5 for only 10 of them. Even without using any membrane proteins to train our deep learning models, our method still performs very well on membrane protein contact prediction. Recent blind test of our method in CAMEO shows that our method successfully folded 4 targets with a new fold and only 0.3L-2.3L effective sequence homologs. ]]> Sheng Wang Siqi Sun Zhen Li Renyu Zhang Jinbo Xu 2016-09-03 doi:10.1101/073239 Cold Spring Harbor Laboratory Press 2016-09-03 <![CDATA[ Selectivity matters: rules of thumb for management of plate-sized, sex-changing fish in the live reef food fish trade ]]> https://biorxiv.org/content/10.1101/098624v1?rss=1 Kindsvater, H. Reynolds, J. Sadovy de Mitcheson, Y. Mangel, M. 2017-01-05 doi:10.1101/098624 Cold Spring Harbor Laboratory Press 2017-01-05 <![CDATA[ The role of glycaemic and lipid risk factors in mediating the effect of BMI on coronary heart disease: A two-step, two-sample Mendelian randomization study ]]> https://biorxiv.org/content/10.1101/118133v1?rss=1 XU, L. Borges, M. C. Hemani, G. Lawlor, D. A. 2017-03-19 doi:10.1101/118133 Cold Spring Harbor Laboratory Press 2017-03-19 <![CDATA[ RETA: An R Package For Whole Exome And Targeted Region Sequencing Data Analysis ]]> https://biorxiv.org/content/10.1101/121384v1?rss=1 Guo, M. Yang, J. Lau, Y.-L. Yang, W. 2017-03-28 doi:10.1101/121384 Cold Spring Harbor Laboratory Press 2017-03-28 <![CDATA[ NFATc2 enhances tumor-initiating phenotypes through the NFATc2/SOX2/ALDH axis in lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/131987v1?rss=1 XIAO, Z.-J. Liu, J. Wang, S.-Q. Zhu, Y. Gao, X.-Y. Tin, V. P.-C. Qin, J. Wang, J.-W. Wong, M. P. 2017-04-28 doi:10.1101/131987 Cold Spring Harbor Laboratory Press 2017-04-28 <![CDATA[ Demoralization among cancer patients in mainland China: validity of the Demoralization Scale (DS) ]]> https://biorxiv.org/content/10.1101/144865v1?rss=1 30, low[less double equals]30) cross-tabulated against PHQ-9 score (mood) scores revealed 47% of patients exceeded demoralization cut-off, 60% of whom were not depressed. Using mean value{+/-}SD indicated demoralization cutoffs at <17.4 (low), 17.4-43.4 (medium) and >43.4 (high). Overall 71% met criteria for medium demoralization, and 15% for high demoralization. Sixty percent of all medium demoralization patients were not depressed, but only 5% of high demoralization patients were not depressed. The conclusion is that the Mainland Chinese Demoralization Scale is useful for detecting mild-to-moderate demoralization in cancer patients but at higher scores has poor specificity against depression. ]]> Deng, L. Pang, Y. He, Y. Zhang, Y. Fielding, R. Tang, L. 2017-06-08 doi:10.1101/144865 Cold Spring Harbor Laboratory Press 2017-06-08 <![CDATA[ GEOracle: Mining perturbation experiments using free text metadata in Gene Expression Omnibus ]]> https://biorxiv.org/content/10.1101/150896v1?rss=1 Djordjevic, D. Chen, Y. X. Kwan, S. L. S. Ling, R. W. K. Qian, G. Woo, C. Y. Y. Ellis, S. J. Ho, J. W. K. 2017-06-16 doi:10.1101/150896 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ Extracellular DNA promotes efficient extracellular electron transfer by pyocyanin in Pseudomonas aeruginosa biofilms ]]> https://biorxiv.org/content/10.1101/2019.12.12.872085v1?rss=1 Saunders, S. H. Tse, E. C. M. Yates, M. D. Jimenez Otero, F. Trammell, S. A. Stemp, E. D. A. Barton, J. K. Tender, L. M. Newman, D. K. 2019-12-12 doi:10.1101/2019.12.12.872085 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ In-depth 15 H7N9 Human Serum Proteomics Profiling Study ]]> https://biorxiv.org/content/10.1101/2020.01.06.896829v1?rss=1 Yang, Z. Guan, W. Zhou, S. Chen, L. Mok, C. K. P. Huang, J. Wu, S. Zhou, H. Liu, Y. Peiris, J. S. M. Liu, X. Li, Y. Zhong, N. 2020-01-07 doi:10.1101/2020.01.06.896829 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ The dynamic surface proteomes of allergenic fungal conidia ]]> https://biorxiv.org/content/10.1101/2020.01.10.902015v1?rss=1 Blango, M. G. Pschibul, A. Rivieccio, F. Krueger, T. Rafiq, M. Jia, L.-J. Zheng, T. Goldmann, M. Voltersen, V. Li, J. Panagiotou, G. Kniemeyer, O. Brakhage, A. A. 2020-01-11 doi:10.1101/2020.01.10.902015 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Activation of Src-family kinases orchestrate secretion of flaviviruses by targeting mature progeny virions to secretory autophagosomes ]]> https://biorxiv.org/content/10.1101/2020.01.12.903062v1?rss=1 Li, M. Y. Naik, T. S. Siu, L. Y. L. Acuto, O. Spooner, E. Wang, P. Yang, X. Lin, Y. Bruzzone, R. Ashour, J. Sanyal, S. 2020-01-14 doi:10.1101/2020.01.12.903062 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Alteration of fecal microbial compositions and bacterial taxa in female osteoporotic patients ]]> https://biorxiv.org/content/10.1101/2020.01.21.914903v1?rss=1 Zhu, C. Xu, A. Wang, K. Pan, Y. Liu, J. Pan, Y. Fan, Y. Jin, L. Liu, Y. Zhang, Z. Gan, Y. Tang, W. Li, J. Xionga, Z. Xu, G. Lin, X. Zhang, Y. Cai, J. Yang, M. Zhang, L. Xiao, L. 2020-01-23 doi:10.1101/2020.01.21.914903 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak ]]> https://biorxiv.org/content/10.1101/2020.01.23.916395v1?rss=1 Zhao, S. Ran, J. MUSA, S. S. Yang, G. Lou, Y. Gao, D. Yang, L. He, D. 2020-01-24 doi:10.1101/2020.01.23.916395 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Molecular and cellular heterogeneity of gastric cancer explained by methylation-driven key regulators ]]> https://biorxiv.org/content/10.1101/2020.01.27.920744v1?rss=1 Yoo, S. Chen, Q. Wang, L. Wang, W. Chakravarthy, A. Busuttil, R. A. Boussioutas, A. Liu, D. She, J. Fenton, T. R. Zhang, J. Fan, X. Leung, S. y. Zhu, J. 2020-01-28 doi:10.1101/2020.01.27.920744 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Breaking down of the healthcare system: Mathematical modelling for controlling the novel coronavirus (2019-nCoV) outbreak in Wuhan, China ]]> https://biorxiv.org/content/10.1101/2020.01.27.922443v1?rss=1 Ming, W.-k. Huang, J. Zhang, C. J. P. 2020-01-28 doi:10.1101/2020.01.27.922443 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Altered Temporal Variability of Local and Large-scale Resting-state Brain Functional Connectivity Patterns in Schizophrenia and Bipolar Disorder ]]> https://biorxiv.org/content/10.1101/2020.02.04.934638v1?rss=1 Long, Y. Liu, Z. Chan, C. K.-y. Wu, G. Xue, Z. Pan, Y. Chen, X. Huang, X. Pu, W. 2020-02-05 doi:10.1101/2020.02.04.934638 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Trait-similarity and trait-hierarchy jointly determine co-occurrences of resident and invasive ant species ]]> https://biorxiv.org/content/10.1101/2020.02.05.935858v1?rss=1 Wong, M. K. L. Tsang, T. P. N. Lewis, O. T. Guenard, B. 2020-02-07 doi:10.1101/2020.02.05.935858 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ F-box protein MEC-15 promotes microtubule stability and neurite growth by antagonizing the HSP90 chaperone network in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2020.02.13.944967v1?rss=1 Zheng, C. Atlas, E. Lee, H. M. T. Jao, S. L. J. Nguyen, K. C. Q. Hall, D. H. Chalfie, M. 2020-02-13 doi:10.1101/2020.02.13.944967 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China ]]> https://biorxiv.org/content/10.1101/2020.02.13.945485v1?rss=1 Lam, T. T.-Y. Shum, M. H.-H. Zhu, H.-C. Tong, Y.-G. Ni, X.-B. Liao, Y.-S. Wei, W. Cheung, W. Y.-M. Li, W.-J. Li, L.-F. Leung, G. M. Holmes, E. C. Hu, Y.-L. Guan, Y. 2020-02-18 doi:10.1101/2020.02.13.945485 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Multivariate Analyses of Codon Usage in 2019 Novel Coronavirus on the Genomic Landscape of Betacoronavirus ]]> https://biorxiv.org/content/10.1101/2020.02.15.950568v1?rss=1 Gu, H. Chu, D. K. W. Peiris, J. S. M. Poon, L. L. M. 2020-02-20 doi:10.1101/2020.02.15.950568 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Estimating indirect parental genetic effects on offspring phenotypes using virtual parental genotypes derived from sibling and half sibling pairs ]]> https://biorxiv.org/content/10.1101/2020.02.21.959114v1?rss=1 Hwang, L.-D. Tubbs, J. D. Luong, J. Moen, G.-H. Sham, P. C. Cuellar Partida, G. Evans, D. M. 2020-02-25 doi:10.1101/2020.02.21.959114 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Probing SWATH-MS as a tool for proteome level quantification in a non-model fish ]]> https://biorxiv.org/content/10.1101/2020.02.23.946913v1?rss=1 Monroe, A. A. Zhang, H. Schunter, C. Ravasi, T. 2020-02-23 doi:10.1101/2020.02.23.946913 Cold Spring Harbor Laboratory Press 2020-02-23 <![CDATA[ Synthesis of diagnostic quality cancer pathology images ]]> https://biorxiv.org/content/10.1101/2020.02.24.963553v1?rss=1 Levine, A. B. Peng, J. Farnell, D. Nursey, M. Wang, Y. Naso, J. R. Ren, H. Farahani, H. Chen, C. Chiu, D. Talhouk, A. Sheffield, B. Riazy, M. Ip, P. P. Parra-Herran, C. Mills, A. Singh, N. Tessier-Cloutier, B. Salisbury, T. Lee, J. Salcudean, T. Jones, S. J. M. Huntsman, D. G. Gilks, C. B. Yip, S. Bashashati, A. 2020-02-26 doi:10.1101/2020.02.24.963553 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Emotional contagion of pain across different social cues shares common and process-specific neural representations ]]> https://biorxiv.org/content/10.1101/2020.02.24.963595v1?rss=1 Zhou, F. Li, J. Zhao, W. Xu, L. Zheng, X. Fu, M. Yao, S. Kendrick, K. M. Wager, T. D. Becker, B. 2020-02-25 doi:10.1101/2020.02.24.963595 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Genome-centric portrait of the microbes' cellulolytic competency ]]> https://biorxiv.org/content/10.1101/2020.03.09.984823v1?rss=1 Wang, Y. Li, L. Xia, Y. Ju, F. Zhang, T. 2020-03-11 doi:10.1101/2020.03.09.984823 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV ]]> https://biorxiv.org/content/10.1101/2020.03.13.991570v1?rss=1 Yuan, M. Wu, N. C. Zhu, X. Lee, C.-C. D. So, R. T. Y. Lv, H. Mok, C. K. P. Wilson, I. A. 2020-03-14 doi:10.1101/2020.03.13.991570 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Cross-reactive antibody response between SARS-CoV-2 and SARS-CoV infections ]]> https://biorxiv.org/content/10.1101/2020.03.15.993097v1?rss=1 Lv, H. Wu, N. C. Tsang, O. T.-Y. Yuan, M. Perera, R. A. P. M. Leung, W. S. So, R. T. Y. Chan, J. M. C. Yip, G. K. Chik, T. S. H. Wang, Y. Choi, C. Y. C. Lin, Y. Ng, W. W. Zhao, J. Poon, L. L. M. Peiris, J. S. M. Wilson, I. A. Mok, C. K. P. 2020-03-17 doi:10.1101/2020.03.15.993097 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ Molecular Typing of Human Respiratory Adenoviruses with Universal PCR and Sequencing Primers for Three Major Capsid Genes: Penton base, Hexon, and Fiber ]]> https://biorxiv.org/content/10.1101/2020.03.17.995373v1?rss=1 Zhang, J. Sridhar, S. Lau, S. K. P. Liu, J. Ou, J. Yan, Y. Zhao, S. Lan, W. Guan, W. Wu, J. Woo, P. C. Y. Seto, D. Zhang, Q. 2020-03-19 doi:10.1101/2020.03.17.995373 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ Siderophores provoke extracellular superoxide production by carbon-starving Arthrobacter strains when carbon sources recover ]]> https://biorxiv.org/content/10.1101/2020.03.20.000083v1?rss=1 Ning, X. Liang, J. Men, Y. Chang, Y. Bai, Y. Liu, H. Wang, A. Zhang, T. Qu, J. 2020-03-21 doi:10.1101/2020.03.20.000083 Cold Spring Harbor Laboratory Press 2020-03-21 <![CDATA[ A potent antibiofilm agent inhibits and eradicates mono- and multi-species biofilms ]]> https://biorxiv.org/content/10.1101/2020.03.25.009126v1?rss=1 LONG, L. wang, r. Chiang, H. Y. li, y. chen, f. Qian, P.-Y. 2020-03-27 doi:10.1101/2020.03.25.009126 Cold Spring Harbor Laboratory Press 2020-03-27 <![CDATA[ Revealing cellular heterogeneity and in vitro differentiation trajectory of cultured human endometrial mesenchymal-like stem cells using single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2020.04.03.004523v1?rss=1 CAO, D. Chan, R. W. S. Ng, E. H. Y. Danielsson, K. G. Yeung, W. S. B. 2020-04-04 doi:10.1101/2020.04.03.004523 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Whole-genome analysis of noncoding genetic variations identifies multigranular regulatory element perturbations associated with Hirschsprung disease ]]> https://biorxiv.org/content/10.1101/2020.04.08.032045v1?rss=1 Fu, A. X. Lui, K. N.-C. Tang, C. S.-M. Ng, R. K. Lai, F. P.-L. Lau, S.-T. Li, Z. Gracia-Barcelo, M.-M. Sham, P. Tam, P. K.-H. Ngan, E. S.-W. Yip, K. Y. 2020-04-09 doi:10.1101/2020.04.08.032045 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ RbAp46/48LIN-53 and HAT-1 are required for initial CENP-AHCP-3 deposition and de novo centromere formation in Caenorhabditis elegans embryos ]]> https://biorxiv.org/content/10.1101/2020.04.12.019257v1?rss=1 Lin, Z. Yuen, K. W. Y. 2020-04-13 doi:10.1101/2020.04.12.019257 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity that may underly population disparities in this disease ]]> https://biorxiv.org/content/10.1101/2020.04.12.037622v1?rss=1 Wang, Y.-F. Zhang, Y. Lin, Z. Zhang, H. Wang, T.-Y. Cao, Y. Morris, D. L. Sheng, Y. Yin, X. Zhong, S.-L. Gu, X. Yao, L. He, J. Wu, Q. Shen, J. J. Yang, J. Lam, T.-H. Lin, J.-H. Mai, Z.-M. Guo, M. Tang, Y. Chen, Y. Song, Q. Ban, B. Mok, C. C. Cui, Y. Lu, L. Shen, N. Sham, P. C. Lau, C. S. Smith, D. K. Vyse, T. J. Zhang, X. Lau, Y. L. Yang, W. 2020-04-12 doi:10.1101/2020.04.12.037622 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ DNA Sequence Preference for De Novo Centromere Formation on a Caenorhabditis elegans Artificial Chromosome ]]> https://biorxiv.org/content/10.1101/2020.04.12.037994v1?rss=1 Lin, Z. Yuen, K. W. Y. 2020-04-13 doi:10.1101/2020.04.12.037994 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals ]]> https://biorxiv.org/content/10.1101/2020.04.16.044016v1?rss=1 10 years, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we profiled a library of known drugs encompassing approximately 12,000 clinical-stage or FDA-approved small molecules. Here, we report the identification of 30 known drugs that inhibit viral replication. Of these, six were characterized for cellular dose-activity relationships, and showed effective concentrations likely to be commensurate with therapeutic doses in patients. These include the PIKfyve kinase inhibitor Apilimod, cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825, and ONO 5334, and the CCR1 antagonist MLN-3897. Since many of these molecules have advanced into the clinic, the known pharmacological and human safety profiles of these compounds will accelerate their preclinical and clinical evaluation for COVID-19 treatment. ]]> Riva, L. Yuan, S. Yin, X. Martin-Sancho, L. Matsunaga, N. Burgstaller, S. Pache, L. De Jesus, P. Hull, M. V. Chang, M. Chan, J. F. W. Cao, J. Kwok-Man Poon, V. Herbert, K. Nguyen, T.-T. Pu, Y. Nguyen, C. Rubanov, A. Martinez-Sobrido, L. Lui, W.-C. Miorin, L. White, K. Johnson, J. R. Benner, C. Sun, R. Schultz, P. Su, A. I. Garcia-Sastre, A. Chatterjee, A. Yuen, K.-Y. Chanda, S. 2020-04-17 doi:10.1101/2020.04.16.044016 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Powered flight potential approached by wide range of close avian relatives but achieved selectively ]]> https://biorxiv.org/content/10.1101/2020.04.17.046169v1?rss=1 Pei, R. Pittman, M. Goloboff, P. A. Dececchi, T. A. Habib, M. B. Kaye, T. G. Larsson, H. C. Norell, M. A. Brusatte, S. L. Xu, X. 2020-04-18 doi:10.1101/2020.04.17.046169 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Single-cell transcriptomic analysis identifies neocortical developmental differences between human and mouse ]]> https://biorxiv.org/content/10.1101/2020.04.23.056390v1?rss=1 Zhou, Z. Wang, S. Zhang, D. Jiang, X. Li, J. Gu, Y. Sun, H. 2020-04-25 doi:10.1101/2020.04.23.056390 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Mapping the Immunodominance Landscape of SARS-CoV-2 Spike Protein for the Design of Vaccines against COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.04.23.056853v1?rss=1 Huang, J.-D. Zhang, B.-z. Hu, Y.-f. 2020-04-24 doi:10.1101/2020.04.23.056853 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ TRPM7 kinase-mediated immunomodulation in macrophage plays a central role in magnesium ion-induced bone regeneration ]]> https://biorxiv.org/content/10.1101/2020.04.24.059881v1?rss=1 Qiao, W. Wong, K. H. M. Shen, J. Wang, W. Wu, J. Li, J. Lin, Z. Chen, Z. Matinlinna, J. P. Zheng, Y. Wu, S. Liu, X. Lai, K. P. Chen, Z. Lam, Y. W. Cheung, K. M. C. Yeung, K. W. K. 2020-04-25 doi:10.1101/2020.04.24.059881 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions ]]> https://biorxiv.org/content/10.1101/2020.04.24.060574v1?rss=1 Soares Souza, G. B. Amaral, D. Batista, D. Torres, A. Q. Serra, A. C. S. Uliano-Silva, M. Leomil, L. Reis, A. C. Matos, E. M. Calderon, E. Yu, V. Dondero, F. Sousa, S. M. Baker, D. Romão-Dumaresq, A. S. REBELO, M. D. F. 2020-04-25 doi:10.1101/2020.04.24.060574 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Role of 1'-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit both Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication ]]> https://biorxiv.org/content/10.1101/2020.04.27.063859v1?rss=1 Zhang, L. Zhang, D. Yuan, C. Wang, X. Li, Y. Jia, X. Gao, X. Yen, H.-L. Cheung, P. Huang, X. 2020-04-27 doi:10.1101/2020.04.27.063859 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Dropout in Neural Networks Simulates theParadoxical Effects of Deep Brain Stimulation onMemory ]]> https://biorxiv.org/content/10.1101/2020.05.01.073486v1?rss=1 Tan, S. Z. K. Du, R. Perucho, J. A. U. Chopra, S. S. Vardhanabhut, V. Lim, L. W. 2020-05-03 doi:10.1101/2020.05.01.073486 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causing Streptococcus pyogenes ]]> https://biorxiv.org/content/10.1101/2020.05.17.095000v1?rss=1 Brouwer, S. Barnett, T. C. Ly, D. Kasper, K. J. De Oliveira, D. M. Rivera-Hernandez, T. Cork, A. J. McIntyre, L. Jespersen, M. G. Richter, J. Schulz, B. L. Dougan, G. Nizet, V. Yuen, K.-Y. You, Y. McCormick, J. K. Sanderson-Smith, M. L. Davies, M. R. Walker, M. J. 2020-05-17 doi:10.1101/2020.05.17.095000 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Enantiomers of Chloroquine and Hydroxychloroquine Exhibit Different Activities Against SARS-CoV-2 in vitro, Evidencing S-Hydroxychloroquine as a Potentially Superior Drug for COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.05.26.114033v1?rss=1 Li, G. Sun, J. Li, Y. Shi, Y. Zhao, J. Zhang, T. Y. Zhang, X. 2020-05-27 doi:10.1101/2020.05.26.114033 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ NON-AVIAN DINOSAUR EGGSHELL CALCITE CONTAINS ANCIENT, ENDOGENOUS AMINO ACIDS ]]> https://biorxiv.org/content/10.1101/2020.06.02.129999v1?rss=1 Saitta, E. T. Vinther, J. Crisp, M. K. Abbott, G. D. Kaye, T. G. Pittman, M. Bull, I. Fletcher, I. Chen, X. Collins, M. J. Sakalauskaite, J. Mackie, M. Dal Bello, F. Dickinson, M. R. Stevenson, M. A. Donohoe, P. Heck, P. R. Demarchi, B. Penkman, K. E. H. 2020-06-03 doi:10.1101/2020.06.02.129999 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Quantitative longitudinal predictions of Alzheimer's disease by multi-modal predictive learning ]]> https://biorxiv.org/content/10.1101/2020.06.04.133645v1?rss=1 Prakash, M. Abdelaziz, M. Zhang, L. Strange, B. A. Tohka, J. 2020-06-05 doi:10.1101/2020.06.04.133645 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Scaling of gene transcriptional gradients with brain size across mouse development ]]> https://biorxiv.org/content/10.1101/2020.06.04.135525v1?rss=1 Lau, H. Y. G. Fulcher, B. D. Fornito, A. 2020-06-05 doi:10.1101/2020.06.04.135525 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Impact of trimethoprim on the river microbiome and antimicrobial resistance. ]]> https://biorxiv.org/content/10.1101/2020.06.05.133348v1?rss=1 Delaney, J. Raguideau, S. Holden, J. Zhang, L. Tipper, H. Hill, G. Klumper, U. Zhang, T. James, R. S. Travis, E. R. Bowes, M. J. Hawkey, P. M. Lindstrom, H. S. Tang, C. Gaze, W. H. Mead, A. Quince, C. R. Singer, A. C. Wellington, E. M. 2020-06-08 doi:10.1101/2020.06.05.133348 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Potent Neutralizing Monoclonal Antibodies Directed to Multiple Epitopes on the SARS-CoV-2 Spike ]]> https://biorxiv.org/content/10.1101/2020.06.17.153486v1?rss=1 Ho, D. D. Lihong, L. Wang, P. Nair, M. S. Jian, Y. Huang, Y. Rapp, M. A. Wang, Q. Luo, Y. Sahi, V. Figueroa, A. Guo, X. V. Cerutti, G. Bimela, J. Gorman, J. Zhou, T. Kwong, P. D. G. Sodroski, J. G. Yin, M. T. Sheng, Z. Shapiro, L. 2020-06-18 doi:10.1101/2020.06.17.153486 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases ]]> https://biorxiv.org/content/10.1101/2020.07.04.186619v1?rss=1 Jiang, L. Jiang, H. Dai, S. Chen, Y. Song, Y.-Q. Tang, C. Wang, B. Garcia-Barcelo, M.-M. Tam, P. Cherny, S. Sham, P. C. Li, M. 2020-07-04 doi:10.1101/2020.07.04.186619 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Improving FnCas12a genome editing by exonuclease fusion ]]> https://biorxiv.org/content/10.1101/2020.07.07.191130v1?rss=1 Yongqiang Wu Qichen Yuan Yufeng Zhu Xiang Gao Jiabao Song Ziru Yin 2020-07-08 doi:10.1101/2020.07.07.191130 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2020.07.09.194670v1?rss=1 Fuqiang Ma Chaogu Zheng 2020-07-10 doi:10.1101/2020.07.09.194670 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ The spatial proteome of the human intervertebral disc reveals architectural changes in health, ageing and degeneration ]]> https://biorxiv.org/content/10.1101/2020.07.11.192948v1?rss=1 Vivian Tam Peikai Chen Anita Yee Nestor Solis Theo Klein Mateusz Kudelko Rakesh Sharma Wilson CW Chan Christopher M Overall Lisbet Haglund Pak C Sham Kathryn SE Cheah Danny Chan 2020-07-12 doi:10.1101/2020.07.11.192948 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ High neutralizing potency of swine glyco-humanized polyclonal antibodies against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.07.25.217158v1?rss=1 Vanhove, B. Duvaux, O. Rousse, J. Royer, P.-J. Evanno, G. Ciron, C. Lheriteau, E. Vacher, L. Gervois, N. Oger, R. Jacques, Y. Salama, A. Duchi, R. Perota, A. Delahaut, P. Ledure, M. Paulus, M. So, R. Mok, C. K. P. Bruzzone, R. Bouillet, M. Brouard, S. Cozzi, E. Galli, C. Blanchard, D. Bach, J.-M. Soulillou, J.-P. 2020-07-25 doi:10.1101/2020.07.25.217158 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Transposable Element-Gene Splicing Modulates the Transcriptional Landscape of Human Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.07.26.220608v1?rss=1 Babarinde, I. A. Ma, G. Li, Y. Deng, B. Luo, Z. Liu, H. Abdul, M. Ward, C. Chen, M. Fu, X. Duttlinger, M. He, J. Sun, L. Li, W. Zhuang, Q. Frampton, J. Cazier, J.-B. Chen, J. Jauch, R. Esteban, M. A. Hutchins, A. 2020-07-26 doi:10.1101/2020.07.26.220608 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Predicting the future development of mild cognitive impairment in the cognitively healthy elderly ]]> https://biorxiv.org/content/10.1101/2020.07.30.227496v1?rss=1 0.9, identifying only delayed verbal memory and left EC GMD as relevant predictors for classification. This performance was maintained on test classification of out-of-sample converters and controls. Our results suggest a parsimonious but powerful predictive model for MCI development in the cognitively healthy elderly. ]]> Strange, B. Zhang, L. Sierra-Marcos, A. Alfayate, E. Tohka, J. Medina, M. 2020-07-31 doi:10.1101/2020.07.30.227496 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ De novo design of ACE2 protein decoys to neutralize SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.08.03.231340v1?rss=1 Linsky, T. W. Vergara, R. Codina, N. Nelson, J. W. Walker, M. J. Su, W. Hsiang, T.-Y. Esser-Nobis, K. Yu, K. Hou, Y. J. Priya, T. Mitsumoto, M. Pong, A. Lau, U. Y. Mason, M. L. Chen, J. Chen, A. Berrocal, T. Peng, H. Clairmont, N. S. Castellanos, J. Lin, Y.-R. Josephson-Day, A. Baric, R. S. Walkey, C. D. Swanson, R. Blancas-Mejia, L. M. Gale, M. Yen, H.-L. Silva, D.-A. 2020-08-03 doi:10.1101/2020.08.03.231340 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Modeling Parent-Specific Genetic Nurture in Families with Missing Parental Genotypes: Application to Birthweight and BMI ]]> https://biorxiv.org/content/10.1101/2020.08.06.239178v1?rss=1 Tubbs, J. D. Hwang, L.-D. Luong, J. Evans, D. M. Sham, P. C. 2020-08-07 doi:10.1101/2020.08.06.239178 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Trans-cinnamaldehyde potently kills Enterococcus faecalis biofilm cells and prevents biofilm recovery ]]> https://biorxiv.org/content/10.1101/2020.08.09.243485v1?rss=1 Ali, I. A. A. Cheung, B. P. K. Matinlinna, J. P. Levesque, C. Neelakantan, P. 2020-08-10 doi:10.1101/2020.08.09.243485 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Curcumin-Sophorolipid nano-conjugate inhibits Candida albicans filamentation and biofilm development ]]> https://biorxiv.org/content/10.1101/2020.08.12.244186v1?rss=1 Rajasekar, V. Darne, P. Prabhune, A. Kao, R. Y. T. Solomon, A. P. Ramage, G. Samaranayake, L. Neelakantan, P. 2020-08-12 doi:10.1101/2020.08.12.244186 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Sex-Dependent Shared and Non-Shared Genetic Architecture Across Mood and Psychotic Disorders ]]> https://biorxiv.org/content/10.1101/2020.08.13.249813v1?rss=1 Blokland, G. A. Grove, J. Chen, C.-Y. Cotsapas, C. Tobet, S. Handa, R. Schizophrenia Working Group of the Psychiatric Genomics Consortium, St Clair, D. Lencz, T. Mowry, B. J. Periyasamy, S. Cairns, M. J. Tooney, P. A. Wu, J. Q. Kelly, B. Kirov, G. Sullivan, P. F. Corvin, A. Riley, B. P. Esko, T. Milani, L. Jönsson, E. G. Palotie, A. Ehrenreich, H. Begemann, M. Steixner-Kumar, A. Sham, P. C. Iwata, N. Weinberger, D. R. Gejman, P. V. Sanders, A. R. Buxbaum, J. D. Rujescu, D. Giegling, I. Konte, B. Hartmann, A. M. Bramon, E. Murray, R. M. Pato, M. T. Lee, 2020-08-17 doi:10.1101/2020.08.13.249813 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ NLRP3 inflammasome contributes to host defense against Talaromyces marneffei infection ]]> https://biorxiv.org/content/10.1101/2020.08.17.253518v1?rss=1 Ma, H. Chan, J. F.-W. Tan, Y. P. Kui, L. Tsang, C.-C. Pei, S. L. Lau, Y.-L. Woo, P. C. Lee, P. P. 2020-08-23 doi:10.1101/2020.08.17.253518 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Pathogenicity, immunogenicity, and protective ability of an attenuated SARS-CoV-2 variant with a deletion at the S1/S2 junction of the spike protein ]]> https://biorxiv.org/content/10.1101/2020.08.24.264192v1?rss=1 Wang, P. Lau, S.-Y. Deng, S. Chen, P. Mok, B. W.-Y. Zhang, A. J. Lee, A. C.-Y. Chan, K.-H. Song, W. To, K. K.-W. Chen, J. F.-W. Yuen, K.-Y. Chen, H. 2020-08-24 doi:10.1101/2020.08.24.264192 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Three-dimensionally preserved 'Stage IIIb' fossil down feather supports developmental modularity in feather evolution ]]> https://biorxiv.org/content/10.1101/2020.08.26.268060v1?rss=1 Roy, A. Miller, C. V. Pittman, M. Kaye, T. G. Peretti, A. 2020-08-27 doi:10.1101/2020.08.26.268060 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ SARS-CoV-2 spike D614G variant exhibits highly efficient replication and transmission in hamsters ]]> https://biorxiv.org/content/10.1101/2020.08.28.271635v1?rss=1 Mok, B. W. Y. Cremin, C. J. Lau, S.-Y. Deng, S. Chen, P. Zhang, A. J. Lee, A. C.-Y. Liu, H. Liu, S. Ng, T. T.-L. Lao, H.-Y. Lee, E. L.-K. Leung, K. S.-S. Wang, P. To, K. K.-W. Chan, J. F.-W. Chan, K.-H. Yuen, K.-Y. Siu, G. K.-H. Chen, H. 2020-08-28 doi:10.1101/2020.08.28.271635 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ EEG Artifact to Signal: Predicting Horizontal Gaze Position from SOBI-DANS Identified Ocular Artifact Components ]]> https://biorxiv.org/content/10.1101/2020.08.29.272187v1?rss=1 Sun, R. Cynthia, C. Hsiao, J. Tang, A. 2020-08-31 doi:10.1101/2020.08.29.272187 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ starmapVR: immersive visualisation of single cell spatial omic data ]]> https://biorxiv.org/content/10.1101/2020.09.01.277079v1?rss=1 Yang, A. Yao, Y. Fang, X. Li, J. Xia, Y. Kwok, C. S. M. Lo, M. C. K. Siu, D. M. D. Tsia, K. K. Ho, J. W. K. 2020-09-04 doi:10.1101/2020.09.01.277079 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Efficient cooperation of chloroplasts and mitochondria enhances ATP and sucrose production ]]> https://biorxiv.org/content/10.1101/2020.09.09.289967v1?rss=1 Voon, C. P. Law, Y.-S. Guan, X. Xu, Z. Chu, W.-T. Zhang, R. Sun, F. Labs, M. Pribil, M. Leister, D. Hronkova, M. Kubasek, J. Cui, Y. Jiang, L. Tsuyama, M. Gardestrom, P. Tikkanen, M. Lim, B. L. 2020-09-11 doi:10.1101/2020.09.09.289967 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Reduction of neuronal activity mediated by blood-vessel regression in the brain ]]> https://biorxiv.org/content/10.1101/2020.09.15.262782v1?rss=1 Gao, X. Li, J.-L. Chen, X. Ci, B. Chen, F. Lu, N. Shen, B. Zheng, L. Jia, J. Yi, Y. Zhang, S. Shi, Y. Shi, K. Propson, N. E. Huang, Y. Poinsatte, K. Zhang, Z. Yue, Y. Bosco, D. B. Lu, Y.-m. Yang, S.-b. Adams, R. H. Lindner, V. Huang, F. Wu, L.-J. Zheng, H. Han, F. Hippenmeyer, S. Stowe, A. M. Peng, B. Margeta, M. Wang, X. Liu, Q. Korbelin, J. Trepel, M. Lu, H. Zhou, B. O. Zhao, H. Sun, W. Bachoo, R. M. Ge, W.-p. 2020-09-15 doi:10.1101/2020.09.15.262782 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Biochemical reconstitutions reveal principles of human γ-TuRC assembly and function ]]> https://biorxiv.org/content/10.1101/2020.09.21.306845v1?rss=1 31 proteins includes{gamma} -tubulin and GCP2-6, as well as MZT1 and an actin-like protein in a "lumenal bridge". The challenge of reconstituting the{gamma} -TuRC has limited dissections of its assembly and function. Here, we report a complete biochemical reconstitution of the human{gamma} -TuRC ({gamma}-TuRC-GFP), a [~]35S complex that nucleates microtubules in vitro. We extend our approach to generate a stable subcomplex,{gamma} -TuRCmini-GFP, which lacks MZT1 and actin. Using mutagenesis, we show that{gamma} -TuRCmini-GFP nucleates microtubules in a guanine nucleotide-dependent manner and proceeds with similar kinetics as reported for native{gamma} -TuRCs. Electron microscopy reveals that{gamma} -TuRC-GFP resembles the native{gamma} -TuRC architecture, while{gamma} -TuRCmini-GFP adopts a partial cone shape presenting only 8-10{gamma} -tubulin subunits and lacks a well-ordered lumenal bridge. Our structure-function analysis suggests that the lumenal bridge facilitates the self-assembly of regulatory interfaces around a microtubule-nucleating "core" in the{gamma} -TuRC. ]]> Wieczorek, M. Ti, S.-C. Urnavicius, L. Molloy, K. R. Aher, A. Chait, B. T. Kapoor, T. M. 2020-09-21 doi:10.1101/2020.09.21.306845 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Hits-Based Quantitative Characterization of SOBI-Recovered P3 Network Configuration: an EEG Source-Imaging Study ]]> https://biorxiv.org/content/10.1101/2020.09.24.312587v1?rss=1 Privitera, A. J. Fung, R. Hua, Y. Tang, A. C. 2020-09-25 doi:10.1101/2020.09.24.312587 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Longitudinal multi-omics along gingivitis development reveal a suboptimal-health gum state with periodontitis-like microbiome ]]> https://biorxiv.org/content/10.1101/2020.09.26.315127v1?rss=1 Huang, S. He, T. Yue, F. Xu, V. Wang, S. Zhu, P. Teng, F. Sun, Z. Liu, X. Jing, G. Su, X. Jin, L. Liu, J. Xu, J. 2020-09-27 doi:10.1101/2020.09.26.315127 Cold Spring Harbor Laboratory Press 2020-09-27 <![CDATA[ Task-Free Recovery and Spatial Characterization of a P3-Like Global Network from Resting-State EEG ]]> https://biorxiv.org/content/10.1101/2020.09.27.316141v1?rss=1 Tang, A. C. Privitera, A. J. 2020-09-28 doi:10.1101/2020.09.27.316141 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Transposable element expression at unique loci in single cells with CELLO-seq ]]> https://biorxiv.org/content/10.1101/2020.10.02.322073v1?rss=1 Marioni, J. C. Berrens, R. V. Yang, A. Lun, A. T. Laumer, C. E. Lan, G. Bieberich, F. Law, C.-T. Imaz, M. Gaffney, D. 2020-10-02 doi:10.1101/2020.10.02.322073 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ exosome-LncPICALM-AU1 regulates endothelial-mesenchymal transition in hepatopulmonary syndrome ]]> https://biorxiv.org/content/10.1101/2020.10.06.327874v1?rss=1 Yang, C. Yang, Y. Chen, Y. Huang, J. Li, Y. Zhi, H. Tang, X. Wang, X. Belguise, K. Xia, Z. Ning, J. Gu, J. Yi, B. lu, K. 2020-10-09 doi:10.1101/2020.10.06.327874 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ The transcription factor BCL11A defines a distinctive subset of dopamine neurons in the developing and adult midbrain ]]> https://biorxiv.org/content/10.1101/2020.10.06.327940v1?rss=1 Tolve, M. Ulusoy, A. Islam, K. U. S. Bodea, G. O. Öztürk, E. Broske, B. Mentani, A. Wagener, A. van Loo, K. Britsch, S. Liu, P. T. Khaled, W. Baader, S. L. Di Monte, D. A. Blaess, S. 2020-10-07 doi:10.1101/2020.10.06.327940 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ piRPheno: a manually curated database to prioritize and analyze human disease related piRNAs ]]> https://biorxiv.org/content/10.1101/2020.10.09.334219v1?rss=1 Zhang, W. Wu, S. Zhang, H. Guan, W. Zeng, B. Wei, Y. Chan, G. C.-F. Li, W. Zhang, W. 2020-10-10 doi:10.1101/2020.10.09.334219 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ A crocodylian-style cloaca in a non-avialan dinosaur ]]> https://biorxiv.org/content/10.1101/2020.10.11.335398v1?rss=1 Bell, P. R. Pittman, M. Kaye, T. G. Hendrickx, C. 2020-10-12 doi:10.1101/2020.10.11.335398 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Between-subject correlation of heart rate variability predicts movie preferences ]]> https://biorxiv.org/content/10.1101/2020.10.12.335646v1?rss=1 So, T. Y. Li, M. Y. E. Lau, H. 2020-10-12 doi:10.1101/2020.10.12.335646 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Evidence of antigenic imprinting in sequential Sarbecovirus immunization ]]> https://biorxiv.org/content/10.1101/2020.10.14.339465v1?rss=1 Lv, H. So, R. T. Y. Yuan, M. Liu, H. Lee, C.-C. D. Yip, G. K. Ng, W. W. Wilson, I. A. Peiris, J. S. M. Wu, N. C. Mok, C. K. P. 2020-10-15 doi:10.1101/2020.10.14.339465 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Cross Sectional Study Of Middle East Respiratory Syndrome (MERS-CoV Infection) In Camels At Selected Sites Of Amibara District, Afar Region, Ethiopia ]]> https://biorxiv.org/content/10.1101/2020.10.25.353227v1?rss=1 0.05). In multivariable logistic regression analysis, age (OR=7.39, 95% CI:3.43-15.91), season (OR=4.83, 95% CI:-2.14-10.90), and in adult female camel reproduction status (OR=7.39,95% C I:3.43-15.91) showed statistically significant difference among the groups for MERS CoV antibody detection while risk factors of origin, animal sex and herd size difference were statistically insignificant. A total of 857 nasal swab samples were collected for the detection of MERS-CoV RNA particle. However, all swab samples tested by Real-time reverse transcription polymerase chain reaction (RT-PCR) technique were Negative for the virus. ConclusionIn conclusion, the present study revealed a high seroprevalance of MERS CoV in adult camels. However, in spite of high seroprevalance the lack of any RNA viral particle in the study suggests the need for further in depth longitudinal study to detect the circulating virus focusing on juveniles and young camels whereby seroprevalance of antibody is low when compared with adult camel in order to get the active virus before the camel develop antibody. Moreover, the zoonotic significance and potential transmission routes of MERS CoV to pastoral communities should also be investigated and design strategy for the preparedness in control of the diseases in Ethiopia. ]]> Lobago, D. S. Mamo, G. Aklilu, F. Zewde, D. Walelign, E. Muluneh, A. Aliy, A. Mirkena, T. Tewolde, N. Gari, G. van't Klooster, G. Elmasry, I. VonDobschuetz, S. Peiris, J. S. M. S. Chu, D. K. W. Perera, R. A. P. M. Jobire, Y. 2020-10-25 doi:10.1101/2020.10.25.353227 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Tracking cytosine depletion in SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.10.26.354787v1?rss=1 Luo, R. Wong, Y.-S. Lam, T.-W. 2020-10-26 doi:10.1101/2020.10.26.354787 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Computational identification of splicing phenotypes from single cell transcriptomic experiments ]]> https://biorxiv.org/content/10.1101/2020.11.04.368019v1?rss=1 Huang, Y. Sanguinetti, G. 2020-11-05 doi:10.1101/2020.11.04.368019 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Acrylamide Fragment Inhibitors that Induce Unprecedented Conformational Distortions in Enterovirus 71 3C and SARS-CoV-2 Main Protease ]]> https://biorxiv.org/content/10.1101/2020.11.06.370916v1?rss=1 Qin, B. Craven, G. B. Hou, P. Lu, X. Child, E. S. Morgan, R. M. L. Armstrong, A. Mann, D. J. Cui, S. 2020-11-06 doi:10.1101/2020.11.06.370916 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Systematic comparative analysis of Mendelian randomization methods for inferring causal genes of complex phenotypes and the application to psychiatric diseases ]]> https://biorxiv.org/content/10.1101/2020.11.09.374298v1?rss=1 Jiang, L. Yi, G. Li, X. Xue, C. Li, J. Huang, H. Li, M. 2020-11-10 doi:10.1101/2020.11.09.374298 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Deficiency in DNA mismatch repair of methylation damage is a major mutational process in cancer ]]> https://biorxiv.org/content/10.1101/2020.11.18.388108v1?rss=1 Fang, H. Zhu, X. Oh, J. Barbour, J. A. Wong, J. W. H. 2020-11-18 doi:10.1101/2020.11.18.388108 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Central Neural Regulation of Parathyroid Hormone ]]> https://biorxiv.org/content/10.1101/2020.11.30.403279v1?rss=1 Zhang, L. Liu, N. Shao, J. Gao, D. Liu, Y. Chen, D. Wang, L. Lu, W. W. Yang, F. 2020-11-30 doi:10.1101/2020.11.30.403279 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain ]]> https://biorxiv.org/content/10.1101/2020.11.30.404905v1?rss=1 Wu, C. Qavi, A. J. Hachim, A. Kavian, N. Cole, A. R. Moyle, A. B. Wagner, N. D. Sweeney-Gibbons, J. Rohrs, H. W. Gross, M. L. Peiris, J. S. M. Basler, C. F. Farnsworth, C. W. Valkenburg, S. A. Amarasinghe, G. K. Leung, D. W. 2020-11-30 doi:10.1101/2020.11.30.404905 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models. ]]> https://biorxiv.org/content/10.1101/2020.12.01.404483v1?rss=1 Ho, J. S. Y. Mok, B. W.-Y. Campisi, L. Jordan, T. Yildiz, S. Parameswaran, S. Wayman, J. A. Gaudreault, N. N. Meekins, D. A. Indran, S. V. Morozov, I. Trujillo, J. D. Fstkchyan, Y. S. Rathnasinghe, R. Zhu, Z. Zheng, S. Zhao, N. White, K. Ray-Jones, H. Malysheva, V. Thiecke, M. J. Lau, S.-Y. Liu, H. Zhang, A. J. Lee, A. C.-Y. Liu, W.-C. Aydillo, T. Melo, B. S. Guccione, E. Sebra, R. Shum, E. Bakker, J. Kaufman, D. A. Moreira, A. Carossino, M. Balasuriya, U. B. R. Byun, M. Miraldi, E. R. Albrecht, R. A. Schotsaert, M. Garcia-Sastre, A. Chanda, S. K. Jeya 2020-12-01 doi:10.1101/2020.12.01.404483 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Critical Thermal maximum measurements and its biological relevance: the case of ants ]]> https://biorxiv.org/content/10.1101/2020.12.09.417410v1?rss=1 Leong, C.-M. Tsang, T. P. N. Guenard, B. 2020-12-10 doi:10.1101/2020.12.09.417410 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Evidence for distinct genetic and environmental influences on fear acquisition and extinction ]]> https://biorxiv.org/content/10.1101/2020.12.18.423504v1?rss=1 Purves, K. L. Krebs, G. McGregor, T. Constantinou, E. Lester, K. J. Barry, T. J. Craske, M. G. Young, K. S. Breen, G. Eley, T. C. 2020-12-18 doi:10.1101/2020.12.18.423504 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Sterilizing immunity against SARS-CoV-2 in hamsters conferred by a novel recombinant subunit vaccine ]]> https://biorxiv.org/content/10.1101/2020.12.18.423552v1?rss=1 wu, y. Huang, X. Yuan, L. Wang, S. Zhang, Y. Xiong, H. Chen, R. Ma, J. Qi, R. Nie, M. Xu, J. Zhang, Z. Chen, L. Wei, M. Zhou, M. Cai, M. Shi, Y. Zhang, L. Yu, H. Hong, J. Wang, Z. Hong, Y. Yue, M. Li, Z. Chen, D. Zheng, Q. Li, S. Chen, Y. Cheng, T. Zhang, J. Zhang, T. Zhu, H. Zhao, Q. Yuan, Q. Guan, Y. Xia, N. 2020-12-20 doi:10.1101/2020.12.18.423552 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Matrix stiffness and blood pressure together regulate vascular smooth muscle cell phenotype switching and cofilin dependent podosome formation ]]> https://biorxiv.org/content/10.1101/2020.12.27.424498v1?rss=1 Sit, B. Feng, Z. Xanthis, I. Marhuenda, E. Zingaro, S. Shanahan, C. Jones, G. Yu, C.-h. Iskratsch, T. 2020-12-28 doi:10.1101/2020.12.27.424498 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ The comprehensive roadmaps of reprogramming and transformation unveiled antagonistic roles for bHLH transcription factors in the control of cellular plasticity ]]> https://biorxiv.org/content/10.1101/2020.12.28.424606v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@1718383org.highwire.dtl.DTLVardef@1714ab8org.highwire.dtl.DTLVardef@e0958borg.highwire.dtl.DTLVardef@7a0643_HPS_FORMAT_FIGEXP M_FIG C_FIG One-sentence summaryComparative roadmaps of cellular plasticity acquisition during pluripotent reprogramming and malignant transformation. ]]> Huyghe, A. Furlan, G. Schroeder, J. Studer, F. Mugnier, F. de Matteo, L. Wang, J. Yu, Y. Rama, N. Gibert, B. Wajda, P. Goddard, I. Gadot, N. Brevet, M. Siouda, M. Mulligan, P. Dante, R. Liu, P. Gronemeyer, H. Mendoza-Parra, M. A. Polo, J. M. Lavial, F. 2020-12-28 doi:10.1101/2020.12.28.424606 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Population Differentiation of Rhodobacteraceae Along Coral Compartments ]]> https://biorxiv.org/content/10.1101/2020.12.31.424895v1?rss=1 Luo, H. Luo, D. Wang, X. Feng, X. Tian, M. Wang, S. Tang, S.-L. Ang, P. O. Yan, A. 2021-01-05 doi:10.1101/2020.12.31.424895 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Cellsnp-lite: an efficient tool for genotyping single cells ]]> https://biorxiv.org/content/10.1101/2020.12.31.424913v1?rss=1 Huang, X. Huang, Y. 2021-01-03 doi:10.1101/2020.12.31.424913 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses ]]> https://biorxiv.org/content/10.1101/2020.12.31.424987v1?rss=1 Banach, B. B. Cerutti, G. Fahad, A. S. Shen, C.-H. Oliveira de Souza, M. Katsamba, P. S. Tsybovsky, Y. Wang, P. Nair, M. S. Huang, Y. Francino Urdaniz, I. M. Steiner, P. J. Gutierrez-Gonzalez, M. Liu, L. Lopez Acevedo, S. N. Nazzari, A. Wolfe, J. R. Luo, Y. Olia, A. S. Teng, I.-T. Yu, J. Zhou, T. Reddem, E. R. Bimela, J. Pan, X. Madan, B. Laflin, A. D. Nimrania, R. Yuen, K.-T. Whitehead, T. A. Ho, D. D. Kwong, P. D. Shapiro, L. DeKosky, B. J. 2021-01-03 doi:10.1101/2020.12.31.424987 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ The repertoire of testicular extracellular vesicles cargoes and their involvement in inter-compartmental communication required for spermatogenesis ]]> https://biorxiv.org/content/10.1101/2021.01.08.426002v1?rss=1 Choy, K. H. K. Chan, S. Y. Lam, W. Jin, J. Zheng, T. Yu, S. S. Wang, W. Li, L. Xie, G. Yim, H. C. H. Chen, H. FOK, E. K. L. 2021-01-09 doi:10.1101/2021.01.08.426002 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Deciphering 3D Human Sphygmopalpation Pulse Patterns using "X-ray" Images Acquired from Tactile Robotic Fingers ]]> https://biorxiv.org/content/10.1101/2021.01.10.426152v1?rss=1 KONG, K. W. CHAN, H.-y. XIE, J. LEE, F. C. S. LEUNG, A. Y. L. GUAN, B. SHEN, J. TAAM WONG, V. C.-W. LI, W. J. 2021-01-11 doi:10.1101/2021.01.10.426152 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ CD8+ T cell epitope variations suggest a potential antigen presentation deficiency for spike protein of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.01.22.427863v1?rss=1 F significantly decreased the proportion of specific T cell activation; n-Sp1 epitope 8L>V variant showed significantly reduced binding to HLA-A2 and decreased the proportion of n-Sp1-specific CD8+ T cell, which potentially contributes to the immune escape of SAR-CoV-2. ]]> Qiu, C. Xiao, C. Wang, Z. Zhu, G. Chen, X. Gao, L. Den, J. Su, J. Su, H. Fang, E. F. Zhang, Z. Zhang, J. Luo, O. J. Wang, P. Chen, G. 2021-01-24 doi:10.1101/2021.01.22.427863 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ Design of a novel DNA Gyrase B inhibitor with a rhodanine scaffold: in silico and in vitro approaches ]]> https://biorxiv.org/content/10.1101/2021.01.24.428017v1?rss=1 Pudipeddi, A. Vasudevan, S. Shanmugam, K. Stanley, A. P, V. Neelakantan, P. Solomon, A. P. 2021-01-25 doi:10.1101/2021.01.24.428017 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Strain dynamics of specific contaminant bacteria modulate the performance of ethanol biorefineries ]]> https://biorxiv.org/content/10.1101/2021.02.07.430133v1?rss=1 Lino, F. S. d. O. Misiakou, M.-A. Kang, K. Li, S. da Costa, B. L. V. Basso, T. O. Panagiotou, G. Sommer, M. O. A. 2021-02-08 doi:10.1101/2021.02.07.430133 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ A transferrable and integrative type I-F Cascade for heterologous genome editing and transcription modulation ]]> https://biorxiv.org/content/10.1101/2021.02.08.430362v1?rss=1 Xu, Z. Li, Y. Cao, H. Si, M. Zhang, G. Woo, P. C. Yan, A. 2021-02-09 doi:10.1101/2021.02.08.430362 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ VIA: Generalized and scalable trajectory inference in single-cell omics data ]]> https://biorxiv.org/content/10.1101/2021.02.10.430705v1?rss=1 stassen, S. V. Yip, G. Ho, J. W. K. Wong, K. K. Y. Tsia, K. 2021-02-11 doi:10.1101/2021.02.10.430705 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Surface-aerosol stability and pathogenicity of diverse MERS-CoV strains from 2012 - 2018 ]]> https://biorxiv.org/content/10.1101/2021.02.11.429193v1?rss=1 van Doremalen, N. Letko, M. C. Fischer, R. Bushmaker, T. Yinda, K. C. Schulz, J. Seifert, S. N. Kim, N. J. Hemida, M. G. Kayali, G. Park, W. B. Perera, R. Tamin, A. Thornburg, N. J. Tong, S. Queen, K. Van Kerkhove, M. D. Choi, Y. K. Oh, M.-d. Assiri, A. M. Peiris, J. S. M. Gerber, S. Munster, V. 2021-02-12 doi:10.1101/2021.02.11.429193 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Homologous and heterologous serological response to the N-terminal domain of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.02.17.431722v1?rss=1 Lv, H. Tsang, O. T.-Y. So, R. T. Y. Wang, Y. Liu, H. Yip, G. K. Teo, Q. W. Lin, Y. Liang, W. Wang, J. Ng, W. W. Wilson, I. A. Peiris, M. Wu, N. C. Mok, C. K. P. 2021-02-18 doi:10.1101/2021.02.17.431722 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Combinatorial engineering of bulk-assembled monodisperse coacervate droplets towards logically integrated protocells ]]> https://biorxiv.org/content/10.1101/2021.02.19.432011v1?rss=1 Li, Q. Song, Q. Wei, J. Cao, Y. Chen, D. Shum, H. C. 2021-02-19 doi:10.1101/2021.02.19.432011 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ A neural circuit basis for bilateral olfactory input-enhanced chemosensory avoidance navigation ]]> https://biorxiv.org/content/10.1101/2021.02.20.431946v1?rss=1 Sy, S. K. H. Chan, D. C. W. Lai, H.-M. Li, Z. Wong, K. K. Y. Choi, C. H. J. Mok, V. C. T. Hu, Y. Ko, H. 2021-02-20 doi:10.1101/2021.02.20.431946 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing among full-sibs ]]> https://biorxiv.org/content/10.1101/2021.03.01.432833v1?rss=1 Fraimout, A. Li, Z. Sillanpaa, M. J. Rastas, P. Merila, J. 2021-03-01 doi:10.1101/2021.03.01.432833 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Periodic synchronization of dengue epidemics in Thailand: the roles played by temperature and immunity ]]> https://biorxiv.org/content/10.1101/2021.03.01.433325v1?rss=1 Garcia-Carreras, B. Yang, B. Grabowski, M. K. Sheppard, L. W. Huang, A. T. Salje, H. Clapham, H. E. Iamsirithaworn, S. Doung-Ngern, P. Lessler, J. Cummings, D. A. T. 2021-03-01 doi:10.1101/2021.03.01.433325 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Trans -cinnamaldehyde attenuates Enterococcus faecalis virulence and inhibits biofilm formation ]]> https://biorxiv.org/content/10.1101/2021.03.15.435450v1?rss=1 Ali, I. A. A. Matinlinna, J. Levesque, C. Neelakantan, P. 2021-03-15 doi:10.1101/2021.03.15.435450 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ RENET2: High-Performance Full-text Gene-Disease Relation Extraction with Iterative Training Data Expansion ]]> https://biorxiv.org/content/10.1101/2021.03.18.436005v1?rss=1 Su, J. Wu, Y. Ting, H.-F. Lam, T.-W. Luo, R. 2021-03-19 doi:10.1101/2021.03.18.436005 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Representation learning of RNA velocity reveals robust cell transitions ]]> https://biorxiv.org/content/10.1101/2021.03.19.436127v1?rss=1 Qiao, C. Huang, Y. 2021-03-20 doi:10.1101/2021.03.19.436127 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Genome-wide screen identifies curli amyloid fibril as a bacterial component promoting host neurodegeneration ]]> https://biorxiv.org/content/10.1101/2021.03.22.436366v1?rss=1 WANG, C. Lau, C. Y. Ma, F. Zheng, C. 2021-03-22 doi:10.1101/2021.03.22.436366 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ MQuad enables clonal substructure discovery using single cell mitochondrial variants ]]> https://biorxiv.org/content/10.1101/2021.03.27.437331v1?rss=1 Huang, Y. Ho, J. W. K. Kwok, A. W. C. Qiao, C. Huang, R. Sham, M. H. 2021-03-29 doi:10.1101/2021.03.27.437331 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Organ-specific microbiota enhances the terrestrial lifestyle of a brachyuran crab ]]> https://biorxiv.org/content/10.1101/2021.03.30.437674v1?rss=1 Bacci, G. Fratini, S. Meriggi, N. Cheng, C. L. Y. Ng, K. H. Iannucci, A. Mengoni, A. Cavalieri, D. Cannicci, S. 2021-03-31 doi:10.1101/2021.03.30.437674 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Time-varying Dynamic Network Model For Dynamic Resting State Functional Connectivity in fMRI and MEG imaging ]]> https://biorxiv.org/content/10.1101/2021.04.01.438060v1?rss=1 Jiang, F. Jin, H. Bao, Y. Xie, X. Cummings, J. Raj, A. Nagarajan, S. 2021-04-02 doi:10.1101/2021.04.01.438060 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ XAV-19, a novel swine glyco-humanized polyclonal antibody against SARS-CoV-2 spike, efficiently neutralizes B.1.1.7 British and B.1.351 South-African variants. ]]> https://biorxiv.org/content/10.1101/2021.04.02.437747v1?rss=1 Vanhove, B. Marot, S. S. Gaborit, B. Evanno, G. Malet, I. Ciron, C. Royer, P.-J. Lheriteau, E. Denie, S. Raffi, F. Duvaux, O. Marcelin, A.-G. Calvez, V. 2021-04-05 doi:10.1101/2021.04.02.437747 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ ECNano: A Cost-Effective Workflow for Target Enrichment Sequencing and Accurate Variant Calling on 4,800 Clinically Significant Genes Using a Single MinION Flowcell ]]> https://biorxiv.org/content/10.1101/2021.04.05.438455v1?rss=1 100x and >98% uniformity using one MinION flowcell. For accurate ONT variant calling, the generated reads sufficiently covered 98.9% of pathogenic positions listed in ClinVar, with 98.96% having at least 30x DoC. ECNano obtained an average read length of 1,000 bp. The long reads of ECNano also covered the adjacent splice sites well, with 98.5% of positions having [≥] 30x DoC. Clair-ensemble achieved >99% recall and accuracy for SNV calling. The whole workflow from wet-lab protocol to variant detection was completed within three days. ConclusionWe presented ECNano, an out-of-the-box workflow comprising (1) a wet-lab protocol for ONT target enrichment sequencing and (2) a downstream variant detection workflow, Clair-ensemble. The workflow is cost-effective, with a short turnaround time for high accuracy variant calling in 4,800 clinically significant genes and regions using a single MinION flowcell. The long-read exon captured data has potential for further development, promoting the application of long-read sequencing in personalized disease treatment and risk prediction. ]]> Leung, A. W.-S. Leung, H. C.-M. Wong, C.-L. Zheng, Z.-X. Lui, W.-W. Luk, H.-M. Lo, I. F.-M. Luo, R. Lam, T.-W. 2021-04-06 doi:10.1101/2021.04.05.438455 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Plasma exosomal miRNA analysis of Alzheimer's disease reveals the dysfunction of a neural network ]]> https://biorxiv.org/content/10.1101/2021.04.12.439575v1?rss=1 Yuzhe, S. Zhen, H. Wang, L. Li, B. Song, Z. Deng, Y. Liu, Z. Ding, J. Li, T. Zhang, W. Nie, C. Rong, S. 2021-04-14 doi:10.1101/2021.04.12.439575 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ MicroRNA-202 safeguards meiotic progression by preventing premature degradation of REC8 mediated by separase ]]> https://biorxiv.org/content/10.1101/2021.04.14.439735v1?rss=1 Chen, J. Gao, C. Zheng, C. Lin, X. Ning, Y. Ma, L. He, W. Xie, D. Liu, K. Han, C. 2021-04-14 doi:10.1101/2021.04.14.439735 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Age-dependent genetic architecture underlines similar heritability of body size in sticklebacks ]]> https://biorxiv.org/content/10.1101/2021.04.19.440387v1?rss=1 Fraimout, A. Li, Z. Sillanpaa, M. Merila, J. 2021-04-20 doi:10.1101/2021.04.19.440387 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Low dose inocula of SARS-CoV-2 B.1.1.7 variant initiate more robust infections in the upper respiratory tract of hamsters than earlier D614G variants ]]> https://biorxiv.org/content/10.1101/2021.04.19.440414v1?rss=1 Mok, B. W.-Y. Liu, H. Lau, S.-Y. Deng, S. D. Liu, S. Tam, R. C.-Y. Ng, T. T.-L. Leung, J. S.-L. Wang, P. To, K. K.-W. Chan, J. F.-W. Chan, K.-H. Yuen, K.-Y. Siu, G. K.-H. Chen, H. 2021-04-19 doi:10.1101/2021.04.19.440414 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ SENSV: Detecting Structural Variations with Precise Breakpoints using Low-Depth WGS Data from a Single Oxford Nanopore MinION Flowcell ]]> https://biorxiv.org/content/10.1101/2021.04.20.440583v1?rss=1 Leung, H. C. Yu, H. Zhang, Y. Leung, W. S. Lo, I. F. Luk, H. M. Law, W.-C. Ma, K. K. Wong, C. L. Wong, Y. S. Luo, R. Lam, T.-W. 2021-04-21 doi:10.1101/2021.04.20.440583 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ DNA methylation affects pre-mRNA transcriptional initiation and processing in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.04.29.441938v1?rss=1 Li, Q. Chen, S. Leung, A. W.-S. Liu, Y. Xin, Y. Zhang, L. LAM, H.-M. Luo, R. Zhang, S. 2021-04-30 doi:10.1101/2021.04.29.441938 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Genomic sequences and RNA binding proteins predict RNA splicing kinetics in various single-cell contexts ]]> https://biorxiv.org/content/10.1101/2021.05.02.442314v1?rss=1 Hou, R. Huang, Y. 2021-05-02 doi:10.1101/2021.05.02.442314 Cold Spring Harbor Laboratory Press 2021-05-02 <![CDATA[ Desert fish populations tolerate extreme salinity change to overcome hydrological constraints ]]> https://biorxiv.org/content/10.1101/2021.05.14.444120v1?rss=1 Schunter, C. Bonzi, L. C. Norstog, J. Sourisse, J. Berumen, M. L. Angel, Y. Parkes, S. D. McCabe, M. F. Ravasi, T. 2021-05-16 doi:10.1101/2021.05.14.444120 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Hypertrophic Chondrocytes Serve as a Reservoir for Unique Marrow Associated Skeletal Stem and Progenitor Cells, Osteoblasts, and Adipocytes During Skeletal Development ]]> https://biorxiv.org/content/10.1101/2021.05.18.444731v1?rss=1 Long, J. T. Leinroth, A. Liao, Y. Ren, Y. Mirando, A. J. Nguyen, T. Guo, W. Sharma, D. Wu, C. Cheah, K. Karner, C. M. Hilton, M. J. 2021-05-18 doi:10.1101/2021.05.18.444731 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Differences in social brain function in autism spectrum disorder are linked to the serotonin transporter ]]> https://biorxiv.org/content/10.1101/2021.05.28.446151v1?rss=1 Wong, N. M. L. Dipasquale, O. Turkheimer, F. E. Findon, J. L. Wichers, R. H. Dimitrov, M. Murphy, C. M. Stoencheva, V. Robertson, D. M. Murphy, D. G. Daly, E. McAlonan, G. M. 2021-05-28 doi:10.1101/2021.05.28.446151 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Ring Finger Protein 213 Assembles into a Sensor for ISGylated Proteins with Antimicrobial Activity ]]> https://biorxiv.org/content/10.1101/2021.06.03.446796v1?rss=1 Thery, F. Martina, L. Asselman, C. Repo, H. Zhang, Y. Sedeyn, K. Moschonas, G. D. Bredow, C. Teo, Q. W. Zhang, J. Vessely, M. Leandro, K. Eggermont, D. De Sutter, D. Boucher, K. Hochepied, T. Festjens, N. Callewaert, N. Saelens, X. Dermaut, B. Knobeloch, K.-P. Beling, A. Sanyal, S. Radoshevich, L. Eyckerman, S. Impens, F. 2021-06-03 doi:10.1101/2021.06.03.446796 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq ]]> https://biorxiv.org/content/10.1101/2021.06.08.447604v1?rss=1 Engel, K. L. Lo, H.-Y. G. Goering, R. Li, Y. Spitale, R. Taliaferro, M. 2021-06-08 doi:10.1101/2021.06.08.447604 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ MCGA: a multi-strategy conditional gene-based association framework integrating with isoform-level expression profiles reveals new susceptible and druggable candidate genes of schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.06.08.447608v1?rss=1 Li, X. Jiang, L. Xue, C. Li, M. J. Li, M. 2021-06-09 doi:10.1101/2021.06.08.447608 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ The benefits of herbivory outweigh the costs of bioerosion in a eutrophic coral community ]]> https://biorxiv.org/content/10.1101/2021.06.08.447634v1?rss=1 Dytnerski, J. K. Marshall, K. E. Baker, D. M. Russell, B. D. 2021-06-09 doi:10.1101/2021.06.08.447634 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ HKG: An open genetic variant database of 205 Hong Kong Cantonese exomes ]]> https://biorxiv.org/content/10.1101/2021.06.15.448515v1?rss=1 Ou, M. Leung, H. C.-M. Leung, A. W.-S. Luk, H.-M. Yan, B. Liu, C.-M. Tong, T. M.-F. Mok, M. T.-S. Ko, W. M.-Y. Law, W.-C. Lam, T.-W. Lo, I. F.-M. Luo, R. 2021-06-16 doi:10.1101/2021.06.15.448515 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Diversity of Treponema denticola and other oral treponeme lineages in subjects with periodontitis and gingivitis ]]> https://biorxiv.org/content/10.1101/2021.06.24.449858v1?rss=1 Zeng, H. Chan, Y. Gao, W. Leung, W. K. Watt, R. M. 2021-06-25 doi:10.1101/2021.06.24.449858 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ MicroRNA-202 prevents precocious spermatogonial differentiation and meiotic initiation during mouse spermatogenesis ]]> https://biorxiv.org/content/10.1101/2021.06.27.449895v1?rss=1 Chen, J. Gao, C. Lin, X. Ning, Y. He, W. Zheng, C. Zhang, D. Yan, L. Jiang, B. Zhao, Y. Hossen, M. A. Han, C. 2021-06-28 doi:10.1101/2021.06.27.449895 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Untangling Microbiota Diversity and Assembly Patterns in the World's Largest Water Diversion Canal ]]> https://biorxiv.org/content/10.1101/2021.07.26.453773v1?rss=1 Zhang, L. Yin, W. Wang, C. Zhang, A. Zhang, H. Zhang, T. Ju, F. 2021-07-26 doi:10.1101/2021.07.26.453773 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Correlational networking guides the discovery of cryptic proteases for lanthipeptide maturation ]]> https://biorxiv.org/content/10.1101/2021.07.26.453782v1?rss=1 Xue, D. Older, E. A. Zhong, Z. Shang, Z. Chen, N. Walla, M. D. Dong, S.-H. Tang, X. Nagarkatti, P. Nagarkatti, M. Li, Y.-X. Li, J. 2021-07-26 doi:10.1101/2021.07.26.453782 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ The generation of a Bcl11a lineage tracing mouse model ]]> https://biorxiv.org/content/10.1101/2021.07.26.453822v1?rss=1 Pensa, S. Liu, P. Khaled, W. T. 2021-07-26 doi:10.1101/2021.07.26.453822 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ ACE2 Pathway Regulates Thermogenesis and Energy Metabolism ]]> https://biorxiv.org/content/10.1101/2021.08.10.455823v1?rss=1 Cao, X. Shi, T. Zhang, C. Jin, W. Song, L. Zhang, Y. Liu, J. Yang, F. Rotimi, C. N. Xu, A. Yang, J. 2021-08-10 doi:10.1101/2021.08.10.455823 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Modeling the SARS-CoV-2 mutation based on geographical regions and time ]]> https://biorxiv.org/content/10.1101/2021.08.11.455941v1?rss=1 Wei, B. Sun, Y. 2021-08-11 doi:10.1101/2021.08.11.455941 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-care Platform ]]> https://biorxiv.org/content/10.1101/2021.08.18.456880v1?rss=1 Donia, A. Shahid, M. F. Ahmad, A. Javed, A. Nawaz, M. Yaqub, T. Bokhari, H. 2021-08-18 doi:10.1101/2021.08.18.456880 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Covalent inhibition of endoplasmic reticulum chaperone GRP78 disconnects the transduction of ER stress signals to inflammation and lipid accumulation in diet-induced obese mice ]]> https://biorxiv.org/content/10.1101/2021.08.20.457085v1?rss=1 Rong, J. Luo, D. Fan, N. Zhang, X. Ngo, F. Y. Zhao, J. Zhao, W. Huang, M. Li, D. Wang, Y. 2021-08-20 doi:10.1101/2021.08.20.457085 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Diterpenoid Vinigrol activates ATF4/DDIT3-mediated PERK/eIF2 arm of unfolded protein response to drive breast cancer cell death ]]> https://biorxiv.org/content/10.1101/2021.08.25.457587v1?rss=1 Wei, W. Li, Y. Wang, C. Gao, S. wang, h. Zhao, Y. Gao, Z. Jiang, Y. Gao, H. Yao, X. Hu, Y. 2021-08-26 doi:10.1101/2021.08.25.457587 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Stem cell-derived macrophages as a new platform for studying host-pathogen interactions in livestock ]]> https://biorxiv.org/content/10.1101/2021.09.10.459580v1?rss=1 Meek, S. Watson, T. Eory, L. McFarlane, G. Wynne, F. J. McCleary, S. Dunn, L. E. M. Charlton, E. M. Craig, C. Shih, B. Regan, T. Taylor, R. M. Sutherland, L. Gossner, A. Chintoan-Uta, C. Fletcher, S. Beard, P. M. Hassan, M. A. Grey, F. Hope, J. C. Stevens, M. P. Nowak-imialek, M. Niemann, H. ROSS, P. J. Tait-Burkard, C. Brown, S. M. Lefevre, L. Thompson, G. McColl, B. M. Lawrence, A. B. Archibald, A. L. Steinbach, F. Crooke, H. R. Gao, X. Liu, P. Burdon, T. 2021-09-10 doi:10.1101/2021.09.10.459580 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Predictors of human-infective RNA virus discovery in the United States, China and Africa, an ecological study ]]> https://biorxiv.org/content/10.1101/2021.09.13.460031v1?rss=1 Zhang, F. Chase-Topping, M. Guo, C.-G. Woolhouse, M. 2021-09-15 doi:10.1101/2021.09.13.460031 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Functional and Highly Crosslinkable HIV-1 Envelope Glycoproteins Enriched in a Pretriggered Conformation ]]> https://biorxiv.org/content/10.1101/2021.09.27.462085v1?rss=1 Nguyen, H. T. Qualizza, A. Anang, S. Zhao, M. Zou, S. Zhou, R. Wang, Q. Zhang, S. Deshpande, A. A. Ding, H. Smith, A. B. Kappes, J. C. Sodroski, J. G. 2021-09-30 doi:10.1101/2021.09.27.462085 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Why can we detect lianas from space? ]]> https://biorxiv.org/content/10.1101/2021.09.30.462145v1?rss=1 Visser, M. D. Detto, M. Meunier, F. Wu, J. Bongalov, B. Coomes, D. Nunes, M. H. Guzman Q., J. A. Sanchez-Azofeifa, A. Foster, J. Broadbent, E. Verbeeck, H. Marvin, D. Chandler, C. J. van der Heijden, G. M. F. Boyd, D. S. Foody, G. M. Cutler, M. E. J. Serbin, S. Schnitzer, S. A. Rodriguez-Ronderos, M. E. Pacala, S. W. 2021-10-01 doi:10.1101/2021.09.30.462145 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Salicylaldehyde ester-mediated protein semi-synthesis enables studies on the tetra-acetylation of HMGB1 ]]> https://biorxiv.org/content/10.1101/2021.10.05.463167v1?rss=1 Wei, T. Liu, J. Tan, Y. Wei, R. Wang, J. Wu, H. Tang, Y. Li, X. 2021-10-06 doi:10.1101/2021.10.05.463167 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ SARS-CoV-2 hijacks neutralizing dimeric IgA for enhanced nasal infection and injury ]]> https://biorxiv.org/content/10.1101/2021.10.05.463282v1?rss=1 Zhou, B. Zhou, R. Chan, J. F.-W. Zeng, J. Zhang, Q. Yuan, S. Liu, L. Robinot, R. Shan, S. Ge, J. Kwong, H. Y.-H. Zhou, D. Xu, H. Chan, C. C.-S. Poon, V. K.-M. Chu, H. Yue, M. Kwan, K.-Y. Chan, C.-Y. Liu, N. Chan, C. C.-Y. Chik, K. K.-H. Du, Z. Au, K.-K. Huang, H. Man, H.-O. Cao, J. Li, C. Wang, Z. Zhou, J. Song, Y. Yeung, M.-L. To, K. K.-W. Ho, D. D. Chakrabarti, L. A. Wang, X. Zhang, L. Yuen, K.-Y. Chen, Z. 2021-10-06 doi:10.1101/2021.10.05.463282 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ Developmental cell death of cortical projection neurons is controlled by a Bcl11a/Bcl6-dependent pathway ]]> https://biorxiv.org/content/10.1101/2021.10.06.463323v1?rss=1 Wiegreffe, C. Wahl, T. Natalie, J. S. Bonnefont, J. Vanderhaeghen, P. Liu, P. Britsch, S. 2021-10-07 doi:10.1101/2021.10.06.463323 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters ]]> https://biorxiv.org/content/10.1101/2021.10.08.463665v1?rss=1 View larger version (81K): org.highwire.dtl.DTLVardef@ada9b8org.highwire.dtl.DTLVardef@1617fcaorg.highwire.dtl.DTLVardef@cdcd3org.highwire.dtl.DTLVardef@75a0ab_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractSARS-CoV-2 infection causes pathological bone loss in golden Syrian hamsters through induction of cytokine storm and inflammation-induced osteoclastogenesis. ]]> Qiao, W. Lau, H. E. Xie, H. Poon, V. K. M. Chan, C. C. S. Chu, H. Yuan, S. Yuen, T. T. T. Chik, K. K. H. Tsang, J. O. L. Chan, C. C. Y. Cai, J.-P. Luo, C. Yuen, K.-Y. Cheung, K. M. C. Chan, J. F. W. Yeung, K. W. K. 2021-10-09 doi:10.1101/2021.10.08.463665 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2021.10.13.464307v1?rss=1 Wang, P. Casner, R. G. Nair, M. S. Yu, J. Guo, Y. Wang, M. Chan, J. F. W. Cerutti, G. Iketani, S. Liu, L. Sheng, Z. Chen, Z. Yuen, K.-Y. Kwong, P. D. Huang, Y. Shapiro, L. Ho, D. D. 2021-10-14 doi:10.1101/2021.10.13.464307 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Neural dynamics of retrieval suppression in abolishing item-specific cortical pattern of unwanted emotional memories ]]> https://biorxiv.org/content/10.1101/2021.10.17.464746v1?rss=1 Lin, X. Chen, D. Yao, Z. Anderson, M. Hu, X. 2021-10-18 doi:10.1101/2021.10.17.464746 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Nasal prevention of SARS-CoV-2 infection by intranasal influenza-based boost vaccination ]]> https://biorxiv.org/content/10.1101/2021.10.21.465252v1?rss=1 Zhou, R. Wang, P. Wong, Y.-C. Xu, H. Lau, S.-Y. Liu, L. Mok, B. W.-Y. Peng, Q. Liu, N. Deng, S. Tam, R. C.-Y. Huang, H. Zhang, A. J. Zhou, D. Zhou, B. Chan, C.-Y. Du, Z. Yang, D. Au, K.-K. Yuen, K.-Y. Chen, H. Chen, Z. 2021-10-22 doi:10.1101/2021.10.21.465252 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ Identifying barriers to gene flow and hierarchical conservation units from seascape genomics: a modelling framework applied to a marine predator ]]> https://biorxiv.org/content/10.1101/2021.10.25.465682v1?rss=1 Boussarie, G. Momigliano, P. Robbins, W. D. Bonnin, L. Cornu, J.-F. Fauvelot, C. Kiszka, J. J. Manel, S. Mouillot, D. Vigliola, L. 2021-10-26 doi:10.1101/2021.10.25.465682 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Global Increases in Human Immunodeficiency Virus Neutralization Sensitivity Due to Alterations in the Membrane-Proximal External Region of the Envelope Glycoprotein Can be Minimized by Distant State 1-Stabilizing Changes ]]> https://biorxiv.org/content/10.1101/2021.11.01.466860v1?rss=1 Wang, Q. Esnault, F. Zhao, M. Chiu, T.-J. Smith, A. B. Nguyen, H. T. Sodroski, J. G. 2021-11-04 doi:10.1101/2021.11.01.466860 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ A phosphoinositide and RAB switch controls early macropinocytosis ]]> https://biorxiv.org/content/10.1101/2021.11.03.467145v1?rss=1 Spangenberg, H. Sneeggen, M. Mateo Tortola, M. Valenzuela-Montenegro, C. Chang, Y.-Y. Stenmark, H. Raiborg, C. Schink, K. O. 2021-11-04 doi:10.1101/2021.11.03.467145 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Construction of lux-based promoter-reporter platforms in Mycobacterium bovis BCG for screening of drug repurposing small-molecule compounds as new anti-tuberculosis drugs ]]> https://biorxiv.org/content/10.1101/2021.11.05.467536v1?rss=1 Zhu, L. Lee, A. W.-t. WU, K. K.-L. GAO, P. Tam, K. K.-G. Rajwani, R. CHABURTE, G. C. NG, T. T.-L. Chan, C. T. M. Lao, H.-Y. Yam, W.-C. Kao, R. Y.-T. Siu, G. K. H. 2021-11-06 doi:10.1101/2021.11.05.467536 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ A live attenuated influenza virus-vectored intranasal COVID-19 vaccine provides rapid, prolonged, and broad protection against SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.11.13.468472v1?rss=1 Chen, J. Wang, P. Yuan, L. Zhang, L. Zhang, L. Zhao, H. Chen, C. Chen, Y. Han, J. Jia, J. Lu, Z. Hong, J. Chen, L. Fan, C. Lu, Z. Wang, Q. Chen, R. Cai, M. Qi, R. Wang, X. Ma, J. Zhou, M. Yu, H. Zhuang, C. Liu, X. Han, Q. Wang, G. Su, Y. Yuan, Q. Cheng, T. Wu, T. Ye, X. Li, C. Zhang, T. Zhang, J. Zhu, H. Chen, Y. Chen, H. Xia, N. 2021-11-15 doi:10.1101/2021.11.13.468472 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ The global spread and invasion capacities of alien ants ]]> https://biorxiv.org/content/10.1101/2021.11.19.469299v1?rss=1 145,000 records spanning 602 regions, we identify 522 ant species exhibiting human-mediated spread, doubling recent estimates of their diversity. We show that movements of alien ant species across regions globally are non-random and, moreover, that these flows differ by the extents to which species invade--ranging from arrival to indoor establishment, naturalization, and harmful status. Importantly, we find that almost two-thirds of the 309 species that naturalize globally--most of which are ground- and litter-dwelling--are absent from customs interceptions, which record disproportionately high numbers of arboreal species. Our results illustrate the vast, yet uneven extent of ant invasions globally, and suggest that most alien species bypass biosecurity controls while spreading successfully worldwide. This raises doubts on the efficacy of current customs interceptions procedures and highlights a need for radically new approaches. Significance statementBiological invasions impact humans and ecosystems tremendously. Invasions are difficult to address because little is known about large-scale patterns of spread, species capacities to invade ecosystems, and the efficacy of existing biosecurity measures. This paper tackles these issues for alien ants, one of the most damaging groups of invasive animals. An unprecedented dataset reveals that 522 ant species exhibit human-mediated spread, 270 more than previously known. Species are grouped under four levels of invasion capacity corresponding to different invasion barriers. Geographic sources and sinks for the groups differ globally. Two-thirds of species with naturalization capacity have never been recorded at customs interceptions, which fail to detect many litter-dwelling species. Novel detection and control strategies for inconspicuous alien organisms are needed. ]]> Wong, M. K. L. Economo, E. P. Guenard, B. 2021-11-20 doi:10.1101/2021.11.19.469299 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Australia as a global sink for the genetic diversity of avian influenza A virus ]]> https://biorxiv.org/content/10.1101/2021.11.30.470533v1?rss=1 Wille, M. Grillo, V. Ban de Gouvea Pedroso, S. Burgess, G. W. Crawley, A. Dickason, C. Hansbro, P. M. Hoque, M. A. Horwood, P. F. Kirkland, P. D. Kung, N. Y.-H. Lynch, S. E. Martin, S. McArthur, M. ORiley, K. Read, A. J. Warner, S. Hoye, B. J. Lisovski, S. Leen, T. Hurt, A. C. Butler, J. Broz, I. Davies, K. R. Mileto, P. Neave, M. Stevens, V. Breed, A. Lam, T. T. Y. Holmes, E. C. Klaassen, M. Wong, F. Y. K. 2021-12-01 doi:10.1101/2021.11.30.470533 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR- V7 splice variant chromatin binding and transcriptional activities ]]> https://biorxiv.org/content/10.1101/2021.12.06.471341v1?rss=1 Paul, B. Robertson, M. J. Bingman, W. E. Dash, A. K. Krause, W. C. Shafi, A. A. Piyarathna, B. Coarfa, C. Weigel, N. L. 2021-12-06 doi:10.1101/2021.12.06.471341 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Isolation and comparative analysis of antibodies that broadly neutralize sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2021.12.11.472236v1?rss=1 Liu, L. Iketani, S. Guo, Y. Casner, R. Reddem, E. Nair, M. S. Yu, J. Chan, J. Wang, M. Cerutti, G. Li, Z. Castagna, C. Corredor, L. Chu, H. Yuan, S. Poon, V. Chan, C. Chen, Z. Luo, Y. Cunningham, M. Chavez, A. Yin, M. Perlin, D. Tsuji, M. Yuen, K.-Y. Kwong, P. Sheng, Z. Huang, Y. Shapiro, L. Ho, D. D. 2021-12-14 doi:10.1101/2021.12.11.472236 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.12.14.472719v1?rss=1 Liu, L. Iketani, S. Guo, Y. Chan, J. F.-W. Wang, M. Liu, L. Luo, Y. Chu, H. Huang, Y. Nair, M. S. Yu, J. Chik, K. K.-H. Yuen, T. T.-T. Yoon, C. To, K. K.-W. Chen, H. Yin, M. T. Sobieszczyk, M. E. Huang, Y. Wang, H. H. Sheng, Z. Yuen, K.-Y. Ho, D. D. 2021-12-15 doi:10.1101/2021.12.14.472719 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ Declining population sizes and loss of genetic diversity in commercial fishes: a simple method for a first diagnostic ]]> https://biorxiv.org/content/10.1101/2021.12.16.472909v1?rss=1 Petit-Marty, N. P. Min, L. Tan, I. Z. Chung, A. Terrasa, B. Guijarro, B. Ordines, F. Ramirez-Amaro, S. Massuti, E. Schunter, C. 2021-12-17 doi:10.1101/2021.12.16.472909 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Gene expression is a poor predictor of the metabolite abundance in cancer cells ]]> https://biorxiv.org/content/10.1101/2021.12.19.473333v1?rss=1 Li, H. Barbour, J. A. Zhu, X. Wong, J. W. H. 2021-12-20 doi:10.1101/2021.12.19.473333 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Waning immune responses against SARS-CoV-2 among vaccinees in Hong Kong ]]> https://biorxiv.org/content/10.1101/2021.12.22.473934v1?rss=1 Peng, Q. Zhou, R. Wang, Y. Zhao, M. Liu, N. Li, S. Huang, H. Yang, D. Au, K.-K. Wang, H. Man, K. Yuen, K.-Y. Chen, Z. 2021-12-23 doi:10.1101/2021.12.22.473934 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Vaccine-breakthrough infection by the SARS-CoV-2 Omicron variant elicits broadly cross-reactive immune responses ]]> https://biorxiv.org/content/10.1101/2021.12.27.474218v1?rss=1 Zhou, R. To, K. K.-W. Peng, Q. Chan, J. M.-C. Huang, H. Yang, D. Lam, B. H.-S. Chuang, V. W.-M. Cai, J.-P. Liu, N. Au, K.-K. Tsang, O. T.-Y. Yuen, K.-Y. Chen, Z. 2021-12-28 doi:10.1101/2021.12.27.474218 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Symphonizing pileup and full-alignment for deep learning-based long-read variant calling ]]> https://biorxiv.org/content/10.1101/2021.12.29.474431v1?rss=1 Zheng, Z. Li, S. Su, J. Leung, A. W.-S. Lam, T.-W. Luo, R. 2021-12-30 doi:10.1101/2021.12.29.474431 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Robust expansion of phylogeny for fast-growing genome sequence data ]]> https://biorxiv.org/content/10.1101/2021.12.30.474610v1?rss=1 Ye, Y. Shum, M. Tsui, J. Yu, G. Smith, D. Zhu, H. Wu, J. Guan, Y. Lam, T. T.-Y. 2022-01-03 doi:10.1101/2021.12.30.474610 Cold Spring Harbor Laboratory Press 2022-01-03 <![CDATA[ An elite broadly neutralizing antibody protects SARS-CoV-2 Omicron variant challenge ]]> https://biorxiv.org/content/10.1101/2022.01.05.475037v1?rss=1 Zhou, B. Zhou, R. Chan, J. F.-W. Luo, M. Peng, Q. Yuan, S. Mok, B. W.-Y. Chen, B. Wang, P. Poon, V. K.-M. Chu, H. Chan, C. C.-S. Tsang, J. O.-L. Chan, C. C.-Y. Au, K.-K. Man, H.-O. Lu, L. To, K. K.-W. Chen, H. Yuen, K.-Y. Chen, Z. 2022-01-05 doi:10.1101/2022.01.05.475037 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Relaxed risk of predation drives parallel evolution of stickleback behaviour ]]> https://biorxiv.org/content/10.1101/2022.01.05.475046v1?rss=1 Fraimout, A. Päiviö, E. Merilä, J. 2022-01-06 doi:10.1101/2022.01.05.475046 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ APOE ε4 effects on hippocampal atrophy in the healthy elderly reflect future cognitive decline ]]> https://biorxiv.org/content/10.1101/2022.01.07.475319v1?rss=1 Zhang, L. Calero, M. Medina, M. Strange, B. 2022-01-14 doi:10.1101/2022.01.07.475319 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ The SARS-CoV-2 Omicron (B.1.1.529) variant exhibits altered pathogenicity, transmissibility, and fitness in the golden Syrian hamster model ]]> https://biorxiv.org/content/10.1101/2022.01.12.476031v1?rss=1 Yuan, S. Ye, Z.-W. Liang, R. Tang, K. Zhang, A. J. Lu, G. Ong, C. P. Poon, V. K.-M. Chan, C. C.-S. Mok, B. W. Y. Qin, Z. Xie, Y. Sun, H. Tsang, J. O.-L. Yuen, T. T.-T. Chik, K. K.-H. Chan, C. C.-Y. Cai, J.-P. Luo, C. Lu, L. Yip, C. C.-Y. Chu, H. To, K. K.-W. Chen, H. Jin, D.-Y. Yuen, K.-Y. Chan, J. F. W. 2022-01-13 doi:10.1101/2022.01.12.476031 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ FRET monitoring of transcription factor activities in living bacteria ]]> https://biorxiv.org/content/10.1101/2022.01.14.476424v1?rss=1 Wang, P. Zhang, G. Xu, Z. Chen, Z. Liu, X. Wang, C. Zheng, C. Wang, J. Zhang, H. Yan, A. 2022-01-15 doi:10.1101/2022.01.14.476424 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Computation of Antigenicity Predicts SARS-CoV-2 Vaccine Breakthrough Variants ]]> https://biorxiv.org/content/10.1101/2022.01.19.477009v1?rss=1 Hu, Y.-f. Hu, J.-c. Gong, H.-R. Danchin, A. Sun, R. Chu, H. Hung, I. F.-N. Yuen, K. Y. To, K. K.-W. Zhang, B.-Z. Yau, T. Huang, J.-D. 2022-01-20 doi:10.1101/2022.01.19.477009 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ XPD protects CTCF-Cohesin binding sites from somatic mutagenesis ]]> https://biorxiv.org/content/10.1101/2022.01.21.477237v1?rss=1 T]N mutations (SBS2) with altered correlation with replication timing. At a locoregional genomic level, mutant XPD BLCA had striking T>G mutation hotspots at CTCF-cohesin binding sites (CBS) with evidence linking XPD to genomic uracil repair. Leveraging differential distribution of somatic mutations, we developed a machine-learning model for predicting pathogenic XPD mutations, which we validated in an independent TCGA cohort with 100% accuracy. Our model enabled the discovery of missed XPD mutation calls and uncovered pathogenic non-hotspot XPD mutations in bladder cancer. Our study reveals how XPD mutations redistribute somatic mutations in cancer genomes and provides a genome sequencing approach to differentiate driver and passenger XPD mutations. ]]> Barbour, J. A. Ou, T. Fang, H. Yue, N. C. Zhu, X. Wong-Brown, M. Yang, H. Wong, Y. T. Wu, S. Wong, J. W. H. 2022-01-21 doi:10.1101/2022.01.21.477237 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Global success in oyster reef restoration despite ongoing recovery debt ]]> https://biorxiv.org/content/10.1101/2022.01.23.477429v1?rss=1 35% per annum. Therefore, while efficient restoration methods will produce enhanced recovery success and minimise recovery debt, potential future coastal development should be weighed up against not just the instantaneous damage to ecosystem functions and services but also the potential for generational loss of services and long-term recovery. ]]> Hemraj, D. A. Bishop, M. J. Hancock, B. Minuti, J. J. Thurstan, R. H. Zu Ermgassen, P. S. E. Russell, B. D. 2022-01-24 doi:10.1101/2022.01.23.477429 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine ]]> https://biorxiv.org/content/10.1101/2022.01.25.477789v1?rss=1 Wu, Y. Wang, S. Zhang, Y. Yuan, L. Zheng, Q. Wei, M. Shi, Y. Wang, Z. Ma, J. Wang, K. Nie, M. Xiao, J. Huang, Z. Chen, P. Guo, H. Lan, M. Xu, J. Hou, W. Hong, Y. Chen, D. Sun, H. Xiong, H. Zhou, M. Liu, C. Guo, W. Guo, H. Gao, J. Li, Z. Zhang, H. Wang, X. Li, S. Cheng, T. Zhao, Q. Chen, Y. Wu, T. Zhang, T. Zhang, J. Cao, H. Zhu, H. Yuan, Q. Guan, Y. Xia, N. 2022-01-26 doi:10.1101/2022.01.25.477789 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Peptide location fingerprinting identifies species- and tissue-conserved structural remodelling of proteins as a consequence of ageing and disease ]]> https://biorxiv.org/content/10.1101/2022.01.31.478441v1?rss=1 Eckersley, A. Ozols, M. Chen, P. Tam, V. Ward, L. J. Hoyland, J. A. Trafford, A. Yuan, X.-M. Schiller, H. B. Chan, D. Sherratt, M. J. 2022-01-31 doi:10.1101/2022.01.31.478441 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Egg-adaptation pathway of human influenza H3N2 virus is contingent on natural evolution ]]> https://biorxiv.org/content/10.1101/2022.01.31.478576v1?rss=1 Liang, W. Tan, T. J. C. Wang, Y. Lv, H. Sun, Y. Bruzzone, R. Mok, C. K. P. Wu, N. C. 2022-02-01 doi:10.1101/2022.01.31.478576 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Perivascular macrophages collaborate to facilitate chemotherapy resistance in cancer ]]> https://biorxiv.org/content/10.1101/2022.02.03.478952v1?rss=1 Anstee, J. E. Opzoomer, J. W. Dean, I. Muller, H. P. Bahri, M. Liakath-Ali, K. Liu, Z. Choy, D. Caron, J. Sosnowska, D. Beatson, R. Muliaditan, T. An, Z. Gillett, C. E. Lan, G. Zou, X. Watt, F. M. Ng, T. Burchell, J. M. Kordasti, S. Withers, D. R. Lawrence, T. Arnold, J. N. 2022-02-04 doi:10.1101/2022.02.03.478952 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ The Role of Notch Signaling in Endometrial Mesenchymal Stromal/Stem-like Cells Maintenance ]]> https://biorxiv.org/content/10.1101/2022.02.09.479815v1?rss=1 Zhang, S. Chan, R. W. Ng, E. H. Yeung, W. S. 2022-02-10 doi:10.1101/2022.02.09.479815 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ CRISPR-Detector: Fast and Accurate Detection, Visualization, and Annotation of Genome Wide Mutations Induced by Gene Editing Events ]]> https://biorxiv.org/content/10.1101/2022.02.16.480781v1?rss=1 Huang, L. Wang, D. Chen, H. Hu, J. Dai, X. Liu, C. Li, A. Shen, X. Qi, C. Sun, H. Zhang, D. Chen, T. Jiang, Y. 2022-02-19 doi:10.1101/2022.02.16.480781 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Phenethylamine-producing gut bacteria induces diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis ]]> https://biorxiv.org/content/10.1101/2022.03.05.483096v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@48400aorg.highwire.dtl.DTLVardef@1645aedorg.highwire.dtl.DTLVardef@18d878dorg.highwire.dtl.DTLVardef@be4b30_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhai, L. Huang, C. Ning, Z. Zhang, Y. Zhuang, M. Yang, W. Wang, X. Wang, J. Zhang, E. L. Xiao, H. Zhao, L. Lam, Y. Y. Chow, C. F. W. Huang, J. Yuan, S. Chan, K. M. Wong, H. L. X. Bian, Z.-x. 2022-03-05 doi:10.1101/2022.03.05.483096 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ Angiotensin converting enzyme 2 (ACE2): Virus accomplice or host defender ]]> https://biorxiv.org/content/10.1101/2022.03.06.483197v1?rss=1 View larger version (70K): org.highwire.dtl.DTLVardef@b51fcforg.highwire.dtl.DTLVardef@13b7f9corg.highwire.dtl.DTLVardef@136fe46org.highwire.dtl.DTLVardef@16fc92a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, J. Chang, H. Qiao, Y. Sun, H. Li, X. Yuan, S. Zhang, S. Shan, C. 2022-03-07 doi:10.1101/2022.03.06.483197 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ SARS-CoV-2 Omicron variant is more stable than the ancestral strain on various surfaces ]]> https://biorxiv.org/content/10.1101/2022.03.09.483703v1?rss=1 Chin, A. Lai, A. Peiris, M. Poon, L. 2022-03-10 doi:10.1101/2022.03.09.483703 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Dynamic evolution of recently duplicated genes in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.03.10.483751v1?rss=1 Ma, F. Lau, C. Y. Zheng, C. 2022-03-12 doi:10.1101/2022.03.10.483751 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Inbreeding depression in an outbred nine-spined stickleback (Pungitius pungitius) population ]]> https://biorxiv.org/content/10.1101/2022.03.15.483967v1?rss=1 Fraimout, A. Rastas, P. Lv, L. Merilä, J. 2022-03-17 doi:10.1101/2022.03.15.483967 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ DCATS: differential composition analysis for complex single-cell experimental designs ]]> https://biorxiv.org/content/10.1101/2022.03.21.485232v1?rss=1 Lin, X. Chau, C. Huang, Y. Ho, J. W. K. 2022-03-23 doi:10.1101/2022.03.21.485232 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ The Graphical R2D2 Estimator for the Precision Matrices ]]> https://biorxiv.org/content/10.1101/2022.03.22.485374v1?rss=1 Gan, D. Yin, G. Zhang, Y. 2022-03-25 doi:10.1101/2022.03.22.485374 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ Multiethnic Polygenic Risk Prediction in Diverse Populations through Transfer Learning ]]> https://biorxiv.org/content/10.1101/2022.03.30.486333v1?rss=1 Tian, P. Chan, T. H. Wang, Y.-F. Yang, W. Yin, G. Zhang, Y. D. 2022-03-30 doi:10.1101/2022.03.30.486333 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Variable Selection via Grace-AKO with Applications in Genomics ]]> https://biorxiv.org/content/10.1101/2022.03.30.486361v1?rss=1 Tian, P. Hu, Y. Liu, Z. Zhang, Y. D. 2022-03-31 doi:10.1101/2022.03.30.486361 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Prediction of brain functions from structural connectome using graph neural network ]]> https://biorxiv.org/content/10.1101/2022.03.31.484925v1?rss=1 Hui, E. S. Sun, Y. Ko, H. Chan, C. C. H. Cao, P. 2022-04-01 doi:10.1101/2022.03.31.484925 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Robustness of the ferret model for influenza risk assessment studies: a cross-laboratory exercise ]]> https://biorxiv.org/content/10.1101/2022.04.02.486825v1?rss=1 Belser, J. A. Lau, E. H. Barclay, W. Barr, I. G. Chen, H. Fouchier, R. A. Hatta, M. Herfst, S. Kawaoka, Y. Lakdawala, S. S. Lee, L. Y. Y. Neumann, G. Peiris, M. Perez, D. R. Russell, C. J. Subbarao, K. Sutton, T. C. Webby, R. J. Yang, H. Yen, H.-L. Bestebroer, T. Bhagwat, A. Blanchard, E. Caceres, C. J. Carnaccini, S. Chiba, S. Choy, K.-T. DeBeauchamp, J. L. de Meulder, D. Ferreri, L. M. Frise, R. Geiger, G. Hu, M. Hurt, A. C. Jeevan, T. Jones, J. E. Kercher, L. A. Kormuth, K. A. Le Sage, V. Lexmond, P. Li, C. Maines, T. R. Patel, D. R. Septer, K. M. 2022-04-02 doi:10.1101/2022.04.02.486825 Cold Spring Harbor Laboratory Press 2022-04-02 <![CDATA[ Key mutations on spike protein altering ACE2 receptor utilization and potentially expanding host range of emerging SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2022.04.11.487828v1?rss=1 Wang, Q. Ye, S.-B. Zhou, Z.-J. Li, J.-Y. Lv, J.-Z. Hu, B. Yuan, S. Qiu, Y. Ge, X.-Y. 2022-04-11 doi:10.1101/2022.04.11.487828 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Tomographic-encoded multiphoton (TEMP) microscopy ]]> https://biorxiv.org/content/10.1101/2022.04.11.487875v1?rss=1 He, H. Dong, X. Ren, Y.-X. Lai, C. S. W. Tsia, K. K. Wong, K. K. Y. 2022-04-11 doi:10.1101/2022.04.11.487875 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference ]]> https://biorxiv.org/content/10.1101/2022.04.27.489808v1?rss=1 Gao, M. Qiao, C. Huang, Y. 2022-04-29 doi:10.1101/2022.04.27.489808 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Multi-task learning uncovers robust translation cis-regulatory features ]]> https://biorxiv.org/content/10.1101/2022.05.03.490410v1?rss=1 Zheng, W. Fong, J. H. C. Wan, Y. K. Chu, A. H. Y. Huang, Y. Wong, A. S. L. Ho, J. W. K. 2022-05-04 doi:10.1101/2022.05.03.490410 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Clair3-Trio: high-performance Nanopore long-read variant calling in family trios with Trio-to-Trio deep neural networks ]]> https://biorxiv.org/content/10.1101/2022.05.03.490460v1?rss=1 Su, J. Zheng, Z. Ahmed, S. S. Lam, T.-W. Luo, R. 2022-05-04 doi:10.1101/2022.05.03.490460 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ ACE2 nanoparticles prevent cell entry of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.05.05.490805v1?rss=1 Sauvanet, C. Lemos, M. Bezault, A. Rodriguez de Francisco, B. Chan, M. C. Hui, K. P. Ng, K.-c. Nicholls, J. M. Volkmann, N. Hanein, D. 2022-05-06 doi:10.1101/2022.05.05.490805 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Assembly-free discovery of human novel sequences using long reads ]]> https://biorxiv.org/content/10.1101/2022.05.06.490971v1?rss=1 Li, Q. Yan, B. Lam, T.-W. Luo, R. 2022-05-09 doi:10.1101/2022.05.06.490971 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Three-dose vaccination-induced immune responses protect against SARS-CoV-2 Omicron-BA.2 ]]> https://biorxiv.org/content/10.1101/2022.05.09.491254v1?rss=1 Zhou, R. Liu, N. Li, X. Peng, Q. Yiu, C.-K. Huang, H. Yang, D. Du, Z. Kwok, H.-Y. Au, K.-K. Cai, J.-P. Hung, I. F.-N. To, K. K.-W. Xu, X. Yuen, K.-Y. Chen, Z. 2022-05-11 doi:10.1101/2022.05.09.491254 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Hippocampus Modulates Natural Sound Processing at Early Auditory Centers ]]> https://biorxiv.org/content/10.1101/2022.05.11.491576v1?rss=1 Wong, E. C. Wang, X. Wu, E. X. Leong, A. T. L. 2022-05-12 doi:10.1101/2022.05.11.491576 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ Molecular analysis of a public cross-neutralizing antibody response to SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.05.17.492220v1?rss=1 Yuan, M. Wang, Y. Lv, H. Wilson, I. A. Wu, N. C. 2022-05-18 doi:10.1101/2022.05.17.492220 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Ecological Dynamics Imposes Fundamental Challenges in Microbial Source Tracking ]]> https://biorxiv.org/content/10.1101/2022.05.21.492809v1?rss=1 Wang, X.-W. Wu, L. Dai, L. Ying, X. Zhang, T. Weiss, S. Liu, Y.-Y. 2022-05-21 doi:10.1101/2022.05.21.492809 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Morphological profiling by high-throughput single-cell biophysical fractometry ]]> https://biorxiv.org/content/10.1101/2022.05.24.493226v1?rss=1 Zhang, Z. Lee, K. C. M. Siu, D. M. D. Lai, Q. T. K. Lam, E. Y. M. Tsia, K. K. M. 2022-05-24 doi:10.1101/2022.05.24.493226 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ CSR-1 RNA interference pathway restricts holocentromere protein CENP-A/HCP-3 localization in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.05.26.493264v1?rss=1 Wong, C. Y. Y. Yuen, K. W. Y. Y. 2022-05-26 doi:10.1101/2022.05.26.493264 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ SARS-CoV-2 Omicron BA.2.12.1, BA.4, and BA.5 subvariants evolved to extend antibody evasion ]]> https://biorxiv.org/content/10.1101/2022.05.26.493517v1?rss=1 Wang, Q. Guo, Y. Iketani, S. Li, Z. Mohri, H. Wang, M. Yu, J. Bowen, A. D. Chan, J. Y. Shah, J. G. Nguyen, N. Meyers, K. Yin, M. T. Sobieszczyk, M. E. Sheng, Z. Huang, Y. Liu, L. Ho, D. 2022-05-26 doi:10.1101/2022.05.26.493517 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Invigorating human MSCs for transplantation therapy via Nrf2/DKK1 co- stimulation in a mice acute-on-chronic liver failure model ]]> https://biorxiv.org/content/10.1101/2022.05.29.493908v1?rss=1 Chen, F. Che, Z. Liu, Y. Luo, P. Xiao, L. Song, Y. Wang, C. Dong, Z. Li, M. Tipoe, G. L. Wu, D. Yang, M. Lv, Y. Wang, F. Wang, H. Xiao, J. 2022-05-30 doi:10.1101/2022.05.29.493908 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Application of metallo-supramolecular branched polymer improves particle distribution and orientation in single-particle cryo-EM ]]> https://biorxiv.org/content/10.1101/2022.06.08.495397v1?rss=1 Xu, Y. Wang, L. Qin, Y. Zhang, Y. Wang, Y. Dang, S. 2022-06-09 doi:10.1101/2022.06.08.495397 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Inferring CTCF insulators and anchored loops across human tissues and cell types ]]> https://biorxiv.org/content/10.1101/2022.06.15.496356v1?rss=1 Xu, H. Yi, X. Wang, W. Chu, X. Huang, D. Zhang, S. Dong, X. Wang, Z. Wang, J. Zhou, Y. Zhao, K. Yao, H. Wang, J. Chen, K. Plewczynski, D. Sham, P. C. Li, M. J. 2022-06-17 doi:10.1101/2022.06.15.496356 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Long non-coding RNA as environmental regulator in a non-model fish ]]> https://biorxiv.org/content/10.1101/2022.06.17.496488v1?rss=1 Kang, J. Chung, A. Suresh, S. Bonzi, L. C. Sourisse, J. M. Ramirez-Calero, S. Romeo, D. Petit-Marty, N. Pegueroles, C. Schunter, C. 2022-06-17 doi:10.1101/2022.06.17.496488 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ The domain-separation low-dimensional language network dynamics in the resting-state support the flexible functional segregation and integration during language and speech processing ]]> https://biorxiv.org/content/10.1101/2022.06.19.496753v1?rss=1 55%), the language network kept inactive in state 4. Machine learning-based dFC-linguistics prediction analyses showed that dFCs of the four states significantly predicted individual linguistic performance. These findings suggest a domain-separation manner of language network dynamics in the resting-state, which forms a dynamic "meta-networking" (network of networks) framework. HighlightsO_LIThe time-varying language network in the resting-state is robustly clustered into four low-dimensional states. C_LIO_LISpatially, the first three dFC states are cognitively meaningful, which highly resemble the neurobiology of primary auditory processing and lexical-phonological representation, speech production processing, and semantic processing, respectively. C_LIO_LITemporally, the first three states appeared exclusively in limited time bins ([~]15%), and most of the time (> 55%), the language network kept inactive in state 4. C_LIO_LIA dynamic "meta-networking" framework of language network in the resting-state is proposed. C_LI ]]> Yuan, B. Xie, H. Wang, Z. Xu, Y. Zhang, H. Liu, J. Chen, L. Li, C. Tan, S. Lin, Z. Hu, X. Gu, T. Lu, J. Liu, D.-Q. Wu, J. 2022-06-20 doi:10.1101/2022.06.19.496753 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ DNA packaging via hierarchical chromatin structures revealed by live-cell 3D imaging ]]> https://biorxiv.org/content/10.1101/2022.06.22.497271v1?rss=1 ZHENG, Y. Ye, S. Li, S. Liu, C. Luo, S. Chen, Y. Li, Y. Huang, L. Deng, S. Chen, P. Zhang, Y. Ji, W. Luo, R. Li, G. Yang, D. 2022-06-25 doi:10.1101/2022.06.22.497271 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ Improving the workflow to crack Small, Unbalanced, Noisy, but Genuine (SUNG) datasets in bioacoustics: the case of bonobo calls ]]> https://biorxiv.org/content/10.1101/2022.06.26.497684v1?rss=1 Arnaud, V. Pellegrino, F. Keenan, S. St-Gelais, X. Mathevon, N. Levrero, F. Coupe, C. 2022-06-29 doi:10.1101/2022.06.26.497684 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ A Chromosome-level Assembly of the Japanese Eel Genome, Insights into Gene Duplication and Chromosomal Reorganization ]]> https://biorxiv.org/content/10.1101/2022.06.28.497880v1?rss=1 WANG, H. WAN, H. T. WU, B. JIAN, J. NG, A. H. CHUNG, C. Y.-L. CHOW, E. Y.-C. ZHANG, J. WONG, A. O. LAI, K. P. CHAN, T. F. Zhang, E. L. WONG, C. K.-C. 2022-07-01 doi:10.1101/2022.06.28.497880 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ CoxMKF: A Knockoff Filter for High-Dimensional Mediation Analysis with a Survival Outcome in Epigenetic Studies ]]> https://biorxiv.org/content/10.1101/2022.06.29.498077v1?rss=1 Tian, P. Yao, M. Huang, T. Liu, Z. 2022-07-02 doi:10.1101/2022.06.29.498077 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ A systematic investigation of lactic acid bacteria-derived biosynthetic gene clusters reveals diverse antagonistic bacteriocins in the human microbiome ]]> https://biorxiv.org/content/10.1101/2022.07.03.498435v1?rss=1 Zhang, D. Zhang, J. Kalimuthu, S. Liu, J. Song, Z. He, B. Cai, P. Zhong, Z. Feng, C. Neelakantan, P. LI, Y.-x. 2022-07-04 doi:10.1101/2022.07.03.498435 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ Duet: SNP-Assisted Structural Variant Calling and Phasing Using Oxford Nanopore Sequencing ]]> https://biorxiv.org/content/10.1101/2022.07.04.498779v1?rss=1 Zhou, Y. Leung, A. W.-S. Ahmed, S. S. Lam, T.-W. Luo, R. 2022-07-05 doi:10.1101/2022.07.04.498779 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Updating memories of unwanted emotions during human sleep ]]> https://biorxiv.org/content/10.1101/2022.07.18.500414v1?rss=1 Xia, T. Yao, Z. Guo, X. Liu, J. Chen, D. Liu, Q. Ken, P. A. Hu, X. 2022-07-20 doi:10.1101/2022.07.18.500414 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Organic Electrochemical Transistor as an On-site Signal Amplifier for Electrochemical Aptamer-based Sensing ]]> https://biorxiv.org/content/10.1101/2022.07.18.500444v1?rss=1 Ji, X. Lin, X. Rivnay, J. 2022-07-19 doi:10.1101/2022.07.18.500444 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Testis-specific H2BFWT disrupts nucleosome integrity through reductions of DNA-histone interactions ]]> https://biorxiv.org/content/10.1101/2022.07.20.500751v1?rss=1 Ding, D. Pang, M. Y. H. Deng, M. Nguyen, T. T. Sun, X. Xu, Z. Zhang, Y. Zhai, Y. Yan, Y. Ishibashi, T. 2022-07-21 doi:10.1101/2022.07.20.500751 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Symbiosis-driven development in an early branching metazoan ]]> https://biorxiv.org/content/10.1101/2022.07.21.500558v1?rss=1 Ohdera, A. H. Darymple, J. Avila-Magana, V. Sharp, V. Watson, K. McCauley, M. Steinworth, B. Diaz-Almeyda, E. M. Kitchen, S. A. Poole, A. Z. Bellantuono, A. J. Haridas, S. Grigoriev, I. V. Goentoro, L. Vallen, E. Baker, D. M. LaJeunesse, T. C. Loesgen, S. martindale, m. q. DeGennaro, M. Fitt, W. K. Medina, M. 2022-07-22 doi:10.1101/2022.07.21.500558 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Age-related seroprevalence trajectories of seasonal coronaviruses in children ]]> https://biorxiv.org/content/10.1101/2022.07.26.501649v1?rss=1 Luo, Y. Lv, H. Zhao, S. Sun, Y. Liu, C. Chen, C. Liang, W. Kwok, K.-o. Teo, Q. W. So, R. T. Lin, Y. Deng, Y. Li, B. Dai, Z. Zhu, J. Zhang, D. Fernando, J. Wu, N. C. Tun, H. M. Bruzzone, R. Mok, C. K. Mu, X. 2022-07-28 doi:10.1101/2022.07.26.501649 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLpro ]]> https://biorxiv.org/content/10.1101/2022.08.10.503531v1?rss=1 Hou, N. Shuai, L. Zhang, L. Xie, X. Tang, K. Zhu, Y. Yu, Y. Zhang, W. Tan, Q. Zhong, G. Wen, Z. Wang, C. He, X. Huo, H. Gao, H. Xu, Y. Xue, J. Peng, C. Zou, J. Schindewolf, C. Menachery, V. Su, W. Yuan, Y. Shen, Z. Zhang, R. Yuan, S. Yu, H. Shi, P.-Y. Bu, Z. Huang, J. Hu, Q. 2022-08-11 doi:10.1101/2022.08.10.503531 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ ERStruct: A Python Package for Inferring the Number of Top Principal Components from Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/2022.08.15.503962v1?rss=1 Yang, J. Xu, Y. Liu, Z. 2022-08-15 doi:10.1101/2022.08.15.503962 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ MMP14 cleaves PTH1R in the chondrocyte derived osteoblast lineage, curbing signaling intensity for proper bone anabolism ]]> https://biorxiv.org/content/10.1101/2022.08.17.504252v1?rss=1 Chu, T. L. Chen, P. Yu, A. X. Kong, M. P. Tan, Z. Tsang, K. Y. Zhou, Z. Cheah, K. S. E. 2022-08-17 doi:10.1101/2022.08.17.504252 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ SpatialDM: Rapid identification of spatially co-expressed ligand-receptor reveals cell-cell communication patterns ]]> https://biorxiv.org/content/10.1101/2022.08.19.504616v1?rss=1 LI, Z. Wang, T. Liu, P. Huang, Y. 2022-08-22 doi:10.1101/2022.08.19.504616 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis ]]> https://biorxiv.org/content/10.1101/2022.09.02.505700v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@1710d00org.highwire.dtl.DTLVardef@10ca8e0org.highwire.dtl.DTLVardef@2310d1org.highwire.dtl.DTLVardef@252728_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chao, Y. Xiang, Y. Xiao, J. Zhang, S. Zheng, W. Wan, X. LI, Z. Gao, M. Wang, G. Chen, Z. Ebrahimkhani, M. Yang, C. Wu, A. R. Liu, P. Huang, Y. Sugimura, R. 2022-09-03 doi:10.1101/2022.09.02.505700 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Positive effects of tree diversity on tropical forest restoration in a field-scale experiment ]]> https://biorxiv.org/content/10.1101/2022.09.09.507141v1?rss=1 Veryard, R. Wu, J. O'Brien, M. J. Anthony, R. Both, S. Burslem, D. F. R. P. Chen, B. Fernandez-Miranda Cagigal, E. Godfray, H. C. J. Godoong, E. Liang, S. Saner, P. Schmid, B. Sau Wai, Y. Xie, J. Reynolds, G. Hector, A. 2022-09-13 doi:10.1101/2022.09.09.507141 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ A dynamic template complex mediates Munc18-chaperoned SNARE assembly ]]> https://biorxiv.org/content/10.1101/2022.09.09.507208v1?rss=1 Yang, J. Jin, H. Liu, Y. Guo, Y. Zhang, Y. 2022-09-09 doi:10.1101/2022.09.09.507208 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Environment-wide and epigenome-wide association study of adiposity in "Children of 1997" birth cohort ]]> https://biorxiv.org/content/10.1101/2022.09.12.507623v1?rss=1 Zhao, J. Fan, B. Huang, J. Cowling, B. J. Au Yeung, S. L. R. Baccarelli, A. M. Leung, G. Schooling, C. M. 2022-09-15 doi:10.1101/2022.09.12.507623 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Mechanistic insights into zearalenone-accelerated colorectal cancer in mice using integrative multi-omics approaches ]]> https://biorxiv.org/content/10.1101/2022.09.21.508814v1?rss=1 Lo, E. K. K. Wang, x. Lee, P.-K. Wong, H.-C. Lee, J. C.-Y. Gallego, C. G. Zhao, D. El-Nezami, H. Li, J. 2022-09-21 doi:10.1101/2022.09.21.508814 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Enhancing Sox/Oct cooperativity induces higher-grade developmental reset ]]> https://biorxiv.org/content/10.1101/2022.09.23.509242v1?rss=1 MacCarthy, C. M. Malik, V. Wu, G. Velychko, T. Keshet, G. Jauch, R. Cojocaru, V. Scholer, H. Velychko, S. 2022-09-25 doi:10.1101/2022.09.23.509242 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ Deciphering Spatial Domains by Integrating Histopathological Image and Transcriptomics via Contrastive Learning ]]> https://biorxiv.org/content/10.1101/2022.09.30.510297v1?rss=1 Zeng, Y. Yin, R. Luo, M. Chen, J. Pan, Z. Lu, Y. Yu, W. Yang, Y. 2022-10-03 doi:10.1101/2022.09.30.510297 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response ]]> https://biorxiv.org/content/10.1101/2022.10.03.510566v1?rss=1 Zhang, L. Jiang, Y. He, J. Chen, J. Qi, R. Yuan, L. Shao, T. Chen, C. Chen, Y. Wang, X. Lei, X. Gao, Q. Zhuang, C. Zhou, M. Ma, J. Liu, W. Yang, M. Fu, R. Wu, Y. Chen, F. Xiong, H. Nie, M. Chen, Y. Wu, K. Fang, M. Wang, Y. Zheng, Z. Huang, S. Ge, S. Cheng, S.-C. Zhu, H. Chen, T. Yuan, Q. Wu, T. Zhang, J. Chen, Y. Zhang, T. Qi, H. Guan, Y. Xia, N. 2022-10-03 doi:10.1101/2022.10.03.510566 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ An integrated cell barcoding and computational analysis pipeline for scalable analysis of differentiation at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2022.10.12.511862v1?rss=1 Shen, S. Werner, T. Sun, Y. Shim, W. J. Lukowski, S. Andersen, S. Chiu, H. S. Xia, D. Chen, X. Pham, D. Su, Z. Powell, J. E. Tam, P. P. L. Boden, M. Ho, J. W. K. Nguyen, Q. Palpant, N. J. 2022-10-14 doi:10.1101/2022.10.12.511862 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity ]]> https://biorxiv.org/content/10.1101/2022.10.12.512003v1?rss=1 Sun, Y. Shim, W. J. Shen, S. Sinniah, E. Pham, D. Su, Z. White, M. D. Ho, J. W. K. Nguyen, Q. Boden, M. Palpant, N. 2022-10-17 doi:10.1101/2022.10.12.512003 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Genetic architecture of behavioural resilience to ocean acidification ]]> https://biorxiv.org/content/10.1101/2022.10.18.512656v1?rss=1 Lehmann, R. Schunter, C. Welch, M. J. Arold, S. T. Nilsson, G. E. tegner, j. Munday, P. L. Ravasi, T. 2022-10-21 doi:10.1101/2022.10.18.512656 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ PAM-less Exonuclease-assisted Cas12a for visual detection of Vibrio Species ]]> https://biorxiv.org/content/10.1101/2022.10.21.513145v1?rss=1 Zhang, D. H. Raykar, S. Ng, K. T. C. 2022-10-21 doi:10.1101/2022.10.21.513145 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ INSIDER: Interpretable Sparse Matrix Decomposition for Bulk RNA Expression Data Analysis ]]> https://biorxiv.org/content/10.1101/2022.11.10.515904v1?rss=1 ZHAO, K. HUANG, S. LIN, C. Sham, P. C. SO, H.-C. Lin, Z. 2022-11-13 doi:10.1101/2022.11.10.515904 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Human Early Syncytiotrophoblasts Are Highly Susceptible to SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2022.11.17.516978v1?rss=1 Liu, P. RUAN, D. Ye, Z.-W. Yuan, S. Li, Z. Zhang, W. Ong, C. P. Tang, K. Guo, J. Xuan, Y. Tam, T. T. K. K. Huang, Y. Zhang, Q. Lee, C.-L. Chiu, P. C. N. Liu, F. Jin, D.-Y. 2022-11-18 doi:10.1101/2022.11.17.516978 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Environmental and genetic drivers of population differences in SARS-CoV-2 immune responses ]]> https://biorxiv.org/content/10.1101/2022.11.22.517073v1?rss=1 Aquino, Y. Bisiaux, A. Li, Z. O'Neill, M. Mendoza-Revilla, J. Merkling, S. H. Kerner, G. Hasan, M. Libri, V. Bondet, V. Smith, N. de Cevins, C. Menager, M. M. Luca, F. Pique-Regi, R. Barba-Spaeth, G. Pietropaoli, S. Schwartz, O. Leroux-Roels, G. Lee, C.-K. Leung, K. Wu, J. T. K. Peiris, J. S. M. Bruzzone, R. Abel, L. Casanova, J.-L. Valkenburg, S. A. Duffy, D. A. Patin, E. Rotival, M. Quintana-Murci, L. 2022-11-22 doi:10.1101/2022.11.22.517073 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Region- and variance-based DNA methylation analyses reveal novel disease genes and pathways for systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/2022.11.23.516835v1?rss=1 Guo, M. Wang, T.-Y. Shen, J. J. Wang, Y.-F. Lau, Y.-L. Yang, W. 2022-11-24 doi:10.1101/2022.11.23.516835 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Reactivating Positive Personality Traits During Sleep Impacts Self-Evaluative Memories ]]> https://biorxiv.org/content/10.1101/2022.11.27.518064v1?rss=1 Yao, Z. Xia, T. Zhang, Z. Lin, X. Qin, P. Ma, Y. Hu, X. 2022-11-27 doi:10.1101/2022.11.27.518064 Cold Spring Harbor Laboratory Press 2022-11-27 <![CDATA[ Bioavailability of Schisandrin B and its effect on 5-Fluorouracil metabolism in a xenograft mouse model of colorectal cancer ]]> https://biorxiv.org/content/10.1101/2022.11.28.518277v1?rss=1 Lee, P.-K. Co, V. A. Yang, Y. Wan, M. L. Y. El-Nezami, H. Zhao, D. 2022-11-29 doi:10.1101/2022.11.28.518277 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Modulating the epigenetic state promotes the reprogramming of transformed cells to pluripotency in a line-specific manner ]]> https://biorxiv.org/content/10.1101/2022.12.01.518778v1?rss=1 Fu, X. Zhuang, Q. Babarinde, I. A. Shi, L. Ma, G. Hu, H. Li, Y. Chen, J. Xiao, Z. Deng, B. Sun, L. Jauch, R. Hutchins, A. 2022-12-02 doi:10.1101/2022.12.01.518778 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Covidscope: An atlas-scale COVID-19 resource for single-cell meta analysis at sample and cell levels ]]> https://biorxiv.org/content/10.1101/2022.12.03.518997v1?rss=1 Yin, D. Cao, Y. Chen, J. Mak, C. L. Y. Yu, K. H. O. Lin, Y. Ho, J. W. K. Yang, J. Y. H. 2022-12-05 doi:10.1101/2022.12.03.518997 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ PD-L1 regulates inflammatory macrophage development from human pluripotent stem cells by maintaining interferon-gamma signal ]]> https://biorxiv.org/content/10.1101/2022.12.14.520176v1?rss=1 Cao, H. Xiang, Y. Zhang, S. Chao, Y. Guo, J. Ho, J. W. K. Huang, Y. Liu, P. Sugimura, R. 2022-12-16 doi:10.1101/2022.12.14.520176 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Identification of a key genetic factor governing arabinan utilization in the gut microbiome suggests a novel therapeutic target for constipation ]]> https://biorxiv.org/content/10.1101/2022.12.15.518621v1?rss=1 Zhang, C. Yu, L. Ma, C. Jiang, S. Wang, S. Tian, F. Xue, Y. Zhao, J. Zhang, H. Liu, L. Chen, W. Huang, S. Zhang, J. Zhai, Q. 2022-12-15 doi:10.1101/2022.12.15.518621 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ ClpP/ClpX deficiency impairs mitochondrial functions and mTORC1 signaling during spermatogenesis and meiosis ]]> https://biorxiv.org/content/10.1101/2022.12.16.520702v1?rss=1 Guo, C. Xiao, Y. Gu, J. Hu, Z. Zheng, J. Hua, R. Hai, Z. Su, J. Zhang, J. Yeung, W. S. B. Wang, T. 2022-12-16 doi:10.1101/2022.12.16.520702 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Evaluation of Mycobacterium Tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling ]]> https://biorxiv.org/content/10.1101/2022.12.17.520855v1?rss=1 Su, J. Lui, W. W. Lee, Y. Zheng, Z. Siu, G. K.-H. Ng, T. T.-L. Zhang, T. Lam, T. T.-Y. Lao, H.-Y. Yam, W.-C. Tam, K. K.-G. Leung, K. S.-S. Lam, T.-W. Leung, A. W.-S. Luo, R. 2022-12-17 doi:10.1101/2022.12.17.520855 Cold Spring Harbor Laboratory Press 2022-12-17 <![CDATA[ The episodic resurgence of highly pathogenic avian influenza H5 virus ]]> https://biorxiv.org/content/10.1101/2022.12.18.520670v1?rss=1 Xie, R. Edwards, K. M. Wille, M. Wei, X. Wong, S.-S. Zanin, M. El-Shesheny, R. Ducatez, M. Poon, L. L. M. Kayali, G. Webby, R. J. Dhanasekaran, V. 2022-12-18 doi:10.1101/2022.12.18.520670 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ A converged ubiquitin-proteasome pathway for the degradation of TOC and TOM tail-anchored receptors ]]> https://biorxiv.org/content/10.1101/2023.01.07.523072v1?rss=1 Yang, M. Chen, S. Lim, S.-L. Yang, L. Zhong, J. Y. Chan, K. C. Zhao, Z. Wong, K.-B. Wang, J. Lim, B. L. 2023-01-08 doi:10.1101/2023.01.07.523072 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ High-throughput quantification of camelid cytokine mRNA expression in PBMCs by microfluidic qPCR technology ]]> https://biorxiv.org/content/10.1101/2023.01.15.524100v1?rss=1 Rodon, J. Te, N. Ballester, M. Segales, J. Vergara-Alert, J. Bensaid, A. 2023-01-18 doi:10.1101/2023.01.15.524100 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Towards a reliable spatial analysis of missing features via spatially-regularized imputation ]]> https://biorxiv.org/content/10.1101/2023.01.20.524992v1?rss=1 Qiao, C. Huang, Y. 2023-01-23 doi:10.1101/2023.01.20.524992 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Item-specific memory reactivation supports overnight memory consolidation ]]> https://biorxiv.org/content/10.1101/2023.01.25.525599v1?rss=1 Liu, J. Xia, T. Chen, D. Yao, Z. Zhu, M. Antony, J. W. Lee, T. M. Hu, X. 2023-01-26 doi:10.1101/2023.01.25.525599 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling ]]> https://biorxiv.org/content/10.1101/2023.01.26.525795v1?rss=1 Zhou, H.-Y. Fu, Y. Zhang, Z. Bian, C. Yu, Y. 2023-01-27 doi:10.1101/2023.01.26.525795 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Stochastic dispersal assembly dominates tropical invertebrate community assembly regardless of land use intensity. ]]> https://biorxiv.org/content/10.1101/2023.01.30.526177v1?rss=1 Granville, N. R. Barclay, M. V. L. Boyle, M. J. W. Fayle, T. M. Hardwick, J. L. Kinneen, L. Kitching, R. L. Maunsell, S. C. Miller, J. A. Sharp, A. C. Stork, N. E. Ewers, R. M. 2023-02-01 doi:10.1101/2023.01.30.526177 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Unraveling the causal genes and transcriptomic determinants of human telomere length ]]> https://biorxiv.org/content/10.1101/2023.02.01.526642v1?rss=1 Cao, J. Shen, Y. Fan, X. Yang, H. Dong, X. Zhang, S. Yi, X. Shuai, L. Shi, L. Liu, Z. Yang, J. Hao, J. Chen, K. Huang, D. Wang, F. Li, M. J. 2023-02-03 doi:10.1101/2023.02.01.526642 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Imprinted anti-hemagglutinin and anti-neuraminidase antibody responses after childhood infections of A(H1N1) and A(H1N1)pdm09 influenza viruses ]]> https://biorxiv.org/content/10.1101/2023.02.01.526741v1?rss=1 Daulagala, P. Mann, B. Leung, K. Lau, E. Yung, L. Lei, R. Nizami, S. I. N. Wu, J. T. Chiu, S. S. Daniels, R. S. Wu, N. C. Wentworth, D. E. Peiris, J. S. M. Yen, H.-L. 2023-02-02 doi:10.1101/2023.02.01.526741 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Lack of neutralizing antibodies against the current circulating influenza viruses during the Omicron outbreak in Hong Kong ]]> https://biorxiv.org/content/10.1101/2023.02.07.527570v1?rss=1 Liang, W. Lv, H. Chen, C. Sun, Y. Hui, D. S. Mok, C. K. P. 2023-02-08 doi:10.1101/2023.02.07.527570 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Structural stability of the oyster gut microbiome contributes to the host's physiological tolerance to temperature fluctuations on tropical rocky shores ]]> https://biorxiv.org/content/10.1101/2023.02.08.527599v1?rss=1 Arromrak, B. S. Wong, A. T. C. Hui, T. Y. Leung, K. S. Williams, G. A. Ganmanee, M. Durand, T. Lee, J. C. Y. Gaitan-Espitia, J. D. 2023-02-08 doi:10.1101/2023.02.08.527599 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ In-group Social Conformity Updates the Neural Representation of Facial Attractiveness ]]> https://biorxiv.org/content/10.1101/2023.02.08.527779v1?rss=1 Chen, D. Yao, Z. Liu, J. Wu, H. Hu, X. 2023-02-10 doi:10.1101/2023.02.08.527779 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Long-term epidemiology and evolution of swine influenza viruses in Vietnam ]]> https://biorxiv.org/content/10.1101/2023.02.08.527780v1?rss=1 Cheung, J. Bui, A. N. Younas, S. Edwards, K. M. Nguyen, H. Q. Pham, N. T. Bui, V. N. Peiris, M. Dhanasekaran, V. 2023-02-11 doi:10.1101/2023.02.08.527780 Cold Spring Harbor Laboratory Press 2023-02-11 <![CDATA[ ImmuneMirror: a Machine Learning-based Integrative Pipeline and Web Server for Neoantigen Prediction ]]> https://biorxiv.org/content/10.1101/2023.02.09.527828v1?rss=1 10 mutations per Mbp). Although the efficacy of PD-1 blockade has been demonstrated in advanced MSI-H patients, almost half of such patients do not respond well. Our study may identify MSI-H patients who do not benefit from this treatment. Additionally, the neopeptide YMCNSSCMGV-TP53G245V, derived from a hotspot mutation restricted by HLA-A02, was identified as an actionable target in esophageal squamous cell carcinoma (ESCC). This is the largest study to comprehensively evaluate neoantigen prediction models using experimentally validated neopeptides. Our results demonstrate the reliability and effectiveness of ImmuneMirror for neoantigen prediction. ]]> Chuwdhury, G. S. Guo, Y. Cheung, C.-L. Lam, K.-O. Kam, N.-W. Liu, Z. Dai, W. 2023-02-10 doi:10.1101/2023.02.09.527828 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Vulture: Cloud-enabled scalable mining of microbial reads in public scRNA-seq data ]]> https://biorxiv.org/content/10.1101/2023.02.13.528411v1?rss=1 Chen, J. Yin, D. Wong, H. Y. H. Duan, X. Yu, K. H. O. Ho, J. W. K. 2023-02-15 doi:10.1101/2023.02.13.528411 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Orthographic deficits but typical visual perceptual processing in Chinese adults with reading disability ]]> https://biorxiv.org/content/10.1101/2023.02.13.528424v1?rss=1 Yan, X. Chen, J. Fu, Y. Wu, Y. Ku, Y. Cao, F. 2023-02-14 doi:10.1101/2023.02.13.528424 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Positive coping supports children's emotional wellness: Behavioral evidence and neuroendocrine mechanisms ]]> https://biorxiv.org/content/10.1101/2023.02.19.526965v1?rss=1 Tian, T. Chen, B. Zhao, Y. Gao, H. Chen, M. He, Y. Xu, J. Jiang, M. Xiong, B. Qin, S. 2023-02-21 doi:10.1101/2023.02.19.526965 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Retrieved Sequence Augmentation for Protein Representation Learning ]]> https://biorxiv.org/content/10.1101/2023.02.22.529597v1?rss=1 Ma, C. Zhao, H. Zheng, L. Xin, J. Li, Q. Wu, L. Deng, Z. Lu, Y. Liu, Q. Kong, L. 2023-02-23 doi:10.1101/2023.02.22.529597 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ APLNR marks a cardiac progenitor derived with human induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2023.02.22.529606v1?rss=1 Lam, Y. Y. Chan, C. H. Geng, L. Wong, N. Keung, W. Cheung, Y. F. 2023-02-23 doi:10.1101/2023.02.22.529606 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ How is Emotional Evidence from Multiple Sources Used in Perceptual Decision Making? ]]> https://biorxiv.org/content/10.1101/2023.02.28.530147v1?rss=1 Ngai, H. H. Hsiao, J. H. Luhmann, C. Mohanty, A. Jin, J. 2023-03-01 doi:10.1101/2023.02.28.530147 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Long-term reliable neural decoding based on flexible implantable microelectronics and machine learning for seizure prediction application ]]> https://biorxiv.org/content/10.1101/2023.03.08.531452v1?rss=1 He, Z. Zheng, J. Duan, J. Jin, Z. Huang, Z. Wu, S. He, Q. So, K.-F. Zhang, S. Xiong, Z. 2023-03-10 doi:10.1101/2023.03.08.531452 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ SpatialScope: A unified approach for integrating spatial and single-cell transcriptomics data using deep generative models ]]> https://biorxiv.org/content/10.1101/2023.03.14.532529v1?rss=1 Wan, X. Xiao, J. Tam, S. S. T. Cai, M. Sugimura, R. Wang, Y. Wan, X. Lin, Z. Wu, A. Yang, C. 2023-03-15 doi:10.1101/2023.03.14.532529 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ De novo mutation rates in sticklebacks ]]> https://biorxiv.org/content/10.1101/2023.03.16.532904v1?rss=1 50x) whole genome re-sequencing and a high-quality reference genome. After stringent filtering, we discovered 295 germline mutations from 106 offspring translating to {micro} = 4.64 x 10-9 and {micro} = 4.08 x 10-9 per base, per generation, in the two populations, respectively. Twenty percent of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated {micro} was 3.2 times smaller than the commonly used substitution rate, recalibration with {micro} led to substantial increase in estimated divergence times between different stickleback species. Our estimates of de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular. ]]> Zhang, C. Reid, K. Sands, A. F. Fraimout, A. Schierup, M. H. Merila, J. 2023-03-19 doi:10.1101/2023.03.16.532904 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ Determinants of genetic diversity in sticklebacks ]]> https://biorxiv.org/content/10.1101/2023.03.17.533073v1?rss=1 Kivikoski, M. Feng, X. Loytynoja, A. Momigliano, P. Merila, J. 2023-03-17 doi:10.1101/2023.03.17.533073 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression ]]> https://biorxiv.org/content/10.1101/2023.03.21.533716v1?rss=1 Lee, S. Barbour, J. A. Tam, Y. M. Yang, H. Huang, Y. Wong, J. W. H. 2023-03-23 doi:10.1101/2023.03.21.533716 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Mutation nsp6 L232F associated with MERS-CoV zoonotic transmission confers higher viral replication in human respiratory tract cultures ex-vivo ]]> https://biorxiv.org/content/10.1101/2023.03.27.534490v1?rss=1 So, R. T. Chu, D. K. W. Hui, K. P. Y. Mok, C. K.-P. Sanyal, S. Nicholls, J. M. Ho, J. C. W. Cheung, M. C. NG, K. C. Yeung, H. W. Chan, M. C. W. Poon, L. L. M. Zhao, J. Peiris, J. S. M. 2023-03-28 doi:10.1101/2023.03.27.534490 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ XClone: detection of allele-specific subclonal copy number variations from single-cell transcriptomic data ]]> https://biorxiv.org/content/10.1101/2023.04.03.535352v1?rss=1 Huang, R. Huang, X. Tong, Y. Yan, H. Y. N. Leung, S. Y. Stegle, O. Huang, Y. 2023-04-05 doi:10.1101/2023.04.03.535352 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ A statistical framework for quantifying the nuclear export rate of influenza viral mRNAs. ]]> https://biorxiv.org/content/10.1101/2023.04.07.536075v1?rss=1 Miura, M. Kiuchi, N. Lau, S.-Y. Mok, B. W.-Y. Ushirogawa, H. Naito, T. Chen, H. Saito, M. 2023-04-08 doi:10.1101/2023.04.07.536075 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking ]]> https://biorxiv.org/content/10.1101/2023.04.08.536123v1?rss=1 Liu, L. Casner, R. G. Guo, Y. Wang, Q. Iketani, S. Chan, J. F.-W. Yu, J. Dadonaite, B. Nair, M. S. Mohri, H. Reddem, E. R. Yuan, S. Poon, V. K.-M. Chan, C. C.-S. Yuen, K.-Y. Sheng, Z. Huang, Y. Bloom, J. D. Shapiro, L. Ho, D. D. 2023-04-10 doi:10.1101/2023.04.08.536123 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data ]]> https://biorxiv.org/content/10.1101/2023.04.17.536840v1?rss=1 Hou, R. Hon, C.-C. Huang, Y. 2023-04-18 doi:10.1101/2023.04.17.536840 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Cell Type-Specific Regulation by a Heptad of Transcription Factors in Human Hematopoietic Stem and Progenitor Cells ]]> https://biorxiv.org/content/10.1101/2023.04.18.537282v1?rss=1 Subramanian, S. Thoms, J. Huang, Y. Cornejo, P. Koch, F. C. Jacquelin, S. Shen, S. Song, E. Joshi, S. Brownlee, C. Woll, P. S. Fajardo, D. C. Beck, D. Curtis, D. J. Yehson, K. Antonenas, V. O'Brien, T. Trickett, A. Powell, J. A. Lewis, I. D. Pitson, S. M. Gandhi, M. K. Lane, S. W. Vafaee, F. Wong, E. Gottgens, B. Rokny, H. A. Wong, J. W. H. Pimanda, J. E. 2023-04-18 doi:10.1101/2023.04.18.537282 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Sensory Eye Dominance Plasticity in the Human Adult Visual Cortex ]]> https://biorxiv.org/content/10.1101/2023.04.21.537873v1?rss=1 KAM, K. Y. Chang, D. H. F. 2023-04-22 doi:10.1101/2023.04.21.537873 Cold Spring Harbor Laboratory Press 2023-04-22 <![CDATA[ The Association between Commensal Flagellated Bacteria and Cardiovascular Benefits in Humans ]]> https://biorxiv.org/content/10.1101/2023.05.04.539500v1?rss=1 Yiu, J. H. C. Cai, J. Cheung, S. W. Chin, K. T. C. Chan, C. F. Ma, E. S. C. Sharma, R. Dorweiler, B. Woo, C. W. H. 2023-05-07 doi:10.1101/2023.05.04.539500 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Endogenous fine-mapping of functional regulatory elements in complex genetic loci ]]> https://biorxiv.org/content/10.1101/2023.05.06.539696v1?rss=1 Zhao, K. Zhou, Y. Wu, C. Wang, J. Yao, H. Cheng, X. Zhao, L. Wang, W. Chu, X. Yi, X. Chen, Y. Li, M. Lu, W. Chen, K. Sham, P. C. Li, M. J. 2023-05-08 doi:10.1101/2023.05.06.539696 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Bacterial Cytochrome P450-catalyzed Post-translational Macrocyclization ]]> https://biorxiv.org/content/10.1101/2023.05.08.539676v1?rss=1 He, B.-B. Cheng, Z. Liu, J. Zhong, Z. Gao, Y. Liu, H. Li, Y.-X. 2023-05-08 doi:10.1101/2023.05.08.539676 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Paternal CHH methylation potentiates stress responses against Pseudomonas syringae in Arabidopsis progenies ]]> https://biorxiv.org/content/10.1101/2023.05.10.540197v1?rss=1 Li, Y. Liu, T. Leung, E. Y. M. Zhao, X. Zhu, G. Ng, D. W.-K. 2023-05-12 doi:10.1101/2023.05.10.540197 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Exonuclease assisted mapping of protein-RNA interactions (ePRINT) ]]> https://biorxiv.org/content/10.1101/2023.05.16.540978v1?rss=1 Hawkins, S. Mondaini, A. Namboori, S. C. Javed, A. Bhinge, A. 2023-05-16 doi:10.1101/2023.05.16.540978 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Deep learning and host variable embedding augment microbiome-based simultaneous detection of multiple diseases ]]> https://biorxiv.org/content/10.1101/2023.05.16.541058v1?rss=1 Wu, S. Li, Z. Chen, Y. Zhang, M. Sun, Y. Xing, J. Zhao, F. Huang, S. Knight, R. Su, X. 2023-05-18 doi:10.1101/2023.05.16.541058 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ ChAdOx1 COVID vaccines express RBD open prefusion SARS-CoV-2 spikes on the cell surface ]]> https://biorxiv.org/content/10.1101/2023.05.22.541685v1?rss=1 Zhang, P. Gilbert, S. Radecke, J. Ni, T. Mendonca, L. Zhu, Y. Howe, A. Shah, P. M. Sheng, Y. Krebs, A.-S. Duyvesteyn, H. M. E. Allen, E. Lambe, T. Bissett, C. Morris, S. Spencer, A. Stuart, D. I. 2023-05-24 doi:10.1101/2023.05.22.541685 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Regulation of hippocampal mossy fiber-CA3 synapse function by a Bcl11b/C1ql2/Nrxn3(25b+) pathway ]]> https://biorxiv.org/content/10.1101/2023.05.23.541921v1?rss=1 Britsch, S. Koumoundourou, A. Rannap, M. De Bruyckere, E. Nestel, S. Reissner, C. Egorov, A. Liu, P. Missler, M. Heimrich, B. Draguhn, A. 2023-05-25 doi:10.1101/2023.05.23.541921 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Association of an estrogen-sensitive Pax1-Col11a1-Mmp3 signaling axis with adolescent idiopathic scoliosis ]]> https://biorxiv.org/content/10.1101/2023.05.26.542293v1?rss=1 T; p.(Pro1335Leu); P=7.07e-11, OR=1.118). Using CRISPR mutagenesis we generated Pax1 knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (1) XI protein both localize within the intervertebral disc (IVD)-vertebral junction region encompassing the growth plate, with less collagen (1) XI detected in Pax1-/- spines compared to wildtype. By genetic targeting we found that wildtype Col11a1 expression in costal chondrocytes suppresses expression of Pax1 and of Mmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, this suppression was abrogated in the presence of the AIS-associated COL11A1P1335L mutant. Further, we found that either knockdown of the estrogen receptor gene Esr2, or tamoxifen treatment, significantly altered Col11a1 and Mmp3 expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering a Pax1-Col11a1-Mmp3 signaling axis in spinal chondrocytes. ]]> Wise, C. Yu, H. Khanshour, A. M. Ushiki, A. Otomo, N. Koike, Y. Einarsdottir, E. Fan, Y. Antunes, L. Kidane, Y. H. Sheng, R. Zhang, Y. Pei, J. Grishin, N. V. Evers, B. M. V. Cheung, J. P. Y. Herring, J. A. Terao, C. Song, Y.-Q. Gurnett, C. Gerdhem, P. Ikegawa, S. Rios, J. J. Ahituv, N. 2023-05-27 doi:10.1101/2023.05.26.542293 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Heterogeneous genomic architecture of skeletal armour traits in sticklebacks ]]> https://biorxiv.org/content/10.1101/2023.05.28.542672v1?rss=1 Yi, X. Kemppainen, P. Reid, K. Chen, Y. Rastas, P. Fraimout, A. Merilae, J. 2023-05-31 doi:10.1101/2023.05.28.542672 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning ]]> https://biorxiv.org/content/10.1101/2023.05.30.542904v1?rss=1 Zhao, H. Liu, S. Ma, C. Xu, H. Fu, J. Deng, Z.-H. Kong, L. Liu, Q. 2023-06-01 doi:10.1101/2023.05.30.542904 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP ]]> https://biorxiv.org/content/10.1101/2023.05.31.543184v1?rss=1 Yu, H. Zheng, Z. Su, J. Lam, T.-W. Luo, R. 2023-06-06 doi:10.1101/2023.05.31.543184 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome ]]> https://biorxiv.org/content/10.1101/218347v1?rss=1 Jiang, X.-T. Yu, K. Li, L.-G. Yin, X. L. Li, A. D. Zhang, T. 2017-11-13 doi:10.1101/218347 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Assessment of the aging of the brown adipose tissue by 18F-FDG PET/CT imaging in the progeria mouse model LmnaG609G/G609G ]]> https://biorxiv.org/content/10.1101/220061v1?rss=1 Wang, Z. Xu, X. Liu, Y. Gao, Y. Ma, W. Yang, W. Kang, F. Liu, B. Wang, J. 2017-11-15 doi:10.1101/220061 Cold Spring Harbor Laboratory Press 2017-11-15 <![CDATA[ Polygenic scores without external summary statistics ]]> https://biorxiv.org/content/10.1101/252270v1?rss=1 Mak, T. Porsch, R. M. Choi, S. W. Sham, P. C. 2018-01-23 doi:10.1101/252270 Cold Spring Harbor Laboratory Press 2018-01-23 <![CDATA[ clusterProfiler: universal enrichment tool for functional and comparative study ]]> https://biorxiv.org/content/10.1101/256784v1?rss=1 Yu, G. 2018-01-31 doi:10.1101/256784 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Inflation versus filling-in: why we feel we see more than we actually do in peripheral vision ]]> https://biorxiv.org/content/10.1101/263244v1?rss=1 Odegaard, B. Chang, M. Y. Lau, H. Cheung, S.-H. 2018-02-12 doi:10.1101/263244 Cold Spring Harbor Laboratory Press 2018-02-12 <![CDATA[ Rifampicin or capreomycin induced remodelling of the Mycobacterium smegmatis mycolic acid layer is mitigated in synergistic combinations with cationic antimicrobial peptides ]]> https://biorxiv.org/content/10.1101/269324v1?rss=1 Man, D. K.-W. Kanno, T. Manzo, G. Robertson, B. D. Lam, J. K. Mason, A. J. 2018-02-21 doi:10.1101/269324 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Role of anterograde motor Kif5b in clathrin-coated vesicle uncoating and clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/284166v1?rss=1 Ni, Y.-X. Xue, W.-Q. Zhou, N. Yung, W.-H. Lin, R.-Z. Kao, Y.-T. Duan, Z.-G. Tang, X.-M. Liu, M.-F. Zhang, W. Qi, S. Lu, X.-B. Hu, J.-j. Chung, S. Song, Y.-Q. Huang, J.-d. 2018-03-18 doi:10.1101/284166 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ Inheritance of neural substrates for motivation and pleasure experience ]]> https://biorxiv.org/content/10.1101/294090v1?rss=1 Li, Z. Wang, Y. Yan, C. Li, K. Zeng, Y.-w. Cheung, E. F. C. Docherty, A. R. Sham, P. C. Gur, R. E. Gur, R. C. Chan, R. C. K. 2018-04-03 doi:10.1101/294090 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Germline genetics encode the resistance, risk, and lymphatic metastasis of triple-negative breast cancer in the southern Chinese population ]]> https://biorxiv.org/content/10.1101/302398v1?rss=1 Yang, M. Fan, Y. Zhang, Q. Han, S. Li, X. Zhu, T. Cheng, M. Xu, J. Yang, C. Gao, H. Zhang, C. Zhang, M. Q. Song, Y.-Q. Niu, G. Wang, K. 2018-04-16 doi:10.1101/302398 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing ]]> https://biorxiv.org/content/10.1101/310458v1?rss=1 Luo, R. Sedlazeck, F. J. Lam, T.-W. Schatz, M. 2018-04-28 doi:10.1101/310458 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants ]]> https://biorxiv.org/content/10.1101/311985v1?rss=1 Luo, R. Lam, T.-W. Schatz, M. 2018-05-01 doi:10.1101/311985 Cold Spring Harbor Laboratory Press 2018-05-01 <![CDATA[ Further expansion of methane metabolism in the Archaea ]]> https://biorxiv.org/content/10.1101/312082v1?rss=1 Wang, Y. Huang, Z. Goh, K. M. Evans, P. N. Liu, L. Mao, Y. Hugenholtz, P. Tyson, G. W. Li, W. Zhang, T. 2018-05-01 doi:10.1101/312082 Cold Spring Harbor Laboratory Press 2018-05-01 <![CDATA[ Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci ]]> https://biorxiv.org/content/10.1101/314880v1?rss=1 Azarian, T. Mitchell, P. Georgieva, M. Thompson, C. M. Ghoulia, A. Pollard, A. J. von Gottberg, A. du Plessis, M. Antonio, M. Kwambana-Adams, B. A. Clarke, S. C. Everett, D. Cornick, J. Sadowy, E. Hryniewicz, W. Skoczynska, A. Moisi, J. McGee, L. Beall, B. Metcalf, B. J. Breiman, R. F. Ho, P. Reid, R. O'Brien, K. L. Gladstone, R. Bentley, S. D. Hanage, W. P. 2018-05-04 doi:10.1101/314880 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Polymer brush bilayers at thermal equilibrium: A theoretical approach ]]> https://biorxiv.org/content/10.1101/316141v1?rss=1 Farzin, M. 2018-05-08 doi:10.1101/316141 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ Trans-ethnic polygenic analysis supports genetic overlaps of lumbar disc degeneration with height, body mass index, and bone mineral density ]]> https://biorxiv.org/content/10.1101/316737v1?rss=1 Zhou, X. Cheung, C.-L. Karasugi, T. Karppinen, J. Samartzis, D. Hsu, Y.-H. Mak, T. S. H. Song, Y.-Q. Chiba, K. Kawaguchi, Y. Li, Y. Chan, D. Cheung, K. M.-C. Ikegawa, S. Cheah, K. S.-E. Sham, P. C. 2018-05-07 doi:10.1101/316737 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ NOVEL INSIGHTS INTO SELECTION FOR ANTIBIOTIC RESISTANCE IN COMPLEX MICROBIAL COMMUNITIES ]]> https://biorxiv.org/content/10.1101/323634v1?rss=1 Murray, A. Zhang, L. Yin, X. Zhang, T. Buckling, A. Snape, J. Gaze, W. 2018-05-16 doi:10.1101/323634 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ CardiacProfileR: An R package for extraction and visualisation of heart rate profiles from wearable fitness trackers ]]> https://biorxiv.org/content/10.1101/324004v1?rss=1 Djordjevic, D. Cawood, B. K. Rispin, S. K. Yim, L. H. H. Hayward, C. S. Ho, J. W. K. 2018-05-16 doi:10.1101/324004 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Replication of MERS and SARS coronaviruses in bat cells offers insights to their ancestral origins ]]> https://biorxiv.org/content/10.1101/326538v1?rss=1 Lau, S. Fan, R. Y. Luk, H. K. H. Zhu, L. Fung, J. Li, K. S. Wong, E. Y. M. Ahmed, S. S. Chan, J. F. W. Kok, K.-H. Chan, K.-H. Wernery, U. Yuen, K.-y. Woo, P. C. Y. 2018-05-20 doi:10.1101/326538 Cold Spring Harbor Laboratory Press 2018-05-20 <![CDATA[ New sequential touch method for determining bacterial contact transfer rate from finger to surface ]]> https://biorxiv.org/content/10.1101/328971v1?rss=1 Zhao, P. Li, Y. 2018-05-23 doi:10.1101/328971 Cold Spring Harbor Laboratory Press 2018-05-23 <![CDATA[ Age-specific differences in the dynamics of protective immunity to influenza ]]> https://biorxiv.org/content/10.1101/330720v1?rss=1 Ranjeva, S. Subramanian, R. Fang, V. J. Leung, G. M. Ip, D. K. M. Perera, R. A. P. M. Peiris, J. S. M. Cowling, B. J. Cobey, S. 2018-05-25 doi:10.1101/330720 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity ]]> https://biorxiv.org/content/10.1101/335620v1?rss=1 Pan, Q. Law, C. O. K. Yung, M. M. H. Han, K. C. Pon, Y. L. Lau, T. c. k. 2018-05-31 doi:10.1101/335620 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ ARGs-OSP: online searching platform for antibiotic resistance genes distribution in metagenomic database and bacterial whole genome database ]]> https://biorxiv.org/content/10.1101/337675v1?rss=1 Zhang, A. N. Hou, C.-J. Li, L.-G. Zhang, T. 2018-06-04 doi:10.1101/337675 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ KS-Burden: Assessing distributional differences of rare variants in dichotomous traits ]]> https://biorxiv.org/content/10.1101/368696v1?rss=1 Porsch, R. M. Mak, T. Tang, C. Sham, P. 2018-07-13 doi:10.1101/368696 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Whole-Genome Genomics Correlates of Response To Anti-PD1 Therapy in Relapsed/Refractory Natural Killer/T Cell Lymphoma ]]> https://biorxiv.org/content/10.1101/372383v1?rss=1 Lim, J. Q. Tang, T. Cai, Q.-q. Tan, D. Nairismagi, M.-L. Laurensia, Y. Chia, B. K. H. Peng, R.-J. Iqbal, J. Huang, D. Song, T. Pang, W. L. Cheah, D. M. Z. Ng, C. C. Y. Rajasegaran, V. Hong, H. Tse, E. Mow, B. Cai, Q.-C. Poon, L.-M. Tan, J. Grigoropoulos, N. F. Goh, Y. T. Phipps, C. Rotzschke, O. Cheng, C. L. Lee, Y. S. Loh, Y. Tao, M. Farid, M. Au-Yeung, R. Chan, T. S.-Y. Ng, S.-B. Kwong, Y.-L. Hwang, W. Chng, W.-J. Tousseyn, T. Tan, P. Teh, B. T. Khor, C. C. Rozen, S. Bei, J.-X. Lin, T. Lim, S. T. Ong, C. K. 2018-07-19 doi:10.1101/372383 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Increased GITRL impairs the function of MDSCs and exacerbates primary Sjögren’s syndrome ]]> https://biorxiv.org/content/10.1101/373753v1?rss=1 Tian, J. Rui, K. Hong, Y. Lin, X. Wang, X. Xiao, F. Xu, H. Lu, L. Wang, S. 2018-07-21 doi:10.1101/373753 Cold Spring Harbor Laboratory Press 2018-07-21 <![CDATA[ Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes ]]> https://biorxiv.org/content/10.1101/374165v1?rss=1 Cai, M. Liu, Y. Zhou, Z. Yang, Y. Pan, J. Gu, J.-D. Li, M. 2018-07-23 doi:10.1101/374165 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ Mini viral RNAs act as innate immune agonists during influenza virus infection ]]> https://biorxiv.org/content/10.1101/385716v1?rss=1 te Velthuis, A. Long, J. Bauer, D. L. Fan, R. Yen, H.-L. Sharps, J. Siegers, J. Killip, M. French, H. Oliva-Martin, M. J. Randall, R. de Wit, E. van Riel, D. Poon, L. Fodor, E. 2018-08-06 doi:10.1101/385716 Cold Spring Harbor Laboratory Press 2018-08-06 <![CDATA[ Are these cardiomyocytes? Protocol development reveals impact of sample preparation on the accuracy of identifying cardiomyocytes by flow cytometry ]]> https://biorxiv.org/content/10.1101/388926v1?rss=1 Waas, M. Weerasekera, R. Kropp, E. M. Romero-Tejeda, M. Poon, E. Boheler, K. R. Burridge, P. W. Gundry, R. 2018-08-09 doi:10.1101/388926 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Mesenchymal stem cells protect retinal ganglion cells from degeneration via mitochondrial donation ]]> https://biorxiv.org/content/10.1101/393959v1?rss=1 JIANG, D. Feng, H. Zhang, Z. Yan, B. Chen, L. Ma, C. Li, C. Han, S. Zhang, Y. Chen, P. Tse, H.-F. Fu, Q. Chiu, K. Lian, Q. 2018-08-19 doi:10.1101/393959 Cold Spring Harbor Laboratory Press 2018-08-19 <![CDATA[ Ultrafast clustering of single-cell flow cytometry data using FlowGrid ]]> https://biorxiv.org/content/10.1101/394189v1?rss=1 Ye, X. Ho, J. W. K. 2018-08-17 doi:10.1101/394189 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ The effect of liver enzymes on adiposity: a Mendelian randomization study ]]> https://biorxiv.org/content/10.1101/404319v1?rss=1 LIU, J. Au Yeung, S. L. Kwok, M. K. Leung, J. Y. Y. Lin, S. L. Hui, L. L. Leung, G. M. Schooling, C. M. 2018-09-12 doi:10.1101/404319 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Divergence in the face of gene flow in two Charadrius plovers along the Chinese coast ]]> https://biorxiv.org/content/10.1101/406041v1?rss=1 Wang, X. Que, P. Heckel, G. Hu, J. Zhang, X. Chiang, C.-Y. Huang, Q. Liu, S. Martinez, J. Zhang, N. Pagani-Nunez, E. Dingle, C. Yan, L. Y. Szekely, T. Zhang, Z. Liu, Y. 2018-08-31 doi:10.1101/406041 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Radiomics Analysis Using Stability Selection Supervised Principal Component Analysis for Right-censored Survival Data ]]> https://biorxiv.org/content/10.1101/408831v1?rss=1 Yan, K. K. Wang, X. Lam, W. Vardhanabhuti, V. Lee, A. W. M. Pang, H. 2018-09-06 doi:10.1101/408831 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ A multidrug resistant clinical P. aeruginosa isolate in the MLST550 clonal complex: uncoupled quorum sensing modulates the interplay of virulence and resistance ]]> https://biorxiv.org/content/10.1101/415000v1?rss=1 Cao, H. Xia, T. Li, Y. Xu, z. Bougouffa, S. Lo, Y. K. Bajic, V. B. Luo, H. Woo, P. C. Y. Yan, A. 2018-09-12 doi:10.1101/415000 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Sox2 and FGF20 define a temporal separation between specification and differentiation required for organ of Corti development ]]> https://biorxiv.org/content/10.1101/436790v1?rss=1 Yang, L. M. Huh, S.-H. Ornitz, D. M. 2018-10-05 doi:10.1101/436790 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Genomic characterization of additional cancer-driver genes using a weighted iterative regression accurately modelling background mutation rate ]]> https://biorxiv.org/content/10.1101/437061v1?rss=1 Jiang, L. Zheng, J. Kwan, J. Dai, S. Li, C. TO, K. F. Sham, P. Zhu, Y. Li, M. 2018-10-08 doi:10.1101/437061 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Decreased kinesin-1 mitigates NMDA-induced exicitotoxicity and ischemia-evoked neurodegeneration ]]> https://biorxiv.org/content/10.1101/440800v1?rss=1 Lin, R. Duan, Z. Sun, H. Fung, M.-L. Chen, H. Wang, J. Lau, C.-F. Yang, D. Liu, Y. Ni, Y. Wang, Z. Cui, J. Wu, W.-T. Yung, W.-H. Chan, Y. S. Lo, A. C. Y. Xia, J. Shen, J. Huang, J.-D. 2018-10-11 doi:10.1101/440800 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ The Maudsley Environmental Risk Score for Psychosis ]]> https://biorxiv.org/content/10.1101/453936v1?rss=1 Vassos, E. Sham, P. Kempton, M. Trotta, A. Stilo, S. A. Gayer-Anderson, C. Di Forti, M. Lewis, C. M. Murray, R. Morgan, C. 2018-10-26 doi:10.1101/453936 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Reproduction and longevity A Mendelian randomization study of gonadotropin-releasing hormone and ischemic heart disease ]]> https://biorxiv.org/content/10.1101/472548v1?rss=1 Schooling, C. Ng, J. 2018-11-19 doi:10.1101/472548 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk ]]> https://biorxiv.org/content/10.1101/484113v1?rss=1 Satterstrom, F. K. Kosmicki, J. A. Wang, J. Breen, M. De Rubeis, S. An, J.-Y. Peng, M. Collins, R. L. Grove, J. Klei, L. Stevens, C. Reichert, J. Mulhern, M. Artomov, M. Gerges, S. Sheppard, B. Xu, X. Bhaduri, A. Norman, U. Brand, H. Schwartz, G. Nguyen, R. Guerrero, E. Dias, C. Aleksic, B. Anney, R. J. Barbosa, M. Bishop, S. Brusco, A. Bybjerg-Grauholm, J. Carracedo, A. Chan, M. C. Y. Chiocchetti, A. Chung, B. Coon, H. Cuccaro, M. Curro, A. Dalla Bernardina, B. Doan, R. Domenici, E. Dong, S. Fallerini, C. Fernandez-Prieto, M. Ferrero, G. B. Freitag, 2018-11-30 doi:10.1101/484113 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Estimating driver-tissues by robust selective expression of genes associated with complex diseases or traits ]]> https://biorxiv.org/content/10.1101/491878v1?rss=1 Jiang, L. Xue, C. Chen, S. Dai, S. Chen, P. Sham, P. C. Wang, H. Li, M. 2018-12-17 doi:10.1101/491878 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Native CRISPR-Cas mediated in situ genome editing reveals extensive resistance synergy in the clinical multidrug resistant Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/496711v1?rss=1 Xu, Z. Li, M. Li, Y. Cao, H. Xiang, H. Yan, A. 2018-12-17 doi:10.1101/496711 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Modelling the distribution of Aedes aegypti and Aedes albopictus using climate, host density and interspecies competitive effects ]]> https://biorxiv.org/content/10.1101/498238v1?rss=1 Yang, B. Borgert, B. A. Alto, B. W. Boohene, C. K. Brabant, P. Brew, J. Deutsch, K. DeValerio, J. T. Dinglasan, R. R. Dixon, D. Faella, J. M. Fisher-Grainger, S. L. Glass, G. E. Hayes, R. Hoel, D. F. Horton, A. Janusauskaite, A. Kellner, B. Kraemer, M. U. G. Leveen, E. Lucas, K. J. Medina, J. Morreale, R. Petrie, W. Reiner, R. C. Riles, M. T. Salje, H. Smith, D. L. Smith, J. P. Solis, A. Stuck, J. Vasquez, C. Williams, K. F. Xue, R.-D. Cummings, D. A. T. 2018-12-17 doi:10.1101/498238 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Multi-ATOM: Ultrahigh-throughput single-cell quantitative phase imaging with subcellular resolution ]]> https://biorxiv.org/content/10.1101/510693v1?rss=1 10,000 cell/sec, bypassing the need for interferometry which inevitably compromises QPI quality under ultrafast operation. We employ multi-ATOM for large-scale, label-free, multi-variate, cell-type classification (e.g. breast cancer sub-types, and leukemic cells versus peripheral blood mononuclear cells) at high accuracy (>94%). Our results suggest that multi-ATOM could empower new strategies in large-scale biophysical single-cell analysis with applications in biology and enriching disease diagnostics. ]]> Lee, K. Lau, A. Tang, A. Wnag, M. Mok, A. Chung, B. Yan, W. Shum, H. C. Cheah, K. Chan, G. So, H. Wong, K. Tsia, K. 2019-01-03 doi:10.1101/510693 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ An evaluation of the Air Quality Health Index Program on respiratory diseases in Hong Kong: an interrupted time series analysis ]]> https://biorxiv.org/content/10.1101/529313v1?rss=1 Mason, T. G. Linwei, T. Schooling, C. M. King Pan, C. 2019-01-26 doi:10.1101/529313 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Selection for antibiotic resistance is reduced when embedded in a natural microbial community ]]> https://biorxiv.org/content/10.1101/529651v1?rss=1 Klümper, U. Recker, M. Zhang, L. Yin, X. Zhang, T. Buckling, A. Gaze, W. 2019-01-24 doi:10.1101/529651 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Positive effects of low LDL-C and statins on bone mineral density: an integrated epidemiological observation analysis and Mendelian Randomization study ]]> https://biorxiv.org/content/10.1101/531137v1?rss=1 Li, G. H.-Y. Cheung, C.-L. Au, P. C.-M. Tan, K. C.-B. Wong, I. C.-K. Sham, P.-C. 2019-01-26 doi:10.1101/531137 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Deep Brain Stimulation of the Ventromedial Prefrontal Cortex Disrupts Consolidation of Fear Memories ]]> https://biorxiv.org/content/10.1101/537514v1?rss=1 Tan, S. Z. K. Poon, C. H. Chan, Y.-S. Lim, L. W. 2019-02-01 doi:10.1101/537514 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Kilohertz in vivo imaging of neural activity ]]> https://biorxiv.org/content/10.1101/543058v1?rss=1 Wu, J. liang, Y. Hsu, C.-L. Chavarha, M. Evans, S. Shi, D. Lin, M. Tsia, K. Ji, N. 2019-02-06 doi:10.1101/543058 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy ]]> https://biorxiv.org/content/10.1101/555250v1?rss=1 Bertero, A. Fields, P. A. Smith, A. S. Leonard, A. Beussman, K. Sniadecki, N. J. Kim, D.-H. Tse, H.-F. Pabon, L. Shendure, J. Noble, W. S. Murry, C. E. 2019-02-19 doi:10.1101/555250 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ The Ps and Qs of alarmone synthesis in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/562918v1?rss=1 Yang, N. Xie, S. Choi, M. Y. Wang, Y. Watt, R. M. Tang, N.-Y. 2019-02-27 doi:10.1101/562918 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ variant2literature: full text literature search for genetic variants ]]> https://biorxiv.org/content/10.1101/583450v1?rss=1 Lin, Y.-H. Lu, Y.-C. Hsu, J. S. Lee, K.-H. Cheng, Y.-W. Chen, Y.-C. Chen, T.-F. Tu, C.-T. Hsu, C.-M. Chou, C.-C. Chen, P.-L. Tu, Y.-C. E. Chen, C.-Y. 2019-03-21 doi:10.1101/583450 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Genetic risk loadings influence the susceptibility and severity of systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/614867v1?rss=1 Chen, L. Tombleson, P. Bielowka, A. Odhams, C. A. Roberts, A. L. Cunninghame Graham, D. S. Vyse, T. J. Morris, D. L. 2019-04-23 doi:10.1101/614867 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ LFMD: a new likelihood-based method to detect low-frequency mutations without molecular tags ]]> https://biorxiv.org/content/10.1101/617381v1?rss=1 A:T, are significantly increased in the mid-stage group. This is consistent with the Mitochondrial Free Radical Theory of Aging, suggesting that AD may be linked to the aging of brain cells induced by oxidative damage. ]]> Ye, R. Ruan, J. Zhuang, X. Qi, Y. An, Y. Xu, J. Mak, T. Liu, X. Yang, H. Xu, X. Baum, L. Nie, C. Sham, P. C. 2019-04-24 doi:10.1101/617381 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ OTUB1 is a key regulator of RIG-I dependent immune signalling and is targeted for proteasomal degradation by influenza A NS1 ]]> https://biorxiv.org/content/10.1101/634014v1?rss=1 Jahan, A. S. Biquand, E. Munoz-Moreno, R. Le Quang, A. Mok, C. K.-P. Wong, H. H. Teo, Q. W. Doak, S. Chin, A. Poon, L. L. M. te Velthuis, A. Garcia-Sastre, A. Demeret, C. Sanyal, S. 2019-05-15 doi:10.1101/634014 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ The Biogeography of coelurosaurian theropods and its impact on their evolutionary history ]]> https://biorxiv.org/content/10.1101/634170v1?rss=1 Ding, A. Pittman, M. Upchurch, P. O'Connor, J. Field, D. Xu, X. 2019-05-10 doi:10.1101/634170 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Uncovering bi-directional causal relationships between plasma proteins and psychiatric disorders: A proteome-wide study leveraging GWAS summary data ]]> https://biorxiv.org/content/10.1101/648113v1?rss=1 Chau, C. K.-L. Lau, A. L.-C. Sham, P. C. SO, H.-C. 2019-05-24 doi:10.1101/648113 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae ]]> https://biorxiv.org/content/10.1101/652065v1?rss=1 Xue, B. Guo, X. Landis, J. B. Sun, M. Tang, C. C. Soltis, P. S. Soltis, D. E. Saunders, R. M. K. 2019-05-28 doi:10.1101/652065 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ Neuron-Glial Antigen 2 (NG2)-based Glial Induction ofHuman BMSCs: A fast & safe glial progenitor cell-based therapy for congenital myelin disorders of the central nervous system ]]> https://biorxiv.org/content/10.1101/658997v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@104a62corg.highwire.dtl.DTLVardef@399a67org.highwire.dtl.DTLVardef@1c81ee1org.highwire.dtl.DTLVardef@16374da_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Human bone marrow stromal cells (BMSCs) can be programmed to myelinating glia (GPCs, glial progenitor cells), via a novel 14-day in vitro induction protocol - Transplantation of these hBM-GPCs robustly remyelinated myelin deficient shiverer mice. - hBM-GPC transplant significantly extended lifespan, increased body weight and improved motor function ]]> Lam, G. Shea, G. K.-H. Wu, K. L. K. Li, M. T.-S. Kwok, C. H. Wong, C. Y. Tsui, A. Y. P. Shum, D. K. Y. Chan, Y. S. 2019-06-17 doi:10.1101/658997 Cold Spring Harbor Laboratory Press 2019-06-17 <![CDATA[ Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer ]]> https://biorxiv.org/content/10.1101/681767v1?rss=1 T mutations in POLE V411L. In contrast, analysis of other genomic regions showed similar mutation profiles across the different POLE mutants. Notably, we found that POLE mutants with the TP53 R213* mutation, caused by a TT[C>T]GA substitution, have significantly higher relative frequency of this mutational context compared with samples without this mutation. This finding demonstrates that variations in underlying mutation spectra can increase the likelihood of specific driver mutation formation. ]]> Fang, H. Barbour, J. A. Poulos, R. C. Katainen, R. Aaltonen, L. A. Wong, J. W. H. 2019-06-24 doi:10.1101/681767 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Quantifying within-host evolution of H5N1 influenza in humans and poultry in Cambodia ]]> https://biorxiv.org/content/10.1101/683151v1?rss=1 5% frequency within-host. However, short infection times, genetic drift, and purifying selection likely restrict their ability to evolve extensively during a single infection. Applying evolutionary methods to sequence data, we reveal a detailed view of H5N1 virus adaptive potential, and develop a foundation for studying host-adaptation in other zoonotic viruses. Author summaryH5N1 avian influenza viruses can cross species barriers and cause severe disease in humans. H5N1 viruses currently cannot replicate and transmit efficiently among humans, but animal infection studies and modeling experiments have suggested that human adaptation may require only a few mutations. However, data from natural spillover infection has been limited, posing a challenge for risk assessment. Here, we analyze a unique dataset of deep sequence data from H5N1 virus-infected humans and domestic ducks in Cambodia. We find that well-known markers of human receptor binding and replication arise in multiple, independent humans. We also find that 3 mutations detected within-host are enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adapting. However, we also show that within-host evolution in both humans and ducks are shaped heavily by purifying selection and genetic drift, and that a large fraction of within-host variation is never detected on the H5N1 phylogeny. Taken together, our data show that H5N1 viruses do generate human-adapting mutations during natural infection. However, short infection times, purifying selection, and genetic drift may severely limit how much H5N1 viruses can evolve during the course of a single infection. ]]> Moncla, L. H. Bedford, T. Dussart, P. Horm, S. V. Rith, S. Buchy, P. Karlsson, E. A. Li, L. Liu, Y. Zhu, H. Guan, Y. Friedrich, T. C. Horwood, P. F. 2019-06-27 doi:10.1101/683151 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Biases in GWAS - the dog that did not bark ]]> https://biorxiv.org/content/10.1101/709063v1?rss=1 Schooling, C. 2019-07-20 doi:10.1101/709063 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ Serotonergic treatment normalizes midbrain dopaminergic neuron increase after periaqueductal gray stimulation-induced anticipatory fear in a rat model ]]> https://biorxiv.org/content/10.1101/714592v1?rss=1 Tan, S. Z. K. Temel, Y. Chan, A. Y. Mok, A. T. C. Perucho, J. A. U. Blokland, A. Aquili, L. Lim, W. L. Lim, L. W. 2019-07-25 doi:10.1101/714592 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Survival bias and competing risk can severely bias Mendelian Randomization studies of specific conditions ]]> https://biorxiv.org/content/10.1101/716621v1?rss=1 Schooling, C. M. Lopez, P. M. Au Yeung, S. Hunag, J. V. 2019-07-26 doi:10.1101/716621 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Post-EMT: Cadherin-11 mediates cancer hijacking fibroblasts ]]> https://biorxiv.org/content/10.1101/729491v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@11317f1org.highwire.dtl.DTLVardef@88fffaorg.highwire.dtl.DTLVardef@5da692org.highwire.dtl.DTLVardef@62f6ed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kang, W. Fan, Y. Du, Y. Tonkova, E. A. Hsu, Y.-H. Tan, K. V. Alexander, S. Wong, B. S. Yang, H. Luo, J. Yao, K. Yang, J. Hu, X. Liu, T. Gan, Y. Zhang, J. Zhao, J. J. Konstantopoulos, K. Friedl, P. Khong, P. L. Lu, A. Hung, M.-C. Brenner, M. B. Segall, J. E. Gu, Z. 2019-08-09 doi:10.1101/729491 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ The effect of liver enzymes on body composition: a Mendelian randomization study ]]> https://biorxiv.org/content/10.1101/732685v1?rss=1 LIU, J. Au Yeung, S. L. Kwok, M. K. Leung, J. Y. Y. Hui, L. L. Leung, G. M. Schooling, C. M. 2019-08-14 doi:10.1101/732685 Cold Spring Harbor Laboratory Press 2019-08-14 <![CDATA[ Targeted Sequencing Workflows for Comprehensive Drug Resistance Profiling of Mycobacterium tuberculosis cultures using Illumina MiSeq and Nanopore MinION: Comparison of analytical and diagnostic performance, turnaround time and cost ]]> https://biorxiv.org/content/10.1101/760462v1?rss=1 Tafess, K. Ng, T. T. L. Lao, H. Y. Leung, K. S.-S. Tam, K. K.-G. Rajwani, R. Tam, S. T. Y. Ho, L. P. K. Chu, C. M. K. Gonzalez, D. Sayada, C. Ma, O. C.-K. Nega, B. H. Ameni, G. Yam, W.-C. Siu, G. K. H. 2019-09-08 doi:10.1101/760462 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells ]]> https://biorxiv.org/content/10.1101/765628v1?rss=1 1 million cells). Using large single cell mass cytometry, RNA-seq and imaging-based biophysical data, we demonstrate that PARC consistently outperforms state-of-the-art clustering algorithms without sub-sampling of cells, including Phenograph, FlowSOM, and Flock, in terms of both speed and ability to robustly detect rare cell populations. For example, PARC can cluster a single cell data set of 1.1M cells within 13 minutes, compared to >2 hours to the next fastest graph-clustering algorithm, Phenograph. Our work presents a scalable algorithm to cope with increasingly large-scale single-cell analysis.nnAvailability and Implementationhttps://github.com/ShobiStassen/PARC ]]> stassen, s. V. Siu, D. M. D. Lee, K. C. M. Ho, J. W. K. So, H. K. H. Tsia, K. 2019-09-11 doi:10.1101/765628 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Spatial expression pattern of ZNF391 gene in the brains of patients with schizophrenia, bipolar disorders or major depressive disorder identifies new cross-disorder biotypes: A trans-diagnostic, top-down approach ]]> https://biorxiv.org/content/10.1101/768515v1?rss=1 biotype 2 > biotype 1, PRIFOG = 0.0027). Using ZNF391 as instrumental variable (IV), a partial casual path could be linked from RIFOG to working memory ({beta}RIFOG->DMS_TC0D = 4.95, P = 0.0056; {beta} RIFOG->DMS_TC = 2.53, P = 0.059; {beta}RIFOG->DMS_TC_A = 2.57, P = 0.056).nnInterpretationThe general predisposition to several psychiatric disorders may be influenced by variations of ZNF391, through its effects on right inferior frontal orbital gyrus and working memory. This illustrates the potential of a trans-diagnostic, top-down approach in understanding the commonality of psychiatric disorders.nnEvidence before this studyThe results from recent cross-disorder genome-wide association studies (GWAS)using large samples indicate that there is notable genetic overlapping between psychiatric disorders. However, the structural relationship of these disorders at the genomic level and the details of refined disease dimensions affected by the associated loci in a cross-disorder pattern remains unknown. We searched the published studies (up to Sep 7, 2019) in PubMed using the combination of the following keywords "((cross disorder) OR (schizophrenia AND bipolar disorder AND major depressive disorder) AND (genome AND structural equation) AND (cognition OR imaging))", no published study was found. We then removed the term "structural equation", 23 original studies were found. To the best of our knowledge, none of these studies explored the organized structure between three disorders. Further, of 23 articles we found, the majority of them took an approach of either polygenic risk score (PRS) or candidate gene to test the association with either psychological traits such as loneliness or neuroimaging measures in one (schizophrenia) or two (schizophrenia and bipolar) disorders. Hitherto, no study has been conducted to redefine three disorders based on the biological markers generated from the cross-disorder genomic studies.nnAdded value of this studyAdopting a novel approach of genomic structural equation modelling, we used the latest results of GWAS of three major psychiatric disorders to detect their common factor, further, to identify the loci associated with such as a common factor, and the locis transcription consequences in the brain. Propelled by the phenomenon "genes do not read DSM", we used a cutting-edge clustering algorithm to redefine three disorders based on the cerebral spatial expression pattern of associated core gene. Our study provides another piece of evidence as to the potentials of utilizing the signals arising from large population-scale GWAS to dissect and redefine psychiatric disorders.nnImplications of all the available evidenceConsistent with previous case-control cross-disorder GWAS, our study suggests that a common factor exists in three major psychiatric disorders and the biological information of core gene associated with the common factor could be used as an objective marker to explain three disorders and their pathophysiology. ]]> Ren, H. Meng, Y. Zhang, Y. Wang, Q. Ma, X. Li, X. Wang, Y. Sham, P. C. Li, T. 2019-09-16 doi:10.1101/768515 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ The impact of Relative Language Distance on Bilingual Language Control - a functional imaging study ]]> https://biorxiv.org/content/10.1101/771212v1?rss=1 Ramanujan, K. 2019-09-16 doi:10.1101/771212 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Exploring the effect of Relative Language Distance on Bilingual Brain Structure: a cross-sectional VBM study ]]> https://biorxiv.org/content/10.1101/779751v1?rss=1 HE>DE. This might be attributable to the differing articulatory control needs that variation in L1-L2 RLD generates. The present study reveals how the dimension of Relative Language Distance could impact bilingual brain structure. ]]> Ramanujan, K. 2019-09-24 doi:10.1101/779751 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ Choosing Your Battles: Which Resistance Genes Warrant Global Action? ]]> https://biorxiv.org/content/10.1101/784322v1?rss=1 Zhang, A.-N. Li, L. Yin, X. Dai, C. L. Groussin, M. Poyet, M. Topp, E. Gillings, M. R. Hanage, W. P. Tiedje, J. M. Alm, E. J. Zhang, T. 2019-10-03 doi:10.1101/784322 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Cooperative pattern formation in multi-species bacterial colonies ]]> https://biorxiv.org/content/10.1101/798827v1?rss=1 Curatolo, A. I. Zhou, N. Zhao, Y. Liu, C. Daerr, A. Tailleur, J. Huang, J.-D. 2019-10-11 doi:10.1101/798827 Cold Spring Harbor Laboratory Press 2019-10-11 <![CDATA[ Evaluation of Commercially Available Exosomal Isolation Kits from Human Plasma ]]> https://biorxiv.org/content/10.1101/808931v1?rss=1 Yuzhe, S. Zhen, H. Guo, M. Ye, J. Liu, Z. Zhang, X. Yang, Y. Nie, C. 2019-10-18 doi:10.1101/808931 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Identification of a Central Neural Circuit that Regulates Anxiety-induced Bone Loss ]]> https://biorxiv.org/content/10.1101/812875v1?rss=1 Yang, F. Liu, Y. Chen, S. Dai, Z. Yang, D. Gao, D. Shao, J. Wang, Y. Wang, T. Zhang, Z. Zhang, L. Lu, W. W. Tu, J. Li, Y. Wang, L. 2019-10-21 doi:10.1101/812875 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Asymmetric molecular architecture of the human γ-tubulin ring complex ]]> https://biorxiv.org/content/10.1101/820142v1?rss=1 100,000 [A]2) surfaces that could interact with different regulatory factors. We also identify an unanticipated structural bridge that includes an actin-like protein and spans the{gamma} -TuRC lumen. Despite its asymmetric composition and architecture, the human{gamma} -TuRC arranges{gamma} -tubulins into a helical geometry poised to nucleate microtubules. The observed compositional complexity of the{gamma} -TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g. within biological condensates 8 or alongside existing filaments 9. ]]> Wieczorek, M. Urnavicius, L. Ti, S.-C. Molloy, K. R. Chait, B. T. Kapoor, T. M. 2019-10-25 doi:10.1101/820142 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ TP63, SOX2 and KLF5 Establish Core Regulatory Circuitry and Construct Cancer Specific Epigenome in Esophageal Squamous Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/825372v1?rss=1 nView larger version (58K):norg.highwire.dtl.DTLVardef@1a9f923org.highwire.dtl.DTLVardef@238c90org.highwire.dtl.DTLVardef@1e14f58org.highwire.dtl.DTLVardef@120249a_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LISuper-enhancers mediated transcriptional regulatory circuitry is established for ESCCnC_LIO_LITP63, SOX2 and KLF5 as CRC TFs co-localize super-enhancer loci to orchestrate chromatin accessibility and transcriptional dysregulationnC_LIO_LIComplex interaction between functional enhancers and TP63 promoter is mediated by CRC TFsnC_LIO_LIALDH3A1 is a key downstream target of ESCC CRC and is essential for ESCC cell survivalnC_LIO_LIBET degrader-ARV-771 and HDAC inhibitor-Romidepsin synergistically inhibit ESCC tumor growthnC_LI ]]> Jiang, Y. Jiang, Y. Li, C.-Q. Ying, Z. Dakle, P. Deng, J.-W. Lin, R. Y.-T. Kaur, H. Han, L. Xie, J.-J. Mayakonda, A. Hazawa, M. Xu, L. Li, Y. Aswad, L. Jeitany, M. Kanojia, D. Guan, X.-Y. Fullwood, M. J. Lin, D.-C. Koeffler, H. P. 2019-11-06 doi:10.1101/825372 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ The independent and combined influence of schizophrenia polygenic risk score and heavy cannabis use on risk for psychotic disorder: A case-control analysis from the EUGEI study. ]]> https://biorxiv.org/content/10.1101/844803v1?rss=1 Di Forti, M. Wu-Choi, B. Quattrone, D. Richards, A. L. Freeman, T. P. Tripoli, G. Gayer-Anderson, C. Rodriguez, V. Jongsma, H. Ferraro, L. La Cascia, C. Tosato, S. Tarricone, I. Berardi, D. Szoke, A. Arango, C. Bobes, J. Sanjuan, J. Santos, J. L. Arrojo, M. Velthorst, E. BERNARDO, M. Del Ben, C. M. Selten, J.-P. Jones, P. B. Kirkbride, J. B. Rutten, B. N. de Haan, L. van os, J. Lynskey, M. Morgan, C. Vassos, E. O'Donovan, M. Lewis, C. Sham, P. C. Murray, R. M. EU-GEI WP2 Group, 2019-11-16 doi:10.1101/844803 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Emergence of opposite neurons in a decentralized firing-rate model of multisensory integration ]]> https://biorxiv.org/content/10.1101/845743v1?rss=1 Niu, X. Chau, H. Y. Lee, T. S. Zhang, W.-H. 2019-11-17 doi:10.1101/845743 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Highly diverse Asgard archaea participate in organic matter degradation in coastal sediments ]]> https://biorxiv.org/content/10.1101/858530v1?rss=1 Cai, M. Liu, Y. Yin, X. Zhou, Z. Friedrich, M. W. Richter-Heitmann, T. Nimzyk, R. Kulkarni, A. Wang, X. Li, W. Pan, J. Yang, Y. Gu, J.-D. Li, M. 2019-11-29 doi:10.1101/858530 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Clair: Exploring the limit of using a deep neural network on pileup data for germline variant calling ]]> https://biorxiv.org/content/10.1101/865782v1?rss=1 Luo, R. Wong, C.-L. Wong, Y.-S. Tang, C.-I. Liu, C.-M. Leung, H. C. M. Lam, T.-W. 2019-12-05 doi:10.1101/865782 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Sierra: Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/867309v1?rss=1 Patrick, R. Humphreys, D. Oshlack, A. Ho, J. W. K. Harvey, R. P. Lo, K. K. 2019-12-06 doi:10.1101/867309 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Cytokines and schizophrenia revisited: a two-sample multi-marker Mendelian randomization approach ]]> https://biorxiv.org/content/10.1101/870022v1?rss=1 cytokines) were modeled for its underlying structure and subsequent clustering analysis further grouped SCZ-induced cytokines based on their genetic similarities. The multi-phenotype summary statistics of each cytokine module were then used as instrumental variables (IVs) for the second round of MR analysis to detect their effect on brain structure and function. ResultsThe first round of MR analysis identified nine cytokines, the highlight of which includes IL18 (OR = 1.292, P = 8.37 x 10-42) and TNFa (OR = 0.721, P = 7.33 x 10-6), to be causally associated with schizophrenia. These SCZ-induced cytokines could be clustered into three modules. The second round of MR analysis (cytokine module => IDPs) indicated that module B (SCGFb-IP10-CTACK-IL6) significantly increased the level of IDPs including IDP_T1_SIENAX_peripheral_grey_normalised_volume ({beta} = 0.0453, P = 4.40x1010), IDP_dMRI_TBSS_MD_Posterior_corona_radiata_R ({beta}= 0.0584, P = 8.89x 10-16) and IDP_dMRI_TBSS_MD_Cingulum_hippocampus_R ({beta} = 0.0563, P = 9.88x 10-15), with module C (IL18-GROa-TNFa) increasing the level of IDP_dMRI_TBSS_L2_Posterior_thalamic_radiation_R ({beta}= 0.0341, P = 2.67x 10-6). ConclusionOur study, for the first time, mapped the causal link from schizophrenia to the comprehensive immune responses, and the findings suggest immune networks play a role in pathophysiology of schizophrenia by mediating the deviations of total gray matter volume and white matter fibers possibly in the mesolimbic system. ]]> Ren, H. Meng, Y. Zhang, Y. Wang, Q. Deng, W. Ma, X. Zhao, L. Li, X. Wang, Y. Sham, P. C. Li, T. 2019-12-10 doi:10.1101/870022 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Lack of evidence for the presence of an interferon in invertebrate ]]> https://biorxiv.org/content/10.1101/000513v1?rss=1 Pei-Hui Wang 2013-11-16 doi:10.1101/000513 Cold Spring Harbor Laboratory Press 2013-11-16 <![CDATA[ Spatial epidemiology of networked metapopulation: An overview ]]> https://biorxiv.org/content/10.1101/003889v1?rss=1 Lin WANG Xiang Li 2014-06-04 doi:10.1101/003889 Cold Spring Harbor Laboratory Press 2014-06-04 <![CDATA[ A novel computational approach for genome-wide prediction of small RNAs in bacteria ]]> https://biorxiv.org/content/10.1101/011668v1?rss=1 Lei Li Hoi Shan Kwan 2014-11-19 doi:10.1101/011668 Cold Spring Harbor Laboratory Press 2014-11-19 <![CDATA[ Learning Immune-Defectives Graph through Group Tests ]]> https://biorxiv.org/content/10.1101/015149v1?rss=1 Abhinav Ganesan Sidharth Jaggi Venkatesh Saligrama 2015-02-11 doi:10.1101/015149 Cold Spring Harbor Laboratory Press 2015-02-11 <![CDATA[ SumVg: Total heritability explained by all variants in genome-wide association studies based on summary statistics with standard error estimates ]]> https://biorxiv.org/content/10.1101/016857v1?rss=1 Hon-Cheong SO Pak C. SHAM 2015-03-22 doi:10.1101/016857 Cold Spring Harbor Laboratory Press 2015-03-22 <![CDATA[ Modeling Continuous Admixture ]]> https://biorxiv.org/content/10.1101/026278v1?rss=1 Ying Zhou Hongxiang Qiu Shuhua Xu 2015-09-08 doi:10.1101/026278 Cold Spring Harbor Laboratory Press 2015-09-08 <![CDATA[ Quantifying the unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects ]]> https://biorxiv.org/content/10.1101/030841v1?rss=1 James Zou Gregory Valiant Paul Valiant Konrad Karczewski Siu On Chan Kaitlin Samocha Monkol Lek Exome Aggregation Consortium Shamil Sunyaev Mark Daly Daniel MacArthur 2015-11-06 doi:10.1101/030841 Cold Spring Harbor Laboratory Press 2015-11-06 <![CDATA[ Modeling Continuous Admixture ]]> https://biorxiv.org/content/10.1101/033944v1?rss=1 Ying Zhou Hongxiang Qiu Shuhua Xu 2015-12-08 doi:10.1101/033944 Cold Spring Harbor Laboratory Press 2015-12-08 <![CDATA[ Deep, Staged Transcriptomic Resources for the Novel Coleopteran Models Atrachya menetriesi and Callosobruchus maculatus ]]> https://biorxiv.org/content/10.1101/035998v1?rss=1 Matthew Alan Benton Nathan James Kenny Kai Hans Conrads Siegfried Roth Jeremy A Lynch 2016-01-06 doi:10.1101/035998 Cold Spring Harbor Laboratory Press 2016-01-06 <![CDATA[ Fractional Dosing of Yellow Fever Vaccine to Extend Supply: A Modeling Study ]]> https://biorxiv.org/content/10.1101/053421v1?rss=1 Joseph T. Wu Corey M. Peak Gabriel M. Leung Marc Lipsitch 2016-05-14 doi:10.1101/053421 Cold Spring Harbor Laboratory Press 2016-05-14 <![CDATA[ Relating dynamic brain states to dynamic machine states: human and machine solutions to the speech recognition problem ]]> https://biorxiv.org/content/10.1101/074799v1?rss=1 Cai Wingfield Li Su Xunying Liu Chao Zhang Philip Woodland Andrew Thwaites Elisabeth Fonteneau William D Marslen-Wilson 2016-09-12 doi:10.1101/074799 Cold Spring Harbor Laboratory Press 2016-09-12 <![CDATA[ When GWAS meets the Connectivity Map: drug repositioning for seven psychiatric disorders ]]> https://biorxiv.org/content/10.1101/096503v1?rss=1 So, H.-C. Chau, C. K. L. Chiu, W.-T. Ho, K.-S. Lo, C.-P. Yim, S. H.-Y. Sham, P. C. 2016-12-23 doi:10.1101/096503 Cold Spring Harbor Laboratory Press 2016-12-23 <![CDATA[ Distinct projection patterns of different classes of layer 2 principal neurons in the olfactorycortex ]]> https://biorxiv.org/content/10.1101/113134v1?rss=1 Mazo, C. Grimaud, J. Murthy, V. N. Lau, C. G. 2017-03-02 doi:10.1101/113134 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ Discovering the Interactions between Circular RNAs and RNA-binding Proteins from CLIP-seq Data using circScan ]]> https://biorxiv.org/content/10.1101/115980v1?rss=1 Li, B. Zhang, X.-Q. Liu, S.-R. Liu, S. Sun, W.-J. Lin, Q. Luo, Y.-X. Zhou, K.-R. Zhang, C.-M. Tan, Y.-Y. Yang, J.-H. Qu, L.-H. 2017-03-11 doi:10.1101/115980 Cold Spring Harbor Laboratory Press 2017-03-11 <![CDATA[ Translating GWAS Findings Into Therapies For Depression And Anxiety Disorders: Drug Repositioning Using Gene-Set Analyses And Testing For Enrichment Of Psychiatric Drug Classes ]]> https://biorxiv.org/content/10.1101/132563v1?rss=1 So, H.-C. 2017-05-01 doi:10.1101/132563 Cold Spring Harbor Laboratory Press 2017-05-01 <![CDATA[ Element-Free Multiscale Modeling Of Large Deformation Behavior Of Red Blood Cell Membrane With Malaria Infection ]]> https://biorxiv.org/content/10.1101/136648v1?rss=1 Ademiloye, A. S. Zhang, L. W. Liew, K. M. 2017-05-11 doi:10.1101/136648 Cold Spring Harbor Laboratory Press 2017-05-11 <![CDATA[ Does Temperature Change Worsen Or Mitigate The Effect Of Malaria Infection On Erythrocyte Deformability? ]]> https://biorxiv.org/content/10.1101/136796v1?rss=1 Ademiloye, A. S. Zhang, L. W. Liew, K. M. 2017-05-11 doi:10.1101/136796 Cold Spring Harbor Laboratory Press 2017-05-11 <![CDATA[ A Combined Use Of Intravoxel Incoherent Motion MRI Parameters Can Differentiate Early Stage Hepatitis-B Fibrotic Livers From Healthy Livers ]]> https://biorxiv.org/content/10.1101/138958v1?rss=1 Wang, Y.-X. Deng, M. Li, Y. Huang, H. Leung, J. C. S. Chen, W. Lu, P.-X. 2017-05-17 doi:10.1101/138958 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Thoracolumbar Intervertebral Disc Area Morphometry In Elderly Chinese Men And Women: Radiographic Quantifications At Baseline And Changes At Year-4 Follow-Up ]]> https://biorxiv.org/content/10.1101/139402v1?rss=1 60% reduction in disc height). The thoracolumbar disc area loss among men and women during 4-years follow-up period varied between 1.32% and 3.56%, and it was greater for women (mean: 2.44%) than for men (mean: 1.90%, p=0.044). Majority of lumbar DSN progressions during 72 to 76 years old were progression from normal disc space to grade-1DSN. Osteoporosis was associated with greater disc area decrease, both for thoracic and lumbar discs.nnConclusionLumbar DSN can be quantified using DAIL. In elderly Chinese, intervertebral disc narrowing over a 4-year period was greater in women than men, and associated with the presence of osteoporosis. ]]> Wang, J.-Q. Kaplar, Z. Griffith, J. F. Deng, M. Leung, J. C. S. Kwok, A. W. L. Kwok, T. Leung, P. C. Wang, Y.-X. 2017-05-19 doi:10.1101/139402 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ Genetic Overlap Of Depression With Cardiometabolic Diseases And Implications For Drug Repurposing For Comorbidities ]]> https://biorxiv.org/content/10.1101/140590v1?rss=1 Wong, B. C.-F. Chau, C. K.-L. So, H.-C. 2017-05-22 doi:10.1101/140590 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps ]]> https://biorxiv.org/content/10.1101/143040v1?rss=1 2kbp, with 65% of them missed by sequencing-based callers. Independent experimental validations confirmed the high accuracy of these SVs. We also demonstrate how OMSV can incorporate sequencing data to determine precise SV break points and novel sequences in the SVs not contained in the reference. We provide OMSV as open-source software to facilitate systematic studies of large SVs. ]]> Li, L. Kwok, T.-P. Leung, A. K.-Y. Lai, Y. Y. Y. Pang, I. K. Chung, G. T.-Y. Mak, A. C. Y. Poon, A. Chu, C. Li, M. Wu, J. J. K. Lam, E. T. Cao, H. Lin, C. Sibert, J. Yiu, S.-M. Xiao, M. Lo, K.-W. Kwok, P.-Y. Chan, T.-F. Yip, K. Y. 2017-05-27 doi:10.1101/143040 Cold Spring Harbor Laboratory Press 2017-05-27 <![CDATA[ ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology ]]> https://biorxiv.org/content/10.1101/153163v1?rss=1 De Col, V. Fuchs, P. Nietzel, T. Elsaesser, M. Voon, C. P. Candeo, A. Seeliger, I. Fricker, M. Grefen, C. Moller, I. M. Bassi, A. Lim, B. L. Zancani, M. Meyer, A. Costa, A. Wagner, S. Schwarzlaender, M. 2017-06-23 doi:10.1101/153163 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Dependence of Intravoxel Incoherent Motion MR threshold b-value selection for separating perfusion and diffusion compartment and liver fibrosis diagnostic performance. ]]> https://biorxiv.org/content/10.1101/164129v1?rss=1 Li, Y. Lu, P.-X. Huang, H. Leung, J. Chen, W. Wang, Y.-X. 2017-07-15 doi:10.1101/164129 Cold Spring Harbor Laboratory Press 2017-07-15 <![CDATA[ Systematic selection of reference genes for normalization of circulating RNA transcripts in pregnant women based on RNA-seq data ]]> https://biorxiv.org/content/10.1101/165654v1?rss=1 Chim, S. S. C. Wong, K. K. W. Chung, C. Y. L. Lam, S. K. W. Kwok, J. S. L. Lai, C.-Y. Cheng, Y. K. Y. Hui, A. S. Y. Meng, M. Chan, O.-K. Tsui, S. K. W. Lee, K.-Y. Chan, T.-F. Leung, T.-Y. 2017-07-19 doi:10.1101/165654 Cold Spring Harbor Laboratory Press 2017-07-19 <![CDATA[ Pitch discrimination performance of ferrets and humans on a go/no-go task. ]]> https://biorxiv.org/content/10.1101/165852v1?rss=1 Walker, K. M. Davies, A. Bizley, J. K. Schnupp, J. W. King, A. J. 2017-07-20 doi:10.1101/165852 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Exploring repositioning opportunities and side-effects of statins: a Mendelian randomization study of HMG-CoA reductase inhibition with 55 complex traits ]]> https://biorxiv.org/content/10.1101/170241v1?rss=1 So, H.-C. 2017-07-30 doi:10.1101/170241 Cold Spring Harbor Laboratory Press 2017-07-30 <![CDATA[ Liver physiological T1rho dynamics associated with age and gender ]]> https://biorxiv.org/content/10.1101/172478v1?rss=1 Wang, Y.-X. Deng, M. Li, J. Kwok, A. Liu, E. Chen, W. 2017-08-04 doi:10.1101/172478 Cold Spring Harbor Laboratory Press 2017-08-04 <![CDATA[ Implications of de novo mutations in guiding drug discovery: A study of four neuropsychiatric disorders ]]> https://biorxiv.org/content/10.1101/173641v1?rss=1 So, H.-C. Wong, Y.-H. 2017-08-08 doi:10.1101/173641 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ IVIM parameters have good scan-rescan reproducibility when evidential motion contaminated and poorly fitted image data are removed ]]> https://biorxiv.org/content/10.1101/179440v1?rss=1 Chevallier, O. Zhou, N. He, J. Loffroy, R. Wang, Y.-X. 2017-08-22 doi:10.1101/179440 Cold Spring Harbor Laboratory Press 2017-08-22 <![CDATA[ Type 2 diabetes promotes cell centrosome amplification and the role of AKT-ROS-dependent signalling of ROCK1 and 14-3-3σ ]]> https://biorxiv.org/content/10.1101/181214v1?rss=1 Wang, P. Lu, Y. C. Wang, J. Wang, L. Yu, H. Li, Y. F. Kong, A. Chan, J. Lee, S. C. 2017-08-26 doi:10.1101/181214 Cold Spring Harbor Laboratory Press 2017-08-26 <![CDATA[ Folding membrane proteins by deep transfer learning ]]> https://biorxiv.org/content/10.1101/181628v1?rss=1 0.6), and generates three-dimensional models with RMSD less than 4[A] and 5[A] for 57 and 108 MPs, respectively. A rigorous blind test in the continuous automated model evaluation (CAMEO) project shows that our method predicted high-resolution three-dimensional models for two recent test MPs of 210 residues with RMSD [~]2[A]. We estimated that our method could predict correct folds for 1,345-1,871 reviewed human multi-pass MPs including a few hundred new folds, which shall facilitate the discovery of drugs targeting at membrane proteins. ]]> Wang, S. Li, Z. Yu, Y. Xu, J. 2017-08-28 doi:10.1101/181628 Cold Spring Harbor Laboratory Press 2017-08-28 <![CDATA[ Characterization of Azotobacter vinelandii and Kits for Its Synthetic Biology Applications ]]> https://biorxiv.org/content/10.1101/188482v1?rss=1 Leung, K. P. Loo, J. F. C. Seak, L. C. U. Lai, T. F. Yip, K. Y. L. Kong, S. K. Chan, T. F. Chan, K. M. 2017-09-13 doi:10.1101/188482 Cold Spring Harbor Laboratory Press 2017-09-13 <![CDATA[ Cholecystokinin release triggered by presynaptic NMDA receptors produces LTP and sound-sound associative memory formation ]]> https://biorxiv.org/content/10.1101/188839v1?rss=1 Li, X. Xi, C. Wong, Y. T. Wang, H. Feng, H. Zheng, X. Feng, J. Baibado, J. T. Jesky, R. Peng, Y. Wang, Z. Xie, H. Sun, W. Zhang, Z. Zhang, X. He, L. Zhang, N. Zhang, Z. Tang, P. Su, J.-F. Hu, L.-L. Liu, Q. He, X.-B. Tan, A. Sun, X. Li, M. Wong, K. Wang, X. Guo, Y. P. Xu, F. He, J. 2017-09-14 doi:10.1101/188839 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Single-cell RNA-Seq Resolves Cellular Heterogeneity and Transcriptional Dynamics during Spermatogonia Stem Cells Establishment and Differentiation ]]> https://biorxiv.org/content/10.1101/194696v1?rss=1 Liao, J. Ng, S. H. Tu, J. Luk, A. C. S. Qian, Y. Tang, N. L. S. Feng, B. Chan, W.-Y. Fouchet, P. Lee, T.-L. 2017-12-30 doi:10.1101/194696 Cold Spring Harbor Laboratory Press 2017-12-30 <![CDATA[ Forward-reverse mutation cycles between stages of cancer development ]]> https://biorxiv.org/content/10.1101/198309v1?rss=1 TG GOHs and copy-number-variations (CNVs) proximal to these GOHs were detected in the non-tumor tissues, which were extensively reversed in paratumors showing prominent TG>CG LOHs with proximal CNVs, and less so in tumors to form forward-reverse mutation cycles. Lineage effects in the reversions, likely resulting from directional selection, supported a sequential rather than parallel mode of evolution as described in a Stage Specific Populations model of cancer development. ]]> Hu, T. Kumar, Y. Shazia, I. Duan, S.-J. Li, Y. Chen, L. Chen, J.-F. Yin, R. Kwong, A. Leung, G. K.-K. Mat, W.-K. Wu, Z. Long, X. Chan, C.-H. Lee, P. Ng, S.-K. Ho, T. Y. C. Yang, J. Ding, X. Tsang, S.-Y. Zhou, X. Zhang, D.-H. International Cancer Genome Consortium, Zhou, E.-X. Xu, L. Poon, W.-S. Wang, H.-Y. Xue, H. 2017-10-05 doi:10.1101/198309 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ SSEalign: accurate function prediction of bacterial unannotated protein, based on effective training dataset ]]> https://biorxiv.org/content/10.1101/200915v1?rss=1 Yang, Z. Tsui, S. K.-W. 2017-10-10 doi:10.1101/200915 Cold Spring Harbor Laboratory Press 2017-10-10 <![CDATA[ Novel pelagiphages prevail in the ocean ]]> https://biorxiv.org/content/10.1101/2019.12.14.876532v1?rss=1 Zhang, Z. Qin, F. Chen, F. Chu, X. Luo, H. Zhang, R. Du, S. Tian, Z. Zhao, Y. 2019-12-15 doi:10.1101/2019.12.14.876532 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Nilotinib activates endothelial TLR4 to exacerbate atherosclerosis ]]> https://biorxiv.org/content/10.1101/2019.12.14.876599v1?rss=1 Qu, D. Huo, M. Wang, L. Lau, C.-W. Tian, X. Y. Huang, Y. 2019-12-15 doi:10.1101/2019.12.14.876599 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Optical activation of TrkB receptors ]]> https://biorxiv.org/content/10.1101/2019.12.15.876722v1?rss=1 Huang, P. Liu, A. Song, Y. Hope, J. M. Cui, B. Duan, L. 2019-12-15 doi:10.1101/2019.12.15.876722 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Influenza H3 and H1 hemagglutinins have different genetic barriers for resistance to broadly neutralizing stem antibodies ]]> https://biorxiv.org/content/10.1101/2019.12.30.891135v1?rss=1 Wu, N. C. Thompson, A. J. Lee, J. M. Su, W. Arlian, B. M. Xie, J. Lerner, R. A. Yen, H.-L. Bloom, J. D. Wilson, I. A. 2019-12-30 doi:10.1101/2019.12.30.891135 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ The transcriptional landscape of cultivated strawberry (Fragraia x ananassa) and its diploid ancestor (Fragraia x vesca) during fruit development ]]> https://biorxiv.org/content/10.1101/2020.01.02.893453v1?rss=1 Li, Y. Liu, S. Liu, T. Luo, H. 2020-01-03 doi:10.1101/2020.01.02.893453 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ Decoding the regulatory architecture of the maize leaf ]]> https://biorxiv.org/content/10.1101/2020.01.07.898056v1?rss=1 Tu, X. Mejia Guerra, M. K. Franco, J. A. V. Tzeng, D. Chu, P.-Y. Dai, X. Li, P. Buckler, E. S. Zhong, S. 2020-01-08 doi:10.1101/2020.01.07.898056 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Directional motion of membrane vesicles on conical surfaces ]]> https://biorxiv.org/content/10.1101/2020.01.09.899997v1?rss=1 Zhenpeng, G. 2020-01-09 doi:10.1101/2020.01.09.899997 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Millipede genomes reveal unique adaptation of genes and microRNAs during myriapod evolution ]]> https://biorxiv.org/content/10.1101/2020.01.09.900019v1?rss=1 Qu, Z. Nong, W. So, W. L. Barton-Owen, T. Li, Y. Li, C. Leung, T. C. Baril, T. Wong, A. Swale, T. Chan, T. Hayward, A. Ngai, S.-m. Hui, J. 2020-01-09 doi:10.1101/2020.01.09.900019 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Dissociation of connectivity for syntactic irregularity and perceptual ambiguity in musical chord stimuli ]]> https://biorxiv.org/content/10.1101/2020.01.12.903583v1?rss=1 Kim, C. H. Jin, S.-H. Kim, J. S. Kim, Y. Yi, S. W. Chung, C. K. 2020-01-14 doi:10.1101/2020.01.12.903583 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Increased fronto-temporal connectivity by modified melody in real music ]]> https://biorxiv.org/content/10.1101/2020.01.12.903609v1?rss=1 Kim, C. H. Seol, J. Jin, S.-H. Kim, J. S. Kim, Y. Yi, S. W. Chung, C. K. 2020-01-14 doi:10.1101/2020.01.12.903609 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ The effects of seasonal climate variability on dengueannual incidence in Hong Kong: A modellingstudy ]]> https://biorxiv.org/content/10.1101/2020.01.20.912097v1?rss=1 Yuan, H.-Y. Liang, J. Lin, P.-S. Sucipto, K. Tsegaye, M. M. Wen, T.-H. Pfeiffer, S. Pfeiffer, D. P. 2020-01-21 doi:10.1101/2020.01.20.912097 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Genomic and protein structure modelling analysis depicts the origin and infectivity of 2019-nCoV, a new coronavirus which caused a pneumonia outbreak in Wuhan, China ]]> https://biorxiv.org/content/10.1101/2020.01.20.913368v1?rss=1 Dong, N. Yang, X. Chen, K. Chan, E. Yang, M. Chen, S. 2020-01-21 doi:10.1101/2020.01.20.913368 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ A large cross-ancestry meta-analysis of genome-wide association studies identifies 69 novel risk loci for primary open-angle glaucoma and includes a genetic link with Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.01.30.927822v1?rss=1 Gharahkhani, P. Jorgenson, E. Hysi, P. Khawaja, A. P. Pendergrass, S. Han, X. Ong, J. S. Hewitt, A. W. Segre, A. Igo, R. P. Choquet, H. Qassim, A. Josyula, N. S. Cooke Bailey, J. N. Bonnemaijer, P. Iglesias, A. Siggs, O. M. Young, T. Vitart, V. Thiadens, A. A. H. J. Karjalainen, J. Uebe, S. Melles, R. B. Nair, S. Luben, R. Simcoe, M. Amersinghe, N. Cree, A. J. Hohn, R. Poplawski, A. Chen, L. J. Cheng, C.-Y. Vithana, E. N. NEIGHBORHOOD consortium, ANZRAG consortium, Biobank Japan project, FinnGen study, UK Biobank Eye and Vision Consortium, GIGA s 2020-02-03 doi:10.1101/2020.01.30.927822 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments ]]> https://biorxiv.org/content/10.1101/2020.02.01.929851v1?rss=1 Chow, E. Y.-C. Lyu, K. Kwok, C. K. Chan, T.-F. 2020-02-02 doi:10.1101/2020.02.01.929851 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Directed effective connectivity and synaptic weights of invitro neuronal cultures revealed from high-density multielectrode array recordings ]]> https://biorxiv.org/content/10.1101/2020.02.06.936781v1?rss=1 Sun, C. Lin, K. C. Huang, Y.-T. Ching, E. S. C. Lai, P.-Y. Chan, C. K. 2020-02-06 doi:10.1101/2020.02.06.936781 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ An in vitro vesicle formation assay to analyze protein sorting in the secretory transport pathway ]]> https://biorxiv.org/content/10.1101/2020.02.12.945162v1?rss=1 Huang, Y. Yin, H. Tang, X. Wu, Q. Wang, M. Poljak, K. Li, B. Liu, Y. Wu, Z. Jiang, L. Miller, E. A. Yao, Z.-P. Guo, Y. 2020-02-13 doi:10.1101/2020.02.12.945162 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Characterizing Sleep-Wake Circadian Rhythm Consolidation in Early Childhood and Its Association with Motor Development Using Actigraphy ]]> https://biorxiv.org/content/10.1101/2020.02.20.957076v1?rss=1 Li, X. Kane, M. Zhang, Y. Sun, W. Song, Y. Dong, S. Lin, Q. Zhu, Q. Jiang, F. Zhao, H. 2020-02-20 doi:10.1101/2020.02.20.957076 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Increasing Host Cellular Receptor--Angiotensin-Converting Enzyme 2 (ACE2) Expression by Coronavirus may Facilitate 2019-nCoV Infection ]]> https://biorxiv.org/content/10.1101/2020.02.24.963348v1?rss=1 Wang, P.-H. 2020-02-27 doi:10.1101/2020.02.24.963348 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Multithreaded two-pass connected components labelling and particle analysis in ImageJ ]]> https://biorxiv.org/content/10.1101/2020.02.28.969139v1?rss=1 Doube, M. 2020-02-28 doi:10.1101/2020.02.28.969139 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Chromosomal-level reference genome of the incense tree Aquilaria sinensis ]]> https://biorxiv.org/content/10.1101/2020.03.03.972679v1?rss=1 Nong, W. Law, S. T. S. Wong, A. Baril, T. Swale, T. Chu, L. M. Hayward, A. Lau, D. T. W. Hui, J. H. L. 2020-03-05 doi:10.1101/2020.03.03.972679 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak ]]> https://biorxiv.org/content/10.1101/2020.03.08.982637v1?rss=1 Liu, Y. Ning, Z. Chen, Y. Guo, M. Liu, Y. Gali, N. K. Sun, L. Duan, Y. Cai, J. Westerdahl, D. Liu, X. Ho, K.-f. Kan, H. Fu, Q. Lan, K. 2020-03-10 doi:10.1101/2020.03.08.982637 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Rapidly predicting vancomycin resistance of Enterococcus faecium through MALDI-TOF MS spectra obtained in real-world clinical microbiology laboratory ]]> https://biorxiv.org/content/10.1101/2020.03.13.990978v1?rss=1 Wang, H.-Y. Lu, K.-P. Chung, C.-R. Tseng, Y.-J. Lee, T.-Y. Chang, T.-H. Wu, M.-H. Lin, T.-W. Liu, T.-P. Lu, J.-J. 2020-03-15 doi:10.1101/2020.03.13.990978 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Genome architecture and transcription data reveal allelic bias during the cell cycle ]]> https://biorxiv.org/content/10.1101/2020.03.15.992164v1?rss=1 Lindsly, S. M. Jia, W. Chen, H. Ronquist, S. Chen, C. Wen, X. Li, S. C. Wicha, M. Rehemtulla, A. Muir, L. Rajapakse, I. 2020-03-17 doi:10.1101/2020.03.15.992164 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ A high-throughput genome-integrated assay reveals spatial dependencies governing Tcf7l2 binding ]]> https://biorxiv.org/content/10.1101/2020.03.16.993204v1?rss=1 Szczesnik, T. Chu, L. Ho, J. W. Sherwood, R. 2020-03-18 doi:10.1101/2020.03.16.993204 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress ]]> https://biorxiv.org/content/10.1101/2020.03.18.995316v1?rss=1 Stephani, M. Picchianti, L. Gajic, A. Beveridge, R. Skarwan, E. Sanchez de Medina Hernandez, V. Mohseni, A. Clavel, M. Zeng, Y. Naumann, C. Matuszkiewicz, M. Turco, E. Loefke, C. Li, B. Durnberger, G. Schutzbier, M. Chen, H. T. Abdrakhmanov, A. Savova, A. Chia, K.-S. Djamei, A. Schaffner, I. Abel, S. Jiang, L. Mechtler, K. Ikeda, F. Martens, S. Clausen, T. Dagdas, Y. 2020-03-19 doi:10.1101/2020.03.18.995316 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ High-Throughput 5' UTR Engineering for Enhanced Protein Production in Non-Viral Gene Therapies ]]> https://biorxiv.org/content/10.1101/2020.03.24.006486v1?rss=1 Cao, J. Maria Novoa, E. Zhang, Z. Chen, W. C. Liu, D. Choi, G. C. Wong, A. S. Wehrspaun, C. Kellis, M. Lu, T. K. 2020-03-25 doi:10.1101/2020.03.24.006486 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ The type 2 diabetes gene product STARD10 is a phosphoinositide binding protein that controls insulin secretory granule biogenesis ]]> https://biorxiv.org/content/10.1101/2020.03.25.007286v1?rss=1 Carrat, G. R. Haythorne, E. Tomas, A. Haataja, L. Andreas, M. Arvan, P. Piunti, A. Cheng, K. Huang, M. Pullen, T. Georgiadou, E. Stylianides, T. Amirruddin, N. S. Salem, V. Distaso, W. Cakebread, A. Heesom, K. J. Lewis, P. A. Hodson, D. Briant, L. J. Fung, A. C. H. Sessions, R. B. Alpy, F. Kong, A. P. S. Benke, P. I. Torta, F. Teo, A. K. K. Leclerc, I. Solimena, M. Wigley, D. B. Rutter, G. A. 2020-03-25 doi:10.1101/2020.03.25.007286 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ An ectosymbiosis-based mechanism of eukaryogenesis ]]> https://biorxiv.org/content/10.1101/2020.03.25.009100v1?rss=1 Wong, J. T.-F. Long, X. Xue, H. 2020-03-26 doi:10.1101/2020.03.25.009100 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning ]]> https://biorxiv.org/content/10.1101/2020.03.26.009001v1?rss=1 Shang, J. Sun, Y. 2020-03-27 doi:10.1101/2020.03.26.009001 Cold Spring Harbor Laboratory Press 2020-03-27 <![CDATA[ SCYN: Single cell CNV profiling method using dynamic programming ]]> https://biorxiv.org/content/10.1101/2020.03.27.011353v1?rss=1 Feng, X. Chen, L. Qing, Y. Li, R. Li, C. Li, S. C. 2020-03-29 doi:10.1101/2020.03.27.011353 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Coupled Co-clustering-based Unsupervised Transfer Learning for the Integrative Analysis of Single-Cell Genomic Data ]]> https://biorxiv.org/content/10.1101/2020.03.28.013938v1?rss=1 ZENG, P. Lin, Z. 2020-03-29 doi:10.1101/2020.03.28.013938 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2020.03.30.015008v1?rss=1 Boni, M. F. Lemey, P. Jiang, X. Lam, T. T.-Y. Perry, B. Castoe, T. Rambaut, A. Robertson, D. L. 2020-03-31 doi:10.1101/2020.03.30.015008 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Automated Feature Extraction from Population Wearable Device Data Identified Novel Loci Associated with Sleep and Circadian Rhythms ]]> https://biorxiv.org/content/10.1101/2020.03.31.017608v1?rss=1 Li, X. Zhao, H. 2020-04-01 doi:10.1101/2020.03.31.017608 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ CovProfile: profiling the viral genome and gene expressions of SARS-COV2 ]]> https://biorxiv.org/content/10.1101/2020.04.05.026146v1?rss=1 Yu, Y. Li, Z. Li, Y. Yu, L. Jia, W. Ye, F. Li, S. C. 2020-04-06 doi:10.1101/2020.04.05.026146 Cold Spring Harbor Laboratory Press 2020-04-06 <![CDATA[ Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication ]]> https://biorxiv.org/content/10.1101/2020.04.16.045815v1?rss=1 Nong, W. Qu, Z. Li, Y. Owen, T. B. Wong, A. Y. Yip, H. Y. Lee, H. T. Narayana, S. Baril, T. Swale, T. Cao, J. Chan, T. F. Kwan, H. S. Ngai, S. M. Panagiotou, G. Qian, P.-Y. Qiu, J.-w. Yip, K. Y. Ismail, N. Pati, S. John, A. Tobe, S. S. Bendena, W. G. Cheung, S. G. Hayward, A. Hui, J. H. L. 2020-04-18 doi:10.1101/2020.04.16.045815 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells ]]> https://biorxiv.org/content/10.1101/2020.04.19.049254v1?rss=1 Muus, C. Luecken, M. D. Eraslan, G. Waghray, A. Heimberg, G. Sikkema, L. Kobayashi, Y. Vaishnav, E. D. Subramanian, A. Smillie, C. Jagadeesh, K. Duong, E. T. Fiskin, E. Torlai Triglia, E. Ansari, M. Cai, P. Lin, B. Buchanan, J. Chen, S. Shu, J. Haber, A. L. Chung, H. Montoro, D. T. Adams, T. Aliee, H. Allon, S. J. Andrusivova, Z. Angelidis, I. Ashenberg, O. Bassler, K. Becavin, C. Benhar, I. Bergenstrahle, J. Bergenstrahle, L. Bolt, L. Braun, E. Bui, L. T. Chaffin, M. Chichelnitskiy, E. Chiou, J. Conlon, T. M. Cuoco, M. S. Deprez, M. Fischer, D. S. G 2020-04-20 doi:10.1101/2020.04.19.049254 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration ]]> https://biorxiv.org/content/10.1101/2020.05.12.092080v1?rss=1 Sin, S. Y. W. Lu, L. Edwards, S. V. 2020-05-14 doi:10.1101/2020.05.12.092080 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ The plate-to-rod transition in trabecular bone loss is elusive ]]> https://biorxiv.org/content/10.1101/2020.05.14.081042v1?rss=1 Felder, A. Monzem, S. De Souza, R. Mills, D. Boyde, A. Doube, M. 2020-05-15 doi:10.1101/2020.05.14.081042 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Exosomes Facilitate Transmission of SARS-CoV-2 Genome into Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.05.14.093583v1?rss=1 Kwon, Y. Nukala, S. B. Srivastava, S. Miyamoto, H. Ismail, N. I. Ong, S.-B. Lee, W. H. Ong, S.-G. 2020-05-14 doi:10.1101/2020.05.14.093583 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Conjugate graph resolves the complex structures at the virus integration loci with NGS data ]]> https://biorxiv.org/content/10.1101/2020.05.17.100578v1?rss=1 Jia, W. Xu, C. Li, S. C. 2020-05-19 doi:10.1101/2020.05.17.100578 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American Shorthair breed ]]> https://biorxiv.org/content/10.1101/2020.05.19.103788v1?rss=1 120 Mb), by combining multiple advanced genomic technologies, including PacBio long-read sequencing as well as sequence scaffolding by long-range genomic information obtained from Hi-C and optical mapping data. Homology-based and ab initio gene annotation was performed with the Iso-Seq data. Analyzed data is be publicly accessible on Cats genome informatics (Cats-I, https://cat.annotation.jp/), a cat genome database established as a platform to facilitate the accumulation and sharing of genomic resources to improve veterinary care. ]]> Isobe, S. Matsumoto, Y. Chung, C. Sakamoto, M. Chan, T. Hirakawa, H. Ishihara, G. Lam, H.-M. Nakayama, S. Sasamoto, S. Tanizawa, Y. Watanabe, A. Watanabe, K. Yagura, M. Nakamura, Y. 2020-05-19 doi:10.1101/2020.05.19.103788 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients ]]> https://biorxiv.org/content/10.1101/2020.05.20.103549v1?rss=1 Wang, Y. Wang, D. Zhang, L. Sun, W. Zhang, Z. Chen, W. Zhu, A. Huang, Y. Xiao, F. Yao, J. Gan, M. Li, F. luo, L. Huang, X. Zhang, Y. Wong, S.-s. Cheng, X. Ji, J. Ou, Z. Xiao, M. Li, M. Li, J. Ren, P. Deng, Z. Zhong, H. Yang, H. Wang, J. Xu, X. Song, T. Mok, C. Peiris, M. Zhong, N. Zhao, J. Li, Y. Li, J. Zhao, J. 2020-05-20 doi:10.1101/2020.05.20.103549 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Proteomic responses to ocean acidification in the brain of juvenile coral reef fish ]]> https://biorxiv.org/content/10.1101/2020.05.25.115527v1?rss=1 Tsang, H. H. Welch, M. Munday, P. L. Ravasi, T. Schunter, C. 2020-05-28 doi:10.1101/2020.05.25.115527 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Simeprevir suppresses SARS-CoV-2 replication and synergizes with remdesivir ]]> https://biorxiv.org/content/10.1101/2020.05.26.116020v1?rss=1 Lo, H. S. Hui, K. P. Y. Lai, H.-M. Khan, K. S. Kaur, S. Li, Z. Chan, A. K. N. Cheung, H. H.-Y. Ng, K. C. Ho, J. C. W. Che, Y. W. Ma, B. Cheung, P. M.-H. Shin, D. Wang, K. Wu, K.-P. Dikic, I. Liang, P.-H. Zuo, Z. Chan, F. K. L. Hui, D. S. C. Mok, V. C. T. Wong, K.-B. Ko, H. Aik, W. S. Chan, M. C. W. Ng, W.-L. 2020-05-26 doi:10.1101/2020.05.26.116020 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ FIRM: Fast Integration of single-cell RNA-sequencing data across Multiple platforms ]]> https://biorxiv.org/content/10.1101/2020.06.02.129031v1?rss=1 Ming, J. Lin, Z. Wan, X. Yang, C. Wu, A. R. 2020-06-03 doi:10.1101/2020.06.02.129031 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Induction of Muscle Regenerative Multipotent Stem Cells from Human Adipocytes by PDGF-AB and 5-Azacytidine. ]]> https://biorxiv.org/content/10.1101/2020.06.04.130872v1?rss=1 Yeola, A. Subramanian, S. Oliver, R. A. Lucas, C. A. Thoms, J. A. I. Yan, F. Olivier, J. Chacon, D. Tursky, M. L. Hung, T. Power, C. Hardy, P. Ma, D. D. McCarroll, J. Kavallaris, M. Hesson, L. B. Beck, D. Curtis, D. J. Wong, J. W. H. Hardeman, E. C. Walsh, W. R. Mobbs, R. Chandrakanthan, V. Pimanda, J. E. 2020-06-05 doi:10.1101/2020.06.04.130872 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ DNMT3b Dysfunction Promotes DNA cleavages at Centromeric R-loops to Increase Centromere Instability ]]> https://biorxiv.org/content/10.1101/2020.06.04.133272v1?rss=1 Shih, H.-T. Chen, W.-Y. Wang, H.-Y. Huang, H.-D. Chou, C.-H. Chang, Z.-F. 2020-06-04 doi:10.1101/2020.06.04.133272 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ A new pipeline to automatically segment and semi-automatically measure bone length on 3D models obtained by Computed Tomography ]]> https://biorxiv.org/content/10.1101/2020.06.06.137729v1?rss=1 Beltran Diaz, S. Qu, X. Fung, S. de Veer, M. Panagiotopoulou, O. Rosello-Diez, A. 2020-06-07 doi:10.1101/2020.06.06.137729 Cold Spring Harbor Laboratory Press 2020-06-07 <![CDATA[ Ozone nanobubble treatment effectively reduced pathogenic Gram positive and negative bacteria in freshwater and safe for tilapia ]]> https://biorxiv.org/content/10.1101/2020.06.07.138297v1?rss=1 Jhunkeaw, C. Khongcharoen, N. Rungrueng, N. Sangpo, P. Panphut, W. Thapinta, A. Senapin, S. St-Hilaire, S. Dong, H. T. 2020-06-07 doi:10.1101/2020.06.07.138297 Cold Spring Harbor Laboratory Press 2020-06-07 <![CDATA[ The Identification of A ROS Responsive Motif that is regulated by snoRNP in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.06.08.141143v1?rss=1 Cheng, H. Sun, M. Guo, D. 2020-06-09 doi:10.1101/2020.06.08.141143 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ A Rare Deletion in SARS-CoV-2 ORF6 Dramatically Alters the Predicted Three-Dimensional Structure of the Resultant Protein ]]> https://biorxiv.org/content/10.1101/2020.06.09.134460v1?rss=1 Riojas, M. A. Frank, A. M. Puthuveetil, N. P. Flores, B. Parker, M. King, S. P. Peiris, M. Chu, D. K. W. Benton, B. Bradford, R. Hazbon, M. H. Rashid, S. 2020-06-10 doi:10.1101/2020.06.09.134460 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ A reference-guided approach for epigenetic characterization of single cells ]]> https://biorxiv.org/content/10.1101/2020.06.16.155010v1?rss=1 Chen, S. Yan, G. Zhang, W. Li, J. Jiang, R. Lin, Z. 2020-06-17 doi:10.1101/2020.06.16.155010 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Characterization of the evolutionary dynamics of influenza A H3N2 hemagglutinin ]]> https://biorxiv.org/content/10.1101/2020.06.16.155994v1?rss=1 Wang, H. M. Lou, J. Cao, L. Zhao, S. Chan, P. K. Chan, M. C.-W. Chong, M. K. Wu, W. K. Chan, R. W. Wei, Y. Zhang, H. Zee, B. C. Yeoh, E.-k. 2020-06-17 doi:10.1101/2020.06.16.155994 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Unambiguous observation of vesicle fusion in the interior of a cone ]]> https://biorxiv.org/content/10.1101/2020.06.20.162636v1?rss=1 Ge, Z. 2020-06-20 doi:10.1101/2020.06.20.162636 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Stabilizing selection of seasonal influenza receptor binding in populations with partial immunity ]]> https://biorxiv.org/content/10.1101/2020.06.27.175190v1?rss=1 Hay, J. A. Junus, A. Riley, S. Yuan, H.-Y. 2020-06-29 doi:10.1101/2020.06.27.175190 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ SPRDA: a matrix completion approach based on the structural perturbation to infer disease-associated Piwi-Interacting RNAs ]]> https://biorxiv.org/content/10.1101/2020.07.02.185611v1?rss=1 Zheng, K. You, Z.-H. wang, l. Zhou, J.-R. Wong, L. Zhan, Z.-H. 2020-07-04 doi:10.1101/2020.07.02.185611 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ CUT&RUN reveals unique positioning of pre-initiated RNA polymerase II in the steady state of transcription ]]> https://biorxiv.org/content/10.1101/2020.07.07.191478v1?rss=1 270 bp) DNA fragments released by CUT&RUN corresponded to the bimodal peak around the transcription start sites, as previously seen with chromatin immunoprecipitation. However, we found that short (<120 bp) fragments identify a well-defined peak localised at the transcription start sites. This distinct DNA footprint of short fragments, which constituted only about 5% of the total reads, suggests the transient positioning of RNA polymerase II before promoter-proximal pausing, which has not been detected in the physiological settings by standard chromatin immunoprecipitation. We showed that the positioning of the large-size-class DNA footprints around the short-fragment peak was associated with the directionality of transcription, demonstrating the biological significance of distinct CUT&RUN footprints of RNA polymerase II. ]]> Miura, M. Chen, H. 2020-07-07 doi:10.1101/2020.07.07.191478 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Friendly regulates membrane depolarization induced mitophagy in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.07.12.198424v1?rss=1 Juncai Ma Zizhen Liang Jierui Zhao Pengfei Wang Wenlong Ma Juan A. Fernandez Andrade Yonglun Zeng Nenad Grujic Liwen Jiang Yasin Dagdas Byung-Ho Kang 2020-07-12 doi:10.1101/2020.07.12.198424 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum ]]> https://biorxiv.org/content/10.1101/2020.07.14.202424v1?rss=1 Altenburger, A. Cai, H. Li, Q. Drumm, K. Kim, M. Zhu, Y. Garcia-Cuetos, L. Zhan, X. Hansen, P. J. John, U. Li, S. Lundholm, N. 2020-07-15 doi:10.1101/2020.07.14.202424 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Genetic variants for head size share genes and pathways with cancer ]]> https://biorxiv.org/content/10.1101/2020.07.15.191114v1?rss=1 Knol, M. J. Poot, R. A. Evans, T. E. Satizabal, C. L. Mishra, A. van der Auwera, S. Duperron, M.-G. Jian, X. Hostettler, I. C. van Dam-Nolen, D. H. K. Lamballais, S. Pawlak, M. A. Lewis, C. E. Carrion-Castillo, A. van Erp, T. G. M. Reinbold, C. S. Shin, J. Scholz, M. Haberg, A. K. Kämpe, A. Li, G. H. Y. Avinun, R. Atkins, J. R. Hsu, F.-C. Amod, A. R. Lam, M. Tsuchida, A. Teunissen, M. W. A. Beiser, A. S. Beyer, F. Bis, J. C. Bos, D. Bryan, R. N. Bülow, R. Caspers, S. Catheline, G. Cecil, C. A. M. Dalvie, S. Dartigues, J.-F. DeCarli, C. Enlund-Cerullo, 2020-07-16 doi:10.1101/2020.07.15.191114 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ DLPAlign: A Deep Learning based Progressive Alignment for Multiple Protein Sequences ]]> https://biorxiv.org/content/10.1101/2020.07.16.207951v1?rss=1 Kuang, M. 2020-07-17 doi:10.1101/2020.07.16.207951 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Wireless AI-Powered IoT Sensors for Laboratory Mice Behavior Recognition ]]> https://biorxiv.org/content/10.1101/2020.07.23.217190v1?rss=1 Chen, M. Liu, Y. Chan, H.-y. Tam, J. C. Li, X. Chan, C. Li, W. J. 2020-07-24 doi:10.1101/2020.07.23.217190 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism ]]> https://biorxiv.org/content/10.1101/2020.07.23.217620v1?rss=1 Han, Y. Zhuang, Q. Sun, B. Lv, W. Wang, S. Xiao, Q. Chi, P. Pang, B. Zhou, Y. Wang, F. Wang, Q. Li, Z. Zhu, L. Li, F. Deng, D. Chiang, Y.-C. Li, Z. Ren, R. 2020-07-23 doi:10.1101/2020.07.23.217620 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Membrane (M) Protein Inhibits Type I and III Interferon Production by Targeting RIG-I/MDA-5 Signaling ]]> https://biorxiv.org/content/10.1101/2020.07.26.222026v1?rss=1 Wang, P.-H. Zheng, Y. Zhuang, M.-W. Han, L. Zhang, J. Nan, M.-L. Gao, C. 2020-07-27 doi:10.1101/2020.07.26.222026 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ New measures of agency from an adaptive sensorimotor task ]]> https://biorxiv.org/content/10.1101/2020.07.28.223503v1?rss=1 Wang, S. Rajananda, S. Lau, H. Knotts, J. D. 2020-07-29 doi:10.1101/2020.07.28.223503 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Drug Screening with Zebrafish Visual Behavior Identifies Carvedilol as a Potential Treatment for Retinitis Pigmentosa ]]> https://biorxiv.org/content/10.1101/2020.07.28.225789v1?rss=1 Ganzen, L. Ko, M. J. Zhang, M. Xie, R. Chen, Y. Zhang, L. James, R. Mumm, J. van Rijn, R. Zhong, W. Pang, C. P. Zhang, M. Tsujikawa, M. Leung, Y. F. 2020-07-29 doi:10.1101/2020.07.28.225789 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Genetic signatures for lineage/sublineage classification of HPV16, 18, 52 and 58 variants ]]> https://biorxiv.org/content/10.1101/2020.07.30.229112v1?rss=1 98%) by classifying HPV genomes obtained from Chinese females, which included 117 HPV16 variants, 48 HPV18 variants 117 HPV52 variants and 89 HPV58 variants. The circulation of HPV variants posing higher cancer risk in Eastern China, such as HPV16 A4 and HPV58 A3, calls for continuous surveillance in this region. The marker genes and signature nucleotide positions may facilitate cost-effective diagnostic detections of HPV variants in clinical settings. ]]> Ou, Z. Chen, Z. Zhao, Y. Lu, H. Liu, W. Li, W. Geng, C. Hu, G. Wang, X. Ren, P. Liu, N. Zhu, S. Lu, L. Li, J. 2020-07-30 doi:10.1101/2020.07.30.229112 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Time-resolved expression analysis comparing two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative regulatory networks. ]]> https://biorxiv.org/content/10.1101/2020.08.04.236299v1?rss=1 Walker, S. L. Wang, G. Emmerich, K. B. Wang, F. White, D. T. Saxena, M. T. Teng, Y. Qian, J. Mumm, J. S. 2020-08-05 doi:10.1101/2020.08.04.236299 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ The Effect of Task on Object Processing revealed by EEG decoding ]]> https://biorxiv.org/content/10.1101/2020.08.18.255018v1?rss=1 Yip, H. M. K. Cheung, L. Y. T. Wong, Y. K. Wong, A. C.- N. 2020-08-18 doi:10.1101/2020.08.18.255018 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Simultaneous transcriptome and methylome profiles of single mouse oocytes provide novel insights on maturation and aging ]]> https://biorxiv.org/content/10.1101/2020.08.22.260612v1?rss=1 Qian, Y. Cao, Q. Liao, J. Luk, C. S. SUEN, A. H. C. Lee, A. W. T. Chan, T. H. T. Ng, J. K. W. Tang, N. L. S. Chung, H. S. Chow, K. L. Leung, T. Y. Chen, C.-H. Yang, W.-J. Huang, J. Y. J. Chan, W.-Y. Chan, D. Y. L. Li, T. C. Yip, K. Y. Lee, T. L. 2020-08-22 doi:10.1101/2020.08.22.260612 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ The immunodominant and neutralization linear epitopes for SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.08.27.267716v1?rss=1 Lu, S. Xie, X.-x. Zhao, L. Wang, B. Zhu, J. Yang, T.-r. Yang, G.-w. Ji, M. Lv, C.-p. Xue, J. Dai, E.-h. Fu, X.-m. Liu, D.-q. Zhang, L. Hou, S.-j. Yu, X.-l. Wang, Y.-l. Gao, H.-x. Shi, X.-h. Ke, C.-w. Ke, B.-x. Jiang, C.-g. Liu, R.-t. 2020-08-27 doi:10.1101/2020.08.27.267716 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Age and gender dependence of liver diffusion parameters and the evidence of intravoxel incoherent motion modelling of perfusion component is constrained by diffusion component. ]]> https://biorxiv.org/content/10.1101/2020.08.27.271080v1?rss=1 Huang, H. Zheng, C.-J. Wang, L.-F. Che-Nordin, N. Wang, Y.-X. 2020-08-29 doi:10.1101/2020.08.27.271080 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ Exploring the distribution of statistical feature parameters for natural sound textures ]]> https://biorxiv.org/content/10.1101/2020.08.28.271528v1?rss=1 Mishra, A. P. Harper, N. S. Schnupp, J. W. H. 2020-08-28 doi:10.1101/2020.08.28.271528 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ mRNA translation control by Dhx36 binding to 5' UTR G-quadruplex structures is essential for skeletal muscle stem cell regenerative functions ]]> https://biorxiv.org/content/10.1101/2020.08.30.274068v1?rss=1 Chen, X. Yuan, J. Xue, G. Campanario Sanz, S. Wang, D. Wang, W. Mou, X. Umar, M. I. I. Isern, J. Zhao, Y. He, L. Li, Y. Mann, C. J. Yu, X. Wang, L. Perdiguero, E. Chen, W. Xue, Y. Nagamine, Y. Kwok, C.-K. Sun, H. Munoz-Canoves, P. Wang, H. 2020-08-31 doi:10.1101/2020.08.30.274068 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Insulin-Induced Conformational Changes in the Full-Length Insulin Receptor: Structural Insights Gained from Molecular Modeling Analyses ]]> https://biorxiv.org/content/10.1101/2020.09.01.278812v1?rss=1 Yang, Y. X. Li, P. Wang, P. Zhu, B. T. 2020-09-02 doi:10.1101/2020.09.01.278812 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Dating Alphaproteobacteria evolution with eukaryotic fossils ]]> https://biorxiv.org/content/10.1101/2020.09.08.285460v1?rss=1 Wang, S. Luo, H. 2020-09-09 doi:10.1101/2020.09.08.285460 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Unexpectedly high mutation rate of a deep-sea hyperthermophilic anaerobic archaeon ]]> https://biorxiv.org/content/10.1101/2020.09.09.287623v1?rss=1 Gu, J. Wang, X. Ma, X. Sun, Y. Xiao, X. Luo, H. 2020-09-09 doi:10.1101/2020.09.09.287623 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Myogenic Vasoconstriction Requires Canonical Gq/11 Signaling of Angiotensin II Type 1a Receptor in Murine Vasculature ]]> https://biorxiv.org/content/10.1101/2020.09.09.289280v1?rss=1 Cui, Y. Kassmann, M. Nickel, S. Zhang, C. Alenina, N. Anistan, Y. M. Schleifenbaum, J. Bader, M. Welsh, D. G. Huang, Y. Gollasch, M. 2020-09-11 doi:10.1101/2020.09.09.289280 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Nicotinamide mononucleotide (NMN) de-amidation by the gut microbiome and evidence for indirect upregulation of the NAD+ metabolome ]]> https://biorxiv.org/content/10.1101/2020.09.10.289561v1?rss=1 Kim, L.-J. Chalmers, T. J. Smith, G. C. Das, A. Poon, E. W. K. Wang, J. Tucker, S. P. Sinclair, D. A. Quek, L.-E. Wu, L. E. 2020-09-11 doi:10.1101/2020.09.10.289561 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ The gut microbiome stability of a butterflyfish is disrupted on severely degraded Caribbean coral reefs ]]> https://biorxiv.org/content/10.1101/2020.09.21.306712v1?rss=1 Clever, F. Sourisse, J. M. Preziosi, R. F. Eisen, J. A. Guerra, E. C. Scott, J. J. Wilkins, L. G. E. Altieri, A. H. McMillan, W. O. Leray, M. 2020-09-21 doi:10.1101/2020.09.21.306712 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis revealed by its hologenome ]]> https://biorxiv.org/content/10.1101/2020.09.23.308304v1?rss=1 Lan, Y. Sun, J. Chen, C. Sun, Y. Zhou, Y. YANG, Y. Zhang, W. Li, R. Zhou, K. Wong, W. C. Kwan, Y. H. Cheng, A. Bougouffa, S. Van Dover, C. L. Qiu, J.-W. Qian, P.-Y. 2020-09-23 doi:10.1101/2020.09.23.308304 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Neural correlates of auditory pattern learning in the auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.09.24.311464v1?rss=1 Kang, H. Auksztulewicz, R. An, H. Abichacra, N. Sutter, M. L. Schnupp, J. W. H. 2020-09-24 doi:10.1101/2020.09.24.311464 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ Changes in the plasmodesma structure and permeability at the bundle sheath and mesophyll interface during the maize C4 leaf development ]]> https://biorxiv.org/content/10.1101/2020.09.30.320283v1?rss=1 Gao, P. Du, B. Li, P. Kang, B. H. 2020-10-01 doi:10.1101/2020.09.30.320283 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ scATAC-Seq reveals epigenetic heterogeneity associated with an EMT-like process in male germline stem cells and its regulation by G9a ]]> https://biorxiv.org/content/10.1101/2020.10.12.336834v1?rss=1 Liao, J. Suen, H. C. Luk, A. C. S. Lee, A. W. T. Ng, J. K. W. Chan, T. H. T. Cheung, M. Y. Chan, D. Y. L. Li, T. C. Qi, H. Chan, W.-Y. Hobbs, R. M. Lee, T. L. 2020-10-14 doi:10.1101/2020.10.12.336834 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Do auditory mismatch responses differ between acoustic features? ]]> https://biorxiv.org/content/10.1101/2020.10.13.337006v1?rss=1 AN, H. SHING, H. K. Auksztulewicz, R. schnupp, j. w. h. 2020-10-13 doi:10.1101/2020.10.13.337006 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells ]]> https://biorxiv.org/content/10.1101/2020.10.26.353797v1?rss=1 Thoms, J. A. Knezevic, K. Harvey, G. Huang, Y. Seneviratne, J. Carter, D. R. Subramanian, S. Skhinas, J. Chacon, D. Shah, A. de Jong, I. Beck, D. Gottgens, B. Larsson, J. Wong, J. W. Zanini, F. Pimanda, J. E. 2020-10-26 doi:10.1101/2020.10.26.353797 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Light-inducible Deformation of Mitochondria in Live Cells ]]> https://biorxiv.org/content/10.1101/2020.11.01.363663v1?rss=1 Song, Y. Huang, P. Liu, X. Cui, B. Duan, L. 2020-11-01 doi:10.1101/2020.11.01.363663 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Temporal patterns in the evolutionary genetic distance of SARS-CoV-2 during the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2020.11.01.363739v1?rss=1 Lou, J. Zhao, S. Cao, L. Chen, Z. Chan, R. W. Chong, M. K. Zee, B. C. Chan, P. K. Wang, M. H. 2020-11-02 doi:10.1101/2020.11.01.363739 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Non-lesioned subcortical brain volumes are associated with post-stroke sensorimotor behavior across 28 cohorts worldwide: An ENIGMA Stroke Recovery study ]]> https://biorxiv.org/content/10.1101/2020.11.04.366856v1?rss=1 Liew, S.-L. Zavaliangos-Petropulu, A. Schweighofer, N. Jahanshad, N. Lang, C. E. Lohse, K. R. Banaj, N. Barisano, G. Baugh, L. A. Bhattacharya, A. K. Bigjahan, B. Borich, M. R. Boyd, L. A. Brodtmann, A. Buetefisch, C. M. Byblow, W. D. Cassidy, J. M. Ciullo, V. Conforto, A. B. Craddock, R. C. Dula, A. N. Egorova, N. Feng, W. Fercho, K. A. Gregory, C. M. Hanlon, C. A. Hayward, K. S. Holguin, J. A. Hordacre, B. Hwang, D. H. Kautz, S. A. Khlif, M. S. Kim, B. Kuceyeski, A. Liu, J. Lin, D. Lotze, M. Kim, H. MacIntosh, B. J. Margetis, J. L. Mohamed, F. B. Nord 2020-11-05 doi:10.1101/2020.11.04.366856 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Chromosome-level de novo assembly of Coprinopsis cinerea A43mut B43mut pab1-1 #326 and genetic variant identification of mutants using Nanopore MinION sequencing ]]> https://biorxiv.org/content/10.1101/2020.11.09.367581v1?rss=1 Xie, Y. Zhong, Y. Chang, J. Kwan, H. S. 2020-11-09 doi:10.1101/2020.11.09.367581 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology ]]> https://biorxiv.org/content/10.1101/2020.11.13.381178v1?rss=1 Gai, W. Zhou, Z. Agbor-Enoh, S. Fan, X. Lian, S. Jiang, P. Cheng, S. H. Wong, J. Chan, S. L. Jang, M. K. Yang, Y. Liang, R. H. S. Chan, W. K. Ma, E. S. K. Leung, T. Y. Chiu, R. W. K. Valantine, H. Chan, K. C. A. Lo, Y. M. D. 2020-11-13 doi:10.1101/2020.11.13.381178 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ Schizophrenia and autism-associated mutations and disrupted m6A signal by YTHDF1 cause defects in microtubule function and neurodevelopment ]]> https://biorxiv.org/content/10.1101/2020.11.14.382556v1?rss=1 Roy, R. Li, X. Hou, S. Fujiwara, Y. Sukegawa, M. Hong, W.-T. Oomoto, I. Ito, H. Joshi, K. Fan, R. Nagata, K.-i. Lai, K.-o. Wang, D. O. 2020-11-14 doi:10.1101/2020.11.14.382556 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ Memory Transfer of Random Time Patterns Across Modalities ]]> https://biorxiv.org/content/10.1101/2020.11.24.395368v1?rss=1 Kang, H. Auksztulewicz, R. Chan, C. H. Cappotto, D. Rajendran, V. G. Schnupp, J. W. H. 2020-11-24 doi:10.1101/2020.11.24.395368 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Snowball Earths, population bottlenecks, and the evolution of marine photosynthetic bacteria ]]> https://biorxiv.org/content/10.1101/2020.11.24.395392v1?rss=1 ZHANG, H. SUN, Y. Zeng, Q. Crowe, S. A. Luo, H. 2020-11-24 doi:10.1101/2020.11.24.395392 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Multi-Level Attention Graph Neural Network for Clinically Interpretable Pathway-Level Biomarkers Discovery ]]> https://biorxiv.org/content/10.1101/2020.12.03.409755v1?rss=1 Xing, X. Yang, F. Li, H. Jiang, B. Zhang, J. Zhao, Y. Huang, J. Meng, M. Q.- H. Yao, J. 2020-12-04 doi:10.1101/2020.12.03.409755 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ A Synthetic Transcription Platform for Programmable Gene Expression in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2020.12.11.420000v1?rss=1 Chen, W. C. W. Gaidukov, L. Wu, M.-R. Cao, J. Choi, G. C. G. Utomo, R. P. Chen, Y.-C. Wroblewska, L. Zhang, L. Weiss, R. Lu, T. K. 2020-12-11 doi:10.1101/2020.12.11.420000 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Effects of crossover interference on genomic recombination landscape ]]> https://biorxiv.org/content/10.1101/2020.12.14.422614v1?rss=1 Kivikoski, M. Rastas, P. Löytynoja, A. Merilä, J. 2020-12-15 doi:10.1101/2020.12.14.422614 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ A DeepFake framework for prediction of cell type specific transcriptional states induced by drug treatment ]]> https://biorxiv.org/content/10.1101/2020.12.14.422792v1?rss=1 Umarov, R. Arner, E. 2020-12-15 doi:10.1101/2020.12.14.422792 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Transcriptomic and epigenomic profiling of young and aged spermatogonial stem cells reveals molecular targets regulating differentiation ]]> https://biorxiv.org/content/10.1101/2020.12.15.422121v1?rss=1 Liao, J. Suen, H. C. Luk, A. C. S. Lee, T. L. 2020-12-16 doi:10.1101/2020.12.15.422121 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperature ]]> https://biorxiv.org/content/10.1101/2020.12.17.423344v1?rss=1 Lu, Z. Cui, J. Wang, L. Teng, N. Zhang, S. Lam, H.-M. Zhu, Y. Xiao, S. Ke, W. Lin, J. Xu, C. Jin, B. 2020-12-18 doi:10.1101/2020.12.17.423344 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Mitragyna alkaloids derived from the medicinal plant Mitragyna speciosa Korth. and cisplatin synergistically inhibit cell proliferation of Nasopharyngeal Carcinoma (NPC) cell lines ]]> https://biorxiv.org/content/10.1101/2020.12.18.423377v1?rss=1 5-fold, respectively in 2D monolayer culture. The combination of mitragynine and cisplatin also significantly inhibited cell migration of the NPC cell lines. Similarly, combination of mitragynine and cisplatin inhibited growth and invasion of HK-1 spheroids in a dose-dependent manner. Moreover, the spheroids did not rapidly develop resistance to the drug combinations at high concentrations over 10 days. ConclusionCollectively, data shows that both mitragynine and speciociliatine could be potential chemosensitizers for cisplatin. Further extensive drug mechanistic studies and investigations in animal models are necessary to delineate the applicability of M. speciosa alkaloids for NPC therapy. ]]> Domnic, G. Abdul Rahman, S. F. Chear, N. J. Y. Singh, D. Mohana Kumaran, N. 2020-12-18 doi:10.1101/2020.12.18.423377 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ VirStrain: a strain identification tool for RNA viruses ]]> https://biorxiv.org/content/10.1101/2020.12.21.423722v1?rss=1 Liao, H. Cai, D. Sun, Y. 2020-12-22 doi:10.1101/2020.12.21.423722 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Genome-wide reversal of glial and neurovascular cell transcriptomic aging signatures by GLP-1R agonism ]]> https://biorxiv.org/content/10.1101/2020.12.21.423879v1?rss=1 Li, Z. Chen, X. Vong, J. S. L. Zhao, L. Huang, J. Yan, L. Y. C. IP, B. Wing, Y. K. Lai, H.-M. Mok, V. C. T. Ko, H. 2020-12-22 doi:10.1101/2020.12.21.423879 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Rare coding variants in 35 genes associate with circulating lipid levels: a multi-ancestry analysis of 170,000 exomes ]]> https://biorxiv.org/content/10.1101/2020.12.22.423783v1?rss=1 170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels. Ten of these: ALB, SRSF2, JAK2, CREB3L3, TMEM136, VARS, NR1H3, PLA2G12A, PPARG and STAB1 have not been implicated for lipid levels using rare coding variation in population-based samples. We prioritize 32 genes identified in array-based genome-wide association study (GWAS) loci based on gene-based associations, of which three: EVI5, SH2B3, and PLIN1, had no prior evidence of rare coding variant associations. Most of the associated genes showed evidence of association in multiple ancestries. Also, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes, and for genes closest to GWAS index single nucleotide polymorphisms (SNP). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels. ]]> Hindy, G. Dornbos, P. Chaffin, M. D. Liu, D. J. Wang, M. X. Aguilar-Salinas, C. A. Antonacci-Fulton, L. Ardissino, D. Arnett, D. K. Aslibekyan, S. Atzmon, G. Ballantyne, C. M. Barajas-Olmos, F. Barzilai, N. Becker, L. C. Bielak, L. F. Bis, J. C. Blangero, J. Boerwinkle, E. Bonnycastle, L. L. Bottinger, E. Bowden, D. W. Bown, M. J. Brody, J. A. Broome, J. G. Burtt, N. P. Cade, B. E. Centeno-Cruz, F. Chan, E. Chang, Y.-C. Chen, Y.-D. I. Cheng, C.-Y. Choi, W. J. Chowdhury, R. Contreras-Cubas, C. Cordova, E. J. Correa, A. Cupples, L. A. Curran, J. E. Danesh, 2020-12-23 doi:10.1101/2020.12.22.423783 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.12.28.424622v1?rss=1 Xiang, H. Zhao, Y. Li, X. Liu, P. Wang, L. Wang, M. Tian, L. Sun, H. Zhang, W. Xu, Z. Ye, B. Yuan, X. Wang, P. Zhang, N. Gong, Y. Bian, C. Wang, Z. Yu, L. Yan, J. Meng, F. Bai, C. Wang, X. Liu, X. Gao, K. Wu, L. Liu, L. F. Gu, Y. Bi, Y. J. Shi, Y. Zhang, S. Zhu, C. Xu, X. Wu, G. Gao, G. Yang, N. Liu, W. Yang, P. 2020-12-29 doi:10.1101/2020.12.28.424622 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Direct measurement of B lymphocyte gene expression biomarkers in peripheral blood enables early prediction of seroconversion after vaccination ]]> https://biorxiv.org/content/10.1101/2020.12.29.424767v1?rss=1 Huang, D. Liu, A. Y. N. Leung, K.-S. Tang, N. L. S. 2020-12-30 doi:10.1101/2020.12.29.424767 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Single-cell and single-variant resolution analysis of clonal evolution in human liver cancer ]]> https://biorxiv.org/content/10.1101/2020.12.30.424907v1?rss=1 Su, X. Zhao, L. Shi, Y. Zhang, R. Long, Q. Bai, S. Luo, Q. Lin, Y. Zou, X. Ghazanfar, S. Tao, K. yang, g. Wang, L. He, K.-Y. Cui, X. He, J. Wu, J.-X. Han, B. Wang, N. Li, X. Yang, P. Hou, S. Sun, J. Yang, J. Y. H. Chen, J. Han, Z.-G. 2021-01-02 doi:10.1101/2020.12.30.424907 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes ]]> https://biorxiv.org/content/10.1101/2020.12.31.424979v1?rss=1 Sun, J. Li, R. Chen, C. Sigwart, J. D. Kocot, K. 2021-01-02 doi:10.1101/2020.12.31.424979 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data ]]> https://biorxiv.org/content/10.1101/2021.01.12.426467v1?rss=1 Yang, Y. Sun, H. Zhang, Y. Zhang, T. Gong, J. Wei, Y. Duan, Y.-G. Shu, M. Yang, Y. Wu, D. Yu, D. 2021-01-14 doi:10.1101/2021.01.12.426467 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ In vivo structure and dynamics of the RNA genome of SARS-Cov-2 ]]> https://biorxiv.org/content/10.1101/2021.01.15.426526v1?rss=1 Zhang, Y. Huang, K. Xie, D. Lau, J. Y. Shen, W. Li, P. Wang, D. Zou, Z. Shi, S. Ren, H. Jin, M. Kudla, G. Zhao, Z. 2021-01-15 doi:10.1101/2021.01.15.426526 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Mechanisms Driving Genome Reduction of a Novel Roseobacter Lineage Showing Vitamin B12 Auxotrophy ]]> https://biorxiv.org/content/10.1101/2021.01.15.426902v1?rss=1 4 Mbp). These taxonomic minorities are phylogenetically diverse but form a Pelagic Roseobacter Cluster (PRC) at the genome content level. Here, we cultivated eight isolates constituting a novel Roseobacter lineage which we named CHUG. Metagenomic and metatranscriptomic read recruitment analyses showed that CHUG members were globally distributed and active in marine environments. CHUG members possess some of the smallest genomes (~2.52 Mb) among all known roseobacters, but they do not exhibit canonical features of genome streamlining like higher coding density or fewer paralogues and pseudogenes compared to their sister lineages. While CHUG members are clustered with traditional PRC members at the genome content level, they show important differences. Unlike other PRC members, neither the relative abundances of CHUG members nor their gene expression levels are correlated with chlorophyll a concentration across the global samples. Moreover, CHUG members cannot synthesize vitamin B12, a key metabolite made by most roseobacters but not by many phytoplankton species and thus thought to mediate the roseobacter-phytoplankton interactions. This combination of features is evidence for the hypothesis that CHUG members may have evolved a free-living lifestyle decoupled from phytoplankton. This ecological transition was accompanied by the loss of signature genes involved in roseobacter-phytoplankton symbiosis, suggesting that relaxation of purifying selection is likely an important driver of genome reduction in CHUG. ]]> Feng, X. Chu, X. Qian, Y. Henson, M. W. Lanclos, V. C. Qin, F. Zhao, Y. Thrash, C. Luo, H. 2021-01-16 doi:10.1101/2021.01.15.426902 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ Polycomb suppresses a female gene regulatory network in Sertoli cells ]]> https://biorxiv.org/content/10.1101/2021.01.19.427322v1?rss=1 Maezawa, S. Yukawa, M. Hasegawa, K. Sugiyama, R. Hu, M. Vidal, M. Koseki, H. Barski, A. DeFalco, T. Namekawa, S. H. 2021-01-20 doi:10.1101/2021.01.19.427322 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Opposing effects of competitive exclusion determine invasion outcomes and structure ant assemblages ]]> https://biorxiv.org/content/10.1101/2021.01.25.428088v1?rss=1 Wong, M. K. L. Lee, R. H. Leong, C.-M. Lewis, O. T. Guenard, B. 2021-01-26 doi:10.1101/2021.01.25.428088 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Separate neural dynamics underlying the acquisition of different auditory category structures ]]> https://biorxiv.org/content/10.1101/2021.01.25.428107v1?rss=1 Feng, G. Gan, Z. Yi, H. G. Ell, S. Roark, C. L. Wang, S. Wong, P. C. M. Chandresekaran, B. 2021-01-27 doi:10.1101/2021.01.25.428107 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Characterization of novel regulatory modules controlling leaf angle in maize ]]> https://biorxiv.org/content/10.1101/2021.02.02.429433v1?rss=1 Wang, X. Wang, X. Sun, S. Tu, X. Lin, K. Qin, L. Wang, X. Li, G. Zhong, S. Li, P. 2021-02-02 doi:10.1101/2021.02.02.429433 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Horizontal gene transfer of a unique nif island drives convergent evolution of free-living N2-fixing Bradyrhizobium ]]> https://biorxiv.org/content/10.1101/2021.02.03.429501v1?rss=1 Tao, J. Wang, S. Liao, T. Luo, H. 2021-02-03 doi:10.1101/2021.02.03.429501 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Quantifying full-length circular RNAs in cancer ]]> https://biorxiv.org/content/10.1101/2021.02.04.429722v1?rss=1 Yu, K. H.-O. Shi, C. H. Wang, B. Chow, S. H.-C. Chung, G. T.-Y. Tan, K.-E. Lim, Y.-Y. Tsang, A. C.-M. Lo, K.-W. Yip, K. Y. 2021-02-05 doi:10.1101/2021.02.04.429722 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Dopamine modulates visual threat processing in the superior colliculus via D2 receptors ]]> https://biorxiv.org/content/10.1101/2021.02.12.430615v1?rss=1 Montardy, Q. Zhou, Z. Li, L. Yang, Q. Lei, Z. Feng, X. Chen, S. Shi, Q. Zhang, H. Chen, S. Zhang, Z. Zhao, B. Xu, F. Lu, Z. Wang, L. 2021-02-12 doi:10.1101/2021.02.12.430615 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ coupleCoC+: an information-theoretic co-clustering-basedtransfer learning framework for the integrative analysis of single-cell genomic data ]]> https://biorxiv.org/content/10.1101/2021.02.17.431728v1?rss=1 ZENG, P. Lin, Z. 2021-02-18 doi:10.1101/2021.02.17.431728 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Interaural Time Difference Tuning in the Rat Inferior Colliculus is Predictive of Behavioral Sensitivity ]]> https://biorxiv.org/content/10.1101/2021.02.21.432131v1?rss=1 Li, K. Rajendran, V. G. Mishra, A. P. Chan, C. H. K. Schnupp, J. W. H. 2021-02-21 doi:10.1101/2021.02.21.432131 Cold Spring Harbor Laboratory Press 2021-02-21 <![CDATA[ DeepMotifSyn: a deep learning approach to synthesize heterodimeric DNA motifs ]]> https://biorxiv.org/content/10.1101/2021.02.22.432257v1?rss=1 Lin, J. Huang, L. Chen, X. Zhang, S. Wong, K.-C. 2021-02-23 doi:10.1101/2021.02.22.432257 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Progranulin promotes immune evasion of pancreatic adenocarcinoma through regulation of MHCI expression ]]> https://biorxiv.org/content/10.1101/2021.02.24.432700v1?rss=1 Cheung, P. F. Yang, J. Krengel, K. Althoff, K. Yip, C. Siu, E. H. Ng, L. W. Lang, K. S. Cham, L. Engel, D. R. Soun, C. Cima, I. Scheffler, B. Striefler, J. K. Sinn, M. Bahra, M. Pelzer, U. Oettle, H. Markus, P. Smeets, E. M. Aarntzen, E. H. Savvatakis, K. Liffers, S.-T. Neander, C. Bazarna, A. Zhang, X. Paschen, A. Crawford, H. C. Chan, A. W. Cheung, S. T. Siveke, J. T. 2021-02-25 doi:10.1101/2021.02.24.432700 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Permeant Fluorescent Probes Visualize the Activation of SARM1 and Uncover an Anti-neurodegenerative Drug Candidate ]]> https://biorxiv.org/content/10.1101/2021.02.24.432704v1?rss=1 Li, W. H. Huang, K. Cai, Y. Wang, Q. W. Zhu, W. J. Hou, Y. N. Wang, S. Cao, S. Zhao, Z. Y. Xie, X. J. Du, Y. Lee, C. Lee, H. C. Zhang, H. Zhao, Y. J. 2021-02-25 doi:10.1101/2021.02.24.432704 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Spontaneous neural oscillations influence behavior and sensory representations by suppressing neuronal excitability ]]> https://biorxiv.org/content/10.1101/2021.03.01.433450v1?rss=1 Iemi, L. Gwilliams, L. Samaha, J. Auksztulewicz, R. Cycowicz, Y. M. King, J.-R. Nikulin, V. V. Thesen, T. Doyle, W. Devinsky, O. Schroeder, C. E. Melloni, L. Haegens, S. 2021-03-02 doi:10.1101/2021.03.01.433450 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Recovery of high-qualitied Genomes from a deep-inland Salt Lake Using BASALT ]]> https://biorxiv.org/content/10.1101/2021.03.05.434042v1?rss=1 Yu, K. Qiu, Z. Mu, R. Qiao, X. Zhang, L. Lian, C.-A. Deng, C. Wu, Y. Xu, Z. Li, B. Pan, B. Zhang, Y. Fan, L. Liu, Y. Cao, H. Jin, T. Chen, B. Wang, F. Yan, Y. Xie, L. Zhou, L. Yi, S. Chi, S. Zhang, T. Zhuang, W. 2021-03-05 doi:10.1101/2021.03.05.434042 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2021.03.08.434398v1?rss=1 Dumetz, F. Chow, E. Y.-C. Harris, L. M. Umar, M. I. Jensen, A. Chung, B. Chan, T. F. Merrick, C. J. Kwok, C. K. 2021-03-08 doi:10.1101/2021.03.08.434398 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Metapopulation Structure of Diatom-associated Marine Bacteria ]]> https://biorxiv.org/content/10.1101/2021.03.10.434754v1?rss=1 Qu, L. Feng, X. Chen, Y. Li, L. Wang, X. Hu, Z. Wang, H. Luo, H. 2021-03-10 doi:10.1101/2021.03.10.434754 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Different issue types have different signal intensity on b=0 images and its implication on intravoxel incoherent motion (IVIM) analysis: examples of liver MRI ]]> https://biorxiv.org/content/10.1101/2021.03.11.431356v1?rss=1 Xiao, B.-H. Wang, Y.-X. 2021-03-11 doi:10.1101/2021.03.11.431356 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ MR-APSS: a unified approach to Mendelian Randomization accounting for pleiotropy and sample structure using genome-wide summary statistics ]]> https://biorxiv.org/content/10.1101/2021.03.11.434915v1?rss=1 Hu, X. Zhao, J. Lin, Z. Wang, Y. Peng, H. Zhao, H. Wan, X. Yang, C. 2021-03-12 doi:10.1101/2021.03.11.434915 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Ozone nanobubble treatments improve survivability of Nile tilapia (Oreochromis niloticus) challenged with a pathogenic multidrug-resistant Aeromonas hydrophila ]]> https://biorxiv.org/content/10.1101/2021.03.14.435289v1?rss=1 Le, D. T. Nguyen, L. V. Dong, H. T. Rodkhum, C. St. Hilaire, S. Senapin, S. Sangpo, P. 2021-03-14 doi:10.1101/2021.03.14.435289 Cold Spring Harbor Laboratory Press 2021-03-14 <![CDATA[ The single-cell epigenetic regulatory landscape in mammalian perinatal testis development ]]> https://biorxiv.org/content/10.1101/2021.03.17.435776v1?rss=1 Liao, J. Suen, H. C. Rao, S. Luk, A. C. S. Zhang, R. Lee, A. W. T. Chan, T. H. T. Cheung, M. Y. Chu, H. T. So, H. C. Hobbs, R. M. Lee, T. L. 2021-03-17 doi:10.1101/2021.03.17.435776 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Integrative genome-scale metabolic modeling reveals versatile metabolic strategies for methane utilization in Methylomicrobium album BG8 ]]> https://biorxiv.org/content/10.1101/2021.03.21.436352v1?rss=1 1:1 between the oxygen and methane specific uptake rates for optimal growth. Integrative modeling revealed that at a high ratio of oxygen-to-methane uptake flux, carbon dioxide and formate were the preferred excreted compounds; at lower ratios, however, acetate accounted for a larger fraction of the total excreted flux. The results of this study reveal a trade-off between biomass production and organic compound excretion and provide evidence that this trade-off is linked to the ratio between the oxygen and methane specific uptake rates. ]]> Villada, J. C. Duran, M. F. Lim, C. K. Stein, L. Y. Lee, P. K. H. 2021-03-22 doi:10.1101/2021.03.21.436352 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ CNAHap: a germline haplotyping method using tumor allele-specific copy number alteration ]]> https://biorxiv.org/content/10.1101/2021.03.27.437314v1?rss=1 Tan, B. Chen, L. Jia, W. Wang, Y. Li, H. Li, S. 2021-03-29 doi:10.1101/2021.03.27.437314 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ scAMACE: Model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation ]]> https://biorxiv.org/content/10.1101/2021.03.29.437485v1?rss=1 Wangwu, J. Sun, Z. Lin, Z. 2021-03-31 doi:10.1101/2021.03.29.437485 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation ]]> https://biorxiv.org/content/10.1101/2021.03.31.437992v1?rss=1 Umarov, R. Li, Y. Arakawa, T. Takizawa, S. Gao, X. Arner, E. 2021-04-02 doi:10.1101/2021.03.31.437992 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ The entorhinal cortex modulates trace fear memory formation and neuroplasticity in the lateral amygdala via cholecystokinin ]]> https://biorxiv.org/content/10.1101/2021.04.18.440346v1?rss=1 Feng, H. Su, J. Fang, W. Chen, X. He, J. 2021-04-18 doi:10.1101/2021.04.18.440346 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ AIE nanoparticles camouflaged with tumor cell-derived exosomes for NIR-II imaging-guided photothermal therapy ]]> https://biorxiv.org/content/10.1101/2021.04.19.440457v1?rss=1 Li, Y. Fan, X. Li, Y. Chen, R. Ni, H. Zhang, Y. Xia, Q. Feng, Z. Tang, B. Z. Qian, J. Lin, H. 2021-04-20 doi:10.1101/2021.04.19.440457 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ A novel strain of lumpy skin disease virus causes clinical disease in cattle in Hong Kong ]]> https://biorxiv.org/content/10.1101/2021.04.20.440323v1?rss=1 Flannery, J. Shih, B. Haga, I. R. Ashby, M. Corla, A. King, S. Freimanis, G. L. Polo, N. Tse, A. Brackman, C. Chan, J. Pun, P. Ferguson, A. D. Law, A. Lycett, S. J. Batten, C. Beard, P. 2021-04-20 doi:10.1101/2021.04.20.440323 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Multi-tissue integrative analysis of personal epigenomes ]]> https://biorxiv.org/content/10.1101/2021.04.26.441442v1?rss=1 10 assays in four donors (>1500 open-access functional genomic and proteomic datasets, in total). Each dataset is mapped to a matched, diploid personal genome, which has long-read phasing and structural variants. The mappings enable us to identify >1 million loci with allele-specific behavior. These loci exhibit coordinated epigenetic activity along haplotypes and less conservation than matched, non-allele-specific loci, in a fashion broadly paralleling tissue-specificity. Surprisingly, they can be accurately modelled just based on local nucleotide-sequence context. Combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci and enables models for transferring known eQTLs to difficult-to-profile tissues. Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics. ]]> Rozowsky, J. Drenkow, J. Yang, Y. Gursoy, G. Galeev, T. Borsari, B. Epstein, C. Xiong, K. Xu, J. Gao, J. Yu, K. Berthel, A. Chen, Z. Navarro, F. Liu, J. Sun, M. Wright, J. Chang, J. Cameron, C. Shoresh, N. Gaskell, E. Adrian, J. Aganezov, S. Balderrama-Gutierrez, G. Banskota, S. Corona, G. Chee, S. Chhetri, S. Martins, G. Danyko, C. Davis, C. Farid, D. Farrell, N. Gabdank, I. Gofin, Y. Gorkin, D. Gu, M. Hecht, V. Hitz, B. Issner, R. Kirsche, M. Kong, X. Lam, B. Li, S. Li, B. Li, T. Li, X. Lin, K. Luo, R. Mackiewicz, M. Moore, J. Mudge, J. Nel 2021-04-26 doi:10.1101/2021.04.26.441442 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Quantitative multidimensional phenotypes improve genetic analysis of laterality traits ]]> https://biorxiv.org/content/10.1101/2021.04.28.441754v1?rss=1 Schmitz, J. Zheng, M. Lui, K. F. H. McBride, C. Ho, C. S.- H. Paracchini, S. 2021-04-29 doi:10.1101/2021.04.28.441754 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A/T-rich transcriptome ]]> https://biorxiv.org/content/10.1101/2021.04.29.441925v1?rss=1 Dumetz, F. Enright, A. J. Zhao, J. Kwok, C. K. Merrick, C. J. 2021-04-29 doi:10.1101/2021.04.29.441925 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ RNA toxicity and perturbation of rRNA processing in spinocerebellar ataxia type 2 ]]> https://biorxiv.org/content/10.1101/2021.05.07.443200v1?rss=1 Li, P. P. Moulick, R. Feng, H. Sun, X. Arbez, N. Jin, J. Marque, L. O. Hedglen, E. Chan, H. Y. E. Ross, C. A. Pulst, S. M. Margolis, R. L. Woodson, S. Rudnicki, D. D. 2021-05-09 doi:10.1101/2021.05.07.443200 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ iPSC modeling shows uncompensated mitochondrial mediated oxidative stress underlies early heart failure in hypoplastic left heart syndrome ]]> https://biorxiv.org/content/10.1101/2021.05.09.443165v1?rss=1 Xu, X. Jin, K. Bais, A. S. Zhu, W. Yagi, H. Feinstein, T. N. Nguyen, P. Criscione, J. Liu, X. Beutner, G. Karunakaran, K. B. Adams, P. Kuo, C. K. Kostka, D. Pryhuber, G. S. Shiva, S. Ganapathiraju, M. Porter, G. A. Lin, J.-H. I. Aronow, B. J. Lo, C. W. 2021-05-10 doi:10.1101/2021.05.09.443165 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Generalizable predictive modeling of semantic processing ability from functional brain connectivity ]]> https://biorxiv.org/content/10.1101/2021.05.11.443600v1?rss=1 Meng, D. Wang, S. Wong, P. Feng, G. 2021-05-13 doi:10.1101/2021.05.11.443600 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Diel CO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions ]]> https://biorxiv.org/content/10.1101/2021.05.17.444406v1?rss=1 Schunter, C. Jarrold, M. D. Munday, P. L. Ravasi, T. 2021-05-17 doi:10.1101/2021.05.17.444406 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ The time course of molecular acclimation to seawater in a euryhaline fish ]]> https://biorxiv.org/content/10.1101/2021.05.17.444413v1?rss=1 Bonzi, L. C. Monroe, A. A. Lehmann, R. Berumen, M. L. Ravasi, T. Schunter, C. 2021-05-17 doi:10.1101/2021.05.17.444413 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Adapting insect caste concepts to the demands of bio-ontologies. ]]> https://biorxiv.org/content/10.1101/2021.05.18.444717v1?rss=1 Silva, T. S. R. Pie, M. R. 2021-05-20 doi:10.1101/2021.05.18.444717 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Alpha oscillatory activity causally linked to working memory retention: insights from online phase-locking closed-loop transcranial alternating current stimulation (tACS) ]]> https://biorxiv.org/content/10.1101/2021.05.23.445322v1?rss=1 Chen, X. Ma, R. Zhang, W. Wu, Q. Yimiti, A. Xia, X. Cui, J. Zeng, G. Q. Bu, J. Chen, Q. Yu, N. X. Wang, S. Deng, Z.-D. Sack, A. T. Laughlin, M. M. Zhang, X. 2021-05-23 doi:10.1101/2021.05.23.445322 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Phage-Derived Depolymerase as an Antibiotic Adjuvant Against Multidrug-Resistant Acinetobacter Baumannii ]]> https://biorxiv.org/content/10.1101/2021.05.26.445908v1?rss=1 Chen, X. Liu, M. Zhang, P. Xu, M. Yuan, W. Bian, L. Liu, Y. Xia, J. Leung, S. S. Y. 2021-05-27 doi:10.1101/2021.05.26.445908 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Gene Expression Associated with Individual Variability in Intrinsic Functional Connectivity ]]> https://biorxiv.org/content/10.1101/2021.06.01.446504v1?rss=1 Li, L. Wei, Y. Zhang, J. Ma, J. Yi, Y. Gu, Y. Li, L. M. W. Lin, Y. Dai, Z. 2021-06-01 doi:10.1101/2021.06.01.446504 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Molecular classification reveals the diverse genetic features and prognosis of gastric cancer: a multi-omics consensus ensemble clustering ]]> https://biorxiv.org/content/10.1101/2021.06.07.447364v1?rss=1 Hu, X. Wang, Z. Wang, Q. Chen, K. Han, Q. Bai, S. Du, J. Chen, W. 2021-06-07 doi:10.1101/2021.06.07.447364 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ scSVAS: CNV clonal visualization online platform for large scale single-cell genomics ]]> https://biorxiv.org/content/10.1101/2021.06.10.437122v1?rss=1 Chen, L. Qing, Y. Li, R. Li, C. Li, H. Feng, X. Li, S. C. 2021-06-10 doi:10.1101/2021.06.10.437122 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ CRISPRa screen on a genetic risk locus shared by multiple autoimmune diseases identifies a dysfunctional enhancer that affects IRF8 expression through cooperative lncRNA and DNA methylation machinery ]]> https://biorxiv.org/content/10.1101/2021.06.11.448156v1?rss=1 Zhou, T. Zhu, X. Ye, Z. Wang, Y. Yao, C. Xu, N. Zhou, M. Ma, J. Qin, Y. Shen, Y. Tang, Y. Yin, Z. Xu, H. Zhang, Y. Zang, X. Ding, H. Yang, W. Guo, Y. Harley, J. B. Namjou, B. Kaufman, K. M. Kottyan, L. C. Weirauch, M. T. Hou, G. Shen, N. 2021-06-12 doi:10.1101/2021.06.11.448156 Cold Spring Harbor Laboratory Press 2021-06-12 <![CDATA[ OsciDrop: A versatile on-demand droplet generator ]]> https://biorxiv.org/content/10.1101/2021.06.14.448273v1?rss=1 Ye, S. Zheng, X. Li, C. Huang, W. Tao, Y. Yu, Y. Yang, L. Lan, Y. Ma, L. Bian, S. Du, W. 2021-06-15 doi:10.1101/2021.06.14.448273 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Neuro-molecular characterization of fish cleaning interactions ]]> https://biorxiv.org/content/10.1101/2021.06.22.449532v1?rss=1 Ramirez-Calero, S. Paula, J. R. Otjacques, E. Rosa, R. Ravasi, T. Schunter, C. 2021-06-23 doi:10.1101/2021.06.22.449532 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Generation of liver organoids from human induced pluripotent stem cells as liver fibrosis and steatosis models ]]> https://biorxiv.org/content/10.1101/2021.06.29.450347v1?rss=1 Tsang, H. Y. Lo, P. H. Y. Lee, K. K. H. 2021-06-30 doi:10.1101/2021.06.29.450347 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Plakoglobin and HMGB1 mediate intestinal epithelial cell apoptosis induced by Clostridioides difficile TcdB ]]> https://biorxiv.org/content/10.1101/2021.07.02.450318v1?rss=1 Li, Y. Xu, W. Ren, Y. Cheung, H.-C. Huang, P. Kaur, G. Kuo, C.-J. McDonough, S. P. Fubini, S. L. Lipkin, S. M. Deng, X. Chang, Y.-F. Huang, L. 2021-07-03 doi:10.1101/2021.07.02.450318 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Phylogenomics Suggests the Origin of Obligately Anaerobic Anammox Bacteria Correlates with the Great Oxidation Event ]]> https://biorxiv.org/content/10.1101/2021.07.07.451387v1?rss=1 Liao, T. Wang, S. Luo, H. 2021-07-08 doi:10.1101/2021.07.07.451387 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Dual inhibition of anti-apoptotic proteins BCL-XL and MCL-1 enhances cytotoxicity of Nasopharyngeal carcinoma cells. ]]> https://biorxiv.org/content/10.1101/2021.07.07.451410v1?rss=1 Abdul Rahman, S. F. Azlan, A. Lo, K.-W. Azzam, G. Mohana Kumaran, N. 2021-07-08 doi:10.1101/2021.07.07.451410 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Mining bacterial NGS data vastly expands the complete genomes of temperate phages ]]> https://biorxiv.org/content/10.1101/2021.07.15.452192v1?rss=1 Zhang, X. Wang, R. Xie, X. Hu, Y. Wang, J. Sun, Q. Feng, X. Tong, S. Cui, Y. Wang, M. Zhai, S. Niu, Q. Wang, F. Kropinski, A. M. Jiang, X. Peng, S. Li, S. Tong, Y. 2021-07-15 doi:10.1101/2021.07.15.452192 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Gastrodia-Uncaria Water Extract Inhibits Endoplasmic Reticulum Stress and Matrix Metalloproteinase in Protecting against Cerebral Ischemia ]]> https://biorxiv.org/content/10.1101/2021.07.21.452303v1?rss=1 Choi, A. Y. Xian, J. W. Ma, S. Y. Lin, Z. Chan, C. W. 2021-07-22 doi:10.1101/2021.07.21.452303 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ Discriminative and affective touch converge: Somatosensory cortex represents A-beta input in a CT-like manner ]]> https://biorxiv.org/content/10.1101/2021.07.21.453292v1?rss=1 Schirmer, A. Lai, O. McGlone, F. Cham, C. Lau, D. 2021-07-23 doi:10.1101/2021.07.21.453292 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ The precedence effect in spatial hearing emerges only late in the auditory pathway ]]> https://biorxiv.org/content/10.1101/2021.07.21.453295v1?rss=1 Li, K. Auksztulewicz, R. Chan, C. H. K. Mishra, A. P. Schnupp, J. W. H. 2021-07-23 doi:10.1101/2021.07.21.453295 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Self-supervised contrastive learning for integrative single cell RNA-seq data analysis ]]> https://biorxiv.org/content/10.1101/2021.07.26.453730v1?rss=1 Han, W. Cheng, Y. Chen, J. Zhong, H. Hu, Z. Chen, S. Zong, L. King, I. Gao, X. Li, Y. 2021-07-27 doi:10.1101/2021.07.26.453730 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ Deep learning identifies and quantifies recombination hotspot determinants ]]> https://biorxiv.org/content/10.1101/2021.07.29.454133v1?rss=1 Li, Y. Chen, S. Rapakoulia, T. Kuwahara, H. Yip, K. Gao, X. 2021-07-29 doi:10.1101/2021.07.29.454133 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Identification and targeting of G-quadruplex structures in MALAT1 long non-coding RNA ]]> https://biorxiv.org/content/10.1101/2021.08.14.456336v1?rss=1 Mou, X. Liew, S. W. Kwok, C. K. 2021-08-15 doi:10.1101/2021.08.14.456336 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Mechanistic basis for the emergence of EPS1 as a catalyst in plant salicylic acid biosynthesis ]]> https://biorxiv.org/content/10.1101/2021.08.21.457228v1?rss=1 Torrens-Spence, M. P. Li, T. Wang, Z. Glinkerman, C. M. Matos, J. O. Wang, Y. Weng, J.-K. 2021-08-22 doi:10.1101/2021.08.21.457228 Cold Spring Harbor Laboratory Press 2021-08-22 <![CDATA[ Single-shot rAAV5-based Vaccine Provides Long-term Protective Immunity against SARS-CoV-2 and Its Variants ]]> https://biorxiv.org/content/10.1101/2021.08.23.456471v1?rss=1 Liao, G. Fan, x.-x. Lau, H. Liu, Z. Li, C. Xu, Z. Zhang, Y. Qi, X. Li, D. Zhu, Q. Chen, L. ZHOU, H. Zhu, S. Ke, B. Pan, H. Cong, Z. Li, Y. Feng, Q. Lv, Q. Liu, J. Liang, D. Li, A. Hong, W. Li, Y. Bao, L. Zhou, F. Gao, H. liang, s. Huang, B. Wu, M. Qin, C. Ke, C. liu, l. 2021-08-26 doi:10.1101/2021.08.23.456471 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Air-nanobubbles ineffective to reduce pathogenic bacteria in fresh and brackish waters ]]> https://biorxiv.org/content/10.1101/2021.08.27.457885v1?rss=1 Domingos, J. A. Huang, Q. Liu, H. Dong, H. T. Khongcharoen, N. Van, P. T. Nghia, N. H. Giang, P. T. The Viet, P. St-Hilaire, S. 2021-08-27 doi:10.1101/2021.08.27.457885 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Effective and Efficient Neural Networks for Spike Inference from In Vivo Calcium Imaging ]]> https://biorxiv.org/content/10.1101/2021.08.30.458217v1?rss=1 Zhou, Z. Tin, C. 2021-08-31 doi:10.1101/2021.08.30.458217 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Both Simulation and Sequencing Data Reveal Multiple SARS-CoV-2 Variants Coinfection in COVID-19 Pandemic ]]> https://biorxiv.org/content/10.1101/2021.09.06.459196v1?rss=1 Li, Y. Jiang, Y. Li, Z. Yu, Y. Chen, J. Jia, W. Ng, Y. K. Ye, F. Shen, B. Li, S. C. 2021-09-07 doi:10.1101/2021.09.06.459196 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Cell-adaptable dynamic hydrogel reinforced with stem cells improves the functional repair of spinal cord injury by alleviating neuroinflammation ]]> https://biorxiv.org/content/10.1101/2021.09.24.461661v1?rss=1 Yuan, X. Yuan, W. Ding, L. Shi, M. Luo, L. Wan, Y. Oh, J. Zhou, Y. Bian, L. Deng, D. Y. B. 2021-09-24 doi:10.1101/2021.09.24.461661 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Revealing Free Energy Landscape from MD Data via Conditional Angle Partition Tree ]]> https://biorxiv.org/content/10.1101/2021.09.27.461919v1?rss=1 Jiang, H. Huang, X. Li, H. Wong, W. H. Fan, X. 2021-09-27 doi:10.1101/2021.09.27.461919 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Performance-optimized neural networks as an explanatory framework for decision confidence ]]> https://biorxiv.org/content/10.1101/2021.09.28.462081v1?rss=1 Webb, T. W. Miyoshi, K. So, T. Y. Rajananda, S. Lau, H. 2021-09-30 doi:10.1101/2021.09.28.462081 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Host phylogeny and ecological associations best explain Wolbachia host shifts in scale insects ]]> https://biorxiv.org/content/10.1101/2021.10.01.462721v1?rss=1 Sanaei, E. Albery, G. F. Yeoh, Y. K. Lin, Y. P. Cook, L. G. Engelstaedter, J. 2021-10-01 doi:10.1101/2021.10.01.462721 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Metabolic Regulation of Mitochondrial Morphologies in Pancreatic Beta Cells: Bioenergetics-Mitochondrial Dynamics Coupling ]]> https://biorxiv.org/content/10.1101/2021.10.04.462897v1?rss=1 Tseng, W.-W. Chu, C.-H. Chang, C. Lee, Y.-J. Zhao, S. Ho, Y.-P. Wei, A.-C. 2021-10-04 doi:10.1101/2021.10.04.462897 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Clinically applicable rapid susceptibility testing of multi-drug resistant Staphylococcus aureus by mass spectrometry and extreme gradient boosting machine ]]> https://biorxiv.org/content/10.1101/2021.10.05.463151v1?rss=1 Wang, Z. Wang, H.-Y. Pang, Y. Chung, C.-R. Horng, J.-T. Lu, J.-J. Lee, T.-Y. 2021-10-06 doi:10.1101/2021.10.05.463151 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ seRNA PAM-1 regulates skeletal muscle satellite cell activation and aging through trans regulation of Timp2 expression synergistically with Ddx5 ]]> https://biorxiv.org/content/10.1101/2021.10.06.463443v1?rss=1 So, K. K. H. Huang, Y. Zhang, S. He, L. Li, Y. Chen, X. Zhao, Y. Ding, Y. Zhou, J. Yuan, J. Sham, M. H. Sun, H. Wang, H. 2021-10-07 doi:10.1101/2021.10.06.463443 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Simultaneous Mnemonic and Predictive Representations in the Auditory Cortex ]]> https://biorxiv.org/content/10.1101/2021.10.08.463638v1?rss=1 Cappotto, D. Auksztulewicz, R. Kang, H. Li, K. Melloni, L. Schnupp, J. 2021-10-08 doi:10.1101/2021.10.08.463638 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Is there magnocellular facilitation of early neural processes underlying visual word recognition? Evidence from masked repetition priming with ERPs ]]> https://biorxiv.org/content/10.1101/2021.10.10.463440v1?rss=1 Huang, X. Wong, W. L. Tse, C.-Y. Sommer, W. Dimigen, O. Maurer, U. 2021-10-12 doi:10.1101/2021.10.10.463440 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ ATP and Substrate Binding Regulates Conformational Changes of Human Peroxisomal ABC Transporter ALDP ]]> https://biorxiv.org/content/10.1101/2021.10.14.464310v1?rss=1 xiong, c. Jia, L.-N. Shen, M.-H. Xiong, W.-X. Xiong, L.-L. Wang, T.-H. Zhou, D. Liu, Z. Tang, L. 2021-10-14 doi:10.1101/2021.10.14.464310 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Observation of reversal in twist-stretch coupling of RNA suggests a unified mechanism for the opposite couplings of DNA and RNA ]]> https://biorxiv.org/content/10.1101/2021.10.15.464617v1?rss=1 Qiang, X.-W. Zhang, C. Dong, H.-L. Tian, F.-J. Fu, H. Yang, Y.-J. Dai, L. Zhang, X.-H. Tan, Z.-J. 2021-10-19 doi:10.1101/2021.10.15.464617 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Extrasynaptic NMDA receptors bidirectionally modulate intrinsic excitability of inhibitory neurons ]]> https://biorxiv.org/content/10.1101/2021.10.17.464733v1?rss=1 zhou, q. Yao, L. Rong, Y. Ma, X. Li, H. Deng, D. Chen, Y. Yang, S. Peng, T. Ye, T. Liang, F. Xu, N. 2021-10-18 doi:10.1101/2021.10.17.464733 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities ]]> https://biorxiv.org/content/10.1101/2021.10.19.464956v1?rss=1 Esposito, R. Polidori, T. Meise, D. Pulido, C. Chouvardas, P. Forster, S. Schaerer, P. Kobel, A. Schlatter, J. Roemmele, M. Westemeier, E. Zhu, L. Lanzos, A. Guillen-Ramirez, H. Basile, G. Carrozzo, I. Vancura, A. Ullrich, S. Medina, P. Andreades, A. Harvey, D. Ma, P. Haefliger, S. Wang, X. Martinez, I. Ochsenbein, A. Riether, C. Johnson, R. 2021-10-20 doi:10.1101/2021.10.19.464956 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ A multimodal imaging and analysis pipeline for creating a cellular census of the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/2021.10.20.464979v1?rss=1 Costantini, I. Morgan, L. Yang, J. Balbastre, Y. Varadarajan, D. Pesce, L. Scardigli, M. Mazzamuto, G. Gavryusev, V. Castelli, F. M. Roffilli, M. Silvestri, L. Laffey, J. Raia, S. Varghese, M. Wicinski, B. Chang, S. Chen I-Chun, A. Wang, H. Cordero, D. Vera, M. Nolan, J. Nestor, K. Mora, J. Iglesias, J. E. Pallares, E. G. Evancic, K. Augustinack, J. Fogarty, M. Dalca, A. V. Frosch, M. Magnain, C. Frost, R. van der Kouwe, A. Chen, S.-C. Boas, D. A. Pavone, F. S. Fischl, B. Hof, P. R. 2021-10-21 doi:10.1101/2021.10.20.464979 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Deep autoencoder enables interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis ]]> https://biorxiv.org/content/10.1101/2021.10.26.465846v1?rss=1 Chen, Y. Wang, Y. Chen, Y. Wei, Y. Li, Y. Chan, T.-F. Li, Y. 2021-10-27 doi:10.1101/2021.10.26.465846 Cold Spring Harbor Laboratory Press 2021-10-27 <![CDATA[ Chronic stroke sensorimotor impairment is related to smaller hippocampal volumes: An ENIGMA analysis ]]> https://biorxiv.org/content/10.1101/2021.10.26.465924v1?rss=1 180 days post-stroke) compiled from 18 research cohorts worldwide in the ENIGMA Stroke Recovery Working Group (age: median = 61 years, interquartile range = 18, range = 23-93; 135 women and 222 men). Sensorimotor impairment was estimated from the Fugl-Meyer Assessment of Upper Extremity scores. Robust mixed-effects linear models were used to test associations between post-stroke sensorimotor impairment and hippocampal volumes (ipsilesional and contralesional separately; Bonferroni-corrected, p-value < 0.025), controlling for age, sex, lesion volume, and lesioned hemisphere. We also performed an exploratory analysis to test whether sex differences influence the relationship between sensorimotor impairment and hippocampal volume. Upper limb sensorimotor impairment was positively associated with ipsilesional (p = 0.005; d = 0.33) but not contralesional (p = 0.96; d = 0.01) hippocampal volume, such that impairment was worse for participants with smaller ipsilesional hippocampal volume. This association remained significant independent of lesion volume or other covariates (p = 0.001; d = 0.36). Evidence indicates an interaction between sensorimotor impairment and sex for both ipsilesional (p = 0.008; d = -0.29) and contralesional (p = 0.006; d = -0.30) hippocampal volumes, whereby women showed progressively worsening sensorimotor impairment with smaller hippocampal volumes compared to men. The present study has identified a novel association between chronic post-stroke sensorimotor impairment and ipsilesional, but not contralesional, hippocampal volume. This finding was not due to lesion size and may be stronger in women. We also provide supporting evidence that smaller hippocampal volume post-stroke is likely a consequence of ipsilesional damage, which could provide a link between vascular disease and other disorders, such as dementia. ]]> Zavaliangos-Petropulu, A. Lo, B. Donnelly, M. R. Schweighofer, N. Lohse, K. Jahanshad, N. Barisano, G. Banaj, N. Borich, M. R. Boyd, L. A. Buetefisch, C. M. Byblow, W. D. Cassidy, J. M. Charalambous, C. C. Conforto, A. B. DiCarlo, J. A. Dula, A. N. Egorova-Brumley, N. Etherton, M. R. Feng, W. Fercho, K. A. Geranmayeh, F. Hanlon, C. A. Hayward, K. S. Hordacre, B. Kautz, S. A. Khlif, M. S. Kim, H. Kuceyeski, A. Lin, D. J. Lotze, M. Liu, J. MacIntosh, B. J. Margetis, J. L. Piras, F. Ramos-Murguialday, A. Revill, K. P. Roberts, P. S. Robertson, A. D. Schambra 2021-10-28 doi:10.1101/2021.10.26.465924 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ A novel mechanism of Euonymine inhibits in-stent restenosis through enhancing contractile phenotype of VSMCs by targeting AKT1 and p38MAPK ]]> https://biorxiv.org/content/10.1101/2021.10.29.466441v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@1582ef9org.highwire.dtl.DTLVardef@73e133org.highwire.dtl.DTLVardef@1c5f318org.highwire.dtl.DTLVardef@daca49_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhang, L. Tao, Y. T. Hu, Q. Yang, R. H. Jia, J. Jin, H. N. Yang, Y. Z. Yang, Y. Yu, M. Y. Wang, Y. T. Shi, J. N. Yu, D. Tang, G. P. Xu, J. Xiong, B. Shen, Z. Q. Yu, Z. Qin, H. T. Chen, P. 2021-11-02 doi:10.1101/2021.10.29.466441 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites ]]> https://biorxiv.org/content/10.1101/2021.11.02.467032v1?rss=1 Ma, R. Li, S. Li, W. Yao, L. Huang, H.-D. Lee, T.-Y. 2021-11-04 doi:10.1101/2021.11.02.467032 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Genome-wide association analyses of individual differences in quantitatively assessed reading- and language-related skills in up to 34,000 people ]]> https://biorxiv.org/content/10.1101/2021.11.04.466897v1?rss=1 Eising, E. Mirza-Schreiber, N. de Zeeuw, E. L. Wang, C. A. Truong, D. T. Allegrini, A. G. Shapland, C. Y. Zhu, G. Wigg, K. G. Gerritse, M. Molz, B. Alagoz, G. Gialluisi, A. Abbondanza, F. Rimfeld, K. Van Donkelaar, M. M. Liao, Z. Jansen, P. R. Andlauer, T. F. M. Bates, T. C. Bernard, M. Blokland, K. Borglum, A. D. Bourgeron, T. Brandeis, D. Ceroni, F. Dale, P. S. de Jong, P. F. DeFries, J. C. Demontis, D. Feng, Y. Gordon, S. D. Guger, S. L. Hayiou-Thomas, M. E. Hernandez-Cabrera, J. A. Hottenga, J.- J. Hulme, C. Kerr, E. N. Koomar, T. Landerl, K. Lovett, 2021-11-04 doi:10.1101/2021.11.04.466897 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ PHOSPHATE STARVATION RESPONSE enables arbuscular mycorrhiza symbiosis ]]> https://biorxiv.org/content/10.1101/2021.11.05.467437v1?rss=1 Das, D. Paries, M. Hobecker, K. Gigl, M. Dawid, C. Lam, H.-M. Zhang, J. Chen, M. Gutjahr, C. 2021-11-06 doi:10.1101/2021.11.05.467437 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ A combinatorial indexing strategy for epigenomic profiling of plant single cells ]]> https://biorxiv.org/content/10.1101/2021.11.07.467612v1?rss=1 Tu, X. Marand, A. P. Schmitz, R. J. Zhong, S. 2021-11-08 doi:10.1101/2021.11.07.467612 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens ]]> https://biorxiv.org/content/10.1101/2021.11.10.467646v1?rss=1 He, W.-T. Hou, X. Zhao, J. Sun, J. He, H. Si, W. Wang, J. Jiang, Z. Yan, Z. Xing, G. Lu, M. Suchard, M. A. Ji, X. Gong, W. He, B. Li, J. Lemey, P. Guo, D. Tu, C. Holmes, E. C. Shi, M. Su, S. 2021-11-12 doi:10.1101/2021.11.10.467646 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Determining the architecture of nuclear ring of Xenopus laevis nuclear pore complex using integrated approaches ]]> https://biorxiv.org/content/10.1101/2021.11.10.468004v1?rss=1 Ren, H. Tai, L. Zhu, Y. Chan, C. Zhao, Q. Xu, J. Wang, X. Ma, X. Zhao, L. Huang, X. Yin, G. Jia, M. Zhu, X. An, Y. Zhao, G. Huang, C. Zhang, L. Fan, J. Sun, F. Zhang, C. 2021-11-11 doi:10.1101/2021.11.10.468004 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Adversarial domain translation networks enable fast and accurate large-scale atlas-level single-cell data integration ]]> https://biorxiv.org/content/10.1101/2021.11.16.468892v1?rss=1 Zhao, J. Wang, G. Ming, J. Lin, Z. Wang, Y. Tabula Microcebus Consortium, Wu, A. R. Yang, C. 2021-11-19 doi:10.1101/2021.11.16.468892 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Divergence and convergence of cortical encoding during word reading in bilinguals ]]> https://biorxiv.org/content/10.1101/2021.11.25.470068v1?rss=1 Geng, S. Guo, W. Xu, K. Jia, T. Zhou, W. Blakemore, C. Tan, L.-H. Cao, M. Feng, J. 2021-11-27 doi:10.1101/2021.11.25.470068 Cold Spring Harbor Laboratory Press 2021-11-27 <![CDATA[ Prediction of drug targets for specific diseases leveraging gene perturbation data: A machine learning approach ]]> https://biorxiv.org/content/10.1101/2021.12.01.470692v1?rss=1 Zhao, K. Shi, Y. SO, H.-C. 2021-12-01 doi:10.1101/2021.12.01.470692 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ CURT1A and CURT1C mediate distinct stages of plastid conversion in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.12.01.470752v1?rss=1 Liang, Z. Yeung, W.-T. Mai, K. K. Ma, J. Liu, Z. Chong, Y.-L. F. Kang, B.-H. 2021-12-01 doi:10.1101/2021.12.01.470752 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ EraSOR: Erase Sample Overlap in polygenic score analyses ]]> https://biorxiv.org/content/10.1101/2021.12.10.472164v1?rss=1 5k) target samples, we recommend that EraSOR be used in all future such PRS studies to mitigate the potential effects of inter-cohort overlap and close relatedness. ]]> Choi, S. W. Mak, T. S. H. Hoggart, C. J. O'Reilly, P. F. 2021-12-13 doi:10.1101/2021.12.10.472164 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration ]]> https://biorxiv.org/content/10.1101/2021.12.12.472268v1?rss=1 Wang, X. Hu, Z. Yu, T. Wang, R. Wei, Y. Shu, J. Zhu, M. Li, Y. 2021-12-13 doi:10.1101/2021.12.12.472268 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Pre-treatment of Nile tilapia (Oreochromis niloticus) with ozone nanobubbles improve efficacy of heat-killed Streptococcus agalactiae immersion vaccine ]]> https://biorxiv.org/content/10.1101/2021.12.13.472363v1?rss=1 Nguyen, L. V. Le, D. T. Sangpo, P. Senapin, S. Thapinta, A. Panphut, W. Sophie, S.-H. Rodkhum, C. Dong, H. T. 2021-12-13 doi:10.1101/2021.12.13.472363 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Automated identification of chicken distress vocalisations using deep learning models ]]> https://biorxiv.org/content/10.1101/2021.12.15.472774v1?rss=1 MAO, A. Giraudet, C. LIU, K. De Almeida Nolasco, I. Xie, Z. Xie, Z. Gao, Y. Theobald, J. Bhatta, D. Stewart, R. G. McElligott, A. 2021-12-16 doi:10.1101/2021.12.15.472774 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Multiscale 3D Genome Reorganization during Skeletal Muscle Stem Cell Lineage Progression and Muscle Aging ]]> https://biorxiv.org/content/10.1101/2021.12.20.473464v1?rss=1 Zhao, Y. DING, Y. HE, L. Li, Y. Chen, X. Sun, H. Wang, H. 2021-12-21 doi:10.1101/2021.12.20.473464 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Single-cell analysis of microglial transcriptomic diversity in subarachnoid hemorrhage ]]> https://biorxiv.org/content/10.1101/2021.12.27.474223v1?rss=1 Chen, J. Sun, L. Lyu, H. Zheng, Z. Lai, H. Wang, Y. Luo, Y. Lu, G. Chan, W. Y. Zhang, Y. Chen, X. Li, Z. Ko, H. Wong, K. C. G. 2022-01-02 doi:10.1101/2021.12.27.474223 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ A taxogenomics approach uncovers a new genus in the phylum Placozoa ]]> https://biorxiv.org/content/10.1101/202119v1?rss=1 25% of genes are not collinear (i.e. they are not in the same order in the two genomes). Finally, a multi-gene distance comparison with other non-bilaterian phyla indicate genus level differences to T. adhaerens. These data highlight the large genomic diversity within the Placozoa and justifies the designation of lineage HI3 as a new species, Xxxxxxxxx yyyyyyyyyyyyy1 gen. et spaec. nov., now the second described placozoan species and the first in a new genus. Phylogenomic analyses furthermore supports a robust placement of the Placozoa as sister to a cnidarian-bilaterian clade. ]]> Eitel, M. Francis, W. Osigus, H.-J. Krebs, S. Vargas, S. Blum, H. Williams, G. A. Schierwater, B. Wörheide, G. 2017-10-12 doi:10.1101/202119 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.01.14.476408v1?rss=1 Zong, Y. Yu, T. Wang, X. Wang, Y. Hu, Z. Li, Y. 2022-01-17 doi:10.1101/2022.01.14.476408 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Structural Insights into Sphingosine-1-phosphate Receptor Activation ]]> https://biorxiv.org/content/10.1101/2022.01.15.475352v1?rss=1 Yu, L. He, L. Gan, B. Ti, R. Xiao, Q. Hu, H. Zhu, L. Wang, S. Ren, R. 2022-01-16 doi:10.1101/2022.01.15.475352 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Splicing factor BUD31 promotes ovarian cancer progression through sustaining the expression of anti-apoptotic BCL2L12 ]]> https://biorxiv.org/content/10.1101/2022.01.19.476862v1?rss=1 Wang, Z. Wang, S. Qin, J. Zhang, X. Lu, G. Liu, H. Guo, H. Wu, L. Shao, C. Kong, B. Liu, Z. 2022-01-21 doi:10.1101/2022.01.19.476862 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ STORM: spectral sparsification helps restore the spatial structure at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2022.01.25.477389v1?rss=1 WANG, J. Li, S. Chen, L. Li, S. 2022-01-28 doi:10.1101/2022.01.25.477389 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Accurate strain-level microbiome composition analysis from short reads ]]> https://biorxiv.org/content/10.1101/2022.01.26.477962v1?rss=1 Liao, H. Ji, Y. Sun, Y. 2022-01-28 doi:10.1101/2022.01.26.477962 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ HiC-LDNet: A general and robust deep learning framework for accurate chromatin loop detection in genome-wide contact maps ]]> https://biorxiv.org/content/10.1101/2022.01.30.478367v1?rss=1 Chen, S. Wang, J. Gao, X. Li, Y. 2022-02-01 doi:10.1101/2022.01.30.478367 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Dissociable neural correlates of multisensory coherence and selective attention ]]> https://biorxiv.org/content/10.1101/2022.02.01.478616v1?rss=1 Peng, F. Bizley, J. K. SCHNUPP, J. auksztulewicz, r. 2022-02-02 doi:10.1101/2022.02.01.478616 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ A Prism Vote Framework for Individualized Risk Prediction of Traits in Genome-wide Sequencing Data of Multiple Populations ]]> https://biorxiv.org/content/10.1101/2022.02.02.478767v1?rss=1 Xia, X. Sun, R. Zhang, Y. Wei, Y. Y. Li, Q. Chong, M. K. C. Wu, W. K. K. Zee, B. C.-Y. Tang, H. Wang, M. H. 2022-02-04 doi:10.1101/2022.02.02.478767 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Resolving single-cell copy number profiling for large datasets ]]> https://biorxiv.org/content/10.1101/2022.02.09.479672v1?rss=1 50,000 cells) within four minutes while other tools failed to finish within the time limit, i.e., 120 hours. We apply SeCNV to single-nucleus sequencing (SNS) datasets from two breast cancer patients and acoustic cell tagmentation (ACT) sequencing datasets from eight breast cancer patients. SeCNV successfully reproduces the distinct subclones and infers tumor heterogeneity. SeCNV is available at https://github.com/deepomicslab/SeCNV. ]]> WANG, R. ZHANG, Y. WANG, M. FENG, X. WANG, J. LI, S. 2022-02-10 doi:10.1101/2022.02.09.479672 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Interaural time difference sensitivity under binaural cochlear implant stimulation even at high pulse rates up to 900 pps ]]> https://biorxiv.org/content/10.1101/2022.02.09.479686v1?rss=1 300 pps in human CI users may not reflect the hard upper limit of biCI ITD performance in the mammalian auditory pathway. Perhaps with training or better CI strategies good binaural hearing may be achievable at pulse rates high enough to allow good sampling of speech envelopes while delivering usable ITDs. ]]> Buck, A. N. Buchholz, S. Schnupp, J. W. Rosskothen-Kuhl, N. 2022-02-10 doi:10.1101/2022.02.09.479686 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ rG4-seq 2.0: enhanced transcriptome-wide RNA G-quadruplex structure sequencing for low RNA input samples ]]> https://biorxiv.org/content/10.1101/2022.02.10.479665v1?rss=1 Zhao, J. Chow, E. Y.-C. Yeung, P. Y. Zhang, Q. C. Chan, T.-F. Kwok, C. K. 2022-02-10 doi:10.1101/2022.02.10.479665 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Omission responses in field potentials but not spikes in rat auditory cortex ]]> https://biorxiv.org/content/10.1101/2022.02.11.479668v1?rss=1 Auksztulewicz, R. Rajendran, V. G. Peng, F. Schnupp, J. W. H. Harper, N. S. 2022-02-11 doi:10.1101/2022.02.11.479668 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Autophagy promotes organelle clearance and organized cell separation of living root cap cells in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2022.02.16.480624v1?rss=1 Goh, T. Sakamoto, K. Wang, P. Kozono, S. Ueno, K. Miyashima, S. Toyokura, K. Fukaki, H. Kang, B. H. Nakajima, K. 2022-02-18 doi:10.1101/2022.02.16.480624 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ CRISPR-mediated correction of skeletal muscle Ca2+ handling in a novel DMD patient-derived pluripotent stem cell model ]]> https://biorxiv.org/content/10.1101/2022.02.17.480850v1?rss=1 Morera, C. Kim, J. Paredes-Redondo, A. Nobles, M. Rybin, D. Moccia, R. Kowala, A. Meng, J. Garren, S. Liu, P. Morgan, J. E. Muntoni, F. Christoforou, N. Owens, J. Tinker, A. Lin, Y.-Y. 2022-02-18 doi:10.1101/2022.02.17.480850 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole ]]> https://biorxiv.org/content/10.1101/2022.02.26.482093v1?rss=1 Zhao, J. Bui, M. T. Ma, J. Kuenzl, F. De La Concepcion, J. C. Chen, Y. Petsangouraki, S. Mohseni, A. Garcia Leon, M. Salas-Gomez, M. Giannini, C. Gwennogan, D. Kobylinska, R. Clavel, M. Schellmann, S. Jaillais, Y. Friml, J. Kang, B.-H. Dagdas, Y. 2022-02-26 doi:10.1101/2022.02.26.482093 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Mettl3-mediated m6A modification of Fgf16 restricts cardiomyocyte proliferation during heart regeneration ]]> https://biorxiv.org/content/10.1101/2022.02.27.482166v1?rss=1 Jiang, F.-Q. Chen, J.-X. Chen, W.-Y. Zhao, W.-L. Song, G.-H. Liang, C.-Q. Zhou, Y.-M. Huang, H.-L. Huang, R.-J. Zhao, H. Park, K.-S. Ju, Z. Cai, D. Qi, X.-F. 2022-03-01 doi:10.1101/2022.02.27.482166 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Label-free three-photon imaging of intact human cerebral organoids: tracking early events in brain development and deficits in Rett Syndrome ]]> https://biorxiv.org/content/10.1101/2022.02.28.482282v1?rss=1 Yildirim, M. Delepine, C. Feldman, D. Pham, V. Chou, S. Ip, J. Nott, A. Tsai, L.-H. Ming, G.-L. So, P. T. Sur, M. 2022-03-01 doi:10.1101/2022.02.28.482282 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ RNA G-quadruplex structure contributes to cold adaptation in plants ]]> https://biorxiv.org/content/10.1101/2022.03.04.482910v1?rss=1 Yang, X. Yu, H. Duncan, S. Zhang, Y. Cheema, J. Miller, J. B. Zhang, J. Kwok, C. K. Zhang, H. DING, Y. 2022-03-04 doi:10.1101/2022.03.04.482910 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Welfare concerns for mounted load carrying by working donkeys in Pakistan ]]> https://biorxiv.org/content/10.1101/2022.03.07.483371v1?rss=1 Bukhari, S. S. U. H. Rosanowski, S. M. McElligott, A. G. Parkes, R. S. V. 2022-03-10 doi:10.1101/2022.03.07.483371 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ New distribution data and phylogenetic approach reveal bioregionalization of the western Palearctic ants ]]> https://biorxiv.org/content/10.1101/2022.03.10.483749v1?rss=1 Wang, R. Kass, J. M. Galkowski, C. Garcia, F. Hamer, M. T. Radchenko, A. Salata, S. Schifani, E. Yusupov, Z. M. Economo, E. P. Guenard, B. 2022-03-12 doi:10.1101/2022.03.10.483749 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Investigating the temporal pattern of neuroimaging-based brain age estimation as a biomarker for Alzheimer's Disease related neurodegeneration ]]> https://biorxiv.org/content/10.1101/2022.03.18.484935v1?rss=1 Taylor, A. Zhang, F. Niu, X. Heywood, A. Stocks, J. Feng, G. Popuri, K. Beg, M. F. Wang, L. 2022-03-20 doi:10.1101/2022.03.18.484935 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ BNIP3 upregulation characterizes cancer cell subpopulation with increased fitness and proliferation ]]> https://biorxiv.org/content/10.1101/2022.03.21.485237v1?rss=1 Zhu, Y. Chen, B. Yan, J. Zhao, W. Dou, P. Sun, N. Wang, Y. Huang, X. 2022-03-23 doi:10.1101/2022.03.21.485237 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ A Conformation-specific Nanobody Targeting the NMN-activated State of SARM1 ]]> https://biorxiv.org/content/10.1101/2022.03.25.485784v1?rss=1 Hou, Y. N. Cai, Y. Li, W. H. He, W. M. Zhao, Z. Y. Zhu, W. J. Wang, Q. Liu, J. Lee, H. C. Goran, S. Zhang, H. Zhao, Y. J. 2022-03-26 doi:10.1101/2022.03.25.485784 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Calcineurin-fusion facilitates Cryo-EM Structure Determination of a Family A GPCR ]]> https://biorxiv.org/content/10.1101/2022.03.27.485993v1?rss=1 Xu, J. Chen, G. Wang, H. Cao, S. Heng, J. Deupi, X. Du, Y. Kobilka, B. K. 2022-03-28 doi:10.1101/2022.03.27.485993 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Noncoding RNA's competing endogenous gene pair as motif in serous ovarian cancer ]]> https://biorxiv.org/content/10.1101/2022.04.04.486923v1?rss=1 Cheng, L. Zheng, X. Leung, K.-S. Wong, M.-H. 2022-04-05 doi:10.1101/2022.04.04.486923 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Electron tomography analysis of the prolamellar body and its transformation into grana thylakoids in the cryofixed Arabidopsis cotyledon ]]> https://biorxiv.org/content/10.1101/2022.04.04.487035v1?rss=1 Liang, Z. Yeung, W.-T. Mai, K. K. Ma, J. Liu, Z. Chong, Y.-L. F. Cai, X. Kang, B.-H. 2022-04-05 doi:10.1101/2022.04.04.487035 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ SMURF: embedding single-cell RNA-seq data with matrix factorization preserving selfconsistency ]]> https://biorxiv.org/content/10.1101/2022.04.22.489140v1?rss=1 Wang, B. Pu, J. Chen, L. Li, S. 2022-04-22 doi:10.1101/2022.04.22.489140 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation ]]> https://biorxiv.org/content/10.1101/2022.05.03.490500v1?rss=1 Meshcheryakov, V. A. Pan, W. Li, T. Wang, Y. Ghosh, G. Wang, V. Y.-F. 2022-05-03 doi:10.1101/2022.05.03.490500 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ Intracortical remodelling increases in highly-loaded bone after exercise cessation ]]> https://biorxiv.org/content/10.1101/2022.05.06.490923v1?rss=1 0.04 mm2) were 1.4x to 18.7x greater in number and area in the third metacarpal bone from rested than exercised animals (p = 0.005- 0.008), but were similar in number and area in ribs from rested and exercised animals (p = 0.575-0.688). An intermediate relationship was present in the tibia, and when large canals and smaller canals that result from partial bony infilling (Ca.Ar > 0.002 mm2) were considered together. The mechanostat may override targeted remodelling during periods of high mechanical load by enhancing bone formation, reducing resorption and suppressing turnover. Both systems may work synergistically in rest periods to remove excess and damaged tissue. ]]> da Silva, R. G. C. Sun, T. C. Mishra, A. P. Boyde, A. Doube, M. Riggs, C. M. 2022-05-08 doi:10.1101/2022.05.06.490923 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Climate and ant richness explain the global distribution of ant-plant mutualisms ]]> https://biorxiv.org/content/10.1101/2022.05.07.490958v1?rss=1 Luo, Y. Taylor, A. Weigelt, P. Guénard, B. Economo, E. P. Nowak, A. Inderjit, I. Kreft, H. 2022-05-08 doi:10.1101/2022.05.07.490958 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Unique gut microbiome signatures among adult patients with moderate to severe atopic dermatitis in southern Chinese ]]> https://biorxiv.org/content/10.1101/2022.05.14.491964v1?rss=1 Wang, Y. Hou, J. Tsui, J. C.-C. Wang, L. Zhou, J. Chan, U. K. Lo, C. J. Y. Siu, P. L. K. Loo, S. K. F. Tsui, S. K.-W. 2022-05-16 doi:10.1101/2022.05.14.491964 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ A live attenuated vaccine confers superior mucosal and systemic immunity to SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2022.05.16.492138v1?rss=1 Nouailles, G. Adler, J. M. Pennitz, P. Peidli, S. Teixeira Alves, G. Baumgart, M. Bushe, J. Voss, A. Langenhagen, A. Pott, F. Kazmierski, J. Goekeri, C. Simmons, S. Xing, N. Langner, C. Martin Vidal, R. Abdelgawad, A. Herwig, S. Cichon, G. Niemeyer, D. Drosten, C. Goffinet, C. Landthaler, M. Blüthgen, N. Wu, H. Witzenrath, M. Gruber, A. D. Praktiknjo, S. D. Osterrieder, N. Wyler, E. Kunec, D. Trimpert, J. 2022-05-16 doi:10.1101/2022.05.16.492138 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Massive Horizontal Gene Transfer in Amphioxus Illuminates the Early Evolution of Deuterostomes ]]> https://biorxiv.org/content/10.1101/2022.05.18.492404v1?rss=1 Xiong, Q. Yang, K. Y. Zeng, X. Wang, M. Ng, P. K.-S. Zhou, J.-W. Ng, J. K.-W. Law, C. T.-Y. Du, Q. Xu, K. Falkenberg, L. J. Mao, B. Chen, J.-Y. Tsui, S. K.-W. 2022-05-19 doi:10.1101/2022.05.18.492404 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ A framework to trace microbial engraftment at the strain level during fecal microbiota transplantation ]]> https://biorxiv.org/content/10.1101/2022.05.18.492592v1?rss=1 Jiang, Y. Wang, S. Wang, Y. Zhang, X. Li, S. 2022-05-19 doi:10.1101/2022.05.18.492592 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Delayed benefits for fallow bucks: more fights decrease same day mating success, but may increase matings the next day ]]> https://biorxiv.org/content/10.1101/2022.05.19.492486v1?rss=1 Bateman-Neubert, A. Briefer, E. F. McElligott, A. G. 2022-05-20 doi:10.1101/2022.05.19.492486 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Goat kid recognition of their mothers' calls is not impacted by changes in source-filter parameters. ]]> https://biorxiv.org/content/10.1101/2022.05.19.492593v1?rss=1 Perroux, T. A. McElligott, A. G. Briefer, E. F. 2022-05-20 doi:10.1101/2022.05.19.492593 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Self-organized canals enable long range directed material transport in bacterial communities ]]> https://biorxiv.org/content/10.1101/2022.05.19.492681v1?rss=1 Li, Y. Liu, S. Zhang, Y. Seng, Z. J. Xu, H. Yang, L. Wu, Y. 2022-05-19 doi:10.1101/2022.05.19.492681 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Epitranscriptomic Modification of MicroRNA Increases Atherosclerosis Susceptibility ]]> https://biorxiv.org/content/10.1101/2022.05.21.492858v1?rss=1 He, M. Dong, J. Zhang, Y. Han, S. Y. Wang, C. Gongol, B. Kang, J. Huang, H.-Y. Shyy, J. Y.-J. 2022-05-21 doi:10.1101/2022.05.21.492858 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ scMinerva: a GCN-featured Interpretable Framework for Single-cell Multi-omics Integration with Random Walk on Heterogeneous Graph ]]> https://biorxiv.org/content/10.1101/2022.05.28.493838v1?rss=1 Yu, T. Zong, Y. Wang, Y. Wang, X. Li, Y. 2022-05-29 doi:10.1101/2022.05.28.493838 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ SARS-CoV-2 impacts the transcriptome and epigenome at the maternal-fetal interface in pregnancy ]]> https://biorxiv.org/content/10.1101/2022.05.31.494153v1?rss=1 Gao, L. Mathur, V. Tam, S. K. M. Zhou, X. Cheung, M. F. Chan, L. Y. Estrada-Gutierrez, G. Leung, B. W. Moungmaithong, S. Wang, C. C. Poon, L. Leung, D. C. Y. 2022-05-31 doi:10.1101/2022.05.31.494153 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ All-optical closed-loop voltage clamp for precise control of muscles and neurons in live animals ]]> https://biorxiv.org/content/10.1101/2022.06.03.494532v1?rss=1 Bergs, A. C. Liewald, J. F. Rodriguez-Rozada, S. Liu, Q. Wirt, C. Bessel, A. Zeitzschel, N. Durmaz, H. Nozownik, A. Vierock, J. Bargmann, C. Hegemann, P. Wiegert, J. S. Gottschalk, A. 2022-06-04 doi:10.1101/2022.06.03.494532 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Identification of a small chemical as a lysosomal calcium mobilizer and characterization of its ability to inhibit autophagy and viral infection ]]> https://biorxiv.org/content/10.1101/2022.06.09.495506v1?rss=1 Zhang, K. Zhang, L. Chen, N. Yue, J. 2022-06-09 doi:10.1101/2022.06.09.495506 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ A pangenome analysis pipeline (PSVCP) provides insights into rice functional gene identification ]]> https://biorxiv.org/content/10.1101/2022.06.15.496234v1?rss=1 Wang, J. Wu, Y. Zhang, S. Hu, H. Yuan, Y. Dong, J. Chen, L. Ma, Y. Yang, T. Zhou, L. Chen, J. Liu, B. Li, C. Edwards, D. Zhao, J. 2022-06-17 doi:10.1101/2022.06.15.496234 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ A Novel Bacterial Speciation Process Observed in a Symbiotic Marine Population ]]> https://biorxiv.org/content/10.1101/2022.06.15.496264v1?rss=1 Wang, X. Uematsu, K. O'Rourke, A. Akita, T. Kimura, K. Tomaru, Y. Voolstra, C. R. Innan, H. Luo, H. 2022-06-15 doi:10.1101/2022.06.15.496264 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ "What" and "When" Predictions Modulate Auditory Processing in a Contextually Specific Manner ]]> https://biorxiv.org/content/10.1101/2022.06.20.496917v1?rss=1 Cappotto, D. Luo, D. Lai, H. W. Peng, F. Melloni, L. Auksztulewicz, R. Schnupp, J. W. H. 2022-06-22 doi:10.1101/2022.06.20.496917 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data ]]> https://biorxiv.org/content/10.1101/2022.06.22.497193v1?rss=1 Cheng, Y. Fan, X. Zhang, J. Li, Y. 2022-06-26 doi:10.1101/2022.06.22.497193 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Thermal Pain and Detection Threshold Modulation in Augmented Reality ]]> https://biorxiv.org/content/10.1101/2022.06.22.497278v1?rss=1 Eckhoff, D. Sandor, C. Cheing, G. L. Y. Schnupp, J. Cassinelli, A. 2022-06-26 doi:10.1101/2022.06.22.497278 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Predicting the antigenic evolution of SARS-COV-2 with deep learning ]]> https://biorxiv.org/content/10.1101/2022.06.23.497375v1?rss=1 Han, W. Chen, N. Wang, Y. Sun, S. Gao, X. 2022-06-24 doi:10.1101/2022.06.23.497375 Cold Spring Harbor Laboratory Press 2022-06-24 <![CDATA[ On the similarities of representations in artificial and brain neural networks for speech recognition ]]> https://biorxiv.org/content/10.1101/2022.06.27.497678v1?rss=1 Wingfield, C. Zhang, C. Devereux, B. Fonteneau, E. Thwaites, A. Liu, X. Woodland, P. Marslen-Wilson, W. Su, L. 2022-06-29 doi:10.1101/2022.06.27.497678 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses ]]> https://biorxiv.org/content/10.1101/2022.07.06.498921v1?rss=1 Brussel, K. V. Mahar, J. E. Ortiz-Baez, A. S. E. Carrai, M. Spielman, D. Boardman, W. S. Baker, M. L. Beatty, J. A. Geoghegan, J. L. Barrs, V. R. Holmes, E. C. 2022-07-06 doi:10.1101/2022.07.06.498921 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ FOXP2 confers oncogenic effects in prostate cancer through activating MET signalling ]]> https://biorxiv.org/content/10.1101/2022.07.06.498943v1?rss=1 Zhu, X. Chen, C. Wei, D. Xu, Y. Liang, S. Jia, W. Li, J. Qu, Y. Zhai, J. Zhang, Y. Wu, P. Hao, Q. Zhang, L. Zhang, W. Yang, X. Pan, L. Qi, R. Li, Y. Wang, F. Yi, R. Yang, Z. Wang, J. Zhao, Y. 2022-07-06 doi:10.1101/2022.07.06.498943 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Oscillatory mechanisms of intrinsic brain networks ]]> https://biorxiv.org/content/10.1101/2022.07.07.499235v1?rss=1 Luo, Y. Meng, X. Zhou, G. Zhou, J. Zelano, C. M. Li, Y. Xu, J. Deng, G. Luo, Y.-j. Ai, H. Xu, P. Chen, F. 2022-07-10 doi:10.1101/2022.07.07.499235 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Plasmid Permissiveness of Wastewater Microbiomes can be Predicted from 16S rDNA sequences by Machine Learning ]]> https://biorxiv.org/content/10.1101/2022.07.09.499415v1?rss=1 Moradigaravand, D. Li, L. Dechesne, A. Nesme, J. Ahmad, H. Banzhaf, M. Sorensen, S. Smets, B. Kreft, J. 2022-07-10 doi:10.1101/2022.07.09.499415 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ The Phylotranscriptomic Hourglass Pattern in Fungi: An Updated Model ]]> https://biorxiv.org/content/10.1101/2022.07.14.500038v1?rss=1 Xie, Y. Kwan, H. S. Chan, P. L. Wu, W. Chiou, J. Chang, J. 2022-07-16 doi:10.1101/2022.07.14.500038 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ GIS-based approach and multivariate statistical analysis for identifying sources of heavy metals in marine sediments from the coast of Hong Kong. ]]> https://biorxiv.org/content/10.1101/2022.07.16.490032v1?rss=1 Huang, F. Chen, C. 2022-07-18 doi:10.1101/2022.07.16.490032 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Apicosome: newly identified cell-type-specific organelle in mouse cochlear and vestibular hair cells ]]> https://biorxiv.org/content/10.1101/2022.07.20.500729v1?rss=1 Li, X. Zhao, Q. Yu, X. Cao, W. Zhang, Y. Feng, W. Jiang, L. He, D. Z. Qi, R. Z. Huang, P. 2022-07-21 doi:10.1101/2022.07.20.500729 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Regulatory roles of three-dimensional structures of topologically associating domains ]]> https://biorxiv.org/content/10.1101/2022.07.22.501196v1?rss=1 Li, K. Y. Cao, Q. Wang, H. Leung, D. C. Y. Yip, K. Y. 2022-07-23 doi:10.1101/2022.07.22.501196 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity ]]> https://biorxiv.org/content/10.1101/2022.07.26.501505v1?rss=1 Fan, S. Sun, W. Fan, L. Wu, N. Sun, W. Ma, H. Chen, S. Li, Z. Li, Y. Zhang, J. Yan, J. 2022-07-26 doi:10.1101/2022.07.26.501505 Cold Spring Harbor Laboratory Press 2022-07-26 <![CDATA[ A molecular mechanism for membrane chaperoning by a late embryogenesis abundant protein ]]> https://biorxiv.org/content/10.1101/2022.07.29.502075v1?rss=1 Li, X.-H. Yu, C. W. H. Gomez-Navarro, N. Stancheva, V. Zhu, H. Guibao, C. Xie, B. Murthy, A. Wozny, M. Leslie, B. Kaminski, M. Malhotra, K. Johnson, C. M. Blackledge, M. Santhanam, B. Green, D. R. Peng, J. Liu, W. Huang, J. Miller, E. A. Freund, S. M. V. Babu, M. M. 2022-07-31 doi:10.1101/2022.07.29.502075 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles ]]> https://biorxiv.org/content/10.1101/2022.07.30.502157v1?rss=1 Schreiber, J. M. Boix, C. A. Lee, J. w. Li, H. Guan, Y. Chang, C.-C. Chang, J.-C. Hawkins-Hooker, A. Schoelkopf, B. Schweikert, G. Rojas Carulla, M. Canakoglu, A. Guzzo, F. Nanni, L. Masseroli, M. Carman, M. J. Pinoli, P. Hong, C. Yip, K. Y. Spence, J. P. Batra, S. S. Song, Y. S. Mahony, S. Zhang, Z. Tan, W. Shen, Y. Sun, Y. Shi, M. Adrian, J. Sandstrom, R. S. Farrell, N. Halow, J. M. Lee, K. Jiang, L. Yang, X. Epstein, C. B. Strattan, J. S. Snyder, M. P. Kellis, M. Noble, W. S. Kundaje, A. B. 2022-08-02 doi:10.1101/2022.07.30.502157 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions ]]> https://biorxiv.org/content/10.1101/2022.08.06.503062v1?rss=1 Chen, J. Hu, Z. Sun, S. Tan, Q. Wang, Y. Yu, Q. Zong, L. Hong, L. Xiao, J. King, I. Li, Y. 2022-08-07 doi:10.1101/2022.08.06.503062 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Nuclear m6A Reader YTHDC1 Promotes Muscle Stem Cell Activation/Proliferation by Regulating mRNA Splicing and Nuclear Export ]]> https://biorxiv.org/content/10.1101/2022.08.07.503064v1?rss=1 Qiao, Y. Sun, Q. Chen, X. Wang, D. Su, R. Xue, Y. Sun, H. Wang, H. 2022-08-07 doi:10.1101/2022.08.07.503064 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ ATF3 Preserves Skeletal Muscle Stem Cell Quiescence by Preventing Precocious Activation ]]> https://biorxiv.org/content/10.1101/2022.08.12.503549v1?rss=1 Zhang, S. Huang, Y. Yang, F. HE, L. Li, Y. Wan, Y. C. E. Ding, Y. Chan, K. M. Xie, T. Sun, H. Wang, H. 2022-08-12 doi:10.1101/2022.08.12.503549 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ Incorporating cell hierarchy to decipher the functional diversity of single cells ]]> https://biorxiv.org/content/10.1101/2022.08.17.504240v1?rss=1 Chen, L. Li, S. 2022-08-17 doi:10.1101/2022.08.17.504240 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ A graph representation of gapped patterns in phage sequences for graph convolutional network ]]> https://biorxiv.org/content/10.1101/2022.08.22.504727v1?rss=1 WANG, R. NG, Y. K. ZHANG, X. WANG, J. Li, S. 2022-08-22 doi:10.1101/2022.08.22.504727 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Active bulging promotes biofilm formation in a bacterial swarm ]]> https://biorxiv.org/content/10.1101/2022.08.25.500950v1?rss=1 Liu, S. Li, Y. Xu, H. Kearns, D. B. Wu, Y. 2022-08-25 doi:10.1101/2022.08.25.500950 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Probabilistic tensor decomposition extracts better latent embeddings from single-cell multiomic data ]]> https://biorxiv.org/content/10.1101/2022.08.26.505382v1?rss=1 WANG, R. WANG, J. Li, S. 2022-08-26 doi:10.1101/2022.08.26.505382 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Unusual Morphological Changes of Rugositalea oryzae, A Novel Wrinkled Bacterium Isolated from The Rice Rhizosphere, Under Nutrient Stress ]]> https://biorxiv.org/content/10.1101/2022.08.29.505124v1?rss=1 Chung, Y. R. Lee, J.-E. Aslam, Z. Chung, E. J. Khan, A. Lee, K. H. Kang, B. H. Niraula, S. Chang, W.-S. 2022-08-30 doi:10.1101/2022.08.29.505124 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Treatment history shapes the evolution of complex carbapenem-resistant phenotypes in Klebsiella spp. ]]> https://biorxiv.org/content/10.1101/2022.08.30.505938v1?rss=1 Lithgow, T. Zhou, T. MCDONALD, M. Rosas, N. Wilksch, J. Barber, J. Li, J. Wang, Y. Sun, Z. Rocker, A. Webb, C. Perlaza-Jimenez, L. Stubenrauch, C. Vijaykrishn, D. Song, J. Taiaroa, G. Davies, M. R. Strugnell, R. Bao, Q. 2022-08-30 doi:10.1101/2022.08.30.505938 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Associations between thinner retinal neuronal layers and suboptimal brain structural integrity: Are the eyes a window to the brain? ]]> https://biorxiv.org/content/10.1101/2022.08.31.506114v1?rss=1 Barrett-Young, A. Abraham, W. C. Cheung, C. Y. Gale, J. Hogan, S. Ireland, D. Keenan, R. Knodt, A. R. Melzer, T. R. Moffitt, T. E. Ramrakha, S. Tham, Y. C. Wilson, G. A. Wong, T. Y. Hariri, A. R. Poulton, R. 2022-09-03 doi:10.1101/2022.08.31.506114 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires ]]> https://biorxiv.org/content/10.1101/2022.09.01.505405v1?rss=1 Jiang, Y. Li, S. C. 2022-09-03 doi:10.1101/2022.09.01.505405 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Endogenous Plasmids and Reductive Genome Evolution in Host-Associated Bacteria ]]> https://biorxiv.org/content/10.1101/2022.09.09.507235v1?rss=1 XIONG, Q. Fung, C. S.-H. Xiao, X. Wan, A. T.-Y. Wang, M. Ren, Y. Yang, K. Y. Cui, Y. Liu, X. Tsui, S. K.-W. 2022-09-10 doi:10.1101/2022.09.09.507235 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation ]]> https://biorxiv.org/content/10.1101/2022.09.11.507502v1?rss=1 Su, Q. Long, Y. Wang, J. Gou, D. 2022-09-13 doi:10.1101/2022.09.11.507502 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Long-distance linguistic dependencies in Chinese and English brains ]]> https://biorxiv.org/content/10.1101/2022.09.12.507571v1?rss=1 Dunagan, D. Stanojevic, M. Coavoux, M. Zhang, S. Bhattasali, S. Li, J. Brennan, J. Hale, J. T. 2022-09-14 doi:10.1101/2022.09.12.507571 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Synaptic Competition Enhances the Discrimination of Interfering Memories ]]> https://biorxiv.org/content/10.1101/2022.09.15.508061v1?rss=1 Fung, C. C. A. Fukai, T. 2022-09-15 doi:10.1101/2022.09.15.508061 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ The Slingshot phosphatase 2 is required for acrosome biogenesis during spermatogenesis in mice ]]> https://biorxiv.org/content/10.1101/2022.09.15.508144v1?rss=1 Xu, K. Su, X. Fang, K. Lv, Y. Lu, G. Chan, W. Chen, Z.-J. Ma, J. Liu, H. 2022-09-17 doi:10.1101/2022.09.15.508144 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Gobies inhabiting natural CO2 seeps reveal acclimation strategies to long-term acidification ]]> https://biorxiv.org/content/10.1101/2022.09.18.508416v1?rss=1 Suresh, S. Mirasole, A. Ravasi, T. Vizzini, S. Schunter, C. 2022-09-19 doi:10.1101/2022.09.18.508416 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ GutMeta: online microbiome analysis and interactive visualization with build-in curated human gut microbiome database ]]> https://biorxiv.org/content/10.1101/2022.09.26.509484v1?rss=1 Jiang, Y. Wang, Y. Che, L. Zhou, Q. Li, S. C. 2022-09-27 doi:10.1101/2022.09.26.509484 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Heterosynaptic Plasticity of the Visuo-auditory Projection Requires Cholecystokinin released from Entorhinal Cortex Afferents ]]> https://biorxiv.org/content/10.1101/2022.10.04.510820v1?rss=1 Sun, W. Wu, H. Peng, Y. Tang, P. Zhao, M. Zheng, C. X. Feng, H. Li, H. Liang, Y. Li, J. Su, J. Chen, X. Hökfelt, T. He, J. 2022-10-05 doi:10.1101/2022.10.04.510820 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A meta-analysis of genome-wide association studies identifies new genetic loci associated with all-cause and vascular dementia ]]> https://biorxiv.org/content/10.1101/2022.10.11.509802v1?rss=1 Fongang, B. Sargurupremraj, M. Jian, X. Mishra, A. Damotte, V. Bis, J. C. Kang-Hsien, F. Li, G. Yang, J. Hilal, S. Knol, M. J. Concas, M. P. Giorgia, G. Riaz, M. Guojunsson, A. Lacaze, P. Naj, A. C. van der Lee, S. J. Goss, M. Ngouongo, Y. W. Skrobot, O. Guonason, V. Launer, L. Oscar, L. Mary, H. Bosnes, I. Dufouil, C. Ganguli, M. Cheung, C.-L. Bennett, D. A. Chen, C. Ilyas, K. M. Satizabal, C. Ikram, A. M. Debette, S. Fornage, M. Qiong, Y. Schellenberg, G. D. Winsvold, B. Kehoe, P. G. Ruiz, A. Lambert, J.-C. Weinstein, G. Seshadri, S. 2022-10-14 doi:10.1101/2022.10.11.509802 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Temporal and regulatory dynamics of the inner ear transcriptome during development in mice ]]> https://biorxiv.org/content/10.1101/2022.10.17.512623v1?rss=1 Cao, R. Takechi, M. Wang, X. Furutera, T. Nojiri, T. Koyabu, D. Li, J. 2022-10-18 doi:10.1101/2022.10.17.512623 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Thermococci-to-Clostridia Pathway for the Evolution of the Bacteria Domain ]]> https://biorxiv.org/content/10.1101/2022.10.20.512992v1?rss=1 Wong, T.-F. Chan, C.-K. Xue, H. 2022-10-21 doi:10.1101/2022.10.20.512992 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ TEINet: a deep learning framework for prediction of TCR-epitope binding specificity ]]> https://biorxiv.org/content/10.1101/2022.10.20.513029v1?rss=1 Jiang, Y. Huo, M. Li, S. 2022-10-21 doi:10.1101/2022.10.20.513029 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Multi-Omic Analysis of Tyrophagus putrescentiae Reveals Insights into the Allergen Complexity of Storage Mites ]]> https://biorxiv.org/content/10.1101/2022.10.21.513148v1?rss=1 Wan, A. T.-Y. XIONG, Q. Xiao, X. Ao, K. F.-K. Jang, S. W. Wong, B. S.-H. Wang, M. Cao, Q. Fung, C. S.-H. Chew, F.-T. Sun, B. Ngai, S.-m. Leung, T.-F. Jeong, K. Y. Liu, X. Tsui, S. K.-W. 2022-10-21 doi:10.1101/2022.10.21.513148 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Styxl2 regulates de novo sarcomere assembly by binding to non-muscle myosin IIs and promoting their degradation ]]> https://biorxiv.org/content/10.1101/2022.10.22.513336v1?rss=1 Chen, X. Li, Y. Xu, J. Cui, Y. Wu, Q. Yin, H. Li, Y. Jiang, L. Wang, H. Wen, Z. Yao, Z. Wu, Z. 2022-10-22 doi:10.1101/2022.10.22.513336 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Eliminate false positives in metagenomic profiling based on type IIB restriction sites ]]> https://biorxiv.org/content/10.1101/2022.10.24.513546v1?rss=1 Sun, Z. Liu, J. Zhang, M. Wang, T. Huang, S. Weiss, S. T. Liu, Y.-Y. 2022-10-25 doi:10.1101/2022.10.24.513546 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Higher habitual FODMAP intake is associated with lower body mass index, lower insulin resistance and higher short-chain fatty acid-producing microbiota in people with prediabetes ]]> https://biorxiv.org/content/10.1101/2022.10.26.513956v1?rss=1 Chu, N. H. He, J. Ling, J. Leung, K. Ma, R. C. Lee, J. Varney, J. Chan, J. C. Muir, J. Chow, E. 2022-10-27 doi:10.1101/2022.10.26.513956 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Mechanical force induces DRP1-dependent asymmetrical mitochondrial fission for quality control ]]> https://biorxiv.org/content/10.1101/2022.10.27.513965v1?rss=1 Liu, X. Xu, L. Song, Y. Li, X. Wong, C.-Y. Rong, C. Feng, J. Chow, H.-M. Yao, S. Gao, S. Liu, X. Duan, L. 2022-10-28 doi:10.1101/2022.10.27.513965 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Protein kinase A gene knockout in Coprinopsis cinerea by CRISPR/Cas9 RNP complex system ]]> https://biorxiv.org/content/10.1101/2022.10.28.513995v1?rss=1 Chan, P. L. Chang, J. Kwan, H. S. 2022-10-30 doi:10.1101/2022.10.28.513995 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ KBPRNA: A novel method integrating bulk RNA-seq data and LINCS-L1000 gene signatures to predict kinase activity based on machine learning ]]> https://biorxiv.org/content/10.1101/2022.11.16.516707v1?rss=1 Zhang, Y. Yao, L. Huang, Y. Zhang, W. Pang, Y. Lee, T.-y. 2022-11-17 doi:10.1101/2022.11.16.516707 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Cholecystokinin from the Rhinal Cortex Facilitates Motor Skill Learning ]]> https://biorxiv.org/content/10.1101/2022.11.21.517378v1?rss=1 Li, H. Feng, J. Chen, M. Xin, M. Chen, X. Wang, K. He, J. 2022-11-22 doi:10.1101/2022.11.21.517378 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses ]]> https://biorxiv.org/content/10.1101/2022.11.23.517609v1?rss=1 Wang, J. Pan, Y. Yang, L.-f. Yang, W.-h. Luo, C.-m. Wang, J. Kuang, G.-p. Wu, W.-c. Gou, Q.-y. Xin, G.-y. Li, B. Luo, H.-l. Chen, Y.-q. Shu, Y.-l. Guo, D. Gao, Z.-h. Liang, G. Li, J. Holmes, E. C. Feng, Y. Shi, M. 2022-11-23 doi:10.1101/2022.11.23.517609 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Inhibitory effect of lactobacilli supernatants on biofilm and filamentation of C. albicans, C. tropicalis, and C. parapsilosis ]]> https://biorxiv.org/content/10.1101/2022.11.26.518025v1?rss=1 Poon, Y. Hui, M. 2022-11-26 doi:10.1101/2022.11.26.518025 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ ABLs and TMKs are co-receptors for extracellular auxin ]]> https://biorxiv.org/content/10.1101/2022.11.28.518138v1?rss=1 Yu, Y. Tang, W. Lin, W. Li, W. Zhou, X. Li, Y. Chen, R. Zheng, R. Qin, G. Cao, W. Perez, P. Huang, R. Ma, J. Lin, J. Jiang, L. Xu, T. Yang, Z. 2022-11-28 doi:10.1101/2022.11.28.518138 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Memory out of context: Spacing effects and decontextualization in a computational model of the medial temporal lobe ]]> https://biorxiv.org/content/10.1101/2022.12.01.518703v1?rss=1 Antony, J. W. Liu, X. L. Zheng, Y. W. Ranganath, C. O'Reilly, R. C. 2022-12-01 doi:10.1101/2022.12.01.518703 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Sequencing-free Tissue-wide Spatial Profiling of Post-transcriptional Regulations ]]> https://biorxiv.org/content/10.1101/2022.12.11.519542v1?rss=1 Ji, X. Fang, P. Zhao, X. Xiong, C. Yang, Q. Wan, Y. Yan Do, R. Wang, Z. Qi, L. Huang, L. Zhang, W. Wang, X. Shi, P. 2022-12-13 doi:10.1101/2022.12.11.519542 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ The structural basis of itch receptor MRGPRX1 activation ]]> https://biorxiv.org/content/10.1101/2022.12.21.521535v1?rss=1 Gan, B. Yu, L. Yang, H. Jiao, H. Pang, B. Chen, Y. Wang, C. Lv, R. Hu, H. Cao, Z. Ren, R. 2022-12-22 doi:10.1101/2022.12.21.521535 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Astrocytic L-lactate signaling in the anterior cingulate cortex is essential for schema memory and neuronal mitochondrial biogenesis ]]> https://biorxiv.org/content/10.1101/2023.01.08.523156v1?rss=1 Akter, M. Hasan, M. Ramkrishnan, A. S. Zheng, X. Iqbal, Z. Fu, Z. Lei, Z. Karim, A. Li, Y. 2023-01-09 doi:10.1101/2023.01.08.523156 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ G3DC: a Gene-Graph-Guided selective Deep Clustering method for single cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2023.01.15.524109v1?rss=1 He, S. Yu, T. Fan, J. 2023-01-18 doi:10.1101/2023.01.15.524109 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Hierarchical Deviant Processing in Auditory Cortex of Awake Mice ]]> https://biorxiv.org/content/10.1101/2023.01.18.524413v1?rss=1 Luo, D. Liu, J. Auksztulewicz, R. Yip, T. K.-W. Kanold, P. O. Schnupp, J. W. H. 2023-01-20 doi:10.1101/2023.01.18.524413 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Cell Instance Segmentation via Multi-Scale Non-local Correlation ]]> https://biorxiv.org/content/10.1101/2023.01.24.525387v1?rss=1 Duan, B. CAO, J. Wang, W. Cai, D. Yan, Y. 2023-01-25 doi:10.1101/2023.01.24.525387 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ A dual diffusion model enables 3D binding bioactive molecule generation and lead optimization given target pockets ]]> https://biorxiv.org/content/10.1101/2023.01.28.526011v1?rss=1 Huang, L. 2023-01-30 doi:10.1101/2023.01.28.526011 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ Quantitative Annotations of T-Cell Repertoire Specificity ]]> https://biorxiv.org/content/10.1101/2023.01.29.526145v1?rss=1 Luo, J. Wang, X. Zou, Y. Chen, L. Liu, W. Zhang, W. Li, S. 2023-01-31 doi:10.1101/2023.01.29.526145 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ How the dominant reading direction changes parafoveal processing: A combined EEG/eye-tracking study ]]> https://biorxiv.org/content/10.1101/2023.01.30.526189v1?rss=1 Huang, X. Ng, H. T.-Y. Lin, C. H. Yan, M. Dimigen, O. Sommer, W. Maurer, U. 2023-02-02 doi:10.1101/2023.01.30.526189 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Protein Sequence Design by Entropy-based Iterative Refinement ]]> https://biorxiv.org/content/10.1101/2023.02.04.527099v1?rss=1 Zhou, X. Chen, G. Ye, J. Wang, E. Zhang, J. Mao, C. Li, Z. Hao, J. Huang, X. Tang, J. Heng, P. A. 2023-02-04 doi:10.1101/2023.02.04.527099 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Taxonomical and ontological analysis of verified natural and laboratory human coronavirus hosts ]]> https://biorxiv.org/content/10.1101/2023.02.05.527173v1?rss=1 Wang, Y. Ye, M. Zhang, F. Freeman, Z. T. Yu, H. Ye, X. He, Y. 2023-02-06 doi:10.1101/2023.02.05.527173 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Genome-wide mining and comparative analysis of microsatellite markers from Orientia tsutsugamushi genomes ]]> https://biorxiv.org/content/10.1101/2023.02.06.527248v1?rss=1 Panda, S. Swain, S. K. Sahu, B. P. Sarangi, R. 2023-02-06 doi:10.1101/2023.02.06.527248 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Probabilistic cell/domain-type assignment of spatial transcriptomics data with SpatialAnno ]]> https://biorxiv.org/content/10.1101/2023.02.08.527590v1?rss=1 Shi, X. Yang, Y. Ma, X. Zhou, Y. Guo, Z. Wang, C. Liu, J. 2023-02-08 doi:10.1101/2023.02.08.527590 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Comprehensive Allergen Profile of Blomia tropicalis Provides Insights into the Component-Resolved Diagnosis of Mite Allergy ]]> https://biorxiv.org/content/10.1101/2023.02.09.527948v1?rss=1 XIONG, Q. Liu, X. Wan, A. T.-Y. Malainual, N. Xiao, X. Tang, M.-F. Ng, J. K.-W. Shin, S.-K. Sio, Y. Y. WANG, M. Sun, B. Leung, T.-F. Chew, F. T. Tungtrongchitr, A. Tsui, S. K.-W. 2023-02-10 doi:10.1101/2023.02.09.527948 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ The effect of glucagon-like peptide-1 receptor agonist (GLP1RA) on hypertensive-induced heart failure with preserved ejection fraction and hypertensive cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2023.02.12.528171v1?rss=1 Zhang, Z. Y. Liao, S.-Y. Zhen, Z. Sun, S. Lai, W.-H. Tsang, A. Hai, J. J. S.-H. 2023-02-12 doi:10.1101/2023.02.12.528171 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ The clock transcription factor BMAL1 is a key regulator of extracellular matrix homeostasis and cell fate in the intervertebral disc ]]> https://biorxiv.org/content/10.1101/2023.02.12.528214v1?rss=1 Dudek, M. Morris, H. Rogers, N. Pathiranage, D. R. Chan, D. Kadler, K. E. Hoyland, J. A. Meng, Q.-J. 2023-02-12 doi:10.1101/2023.02.12.528214 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ SARS-CoV-2 Neutralizing Antibodies After Bivalent vs. Monovalent Booster ]]> https://biorxiv.org/content/10.1101/2023.02.13.528341v1?rss=1 Wang, Q. Bowen, A. D. Tam, A. R. Valdez, R. Stoneman, E. Mellis, I. A. Gordon, A. Liu, L. Ho, D. D. 2023-02-14 doi:10.1101/2023.02.13.528341 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ An explainable artificial intelligence-based typification of chronic inflammatory responses enhances glioma prognosis ]]> https://biorxiv.org/content/10.1101/2023.02.28.530381v1?rss=1 Chowdhury, D. YIP, H. F. Li, Z. Ren, Q. Liu, H. Tai, X. Zhang, L. Lu, A. 2023-03-01 doi:10.1101/2023.02.28.530381 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ BRD9-SMAD2/3 orchestrates stemness and tumorigenesis in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.03.02.530770v1?rss=1 Feng, Y. Cai, L. Pook, M. Liu, F. Chang, C.-H. Mouti, M. A. Nibhani, R. Wu, S. Deng, S. Militi, S. Dunford, J. Philpott, M. Fan, Y. Fan, G.-C. Liu, Q. Qi, J. Sadayappan, S. Jegga, A. G. Oppermann, U. Wang, Y. Huang, W. Jiang, L. Pauklin, S. 2023-03-02 doi:10.1101/2023.03.02.530770 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Differentiating shame- and guilt-proneness with heart rate variability in Chinese young adults ]]> https://biorxiv.org/content/10.1101/2023.03.02.530780v1?rss=1 Ip, I. Ching, F. Chiu, H. T. Keung, A. Wong, S. 2023-03-02 doi:10.1101/2023.03.02.530780 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Inferring B-cell derived T-cell receptor induced multi epitope-based vaccine candidate against enterovirus 71 (EV 71): A reverse vaccinology approach. ]]> https://biorxiv.org/content/10.1101/2023.03.04.531076v1?rss=1 Panda, S. Swain, S. K. Sahu, B. P. Mahapatra, S. R. Dey, J. Mishra, N. Sarangi, R. 2023-03-04 doi:10.1101/2023.03.04.531076 Cold Spring Harbor Laboratory Press 2023-03-04 <![CDATA[ A bootstrap model comparison test for identifying genes with context-specific patterns of genetic regulation ]]> https://biorxiv.org/content/10.1101/2023.03.06.531446v1?rss=1 Malakhov, M. M. Dai, B. Shen, X. T. Pan, W. 2023-03-07 doi:10.1101/2023.03.06.531446 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Distance-dependent reconfiguration of hubs in Alzheimer's disease:a cross-tissue functional network study ]]> https://biorxiv.org/content/10.1101/2023.03.24.532772v1?rss=1 Zhang, X. Li, Y. Guan, Q. Dong, D. Zhang, J. Meng, X. Chen, F. Luo, Y. Zhang, H. 2023-03-25 doi:10.1101/2023.03.24.532772 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Structural insights into ligand recognition and selectivity of the human hydroxycarboxylic acid receptor HCAR2 ]]> https://biorxiv.org/content/10.1101/2023.03.28.534513v1?rss=1 pan, x. ye, f. Ning, P. Zhang, Z. Zhang, B. Chen, G. Gao, W. Qiu, C. Wu, Z. Gong, K. Li, J. Xia, J. Du, Y. 2023-03-29 doi:10.1101/2023.03.28.534513 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ XMAP: Cross-population fine-mapping by leveraging genetic diversity and accounting for confounding bias ]]> https://biorxiv.org/content/10.1101/2023.03.30.534832v1?rss=1 Cai, M. Wang, Z. Xiao, J. Hu, X. Chen, G. Yang, C. 2023-04-02 doi:10.1101/2023.03.30.534832 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ PanGraphViewer: A Versatile Tool to Visualize Pangenome Graphs ]]> https://biorxiv.org/content/10.1101/2023.03.30.534931v1?rss=1 Yuan, Y. Ma, K. Chan, T. 2023-04-02 doi:10.1101/2023.03.30.534931 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of skeletal muscle. ]]> https://biorxiv.org/content/10.1101/2023.03.30.534956v1?rss=1 Oprescu, S. N. Baumann, N. Chen, X. Sun, Q. Zhao, Y. Yue, F. Wang, H. Kuang, S. 2023-04-01 doi:10.1101/2023.03.30.534956 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ TCR2vec: a deep representation learning framework of T-cell receptor sequence and function ]]> https://biorxiv.org/content/10.1101/2023.03.31.535142v1?rss=1 Jiang, Y. Huo, M. Zhang, P. Zou, Y. Li, S. 2023-04-02 doi:10.1101/2023.03.31.535142 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ Transcriptional Regulation of the P-bodies Associated Psoriasis Candidate Gene CCHCR1 ]]> https://biorxiv.org/content/10.1101/2023.04.08.535951v1?rss=1 Ling, Y. H. Chen, Y. Y. Leung, K. N. Chan, K. M. Liu, W. K. 2023-04-08 doi:10.1101/2023.04.08.535951 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Syncytiotrophoblast 5'-tRNA fragments are placental endocrine signals contributing to sterile inflammation in preeclampsia ]]> https://biorxiv.org/content/10.1101/2023.04.11.536371v1?rss=1 900 small RNA fragments are differentially expressed in preeclampsia STB-EVs. Preeclampsia-dysregulated 5-tRFs are detectable in maternal plasma, where we identified a placentally-derived load. 5-tRF-Glu-CTC, the most abundant preeclampsia-upregulated 5-tRF in perfusion STB-EVs, is also increased in preeclampsia STB-EVs from maternal plasma. 5-tRF-Glu-CTC induced inflammation in macrophages but not monocytes. The conditioned media from 5-tRF-Glu-CTC-activated macrophages reduced eNOS expression in endothelial cells. ConclusionsIncreased release of syncytiotrophoblast-derived vesicle-bound 5-tRF-Glu-CTC contributes to preeclampsia pathophysiology. ]]> Cooke, W. R. Jiang, P. Ji, L. Bai, J. Jones, G. D. Lo, Y. M. D. Redman, C. Vatish, M. 2023-04-11 doi:10.1101/2023.04.11.536371 Cold Spring Harbor Laboratory Press 2023-04-11 <![CDATA[ Generalized mutualisms promote range expansion in both plant and ant partners ]]> https://biorxiv.org/content/10.1101/2023.04.12.536632v1?rss=1 Nathan, P. Guenard, B. Economo, E. P. Simonsen, A. Frederickson, M. 2023-04-14 doi:10.1101/2023.04.12.536632 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Dissociable roles of the auditory midbrain and cortex in processing the statistical features of natural sound textures ]]> https://biorxiv.org/content/10.1101/2023.04.12.536666v1?rss=1 Peng, F. Harper, N. S. Mishra, A. P. Auksztulewicz, R. Schnupp, J. W. H. 2023-04-13 doi:10.1101/2023.04.12.536666 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Migratory herbivorous waterfowl couple the seed wave and the green wave during spring migration ]]> https://biorxiv.org/content/10.1101/2023.04.14.536842v1?rss=1 Xu, F. Wu, W. Wei, J. Xin, Q. Wielstra, B. La Sorte, F. A. Ma, Z. Lei, G. Lei, J. Wu, W. Yang, Y. Gong, P. Xu, B. Si, Y. 2023-04-17 doi:10.1101/2023.04.14.536842 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Integrin beta4 promotes DNA damage drug resistance in triple-negative breast cancer via TNFAIP2/IQGAP1/Rac1 ]]> https://biorxiv.org/content/10.1101/2023.04.17.537130v1?rss=1 Fang, H. Ren, W. Cui, Q. Liang, H. Yang, C. Liu, W. Wang, X. Liu, X. Shi, Y. Feng, J. Chen, C. 2023-04-17 doi:10.1101/2023.04.17.537130 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Artificial intelligence redefines RNA virus discovery ]]> https://biorxiv.org/content/10.1101/2023.04.18.537342v1?rss=1 Hou, X. He, Y. Fang, P. Mei, S.-Q. Xu, Z. Wu, W.-C. Tian, J.-H. Zhang, S. Zeng, Z.-Y. Gou, Q.-Y. Xin, G.-Y. Le, S.-J. Xia, Y.-Y. Zhou, Y.-L. Hui, F.-M. Pan, Y.-F. Eden, J.-S. Yang, Z.-H. Han, C. Shu, Y.-L. Guo, D. Li, J. Holmes, E. C. Li, Z.-R. Shi, M. 2023-04-18 doi:10.1101/2023.04.18.537342 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ SurVIndel2: improving local CNVs calling from next-generation sequencing using novel hidden information ]]> https://biorxiv.org/content/10.1101/2023.04.23.538018v1?rss=1 Rajaby, R. Sung, W.-K. 2023-04-25 doi:10.1101/2023.04.23.538018 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ LSM14B is essential for mitochondrial clustering in the oocyte meiosis ]]> https://biorxiv.org/content/10.1101/2023.04.24.538190v1?rss=1 Wan, Y. Yang, S. Li, T. Cai, Y. Zhang, M. Huang, T. Lv, Y. Lu, G. Li, J. Sha, Q. Chen, Z.-J. Liu, H. 2023-04-28 doi:10.1101/2023.04.24.538190 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Deep immunological imprinting due to the ancestral spike in the current bivalent COVID-19 vaccine ]]> https://biorxiv.org/content/10.1101/2023.05.03.539268v1?rss=1 Wang, Q. Guo, Y. Tam, A. R. Valdez, R. Gordon, A. Lihong, L. Ho, D. D. 2023-05-04 doi:10.1101/2023.05.03.539268 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Sex and dominance status affect allogrooming in free-ranging feral cattle ]]> https://biorxiv.org/content/10.1101/2023.05.08.539791v1?rss=1 Hodgson, G. M. W. Flay, K. J. Perroux, T. A. Chan, W. Y. McElligott, A. G. 2023-05-09 doi:10.1101/2023.05.08.539791 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Deficits in neural encoding of speech in preterm infants ]]> https://biorxiv.org/content/10.1101/2023.05.09.539966v1?rss=1 Novitskiy, N. Chan, P. H. Y. Chan, M. Lai, C. M. Leung, T. Y. Leung, T. F. Bornstein, M. H. Lam, H. S. Wong, P. C. M. 2023-05-10 doi:10.1101/2023.05.09.539966 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Molecular motor tug-of-war regulates elongasome cell wall synthesis dynamics in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2023.05.10.540107v1?rss=1 Middlemiss, S. Roberts, D. M. Grimshaw, J. Edwards, J. M. Sun, Z. Whitley, K. D. Blu, T. Strahl, H. Holden, S. 2023-05-10 doi:10.1101/2023.05.10.540107 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ In vivo Ontogeny of human forebrain neural progenitor cell grafts in adult rats: an immunohistological study ]]> https://biorxiv.org/content/10.1101/2023.05.15.539796v1?rss=1 Liu, C. Lin, A. Xing, Q. Zhang, D. Meng, W. Wu, R. Shi, H. Huang, W. Huang, X. Qin, D. Wang, X. Zhong, X. Guo, Y. 2023-05-15 doi:10.1101/2023.05.15.539796 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Bearskin2 mediates the coordinated secretion of xylogalacturonan and root cap polygalacturonase in Arabidopsis border-like cells ]]> https://biorxiv.org/content/10.1101/2023.05.21.541628v1?rss=1 Liu, Z. Wang, P. Goh, T. Nakajima, K. Kang, B. H. 2023-05-22 doi:10.1101/2023.05.21.541628 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution ]]> https://biorxiv.org/content/10.1101/2023.05.22.541674v1?rss=1 Mai, L. Wen, Z. Zhang, Y. Gao, Y. Lin, G. Lian, Z. Yang, X. Zhou, J. Lin, X. Luo, C. Peng, W. Chen, C. Liu, D. Zhang, J. Marjani, S. L. Tao, Q. Wu, X. Weissman, S. M. Pan, X. 2023-05-24 doi:10.1101/2023.05.22.541674 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Estimating recent and historical effective population size of marine and freshwater sticklebacks ]]> https://biorxiv.org/content/10.1101/2023.05.22.541730v1?rss=1 Feng, X. Loytynoja, A. Merila, J. 2023-05-24 doi:10.1101/2023.05.22.541730 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Multi-Scale Label-free Human Brain Imaging with Integrated Serial Sectioning Polarization Sensitive Optical Coherence Tomography and Two-Photon Microscopy ]]> https://biorxiv.org/content/10.1101/2023.05.22.541785v1?rss=1 Chang, S. Yang, J. Novoseltseva, A. Fu, X. Li, C. Chen, S.-C. Augustinack, J. C. Magnain, C. Fischl, B. McKee, A. C. Boas, D. A. Chen, I. A. Wang, H. 2023-05-24 doi:10.1101/2023.05.22.541785 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Goat Discrimination of Emotional Valence in the Human Voice ]]> https://biorxiv.org/content/10.1101/2023.05.26.542400v1?rss=1 Mason, M. A. Semple, S. Marshall, H. H. McElligott, A. G. 2023-05-26 doi:10.1101/2023.05.26.542400 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Accurate identification of structural variations from cancer samples ]]> https://biorxiv.org/content/10.1101/2023.05.31.543104v1?rss=1 Li, L. Hong, C. Xu, J. Chung, C. Y.-L. Leung, A. K.-Y. Boncan, D. A. T. Cheng, L. Lo, K.-W. Lai, P. B. S. Wong, J. Zhou, J. Cheng, A. S.-L. Chan, T.-F. Yue, F. Yip, K. Y. 2023-06-04 doi:10.1101/2023.05.31.543104 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ Cryo-EM structure of the human G-protein coupled receptor 1 (GPR1) - Gi protein complex bound to the chemerin C-terminal nonapeptide ]]> https://biorxiv.org/content/10.1101/2023.06.03.543554v1?rss=1 Liu, A. Liu, Y. Chen, G. Lyu, W. Wang, J. Ye, F. Zhu, L. Du, Y. Ye, R. D. 2023-06-05 doi:10.1101/2023.06.03.543554 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Draft genomes of the fungal pathogen Phellinus noxius in Hong Kong ]]> https://biorxiv.org/content/10.1101/209312v1?rss=1 Tsang, K. S. W. Lam, R. Y. C. Kwan, H. S. 2017-10-26 doi:10.1101/209312 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Sensory cortex is optimised for prediction of future input ]]> https://biorxiv.org/content/10.1101/224758v1?rss=1 Singer, Y. Teramoto, Y. Willmore, B. Schnupp, J. W. H. King, A. J. Harper, N. S. 2017-11-24 doi:10.1101/224758 Cold Spring Harbor Laboratory Press 2017-11-24 <![CDATA[ Subjective inflation of color saturation in the periphery under temporal overload ]]> https://biorxiv.org/content/10.1101/227074v1?rss=1 Rajananda, S. A.K. Peters, M. Lau, H. Odegaard, B. 2017-12-01 doi:10.1101/227074 Cold Spring Harbor Laboratory Press 2017-12-01 <![CDATA[ The fruitENCODE project sheds light on the genetic and epigenetic basis of convergent evolution of climacteric fruit ripening ]]> https://biorxiv.org/content/10.1101/231258v1?rss=1 Lv, P. Yu, S. Zhu, N. Chen, Y.-R. Zhou, B. Pan, Y. Tzeng, D. Paulo Fabi, J. Garcia-Mas, J. Ye, N. Zhang, J. Grierson, D. Fei, Z. Giovannoni, J. zhong, s. 2017-12-08 doi:10.1101/231258 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ GORAB, a Golgi protein required for centriole structure and duplication ]]> https://biorxiv.org/content/10.1101/232272v1?rss=1 Kovacs, L. Chao-Chu, J. Schneider, S. Gottardo, M. Tzolovsky, G. Dzhindzhev, N. S. Riparbelli, M. G. Callaini, G. Glover, D. M. 2017-12-14 doi:10.1101/232272 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ Long-range infra-sound acoustic signaling inhuman in vivo ]]> https://biorxiv.org/content/10.1101/233353v1?rss=1 Chang, X. Zhang, L. Wei, X. Peng, Z. Zhang, Z. Liu, Z. Li, P.-W. Lai, P. T. Chan, S. C. Yang, E. 2017-12-14 doi:10.1101/233353 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ Global phylogenomics of multidrug-resistant Staphylococcus aureus sequence type 772: the Bengal Bay clone ]]> https://biorxiv.org/content/10.1101/233395v1?rss=1 Steinig, E. J. Duchene, S. Robinson, D. A. Monecke, S. Yokoyama, M. Laabei, M. Slickers, P. Andersson, P. Williamson, D. Kearns, A. Goering, R. Dickson, E. Ehricht, R. Ip, M. O'Sullivan, M. V. Coombs, G. W. Petersen, A. Brennan, G. Shore, A. C. Coleman, D. C. Pantosti, A. de Lencastre, H. Westh, H. Kobayashi, N. Heffernan, H. Strommenger, B. Layer, F. Weber, S. Aamot, H. Skakni, L. Peacock, S. J. Sarovich, D. Giffard, P. Harris, S. Parkhill, J. Massey, R. C. Holden, M. T. Bentley, S. D. Tong, S. Y. 2017-12-13 doi:10.1101/233395 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Boosting ATM Activity Promotes Longevity in Nematodes and Mice ]]> https://biorxiv.org/content/10.1101/240606v1?rss=1 Qian, M. Liu, Z. Peng, L. Meng, F. Tang, X. Ao, Y. Shi, L. Zhou, M. Wang, M. Qin, B. Cao, X. Wang, Z. Zhou, Z. Liu, B. 2017-12-28 doi:10.1101/240606 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ Unconsciously Implanted Visuoauditory Memory in the Presence of Cholecystokinin Retrieved in Behavioral Contexts ]]> https://biorxiv.org/content/10.1101/241141v1?rss=1 Zhang, Z. Zheng, C. X. Peng, Y. Guo, Y. Lu, D. Li, X. Sun, W. Tang, P. He, S. L. Li, M. Liu, Q. Xu, F. Ng, G. Chen, X. He, J. 2017-12-30 doi:10.1101/241141 Cold Spring Harbor Laboratory Press 2017-12-30 <![CDATA[ Profile of Molecular Subtypes of Breast Cancer Among Bangladeshi Women - Audit of Initial Experience ]]> https://biorxiv.org/content/10.1101/253781v1?rss=1 RAHMAN, M. Z. Karim, M. A. 2018-01-25 doi:10.1101/253781 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome ]]> https://biorxiv.org/content/10.1101/261511v1?rss=1 Cheng, L. Leung, K.-S. 2018-02-07 doi:10.1101/261511 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Establishment of signaling interactions with cellular resolution for every cell cycle of embryogenesis ]]> https://biorxiv.org/content/10.1101/285007v1?rss=1 Zhao, Z. Chen, L. Ho, V. W. Wong, M.-K. Huang, X. Chan, L.-y. Ng, K. H. Ren, X. Yan, H. 2018-03-19 doi:10.1101/285007 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Small effect size leads to reproducibility failure in resting-state fMRI studies ]]> https://biorxiv.org/content/10.1101/285171v1?rss=1 Jia, X.-Z. Zhao, N. Barton, B. Burciu, R. Carriere, N. Cerasa, A. Chen, B.-Y. Chen, J. Coombes, S. Defebvre, L. Delmaire, C. Dujardin, K. Esposito, F. Fan, G.-G. Federica, D. N. Feng, Y.-X. Fling, B. W. Garg, S. Gilat, M. Gorges, M. Ho, S.-L. Horak, F. B. Hu, X. Hu, X.-F. Huang, B. Huang, P.-Y. Jia, Z.-J. Jones, C. Kassubek, J. Krajcovicova, L. Kurani, A. Li, J. Li, Q. Liu, A.-P. Liu, B. Liu, H. Liu, W.-G. Lopes, R. Lou, Y.-T. Luo, W. Madhyastha, T. Mao, N.-N. McAlonan, G. McKeown, M. J. Pang, S. Y. Quattrone, A. Rektorova, I. Sarica, A. Shang, H 2018-03-20 doi:10.1101/285171 Cold Spring Harbor Laboratory Press 2018-03-20 <![CDATA[ A statistical framework for cross-tissue transcriptome-wide association analysis ]]> https://biorxiv.org/content/10.1101/286013v1?rss=1 Hu, Y. Li, M. Lu, Q. Weng, H. Wang, J. Zekavat, S. M. Yu, Z. Li, B. Muchnik, S. Shi, Y. Kunkle, B. W. Mukherjee, S. Natarajan, P. Naj, A. Kuzma, A. Zhao, Y. Crane, P. K. Alzheimer's Disease Genetics Consortium, Zhao, H. 2018-03-21 doi:10.1101/286013 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Toward Precision Molecular Surgery: Robust, Selective Induction of Microhomology-mediated End Joining in vivo ]]> https://biorxiv.org/content/10.1101/291187v1?rss=1 Ata, H. Ekstrom, T. L. Martinez-Galvez, G. Mann, C. M. Dvornikov, A. V. Schaefbauer, K. J. Ma, A. C. Dobbs, D. Clark, K. J. Ekker, S. C. 2018-03-28 doi:10.1101/291187 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Evolutionary dynamics of sex chromosomes of palaeognathous birds ]]> https://biorxiv.org/content/10.1101/295089v1?rss=1 Xu, L. Sin, S. Y. W. Y. W. Grayson, P. Janes, D. E. Edwards, S. V. Sackton, T. B. 2018-04-05 doi:10.1101/295089 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Evolution of the latitudinal diversity gradient in the hyperdiverse ant genus Pheidole ]]> https://biorxiv.org/content/10.1101/295386v1?rss=1 1100 species) ant radiation, Pheidole, and evaluate the roles of three general explanations for the latitudinal gradient: variation in diversification rate, tropical conservatism, and ecological regulation.nnLocationGlobal.nnTime PeriodThe past 35 million years.nnMajor taxa studiedThe hyperdiverse ant genus Pheidole Westwood.nnMethodsWe assembled geographic data for 1499 species and morphospecies, and inferred a dated phylogeny of Pheidole of 449 species, including 150 species newly sequenced for this study. We tested correlations between diversification rate and latitude with BAMM, HiSSE, GeoSSE, and FiSSE, and examined patterns of diversification as Pheidole spread around the globe.nnResultsWe found that Pheidole diversification occurred in series of bursts when new continents were colonized, followed by a slowdown in each region. There was no evidence of systematic variation of net diversification rates with latitude across any of the methods. Additionally, we found latitudinal affinity is moderately conserved with a Neotropical ancestor and phylogenetic inertia alone is sufficient to produce the gradient pattern.nnMain ConclusionsOverall our results are consistent with tropical conservatism explaining the diversity gradient, while providing no evidence that diversification rate varies systematically with latitude. There is evidence of ecological regulation on continental scales through the pattern of diversification after colonization. These results shed light on the mechanisms underlying the diversity gradient, while contributing toward a much-needed invertebrate perspective on global biodiversity dynamics. ]]> Economo, E. P. Huang, J.-P. Fischer, G. Sarnat, E. M. Narula, N. Janda, M. Guenard, B. Longino, J. T. Knowles, L. L. 2018-04-05 doi:10.1101/295386 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Genome Wide Association Scan identifies new variants associated with a cognitive predictor of dyslexia. ]]> https://biorxiv.org/content/10.1101/309336v1?rss=1 Gialluisi, A. Andlauer, T. F. Mirza-Schreiber, N. Moll, K. Hoffmann, P. Ludwig, K. U. Czamara, D. Francks, C. St Pourcain, B. Brandler, W. Honbolygo, F. Toth, D. Csepe, V. Huguet, G. Morris, A. P. Hulslander, J. Willcutt, E. G. DeFries, J. C. Olson, R. K. Smith, S. D. Pennington, B. F. Vaessen, A. Maurer, U. Lyytinen, H. Peyrard-Janvid, M. Leppanen, P. H. Brandeis, D. Bonte, M. Stein, J. F. Talcott, J. Fauchereau, F. Bourgeron, T. Monaco, A. P. Ramus, F. Landerl, K. Kere, J. Scerri, T. S. Paracchini, S. Fisher, S. E. Schumacher, J. Nothen, M. M. Muller- 2018-05-02 doi:10.1101/309336 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Differential contributions of subthalamic beta rhythms and neural noise to Parkinson motor symptoms ]]> https://biorxiv.org/content/10.1101/312819v1?rss=1 Martin, S. Iturrate, I. Chavarriaga, R. Leeb, R. Sobolewski, A. Li, A. M. Zaldivar, J. Peciu-Florianu, I. Pralong, E. Castro-Jimenez, M. Benninger, D. Vingerhoets, F. Knight, R. T. Bloch, J. Millan, J. d. R. 2018-05-02 doi:10.1101/312819 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Pathogenic DDX3X mutations impair RNA metabolism and neurogenesis during fetal cortical development ]]> https://biorxiv.org/content/10.1101/317974v1?rss=1 Lennox, A. L. Jiang, R. Suit, L. Fregeau, B. Sheehan, C. J. Aldinger, K. A. Moey, C. Lobach, I. Mirzaa, G. Afenjar, A. Babovic-Vuksanovic, D. Bezieau, S. Blackburn, P. R. Bunt, J. Burglen, L. Charles, P. Chung, B. H. Y. Cogne, B. DeBrosse, S. Di Donato, N. Faivre, L. Heron, D. Innes, A. M. Isidor, B. Johnson-Kerner, B. L. Keren, B. Kimball, A. Klee, E. W. Kuentz, P. Küry, S. Martin-Coignard, D. Mignot, C. Miyake, N. Nava, C. Nizon, M. Rodriguez, D. Snijders Blok, L. Thauvin, C. Thevenon, J. Vincent, M. Ziegler, A. Dobyns, W. Richards, L. J. Ba 2018-05-11 doi:10.1101/317974 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Post-reactivation new learning impairs and updates human episodic memory through dissociable processes ]]> https://biorxiv.org/content/10.1101/320101v1?rss=1 Zhu, Z. Wang, Y. Jia, J. Huang, L. Rao, Y. Wu, Y. 2018-05-11 doi:10.1101/320101 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea ]]> https://biorxiv.org/content/10.1101/325217v1?rss=1 Lau, A. Y.-T. Cheng, X. Cheng, C. K. Nong, W. Cheung, M. K. Chan, R. H.-F. Hui, J. H. L. Kwan, H. S. 2018-05-17 doi:10.1101/325217 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Genetic determinants of resistance and virulence among carbapenemase-producing Klebsiella pneumoniae from Sri Lanka. ]]> https://biorxiv.org/content/10.1101/330951v1?rss=1 Zhu, C. Liyanapathirana, V. C. Li, C. Pinto, V. Hui, M. Lo, N. W.-S. Wong, K.-T. Dissanayake, N. Ip, M. 2018-05-25 doi:10.1101/330951 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation ]]> https://biorxiv.org/content/10.1101/334318v1?rss=1 Li, L. Gao, Y. Wu, Q. Cheng, A. S. L. Yip, K. Y. 2018-05-30 doi:10.1101/334318 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ The role of two-component system response regulator BceR in antimicrobial resistance, virulence, biofilm formation, and stress response of group B Streptococcus. ]]> https://biorxiv.org/content/10.1101/340679v1?rss=1 YANG, Y. LUO, M. ZHOU, H. Li, C. Luk, A. W. S. ZHAO, G. Fung, K. Ip, M. 2018-06-06 doi:10.1101/340679 Cold Spring Harbor Laboratory Press 2018-06-06 <![CDATA[ Weighted Network Density Predicts Range of Latent Variable Model Accuracy ]]> https://biorxiv.org/content/10.1101/343285v1?rss=1 Palmerston, J. B. She, Q. Chan, R. 2018-06-11 doi:10.1101/343285 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ NFAT5 participates in Inducible Nitric Oxide Synthase activation by hypoxia in MEF cells. ]]> https://biorxiv.org/content/10.1101/347302v1?rss=1 Serman, Y. Fuentealba, R. A. Pasten, C. Rocco, J. Ko, B. Carrion, F. Irarrazabal, C. E. 2018-06-14 doi:10.1101/347302 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Regulatory T-cells are required for neonatal heart regeneration ]]> https://biorxiv.org/content/10.1101/355065v1?rss=1 Li, J. Yang, K. Y. Tam, R. C. Y. Chan, V. W. Sheng, B. Hori, S. Zhou, B. Lo, Y. M. D. Lui, K. O. 2018-06-25 doi:10.1101/355065 Cold Spring Harbor Laboratory Press 2018-06-25 <![CDATA[ Acquiring absolute pitch in adulthood is difficult but possible ]]> https://biorxiv.org/content/10.1101/355933v1?rss=1 Wong, Y. K. Lui, K. F. H. Yip, K. H. M. Wong, A. C.- N. 2018-07-03 doi:10.1101/355933 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis ]]> https://biorxiv.org/content/10.1101/362046v1?rss=1 Fan, G. Fu, Y. Yang, B. Liu, M. Zhang, H. Liang, X. Shi, C. Ma, K. Wang, J. Liu, W. Shao, L. Huang, C. Guo, M. Cai, J. Wong, A. K. Li, C. Zhuang, D. Chen, K. Cong, W. Sun, X. Liu, X. Xu, X. Tsui, S. K. Chen, W. Lee, S. M. 2018-07-04 doi:10.1101/362046 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ Infer related genes from large gene expression dataset with embedding ]]> https://biorxiv.org/content/10.1101/362848v1?rss=1 Choy, C. T. Wong, C. H. Chan, S. L. 2018-07-05 doi:10.1101/362848 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ Causal relationships between blood lipids and depression phenotypes: A Mendelian randomization analysis ]]> https://biorxiv.org/content/10.1101/363119v1?rss=1 So, H.-C. Cheng, Y.-y. Chau, C. K.-l. 2018-07-06 doi:10.1101/363119 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Selective Permeability of Carboxysome Shell Pores to Anionic Molecules ]]> https://biorxiv.org/content/10.1101/367714v1?rss=1 Mahinthichaichan, P. Morris, D. M. Wang, Y. Jensen, G. J. Tajkhorshid, E. 2018-07-11 doi:10.1101/367714 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Hydrogen sulfide promotes nodulation and nitrogen fixation in soybean-rhizobia symbiotic system ]]> https://biorxiv.org/content/10.1101/367896v1?rss=1 Zou, H. Zhang, N.-N. Pan, Q. Zhang, J.-H. Chen, J. Wei, G.-H. 2018-07-12 doi:10.1101/367896 Cold Spring Harbor Laboratory Press 2018-07-12 <![CDATA[ Alternative splicing and translation play important roles in parallel with transcriptional regulation during rice hypoxic germination ]]> https://biorxiv.org/content/10.1101/371583v1?rss=1 Chen, M.-X. Zhu, F.-Y. Wang, F.-Z. Ye, N.-H. Gao, B. Chen, X. Zhao, S.-S. Fan, T. Cao, Y.-Y. Liu, T.-Y. Su, Z.-Z. Xie, L.-J. Hu, Q.-J. Wu, H.-J. Xiao, S. Zhang, J. Liu, Y.-G. 2018-07-18 doi:10.1101/371583 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Osteoblastic PLEKHO1 contributes to joint inflammation in rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/380303v1?rss=1 He, X. Liu, J. Liang, C. Shaikh, A. B. Zheng, K. Dang, L. Guo, B. Li, D. Lu, C. Guo, Q. Fan, D. Bian, Y. Feng, H. Xiao, L. Pan, X. Xiao, C. Zhang, B.-T. Zhang, G. Lu, A. 2018-07-30 doi:10.1101/380303 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ A cross-organism framework for supervised enhancer prediction with epigenetic pattern recognition and targeted validation ]]> https://biorxiv.org/content/10.1101/385237v1?rss=1 Sethi, A. Gu, M. Gumusgoz, E. Chan, L. Yan, K.-K. Rozowsky, J. S. Barozzi, I. Afzal, V. Akiyama, J. Plajzer-Frick, I. Yan, C. Pickle, C. Kato, M. Garvin, T. Pham, Q. Harrington, A. Mannion, B. Lee, E. Fukuda-Yuzawa, Y. Visel, A. Dickle, D. E. Yip, K. Sutton, R. Pennacchio, L. A. Gerstein, M. 2018-08-05 doi:10.1101/385237 Cold Spring Harbor Laboratory Press 2018-08-05 <![CDATA[ On the Number of Driver Nodes for Controlling a Boolean Network to Attractors ]]> https://biorxiv.org/content/10.1101/395442v1?rss=1 Hou, W. Ruan, P. Ching, W.-K. Akutsu, T. 2018-08-20 doi:10.1101/395442 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ tmap: topological analysis of population-scale microbiome data ]]> https://biorxiv.org/content/10.1101/396960v1?rss=1 Liao, T. Wei, Y. Luo, M. Zhao, G. Zhou, H. 2018-08-21 doi:10.1101/396960 Cold Spring Harbor Laboratory Press 2018-08-21 <![CDATA[ Mate-pair Library Construction with Controlled Polymerization Enables Comprehensive Structural Rearrangement Detection ]]> https://biorxiv.org/content/10.1101/400689v1?rss=1 Zirui, D. Xia, Z. Qiaoling, L. Zhenjun, Y. Yang, X. Andrei, A. Hanjie, S. Ou, W. Jie, R. Han, R. Hanmin, W. Xiaojuan, Q. Jiguang, L. Xiaofan, Z. Dai, P. Kong, X. Oleg, A. Shane, G. Jennifer, Y. Bahram G., K. Killeen, K. Chao, D. Pengjuan, L. Zilan, M. Wenwei, Z. Xun, X. Radoje, D. Kwong Wai, C. Yuan, J. 2018-08-26 doi:10.1101/400689 Cold Spring Harbor Laboratory Press 2018-08-26 <![CDATA[ Microbial Cells Harboring a Mitochondrial Gene Are Capable of CO2 Capture ]]> https://biorxiv.org/content/10.1101/411090v1?rss=1 Zhou, Y. Ouyang, L. Yi, X. Gan, T. Qi, J. Wan, Y. Wang, Y. An, S. Shi, Y. Yang, W. Chen, W. Luo, Z. Li, J. Luo, J. Nuertai, X. Zhu, X. Yang, F. Zhang, X. Weng, S. Liu, Q. Cao, W. He, J. 2018-09-07 doi:10.1101/411090 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ eQTL network analysis reveals that regulatory genes are evolutionarily older and bearing more types of PTM sites in Coprinopsis cinerea ]]> https://biorxiv.org/content/10.1101/413062v1?rss=1 Chang, J. Au, C. H. Cheng, C. Kwan, H. S. 2018-09-20 doi:10.1101/413062 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies ]]> https://biorxiv.org/content/10.1101/415109v1?rss=1 Luo, X. Yang, C. Wei, Y. 2018-09-12 doi:10.1101/415109 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ A guide to performing Polygenic Risk Score analyses ]]> https://biorxiv.org/content/10.1101/416545v1?rss=1 Choi, S. W. Mak, T. S. H. O'Reilly, P. 2018-09-14 doi:10.1101/416545 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Dietary fatty acids promote lipid droplet diversity through seipin enrichment in an ER subdomain ]]> https://biorxiv.org/content/10.1101/424663v1?rss=1 Cao, Z. Hao, Y. Lee, Y. Y. Wang, P. Li, X. Xie, K. Lam, W. J. Qiu, Y. Shui, G. Liu, P. Qu, J. Kang, B.-H. Mak, H. Y. 2018-09-22 doi:10.1101/424663 Cold Spring Harbor Laboratory Press 2018-09-22 <![CDATA[ 5-Hydroxymethylcytosines from Circulating Cell-free DNA as Diagnostic and Prognostic Markers for Hepatocellular Carcinoma ]]> https://biorxiv.org/content/10.1101/424978v1?rss=1 Cai, J. Chen, L. Zhang, Z. Zhang, X. Lu, X. Liu, W. Shi, G. Ge, Y. Gao, P. Yang, Y. Ke, A. Xiao, L. Dong, R. Zhu, Y. Yang, X. Wang, J. Zhu, T. Yang, D. Huang, X. Sui, C. Qiu, S. Shen, F. Sun, H. Zhou, W. Zhou, J. Nie, J. Zhang, X. Chiu, B. C.-H. Lau, W. Y. He, C. Wang, H. Zhang, W. Fan, J. 2018-09-23 doi:10.1101/424978 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ GRID-seq assisted computational prediction of transcription factor binding motifs using multivariate mahalanobis distance analysis reveals that RNA-chromosomal interaction may act as a proxy indicator of true positive transcriptional activity. ]]> https://biorxiv.org/content/10.1101/429332v1?rss=1 Veldsman, W. P. 2018-09-27 doi:10.1101/429332 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants ]]> https://biorxiv.org/content/10.1101/429795v1?rss=1 Liou, G. Chiang, Y.-C. Wang, Y. Weng, J.-K. 2018-09-28 doi:10.1101/429795 Cold Spring Harbor Laboratory Press 2018-09-28 <![CDATA[ Comparison of tri-exponential decay vs. bi-exponential decay and full fitting vs. segmented fitting for modeling liver intravoxel incoherent motion diffusion MRI ]]> https://biorxiv.org/content/10.1101/429977v1?rss=1 Chevallier, O. Zhou, N. Cercueil, J.-P. He, J. Loffroy, R. Wang, Y.-X. 2018-09-29 doi:10.1101/429977 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning ]]> https://biorxiv.org/content/10.1101/434803v1?rss=1 Wang, H. Liu, X. Tao, Y. Ye, W. Jin, Q. Cohen, W. W. Xing, E. P. 2018-10-05 doi:10.1101/434803 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ D-GPM: a deep learning method for gene promoter methylation inference ]]> https://biorxiv.org/content/10.1101/438218v1?rss=1 Pan, X. Liu, B. Wen, X. Liu, Y. Zhang, X. Li, S. 2018-10-09 doi:10.1101/438218 Cold Spring Harbor Laboratory Press 2018-10-09 <![CDATA[ Comparative genetic architectures of schizophrenia in East Asian and European populations ]]> https://biorxiv.org/content/10.1101/445874v1?rss=1 Lam, M. Chen, C.-Y. Li, Z. Martin, A. Bryois, J. Ma, X. Gaspar, H. Ikeda, M. Benyamin, B. Brown, B. Liu, R. Zhou, W. Huan, L. Kamatani, Y. Kim, S.-W. Kubo, M. Kusumawardhani, A. Liu, C.-M. Ma, H. Periyasamy, S. Takahashi, A. Wang, Q. Xu, Z. Yu, H. Zhu, F. Psychiatric Genomics Consortium - Schizophrenia Working Group, Indonesia Schizophrenia Consortium, Genetic REsearch on schizophreniA neTwork-China and Netherland (GREAT-CN), Chen, W. Faraone, S. Glatt, S. He, L. Hyman, S. Hwu, H.-G. Li, T. McCarroll, S. Neale, B. Sklar, P. Wildenauer, D. Yu, X. Zh 2018-10-17 doi:10.1101/445874 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Optical Sectioning of Live Mammal with Near-Infrared Light Sheet ]]> https://biorxiv.org/content/10.1101/447433v1?rss=1 Wang, F. Wan, H. Yue, J. Zhang, M. Ma, Z. Sun, Q. Qu, L. Ma, H. Zhong, Y. Tian, Y. Hong, G. Li, W. J. Liang, Y. Liu, L. Dai, H. 2018-10-18 doi:10.1101/447433 Cold Spring Harbor Laboratory Press 2018-10-18 <![CDATA[ Single Agent and Synergistic Activity of Maritoclax with ABT-263 in Nasopharyngeal Carcinoma (NPC) Cell Lines ]]> https://biorxiv.org/content/10.1101/471888v1?rss=1 Lian, B. S. X. Lo, K.-W. Khoo, A. S.-B. Mohana Kumaran, N. 2018-11-16 doi:10.1101/471888 Cold Spring Harbor Laboratory Press 2018-11-16 <![CDATA[ Beat-Relevant Signals in Auditory Cortical Responses to Musical Excerpts ]]> https://biorxiv.org/content/10.1101/481473v1?rss=1 Rajendran, V. G. Harper, N. S. Schnupp, J. W. H. 2018-11-29 doi:10.1101/481473 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Transcriptional profiling elucidates the essential role of glycogen synthase kinase 3 to fruiting body formation in Coprinopsis cinerea ]]> https://biorxiv.org/content/10.1101/492397v1?rss=1 Chan, K. P. Chang, J. Xie, Y. Cheung, M. K. Ma, K. L. Kwan, H. 2018-12-10 doi:10.1101/492397 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Consensus interpretation of the Met34Thr and Val37Ile variants in GJB2 by the ClinGen Hearing Loss Expert Panel ]]> https://biorxiv.org/content/10.1101/493130v1?rss=1 C/p.Met34Thr and c.109G>A/p.Val37Ile in GJB2 are controversial. Therefore, an expert consensus is required for the interpretation of these two variants.nnMETHODSThe ClinGen Hearing Loss Expert Panel (HL-EP) collected published data and shared unpublished information from participating laboratories regarding the two variants. Functional, computational, allelic, and segregation data were also obtained.nnRESULTSThe panel reviewed the synthesized information, and classified the Met34Thr and Val37Ile variants according to professional variant interpretation guidelines. We found that Met34Thr and Val37Ile are significantly overrepresented in hearing loss patients, compared to the general population. Met34Thr or Val37Ile homozygotes or compound heterozygotes typically manifest mild to moderate hearing loss. Several other types of evidence also support pathogenic roles for those two variants.nnCONCLUSIONResolving controversies in variant classification requires coordinated effort among a panel of international multi-institutional experts to share data, standardize classification rules, review evidence, and reach a consensus. The ClinGen HL-EP concluded that Met34Thr and Val37Ile variants in GJB2 are pathogenic for autosomal recessive nonsyndromic hearing loss with variable expressivity and age-dependent penetrance. ]]> Shen, J. Oza, A. del Castillo, I. Duzkale, H. Matsunaga, T. Pandya, A. Kang, H. Mar-Heyming, R. Guha, S. Moyer, K. Lo, C. Kenna, M. Alexander, J. Zhang, Y. Hirsch, Y. Luo, M. Cao, Y. Wai Choy, K. Cheng, Y.-F. Avraham, K. Hu, X. Garrido, G. Moreno-Pelayo, M. Greinwald, J. Zhang, K. Zeng, Y. Brownstein, Z. Basel-Vanagaite, L. Davidov, B. Frydman, M. Weiden, T. Nagan, N. Willis, A. Hemphill, S. Grant, A. Siegert, R. DiStefano, M. Amr, S. Rehm, H. Abou Tayoun, A. The ClinGen Hearing Loss Working Group, 2018-12-11 doi:10.1101/493130 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Modified recipe to inhibit GSK-3 for the living fungal biomaterial manufacture ]]> https://biorxiv.org/content/10.1101/496265v1?rss=1 Jinhui, C. Chan, K. P. Xie, Y. Ma, K. L. Kwan, H. S. 2018-12-13 doi:10.1101/496265 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Pleistocene Mammal Population Fluctuation Patterns Inferred by Their Genomes ]]> https://biorxiv.org/content/10.1101/505131v1?rss=1 Liu, Y. Liu, B. Pan, X. Shi, Q. Xiao, Z. Li, S. Li, S. 2018-12-23 doi:10.1101/505131 Cold Spring Harbor Laboratory Press 2018-12-23 <![CDATA[ 10Kin1day: A bottom-up neuroimaging initiative ]]> https://biorxiv.org/content/10.1101/509554v1?rss=1 van den Heuvel, M. Scholtens, L. van der Burgh, H. Agosta, F. Alloza, C. Avancini, T. Baron-Cohen, S. Basaia, S. Beyer, F. Booij, L. Cannon, D. Chan, S. Chen, E. Cambridge Child Development Project, Crespo-Facorro, B. Crone, E. Dannlowski, U. de Zwarte, S. Diaz-Zuluaga, A. Dietsche, B. Donohoe, G. Du Plessis, S. Durston, S. Emsley, R. Filho, G. Filippi, M. Frodl, T. Gasecki, D. Goc, J. Gorges, M. Graff, B. Grotegerd, D. Hall, J. Holleran, L. Hopman, H. Jäncke, L. Jansen, A. Jodzio, K. Kaleda, V. Kassubek, J. Kharabian Masouleh, S. Kircher, T. Koevoe 2019-01-16 doi:10.1101/509554 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Tombusvirus p19 captures RNase III-cleaved double-stranded RNAs formed by overlapping sense and antisense transcripts in E. coli ]]> https://biorxiv.org/content/10.1101/510842v1?rss=1 Huang, L. Deighan, P. Jin, J. Li, Y. Lee, E. Mo, S. S. Hoover, H. Abubucker, S. Finkel, N. McReynolds, L. Hochschild, A. Lieberman, J. 2019-01-04 doi:10.1101/510842 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ Immune gene expression profiling reveals heterogeneity in luminal breast tumors ]]> https://biorxiv.org/content/10.1101/515486v1?rss=1 Zhu, B. Tse, S. L. A. Wang, D. Koka, H. Zhang, T. Abubakar, M. Lee, P. Wang, F. Wu, C. Tsang, K. H. Chan, W.-c. Law, S. H. Li, M. Li, W. Wu, S. Liu, Z. Huang, B. Zhang, H. Tang, E. Kan, Z. Lee, S. Park, Y. H. Nam, S. J. Wang, M. Sun, X. Jones, K. Zhu, B. Hutchinson, A. Hicks, B. Prokunina-Olsson, L. Shi, J. Garcia-Closas, M. Chanock, S. Yang, X. R. 2019-01-09 doi:10.1101/515486 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ O-GlcNAc transferase suppresses necroptosis and liver fibrosis ]]> https://biorxiv.org/content/10.1101/519975v1?rss=1 Zhang, B. Li, M.-D. Yin, R. Liu, Y. Yang, Y. Mitchell-Richards, K. A. Nam, J. H. Li, R. Wang, L. Iwakiri, Y. Chung, D. Robert, M. E. Ehrlich, B. E. Bennett, A. M. Yu, J. Nathanson, M. Yang, X. 2019-01-14 doi:10.1101/519975 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ Ultra-rare genetic variation in the epilepsies: a whole-exome sequencing study of 17,606 individuals ]]> https://biorxiv.org/content/10.1101/525683v1?rss=1 Epi25 Collaborative, Feng, Y.-C. A. Howrigan, D. P. Abbott, L. E. Tashman, K. Cerrato, F. Singh, T. Heyne, H. Byrnes, A. Churchhouse, C. Lal, D. Heinzen, E. L. Cavalleri, G. L. Hakonarson, H. Helbig, I. Krause, R. May, P. Weckhuysen, S. Petrovski, S. Kamalakaran, S. Sisodiya, S. M. Cossette, P. Cotsapas, C. De Jonghe, P. Dixon-Salazar, T. Guerrini, R. Kwan, P. Marson, A. G. Stewart, R. Depondt, C. Dlugos, D. J. Scheffer, I. E. Striano, P. Freyer, C. McKenna, K. Regan, B. M. Bellows, S. T. Leu, C. Bennett, C. A. Johns, E. M. C. Macdonald, A. Shilling, 2019-01-21 doi:10.1101/525683 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Seascape genetics at its finest: dispersal patchiness within a well-connected population ]]> https://biorxiv.org/content/10.1101/530451v1?rss=1 Schunter, C. Pascual, M. Raventos, N. Garriga, J. Garza, J. C. Bartumeus, F. Macpherson, E. 2019-01-26 doi:10.1101/530451 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Flexible Experimental Designs for Valid Single-cell RNA-sequencing Experiments Allowing Batch Effects Correction ]]> https://biorxiv.org/content/10.1101/533372v1?rss=1 Song, F. Chan, G. M. Wei, Y. 2019-01-29 doi:10.1101/533372 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Illuminating the dark depths inside coral ]]> https://biorxiv.org/content/10.1101/534842v1?rss=1 Liu, C. Cheng, S. H. Lin, S. 2019-01-30 doi:10.1101/534842 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Genome-wide copy number variation-, validation- and screening study implicates a novel copy number polymorphism associated with suicide attempts in major depressive disorder ]]> https://biorxiv.org/content/10.1101/534909v1?rss=1 Rao, S. Shi, M. Han, X. Lam, M. H. B. Liu, G. Wing, Y. K. So, H.-C. Waye, M. M. Y. 2019-01-30 doi:10.1101/534909 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Antibiotic treatment drives the diversification of the human gut resistome ]]> https://biorxiv.org/content/10.1101/537670v1?rss=1 Li, J. Rettedal, E. van der Helm, E. Ellabaan, M. M. H. Panagiotou, I. Sommer, M. O. A. 2019-02-01 doi:10.1101/537670 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ The unique coding sequence of pmoCAB operon from type Ia methanotrophs simultaneously optimizes transcription and translation ]]> https://biorxiv.org/content/10.1101/543546v1?rss=1 Villada, J. C. Duran, M. F. Lee, P. K. H. 2019-02-07 doi:10.1101/543546 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Clinical investigation and genetic analysis of a peripheral sclerocornea pedigree ]]> https://biorxiv.org/content/10.1101/547547v1?rss=1 Zhang, B. N. Chan, T. C. Y. Tam, P. O. S. Liu, Y. Pang, C. P. Jhanji, V. Chen, L. J. Chu, W. K. 2019-02-12 doi:10.1101/547547 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ 3D computational models explain muscle activation patterns and energetic functions of internal structures in fish swimming ]]> https://biorxiv.org/content/10.1101/556126v1?rss=1 Ming, T. Jin, B. Song, J. Luo, H. Du, R. Ding, Y. 2019-02-20 doi:10.1101/556126 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia. ]]> https://biorxiv.org/content/10.1101/557785v1?rss=1 Wyres, K. L. Nguyen, T. N. Lam, M. M. Judd, L. M. van Vinh Chau, N. Dance, D. A. Ip, M. Karkey, A. Ling, C. L. Miliya, T. Newton, P. Nguyen, L. Sengduangphachanh, A. Turner, P. Veeraraghavan, B. Voong Vinh, P. Vongsouvath, M. Thomson, N. R. Baker, S. Holt, K. E. 2019-02-26 doi:10.1101/557785 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Tuned normalization in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior ]]> https://biorxiv.org/content/10.1101/558858v1?rss=1 Maniscalco, B. Odegaard, B. Grimaldi, P. Cho, S. H. Basso, M. A. Lau, H. Peters, M. A. K. 2019-02-24 doi:10.1101/558858 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Interaction Effects of Apolipoprotein E ε 4 and Cognitive Status on the Functional Connectivity within Default Mode Network in Individuals at Risk of Cognitive Impairments ]]> https://biorxiv.org/content/10.1101/565812v1?rss=1 Lu, H. Ma, S. L. Wing, W. C. C. Wong, S. W. H. Lam, L. C. W. 2019-03-06 doi:10.1101/565812 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains ]]> https://biorxiv.org/content/10.1101/567883v1?rss=1 Dong, P. Tu, X. Li, H. Zhang, J. Grierson, D. Li, P. zhong, s. 2019-03-05 doi:10.1101/567883 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Cannabis-associated symptom profiles in patients with first episode psychosis and population controls ]]> https://biorxiv.org/content/10.1101/577932v1?rss=1 Quattrone, D. Ferraro, L. Tripoli, G. La Cascia, E. Quigley, H. EU-GEI WP2 group, Gayer-Anderson, C. Jones, P. B. Kirkbride, J. B. La Barbera, D. Tarricone, I. Lynskey, M. T. Freeman, T. P. Sham, P. C. Cardno, A. Vassos, E. van Os, J. Morgan, C. Reininghaus, U. Lewis, C. M. Murray, R. M. Di Forti, M. 2019-03-16 doi:10.1101/577932 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ On triangular inequalities of correlation-based distances for gene expression profiles ]]> https://biorxiv.org/content/10.1101/582106v1?rss=1 Jiaxing, C. Ng, Y. K. Lin, L. Jiang, Y. Li, S. 2019-03-19 doi:10.1101/582106 Cold Spring Harbor Laboratory Press 2019-03-19 <![CDATA[ Whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants ]]> https://biorxiv.org/content/10.1101/583237v1?rss=1 Zhang, S. He, Y. Liu, H. Zhai, H. Huang, D. Yi, X. Dong, X. Wang, Z. Zhao, K. Zhou, Y. Wang, J. Yao, H. Xu, H. Yang, Z. Sham, P. C. Chen, K. Li, M. J. 2019-03-20 doi:10.1101/583237 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Uncovering complex disease subtypes by integrating clinical data and imputed transcriptome from genome-wide association studies: Applications in psychiatry and cardiovascular medicine ]]> https://biorxiv.org/content/10.1101/595488v1?rss=1 Yin, L. Chau, C. K. L. Sham, P.-C. So, H.-C. 2019-04-03 doi:10.1101/595488 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Evolution of Auxin Response Factors in plants characterized by phylogenomic synteny network analyses ]]> https://biorxiv.org/content/10.1101/603175v1?rss=1 Gao, B. Wang, L. Oliver, M. Chen, M. Zhang, J. 2019-04-09 doi:10.1101/603175 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses ]]> https://biorxiv.org/content/10.1101/603191v1?rss=1 Gao, B. Chen, M. Li, X. Liang, Y. Zhang, D. Wood, A. Oliver, M. Zhang, J. 2019-04-10 doi:10.1101/603191 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ The cryptic impacts of invasion: functional homogenization of tropical ant communities by invasive fire ants ]]> https://biorxiv.org/content/10.1101/611749v1?rss=1 Wong, M. K. Guenard, B. Lewis, O. T. 2019-04-18 doi:10.1101/611749 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Estrogen accelerates heart regeneration by promoting inflammatory responses in zebrafish ]]> https://biorxiv.org/content/10.1101/616250v1?rss=1 Shisan, X. Fangjing, X. Samane, F. Fariba, B. Lina, Z. Kin Fung, W. Yinmin, L. Rajkumar, R. Lei, S. Xin, W. Yun Wah, L. Shuk Han, C. 2019-04-23 doi:10.1101/616250 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ Neo-sex chromosomes and demography shape genetic diversity in the Critically Endangered Raso lark ]]> https://biorxiv.org/content/10.1101/617563v1?rss=1 Dierickx, E. G. Sin, S. Y. W. van Veelen, P. Brooke, M. d. L. Liu, Y. Edwards, S. V. Martin, S. H. 2019-04-24 doi:10.1101/617563 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ Efficient and accurate prediction of transmembrane topology from amino acid sequence only ]]> https://biorxiv.org/content/10.1101/627307v1?rss=1 Wang, Q. Ni, C. Li, Z. Li, X. Han, R. Zhao, F. Xu, J. Gao, X. Wang, S. 2019-05-05 doi:10.1101/627307 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ A Clostridia-rich microbiota contributes to increased excretion of bile acids in diarrhea-predominant irritable bowel syndrome ]]> https://biorxiv.org/content/10.1101/630350v1?rss=1 Zhao, L. Yang, W. Chen, Y. Huang, F. Lu, L. Lin, C. Huang, T. Ning, Z. Zhai, L. Zhong, L. L. Lam, W. Yang, Z. Zhang, X. Cheng, C. Han, L. Qiu, Q. Shang, X. Huang, R. Ren, Z. Chen, D. Sun, S. El-Nezami, H. Lu, A. Fang, X. Jia, W. Bian, Z. 2019-05-12 doi:10.1101/630350 Cold Spring Harbor Laboratory Press 2019-05-12 <![CDATA[ Validation study of a diffusion MRI derived vessel density biomarker for detecting viral hepatitis-b induced liver fibrosis ]]> https://biorxiv.org/content/10.1101/633024v1?rss=1 Wang, Y.-X. Xiao, B.-H. Wang, L.-F. Qiu, S.-W. Yun, Y.-X. Huang, H. 2019-05-09 doi:10.1101/633024 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Prenatal Diagnosis of Fetuses with Increased Nuchal Translucency by Genome Sequencing Analysis ]]> https://biorxiv.org/content/10.1101/667311v1?rss=1 30-fold) for fetuses with increased NT ([≥]3.5-mm), who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy-number variants and structural rearrangements was performed simultaneously and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available.nnResultsOverall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a 2-fold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion which disrupted an OMIM autosomal dominant disease-causing gene at the inserted site.nnConclusionsOur study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turn-around-time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT. ]]> Choy, K. W. Wang, H. Shi, M. Chen, J. Yang, Z. Zhang, R. Yan, H. Wang, Y. Chen, S. Chau, M. H. K. Cao, Y. Chan, O. Y. Kwok, Y. K. Zhu, Y. Chen, M. Leung, T. Y. Dong, Z. 2019-06-11 doi:10.1101/667311 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ A multimodal framework for detecting direct and indirect gene-gene interactions from large expression compendium ]]> https://biorxiv.org/content/10.1101/680116v1?rss=1 Zhang, L. Chen, J. Li, S. 2019-06-23 doi:10.1101/680116 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ Identification of type 2 diabetes loci in 433,540 East Asian individuals ]]> https://biorxiv.org/content/10.1101/685172v1?rss=1 240 loci associated with type 2 diabetes (T2D), however most loci have been identified in analyses of European-ancestry individuals. To examine T2D risk in East Asian individuals, we meta-analyzed GWAS data in 77,418 cases and 356,122 controls. In the main analysis, we identified 298 distinct association signals at 178 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 56 loci newly implicated in T2D predisposition. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. New associations include signals in/near GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect muscle and adipose differentiation. At another locus, eQTLs at two overlapping T2D signals act through two genes, NKX6-3 and ANK1, in different tissues. Association studies in diverse populations identify additional loci and elucidate disease genes, biology, and pathways.nnType 2 diabetes (T2D) is a common metabolic disease primarily caused by insufficient insulin production and/or secretion by the pancreatic {beta} cells and insulin resistance in peripheral tissues1. Most genetic loci associated with T2D have been identified in populations of European (EUR) ancestry, including a recent meta-analysis of genome-wide association studies (GWAS) of nearly 900,000 individuals of European ancestry that identified >240 loci influencing the risk of T2D2. Differences in allele frequency between ancestries affect the power to detect associations within a population, particularly among variants rare or monomorphic in one population but more frequent in another3,4. Although smaller than studies in European populations, a recent T2D meta-analysis in almost 200,000 Japanese individuals identified 28 additional loci4. The relative contributions of different pathways to the pathophysiology of T2D may also differ between ancestry groups. For example, in East Asian (EAS) populations, T2D prevalence is greater than in European populations among people of similar body mass index (BMI) or waist circumference5. We performed the largest meta-analysis of East Asian individuals to identify new genetic associations and provide insight into T2D pathogenesis. ]]> Spracklen, C. N. Horikoshi, M. Kim, Y. J. Lin, K. Bragg, F. Moon, S. Suzuki, K. Tam, C. Tabara, Y. Kwak, S.-H. Takeuchi, F. Long, J. Lim, V. Chai, J.-F. Chen, C.-H. Nakatochi, M. Yao, J. Choi, H. S. Iyengar, A. K. Perrin, H. J. Brotman, S. M. van de Bunt, M. Gloyn, A. L. Below, J. L. Boehnke, M. Bowden, D. W. Chambers, J. C. Mahajan, A. McCarthy, M. I. Ng, M. C. Petty, L. E. Zhang, W. Morris, A. P. Adair, L. S. Bian, Z. Chan, J. Chang, L.-C. Chee, M.-L. Chen, Y.-D. I. Chen, Y.-T. Chen, Z. Chuang, L.-M. Du, S. Gordon-Larsen, P. Gross, M. Guo, X. Guo 2019-06-28 doi:10.1101/685172 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma ]]> https://biorxiv.org/content/10.1101/695304v1?rss=1 Lee, B.-Y. Kim, M.-S. Choi, B.-S. Nagano, A. Au, D. W. T. Wu, R. Takehana, Y. Lee, J.-S. 2019-07-08 doi:10.1101/695304 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Genomic signature of shifts in selection in a sub-alpine ant and its physiological adaptations ]]> https://biorxiv.org/content/10.1101/696948v1?rss=1 Cicconardi, F. Krapf, P. D'Annessa, I. Gamisch, A. Wagner, H. C. Nguyen, A. D. Economo, E. P. Mikheyev, A. S. Guenard, B. Grabherr, R. Arthofer, W. di Marino, D. Steiner, F. Schlick-Steiner, B. C. 2019-07-09 doi:10.1101/696948 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Diverse, abundant and novel viruses infecting \"unculturable\" but abundant marine bacteria ]]> https://biorxiv.org/content/10.1101/699256v1?rss=1 Zhang, Z. Chen, F. Chu, X. Zhang, H. Luo, H. Qin, F. Zhai, Z. Yang, M. Sun, J. Zhao, Y. 2019-07-11 doi:10.1101/699256 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ MicroRNA-378 suppressed osteogenesis of mesenchymal stem cells and impaired bone formation via inactivating Wnt/β-catenin signaling ]]> https://biorxiv.org/content/10.1101/699355v1?rss=1 Li, G. Feng, L. Zhang, J. Shi, L. Yang, Z. Wu, T. Wang, H. Lin, W. Lu, Y. Lo, J. H. T. Zhu, D. 2019-07-11 doi:10.1101/699355 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Alternative splicing modulation by G-quadruplexes ]]> https://biorxiv.org/content/10.1101/700575v1?rss=1 Georgakopoulos Soares, I. Parada, G. E. Wong, H. Y. Miska, E. A. Kwok, C. K. K. Hemberg, M. 2019-07-12 doi:10.1101/700575 Cold Spring Harbor Laboratory Press 2019-07-12 <![CDATA[ Molecular mechanism of mitochondrial phosphatidate transfer by Ups1/Mdm35 ]]> https://biorxiv.org/content/10.1101/702415v1?rss=1 Lu, J. Chan, K. Yu, L. Fan, J. Zhai, Y. Sun, F. 2019-07-14 doi:10.1101/702415 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ A binning tool to reconstruct viral haplotypes from assembled contigs ]]> https://biorxiv.org/content/10.1101/704288v1?rss=1 Chen, J. Shang, J. Wang, J. Sun, Y. 2019-07-16 doi:10.1101/704288 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ An integrative ENCODE resource for cancer genomics ]]> https://biorxiv.org/content/10.1101/706424v1?rss=1 Zhang, J. Lee, D. Dhiman, V. Jiang, P. Xu, J. McGillivray, P. Yang, H. Liu, J. Meyerson, W. Clarke, D. Gu, M. Li, S. Lou, S. Xu, J. Lochovsky, L. Ung, M. Ma, L. Yu, S. Cao, Q. Harmanci, A. Yan, K.-K. Sethi, A. Gursoy, G. Schoenberg, M. R. Rozowsky, J. Warrell, J. Emani, P. Yang, Y. T. Galeev, T. Kong, X. Liu, S. Li, X. Krishnan, J. Feng, Y. Rivera-Mulia, J. C. Adrian, J. Broach, J. R. Bolt, M. Moran, J. Fitzgerald, D. Dileep, V. Liu, T. Mei, S. Sasaki, T. Trevilla-Garcia, C. Wang, S. Wang, Y. Zang, C. Wang, D. Klein, R. Snyder, M. Gilbert, D. 2019-07-18 doi:10.1101/706424 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Varying constraints impact the miR-6/5/4/286/3/309 microRNA cluster in Drosophila leg development ]]> https://biorxiv.org/content/10.1101/714766v1?rss=1 Qu, Z. Yiu, W. C. Yip, H. Y. Nong, W. Yu, C. W. C. Lee, I. H. T. Wong, A. Y. P. Wong, N. W. Y. Cheung, F. K. M. Chan, T. F. Lau, K. F. Zhong, S. Chu, K. H. Tobe, S. S. Ferrier, D. E. K. Bendena, W. G. Hui, J. H. L. 2019-07-25 doi:10.1101/714766 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Reference intervals of spot urine copper excretion in preschool children and potential application in pre-symptomatic screening of Wilson’s disease ]]> https://biorxiv.org/content/10.1101/719369v1?rss=1 Tang, N. L.-s. Hui, J. Huang, D. Tang, M. F. Wang, X. Wu, J. Chan, I. Leung, T.-f. 2019-07-31 doi:10.1101/719369 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ K-mer counting with low memory consumption enables fast clustering of single-cell sequencing data without read alignment ]]> https://biorxiv.org/content/10.1101/723833v1?rss=1 Shi, C. H. Yip, K. Y. 2019-08-02 doi:10.1101/723833 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird ]]> https://biorxiv.org/content/10.1101/723924v1?rss=1 Sin, S. Y. W. Cloutier, A. Nevitt, G. Edwards, S. V. 2019-08-12 doi:10.1101/723924 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Global Genetic Cartography of Urban Metagenomes andAnti-Microbial Resistance ]]> https://biorxiv.org/content/10.1101/724526v1?rss=1 Danko, D. C. Bezdan, D. Afshinnekoo, E. Ahsanuddin, S. Alicea, J. Bhattacharya, C. Bhattacharyya, M. Blekhman, R. Butler, D. J. Castro-Nallar, E. Canas, A. M. Chatziefthimiou, A. D. Chng, K. R. Coil, D. A. Court, D. S. Crawford, R. W. Desnues, C. Dias-Neto, E. Donnellan, D. Dybwad, M. Eisen, J. A. Elhaik, E. Ercolini, D. De Filippis, F. Frolova, A. Graf, A. B. Green, D. C. Lee, P. K. H. Hecht, J. Hernandez, M. Jang, S. Kahles, A. Karasikov, M. Knights, K. Kyrpides, N. C. Ljungdahl, P. Lyons, A. Mason-Buck, G. McGrath, K. Mongodin, E. F. Mustafa, H. Muta 2019-08-05 doi:10.1101/724526 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Biological Pathways and Gene Networks Link Inflammation and Vascular Remodeling to Both Heart Failure with Preserved and Reduced Ejection Fraction in Women across Ethnicities ]]> https://biorxiv.org/content/10.1101/726208v1?rss=1 Liu, Q. Chan, K. H. K. Morrison, A. R. McGarvey, S. T. Luo, X. Wilson, J. G. Correa, A. Reiner, A. P. Li, J. Liu, S. Wu, W.-C. 2019-08-06 doi:10.1101/726208 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Using Machine Learning and Gene Nonhomology Features to Predict Gene Ontology ]]> https://biorxiv.org/content/10.1101/730473v1?rss=1 Dai, X. Xu, Z. Liang, Z. Tu, X. Zhong, S. Schnable, J. C. Li, P. 2019-08-09 doi:10.1101/730473 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Massive parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity ]]> https://biorxiv.org/content/10.1101/740837v1?rss=1 Suiter, C. C. Moriyama, T. Matreyek, K. A. Yang, W. Scaletti, E. R. Nishii, R. Yang, W. Hoshitsuki, K. Singh, M. Trehan, A. Parish, C. Smith, C. Bhojwani, D. Yuen, L. Y. Li, C.-k. Li, C.-h. Yang, Y.-l. Walker, G. J. Goodhand, J. R. Kennedy, N. A. Klussmann, F. A. Bhatia, S. Relling, M. V. Kato, M. Hori, H. Bhatia, P. Ahmad, T. Yoeh, A. E. J. Stenmark, P. Fowler, D. M. Yang, J. J. 2019-08-20 doi:10.1101/740837 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ DeepMF: Deciphering the Latent Patterns in Omics Profiles with a Deep Learning Method ]]> https://biorxiv.org/content/10.1101/744706v1?rss=1 Chen, L. Xu, J. Li, S. C. 2019-08-22 doi:10.1101/744706 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Hierarchical learning of statistical regularities over multiple timescales of sound sequence processing: A dynamic causal modelling study ]]> https://biorxiv.org/content/10.1101/768846v1?rss=1 Fitzgerald, K. Auksztulewicz, R. Provost, A. Paton, B. Howard, Z. Todd, J. 2019-09-13 doi:10.1101/768846 Cold Spring Harbor Laboratory Press 2019-09-13 <![CDATA[ Dissociable neural effects of temporal expectations due to passage of time and contextual probability ]]> https://biorxiv.org/content/10.1101/769372v1?rss=1 Todorovic, A. Auksztulewicz, R. 2019-09-14 doi:10.1101/769372 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ I-Impute: a self-consistent method to impute single cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/772723v1?rss=1 FENG, X. Chen, L. Wang, Z. Li, S. C. 2019-09-18 doi:10.1101/772723 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Glutamatergic and GABAergic neuronal populations in thedorsolateral Periacqueductual Gray have differentfunctional roles in fear conditioning ]]> https://biorxiv.org/content/10.1101/781187v1?rss=1 Montardy, Q. Zhou, Z. Liu, X. Lei, Z. Zeng, P. Chen, C. Liu, Y. Huang, K. Wei, M. Wang, L. 2019-09-27 doi:10.1101/781187 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ Analysis of spatiotemporal specificity of small RNAs regulating hPSC differentiation and beyond ]]> https://biorxiv.org/content/10.1101/784819v1?rss=1 Li, L. Li, J. F. Cao, D. D. Papadopoulos, V. Chan, W. Y. 2019-09-27 doi:10.1101/784819 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ Isolation and Characterization of a Rhizobium Bacterium Associated with the Toxic Dinoflagellate Gambierdiscus balechii ]]> https://biorxiv.org/content/10.1101/789107v1?rss=1 WU, Z. Yang, X. Lin, S. Lee, W. H. Lam, P. K. S. 2019-10-01 doi:10.1101/789107 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ CircFOXK2 Promotes Tumor Growth and Metastasis of Pancreatic Ductal Adenocarcinoma via Complexing with RNA Binding Proteins and Sponging MiR-942 ]]> https://biorxiv.org/content/10.1101/792101v1?rss=1 Wong, C. H. Lou, U. K. Li, Y. Chan, S. L. Tong, J. H.-M. To, K.-F. Chen, Y. 2019-10-03 doi:10.1101/792101 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Establishment of morphological atlas of Caenorhabditis elegans embryo with cellular resolution using deep-learning-based 4D segmentation ]]> https://biorxiv.org/content/10.1101/797688v1?rss=1 Cao, J. Guan, G. Wong, M.-K. Chan, L.-Y. Tang, C. Zhao, Z. Yan, H. 2019-10-08 doi:10.1101/797688 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ In Vivo Study of Key Transcription Factors in Muscle Satellite Cells by CRISPR/Cas9/AAV9-sgRNA Mediated Genome Editing ]]> https://biorxiv.org/content/10.1101/797746v1?rss=1 WANG, H. HE, L. Ding, Y. Zhao, Y. SO, K. Peng, X. Li, Y. Yuan, J. Sun, H. 2019-10-08 doi:10.1101/797746 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Zonation-dependent single-endothelial cell transcriptomic changes in the aged brain ]]> https://biorxiv.org/content/10.1101/800318v1?rss=1 Zhao, L. Li, Z. Vong, J. S. L. Chen, X. Lai, H.-M. Yan, L. Y. C. Huang, J. Sy, S. K. H. Tian, X. Huang, Y. Chan, H. Y. E. So, H.-C. Ng, W.-L. Tang, Y. Lin, W.-J. Mok, V. C. T. Ko, H. 2019-10-10 doi:10.1101/800318 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Optimal Multichannel Artifact Prediction and Removal for Brain Machine Interfaces and Neural Prosthetics ]]> https://biorxiv.org/content/10.1101/809640v1?rss=1 Sadeghi, M. Chen, L. Dutta, K. Norris, A. Feng, B. Schnupp, J. Rosskothen-Kuhl, N. Read, H. Escabi, M. 2019-10-17 doi:10.1101/809640 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Tensor Factorization-based Prediction with an Application to Estimating the Risk of Chronic Diseases ]]> https://biorxiv.org/content/10.1101/810556v1?rss=1 Wang, H. Zhang, Q. Chen, Y. F. Leung, E. Wong, E. Yeoh, E.-k. 2019-10-18 doi:10.1101/810556 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Codon usage bias creates a ramp of hydrogen bonding at the 5′-end in prokaryotic ORFeomes ]]> https://biorxiv.org/content/10.1101/811612v1?rss=1 Villada, J. C. Duran, M. F. Lee, P. K. H. 2019-10-21 doi:10.1101/811612 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ The Establishment of CDK9/ RNA PolII/H3K4me3/DNA Methylation Feedback Promotes HOTAIR Expression by RNA Elongation Enhancement in Cancer ]]> https://biorxiv.org/content/10.1101/812776v1?rss=1 Wong, C. H. Li, C. H. He, Q. Tong, J. H. M. To, K.-F. Chen, Y. 2019-10-21 doi:10.1101/812776 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Ectopic HOTTIP Expression Induces Non-canonical Transactivation Pathways to Promote Growth and Invasiveness in Pancreatic Ductal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/812800v1?rss=1 Wong, C. H. Li, C. H. He, Q. Chan, S. L. Tong, J. H.-M. To, K.-F. Chen, Y. 2019-10-21 doi:10.1101/812800 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Single-cell dissection of a rare human prostate basal cell carcinoma ]]> https://biorxiv.org/content/10.1101/818260v1?rss=1 T, T>C and C>A, similar to common prostate cancer. The distribution of the variant allele frequency values indicated these single cells are from the same tumor clone. The transcriptomes of 69 single cells were obtained, and they were clustered into tumor, stromal and immune cells based on their global transcriptomic profiles. The tumor cells specifically express basal cell markers like KRT5, KRT14 and KRT23, and epithelial markers EPCAM, CDH1 and CD24. The transcription factor (TF) co-variance network analysis showed that the BCC tumor cells have distinct regulatory networks. By comparison with current prostate cancer datasets, we found that some of the bulk samples exhibit basal-cell signatures. Interestingly, at single-cell resolution the gene expression patterns of prostate BCC tumor cells show uniqueness compared with that of common prostate cancer-derived circulating tumor cells. This study, for the first time, discloses the comprehensive mutational and transcriptomic landscapes of prostate BCC, which lays a foundation for the understanding of its tumorigenesis mechanism and provides new insights into prostate cancers in general. ]]> Su, X. Long, Q. Bo, J. Shi, Y. Zhao, L.-N. Lin, Y. Luo, Q. Ghazanfar, S. Zhang, C. Liu, Q. Wang, L. He, K.-Y. He, J. Cui, X.-F. Yang, J. Y. H. Han, Z.-G. Sha, J. Yang, G. 2019-10-25 doi:10.1101/818260 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Carbon metabolism, transcriptome and RNA editome in developmental paths differentiation of Coprinopsis cinerea ]]> https://biorxiv.org/content/10.1101/819201v1?rss=1 Xie, Y. Chang, J. Kwan, H. S. 2019-10-28 doi:10.1101/819201 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Insights from two decades of the Student Conference on Conservation Science ]]> https://biorxiv.org/content/10.1101/819623v1?rss=1 Geldmann, J. Alves-Pinto, H. Amano, T. Barlett, H. Christie, A. P. Collas, L. Cooke, S. C. Correa, R. Cripps, I. Doherty, A. Finch, T. Garnett, E. Hua, F. Jones, J. P. G. Kasoar, T. MacFarlane, D. Martin, P. A. Mukherjee, N. Mumby, H. S. Payne, C. Petrovan, S. O. Rocha, R. Russell, K. Simmons, B. I. Wauchope, H. Worthington, T. A. Trevelyan, R. Green, R. Balmford, A. 2019-10-29 doi:10.1101/819623 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Cross-kingdom regulation of tRNAs/tRFs derived from Chinese yew ]]> https://biorxiv.org/content/10.1101/821165v1?rss=1 Cao, K.-Y. Yan, T.-M. Zhang, J.-Z. Chan, T.-F. Li, J. Li, C. Leung, L.-H. Jiang, Z.-H. 2019-10-28 doi:10.1101/821165 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ PointSite: a point cloud segmentation tool for identication of protein ligand binding atoms ]]> https://biorxiv.org/content/10.1101/831131v1?rss=1 Li, Z. Yan, X. Wei, Q. Gao, X. Wang, S. Cui, S. 2019-11-05 doi:10.1101/831131 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Prediction of multiple drug resistant pulmonary tuberculosis against drug sensitive pulmonary tuberculosis by CT nodular consolidation sign ]]> https://biorxiv.org/content/10.1101/833954v1?rss=1 . Drug sensitive pulmonary TB (dsptb) cases were from the TBPP collection (n=112) as well as the Shenzhen Center for Chronic Disease Control (n=111), Shenzhen, China, and we excluded patients with HIV(+) status. Our study shows NC, particularly multiple NCs, is more common in mdrptb than in dsptb, and more common in xdrptb than in mdrptb. For example, 2.24% of dsptb patients, 13.23% of mdrptb patients, and 20.89% of xdrptb patients, respectively, have NCs with diameter >= 10mm equal or more than 2 in number. ]]> Huang, X.-L. Skrahin, A. Lu, P.-X. Alexandru, S. Crudu, V. Astrovko, A. Skrahina, A. Taaffe, J. Harris, M. Long, A. Wollenberg, K. Engle, E. Hurt, D. Akhundova, I. Ismayilov, S. Mammadbayov, E. Gadirova, H. Abuzarov, R. Seyfaddinova, M. Avaliani, Z. Vashakidze, S. Shubladze, N. Nanava, U. Strambu, I. Zaharia, D. Muntean, A. Ghita, E. Bogdan, M. Mindru, R. Spinu, V. Sora, A. Ene, C. Sergueev, E. Kirichenko, V. Lapitski, V. Snezhko, E. Kovalev,, V. Tuzikov, A. Gabrielian, A. Rosenthal, A. Tartakovsky, M. Wang, Y.-X. 2019-11-07 doi:10.1101/833954 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ The histone modification reader ZCWPW1 links histone methylation to repair of PRDM9-induced meiotic double stand breaks ]]> https://biorxiv.org/content/10.1101/836023v1?rss=1 Huang, T. Yuan, S. Li, M. Yu, X. Zhang, J. Yin, Y. Liu, C. Gao, L. Li, W. Liu, J. Chen, Z.-J. Liu, H. 2019-11-08 doi:10.1101/836023 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ RNA G-quadruplex structures exist and function in vivo ]]> https://biorxiv.org/content/10.1101/839621v1?rss=1 Yang, X. Cheema, J. Zhang, Y. Deng, H. Duncan, S. Umar, M. I. Zhao, J. Liu, Q. Cao, X. Kwok, C. K. DING, Y. 2019-11-12 doi:10.1101/839621 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Selective attention to sound features mediates cross-modal activation of visual cortices ]]> https://biorxiv.org/content/10.1101/855882v1?rss=1 Retsa, C. Matusz, P. J. Schnupp, J. W. H. Murray, M. M. 2019-11-26 doi:10.1101/855882 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ LandScape: a web application for interactive genomic summary visualization ]]> https://biorxiv.org/content/10.1101/866087v1?rss=1 Jia, W. Li, H. Li, S. Li, S. 2019-12-06 doi:10.1101/866087 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ SpecHap: a fast haplotyping method based on spectral graph theory ]]> https://biorxiv.org/content/10.1101/870972v1?rss=1 Yu, Y. Chen, L. Tan, B. Jia, W. Li, S. 2019-12-10 doi:10.1101/870972 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Brain Templates for Chinese Babies from Newborn to Three Months of Age ]]> https://biorxiv.org/content/10.1101/2023.06.05.543553v1?rss=1 Geng, X. Chan, P. H. Lam, H. S. Chu, W. C. Wong, P. C. 2023-06-07 doi:10.1101/2023.06.05.543553 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Targeted Protein O-GlcNAcylation Using Bifunctional Small Molecules ]]> https://biorxiv.org/content/10.1101/2023.06.09.544275v1?rss=1 Ma, B. Khan, K. S. Xu, T. Amada, J. X. Guo, Z. Yan, Y. Cheng, A. Ng, W.-L. 2023-06-11 doi:10.1101/2023.06.09.544275 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ GDmicro: classifying host disease status with GCN and Deep adaptation network based on the human gut microbiome data ]]> https://biorxiv.org/content/10.1101/2023.06.12.544696v1?rss=1 Liao, H. Shang, J. Sun, Y. 2023-06-13 doi:10.1101/2023.06.12.544696 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Phylogenetic and population structure of the nod-free but nodulating Bradyrhizobium phylogroup ]]> https://biorxiv.org/content/10.1101/2023.06.14.544914v1?rss=1 Ling, L. Camuel, A. Wang, S. Wang, X. Lin, X. Nouwen, N. Giraud, E. Luo, H. 2023-06-14 doi:10.1101/2023.06.14.544914 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Diversification of Nucleoside Analogues as Potent Antiviral Drug Leads ]]> https://biorxiv.org/content/10.1101/2023.06.17.545395v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@fbd078org.highwire.dtl.DTLVardef@3399a9org.highwire.dtl.DTLVardef@1ad5fcborg.highwire.dtl.DTLVardef@16c2f3d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Scheeff, S. Wang, Y. Lyu, M.-Y. Nasiri Ahmadabadi, B. Hau, S. C. K. Hui, T. K. C. Zhang, Y. Zuo, Z. Chan, R. W. Y. Ng, B. W.-L. 2023-06-17 doi:10.1101/2023.06.17.545395 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ Dating the bacterial tree of life with ancient symbiosis ]]> https://biorxiv.org/content/10.1101/2023.06.18.545440v1?rss=1 Wang, S. Luo, H. 2023-06-21 doi:10.1101/2023.06.18.545440 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Rats synchronize predictively to metronomes ]]> https://biorxiv.org/content/10.1101/2023.06.19.545615v1?rss=1 Rajendran, V. G. Tsdaka, Y. Keung, T. Y. Schnupp, J. W. H. Nelken, I. 2023-06-22 doi:10.1101/2023.06.19.545615 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Genome reduction occurred in early Prochlorococcus with an unusually low effective population size ]]> https://biorxiv.org/content/10.1101/2023.06.25.546417v1?rss=1 Zhang, H. Hellweger, F. L. Luo, H. 2023-06-26 doi:10.1101/2023.06.25.546417 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Unravelling Biosynthesis and Biodegradation Potentials of Microbial Dark Matters in Hypersaline Lakes ]]> https://biorxiv.org/content/10.1101/2023.06.28.546814v1?rss=1 Qiu, Z. Zhu, Y. Zhang, Q. Qiao, X. Mu, R. Xu, Z. Yan, Y. Wang, F. Zhang, T. Yu, K. 2023-06-28 doi:10.1101/2023.06.28.546814 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ BeeDC: An R package and globally synthesised and flagged bee occurrence dataset ]]> https://biorxiv.org/content/10.1101/2023.06.30.547152v1?rss=1 18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducible BeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and we added record-level flags for a series of potential quality issues. These data are provided in two formats, "cleaned" and "flagged-but-uncleaned". The BeeBDC package with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducible R workflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation. ]]> Dorey, J. B. Fischer, E. E. Chesshire, P. R. Nava-Bolanos, A. OReilly, R. L. Bossert, S. Collins, S. M. Lichtenberg, E. M. Tucker, E. M. Smith-Pardo, A. Falcon-Brindis, A. Guevara, D. A. Ribeiro, B. de Pedro, D. Pickering, J. James, K.-L. Parys, K. A. McCabe, L. M. Rogan, M. S. Minckley, R. L. Velazco, S. J. E. Griswold, T. Zarrillo, T. A. Jetz, W. Sica, Y. V. Orr, M. C. Guzman, L. M. Ascher, J. A. Hughes, A. C. Cobb, N. S. 2023-07-02 doi:10.1101/2023.06.30.547152 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Dual-species proteomics and targeted intervention of animal-pathogen interactions ]]> https://biorxiv.org/content/10.1101/2023.07.02.547426v1?rss=1 Liu, S. Y. Zhang, C. Khoo, B. L. Hao, P. Chua, S. L. 2023-07-02 doi:10.1101/2023.07.02.547426 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ A pre-trained large language model for translating single-cell transcriptome to proteome ]]> https://biorxiv.org/content/10.1101/2023.07.04.547619v1?rss=1 Liu, L. Li, W. Wong, K.-c. Yang, F. Yao, J. 2023-07-04 doi:10.1101/2023.07.04.547619 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Structural basis for lipid transfer by the ATG2A-ATG9A complex ]]> https://biorxiv.org/content/10.1101/2023.07.08.548186v1?rss=1 Wang, Y. Dahmane, S. Ti, R. Mai, X. Zhu, L. Carlson, L.-A. Stjepanovic, G. 2023-07-08 doi:10.1101/2023.07.08.548186 Cold Spring Harbor Laboratory Press 2023-07-08 <![CDATA[ Aster-dependent non-vesicular transport facilitates dietary cholesterol uptake ]]> https://biorxiv.org/content/10.1101/2023.07.07.548168v1?rss=1 Ferrari, A. Whang, E. Xiao, X. Kennelly, J. P. Romartinez- Alonso, B. Mack, J. J. Weston, T. Chen, K. Kim, Y. Tol, M. Bideyan, L. Nguyen, A. Gao, Y. Cui, L. Bedard, A. H. Sandhu, J. Lee, S. D. Fairall, L. Williams, K. J. Song, W. Munguia, P. Russell, R. A. Martin, M. G. Jung, M. E. Jiang, H. Schwabe, J. W. Young, S. G. Tontonoz, P. 2023-07-10 doi:10.1101/2023.07.07.548168 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ What explains the high island endemicity of Philippine Rafflesia? A species distribution modeling analysis of three threatened parasitic plant species and their hosts ]]> https://biorxiv.org/content/10.1101/2023.07.10.548437v1?rss=1 Obico, J. J. A. Lapuz, R. S. Barcelona, J. F. Pelser, P. B. 2023-07-11 doi:10.1101/2023.07.10.548437 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ ProFAST: a fast and scalable factor analysis for spatially aware dimension reduction of multi-section spatial transcriptomics data ]]> https://biorxiv.org/content/10.1101/2023.07.11.548486v1?rss=1 2.3 million locations in only 2 hours. More importantly, FAST identified the differential activities of immune-related transcription factors between tumor and non-tumor clusters and also predicted a carcinogenesis factor CCNH as the upstream regulator of differentially expressed genes in a breast cancer Xenium dataset. ]]> Liu, W. Zhang, X. Chai, X. Fan, Z. Lin, H. Chen, J. Sun, L. Yu, T. Yeong, J. Liu, J. 2023-07-12 doi:10.1101/2023.07.11.548486 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ DNAGPT: A Generalized Pretrained Tool for Multiple DNA Sequence Analysis Tasks ]]> https://biorxiv.org/content/10.1101/2023.07.11.548628v1?rss=1 Zhang, D. Zhang, w. He, B. Zhang, J. Qin, C. Yao, J. 2023-07-12 doi:10.1101/2023.07.11.548628 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.07.12.548617v1?rss=1 Pekar, J. E. Lytras, S. Ghafari, M. Magee, A. F. Parker, E. Havens, J. L. Katzourakis, A. Vasylyeva, T. I. Suchard, M. A. Hughes, A. C. Hughes, J. Robertson, D. L. Dellicour, S. Worobey, M. Wertheim, J. O. Lemey, P. 2023-07-12 doi:10.1101/2023.07.12.548617 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ EMDiffuse: a diffusion-based deep learning method augmenting ultrastructural imaging and volume electron microscopy ]]> https://biorxiv.org/content/10.1101/2023.07.12.548636v1?rss=1 Lu, C. Chen, K. Qiu, H. Chen, X. Chen, G. Qi, X. Jiang, H. 2023-07-12 doi:10.1101/2023.07.12.548636 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Theranostic Bottle-Brush Polymers Tailored for Universal Solid-Tumour Targeting ]]> https://biorxiv.org/content/10.1101/2023.07.13.548666v1?rss=1 Zhang, W. Xu, Y. Guo, R. Zhuang, P. Hong, H. Tan, H. Wang, M. 2023-07-15 doi:10.1101/2023.07.13.548666 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Divergent evolution of head morphology between marine and freshwater sticklebacks ]]> https://biorxiv.org/content/10.1101/2023.07.14.549115v1?rss=1 marine) and number, but the degree of divergence in these traits did not exceed neutral expectations. Yet, the direction of divergence in gill raker traits are suggestive of the limnetic feeding mode of pond fish, aligning with the inference from the head morphology analyses. ]]> Fraimout, A. Chen, Y. Reid, K. Merilä, J. 2023-07-15 doi:10.1101/2023.07.14.549115 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Trophic diversity and evolution in Enantiornithes: a synthesis including new insights from Bohaiornithidae ]]> https://biorxiv.org/content/10.1101/2023.07.18.549506v1?rss=1 Miller, C. V. Pittman, M. Wang, X. Zheng, X. Bright, J. A. 2023-07-19 doi:10.1101/2023.07.18.549506 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Neuromolecular responses in disrupted mutualistic cleaning interactions under future environmental conditions ]]> https://biorxiv.org/content/10.1101/2023.07.20.549851v1?rss=1 Ramirez-Calero, S. P. Paula, J. R. Otjacques, E. Ravasi, T. Rosa, R. Schunter, C. 2023-07-21 doi:10.1101/2023.07.20.549851 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Autophagy maintains the homeostatic environment in the male reproductive accessory organs playing a key role in fertility ]]> https://biorxiv.org/content/10.1101/2023.07.21.549845v1?rss=1 Jaulim, A. Cassidy, L. D. Young, A. R. J. Chan, A. S. L. Warren, A. Y. Taylor, A. E. Arlt, W. Lan, G. Blayney, M. L. Davidson, O. Barratt, C. L. R. Pacey, S. Narita, M. 2023-07-21 doi:10.1101/2023.07.21.549845 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Cuprizone drives divergent neuropathological changes in different mouse models of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.07.24.547147v1?rss=1 Cheng, G. W.-Y. Ma, I. W.-T. Huang, J. Yeung, S. H.-S. Ho, P. Chen, Z. Mak, H. K. F. Herrup, K. Chan, K. W. Y. Tse, K.-H. 2023-07-25 doi:10.1101/2023.07.24.547147 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Neural mechanism underlying preview effects and masked priming effects in visual word processing ]]> https://biorxiv.org/content/10.1101/2023.07.24.550196v1?rss=1 Huang, X. Wong, B. W. L. Ng, H. T.-Y. Sommer, W. Dimigen, O. Maurer, U. 2023-07-25 doi:10.1101/2023.07.24.550196 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Butyrate Protects against SARS-CoV-2-induced Tissue Damage in Golden Hamsters. ]]> https://biorxiv.org/content/10.1101/2023.07.27.550811v1?rss=1 Yu, H. Yuan, L. Yan, Z. Zhou, M. Ye, J. Wu, K. Chen, W. Chen, R. Xia, N.-S. Guan, Y. Zhu, H. 2023-07-28 doi:10.1101/2023.07.27.550811 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Immunities Specific to Both of the M Protein Ectodomain and RBD Synergize to Confer Cross-protection against SARS-CoV-2 Infections ]]> https://biorxiv.org/content/10.1101/2023.07.31.551223v1?rss=1 Tang, Y. Tang, K. Hu, Y. Ye, Z.-W. Luo, W. Luo, C. Cao, H. Wang, R. Liu, D. Liu, C. Ge, X. Chen, Y. Yuan, S. Deng, L. 2023-07-31 doi:10.1101/2023.07.31.551223 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ SR2: Sparse Representation Learning for Scalable Single-cell RNA Sequencing Data Analysis ]]> https://biorxiv.org/content/10.1101/2023.07.31.551228v1?rss=1 ZHAO, K. SO, H.-C. Lin, Z. 2023-08-02 doi:10.1101/2023.07.31.551228 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Is Inappropriate Pulse Timing Responsible for Poor Binaural Hearing with Cochlear Implants? ]]> https://biorxiv.org/content/10.1101/2023.08.04.551983v1?rss=1 Schnupp, J. W. Buchholz, S. Buck, A. N. Budig, H. K. Khurana, L. Rosskothen-Kuhl, N. 2023-08-04 doi:10.1101/2023.08.04.551983 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Radiation-induced rescue effect on human breast carcinoma cells is regulated by macrophages ]]> https://biorxiv.org/content/10.1101/2023.08.02.551610v1?rss=1 Pathikonda, S. Tian, L. Cheng, S. H. Lam, Y. W. 2023-08-05 doi:10.1101/2023.08.02.551610 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ DHX36 binding induces RNA structurome remolding and regulates RNA abundance via m6A/YTHDF1 ]]> https://biorxiv.org/content/10.1101/2023.08.06.551902v1?rss=1 Zhang, Y. Zhao, J. Chen, X. Lyu, K. Ding, Y. Sun, H. Kwok, C. K. Wang, H. 2023-08-06 doi:10.1101/2023.08.06.551902 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Shared and distinct molecular effects of regulatory genomic variants provide insight into mechanisms of distal enhancer-promoter communication ]]> https://biorxiv.org/content/10.1101/2023.08.04.551251v1?rss=1 Ray-Jones, H. Song, Z. Haglund, A. Artemov, P. Della Rosa, M. Burden, F. Kreuzhuber, R. Litovskikh, A. Tan, V. X. H. Chan, L. T. Frontini, M. Wallace, C. Malysheva, V. Bottolo, L. Vigorito, E. Spivakov, M. 2023-08-07 doi:10.1101/2023.08.04.551251 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Do Goats Recognise Humans Cross-Modally? ]]> https://biorxiv.org/content/10.1101/2023.08.04.551944v1?rss=1 Mason, M. A. Semple, S. Marshall, H. H. McElligott, A. G. 2023-08-07 doi:10.1101/2023.08.04.551944 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Climatic and biogeographic processes underlying the diversification of the pantropical and early divergent angiosperm family Annonaceae ]]> https://biorxiv.org/content/10.1101/2023.08.08.549183v1?rss=1 Li, W. Wang, R. Liu, M.-F. Folk, R. A. Xue, B. Saunders, R. M. K. 2023-08-09 doi:10.1101/2023.08.08.549183 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Targeting adipocyte ESRRA promotes osteogenesis and vascular formation in adipocyte-rich bone marrow ]]> https://biorxiv.org/content/10.1101/2023.08.14.552932v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1132da3org.highwire.dtl.DTLVardef@19342aorg.highwire.dtl.DTLVardef@afe8d7org.highwire.dtl.DTLVardef@dfb1f9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Huang, T. Lu, Z. Wang, Z. Cheng, L. Gao, L. Gao, J. Zhang, N. Geng, C.-A. Zhao, X. Wang, H. Wong, C.-W. Yeung, K. W. K. Pan, H. Lu, W. W. Guan, M. 2023-08-14 doi:10.1101/2023.08.14.552932 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ High-throughput generic single-entity sequencing using droplet microfluidics ]]> https://biorxiv.org/content/10.1101/2023.08.15.549386v1?rss=1 Wang, G. Zhao, L. Shi, Y. Qu, F. Ding, Y. Liu, W. Liu, C. Luo, G. Li, M. Bai, X. Li, L. Ho, Y.-P. Yu, J. 2023-08-15 doi:10.1101/2023.08.15.549386 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ ClairS: a deep-learning method for long-read somatic small variant calling ]]> https://biorxiv.org/content/10.1101/2023.08.17.553778v1?rss=1 Zheng, Z. Su, J. Chen, L. Lee, Y.-L. Lam, T.-W. Luo, R. 2023-08-21 doi:10.1101/2023.08.17.553778 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Capturing dynamic fear experiences in naturalistic contexts: An ecologically valid fMRI signature integrating brain activation and connectivity ]]> https://biorxiv.org/content/10.1101/2023.08.18.553808v1?rss=1 Zhou, F. Zhang, R. Yao, S. Dong, D. Feng, P. Kranz, G. Feng, T. Becker, B. 2023-08-21 doi:10.1101/2023.08.18.553808 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Schisandrin B suppresses colon cancer growth by inducing cell cycle arrest and apoptosis via the CHOP signalling pathway ]]> https://biorxiv.org/content/10.1101/2023.08.27.554980v1?rss=1 Co, V. A. El-Nezami, H. Liu, Y. Twum, B. Dey, P. Cox, P. A. Joseph, S. Agbodjan, R. Sabzichi, M. Draheim, R. Wan, M. L. Y. 2023-08-27 doi:10.1101/2023.08.27.554980 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses ]]> https://biorxiv.org/content/10.1101/2023.08.28.555221v1?rss=1 Pan, Y.-f. Zhao, H. Gou, Q.-y. Shi, P.-b. Tian, J.-h. Feng, Y. Li, K. Yang, W.-h. Wu, D. Tang, G. Zhang, B. Ren, Z. Peng, S. Luo, G.-y. Le, S.-j. Xin, G.-y. Wang, J. Hou, X. Peng, M.-w. Kong, J.-b. Chen, X.-x. Yang, C.-h. Mei, S.-q. Liao, Y.-q. Cheng, J.-x. Wang, J. n/a, C. Wu, Y.-h. Wang, J.-b. An, T. Huang, X. Eden, J.-S. Li, J. Guo, D. Liang, G. Jin, X. Holmes, E. C. Li, B. Wang, D. Li, J. Wu, W.-c. Shi, M. 2023-08-30 doi:10.1101/2023.08.28.555221 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ High-resolution diploid 3D genome reconstruction using Pore-C data ]]> https://biorxiv.org/content/10.1101/2023.08.29.555243v1?rss=1 Chen, Y. Lin, Z.-B. Wang, S. Wu, B. Niu, L.-J. Zhong, J.-Y. Sun, Y.-M. Bai, X. Liu, L.-R. Xie, W. Luo, R. Hou, C. Luo, F. Xiao, C.-L. 2023-08-31 doi:10.1101/2023.08.29.555243 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Prosocial Decision-Making and Human Brain: A Graph Theory Analysis on Resting-State Functional Magnetic Resonance Image ]]> https://biorxiv.org/content/10.1101/2023.09.01.555856v1?rss=1 Xu, J. Sun, D. 2023-09-05 doi:10.1101/2023.09.01.555856 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Elasticity of adhesion bonds determines multistable mechanosensitive behaviour of living cells. ]]> https://biorxiv.org/content/10.1101/2023.09.04.554585v1?rss=1 Liu, P. Wang, Q. Yao, M. Efremov, A. K. 2023-09-05 doi:10.1101/2023.09.04.554585 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Genetic basis and evolution of structural color polymorphism in an Australian songbird ]]> https://biorxiv.org/content/10.1101/2023.09.03.556140v1?rss=1 Sin, S. Y. W. Ke, F. Chen, G. Huang, P.-Y. Enbody, E. Karubian, J. Webster, M. Edwards, S. V. 2023-09-06 doi:10.1101/2023.09.03.556140 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Emergence of Prochlorococcus in the Tonian oceans and the initiation of Neoproterozoic oxygenation ]]> https://biorxiv.org/content/10.1101/2023.09.06.556545v1?rss=1 Zhang, H. Wang, S. Liao, T. Crowe, S. A. Luo, H. 2023-09-06 doi:10.1101/2023.09.06.556545 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Structural basis for EROS binding to human phagocyte NADPH oxidase NOX2 ]]> https://biorxiv.org/content/10.1101/2023.09.11.557130v1?rss=1 Liang, S. Liu, A. Liu, Y. Wang, F. Zhou, Y. Wang, T. Liu, Z. Ren, R. Ye, R. D. 2023-09-11 doi:10.1101/2023.09.11.557130 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ magpie: a power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing ]]> https://biorxiv.org/content/10.1101/2023.09.08.556896v1?rss=1 Guo, Z. Duan, D. Tang, W. Zhu, J. Bush, W. S. Zhang, L. Zhu, X. Jin, F. Feng, H. 2023-09-12 doi:10.1101/2023.09.08.556896 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ The Effect of Transcranial Direct Current and Magnetic Stimulation on Fear Extinction and Return of Fear: A meta-analysis and Systematic Review ]]> https://biorxiv.org/content/10.1101/2023.09.11.557284v1?rss=1 Lei, G. L. T. Lai, C. S. W. Lee, T. M. C. Lam, C. L. M. 2023-09-13 doi:10.1101/2023.09.11.557284 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Guided Diffusion for molecular generation with interaction prompt ]]> https://biorxiv.org/content/10.1101/2023.09.11.557141v1?rss=1 Song, W. Wu, P. Du, H. Yan, Y. Bai, C. 2023-09-15 doi:10.1101/2023.09.11.557141 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Pre-trained Inspired MocFormer: Efficient and Predictive Models of Drug-target Interactions ]]> https://biorxiv.org/content/10.1101/2023.09.13.557595v1?rss=1 Zhang, Y.-L. Wang, W. Guan, J.-H. Yang, H.-W. 2023-09-17 doi:10.1101/2023.09.13.557595 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Differentiation and migration of hematopoietic stem and progenitor cells cross multiple tissues ]]> https://biorxiv.org/content/10.1101/2023.09.15.557856v1?rss=1 Yu, S. Li, H. Wang, X. Chen, G. Huang, H. Hong, N. Song, Y.-Q. Zhang, X. Jin, W. 2023-09-17 doi:10.1101/2023.09.15.557856 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Single-cell mitochondrial variant enrichment resolved clonal tracking and spatial architecture in human embryonic hematopoiesis ]]> https://biorxiv.org/content/10.1101/2023.09.18.558215v1?rss=1 Xue, Y. Chao, Y. Lin, X. Huang, Y. Ho, J. W. K. Sugimura, R. 2023-09-18 doi:10.1101/2023.09.18.558215 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ A neural signature for the subjective experience of threat anticipation under uncertainty ]]> https://biorxiv.org/content/10.1101/2023.09.20.558716v1?rss=1 Liu, X. Jiao, G. Zhou, F. Kendrick, K. M. Yao, D. Xiang, S. Jia, T. Zhang, X.-Y. Zhang, J. Feng, J. Becker, B. 2023-09-22 doi:10.1101/2023.09.20.558716 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Co-evolution of spheroid fluidization and mechanical fracture in a morphogenic cascade ]]> https://biorxiv.org/content/10.1101/2023.09.25.559247v1?rss=1 Wu, S. K. Ho, C. Z. Sun, F. Lou, Y. Huang, C. B.-X. Xiao, J. Shagirov, M. Yow, I. Chin, J. F. L. Verma, S. Yap, A. Lin, Y. Hiraiwa, T. Low, B. C. 2023-09-26 doi:10.1101/2023.09.25.559247 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Progressive community, biogeochemical and evolutionary remodeling of the soil microbiome underpins long-term desert ecosystem restoration ]]> https://biorxiv.org/content/10.1101/2023.09.26.559499v1?rss=1 Chen, Q. Yuan, M. Jiang, L. Wei, X. Liu, Z. Peng, C. Huang, Z. Tang, D. Wu, X. Sun, J. Liu, Q. Zhu, X. Gao, P. Huang, L. Wang, M. Jiang, M. Jiang, C. 2023-09-26 doi:10.1101/2023.09.26.559499 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Timing specific parental effects of ocean warming in a coral reef fish ]]> https://biorxiv.org/content/10.1101/2023.09.27.559693v1?rss=1 Bonzi, L. C. Spinks, R. K. Donelson, J. M. Munday, P. L. Ravasi, T. Schunter, C. 2023-09-29 doi:10.1101/2023.09.27.559693 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Characterization of Z chromosomal inversion and lineage-specific sweeps reveal widespread local adaptation in Helicoverpa armigera ]]> https://biorxiv.org/content/10.1101/2023.09.28.560065v1?rss=1 Ke, F. 2023-10-01 doi:10.1101/2023.09.28.560065 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ Merging-limited coarsening governs long-term stability of nanoscale condensates ]]> https://biorxiv.org/content/10.1101/2023.10.06.561146v1?rss=1 Chen, F. Zhang, Y. Shum, H. C. 2023-10-09 doi:10.1101/2023.10.06.561146 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Multi-omics analysis reveals novel interplays between intratumoral bacteria and glioma ]]> https://biorxiv.org/content/10.1101/2023.10.08.561332v1?rss=1 Li, T. Zhao, Z. Peng, M. Wang, C. Luo, F. Zeng, M. Sun, K. Fang, Z. Luo, Y. Huang, Q. Xie, Y. Wang, J. Huang, J.-D. Zhou, H. Sun, H. 2023-10-10 doi:10.1101/2023.10.08.561332 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples ]]> https://biorxiv.org/content/10.1101/2023.10.09.561628v1?rss=1 XU, S. Morgan, D. Qian, G. Huang, Y. Ho, J. W. K. 2023-10-10 doi:10.1101/2023.10.09.561628 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ The Role of PKR on Modulating Neuroinflammation and Cognitive Dysfunctions in a Peripheral Inflammation Model ]]> https://biorxiv.org/content/10.1101/2023.10.10.561630v1?rss=1 Cheng, W.-Y. Lee, X.-Z. Lai, M. S.-L. Ho, Y.-S. Chang, R. C.-C. 2023-10-10 doi:10.1101/2023.10.10.561630 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning ]]> https://biorxiv.org/content/10.1101/2023.10.12.562026v1?rss=1 Li, S. Ma, J. Zhao, T. Jia, Y. Liu, B. Luo, R. Huang, Y. 2023-10-17 doi:10.1101/2023.10.12.562026 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Distinct resource utilization by introduced man-made grouper hybrid: an overlooked anthropogenic impact from a longstanding religious practise ]]> https://biorxiv.org/content/10.1101/2023.10.12.562133v1?rss=1 Chung, A. Schunter, C. 2023-10-17 doi:10.1101/2023.10.12.562133 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Structural insights into the distinct protective mechanisms of human antibodies targeting ZIKV NS1 ]]> https://biorxiv.org/content/10.1101/2023.10.16.562450v1?rss=1 Pan, Q. Xiong, X. Yu, J. Chen, Q. Jiao, H. Zhang, W. Wen, Y. Gao, M. Zhao, W. Yu, L. Hu, H. 2023-10-18 doi:10.1101/2023.10.16.562450 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Preventing extinction in an age of species migration and planetary change ]]> https://biorxiv.org/content/10.1101/2023.10.17.562809v1?rss=1 Lundgren, E. J. Wallach, A. D. Svenning, J.-C. Schlaepfer, M. Andersson, A. L. A. Ramp, D. 2023-10-20 doi:10.1101/2023.10.17.562809 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ De novo generation of T-cell receptors with desired epitope-binding property by leveraging a pre-trained large language model ]]> https://biorxiv.org/content/10.1101/2023.10.18.562845v1?rss=1 Yang, J. He, B. Zhao, Y. Jiang, F. Wang, Z. Guo, Y. Xu, Z. Yuan, B. Song, J. Zhang, Q. Yao, J. 2023-10-20 doi:10.1101/2023.10.18.562845 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ ClusterV-Web: A User-Friendly Tool for Profiling HIV Quasispecies and Generating Drug Resistance Reports from Nanopore Long-Read Data ]]> https://biorxiv.org/content/10.1101/2023.10.19.563033v1?rss=1 Su, J. Zheng, Z. Li, S. Lam, T.-W. Luo, R. 2023-10-21 doi:10.1101/2023.10.19.563033 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Biosynthesis- and Metabolomics-guided discovery of antimicrobial cyclopeptides against drug-resistant clinical isolates ]]> https://biorxiv.org/content/10.1101/2023.10.26.563470v1?rss=1 Cheng, Z. He, B.-B. Lei, K. Gao, Y. Shi, Y. Zhong, Z. Liu, H. Liu, R. Zhang, H. Wu, S. Zhang, W. Tang, X. Li, Y.-X. 2023-10-26 doi:10.1101/2023.10.26.563470 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Metabolic interactions of a minimal bacterial consortium drive robust nitritation at acidic pH ]]> https://biorxiv.org/content/10.1101/2023.10.29.564480v1?rss=1 Ni, G. Su, Z. Wang, Y. Wang, Z. Wu, M. Hua, Z. Hu, S. Yuan, Z. Guo, J. Greening, C. Zheng, M. 2023-10-31 doi:10.1101/2023.10.29.564480 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Three-dimensional visualization of blood vessels in human gliomas based on tissue clearing and deep learning ]]> https://biorxiv.org/content/10.1101/2023.10.31.564955v1?rss=1 Wang, X. Yang, X. He, D. Luo, Y. Huang, Q. Li, T. Ye, Z. Ye, C. Zhang, M. Lai, H. Xu, Y. Sun, H. 2023-11-02 doi:10.1101/2023.10.31.564955 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Bio-Mol:Pretraining Multimodality Bioactivity Profile for Enhancing Small Molecule Property Prediction ]]> https://biorxiv.org/content/10.1101/2023.11.02.565401v1?rss=1 Yip, H. F. Wei, X. Li, Z. Ren, Q. Cao, D. Zhang, L. Lu, A. 2023-11-05 doi:10.1101/2023.11.02.565401 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Accurate 3D SMLM localization via Vectorial In-situ PSF Retrieval and Aberration Assessment ]]> https://biorxiv.org/content/10.1101/2023.11.03.565592v1?rss=1 Yang, X. Zhu, H. Sun, Y. Wu, H. Han, Y. Hao, X. Zhou, R. Kuang, C. Liu, X. 2023-11-05 doi:10.1101/2023.11.03.565592 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Cross-Dataset Identification of Human Disease-Specific Cell Subtypes Enabled by the Gene Print-based Algorithm--gPRINT ]]> https://biorxiv.org/content/10.1101/2023.11.05.565588v1?rss=1 Yan, R. Fan, C. Gu, S. Wang, T. Yin, Z. CHEN, X. 2023-11-06 doi:10.1101/2023.11.05.565588 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Pathogenic mechanisms underlying adverse neurodevelopmental outcome in congenital heart disease ]]> https://biorxiv.org/content/10.1101/2023.11.05.565716v1?rss=1 Gabriel, G. C. Yagi, H. Tan, T. Bais, A. S. Glennon, B. Stapleton, M. C. Huang, L. Reynolds, W. T. Shaffer, M. G. Xu, X. Ganapathiraju, M. Simon, D. Panigrahy, A. Wu, Y. L. Lo, C. W. 2023-11-06 doi:10.1101/2023.11.05.565716 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Information-Distilled Generative Label-Free Morphological Profiling Encodes Cellular Heterogeneity ]]> https://biorxiv.org/content/10.1101/2023.11.06.565732v1?rss=1 Lo, M. C. K. Siu, D. M. D. Lee, K. C. M. Wong, J. S. J. Hsin, M. K. Y. Ho, J. C. M. Tsia, K. K. 2023-11-06 doi:10.1101/2023.11.06.565732 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ More is Different: Constructing the Most Comprehensive Human Protein High-Order Interaction Dataset ]]> https://biorxiv.org/content/10.1101/2023.11.06.565906v1?rss=1 Lu, Y. Huang, Y. Li, T. 2023-11-08 doi:10.1101/2023.11.06.565906 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Sex chromosome turnover in hybridizing stickleback lineages ]]> https://biorxiv.org/content/10.1101/2023.11.06.565909v1?rss=1 Yi, X. Wang, D. Reid, K. Feng, X. Löytynoja, A. Merilä, J. 2023-11-08 doi:10.1101/2023.11.06.565909 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Combinatorial in silico approach for cancer-associated 4Fe-4S protein discovery ]]> https://biorxiv.org/content/10.1101/2023.11.08.566327v1?rss=1 Tam, W. W. L. Cheng, M. H. W. Mo, X. He, B.-B. Ngo, U. F. M. Yuen, N. M. H. Yau, A. Y. L. Wu, N. C. Tse, E. C. M. 2023-11-13 doi:10.1101/2023.11.08.566327 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Genome folding principles revealed in condensin-depleted mitotic chromosomes ]]> https://biorxiv.org/content/10.1101/2023.11.09.566494v1?rss=1 Zhao, H. Lin, Y. Lin, E. Liu, F. Shu, L. Jing, D. Wang, B. Wang, M. Shan, F. Zhang, L. Lam, J. Midla, S. Giardine, B. Keller, C. Hardison, R. Blobel, G. Zhang, H. 2023-11-13 doi:10.1101/2023.11.09.566494 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Amplification of avian influenza viruses along poultry marketing chains in Bangladesh: a controlled field experiment ]]> https://biorxiv.org/content/10.1101/2023.11.10.566573v1?rss=1 Kohnle, L. Das, T. Uddin, M. H. Nath, S. C. Mohsin, M. A. S. Mahmud, R. Biswas, P. K. Hoque, M. A. Pfeiffer, D. U. Fournie, G. 2023-11-13 doi:10.1101/2023.11.10.566573 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Ocean acidification alters the transcriptomic response in the nervous system of Aplysia californica during reflex behaviour ]]> https://biorxiv.org/content/10.1101/2023.11.14.567130v1?rss=1 SOURISSE, J. M. Schunter, C. 2023-11-16 doi:10.1101/2023.11.14.567130 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Cross-talk between tissues is critical for intergenerational acclimation to environmental change ]]> https://biorxiv.org/content/10.1101/2023.11.15.567297v1?rss=1 Suresh, S. Welch, M. J. Munday, P. L. Ravasi, T. Schunter, C. 2023-11-17 doi:10.1101/2023.11.15.567297 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ NeuroVelo: interpretable learning of cellular dynamics from single-cell transcriptomic data ]]> https://biorxiv.org/content/10.1101/2023.11.17.567500v1?rss=1 Kouadri Boudjelthia, I. Milite, S. El Kazwini, N. Fernandez-Mateos, J. Valeri, N. Huang, Y. Sottoriva, A. Sanguinetti, G. 2023-11-17 doi:10.1101/2023.11.17.567500 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Quantitative cell morphology in C. elegans embryos reveals regulations of cell volume asymmetry ]]> https://biorxiv.org/content/10.1101/2023.11.20.567849v1?rss=1 View larger version (114K): org.highwire.dtl.DTLVardef@1b7d0fforg.highwire.dtl.DTLVardef@fa28b1org.highwire.dtl.DTLVardef@185a0deorg.highwire.dtl.DTLVardef@478a2_HPS_FORMAT_FIGEXP M_FIG C_FIG Potential Cover/Featured Image: Smiling "ghost" face of C. elegans embryo. Center: shown are skins (colored in red, dorsal view with anterior to the bottom) of a 400-celled C. elegans embryo. Cells not covered by the skins are colored in gray, green, blue, and transparent yellow, respectively. Internal and external circles: confocal fluorescence images (GFP for cell nucleus and mCherry for cell membrane) and reconstructed cell morphologies of the C. elegans embryo from the 2- to 550-cell stages respectively, connected with images of a C. elegans adult expressing the same markers. ]]> Guan, G. Li, Z. Ma, Y. Cao, J. Wong, M.-K. Chan, L.-Y. Yan, H. Tang, C. Zhao, Z. 2023-11-20 doi:10.1101/2023.11.20.567849 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization ]]> https://biorxiv.org/content/10.1101/2023.11.22.567635v1?rss=1 Sun, Q. Zhou, Q. Qiao, Y. Sun, H. Wang, H. 2023-11-23 doi:10.1101/2023.11.22.567635 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Boundary effects cause false signals of range expansions in population genomic data ]]> https://biorxiv.org/content/10.1101/2023.12.06.570483v1?rss=1 Kemppainen, P. Schemberi, R. Momigliano, P. 2023-12-08 doi:10.1101/2023.12.06.570483 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea ]]> https://biorxiv.org/content/10.1101/2023.12.15.571666v1?rss=1 Sahu, B. P. Fazil, M. M. Panda, S. Thiyagarajan, V. 2023-12-15 doi:10.1101/2023.12.15.571666 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ A Dataset for Deep Learning based Cleavage-stage Blastocyst Prediction with Time-lapse Images ]]> https://biorxiv.org/content/10.1101/2023.12.26.573382v1?rss=1 Wang, S. Fan, J. Li, H. Zhao, M. Li, X. Chan, D. Y. L. 2023-12-27 doi:10.1101/2023.12.26.573382 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Structural basis for constitutive activation and CXCL1 recognition of human herpesvirus 8-encoded G protein-coupled receptor KSHV-GPCR ]]> https://biorxiv.org/content/10.1101/2023.12.27.573477v1?rss=1 Liu, A. Liu, Y. Llinas del Torrent Masachs, C. Zhang, W. Pardo, L. Ye, R. D. 2023-12-28 doi:10.1101/2023.12.27.573477 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Auditory training alters the cortical representation of both learned and task irrelevant sound features ]]> https://biorxiv.org/content/10.1101/2023.12.29.573645v1?rss=1 Atilgan, H. Walker, K. M. M. King, A. J. Schnupp, J. Bizley, J. K. 2023-12-30 doi:10.1101/2023.12.29.573645 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ Skeletal Muscle Stem Cells Modulate Niche Function in Duchenne Muscular Dystrophy through YY1-CCL5 Axis ]]> https://biorxiv.org/content/10.1101/2024.01.13.575317v1?rss=1 Li, Y. Li, C. Sun, Q. Chen, F. Cheung, Y. Zhao, Y. Xie, T. Chazaud, B. Sun, H. Wang, H. 2024-01-14 doi:10.1101/2024.01.13.575317 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Tmc7 deficiency causes acrosome biogenesis defects and male infertility in mice ]]> https://biorxiv.org/content/10.1101/2024.01.18.576276v1?rss=1 Wang, J. Yin, Y. Yang, L. Qin, J. Wang, Z. Qiu, C. Gao, Y. Lu, G. Gao, F. Chen, Z.-J. Zhang, X. Liu, H. Liu, Z. 2024-01-22 doi:10.1101/2024.01.18.576276 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Superagers resist typical age-related white matter structural changes ]]> https://biorxiv.org/content/10.1101/2024.01.25.577227v1?rss=1 Garo-Pascual, M. Zhang, L. Valenti-Soler, M. Strange, B. 2024-01-26 doi:10.1101/2024.01.25.577227 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Cell Type Specific Responses of the Endoplasmic Reticulum Dynamics to Environmental Stress ]]> https://biorxiv.org/content/10.1101/2024.01.23.576814v1?rss=1 Zhang, Y. Liu, J. Sun, Z. Guo, J. Yuan, J. Xue, Y. Qiu, T. Wang, P. Yin, B. Yang, H. Zhai, L. Han, H. Li, X. 2024-01-27 doi:10.1101/2024.01.23.576814 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Structural insights into agonist binding and activation of succinate receptor 1 ]]> https://biorxiv.org/content/10.1101/2024.02.03.578529v1?rss=1 Liu, A. Liu, Y. Zhang, W. Ye, R. 2024-02-03 doi:10.1101/2024.02.03.578529 Cold Spring Harbor Laboratory Press 2024-02-03 <![CDATA[ Dating ammonia-oxidizing bacteria with abundant eukaryotic fossils ]]> https://biorxiv.org/content/10.1101/2024.02.23.581699v1?rss=1 Liao, T. Wang, S. Zhang, H. Eva, S. Luo, H. 2024-02-23 doi:10.1101/2024.02.23.581699 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Interleaved intersectional strategy enables genetic lineage tracing with enhanced specificity ]]> https://biorxiv.org/content/10.1101/2024.03.06.583635v1?rss=1 han, m. liu, z. huang, x. liu, l. zhou, b. Lui, K. shu, q. Zhou, B. 2024-03-11 doi:10.1101/2024.03.06.583635 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Buzz-world: Global patterns and drivers of buzzing bees and poricidal plants ]]> https://biorxiv.org/content/10.1101/2024.03.06.583730v1?rss=1 Russell, A. L. Buchmann, S. L. Ascher, J. S. Wang, Z. Kriebel, R. Jolles, D. D. Orr, M. C. Hughes, A. C. 2024-03-11 doi:10.1101/2024.03.06.583730 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Spatiotemporal regulation of Pseudorabies Virus Thymidine kinase UL23 by post-translational modification ]]> https://biorxiv.org/content/10.1101/2024.03.06.583799v1?rss=1 Li, C. Cao, R. Zhang, R. Tang, J. 2024-03-07 doi:10.1101/2024.03.06.583799 Cold Spring Harbor Laboratory Press 2024-03-07 <![CDATA[ High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains ]]> https://biorxiv.org/content/10.1101/2024.03.08.584176v1?rss=1 Loes, A. N. Tarabi, R. A. L. Huddleston, J. Touyon, L. Wong, S. S. Cheng, S. M. Leung, N. H. Hannon, W. W. Bedford, T. Cobey, S. Cowling, B. J. Bloom, J. D. 2024-03-09 doi:10.1101/2024.03.08.584176 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ Deoxynivalenol induced inflammation and increased the adherence of entero-invasive Escherichia coli to intestinal epithelial cells via modulation of mucin and pro-inflammatory cytokine production ]]> https://biorxiv.org/content/10.1101/2024.03.11.584405v1?rss=1 Wan, M. L. Co, V. A. Turner, P. C. Nagendra, S. P. El-Nezami, H. 2024-03-13 doi:10.1101/2024.03.11.584405 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ SLRfinder: a method to detect candidate sex-linked regions with linkage disequilibrium clustering ]]> https://biorxiv.org/content/10.1101/2024.03.11.584532v1?rss=1 Yi, X. Kemppainen, P. Merila, J. 2024-03-14 doi:10.1101/2024.03.11.584532 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ A hemagglutinin and neuraminidase biased immunological memory shapes the dynamics of antibody responses to Influenza A virus ]]> https://biorxiv.org/content/10.1101/2024.03.14.584765v1?rss=1 Lin, X. Wang, J. Ling, S. Xiao, C. Liang, Z. Chow, C. L. Yang, B. Xiao, B. Cowling, B. J. Webby, R. J. Zanin, M. Wong, S.-S. 2024-03-15 doi:10.1101/2024.03.14.584765 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ The somatic mutation landscape of normal gastric epithelium ]]> https://biorxiv.org/content/10.1101/2024.03.17.585238v1?rss=1 Coorens, T. H. H. Collord, G. Jung, H. Wang, Y. Moore, L. Hooks, Y. Mahbubani, K. Saeb-Parsy, K. Campbell, P. J. Martincorena, I. Leung, S. Y. Stratton, M. R. 2024-03-19 doi:10.1101/2024.03.17.585238 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ ΔNp63-restricted viral mimicry response impedes cancer cell viability and remodels tumor microenvironment in esophageal squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2024.03.17.585449v1?rss=1 Yu, V. Z. So, S. S. Lung, B. C.-c. Hou, G. Z. Wong, C. W.-y. Chow, L. K.-y. Chung, M. K.-y. Wong, I. Y.-h. Wong, C. L.-y. Chan, D. K.-k. Chan, F. S.-y. Law, B. T.-t. Xu, K. Tan, Z. Z. Lam, K.-o. Lo, A. W.-i. Lam, A. K.-y. Kwong, D. L.-w. Ko, J. M.-y. Dai, W. Law, S. Lung, M. L. 2024-03-19 doi:10.1101/2024.03.17.585449 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ SARS-CoV-2 infection activates inflammatory macrophages in vascular immune organoids ]]> https://biorxiv.org/content/10.1101/2024.03.20.585837v1?rss=1 Chau, C. W. To, A. Au-Yeung, R. K. H. Tang, K. Xiang, Y. Ruan, D. Zhang, L. Wong, H. Zhang, S. Au, M. T. Chung, S. Song, E. Choi, D.-H. Liu, P. Yuan, S. Wen, C. Sugimura, R. 2024-03-21 doi:10.1101/2024.03.20.585837 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ BRD8 guards the pluripotent state by sensing and maintaining histone acetylation ]]> https://biorxiv.org/content/10.1101/2024.03.20.585857v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@199139forg.highwire.dtl.DTLVardef@d735c6org.highwire.dtl.DTLVardef@10b6e15org.highwire.dtl.DTLVardef@16863cf_HPS_FORMAT_FIGEXP M_FIG C_FIG Key findingsO_LIBRD8 blocks the primed-to-naive transition. C_LIO_LIReduced Brd8 promoted the suppression of somatic and primed genes through reduced chromatin repression. C_LIO_LIReduced Brd8 enabled the accelerated activation of naive-specific genes by opening chromatin. C_LIO_LIBRD8 anchors the histone acetyltransferase KAT5 to acetylated genomic loci. C_LI ]]> Sun, L. Fu, X. Xiao, Z. Ma, G. Zhou, Y. Hu, H. Shi, L. Li, D. Jauch, R. Hutchins, A. 2024-03-20 doi:10.1101/2024.03.20.585857 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Novel assay for endangered Hong Kong grouper (Epinephelus akaara) to assess eDNA shedding, decay, and population status ]]> https://biorxiv.org/content/10.1101/2024.03.21.585953v1?rss=1 Chung, A. Kam, Y. C. Schunter, C. 2024-03-26 doi:10.1101/2024.03.21.585953 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ Paraneoplastic renal dysfunction in fly cancer models driven by inflammatory activation of stem cells ]]> https://biorxiv.org/content/10.1101/2024.03.21.586173v1?rss=1 Kwok, S. H. Liu, Y. Bilder, D. Kim, J. 2024-03-25 doi:10.1101/2024.03.21.586173 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Beyond enumeration: Phenotype independent "labeling-capture-release" process enabling precise detection of circulating tumour cells and downstream applications ]]> https://biorxiv.org/content/10.1101/2024.03.27.586941v1?rss=1 Lao, Z. Ren, X. Zhuang, D. Xie, L. Zhang, Y. Li, W. Jiang, Z. Chen, Y. Li, P. Tong, L. Chu, P. K. Wang, H. 2024-03-30 doi:10.1101/2024.03.27.586941 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ A Robust Statistical Approach for Finding Informative Spatially Associated Pathways ]]> https://biorxiv.org/content/10.1101/2024.03.31.587469v1?rss=1 Tian, L. Xiao, J. Yu, T. 2024-04-01 doi:10.1101/2024.03.31.587469 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Mechano-regulation of GLP-1 production by Piezo1 in intestinal L cells ]]> https://biorxiv.org/content/10.1101/2024.04.01.587569v1?rss=1 Huang, Y. Mo, H. Yang, J. Gao, L. Tao, T. Shu, Q. Guo, W. Zhao, Y. Lyu, J. Wang, Q. Guo, J. Zhai, H. Zhu, L. Chen, H. Xu, G. 2024-04-02 doi:10.1101/2024.04.01.587569 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Combination of oncolytic Maraba virus with immune checkpoint blockade overcomes therapy resistance in an immunologically cold model of advanced melanoma with dysfunctional T cell receptor signalling. ]]> https://biorxiv.org/content/10.1101/2024.04.02.587705v1?rss=1 Armstrong, E. Chiu, M. K. L. Foo, S. Appleton, L. Nenclares, P. Patrikeev, A. Mohan, N. McLaughlin, M. Bozhanova, G. Hoebart, J. Roulstone, V. Patin, E. C. Pedersen, M. Kyula, J. Errington-Mais, F. Bell, J. C. Harrington, K. J. Melcher, A. A. Jennings, V. A. 2024-04-03 doi:10.1101/2024.04.02.587705 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Divergent lineage trajectories and genetic landscapes in human gastric intestinal metaplasia organoids associated with early neoplastic progression ]]> https://biorxiv.org/content/10.1101/2024.04.03.588024v1?rss=1 Yue, S. S. Tong, Y. Siu, H. C. Ho, S. L. Law, S. Y. Tsui, W. Y. Chan, D. Huang, Y. Chan, A. S. Yun, S. W. Hui, H. S. Chan, A. S. Yuen, S. T. Clevers, H. Leung, S. Y. Yan, H. H. 2024-04-05 doi:10.1101/2024.04.03.588024 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Leveraging cross-source heterogeneity to improve the performance of bulk gene expression deconvolution ]]> https://biorxiv.org/content/10.1101/2024.04.07.588458v1?rss=1 Shen, W. Liu, C. Hu, Y. Lei, Y. Wong, H.-S. Wu, S. Zhou, X. M. 2024-04-09 doi:10.1101/2024.04.07.588458 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease ]]> https://biorxiv.org/content/10.1101/2024.04.07.588491v1?rss=1 Wu, W.-C. Pan, Y.-F. Zhou, W.-D. Liao, Y.-Q. Peng, M.-W. Luo, G.-Y. Xin, G.-Y. Peng, Y.-N. An, T. Li, B. Luo, H. Barrs, V. R. Beatty, J. A. Holmes, E. C. Zhao, W. Shu, Y. 2024-04-08 doi:10.1101/2024.04.07.588491 Cold Spring Harbor Laboratory Press 2024-04-08 <![CDATA[ Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor ]]> https://biorxiv.org/content/10.1101/2024.04.08.588650v1?rss=1 Hong Kong Biodiversity Genomics Consortium, Hui, J. H. L. Chan, T.-F. Chan, L. Cheung, S. G. Cheang, C. C. Fang, J. Gaitan-Espitia, J. D. Lau, S. Sung, Y. H. Wong, C. Yip, K. Wei, Y. So, W. L. Nong, W. law, s. Rose-Jeffreys, L. Crow, P. Leong, A. Yip, H. 2024-04-11 doi:10.1101/2024.04.08.588650 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Human cytomegalovirus extensively re-organizes the human genome, diminishing TEAD1 transcription factor activity ]]> https://biorxiv.org/content/10.1101/2024.04.12.588762v1?rss=1 Sayeed, K. Parameswaran, S. Beucler, M. J. Edsall, L. E. VonHandorf, A. Crowther, A. Donmez, O. A. Hass, M. R. Richards, S. Forney, C. R. Wright, J. Leong, M. M. Murray-Nerger, L. A. Gewurz, B. E. Kaufman, K. M. Harley, J. B. Zhao, B. Miller, W. E. Kottyan, L. C. Weirauch, M. T. 2024-04-13 doi:10.1101/2024.04.12.588762 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ InstructPLM: Aligning Protein Language Models to Follow Protein Structure Instructions ]]> https://biorxiv.org/content/10.1101/2024.04.17.589642v1?rss=1 Qiu, J. Xu, J. Hu, J. Cao, H. Hou, L. Gao, Z. Zhou, X. Li, A. Li, X. Cui, B. Yang, F. Peng, S. Sun, N. Wang, F. Pan, A. Tang, J. Ye, J. Lin, J. Tang, J. Huang, X. Heng, P. A. Chen, G. 2024-04-20 doi:10.1101/2024.04.17.589642 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Cleaner gobies can solve a biological market task when the correct cue is larger ]]> https://biorxiv.org/content/10.1101/2024.04.17.589842v1?rss=1 Ranucci, M. Court, M. Pereira, B. P. Romeo, D. Paula, J. R. 2024-04-21 doi:10.1101/2024.04.17.589842 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Differential antigenic imprinting effects between influenza H1N1 hemagglutinin and neuraminidase in a mouse model ]]> https://biorxiv.org/content/10.1101/2024.04.17.589918v1?rss=1 Lv, H. Teo, Q. W. Lee, C.-C. D. Liang, W. Choi, D. Mao, K. J. Bruzzone, R. Wilson, I. A. Wu, N. C. Mok, C. K. 2024-04-22 doi:10.1101/2024.04.17.589918 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Purifying selection and intraspecies recombination may drive the speciation in Crassostrea: evidence from complete mitochondria sequence of Crassostrea hongkongensis and comparative genomic analysis ]]> https://biorxiv.org/content/10.1101/2024.04.17.589994v1?rss=1 Sahu, B. P. Fazil, M. M. Panda, S. Thiyagarajan, V. 2024-04-20 doi:10.1101/2024.04.17.589994 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ scCaT: an explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2024.04.17.590014v1?rss=1 Zheng, X. Meng, D. Chen, D. Wong, W.-K. To, K.-H. Zhu, L. Wu, J. Liang, Y. Leung, K.-S. Wong, M.-H. Cheng, L. 2024-04-20 doi:10.1101/2024.04.17.590014 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ RiboDiffusion: Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models ]]> https://biorxiv.org/content/10.1101/2024.04.18.590187v1?rss=1 Huang, H. Lin, Z. He, D. Hong, L. Li, Y. 2024-04-21 doi:10.1101/2024.04.18.590187 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ The robust, high-throughput, and temporally regulated roxCre and loxCre reporting systems for genetic modifications in vivo ]]> https://biorxiv.org/content/10.1101/2024.04.23.590680v1?rss=1 Shi, M. Li, J. Liu, X. Liu, K. Pu, W. Weng, W. Zhang, S. Zhao, H. Lui, K. Zhou, B. 2024-04-23 doi:10.1101/2024.04.23.590680 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Le Petit Prince Hong Kong (LPPHK): Naturalistic fMRI and EEG data from older Cantonese speakers ]]> https://biorxiv.org/content/10.1101/2024.04.24.590842v1?rss=1 Momenian, M. Ma, Z. Wu, S. Wang, C. Brennan, J. Hale, J. Meyer, L. Li, J. 2024-04-28 doi:10.1101/2024.04.24.590842 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Chromosomal-level genome of fish mint Houttuynia cordata Thunb. (Saururaceae) ]]> https://biorxiv.org/content/10.1101/2024.04.25.590851v1?rss=1 Law, S. T. S. Nong, W. Tsang, S. S. K. Lau, D. T. W. Shaw, P. C. Hui, J. H. L. 2024-04-30 doi:10.1101/2024.04.25.590851 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Genome of tropical bed bug Cimex hemipterus (Cimicidae, Hemiptera) reveals tetraspanin expanded in bed bug ancestor ]]> https://biorxiv.org/content/10.1101/2024.04.25.591052v1?rss=1 Law, S. T. S. Nong, W. Li, C. Chong, T. K. Yip, H. Y. Swale, T. Chiu, S. W. Chung, R. Y.-N. Lam, H.-M. Wong, S. Y. S. Wong, H. Hui, J. H. L. 2024-04-28 doi:10.1101/2024.04.25.591052 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ An ingestible, battery-free, tissue-adhering robotic interface for non-invasive and chronic electrostimulation of the gut ]]> https://biorxiv.org/content/10.1101/2024.04.25.591220v1?rss=1 Nan, K. Wong, K. Li, D. Ying, B. McRae, J. C. Feig, V. R. Wang, S. Yao, K. Zhou, J. Li, J. Jenkins, J. Ishida, K. Kuosmanen, J. Madani, W. Hayward, A. Ramadi, K. Yu, X. Traverso, G. 2024-04-28 doi:10.1101/2024.04.25.591220 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ siRNADesign: A Graph Neural Network for siRNA Efficacy Prediction via Deep RNA Sequence Analysis ]]> https://biorxiv.org/content/10.1101/2024.04.28.591509v1?rss=1 Long, R. Guo, Z. Han, D. Yuan, X. Chen, G. Heng, P. A. Zhang, L. 2024-04-30 doi:10.1101/2024.04.28.591509 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Response of protein coding genes and microRNAs to temperature changes in four insect species ]]> https://biorxiv.org/content/10.1101/2024.04.28.591511v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1037b18org.highwire.dtl.DTLVardef@18683f3org.highwire.dtl.DTLVardef@40dee5org.highwire.dtl.DTLVardef@e9a108_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tsang, S. S. K. Nong, W. Xie, Y. Qu, Z. Yip, H. Y. Gaitan-Espitia, J. D. Tai, A. P. K. Yeung, Y. Y. Tobe, S. S. Bendena, W. G. Hui, J. H. L. 2024-04-28 doi:10.1101/2024.04.28.591511 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Distinct neural computations scale the violation of expected reward and emotion in social transgressions ]]> https://biorxiv.org/content/10.1101/2024.04.29.591585v1?rss=1 Xu, T. Zhang, L. Zhou, F. Fu, K. Gan, X. Chen, Z. Zhang, R. Lan, C. Wang, L. Kendrick, K. K. Yao, D. Becker, B. 2024-04-30 doi:10.1101/2024.04.29.591585 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ MBL-1/Muscleblind regulates neuronal differentiation and controls the splicing of a terminal selector in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.04.29.591598v1?rss=1 Lee, H. M. T. Lim, H. Y. He, H. Lau, C. Y. Zheng, C. 2024-04-30 doi:10.1101/2024.04.29.591598 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Dynamical Responses Predict a Distal Site that Modulates Activity in an Antibiotic Resistance Enzyme ]]> https://biorxiv.org/content/10.1101/2024.04.29.591639v1?rss=1 Beer, M. Oliveira, A. S. F. Tooke, C. L. Hinchliffe, P. Li, A. T. Y. Balega, B. Spencer, J. Mulholland, A. J. 2024-04-29 doi:10.1101/2024.04.29.591639 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Functional selection in SH3-mediated activation of the PI3 kinase ]]> https://biorxiv.org/content/10.1101/2024.04.30.591319v1?rss=1 Aljedani, S. S. Aldehaiman, A. Sandholu, A. Alharb, S. Mak, V. C. Y. Wu, H. Lugari, A. Jaremko, M. Morelli, X. Backer, J. Ladbury, J. E. Nowakowski, M. Cheung, L. W. T. Arold, S. T. 2024-04-30 doi:10.1101/2024.04.30.591319 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ The global fish and invertebrate abundance value of mangroves ]]> https://biorxiv.org/content/10.1101/2024.05.02.591889v1?rss=1 zu Ermgassen, P. Worthington, T. A. Gair, J. R. Garnett, E. E. Mukherjee, N. Longley-Wood, K. Nagelkerken, I. Abrantes, K. Aburto-Oropeza, O. Acosta, A. Araujo, A. R. d. R. Baker, R. Barnett, A. Beitl, C. M. Benzeev, R. Brookes, J. Castellanos-Galindo, G. A. Ching Chong, V. Connolly, R. M. Cunha-Lignon, M. Dahdouh-Guebas, F. Diele, K. Dwyer, P. G. Friess, D. A. Grove, T. Hoq, M. E. Huijbers, C. Hutchinson, N. Johnson, A. F. Johnson, R. Knight, J. Krumme, U. Kuguru, B. Lee, S. Y. Lobo, A. S. Lugendo, B. R. Meynecke, J.-O. Nzaka Munga, C. Olds, A. D. Parret 2024-05-05 doi:10.1101/2024.05.02.591889 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Genomes of two indigenous clams Anomalocardia flexuosa (Linnaeus, 1767) and Meretrix petechialis (Lamarck, 1818) ]]> https://biorxiv.org/content/10.1101/2024.05.03.592324v1?rss=1 law, S. T. S. Nong, W. Au, M. F. F. Cheung, L. H. T. Shum, C. W. Y. Lee, S. Y. Cheung, S. G. Hui, J. H. L. 2024-05-05 doi:10.1101/2024.05.03.592324 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage ]]> https://biorxiv.org/content/10.1101/2024.05.06.590709v1?rss=1 Clavel, M. Bianchi, A. Kobylinska, R. Groh, R. Ma, J. Papareddy, R. K. Grujic, N. Picchianti, L. Stewart, E. Schutzbier, M. Stejskal, K. de la Concepcion, J. C. Hernandez, V. S. d. M. Voichek, Y. Clauw, P. Gunis, J. Durnberger, G. Muelders, J. C. Grimm, A. Sedivy, A. Erhardt, M. Vyboishchikov, V. Gao, P. Lechner, E. Vantard, E. Jez, J. Roitinger, E. Genschik, P. Kang, B.-H. Dagdas, Y. 2024-05-06 doi:10.1101/2024.05.06.590709 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Functional and multi-omic aging rejuvenation with GLP-1R agonism ]]> https://biorxiv.org/content/10.1101/2024.05.06.592653v1?rss=1 Huang, J. Kwok, A. J. Li, J. C. Y. Chiu, C. L. H. Ip, B. Y. M. Tung, L. Y. Zheng, X. Chow, H. T. Lo, M. P. S. Li, Z. Chan, R. C. H. Lin, N. Wang, Z. Wang, M. Yan, L. Y. C. Chan, D. C. W. Wu, W. K. K. Chow, H.-M. Lin, W.-J. Tang, Y. Ng, B. W.-L. Wong, S. H. Leung, T. W. Mok, V. C. T. Ko, H. 2024-05-08 doi:10.1101/2024.05.06.592653 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Metagenomic coverage bias at transcription start sites is correlated with gene expression ]]> https://biorxiv.org/content/10.1101/2024.05.09.593333v1?rss=1 Qian, G. Coleman, I. Korem, T. Ho, J. W. K. 2024-05-13 doi:10.1101/2024.05.09.593333 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ LucaOne: Generalized Biological Foundation Model with Unified Nucleic Acid and Protein Language ]]> https://biorxiv.org/content/10.1101/2024.05.10.592927v1?rss=1 He, Y. Fang, P. Shan, Y. Pan, Y. Wei, Y. Chen, Y. Chen, Y. Liu, Y. Zeng, Z. Zhou, Z. Zhu, F. Holmes, E. C. Ye, J. Li, J. Shu, Y. Shi, M. Li, Z. 2024-05-14 doi:10.1101/2024.05.10.592927 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Giraffe: a tool for comprehensive processing andvisualization of multiple long-read sequencing data ]]> https://biorxiv.org/content/10.1101/2024.05.10.593289v1?rss=1 Liu, X. Shao, Y. Guo, Z. Ni, Y. Sun, X. Leung, Y. H. A. Li, R. 2024-05-14 doi:10.1101/2024.05.10.593289 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ "What" and "when" predictions jointly modulate speech processing ]]> https://biorxiv.org/content/10.1101/2024.05.10.593519v1?rss=1 Auksztulewicz, R. Ödül, O. B. Helbling, S. Böke, A. Cappotto, D. Luo, D. Schnupp, J. Melloni, L. 2024-05-10 doi:10.1101/2024.05.10.593519 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Combination of bortezomib and venetoclax targets the pro-survival function of LMP-1 and EBNA-3C of Epstein-Barr virus in post-transplant lymphoproliferative disorder ]]> https://biorxiv.org/content/10.1101/2024.05.13.593820v1?rss=1 Tam, K. P. Xie, J. Au-Yeung, R. K. H. Chiang, A. K. S. 2024-05-13 doi:10.1101/2024.05.13.593820 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Persistent lung inflammation and alveolar-bronchiolization due to Notch signaling dysregulation in SARS-CoV-2 infected hamster ]]> https://biorxiv.org/content/10.1101/2024.05.13.593878v1?rss=1 Li, C. Xiao, N. Song, W. Lam, A. H.-C. Liu, F. Cui, X. Ye, Z. Chen, Y. Ren, P. Cai, J. Lee, A. C.-Y. Chen, H. Ou, Z. Chan, J. F.-W. Yuen, K.-Y. Chu, H. Zhang, A. J.-X. 2024-05-13 doi:10.1101/2024.05.13.593878 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure ]]> https://biorxiv.org/content/10.1101/2024.05.14.594047v1?rss=1 zhan, x. Deng, l. Lian, Y. Shu, Z. Xu, Y. Mai, X. Krishna, M. S. Xiong, C. Lu, R. Wang, A. Bai, S. Xu, Y. Ni, J. Vandana, J. Wang, Z. Li, Y. Sun, D. Huang, S. Liu, J. Cheng, G. Wu, S. Chiang, C.-C. Stjepanovic, G. Jiang, C. Shao, Y. Chen, G. 2024-05-14 doi:10.1101/2024.05.14.594047 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Recognition of RNA secondary structures with a programmable peptide nucleic acid-based platform ]]> https://biorxiv.org/content/10.1101/2024.05.14.594238v1?rss=1 Lu, R. Deng, L. Lian, Y. Ke, X. Yang, L. Xi, K. Ong, A. A. L. Chen, Y. Zhou, H. Meng, Z. Lin, R. Fan, S. Liu, Y. Toh, D.-F. K. Zhan, X. S. Krishna, M. M. Patil, K. Lu, Y. Liu, Z. Zhu, L. Wang, H. Li, G. Chen, G. 2024-05-15 doi:10.1101/2024.05.14.594238 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Connection Building Method: High-Accuracy MicroRNA Target Prediction Using Disease Semantic Strings ]]> https://biorxiv.org/content/10.1101/2024.05.17.594604v1?rss=1 Chen, B. Huang, H.-Y. 2024-05-17 doi:10.1101/2024.05.17.594604 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Millennial-scale societal shifts drive the widespread loss of a marine ecosystem ]]> https://biorxiv.org/content/10.1101/2024.05.19.594609v1?rss=1 750 km of coastline in the Pearl River Delta, and their exploitation underpinned the regions development into Chinas first economic hub in the 6th century. Millennial-scale overexploitation alongside societal shifts were central in their regional extirpation by the 19th century, but the enduring cultural importance of oysters is maintained by aquaculture expansion. Informed conservation practices can be developed from reconstructing the temporal interplay between human societies and the natural environment. ]]> Lau, S. C. Y. Thomas, M. Williams, J. M. Thurstan, R. H. Hancock, B. Russell, B. D. 2024-05-20 doi:10.1101/2024.05.19.594609 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Signatures of social pain empathy: general and process-specific brain-wide representations of social exclusion and separation ]]> https://biorxiv.org/content/10.1101/2024.05.19.594630v1?rss=1 Zhang, X. Qing, P. Liu, Q. Liu, C. Liu, L. Gan, X. Fu, K. Lan, C. Zhou, X. Kendrick, K. M. Becker, B. Zhao, W. 2024-05-20 doi:10.1101/2024.05.19.594630 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ iResNetDM: Interpretable deep learning approach for four types of DNA modification prediction ]]> https://biorxiv.org/content/10.1101/2024.05.19.594892v1?rss=1 Yang, Z. Shao, W. Matsuda, Y. Song, L. 2024-05-21 doi:10.1101/2024.05.19.594892 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ AptaGPT: Advancing aptamer design with a generative pre-trained language model ]]> https://biorxiv.org/content/10.1101/2024.05.23.594910v1?rss=1 Ding, S. Yang, X. Chan, C. H. Ma, Y. Yu, S. Wang, L. Lyu, A. Zhang, B. Yu, Y. Zhang, G. 2024-05-28 doi:10.1101/2024.05.23.594910 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage ]]> https://biorxiv.org/content/10.1101/2024.05.28.596239v1?rss=1 Lanclos, V. C. Feng, X. Cheng, C. Yang, M. Hider, C. J. Coelho, J. T. Kojima, C. Y. Barnes, S. J. Cleveland, C. Xie, M. Zhao, Y. Luo, H. Thrash, J. C. 2024-05-28 doi:10.1101/2024.05.28.596239 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ PITPβ promotes COPI vesicle fission through lipid transfer and membrane contact formation ]]> https://biorxiv.org/content/10.1101/2024.05.27.596058v1?rss=1 Park, K. Ju, S. Choi, H. Gao, P. Bang, G. Choi, J. H. Jang, J. Morris, A. Kang, B.-H. Hsu, V. W. Park, S.-Y. 2024-05-29 doi:10.1101/2024.05.27.596058 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ INSIHGT: Accessible multimodal systems biology with quantitative molecular phenotyping in 3D ]]> https://biorxiv.org/content/10.1101/2024.05.24.595771v1?rss=1 Yau, C. N. Hung, J. T. S. Wong, T. C. Y. Huang, B. Wong, B. T. Y. Chow, N. K. N. Tsoi, E. P. L. Tan, Y. Li, J. J. X. Wing, Y. K. Lai, H. M. 2024-05-30 doi:10.1101/2024.05.24.595771 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Mechanism of RSL3-Induced Ferroptotic Cell Death in HT22 Cells: Contributing Role of Protein Disulfide Isomerase ]]> https://biorxiv.org/content/10.1101/2024.05.27.596002v1?rss=1 Hou, M.-J. Huang, X. Zhu, B. T. 2024-05-30 doi:10.1101/2024.05.27.596002 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Emergence of a dynamical state of coherent bursting with power-law distributed avalanches from collective stochastic dynamics of adaptive neurons ]]> https://biorxiv.org/content/10.1101/2024.05.28.596196v1?rss=1 Ching, E. S. C. Chan, L.-C. Kok, T.-F. 2024-06-01 doi:10.1101/2024.05.28.596196 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Femtosecond X-ray snapshots reveal correlated displacements of specific distal atoms in a protein crystal ]]> https://biorxiv.org/content/10.1101/2024.05.29.596429v1?rss=1 Gagner, V. A. Jensen, M. Olsson, T. N. Sanchez, J. C. Bengtsson, A. U. J. Ekström, J. C. Zhang, Z. Jurgilaitis, A. Kroon, D. Pham, V.-T. Checchia, S. Coudert-Alteirac, H. Rodilla, H. Stake, J. Zhaunerchyk, V. Friedman, R. Larsson, J. Mezzasalma, S. A. Katona, G. 2024-06-02 doi:10.1101/2024.05.29.596429 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Hepatic Macrophage Migration Inhibitory Factor Promotes Pancreatic Cancer Liver Metastasis in NAFLD ]]> https://biorxiv.org/content/10.1101/2024.06.02.595997v1?rss=1 YU, Q. Song, H. Zhu, L. Shi, X.-y. Wang, H.-z. Wang, Y.-l. Gong, R.-n. Cui, J.-f. Yang, X.-n. Wang, J.-g. Liang, Y. Chen, Y. Dong, X.-w. Lu, G.-t. Li, C. Zhang, H. Tian, Y.-t. Hu, H.-t. Shao, X.-x. Hu, Y.-b. Saluja, A. K. Li, Y. Mo, M.-g. Ren, H. 2024-06-03 doi:10.1101/2024.06.02.595997 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Parental thermal conditions affect the brain activity response to alarm cue in larval zebrafish ]]> https://biorxiv.org/content/10.1101/2024.06.02.597016v1?rss=1 Sourisse, J. M. Semmelhack, J. Schunter, C. 2024-06-03 doi:10.1101/2024.06.02.597016 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ P-cadherin mechanoactivates tumor- mesothelium metabolic coupling to promote ovarian cancer metastasis ]]> https://biorxiv.org/content/10.1101/2024.06.02.597059v1?rss=1 Ma, J. To, S. K. Y. Fung, K. S. W. Wang, K. Zhang, J. Ngan, A. H. W. Yung, S. Chan, T.-M. Wong, C. C. L. Ip, P. P. C. Peng, L. Guo, H.-Y. Chan, C. B. Wong, A. S. T. 2024-06-03 doi:10.1101/2024.06.02.597059 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Prioritising Functionally Distinct and Globally Endangered (FuDGE) sharks for conservation action ]]> https://biorxiv.org/content/10.1101/2024.06.05.597292v1?rss=1 Webster, C. Barker, J. Curnick, D. Gollock, M. Hansford, J. Hoffmann, M. Pettorelli, N. Turvey, S. T. Walkden, P. A. Wang, J. Rosindell, J. Gumbs, R. 2024-06-06 doi:10.1101/2024.06.05.597292 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Potent and broadly neutralizing antibodies against sarbecoviruses elicited by single ancestral SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2024.06.06.597720v1?rss=1 Yu, L. Wang, Y. Liu, Y. Xing, X. Li, C. Wang, X. Shi, J. Ma, W. Li, J. Chen, Y. Qiao, R. ZHAO, X. Gao, M. Wen, S. Xue, Y. Guan, Y. Chu, H. Sun, L. Wang, P. 2024-06-07 doi:10.1101/2024.06.06.597720 Cold Spring Harbor Laboratory Press 2024-06-07 <![CDATA[ Fast and Tuning-free Nonlinear Data Embedding and Integration based on DCOL ]]> https://biorxiv.org/content/10.1101/2024.06.06.597744v1?rss=1 Liu, S. Yu, T. 2024-06-09 doi:10.1101/2024.06.06.597744 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Bola-amphiphilic dendrimer empowers imatinib to target metastatic ovarian cancer stem cells via beta-catenin-HRP2 signaling axis ]]> https://biorxiv.org/content/10.1101/2024.06.07.597857v1?rss=1 Shi, Z. Artemenko, M. Zhang, M. Yi, C. Chen, P. Lin, S. Bian, Z. Lian, B. Meng, F. Chen, J. Roussel, T. Li, Y. Chan, K. K. L. Ip, P. P. C. Lai, H.-C. Liu, X. Peng, L. Wong, A. S.-T. 2024-06-09 doi:10.1101/2024.06.07.597857 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Adaptation-induced oscillatory phototaxis and emergence of ordered density bands in the microswimmer Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2024.06.09.598154v1?rss=1 Wang, Z. Tsang, A. C. H. 2024-06-10 doi:10.1101/2024.06.09.598154 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Microglia replacement effectively attenuates the disease progress of ALSP in the mouse model and human patient ]]> https://biorxiv.org/content/10.1101/2024.06.11.598496v1?rss=1 Wu, J. Wang, Y. Li, X. Cai, Y. Ouyang, P. He, Y. Zhang, M. Luan, X. Jin, Y. Liu, T. Li, Y. Huang, X. Mao, Y. Rao, Y. Cao, L. Peng, B. 2024-06-11 doi:10.1101/2024.06.11.598496 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Neural Mechanisms of Mutualistic Fish Cleaning Behaviour: a Study in the Wild ]]> https://biorxiv.org/content/10.1101/2024.06.12.598765v1?rss=1 Romeo, D. Ramirez-Calero, S. Ravasi, T. Rodolfo-Metalpa, R. Schunter, C. 2024-06-13 doi:10.1101/2024.06.12.598765 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Aerial litter mimicry: a novel form of floral deception mediated by a monoterpene synthase ]]> https://biorxiv.org/content/10.1101/2024.06.12.596753v1?rss=1 Liu, M.-F. Chen, J. Goodrich, K. R. Chiu, S. K. Pang, C.-C. Scharaschkin, T. Saunders, R. M. K. 2024-06-14 doi:10.1101/2024.06.12.596753 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Cerebrospinal Fluid Dynamics: Uncovering Alternative Blood Vessel Clearance Mechanisms ]]> https://biorxiv.org/content/10.1101/2024.06.13.598807v1?rss=1 Yuan, Q. Satyanarayanan, S. K. Lee, S. M.-Y. Yan, L. Wang, Y. Xian, Y.-F. He, L. Zhou, Y. Wu, W. Song, Y.-Q. Su, H. Lin, Z.-X. Qin, D. 2024-06-14 doi:10.1101/2024.06.13.598807 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Disruption of sustained attention and orbitofrontal cortex engagement by incoming social media messages vary as a function of problematic social media use ]]> https://biorxiv.org/content/10.1101/2024.06.13.598945v1?rss=1 Liu, X. Liu, H. Kendrick, K. M. Montag, C. Becker, B. 2024-06-14 doi:10.1101/2024.06.13.598945 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Sulfur oxidation through rDsr in a novel Sox-free marine Roseobacter lineage ]]> https://biorxiv.org/content/10.1101/2024.06.14.599071v1?rss=1 Lin, X. Feng, X. Wang, X. Long, H. Crowe, S. A. Luo, H. 2024-06-17 doi:10.1101/2024.06.14.599071 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Multiomics mapping and characterization of cellular senescence in aging human muscle uncovers novel senotherapeutics for sarcopenia ]]> https://biorxiv.org/content/10.1101/2024.06.20.599817v1?rss=1 Li, Y. Li, C. Zhou, Q. Liu, X. Qiao, Y. Xie, T. Sun, H. Ong, M. T.-Y. Wang, H. 2024-06-21 doi:10.1101/2024.06.20.599817 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ A genome resource for the marine annelid Platynereis dumerilii ]]> https://biorxiv.org/content/10.1101/2024.06.21.600153v1?rss=1 Mutemi, K. N. Simakov, O. Pan, L. Santangeli, L. Null, R. W. Handberg-Thorsager, M. Vellutini, B. C. Larsson, T. Savage, E. L. Lopez, M. O. Hercog, R. Provaznik, J. Ordonez-Rueda, D. Azevedo, N. Gazave, E. Vervoort, M. Tomancak, P. Tan, W. Winkler, S. Benes, V. Hui, J. Helm, C. Ozpolat, B. D. Arendt, D. 2024-06-23 doi:10.1101/2024.06.21.600153 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ Multi-talker speech comprehension at different temporal scales in listeners with normal and impaired hearing ]]> https://biorxiv.org/content/10.1101/2024.06.20.599315v1?rss=1 Li, J. Wang, Q. Zhou, Q. Yang, L. Shen, Y. Huang, S. Wang, S. Pylkkänen, L. Huang, Z. 2024-06-26 doi:10.1101/2024.06.20.599315 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ Polymerization of Tspan7 into Helical Transmembrane Skeletons for Membrane Tether Stabilization ]]> https://biorxiv.org/content/10.1101/2024.06.27.600806v1?rss=1 Wang, D. Jia, X. Zhang, Q. Xu, K. Zheng, Y. Zhang, Q. Liu, N. Wang, H. Yu, L. 2024-06-29 doi:10.1101/2024.06.27.600806 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Dual roles of idling moments in past and future memories ]]> https://biorxiv.org/content/10.1101/2024.06.27.600961v1?rss=1 Inokuchi, K. Ghandour, K. Haga, T. Ohkawa, N. FUNG, C. C. A. Nomoto, M. Fayed, M. R. Asai, H. Sato, M. Fukai, T. 2024-07-01 doi:10.1101/2024.06.27.600961 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ ADM: Adaptive Graph Diffusion for Meta-Dimension Reduction ]]> https://biorxiv.org/content/10.1101/2024.06.28.601128v1?rss=1 Feng, J. Yong, L. Yu, T. 2024-07-02 doi:10.1101/2024.06.28.601128 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ New soft tissue data of pterosaur tail vane reveals sophisticated, dynamic tensioning usage and expands its evolutionary origins ]]> https://biorxiv.org/content/10.1101/2024.07.01.601487v1?rss=1 Jagielska, N. Kaye, T. G. Habib, M. B. Hirasawa, T. Pittman, M. 2024-07-03 doi:10.1101/2024.07.01.601487 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ An emerging PB2-627 polymorphism increases the pandemic potential of avian influenza virus by breaking through ANP32 host restriction in mammalian and avian hosts ]]> https://biorxiv.org/content/10.1101/2024.07.03.601996v1?rss=1 Guo, Y. Shu, S. Zhou, Y. Peng, W. Jiang, Z. Li, Y. Li, T. Du, F. Wang, L. Chen, X. Dong, J. Zhao, C. Wang, M. H. Sun, Y. Sun, H. Lu, L. Digard, P. Chang, K.-c. Yen, H.-L. Liu, J. Pu, J. 2024-07-04 doi:10.1101/2024.07.03.601996 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Interpretable variational encoding of genotypes identifiescomprehensive clonality and lineages in single cells geometrically ]]> https://biorxiv.org/content/10.1101/2024.07.04.602109v1?rss=1 Chung, H. M. Huang, Y. 2024-07-09 doi:10.1101/2024.07.04.602109 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data ]]> https://biorxiv.org/content/10.1101/2024.07.05.602174v1?rss=1 Hou, R. Huang, Y. 2024-07-09 doi:10.1101/2024.07.05.602174 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ VirID: Beyond Virus Discovery - An Integrated Platform for Comprehensive RNA Virus Characterization ]]> https://biorxiv.org/content/10.1101/2024.07.05.602175v1?rss=1 Yang, Z. Shan, Y. Liu, X. Chen, G. Pan, Y. Gou, Q. Zou, J. Chang, Z. Zeng, Q. Yang, C. Kong, J. Sun, Y. Li, S. Zhang, X. Wu, W. Li, C. Peng, H. Holmes, E. C. Guo, D. Shi, M. 2024-07-09 doi:10.1101/2024.07.05.602175 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ Human microbiome-derived peptide affects the development of experimental autoimmune encephalomyelitis via molecular mimicry ]]> https://biorxiv.org/content/10.1101/2024.07.05.602171v1?rss=1 Ma, X. Zhang, J. Jiang, Q. Li, Y. Yang, G. 2024-07-10 doi:10.1101/2024.07.05.602171 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication ]]> https://biorxiv.org/content/10.1101/2024.07.10.602835v1?rss=1 Yin, X. Pu, Y. Yuan, S. Pache, L. Churas, C. Weston, S. Riva, L. Simons, L. M. Cisneros, W. Clausen, T. de Jesus, P. Kim, H. N. Fuentes, D. Whitelock, J. Esko, J. Lord, M. Mena, I. Garcia-Sastre, A. Hultquist, J. Frieman, M. Ideker, T. Pratt, D. Martin-Sancho, L. Chanda, S. 2024-07-10 doi:10.1101/2024.07.10.602835 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Unveiling Clonal Cell Fate and Differentiation Dynamics: A Hybrid NeuralODE-Gillespie Approach ]]> https://biorxiv.org/content/10.1101/2024.07.08.602444v1?rss=1 Gao, M. Barile, M. Chabra, S. Haltalli, M. Calderbank, E. Chao, Y. Laurenti, E. Gottgens, B. Huang, Y. 2024-07-11 doi:10.1101/2024.07.08.602444 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ ANASFV: a workflow for ASFV whole genome sequencing, assembly, and evaluation ]]> https://biorxiv.org/content/10.1101/2024.07.08.602471v1?rss=1 Li, K. Han, X. Shao, Y. Zhao, X. Johnson, E. W. Li, R. 2024-07-11 doi:10.1101/2024.07.08.602471 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life ]]> https://biorxiv.org/content/10.1101/2024.07.09.602008v1?rss=1 Chantzi, N. Nayak, A. Baltoumas, F. A. Aplakidou, E. Liew, S. W. Galuh, J. E. Patsakis, M. Moeckel, C. Mouratidis, I. Sazed, S. A. Guiblet, W. Montgomery, A. Karmiris-Obratanski, P. Guliang, W. Zaravinos, A. Vasquez, K. M. Kwok, C. K. Pavlopoulos, G. Georgakopoulos-Soares, I. 2024-07-11 doi:10.1101/2024.07.09.602008 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ BOOST: a robust ten-fold expansion method on hour-scale ]]> https://biorxiv.org/content/10.1101/2024.07.11.603043v1?rss=1 Guo, J. Yang, H. Lu, C. Cui, D. Zhao, M. Li, C. Chen, W. Yang, Q. Li, Z. Chen, M. Zhao, S. Zhou, J. He, J. Jiang, H. 2024-07-16 doi:10.1101/2024.07.11.603043 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Muller glia cell cycle re-activation by simultaneous cyclin D1 overexpression and p27kip1 knockdown promotes retinal regeneration in mice ]]> https://biorxiv.org/content/10.1101/2024.07.12.603194v1?rss=1 Wu, Z. Liao, B. Ying, J. Keung, J. Zheng, Z. Ahola, V. Xiong, W. 2024-07-16 doi:10.1101/2024.07.12.603194 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Elucidating the Diversity and Potential Function of Ribosomally Synthesized and Post-translationally Modified Peptides in the Human Microbiome ]]> https://biorxiv.org/content/10.1101/2024.07.16.603675v1?rss=1 ZHANG, J. ZHANG, D. ZHANG, J. GAO, Y. SHI, Y. CAI, P. ZHONG, Z. HE, B. LI, X. LI, Y. 2024-07-16 doi:10.1101/2024.07.16.603675 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Dynamin 1-mediated endocytic recycling of glycosylated N-cadherin sustains the plastic mesenchymal state to promote ovarian cancer metastasis ]]> https://biorxiv.org/content/10.1101/2024.07.16.603672v1?rss=1 Cai, Y. To, S. K. Y. Guan, Z. Tong, Y. Zhang, J. Ip, P. P. C. Peng, L. Wong, A. S. T. 2024-07-19 doi:10.1101/2024.07.16.603672 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ A neurofunctional signature of affective arousal generalizes across valence domains and distinguishes subjective experience from autonomic reactivity ]]> https://biorxiv.org/content/10.1101/2024.07.17.604003v1?rss=1 Zhang, R. Gan, X. Xu, T. Yu, F. Wang, L. Song, X. Jiao, G. Liu, X. Zhou, F. Becker, B. 2024-07-22 doi:10.1101/2024.07.17.604003 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Olfactory cortical outputs recruit and shape distinct brain-wide spatiotemporal networks ]]> https://biorxiv.org/content/10.1101/2024.07.19.604242v1?rss=1 Ma, T. Wang, X. Lin, X. Wen, J. Xie, L. Cao, P. Leong, A. T. L. Wu, E. X. 2024-07-23 doi:10.1101/2024.07.19.604242 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Spiking neural network models of sound localisation via a massively collaborative process ]]> https://biorxiv.org/content/10.1101/2024.07.19.604252v1?rss=1 Ghosh, M. Habashy, K. G. De Santis, F. Fiers, T. Ercelik, D. F. Meszaros, B. Friedenberger, Z. Bena, G. Hong, M. Abubacar, U. Byrne, R. T. Riquelme, J. L. Liu, Y. H. Aizenbud, I. Bicknell, B. A. Bormuth, V. Antonietti, A. Goodman, D. F. M. 2024-07-23 doi:10.1101/2024.07.19.604252 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Towards a new standard in genomic data privacy: a realization of owner-governance ]]> https://biorxiv.org/content/10.1101/2024.07.23.604393v1?rss=1 Zhang, J. Ren, Y. Au, M. H. Chow, K.-H. Zhou, Y. Chen, L. Zhao, Y. Su, J. Luo, R. 2024-07-24 doi:10.1101/2024.07.23.604393 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Interaural level difference sensitivity in neonatally deafened rats fitted with bilateral cochlear implants ]]> https://biorxiv.org/content/10.1101/2024.07.30.605756v1?rss=1 Buchholz, S. Schnupp, J. W. Arndt, S. Rosskothen-Kuhl, N. 2024-07-30 doi:10.1101/2024.07.30.605756 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Cholecystokinin modulates age-dependent Thalamocortical Neuroplasticity ]]> https://biorxiv.org/content/10.1101/2024.07.31.605964v1?rss=1 Li, X. Feng, J. Hu, X. Zhou, P. Chen, T. Zheng, X. Jendrichovsky, P. Wang, X. Chen, M. Li, H. Chen, X. Zeng, D. Zhang, M. Xiao, Z. He, L. Bello, S. T. He, J. 2024-07-31 doi:10.1101/2024.07.31.605964 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Aging amplifies sex differences in low alpha and low beta EEG oscillations ]]> https://biorxiv.org/content/10.1101/2024.07.31.603949v1?rss=1 Han, C. Cheung, V. C. K. Chan, R. H. M. 2024-08-01 doi:10.1101/2024.07.31.603949 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Extensive mutual influences of SMC complexes shape 3D genome folding ]]> https://biorxiv.org/content/10.1101/2024.07.31.606012v1?rss=1 Zhang, H. Zhao, H. Shu, L. Liu, F. Lin, E. Xia, S. Wang, B. Wang, M. Shan, F. Lin, Y. Zhang, L. Gu, Y. Blobel, G. 2024-08-01 doi:10.1101/2024.07.31.606012 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ EPInformer: A Scalable Deep Learning Framework for Gene Expression Prediction by Integrating Promoter-enhancer Sequences with Multimodal Epigenomic Data ]]> https://biorxiv.org/content/10.1101/2024.08.01.606099v1?rss=1 Lin, J. Luo, R. Pinello, L. 2024-08-01 doi:10.1101/2024.08.01.606099 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ MOSTPLAS: A Self-correction Multi-label Learning Model for Plasmid Host Range Prediction ]]> https://biorxiv.org/content/10.1101/2024.07.31.606102v1?rss=1 Zou, W. Ji, Y. Guan, J. Sun, Y. 2024-08-03 doi:10.1101/2024.07.31.606102 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ Coral microbiomes from the Atlantic and Indo-Pacific oceans have the same alpha diversity but different composition ]]> https://biorxiv.org/content/10.1101/2024.08.16.608269v1?rss=1 Santos, M. E. A. Reimer, J. D. Kiriukhin, B. Wee, H. B. Mizuyama, M. Kise, H. Kitahara, M. V. Iguchi, A. Dudoit, A. Toonen, R. J. Husnik, F. 2024-08-17 doi:10.1101/2024.08.16.608269 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ Enhanced spatially resolved transcriptomics analysis by matching between expression profiles and spatial topology ]]> https://biorxiv.org/content/10.1101/2024.08.16.608230v1?rss=1 Pang, Y. Wang, C. Zhang, Y.-z. Wang, Z. Imoto, S. Lee, T.-Y. 2024-08-19 doi:10.1101/2024.08.16.608230 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ SegFinder: an automated tool for identifying RNA virus genome segments through co-occurrence in multiple sequenced samples ]]> https://biorxiv.org/content/10.1101/2024.08.19.608591v1?rss=1 Liu, X. Kong, J. Shan, Y. Yang, Z. Miao, J. Pan, Y. Luo, T. Shi, Z. Wang, Y. Gou, Q. Yang, C. Li, C. Li, S. Zhang, X. Sun, Y. Holmes, E. C. Guo, D. Shi, M. 2024-08-19 doi:10.1101/2024.08.19.608591 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ FGR Src Family Kinase Causes Signaling and Phenotypic Shift Mimicking Retinoic Acid-Induced Differentiation of Leukemic Cells ]]> https://biorxiv.org/content/10.1101/2024.08.21.608654v1?rss=1 Yen, A. Kazim, N. Yue, J. Wang, P. 2024-08-22 doi:10.1101/2024.08.21.608654 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Endothelial MICU1 protects against vascular inflammation and atherosclerosis by inhibiting mitochondrial calcium uptake ]]> https://biorxiv.org/content/10.1101/2024.08.22.609192v1?rss=1 Sun, L. Leng, R. He, Q. Su, M. Zhang, Z. Liu, Z. Wang, Z. Jiang, H. Liu, M. Wang, L. Huo, Y. Miller, C. L. Banach, M. Huang, Y. Evans, P. C. Pelisek, J. Camici, G. G. Berk, B. C. Offermanns, S. Ge, J. Xu, S. Weng, J. 2024-08-22 doi:10.1101/2024.08.22.609192 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Genomic signatures and demographic history of the widespread and critically endangered yellow-breasted bunting ]]> https://biorxiv.org/content/10.1101/2024.08.26.609693v1?rss=1 Chen, G. Sin, S. Y. W. 2024-08-26 doi:10.1101/2024.08.26.609693 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Foraging niche partitioning of three Myotis bat species and marine fish consumption by Myotis pilosus in a subtropical East Asian region ]]> https://biorxiv.org/content/10.1101/2024.08.26.609698v1?rss=1 Wei, X. Poon, E. S. K. Chung, J. C. T. Chan, D. T. C. Shek, C. T. Tsui, W. C. Zhao, H. Sin, S. Y. W. 2024-08-26 doi:10.1101/2024.08.26.609698 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Differential splice isoforms of mouse CDK2 play functionally redundant roles during mitotic and meiotic division ]]> https://biorxiv.org/content/10.1101/2024.09.03.610967v1?rss=1 Palmer, N. Talib, S. Z. A. Ow, J. R. Tabaglio, T. Goh, C. M. F. Zhao, L. N. Guccione, E. Liu, K. Kaldis, P. 2024-09-04 doi:10.1101/2024.09.03.610967 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ RNase III in Salmonella Enteritidis enhances bacterial virulence by reducing host immune responses ]]> https://biorxiv.org/content/10.1101/2024.09.04.611193v1?rss=1 CHAN, K.-w. B. Li, Y. NI, H. CHAN, W.-c. E. Deng, X. Huang, L. Chen, S. 2024-09-04 doi:10.1101/2024.09.04.611193 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants ]]> https://biorxiv.org/content/10.1101/2024.09.08.611708v1?rss=1 Hernandez, V. S. d. M. Garcia, M. M. N. Clavel, M. Papareddy, R. K. Andreev, V. I. Gao, P. De la Concepcion, J. C. Mathur, V. Picchianti, L. Grujic, N. Kobylinska, R. Abdrakhmanov, A. Duverge, H. Anand, G. Leibrock, N. Bianchi, A. Crawford, T. Argiro, L. Mohseni, A. Leon, M. G. Matuszkiewickz, M. Raffeiner, M. Wun, C.-L. Kanne, J. V. Meinhart, A. Roitinger, E. Baurle, I. Kang, B.-H. Petersen, M. Ustun, S. Kulathu, Y. Clausen, T. Ramundo, S. Dagdas, Y. 2024-09-09 doi:10.1101/2024.09.08.611708 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Biomolecular condensation of ERC1 recruits ATG8 and NBR1 to drive autophagosome formation for plant heat tolerance ]]> https://biorxiv.org/content/10.1101/2024.09.09.611939v1?rss=1 Chung, K. K. Zhao, Z. Law, K. C. Ma, J. Chiang, C. H. J. Leung, K. H. Shrestha, R. Wu, Y. Li, C. Feng, L. Li, X. Lee, K.-M. Wong, K.-B. Xu, S.-L. Gao, C. Zhuang, X. 2024-09-10 doi:10.1101/2024.09.09.611939 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ EmbSAM: Cell boundary localization and Segment Anything Model for fast images of developing embryos ]]> https://biorxiv.org/content/10.1101/2024.09.07.611795v1?rss=1 Zhao, C. Li, Z. Zhang, P. Chen, Y. Ye, P. Wong, M.-K. Chan, L.-Y. Yan, H. Tang, C. Guan, G. Zhao, Z. 2024-09-13 doi:10.1101/2024.09.07.611795 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Unveiling multi-scale architectural features in single-cell Hi-C data using scCAFE ]]> https://biorxiv.org/content/10.1101/2024.09.10.611762v1?rss=1 Wang, F. Lin, J. Alinejad-Rokny, H. Ma, W. Meng, L. Huang, L. Yu, J. Chen, N. Wang, Y. Yao, Z. Xie, W. Li, X. Wong, K.-C. 2024-09-14 doi:10.1101/2024.09.10.611762 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ A Comprehensive Proteogenomic and Spatial Analysis of Innate and Acquired Resistance of Metastatic Melanoma to Immune Checkpoint Blockade Therapies ]]> https://biorxiv.org/content/10.1101/2024.09.12.612675v1?rss=1 wei, s. Du, K. Lan, H. Yang, Z. Deng, Y. Wei, Z. Frederick, D. T. Lee, J. Labrie, M. Tian, T. Moll, T. Chen, Y. Sullivan, R. J. Mills, G. B. Boland, G. M. Flaherty, K. liu, l. Herlyn, M. Zhang, G. 2024-09-15 doi:10.1101/2024.09.12.612675 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Proteogenomic Characterization of Primary Oral Squamous Cell Carcinomas Unveils the Extracellular Matrix Remodeling and Immunosuppressive Microenvironment Linked with Lymph Node Metastasis ]]> https://biorxiv.org/content/10.1101/2024.09.12.612653v1?rss=1 Liu, Y. Yang, Z. Pu, J. J. Zhong, J. Khoo, U. S. Su, Y. R. Zhang, G. 2024-09-17 doi:10.1101/2024.09.12.612653 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Precision Repair of Zone-Specific Meniscal Injuries Using a Tunable Extracellular Matrix-Based Hydrogel System ]]> https://biorxiv.org/content/10.1101/2024.09.12.612723v1?rss=1 Lee, S.-H. Li, Z. Zhang, E. Y. Kim, D. H. Huang, Z. Lee, S. J. Kang, H.-W. Burdick, J. A. Mauck, R. L. Heo, S. C. 2024-09-17 doi:10.1101/2024.09.12.612723 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ CRAK-Velo: Chromatin Accessibility Kinetics integration improves RNA Velocity estimation ]]> https://biorxiv.org/content/10.1101/2024.09.12.612736v1?rss=1 El Kazwini, N. Gao, M. Boudjelthia, I. K. Cai, F. Huang, Y. Sanguinetti, G. 2024-09-17 doi:10.1101/2024.09.12.612736 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Cytosolic CRISPR RNA for RNA-targeting CRISPR-Cas systems ]]> https://biorxiv.org/content/10.1101/2024.09.18.613662v1?rss=1 Kwon, S. C. Cheng, E. C. K. 2024-09-18 doi:10.1101/2024.09.18.613662 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Sidechain chemistry-encoded solid/liquid phase transitions of condensates ]]> https://biorxiv.org/content/10.1101/2024.09.16.613107v1?rss=1 Chen, F. Han, Y. Li, X. Guo, W. Wu, C. Xia, J. Zeng, X. Shum, H. C. 2024-09-19 doi:10.1101/2024.09.16.613107 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Epigenomic analysis of hepatocellular carcinoma reveals aberrant cis-regulatory changes and dysregulated retrotransposons with prognostic potentials ]]> https://biorxiv.org/content/10.1101/2024.09.16.613254v1?rss=1 Cheng, C. C. Y. Cheung, M. F. Lee, A. Y. Wu, Q. Chow, S. H.-C. Ang, J. Y. J. Riquelme Medina, I. Lo, G. Wu, H. Yang, W. Lai, P. B. S. Yip, K. Cheng, A. Leung, D. C. Y. 2024-09-20 doi:10.1101/2024.09.16.613254 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ More than fruity scents: floral biology, scent and spectral reflectance of twelve Annonaceae species ]]> https://biorxiv.org/content/10.1101/2024.09.16.613362v1?rss=1 Liu, M.-F. Chen, J. Pang, C.-C. Scharaschkin, T. Saunders, R. M. K. 2024-09-20 doi:10.1101/2024.09.16.613362 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Fungus-infected Meiogyne flowers offer a brood site for beetle pollinators in a tripartite nursery pollination system ]]> https://biorxiv.org/content/10.1101/2024.09.19.613827v1?rss=1 Liu, M.-F. Chen, J. Xue, B. Wang, R. Saunders, R. M. K. 2024-09-22 doi:10.1101/2024.09.19.613827 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Trait-dependent biogeography offers insights on the dispersal of Meiogyne (Annonaceae) across the Australasia-Pacific region ]]> https://biorxiv.org/content/10.1101/2024.09.19.614018v1?rss=1 Liu, M.-F. Munzinger, J. Chalermglin, P. Chen, J. Xue, B. Saunders, R. M. K. 2024-09-24 doi:10.1101/2024.09.19.614018 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Generalizable Morphological Profiling of Cells by Interpretable Unsupervised Learning ]]> https://biorxiv.org/content/10.1101/2024.09.24.614684v1?rss=1 Murthy, R. S. Stassen, S. V. Siu, D. M. D. Lo, M. C. K. Yip, G. G. K. Tsia, K. K. 2024-09-26 doi:10.1101/2024.09.24.614684 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ State and trait serotonin variations interact to shape the intrinsic connectivity and gradient architecture of the brain: a combined TPH2 genetics and tryptophan depletion study ]]> https://biorxiv.org/content/10.1101/2024.09.29.615637v1?rss=1 Wang, L. Liu, C. Xu, T. Gan, X. Kendrick, K. M. Zhao, W. Montag, C. Becker, B. 2024-09-30 doi:10.1101/2024.09.29.615637 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ P450-Catalyzed Biaryl Macrocyclization of Leaderless Ribosomal Peptides ]]> https://biorxiv.org/content/10.1101/2024.10.06.616194v1?rss=1 Liu, R. Ren, H. Wu, G. He, B. Pang, C. Shen, Z. Liu, J. Zhiman, S. Zhou, J. Li, Y.-x. 2024-10-06 doi:10.1101/2024.10.06.616194 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Cholecystokinin-expressing GABA neurons elicit long-term potentiation in the cortical inhibitory synapses and attenuate sound-shock associative memory ]]> https://biorxiv.org/content/10.1101/2024.10.08.617188v1?rss=1 Zhang, G. Pang, K. K. Chen, X. Huang, F. He, J. 2024-10-08 doi:10.1101/2024.10.08.617188 Cold Spring Harbor Laboratory Press 2024-10-08 <![CDATA[ Pan-cistrome analysis of the leaf accessible chromatin regions of 214 maize inbred lines ]]> https://biorxiv.org/content/10.1101/2024.10.14.618191v1?rss=1 Zhu, Y. Ngan, H. Zhu, T. Nan, L. Li, W. Xiao, Y. Zhuo, L. Chen, D. Tu, X. Gao, K. Yan, J. Zhong, S. Yang, N. 2024-10-16 doi:10.1101/2024.10.14.618191 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Bio-medical Big Data Operating System (Bio-OS): An Integrated Data Mining Environment for Data Intensive Scientific Research ]]> https://biorxiv.org/content/10.1101/2024.10.17.612997v1?rss=1 Liu, J. Yang, L. Xiao, Q. Li, Z. Chen, J. Chen, Z. Zhou, J. Wan, X. Tsung-Hui Chang, T.-H. Zhang, X. Li, Y. 2024-10-20 doi:10.1101/2024.10.17.612997 Cold Spring Harbor Laboratory Press 2024-10-20 <![CDATA[ Chromosomal-level reference genome and microRNAs of the ricefield flatsedge Cyperus iria ]]> https://biorxiv.org/content/10.1101/2024.10.18.619046v1?rss=1 Tsang, S. K. Nong, W. Law, S. T. S. Bede, J. C. Chen, S.-S. Li, S. Xie, Y. Swale, T. Lau, D. T. W. Kai, Z.-p. Chan, T. F. Tobe, S. S. Bendena, W. Hui, J. H. L. 2024-10-20 doi:10.1101/2024.10.18.619046 Cold Spring Harbor Laboratory Press 2024-10-20 <![CDATA[ Does Unfairness Evoke Anger or Disgust? A Quantitative Neurofunctional Dissection Based on 25 Years of Neuroimaging ]]> https://biorxiv.org/content/10.1101/2024.10.17.618853v1?rss=1 Gan, X. Zhang, R. Zheng, Z. Wang, L. Yang, X. Klugah-Brown, B. Xu, T. Qiu, N. Kendrick, K. M. Mathiak, K. Tiwald, J. Yao, D. Becker, B. 2024-10-21 doi:10.1101/2024.10.17.618853 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Low-Rank Full Matrix Factorization for dropout imputation in single cell RNA-seq and benchmarking with imputation algorithms for downstream applications ]]> https://biorxiv.org/content/10.1101/2024.10.21.619343v1?rss=1 Huang, J. Chow, A. C. M. Tang, N. L.-s. Yam, S. C. 2024-10-23 doi:10.1101/2024.10.21.619343 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention ]]> https://biorxiv.org/content/10.1101/2024.10.21.619560v1?rss=1 Li, Q. Li, K. Y. Nicoletti, C. Puri, P. L. Cao, Q. Yip, K. Y. 2024-10-24 doi:10.1101/2024.10.21.619560 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Utilizing data imbalance to enhance compound-protein interaction prediction models ]]> https://biorxiv.org/content/10.1101/2024.10.23.619867v1?rss=1 Lin, W. FUNG, C. C. A. 2024-10-25 doi:10.1101/2024.10.23.619867 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Irx3/5 define the cochlear sensory domain and regulate vestibular and cochlear sensory patterning in the mammalian inner ear ]]> https://biorxiv.org/content/10.1101/2024.10.24.620152v1?rss=1 Liu, Y. Qin, T. Weng, X. Leung, B. So, K. K. H. Wang, B. Feng, W. Marsolais, A. Josselyn, S. Huang, P. Fritzsch, B. Hui, C.-C. Sham, M. H. 2024-10-26 doi:10.1101/2024.10.24.620152 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ PhenoScreen: A Dual-Space Contrastive Learning Framework-based Phenotypic Screening Method by Linking Chemical Perturbations to Cellular Morphology ]]> https://biorxiv.org/content/10.1101/2024.10.23.619752v1?rss=1 Wang, S. Han, Q. Qin, W. Wang, L. Yuan, J. Zhao, Y. Ren, P. Zhang, Y. Tang, Y. Li, R. Li, Z. Zhang, W. Gao, S. Bai, F. 2024-10-28 doi:10.1101/2024.10.23.619752 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Chemosensory modulation of eye-body coordination in larval zebrafish ]]> https://biorxiv.org/content/10.1101/2024.10.27.620486v1?rss=1 Sy, S. K. H. Chan, D. C. W. Zhang, J. J. Lyu, J. Feng, C. Wang, K. Mok, V. C. T. Wong, K. K. Y. Mu, Y. Randlett, O. Hu, Y. Ko, H. 2024-10-28 doi:10.1101/2024.10.27.620486 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data ]]> https://biorxiv.org/content/10.1101/2024.10.27.620451v1?rss=1 Deng, T. Huang, M. Xu, K. Lu, Y. Xu, Y. Chen, S. Tao, Q. Xie, N. Wu, H. Sun, X. 2024-10-29 doi:10.1101/2024.10.27.620451 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Developmental and transcriptomic responses of Hawaiian bobtail squid early stages to ocean warming and acidification ]]> https://biorxiv.org/content/10.1101/2024.10.31.621237v1?rss=1 Otjacques, E. Paula, J. R. Ruby, E. G. Xavier, J. McFall-Ngai, M. J. Rosa, R. Schunter, C. 2024-11-02 doi:10.1101/2024.10.31.621237 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Colchicine Inhibits Smooth Muscle Cell Phenotypic Switch and Aortic Dissection in Mice ]]> https://biorxiv.org/content/10.1101/2024.11.02.621511v1?rss=1 Jiang, H. Zhao, Y. Jin, M. Zhang, Z. Wang, L. Liu, Z. Xu, S. Weng, J. 2024-11-03 doi:10.1101/2024.11.02.621511 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ A high-throughput protein tagging toolkit that retains endogenous UTRs for studying gene regulation in Kinetoplastids. ]]> https://biorxiv.org/content/10.1101/2024.11.02.621556v1?rss=1 Carbajo, C. G. Han, X. Savur, B. Upadhyaya, A. Taha, F. Tinti, M. Wheeler, R. J. Yates, P. A. Tiengwe, C. 2024-11-03 doi:10.1101/2024.11.02.621556 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Interpretable PROTAC degradation prediction with structure-informed deep ternary attention framework ]]> https://biorxiv.org/content/10.1101/2024.11.05.622005v1?rss=1 Chen, Z. Gu, C. Tan, S. Wang, X. Li, Y. He, M. Lu, R. Sun, S. Hsieh, C.-Y. Yao, X. Liu, H. Heng, P.-A. 2024-11-08 doi:10.1101/2024.11.05.622005 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ A CONTRIBUTION TO THE ANATOMY OF TWO RARE CETACEAN SPECIES: THE HOURGLASS DOLPHIN (Lagenorhynchus cruciger) AND THE SPECTACLED PORPOISE (Phocoena dioptrica) ]]> https://biorxiv.org/content/10.1101/2024.11.06.622215v1?rss=1 Graic, J.-M. Gerussi, T. Cozzi, B. Kot, B. C. W. Boys, R. M. Perrott, M. Fleury, K. Burns, E. Webster, T. Betty, E. Howarth, O. Loch, C. White, S. Dawson, S. Rayment, W. Hunter, S. Cole, R. Cox, D. Young, M. Roberts, J. Waterhouse, T. Smith, R. Ogle, M. Fyfe, J. Hendriks, H. van Helden, A. Johnstone, M. Stewart, R. O. Fordyce, R. E. Stockin, K. A. 2024-11-08 doi:10.1101/2024.11.06.622215 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Image-based DNA Sequencing Encoding for Detecting Low-Mosaicism Somatic Mobile Element Insertions ]]> https://biorxiv.org/content/10.1101/2024.11.07.619809v1?rss=1 Tan, M. Lin, Z. Chen, Z. Park, J. He, Z. Zhou, H. Lee, E. A. Gao, Z. Zhu, X. 2024-11-08 doi:10.1101/2024.11.07.619809 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ YY1 Enhances the Stability of HIF-1α Protein by Interacting with NUSAP1 in Macrophages within the Prostate Cancer Microenvironment ]]> https://biorxiv.org/content/10.1101/2024.11.07.622424v1?rss=1 Li, W. Chen, S. Lu, J. Mao, W. Zheng, S. Zhang, M. Wu, T. Chen, Y. Lu, K. Chu, C. Shu, C. Hou, Y. Yang, X. Shi, N. Chen, Z. Zhang, L. Zhang, L. Na, R. Chen, M. Ju, S. Zhang, D. Ma, Y. Xu, B. 2024-11-08 doi:10.1101/2024.11.07.622424 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Accurate prediction of CRISPR editing outcomes in somatic cell lines and zygote with few-shot learning ]]> https://biorxiv.org/content/10.1101/2024.11.08.622621v1?rss=1 Zheng, W. Yu, L. Wang, G. Cao, S. Ho, K. Song, J. Cheng, C. Ho, J. W. K. Liu, X. Wu, M. Liu, Z. Wang, H. Liu, P. Lan, G. Huang, Y. 2024-11-11 doi:10.1101/2024.11.08.622621 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ VIRALpre: Genomic Foundation Model Embedding Fused withK-mer Feature for Virus Identification ]]> https://biorxiv.org/content/10.1101/2024.11.12.623150v1?rss=1 Wang, Z. Yu, Q. Li, Y. 2024-11-15 doi:10.1101/2024.11.12.623150 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Rate of de novo mutations in the three-spined stickleback ]]> https://biorxiv.org/content/10.1101/2024.11.13.623523v1?rss=1 Zhang, C. Reid, K. Schierup, M. H. Wang, H. Candolin, U. Merila, J. 2024-11-15 doi:10.1101/2024.11.13.623523 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Expectation Violations as an Effective Alternative to Complex Mentalizing in Novel Communication ]]> https://biorxiv.org/content/10.1101/2024.11.19.624256v1?rss=1 Buidze, T. Glaescher, J. Yao, Y.-W. 2024-11-21 doi:10.1101/2024.11.19.624256 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ VaxLLM: Leveraging Fine-tuned Large Language Model for automated annotation of Brucella Vaccines ]]> https://biorxiv.org/content/10.1101/2024.11.25.625209v1?rss=1 Li, X. Zheng, Y. Hu, J. Zheng, J. Wang, Z. He, Y. 2024-11-26 doi:10.1101/2024.11.25.625209 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Marine medaka responds differently to dioxin compared with its close freshwater relative, the Japanese medaka: the AHR molecular mechanism ]]> https://biorxiv.org/content/10.1101/2024.12.01.626272v1?rss=1 PCB126 > BNF > indole, mirroring their AHR transactivation potency, but the docking poses and dynamics can vary; 2) one AHR subforms high sensitivity to dioxin--TCDD may extend to DLCs but not to other types of ligands. These insights underscore the difference of AHR biology among species even the close relative species, and finger out the necessity for meticulous consideration when evaluating the toxicity of compounds and when extending predictive toxicity assessments to more species. ]]> Zhang, W. Zong, Y. Sun, R. Xue, Z. Wan, W. Ren, A. Ma, Y. Tian, W. Wang, R. 2024-12-05 doi:10.1101/2024.12.01.626272 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Coverage landscape of the human genome in nucleus DNA and cell-free DNA ]]> https://biorxiv.org/content/10.1101/2024.12.03.626615v1?rss=1 Luo, J. Li, S. 2024-12-07 doi:10.1101/2024.12.03.626615 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Drug Response Modeling across Cancers: Proteomics vs. Transcriptomics ]]> https://biorxiv.org/content/10.1101/2024.12.04.626700v1?rss=1 Zheng, Z. Huang, L. Wang, F. Liu, L. Yu, J. Xie, W. Chen, X. Li, X. Wong, K.-C. 2024-12-07 doi:10.1101/2024.12.04.626700 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Convincing Evidence of Carnivorous Diet in Alvarezsaurian Dinosaur ]]> https://biorxiv.org/content/10.1101/2024.12.06.627300v1?rss=1 WANG, S. Ding, N. Ma, W. Yu, W. Zheng, T. Choiniere, J. Xu, X. 2024-12-10 doi:10.1101/2024.12.06.627300 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Nonuple atg8 mutant provides genetic evidence for functional specialization of ATG8 isoforms in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2024.12.10.627464v1?rss=1 Del Chiaro, A. Grujic, N. Zhao, J. Papareddy, R. K. Gao, P. Ma, J. Loefke, C. Bhattacharya, A. Gruetzner, R. Bourguet, P. Berger, F. Kang, B.-H. Marillonnet, S. Dagdas, Y. 2024-12-10 doi:10.1101/2024.12.10.627464 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Simulating big mechanically-active culture systems (BigMACS) using paired biomechanics-histology FEA modelling to derive mechanobiology design relationships. ]]> https://biorxiv.org/content/10.1101/2024.12.08.627430v1?rss=1 Schoenborn, S. Yuan, M. Fell, C. A. Liu, C. Fletcher, D. F. Pirola, S. Chan, H. F. Woodruff, M. A. Li, Z. Toh, Y.-C. Allenby, M. C. 2024-12-12 doi:10.1101/2024.12.08.627430 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Benchmarking deep learning methods for biologically conserved single-cell integration ]]> https://biorxiv.org/content/10.1101/2024.12.09.627450v1?rss=1 Yi, C. Cheng, J. Liu, W. Liu, J. Li, Y. 2024-12-13 doi:10.1101/2024.12.09.627450 Cold Spring Harbor Laboratory Press 2024-12-13 <![CDATA[ Modulating Prestimulus Alpha and Beta Power with tRNS Establishes Their Causal Role in Visual Perception ]]> https://biorxiv.org/content/10.1101/2024.12.11.627917v1?rss=1 Wei, J. Zou, H. Tang, Q. Yao, Z. Huang, G. Liang, Z. Zhang, L. Zhou, C. Zhang, Z. 2024-12-16 doi:10.1101/2024.12.11.627917 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Mechanism of D-type cyclins recognition by the AMBRA1 E3 ligase receptor ]]> https://biorxiv.org/content/10.1101/2024.12.17.628619v1?rss=1 Wang, Y. Liu, M. Wang, S. Mai, X. Wang, X. Teng, F. Lyu, T. Su, M.-Y. Stjepanovic, G. 2024-12-18 doi:10.1101/2024.12.17.628619 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ The RING-finger domain of Arabidopsis RMR functions as an E3 ligase essential for post-Golgi trafficking ]]> https://biorxiv.org/content/10.1101/2024.12.17.628466v1?rss=1 Chen, S. Zeng, Y. Wong, H. Chen, Y. Yang, L. Luo, F. Gao, C. Jiang, L. Wong, K.-B. 2024-12-20 doi:10.1101/2024.12.17.628466 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ A comprehensive benchmark for multiple highly efficient base editors with broad targeting scope ]]> https://biorxiv.org/content/10.1101/2024.12.17.628899v1?rss=1 Wang, X. Cheng, X. Li, Z. Ma, S. Zhang, H. Chen, Z. Yao, Y. Li, Z. Zhong, C. Li, Y. Zhang, Y. Menon, V. Chao, L. Li, W. Fei, T. 2024-12-20 doi:10.1101/2024.12.17.628899 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Homogeneously crosslinked in situ hydrogel enclosing high-density human-cancer cells promotes vascularized in vivo tumor modeling for immune cell therapy ]]> https://biorxiv.org/content/10.1101/2024.12.17.628981v1?rss=1 Huang, Z. Tsun, Y. M. Liang, C. Wu, Z. Aurich, T. Liu, L. Sugimura, R. Lee, S. J. 2024-12-20 doi:10.1101/2024.12.17.628981 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ I2SIM: Boosting High-Fidelity Isotropic Super-Resolution with Image Interference and Spatial-Spectrum Optimization ]]> https://biorxiv.org/content/10.1101/2024.12.18.629092v1?rss=1 He, E. Sun, Y. Zhu, H. Yang, X. Yin, L. Han, Y. Kuang, C. Liu, X. 2024-12-21 doi:10.1101/2024.12.18.629092 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ HMG-DTI: a drug-target interaction prediction framework combining Hierarchical Molecular Graphs and improved Convolutional Block Attention Module ]]> https://biorxiv.org/content/10.1101/2024.12.21.628851v1?rss=1 Yang, Z. Li, Y. Matsuda, Y. Song, L. 2024-12-22 doi:10.1101/2024.12.21.628851 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Development of a novel peripherally acting alpha2A-adrenergic receptor antagonist for anti-diabetic ]]> https://biorxiv.org/content/10.1101/2024.12.17.628818v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@1d3d7corg.highwire.dtl.DTLVardef@1afbad3org.highwire.dtl.DTLVardef@12a1aborg.highwire.dtl.DTLVardef@1341a02_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hong, F. Wang, J. Chen, D. Wang, Q. Gan, S. Ye, F. Chen, L. Ren, H. Zhang, T. Xie, Y. Jing, X. Wang, R. Xu, Z. Ren, J. Shi, C. Jia, S. Huang, X. Xu, X. Zheng, Y. Lu, J. Lin, W. Dai, J. Wang, L. Chen, L. Tang, C. Liu, H. Xu, T. Xie, X. Liu, X.-a. Du, Y. Nan, F. Chen, Z. 2024-12-23 doi:10.1101/2024.12.17.628818 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ A Systematic Comparison of Single-Cell Perturbation Response Prediction Models ]]> https://biorxiv.org/content/10.1101/2024.12.23.630036v1?rss=1 Li, L. You, Y. Liao, W. Fan, X. Lu, S. Cao, Y. Li, B. Ren, W. Fu, Y. Kong, J. Zheng, S. Chen, J. Liu, X. Tian, L. 2024-12-23 doi:10.1101/2024.12.23.630036 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ PhosF3C: A Feature Fusion Architecture with Fine-Tuned Protein Language Model and Conformer for prediction of general phosphorylation site ]]> https://biorxiv.org/content/10.1101/2024.12.25.630296v1?rss=1 Liu, Y. Zhong, H. Zhai, J. Wang, X. LU, T. 2024-12-25 doi:10.1101/2024.12.25.630296 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Single-cell analysis reveals distinct immune characteristics of hepatocellular carcinoma in HBV-positive versus HBV-negative cases ]]> https://biorxiv.org/content/10.1101/2024.12.30.630656v1?rss=1 Liu, K. Chen, E. Liang, J. Li, Y. Cheng, B. Shi, W. Zhou, Z. Zhou, W. Tian, H. Yang, D. Shao, X. Li, H. 2024-12-30 doi:10.1101/2024.12.30.630656 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Food for thought: Rosy-faced lovebirds (Agapornis roseicollis) are capable of associative symbol learning and inference-based quantity discrimination ]]> https://biorxiv.org/content/10.1101/2024.12.30.630847v1?rss=1 3), the effect of these factors diminished. We conclude that rosy-faced lovebirds are capable of advanced numeracy and quantity discrimination, similar to larger parrot species. ]]> Wang, S. Lo, K. C. H. Shiu, V. W. T. Hung, C. Y. C. Poon, E. S. K. Newman, C. Buesching, C. D. Sin, S. Y. W. 2024-12-31 doi:10.1101/2024.12.30.630847 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Crosslinker-free in situ hydrogel induces self-aggregation of human dental pulp stem cells with enhanced antibacterial activity ]]> https://biorxiv.org/content/10.1101/2024.12.30.630819v1?rss=1 Lee, S. J. Wu, Z. Huang, M. Liang, C. Huang, Z. Siyuan, C. Rajasekar, V. Abdalla, M. M. Nah, H. Heo, D. N. Kwon, I. K. Cho, M.-J. Kim, S. J. Sohn, S. Kim, S.-H. Sugimura, R. R. Yiu, C. K. Y. 2025-01-01 doi:10.1101/2024.12.30.630819 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ Looking for the optimal pathway to stimulate hippocampus in human participants using transcranial ultrasound stimulation (TUS): a simulation study ]]> https://biorxiv.org/content/10.1101/2025.01.05.631158v1?rss=1 Lu, H. Li, Z. Ni, X. Guo, L. Qiu, Z. Meng, L. Yuan, Y. 2025-01-06 doi:10.1101/2025.01.05.631158 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ Genome-wide Viral Nascent RNA Sequencing Unveils Polymerase Pausing Landscape at Single-nucleotide Precision ]]> https://biorxiv.org/content/10.1101/2025.01.08.631631v1?rss=1 Zhu, Z. Fung, C. W. Xu, X. Liang, Z. Gao, Z. Wang, M. H. Li, M. Yeung, S. Y. Wang, J. Tse, C. K. M. Cheung, P. P.-H. 2025-01-08 doi:10.1101/2025.01.08.631631 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment ]]> https://biorxiv.org/content/10.1101/2025.01.07.631789v1?rss=1 Ort, J. T. Shepard, S. S. Zolnoski, S. A. Lam, T. T.- Y. Davis, T. Neher, R. Moncla, L. H. 2025-01-10 doi:10.1101/2025.01.07.631789 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ A cytoskeletal scaffold promotes motile cilia assembly by regulating transition-zone integrity ]]> https://biorxiv.org/content/10.1101/2025.01.10.632296v1?rss=1 Park, H. Choi, M. Cheung, H. O.-L. Zhang, Y. Makino, S. Yoshikawa, Y. Qi, H. Liu, Z. Lan, G. Fu, G. Wang, Q. Guo, S. S. Liu, P. Liu, Z. Ti, S.-C. Wang, W.-J. Li, X. D. Ni, T. Hui, C. C. He, M. 2025-01-10 doi:10.1101/2025.01.10.632296 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Branched chain fatty acid-rich diet promotes lipid droplet enlargement and impacts organismal health in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.01.15.633283v1?rss=1 Li, K. U. R. Lo, W. K. Yang, M. Wang, C. Yin, L. C. Lee, J. C.-Y. Zheng, C. 2025-01-20 doi:10.1101/2025.01.15.633283 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ SpatialFormer: Universal Spatial Representation Learning from Subcellular Molecular to Multicellular Landscapes ]]> https://biorxiv.org/content/10.1101/2025.01.18.633701v1?rss=1 Wang, J. Huang, Y. Winther, O. 2025-01-22 doi:10.1101/2025.01.18.633701 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Primate-specific microRNA-1202 regulates dopaminergic neurogenesis by targeting APC2 and modulates WNT/β-catenin signaling pathway in midbrain organoid ]]> https://biorxiv.org/content/10.1101/2025.01.19.633822v1?rss=1 Long, X. CAO, D. Chan, S.-W. Hao, S. Liu, L. Chan, W.-Y. Cheung, H.-H. 2025-01-22 doi:10.1101/2025.01.19.633822 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ TransHLA: A Hybrid Transformer Model for HLA-Presented Epitope Detection ]]> https://biorxiv.org/content/10.1101/2025.01.20.634002v1?rss=1 LU, T. Wang, X. Nie, W. Huo, M. Li, S. 2025-01-24 doi:10.1101/2025.01.20.634002 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Root Cap-Specific Transcriptomics Identify the NAC Transcription Factor SOMBRERO as a Versatile Regulator of Auxin Gradients ]]> https://biorxiv.org/content/10.1101/2025.01.22.634243v1?rss=1 Wang, P. Zhou, Y. Liu, Z. He, J. Kang, B. H. 2025-01-24 doi:10.1101/2025.01.22.634243 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Direct single cell-type gene expression analysis in Whole blood: Novel ratio-based gene expression biomarkers using 2 novel monocyte reference genes (PSAP and CTSS) for monitoring bacterial infection ]]> https://biorxiv.org/content/10.1101/2025.01.27.634977v1?rss=1 50% transcript of genes in PB are contributed by monocytes alone. Public gene expression datasets were used to generate a list of monocyte informative genes with which DIRECT LS-TA assay is applicable in PB samples. PSAP and CTSS were identified as the monocyte informative reference genes, based on low biological variation (CV <12%) and high monocyte specificity. They were used as the denominator and together with another monocyte informative target gene as the numerator, the value of this new DIRECT LS-TA can be determined which is a kind of ratio-based biomarker (RBB). The clinical utility was the differentiation of patients with bacterial infection from control subjects in a discovery dataset and 4 other replication datasets. Methods to convert DIRECT LS-TA results to multiple of control median (MoM) provided approximations to delta-delta CT values of relative quantification commonly used in qPCR or digital PCR assays. ResultsOver 50 monocyte-informative genes were identified, including key immune response genes like IFI44L, IL1B, VNN1 and NFKBIZ. DIRECT LS-TA results showed excellent correlation with the gold standard results, gene expression in isolated monocyte expression (R2=0.55-0.97). Then, DIRECT LS-TA of these 50 target genes were evaluated to identify the best RBB to detect the host response to bacterial infection. Monocyte DIRECT LS-TA VNN1 RBB showed consistent upregulation across five independent datasets (median fold change 2.7-fold, p<10-8) with strong diagnostic performance (AUC=0.84-0.99). The expected corresponding delta-delta CT value is more than 1.4 cycle which can be reliably measured by qPCR. Additional monocyte-informative genes including NLRC4, CYP1B1, PFKFB3, LILRA5, NFKBIA, and NFKBIZ also demonstrated significant diagnostic ability (AUC>0.8). ConclusionsThe DIRECT LS-TA method (as a simple RBB) provides reliable quantification of monocyte-specific gene expression directly from whole blood samples without cell separation. The robust performance in bacterial infection diagnosis demonstrates its potential clinical utility for rapid infection differentiation and informed antibiotic stewardship. DIRECT LS-TA will emerge as a new kind of in vitro diagnostics (IVD) which can convey single cell-type gene expression information from PB samples. The new kind of IVD and uniqueness of the information, together with the ease of implementation will make it very useful in clinics ]]> Tang, N. L.-s. Kwan, T.-K. Huang, D. Ma, S. L. Leung, K.-S. 2025-01-28 doi:10.1101/2025.01.27.634977 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ A-TWAS: An aggregated transcriptome-wide association study model incorporating multiple Bayesian priors ]]> https://biorxiv.org/content/10.1101/2025.01.27.635054v1?rss=1 Liang, Y. Wang, H. Zhang, Y. D. 2025-01-28 doi:10.1101/2025.01.27.635054 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Decoding Phenotypic Variability in Osteogenesis Imperfecta: Zebrafish as a Model for Molecular and Ultrastructural Insights. ]]> https://biorxiv.org/content/10.1101/2025.01.28.635270v1?rss=1 Debaenst, S. Sahd, L. Debaene, C. Jarayseh, T. De Saffel, H. Bek, J. W. Steyaert, W. Van Haver, D. Dufour, S. Impens, F. Coucke, P. De Clercq, A. Willaert, A. 2025-01-29 doi:10.1101/2025.01.28.635270 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Interactions of Interaural Time and Level Differences in Spatial Hearing with Cochlear Implants ]]> https://biorxiv.org/content/10.1101/2025.01.29.635454v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@15ee6e2org.highwire.dtl.DTLVardef@1881bd4org.highwire.dtl.DTLVardef@db17c7org.highwire.dtl.DTLVardef@1f62f2f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Buchholz, S. Arndt, S. Schnupp, J. W. Rosskothen-Kuhl, N. 2025-01-29 doi:10.1101/2025.01.29.635454 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Novel Pipelines to Extract Differences in Proteome Dynamics Based on Health Status ]]> https://biorxiv.org/content/10.1101/2025.02.01.636015v1?rss=1 Xu, B. Zhao, J. Huang, T. Honfo, S. H. Trumpff, C. Picard, M. Cohen, A. Liu, M. 2025-02-04 doi:10.1101/2025.02.01.636015 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ DNA repair functions are essential for bacterial stress defense but render antibiotic tolerant sub-populations susceptible to ciprofloxacin and gentamicin upon prolonged treatment ]]> https://biorxiv.org/content/10.1101/2025.02.03.636342v1?rss=1 Wan, Y. Zheng, J. Heng, H. Tang, Y. Ye, L. Wai-Chi Chan, E. Chen, S. 2025-02-04 doi:10.1101/2025.02.03.636342 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Time-course Transcriptomic Dataset of Gallic Acid-induced Human Cervical Carcinoma HeLa Cell Death ]]> https://biorxiv.org/content/10.1101/2025.02.03.636357v1?rss=1 Tang, H. M. Cheung, P. C. K. 2025-02-04 doi:10.1101/2025.02.03.636357 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Long non-coding RNA BCAR4 is required for efficient influenza A virus replication ]]> https://biorxiv.org/content/10.1101/2025.02.06.636885v1?rss=1 Cao, Y. Chin, A. W. H. Gu, H. Li, M. Poon, L. L. 2025-02-06 doi:10.1101/2025.02.06.636885 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Unifying Genetic and Chemical Perturbagen Representation through a Hybrid Deep Learning Framework ]]> https://biorxiv.org/content/10.1101/2025.02.02.635055v1?rss=1 Li, Y. Zhu, J. Liu, L. Wang, F. Zeng, M. Huang, L. Yang, F. Li, M. Yao, J. 2025-02-07 doi:10.1101/2025.02.02.635055 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ 'Trans-differentiation of neutrophils from plasmablast' is an artefact caused by over-reliance on machine algorithms in single cell RNA sequencing analysis: Lesson learnt and steps ahead ]]> https://biorxiv.org/content/10.1101/2025.02.07.636761v1?rss=1 Huang, J. Yam, P. S. C. Tang, N. L.-s. 2025-02-07 doi:10.1101/2025.02.07.636761 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ SpecImmune accurately genotypes diverse immune-related gene families using long-read data ]]> https://biorxiv.org/content/10.1101/2025.02.04.636381v1?rss=1 Wang, S. Wang, X. Wang, M. Zhou, Q. Li, S. 2025-02-08 doi:10.1101/2025.02.04.636381 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ scKAN: Interpretable Single-cell Analysis for Cell-type-specific Gene Discovery and Drug Repurposing via Kolmogorov-Arnold Networks ]]> https://biorxiv.org/content/10.1101/2025.02.04.636408v1?rss=1 He, H. Tang, Z. Chen, G. Xu, F. Hu, Y. Feng, Y. Wu, J. Huang, Y.-A. Huang, Z.-A. Tan, K. C. 2025-02-08 doi:10.1101/2025.02.04.636408 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Beyond RNA Structure Alone: Complex-Aware Feature Fusion for Tertiary Structure-based RNA Design ]]> https://biorxiv.org/content/10.1101/2025.02.05.636748v1?rss=1 Zhang, Z. Zheng, J. Zhou, Y. Wang, S. Cui, S. Li, Z. 2025-02-08 doi:10.1101/2025.02.05.636748 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Neocortical Layer-5 tLTD Relies on Non-Ionotropic Presynaptic NMDA Receptor Signaling ]]> https://biorxiv.org/content/10.1101/2025.02.07.637179v1?rss=1 Thomazeau, A. Rannio, S. Brock, J. A. Wong, H. H.-W. Sjöström, P. J. 2025-02-10 doi:10.1101/2025.02.07.637179 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ DNA G-quadruplex Profiling Reveals Functional and Mechanistic Role of G-quadruplexes in Skeletal Muscle Stem Cells ]]> https://biorxiv.org/content/10.1101/2025.02.10.637367v1?rss=1 Chen, X. Yang, F. Zhang, S. Guo, X. Zhao, J. Qiao, Y. He, L. Li, Y. Zhou, Q. Ong, M. T. Y. Kwok, C. K. Sun, H. Wang, H. 2025-02-12 doi:10.1101/2025.02.10.637367 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Sexual dimorphism and phenotypic plasticity in a subtropical feral bovid Bos taurus (Artiodactyla: Bovidae). ]]> https://biorxiv.org/content/10.1101/2025.02.10.637565v1?rss=1 Perroux, T. A. McElligott, A. G. Hodgson, G. M. W. Flay, K. J. 2025-02-12 doi:10.1101/2025.02.10.637565 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Eye blinks synchronize with musical beats during music listening ]]> https://biorxiv.org/content/10.1101/2025.02.10.637582v1?rss=1 Wu, Y. Teng, X. Du, Y. 2025-02-12 doi:10.1101/2025.02.10.637582 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ scWGBS-GPT: A Foundation Model for Capturing Long-Range CpG Dependencies in Single-Cell Whole-Genome Bisulfite Sequencing to Enhance Epigenetic Analysis ]]> https://biorxiv.org/content/10.1101/2025.02.19.638959v1?rss=1 Liang, C. Ye, P. Yan, H. Zheng, P. Sun, J. Wang, Y. Li, Y. Ren, Y. Jiang, Y. Xiang, J. Zhang, S. Jiang, L. Bai, W. Ma, X. Chen, T. Zuo, W. Bai, L. Ouyang, W. Li, J. 2025-02-23 doi:10.1101/2025.02.19.638959 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Emergent modularity in large language models: Insights from aphasia simulations ]]> https://biorxiv.org/content/10.1101/2025.02.22.639416v1?rss=1 Wang, C. Fan, Z. Han, Z. Bi, Y. Li, J. 2025-02-23 doi:10.1101/2025.02.22.639416 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Le Petit Prince (LPP) Multi-talker: Naturalistic 7T fMRI and EEG Dataset ]]> https://biorxiv.org/content/10.1101/2025.02.26.640265v1?rss=1 Wang, Q. Zhou, Q. Ma, Z. Wang, N. Zhang, T. Fu, Y. Li, J. 2025-02-26 doi:10.1101/2025.02.26.640265 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ Distinct Connectivity Signatures of Emotions Enhance Precision of Network Biomarkers in Mood Disorders ]]> https://biorxiv.org/content/10.1101/2025.03.02.641022v1?rss=1 Xu, S. Li, L. Luo, T. Zhang, L. Becker, B. Liang, Z. 2025-03-04 doi:10.1101/2025.03.02.641022 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Deviant functional connectivity patterns in the EEG and their potential use for dyslexia screening ]]> https://biorxiv.org/content/10.1101/2025.03.04.641551v1?rss=1 YANG, Y. Liu, Z. Wong, B. Huo, S. Wang, J. Lee, T. Hoeft, F. Maurer, U. 2025-03-10 doi:10.1101/2025.03.04.641551 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Morphogenesis and morphometry of brain folding patterns across species ]]> https://biorxiv.org/content/10.1101/2025.03.05.641692v1?rss=1 Yin, S. Liu, C. Choi, G. P. T. Jung, Y. Heuer, K. Toro, R. Mahadevan, L. 2025-03-10 doi:10.1101/2025.03.05.641692 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ FACED 2.0 enables large-scale voltage and calcium imaging in vivo ]]> https://biorxiv.org/content/10.1101/2025.03.06.641784v1?rss=1 Zhong, J. Natan, R. G. Zhang, Q. Wong, J. S. J. Miehl, C. Bose, K. Lu, X. St-Pierre, F. Guo, S. Doiron, B. Tsia, K. K. Ji, N. 2025-03-10 doi:10.1101/2025.03.06.641784 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ SARS-CoV-2 Infects Peripheral Sensory Neurons and Promotes Axonal Degeneration via TRPV1 Activation ]]> https://biorxiv.org/content/10.1101/2025.03.06.641885v1?rss=1 Hong, Y. Co, V. A. Liu, S. T. Chun-Yee, R. Mok, B. W. Y. Chen, H. 2025-03-10 doi:10.1101/2025.03.06.641885 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ A functional anatomical shift from the lateral frontal pole to dorsolateral prefrontal cortex in emotion action control underpins elevated levels of anxiety: partial replication and generalization of Bramson et al., 2023 ]]> https://biorxiv.org/content/10.1101/2025.03.09.642129v1?rss=1 Zhuang, Q. Yao, S. Xu, L. Chen, S. Li, J. Zheng, X. Fu, M. Kendrick, K. Becker, B. 2025-03-11 doi:10.1101/2025.03.09.642129 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Oxytocin receptor and HER2 interactions in breast cancer ]]> https://biorxiv.org/content/10.1101/2025.03.09.642136v1?rss=1 Liu, H. Liu, L. Moeller, A. Muttenthaler, M. 2025-03-11 doi:10.1101/2025.03.09.642136 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Hyperactivity of the Amygdala Mediates Depressive-Like Phenotypes and Decreased Serotonin Release ]]> https://biorxiv.org/content/10.1101/2025.03.10.642393v1?rss=1 Kim, K. Lai, Y. Gao, Q. Wang, H. ying, K. T. Asim, M. He, J. 2025-03-11 doi:10.1101/2025.03.10.642393 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Biodiversity modulates the size-abundance relationship in changing environments ]]> https://biorxiv.org/content/10.1101/2025.03.07.642014v1?rss=1 Gjoni, V. Altermatt, F. Garnier, A. Palamara, G. M. Seymour, M. Pontarp, M. Pennekamp, F. 2025-03-12 doi:10.1101/2025.03.07.642014 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Multimodal brain cell atlas across the adult macaque lifespan ]]> https://biorxiv.org/content/10.1101/2025.03.11.641786v1?rss=1 Zhang, X. Lai, G. Guo, X. Ma, W. Yuan, Y. Zhang, H. Fan, P. Liu, X. Guo, P. An, J. Li, J. Huang, K. Zuo, J. Wu, L. Shangguan, S. Yu, F. Xiang, Y. Hu, Y. Huang, Y. Lin, Y. He, D. Pan, M. Chen, L. Li, B. Yang, W. Yin, P. Li, S. Zhang, X. Yang, T. Chen, J. Zhong, Q. Lv, Y. Qin, B. Qing, X. Deng, Q. Huang, Y. Liu, C. Han, L. Liu, S. Qin, D. Liu, Z. Zhou, Y. Qiao, L. Li, C. Zhang, Y. Volpe, G. Graf, S. Diks, I. F. Flotho, M. Krol, R. P. Mulder, J. Hutchins, A. P. Keller, A. Maxwell, P. H. Rubinsztein, D. C. Liu, X. Tse, H.-F. Poo, M. Wang, B 2025-03-12 doi:10.1101/2025.03.11.641786 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ A tumor necrosis factor-α responsive cryptic promoter drives overexpression of the human endogenous retrovirus ERVK-7 ]]> https://biorxiv.org/content/10.1101/2025.03.09.642286v1?rss=1 LEE, S. Ho, Y. Y. Hao, S. Ouyang, Y. Liew, U. L. Goyal, A. Li, S. Barbour, J. A. He, M. Huang, Y. Wong, J. W. H. 2025-03-13 doi:10.1101/2025.03.09.642286 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Harnessing Uniform Design to Enhance AI-Driven Predictions of Physicochemical Properties of Short Peptides ]]> https://biorxiv.org/content/10.1101/2025.03.10.642308v1?rss=1 Zhu, Z. Liu, H. Guo, Y. Xu, M. Li, X. Zhou, H. Wang, J. 2025-03-13 doi:10.1101/2025.03.10.642308 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ How sleeping minds decide: state-specific reconfigurations of lexical decision-making ]]> https://biorxiv.org/content/10.1101/2025.03.10.642374v1?rss=1 Xia, T. Hu, C.-P. Turker, B. Musat, E. M. Naccache, L. Arnulf, I. Oudiette, D. Hu, X. 2025-03-13 doi:10.1101/2025.03.10.642374 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ ClairS-TO: A deep-learning method for long-read tumor-only somatic small variant calling ]]> https://biorxiv.org/content/10.1101/2025.03.10.642523v1?rss=1 Chen, L. Zheng, Z. Su, J. Yu, X. Wong, A. O. K. Zhang, J. Lee, Y.-L. Luo, R. 2025-03-13 doi:10.1101/2025.03.10.642523 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Adaptive behavioural strategies to seasonal challenges by a semi-urban feral ungulate ]]> https://biorxiv.org/content/10.1101/2025.03.12.642745v1?rss=1 Bhattacharjee, D. Flay, K. J. Mumby, H. S. McElligott, A. G. 2025-03-14 doi:10.1101/2025.03.12.642745 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ RPGR regulates motile cilia by interfering with actin dynamics ]]> https://biorxiv.org/content/10.1101/2025.03.13.643176v1?rss=1 Wu, Y. Tavares, E. Liang, B. Wee, W. Mennella, V. Feng, H. Cao, J. Zheng, J. He, M. Stephenson, K. Hanan, L. Li, J. M. Dell, S. D. Heon, E. LIU, Z. 2025-03-14 doi:10.1101/2025.03.13.643176 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition ]]> https://biorxiv.org/content/10.1101/2025.03.14.643063v1?rss=1 A:T driver mutations in KRAS plus short subclonal diversification. LUAD in never smokers showed early occurrence of copy number alterations and EGFR mutations associated with SBS5 and SBS40a mutational signatures. Tumors harboring EGFR mutations exhibited long latency, particularly in females of European-ancestry (EU_N). In EU_N, EGFR mutations preceded the occurrence of other driver genes, including TP53 and RBM10. Tumors from Asian never smokers showed a short clonal evolution and presented with heterogeneous repetitive patterns for the inferred mutational order. Importantly, we found that the mutational signature ID2 is a marker of a previously unrecognized mechanism for LUAD evolution. Tumors with ID2 showed short latency and high L1 retrotransposon activity linked to L1 promoter demethylation. These tumors exhibited an aggressive phenotype, characterized by increased genomic instability, elevated hypoxia scores, low burden of neoantigens, propensity to develop metastasis, and poor overall survival. Re-activated L1 retrotransposition-induced mutagenesis can contribute to the origin of the mutational signature ID2, including through the regulation of the transcriptional factor ZNF695, a member of the KZFP family. The complex nature of LUAD evolution creates both challenges and opportunities for screening and treatment plans. ]]> Zhang, T. Zhao, W. Wirth, C. Diaz-Gay, M. Yin, J. Cecati, M. Marchegiani, F. Hoang, P. H. Leduc, C. Baine, M. K. Travis, W. D. Sholl, L. M. Joubert, P. Sang, J. McElderry, J. P. Klein, A. Khandekar, A. Hartman, C. Rosenbaum, J. Colon-Matos, F. J. Miraftab, M. Saha, M. Lee, O. W. Jones, K. M. Caporaso, N. E. Wong, M. P. Leung, K. C. Hsiung, C. A. Chen, C.-Y. Homer, R. Yang, S.-R. Pesatori, A. C. Consonni, D. Yang, L. Zhu, B. Edell, E. S. Santamaria, J. M. Schabath, M. B. Yendamuri, S. S. Manczuk, M. Lissowska, J. Swiatkowska, B. Mukeria, A. Shangina, O 2025-03-16 doi:10.1101/2025.03.14.643063 Cold Spring Harbor Laboratory Press 2025-03-16 <![CDATA[ Compositional data modeling of high-dimensional single cell RNA-seq (CoDA-hd): its advantages over commonly used normalization approaches ]]> https://biorxiv.org/content/10.1101/2025.03.24.644852v1?rss=1 Huang, J. Yam, P. S. C. Leung, K.-S. Deng, M. Tang, N. L.-S. 2025-03-26 doi:10.1101/2025.03.24.644852 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Characterization of two non-competing antibodies to influenza H3N2 hemagglutinin stem reveals its evolving antigenicity ]]> https://biorxiv.org/content/10.1101/2025.03.24.644842v1?rss=1 Gopal, A. B. Lv, H. Pholcharee, T. Ouyang, W. O. Teo, Q. W. Luo, Y. Tang, Y. S. Luo, M. Mok, C. K. P. Wu, N. C. 2025-03-27 doi:10.1101/2025.03.24.644842 Cold Spring Harbor Laboratory Press 2025-03-27 <![CDATA[ MKFGO: Integrating Multi-Source Knowledge Fusion with Pre-Trained Language Model for High-Accuracy Protein Function Prediction ]]> https://biorxiv.org/content/10.1101/2025.03.27.645685v1?rss=1 Zhu, Y.-H. Zhu, S. Yu, X. Yan, H. Liu, Y. Xie, X. Yu, D.-J. Ye, R. 2025-04-01 doi:10.1101/2025.03.27.645685 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ BABA: Naturalistic fMRI and MEG recordings during viewing of a reality TV show ]]> https://biorxiv.org/content/10.1101/2025.04.03.646958v1?rss=1 Li, J. Wang, Q. Wang, Y. Wang, C. Ma, Z. Xu, R. Feng, S. Jiang, X. Meng, Z. 2025-04-04 doi:10.1101/2025.04.03.646958 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Proterozoic Tectonic Drivers Underpin Flavobacterial Diversification ]]> https://biorxiv.org/content/10.1101/2025.04.01.646730v1?rss=1 ZHANG, H. Luo, H. 2025-04-07 doi:10.1101/2025.04.01.646730 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Imputation Disparities Driven by Recent Selectionand Their Impact on Disease Risk Estimation in East and Southeast Asian Populations ]]> https://biorxiv.org/content/10.1101/2025.04.03.646928v1?rss=1 Li, D. Tangtanatakul, P. Lei, Y. Liu, X. Huang, H.-Y. Lin, Y.-C.-D. Li, C. Chen, Y. Cai, L. Zhao, J. Pisitkul, P. Suangtamai, T. Yu, J. Zhou, Y. Kunhapan, P. Sun, R. Yu, G. Sun, H. Hirankarn, N. Huang, H.-D. Yang, W. Wang, Y.-F. 2025-04-07 doi:10.1101/2025.04.03.646928 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ A Bioinformatic Investigation into the Role of ITGB1 in Cancer Prognosis and Therapeutic Resistance ]]> https://biorxiv.org/content/10.1101/2025.04.06.647487v1?rss=1 Mo, X. 2025-04-09 doi:10.1101/2025.04.06.647487 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Lysosomal cathepsin D regulates bone turnover through distinct mode of actions of the autophagy pathways in osteoblasts and osteoclasts ]]> https://biorxiv.org/content/10.1101/2025.04.09.645406v1?rss=1 Zhang, F. Zhao, Y. He, Q. Schneider, L. E. Zhang, J. Wan, C. 2025-04-10 doi:10.1101/2025.04.09.645406 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Drp1 Proteins Released from Hydrolysis-driven Scaffold Disassembly Trigger Nucleotide-dependent Membrane Remodeling to Promote Scission ]]> https://biorxiv.org/content/10.1101/2025.04.10.648288v1?rss=1 Luo, E. W.-C. Nolden, K. A. Alimohamadi, H. Lee, M. W. Duan, L. Hill, R. B. Wong, G. C. L. 2025-04-16 doi:10.1101/2025.04.10.648288 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ A unified eIF1A+ luminal cells-centered hypoxic and "cold" tumor microenvironment promotes PCa progression among different subtypes ]]> https://biorxiv.org/content/10.1101/2025.04.17.649316v1?rss=1 Wan, L. Huang, E. Xu, Z. Zheng, B. Ding, X. Chu, C. Wu, T. Chen, S. Zhuang, J. Chen, M. Na, R. Ju, S. Zhang, D. Li, W. Cheng, Y. Xu, B. 2025-04-18 doi:10.1101/2025.04.17.649316 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Single-Cell Pharmacogenomic Landscapes of Epigenetic Therapy in Gastric Cancer ]]> https://biorxiv.org/content/10.1101/2025.04.16.649236v1?rss=1 200 GC-related genes across 4 distinct epigenetic drug classes in multiple gastric lines. We captured 17.7 million pharmocogenomic expression interactions in 625,866 cells representing baseline and post-therapeutic molecular phenotypes. This single-cell pharmacogenomic compendium confirmed previously known gene-driven molecular phenotypes, elucidated poorly characterized genes, and uncovered novel gene dosage-molecular phenotype relationships. Molecular phenotypes in post-therapeutic surviving cells revealed diverse gene perturbation-associated pathways causing convergent drug resistance (EMT plasticity, cell cycle alterations, metabolic reprogramming), highlighting combinatorial strategies for restoring sensitivity. Mapping of in vitro molecular phenotypes to primary human GCs imparted prognostic information and insights into spatial heterogeneity. Comparative analysis of gene perturbations across therapies and lines revealed both conserved and context-specific molecular alterations. Our results illustrate how Perturb-seq approaches can systematically map diverse cancer-associated molecular phenotypes across multiple gene/drug/cell line interactions, yielding translational insights. ]]> Xu, C. Ma, H. Sheng, T. Lee, M. H. Abdul Ghani, S. A. B. Perlaza-Jimenez, L. Huang, K. K. Lim, S. K. Srivastava, S. Ong, X. Tay, S. T. Ho, S. W. T. Tan, A. L. K. Zhu, F. Nasca, V. Randon, G. Ashktorab, H. Cheng, A. S.-L. Jeyasekharan, A. D. Li, S. Teh, M. Sundar, R. Powell, D. R. Rosenbluh, J. Pietrantonio, F. Yong, W. P. So, J. B.-Y. Tan, P. 2025-04-21 doi:10.1101/2025.04.16.649236 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Cross-modal Denoising and Integration of Spatial Multi-omics data with CANDIES ]]> https://biorxiv.org/content/10.1101/2025.04.17.649333v1?rss=1 Liu, Y. Zou, W. Li, Y. Wang, J. Cai, M. Cai, H. 2025-04-22 doi:10.1101/2025.04.17.649333 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Cognitive Mode Detectable with Task-Based fMRI: Default Mode B (DMB) ]]> https://biorxiv.org/content/10.1101/2025.04.21.649745v1?rss=1 Ni, Y. Q. Y. Redway, S. Momeni, A. Momeni, A. Jian, L. Yip, L. Woodward, T. S. 2025-04-22 doi:10.1101/2025.04.21.649745 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Predicting Early Transitions in Respiratory Virus Infections via Critical Transient Gene Interactions ]]> https://biorxiv.org/content/10.1101/2025.04.18.649619v1?rss=1 Lyu, C. Jiang, A. Ng, K. H. Liu, X. Chen, L. 2025-04-23 doi:10.1101/2025.04.18.649619 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ A direct RNA-seq-based EBV Latency Transcriptome Offers Insights into the Biogenesis of EBV Gene Products. ]]> https://biorxiv.org/content/10.1101/2025.04.23.648900v1?rss=1 Mamane-Logsdon, A. Zane, I. Chong, C. S. Chou, O. H. I. Rawal, M. Gillman, A. C. T. Wongwiwat, W. Donovan-Banfield, I. Matthews, D. A. White, R. E. 2025-04-23 doi:10.1101/2025.04.23.648900 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ PepSeek: Universal Functional Peptide Discovery with Cooperation Between Specialized Deep Learning Models and Large Language Model ]]> https://biorxiv.org/content/10.1101/2025.04.29.641945v1?rss=1 Gong, H. Wang, Y. Kong, Q. Li, X. Li, L. Wan, B. Zhao, Y. Chen, G. Chen, J. Zhang, J. Yu, Y. Yang, X. Zuo, X. Li, Y. 2025-04-30 doi:10.1101/2025.04.29.641945 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Single-cell analyses reveal scyphozoan conserved and specific genes contribution during tissue regeneration in two jellyfish ]]> https://biorxiv.org/content/10.1101/2025.04.29.650939v1?rss=1 Li, Y. Law, S. T. S. Nong, W. So, W. L. Xie, Y. Leung, T. C. N. Li, T. H. Tse, J. Yip, H. Y. Jin, O. Zhang, J. Chui, A. P. Lau, K. F. John, A. Kai, Z. p. Bendena, W. G. Hayward, A. Wei, Y. Chan, T. F. Ngai, S. M. Hui, J. H. L. 2025-05-01 doi:10.1101/2025.04.29.650939 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Metabolic modulation of intratumoral cholesterol with gut microbiota for the treatment of colorectal cancer ]]> https://biorxiv.org/content/10.1101/2025.05.02.651972v1?rss=1 Wu, J. Lai, Y. Li, J. Zhai, L. Asthana, P. Chen, L. Chen, M. Chen, B. Gurung, S. Lyu, J. Zhang, Y. Lin, L. Huang, S. Kuang, W. Shi, H. Luo, Y. Kong, X. Wong, S. H. Chan, K. M. Yuan, S. Kwan, H. Y. Yuan, X. Huang, W. Ruan, Y. Lu, H. Wong, C. C. Lyu, A. Bian, Z. Ren, Y. Wu, X. Ma, Y. Wong, H. L. X. 2025-05-08 doi:10.1101/2025.05.02.651972 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Monocyte single cell-type gene expression measured in peripheral blood by DIRECT LS-TA method: the ratio-based biomarkers of (IFI27/PSAP) showed superior performance than interferon score in triage patients with viral infection ]]> https://biorxiv.org/content/10.1101/2025.05.08.652590v1?rss=1 0.9 for the target gene IFI44L). This high level of correlation supports that this simple RBB (DIRECT LS-TA) method can replace the tedious cell sorting approach to obtain single-cell-type gene expression data. All DIRECT LS-TA results of ISGs were raised during viral infection. The best clinical performance in triaging viral infection patients was achieved by IFI27/PSAP or IFI27/CTSS across all datasets. For example, in the GSE111368 dataset, IFI27/PSAP achieved an AUC of 0.94 (95% CI 0.90-0.97) with 88% sensitivity and 95% specificity, surpassing the IFN scores AUC of 0.90 (95% CI 0.85-0.94) with 79% sensitivity and 93% specificity. ConclusionThe DIRECT LS-TA method, utilizing the format of simple two-gene ratio-based biomarkers like IFI27/PSAP, provides a robust and accurate measure of monocyte-specific interferon pathway activation directly from peripheral blood. The superior performance of the DIRECT LS-TA method makes it a promising, readily implementable tool for clinical triage. Its ability to provide single-cell-type specific information, rapid turnaround using standard qPCR/dPCR technology, and enhanced biological specificity make it a valuable molecular host response assessment. ]]> Tang, N. L.-s. Kwan, T.-K. Huang, D. Huang, J. Wang, X. Lui, G. C. Ma, S.-L. Leung, K.-S. 2025-05-11 doi:10.1101/2025.05.08.652590 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Lifespan Trajectories of Alpha Rhythm: Dynamic Shifts in Neural Excitation-Inhibition Balance ]]> https://biorxiv.org/content/10.1101/2025.05.14.653960v1?rss=1 Han, C. Cheung, V. C. K. Chan, R. H. M. 2025-05-14 doi:10.1101/2025.05.14.653960 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ SynLS: A novel diffusion-transformer framework for generating high-quality wearable sensor time series data to enhance health monitoring ]]> https://biorxiv.org/content/10.1101/2025.05.11.653212v1?rss=1 Lin, D. Ji, Y. McArt, J. Li, J. 2025-05-15 doi:10.1101/2025.05.11.653212 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Automated behavior classification of julius seizure mutants in Drosophila reveals stereotyped seizure stages with genotype specificity ]]> https://biorxiv.org/content/10.1101/2025.05.13.653908v1?rss=1 Zhang, H. Deitcher, D. L. Lau, C. G. 2025-05-15 doi:10.1101/2025.05.13.653908 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Aligning Neural Population Patterns Facilitates Motor Learning Transfer ]]> https://biorxiv.org/content/10.1101/2025.05.16.654614v1?rss=1 Zhang, X. Song, Z. Shen, X. Chen, S. Huang, Y. Wang, Y. 2025-05-21 doi:10.1101/2025.05.16.654614 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ A First-in-Class Therapy Targeting Transcription-Replication Conflicts Drives Synthetic Lethality in Homologous Recombination Deficient Cancers ]]> https://biorxiv.org/content/10.1101/2025.05.21.655390v1?rss=1 Lim, Y. C. Lai, S. K. Yang, R. H. Chua, Y. K. Patouret, R. Manoj, V. Soh, C. Lebeau, B. Cham, N. Meng, W. Tey, S. K. Yeap, S. L. Zhang, S. Yong, J. Ali, Z. Mutwil, M. Singh, P. Fullwood, M. Zhong, L. Dong, X. Chiba, S. Koh, C. G. Li, H. Y. 2025-05-24 doi:10.1101/2025.05.21.655390 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Impact of Group Size and Habitat Disturbance on Parasitic Infection in Free-ranging Proboscis Monkeys ]]> https://biorxiv.org/content/10.1101/2025.05.21.655443v1?rss=1 Fitri-Suhaimi, M. N. Frias, L. Zimmermann, E. Lambut, P. Tangah, J. Bernard, H. Subbiah, V. K. Matsuda, I. 2025-05-26 doi:10.1101/2025.05.21.655443 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ FoldBench: An All-atom Benchmark for Biomolecular Structure Prediction ]]> https://biorxiv.org/content/10.1101/2025.05.22.655600v1?rss=1 Xu, S. Feng, Q. Qiao, L. Wu, H. Shen, T. Cheng, Y. Zheng, S. Sun, S. 2025-05-27 doi:10.1101/2025.05.22.655600 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Proximity and current alignment drives fertilisation success in a broadcast-spawning coral ]]> https://biorxiv.org/content/10.1101/2025.05.24.654664v1?rss=1 Ricardo, G. F. Doropoulos, C. Humanes, A. Lachs, L. Martinez, H. M. Sartori, G. Chang, T. K. T. Chui, A. P. Y. Wong, E. L. C. Stevens, J. R. Popovic, I. Guest, J. R. Buccheri, E. Idip, D. Mumby, P. J. 2025-05-28 doi:10.1101/2025.05.24.654664 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ The SAFE Labs Handbook: community-driven commitments for group leaders to improve lab culture ]]> https://biorxiv.org/content/10.1101/2025.05.27.655799v1?rss=1 Dona, E. Gahan, J. M. Lau, P. Jeschke, J. Ott, T. Reinhard, K. Sinigaglia, C. Treur, J. L. Vogl, T. Bugeon, S. Mariotti, L. Rossi, F. F. Coen, P. 2025-05-29 doi:10.1101/2025.05.27.655799 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Impact of Peptide Initial Configuration and Membrane Composition on Melittin's Pore-Forming Ability under Unbiased All-Atom Molecular Dynamics Simulations ]]> https://biorxiv.org/content/10.1101/2025.05.28.656502v1?rss=1 Zhao, Z. Guo, Y. Cai, J. Xie, P. Guan, J. Yao, L. Liu, Y. Chung, C.-R. Lee, T.-Y. Chiang, Y.-C. 2025-05-30 doi:10.1101/2025.05.28.656502 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Neural hierarchy for coding articulatory dynamics in speech imagery and production ]]> https://biorxiv.org/content/10.1101/2025.05.27.656311v1?rss=1 Zhao, Z. Wang, Z. Liu, Y. Qian, Y. Yin, Y. Gao, X. Yuan, B. Tong, S. X. Tian, X. Chen, G. Li, Y. Lu, J. Wu, J. 2025-05-31 doi:10.1101/2025.05.27.656311 Cold Spring Harbor Laboratory Press 2025-05-31 <![CDATA[ The Kocurious case of Noodlococcus: genomic insights into Kocuria rhizophila from characterisation of a laboratory contaminant ]]> https://biorxiv.org/content/10.1101/2025.05.28.656266v1?rss=1 McCallum, G. E. Ho, S. F. S. Cummins, E. A. Wildsmith, A. J. McInnes, R. S. Weigel, C. Tong, L. Y. S. Quick, J. van Schaik, W. Moran, R. A. 2025-06-01 doi:10.1101/2025.05.28.656266 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Pyruvate kinase activates SARM1 to exacerbate axonal degeneration in diabetic peripheral neuropathy ]]> https://biorxiv.org/content/10.1101/2025.05.28.656718v1?rss=1 Liu, J. Li, W. Li, C. Jiang, Y. Zhu, W. J. Zhang, Z. Zhao, Y. J. Lin, J. YU, W. 2025-06-01 doi:10.1101/2025.05.28.656718 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Multimodal Validation of the Existence of Transitional Cerebellar Progenitors in the Human Fetal Cerebellum ]]> https://biorxiv.org/content/10.1101/2025.06.01.657310v1?rss=1 Luo, Z. Xia, M. Zhang, F. Xin, D. Rao, R. Kiang, K. Berry, K. Xiong, Y. Liu, H. Lin, Y. Hu, M. Xin, M. Ma, J. Li, H. Taylor, M. D. Zhou, W. Lu, Q. R. 2025-06-03 doi:10.1101/2025.06.01.657310 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ The hemagglutinin proteins of clades 1 and 2.3.4.4b H5N1 highly pathogenic avian influenza viruses exhibit comparable attachment patterns to avian and mammalian tissues ]]> https://biorxiv.org/content/10.1101/2025.06.02.657404v1?rss=1 Zhu, B. Fung, K. Feng, H. H. Beatty, J. A. Hill, F. Tse, A. C. Brackman, C. J. Sit, T. H. Poujade, A. Gaide, N. Ducatez, M. Foucras, G. Peiris, M. Ti, S.-C. Nicholls, J. M. Yen, H.-L. 2025-06-04 doi:10.1101/2025.06.02.657404 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ Remodelled cholesteryl ester enriched lipid droplets fuel flavivirus morphogenesis ]]> https://biorxiv.org/content/10.1101/2025.06.07.658178v1?rss=1 Banducci-Karp, A. Brixton, S. Shah, P. M. Li, M.-Y. Bancroft, J. Riepsaame, J. Dhaliwal, R. Melia, C. E. Malavige, G. N. Sanyal, S. Bancroft, J. 2025-06-09 doi:10.1101/2025.06.07.658178 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Chromosome-level assembly and annotation of the grey reef shark (Carcharhinus amblyrhynchos) genome ]]> https://biorxiv.org/content/10.1101/2025.06.07.658398v1?rss=1 Dahms, C. Vigliola, L. Cheung, L. H. T. Hui, J. H. L. Momigliano, P. 2025-06-10 doi:10.1101/2025.06.07.658398 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/2025.06.11.656869v1?rss=1 0.9) in predicting patient treatment response. Key predictive features and associated spatial transcriptomic profiles revealed the multi-omic landscape of immunotherapy response and resistance. One such feature was an interface niche expressing restrictive extracellular matrix factors that physically separates tumor tissue and lymphoid aggregates in nonresponders. We integrate this and other spatially-resolved signatures into SPARC, a multi-omic "fingerprint" comprising scores for immunotherapy response and resistance mechanisms. This study lays groundwork for future patient stratification and treatment strategies in cancer immunotherapy. ]]> Wu, Z. Boen, J. Jindal, S. Basu, S. Bieniosek, M. He, S. LaPelusa, M. B. Mayer, A. T. Kaseb, A. O. Zou, J. Sharma, P. Trevino, A. E. 2025-06-13 doi:10.1101/2025.06.11.656869 Cold Spring Harbor Laboratory Press 2025-06-13 <![CDATA[ Evolutionary Genomics Guides Scalable Coral Probiotics for Climate Resilience ]]> https://biorxiv.org/content/10.1101/2025.06.16.659728v1?rss=1 Xie, M. Xiang, N. Liao, T. Cheung, C. T. Lee, C. H. Tse, W. Y. Tsang, K. K. Ho, K. E. He, Q. Dörr, M. Manns, H. Li, P. Xian, Z. Wang, X. Luo, D. Hayden, R. Chei, E. Wan, Z. Thompson, P. Brennan, J. Peixoto, R. S. Cui, G. Mcllroy, S. E. Chui, A. P. Y. Voolstra, C. R. Luo, H. 2025-06-16 doi:10.1101/2025.06.16.659728 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories ]]> https://biorxiv.org/content/10.1101/2025.06.17.659820v1?rss=1 Sun, L. Qin, W. Liang, X. Wang, C. Men, W. Duan, Y. Fan, X.-R. Cai, Q. Qiu, S. Wang, M. Gong, Q. Tian, Y. Liang, P. Liu, Z. Zhang, X. Song, H. Ye, Z. Zhang, P. Dong, Q. Tao, S. Zhu, W. Zhang, J. Xie, F. Feng, J. Zhang, J. Liu, C. Qian, Q. Zhang, B. Meng, M. Hu, L. Gao, J.-H. Jiang, T. Zhu, X. Zhang, Y. Liu, L. Liu, H. Liao, W. Wang, D. Wang, H. Guo, T. Dai, Z. Lui, S. Xu, K. Li, L. Xie, P. Feng, C. Cui, G. Wu, J. Yin, X. Ding, G. Xian, J. Zhao, L. Lu, J. Liu, Z. Han, Y. Yuan, Z. Zhang, X. Si, T. Zhou, F. Bi, Y. Wu, D. Gao, F. Wang, 2025-06-18 doi:10.1101/2025.06.17.659820 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ A map of Non-translated RNA (nt-RNA) junctions in cancer genomes: a database resource of unproductive splicing ]]> https://biorxiv.org/content/10.1101/2025.06.15.659434v1?rss=1 Huang, D. Kwan, T.-K. Ma, S.-L. Tang, N. L.-s. 2025-06-19 doi:10.1101/2025.06.15.659434 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ OmicsSankey: Crossing Reduction of Sankey Diagram on Omics Data ]]> https://biorxiv.org/content/10.1101/2025.06.13.659656v1?rss=1 Li, S. Tan, B. Ouyang, S. Ling, Z. Huo, M. Shen, T. WANG, j. Feng, X. 2025-06-20 doi:10.1101/2025.06.13.659656 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Versatile Vasculature Chips for Ultrasound Localization Microscopy ]]> https://biorxiv.org/content/10.1101/2025.06.15.659747v1?rss=1 Wang, R. Liu, Q. Zhao, X. Lee, W.-N. 2025-06-20 doi:10.1101/2025.06.15.659747 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry ]]> https://biorxiv.org/content/10.1101/2025.06.17.660256v1?rss=1 Chantzi, N. Liew, S. W. Wijaya, A. Chan, C. Mouratidis, I. Amaral, E. d. O. S. Uzun, Y. Hemberg, M. Vasquez, K. M. Kwok, C. K. Georgakopoulos Soares, I. 2025-06-23 doi:10.1101/2025.06.17.660256 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Targeting PI3K Signaling for Broad Inhibition of β-Coronavirus Infection ]]> https://biorxiv.org/content/10.1101/2025.06.22.660949v1?rss=1 Xing, J. Wang, Q. Chen, N. Nutsford, A. N. Sullivan-Hill, B. Taylor, J. A. Rewcastle, G. Flanagan, J. U. Li, S. Shepherd, P. R. Yue, J. Netzler, N. E. 2025-06-23 doi:10.1101/2025.06.22.660949 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Arabidopsis RabGDIs are essential for the asymmetric division of zygotes and embryonic patterning ]]> https://biorxiv.org/content/10.1101/2025.06.23.660972v1?rss=1 Yin, G. Wu, Y. Wang, W. Dun, S. Li, S. Jiang, L. Liang, Z. Zhang, Y. Xiong, F. 2025-06-23 doi:10.1101/2025.06.23.660972 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ Biologically Informative NA Deconvolution (BIND) excavates hidden features of the proteome from missing values in large-scale datasets ]]> https://biorxiv.org/content/10.1101/2025.06.19.660508v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@1a9d7c4org.highwire.dtl.DTLVardef@194b2d9org.highwire.dtl.DTLVardef@169d3bborg.highwire.dtl.DTLVardef@cba0de_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> GUO, W. JIN, W. ZHENG, J. PAN, Y. WANG, R. ZHANG, J. FENG, X. CHEN, L. ZHANG, L. 2025-06-24 doi:10.1101/2025.06.19.660508 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Vitamin D attenuates TNF-α-mediated neurotoxicity and improves functional recovery in experimental intracerebral haemorrhage ]]> https://biorxiv.org/content/10.1101/2025.06.22.660985v1?rss=1 Cheng, S. Y. Kiang, K. M. Zhong, Z. Leung, G. K.-K. 2025-06-25 doi:10.1101/2025.06.22.660985 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Pentose Sugars Encode Sequence-Dependent DNA-RNA Segregation for Biomimetic Multiphase Condensates ]]> https://biorxiv.org/content/10.1101/2025.06.23.656378v1?rss=1 Guo, W. Chen, F. Kinghorn, A. B. Li, X. Pan, Y. Luo, R. Wang, Y. Lau, K. K. Mao, T. Wang, F. Yang, Z. Li, X. Chen, Y. Liu, S. Zhang, Y. Song, Y. Zeng, X. Shum, H. C. 2025-06-25 doi:10.1101/2025.06.23.656378 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignment ]]> https://biorxiv.org/content/10.1101/2025.06.22.660968v1?rss=1 Ji, Y. Liao, H. Guan, J. Shang, J. Sun, Y. 2025-06-27 doi:10.1101/2025.06.22.660968 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Assessing the Effectiveness of 3D-Printed Ceramic Structures for Coral Restoration: Growth, Survivorship, and Biodiversity Using Visual Surveys and eDNA ]]> https://biorxiv.org/content/10.1101/2025.06.23.660499v1?rss=1 Yu, V. Corley, A. McIlroy, S. Wong, J. Wan, Z. W. Lau, H. Baker, D. M. 2025-06-27 doi:10.1101/2025.06.23.660499 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ PHbinder and PSGM: A Cascaded Framework for Epitope Prediction and HLA-I Allele Identification ]]> https://biorxiv.org/content/10.1101/2025.06.25.661428v1?rss=1 Wang, Z. WANG, X. Zhai, J. Xu, S. R. LU, T. 2025-06-27 doi:10.1101/2025.06.25.661428 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Computational Design of Next-Gen Peptide Biopesticides: Targeting the Nicotinic Acetylcholine Receptor in Rice Pests Class ]]> https://biorxiv.org/content/10.1101/2025.06.25.661460v1?rss=1 Chen, X. Zhou, H. He, X. Wang, J. 2025-06-27 doi:10.1101/2025.06.25.661460 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Immunomodulatory effect of HLA-G Overexpressed Mesenchymal Stromal Cell in Cell-based Therapy for Myocardial Infarction ]]> https://biorxiv.org/content/10.1101/2025.07.02.662882v1?rss=1 Sun, S.-J. Zhu, W. Kong, J. Li, H.-X. Jiang, T. Zou, C. 2025-07-03 doi:10.1101/2025.07.02.662882 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Unveiling patterns of roadkill of a migratory amphibian in Hong Kong with implications for mitigation ]]> https://biorxiv.org/content/10.1101/2025.07.04.663120v1?rss=1 Brualla, N. Yip, G. Pickett, E. Fung, H. S. Lau, A. 2025-07-07 doi:10.1101/2025.07.04.663120 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS ]]> https://biorxiv.org/content/10.1101/2025.07.08.663251v1?rss=1 Sang, X. Jiao, H. Meng, Q. Fang, X. Sundaram, K. S. Zhou, J. Xu, Y. Alvarado, A. I. W. Nuryyev, R. L. Ourenik, J. Ourednik, V. Huang, I. S. Liu, X. Mei, Y. Qian, T. Ciechanover, A. Pizzo, D. P. Lane, M. A. Zholudeva, L. V. An, J. Snyder, E. Y. Hu, H. Huang, Z. 2025-07-11 doi:10.1101/2025.07.08.663251 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Methyl gallate Attenuates Post-Stroke Emotional and Cognitive Symptoms by Promoting Hippocampal Neurogenesis via PI3K/GSK3 and AMPK Signaling ]]> https://biorxiv.org/content/10.1101/2025.07.08.663507v1?rss=1 Xu, L. Chen, F. Fan, H. Zhang, L. Yang, F. Pang, J. Pan, B. Wu, X. 2025-07-11 doi:10.1101/2025.07.08.663507 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Interspecific variation in cleaning behaviour and honesty among cleaner wrasses ]]> https://biorxiv.org/content/10.1101/2025.07.08.663626v1?rss=1 Romeo, D. Ranucci, M. Court, M. Pereira, B. Paula, J. R. Schunter, C. 2025-07-11 doi:10.1101/2025.07.08.663626 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ EPEPDI: prediction of binding free energy changes from missense mutations in double and single-stranded DNA-binding proteins ]]> https://biorxiv.org/content/10.1101/2025.07.08.663633v1?rss=1 YU, X. 2025-07-11 doi:10.1101/2025.07.08.663633 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Uncovering bacterial pseudaminylation with pan-specific antibody tools ]]> https://biorxiv.org/content/10.1101/2025.07.13.664564v1?rss=1 Karlic, K. I. Tang, A. H. Madiedo Soler, N. Corcilius, L. Lehmann, C. Debowski, A. Dale, A. L. Zavan, L. Cielesh, M. Adewale, A. P. Moulton, K. D. Li, L. Guan, C. Kaparakis-Liaskos, M. Howden, B. P. Wei, R. Li, X. Dube, D. H. Cordwell, S. J. Larance, M. Stubbs, K. A. Carter, G. P. Scott, N. Goddard-Borger, E. D. Payne, R. J. 2025-07-13 doi:10.1101/2025.07.13.664564 Cold Spring Harbor Laboratory Press 2025-07-13 <![CDATA[ Assessing large-scale genomic language models in predicting personal gene expression: promises and limitations ]]> https://biorxiv.org/content/10.1101/2025.07.09.664024v1?rss=1 Li, S. Luo, R. Huang, Y. 2025-07-14 doi:10.1101/2025.07.09.664024 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Inferring Progressive Disconnection in Alzheimer's Disease with Probabilistic Boolean Networks ]]> https://biorxiv.org/content/10.1101/2025.07.10.664143v1?rss=1 Liu, Z. Zhang, L. 2025-07-15 doi:10.1101/2025.07.10.664143 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Autonomous Reef Monitoring Structures (ARMS) Reveal Human-Induced Biodiversity Shifts in Urban Coastal Ecosystems ]]> https://biorxiv.org/content/10.1101/2025.07.11.664282v1?rss=1 WAN, Z. Guibert, I. Chung, W. Y. H. Ho, C. Au, W. C. R. Brennan, J. B. Chan, L. F. M. Chei, E. Conti-Jerpe, I. Corley, A. Cybulski, J. D. Hayden, R. Lee, S. Y. J. McLeod, W. Tompson, P. McIlroy, S. E. Baker, D. M. 2025-07-15 doi:10.1101/2025.07.11.664282 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Prediction of cellular morphology change under perturbations with transcriptome-guided diffusion model ]]> https://biorxiv.org/content/10.1101/2025.07.16.665106v1?rss=1 Wang, X. Fan, Y. Guo, Y. Fu, C. Lee, K. Dallakyan, K. Li, Y. Yin, Q. Li, Y. Song, L. 2025-07-16 doi:10.1101/2025.07.16.665106 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ AtlasAgent: Vision language model and Agent-guided Framework for Evaluation of Atlas-scale Single-cell Integration ]]> https://biorxiv.org/content/10.1101/2025.07.15.663271v1?rss=1 Yin, D. Zhang, Z. Liu, X. Ni, K. Su, H. Li, N. L. L. Dong, H. Zhao, Q. Lin, X. Tian, L. Meng, Y. Ho, J. W. K. 2025-07-18 doi:10.1101/2025.07.15.663271 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ A Deep Learning-based Method for Drug Molecule Representation and Property Prediction ]]> https://biorxiv.org/content/10.1101/2025.07.15.665023v1?rss=1 Zhang, Q. Yu, X. Wei, y. Wang, Z.-H. Yu, D.-J. 2025-07-18 doi:10.1101/2025.07.15.665023 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Molecular Clock Dating of Deep-Time Evolution Using Complex Mixture Models ]]> https://biorxiv.org/content/10.1101/2025.07.17.665246v1?rss=1 Wang, S. Meade, A. 2025-07-21 doi:10.1101/2025.07.17.665246 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ OmicsNavigator: an LLM-driven multi-agent system for autonomous zero-shot biological analysis in spatial omics ]]> https://biorxiv.org/content/10.1101/2025.07.21.665821v1?rss=1 LI, Y. Vakharia, N. Mayer, A. T. Luo, R. Trevino, A. E. Wu, Z. 2025-07-25 doi:10.1101/2025.07.21.665821 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Towards universal modeling of transcript isoform expression levels ]]> https://biorxiv.org/content/10.1101/2025.07.21.665977v1?rss=1 Chow, S. H.-C. Shi, C. H. Deshpande, A. Cao, Q. Yip, K. Y. 2025-07-25 doi:10.1101/2025.07.21.665977 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Can large language models reliably extract human disease genes from full-text scientific literature? ]]> https://biorxiv.org/content/10.1101/2025.07.27.667022v1?rss=1 Yin, D. Leung, M. K. S. Pun, D. W. H. Chen, F. H. Kwon, J. Y. Lin, X. Ho, J. W. K. 2025-07-31 doi:10.1101/2025.07.27.667022 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ MSF-CPMP: A Novel Multi-Source Feature Fusion Model for Prediction of Cyclic Peptide Membrane Permeability ]]> https://biorxiv.org/content/10.1101/2025.07.28.667130v1?rss=1 Zhang, Y. Chen, Z. Wan, Z. Jiang, Q. Lu, X. Yan, B. Qin, J. Liu, Y. Wang, J. 2025-07-31 doi:10.1101/2025.07.28.667130 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ DeepADR: Multi-modal Prediction of Adverse Drug Reaction Frequency by Integrating Early-Stage Drug Discovery Information via Kolmogorov-Arnold Networks ]]> https://biorxiv.org/content/10.1101/2025.07.29.667409v1?rss=1 Wan, J. Jia, C. Dong, D. Chen, Y. Lin, Y.-C.-D. He, Y. Huang, H.-Y. Huang, H.-D. 2025-08-01 doi:10.1101/2025.07.29.667409 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Reliability and precision of thermal imaging measurements to study animal behaviour and welfare ]]> https://biorxiv.org/content/10.1101/2025.07.31.668027v1?rss=1 Bhattacharjee, D. Mason, M. A. McElligott, A. G. 2025-08-01 doi:10.1101/2025.07.31.668027 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Nanopore direct-RNA sequencing reveals TGEV epitranscriptomic and transcriptomic landscapes modulated by gene 7 ]]> https://biorxiv.org/content/10.1101/2025.08.05.668584v1?rss=1 JIANG, Q. GUO, Z. TAN, L. SHAO, Y. ZHAO, X. WANG, H. Li, R. 2025-08-05 doi:10.1101/2025.08.05.668584 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Maternal IBD-related antibodies are associated with early life gut inflammatory status and microbiota composition: insights from cord blood ]]> https://biorxiv.org/content/10.1101/2025.08.04.668517v1?rss=1 Kim, T. Nicoletti, P. Estevinho, M. M. Tarassishin, L. Picker, M. Debebe, A. Nguyen, I. Dutra-Clarke, R. Young, C. Stone, J. Shitrit, A. B.-G. Agrawal, M. Colombel, J.-F. Torres, J. Ng, S. C. Zhang, L. McGovern, D. P. B. Peter, I. 2025-08-06 doi:10.1101/2025.08.04.668517 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Knowledge, attitudes, and practices of para-veterinary workers about ticks and tick-borne diseases in three provinces of Pakistan ]]> https://biorxiv.org/content/10.1101/2025.08.05.668794v1?rss=1 Hussain, A. Hussain, S. Rajput, M. Sajid, M. S. Sparagano, O. Mateus-Pinilla, N. Smith, R. L. 2025-08-07 doi:10.1101/2025.08.05.668794 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Rewired NAD+ metabolism promotes NF-κB-mediated oxidative stress and disrupts lipid homeostasis in liver fibrosis progression ]]> https://biorxiv.org/content/10.1101/2025.08.06.668888v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@e39d72org.highwire.dtl.DTLVardef@175cdc7org.highwire.dtl.DTLVardef@118d707org.highwire.dtl.DTLVardef@1cd3a43_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ngan, H.-L. Cheu, J. W.-S. Kwan, K. K.-L. Wong, C. C.-L. Yan, H. Cai, Z. 2025-08-08 doi:10.1101/2025.08.06.668888 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Spatial proximity and dyadic social relationships affect ungulate behavioral synchrony ]]> https://biorxiv.org/content/10.1101/2025.08.06.668986v1?rss=1 Hodgson, G. M. W. Flay, K. J. Perroux, T. A. McElligott, A. G. 2025-08-09 doi:10.1101/2025.08.06.668986 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Protein Function Prediction via Contig-Aware Multi-Level Feature Integration ]]> https://biorxiv.org/content/10.1101/2025.08.07.669053v1?rss=1 Yang, L. Du, K. Lu, Y. Wang, M. Zhang, H. Yang, S. Lin, Y. Zhuo, J. Zhang, D. Jiang, Y. Zhang, X. Li, S. 2025-08-11 doi:10.1101/2025.08.07.669053 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells ]]> https://biorxiv.org/content/10.1101/2025.08.10.669524v1?rss=1 HE, L. Fu, Y. Wang, Z. Zhou, Q. Sun, H. Wang, H. 2025-08-11 doi:10.1101/2025.08.10.669524 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Light-dependent switching of circling handedness in microswimmer navigation ]]> https://biorxiv.org/content/10.1101/2025.08.08.669292v1?rss=1 Wang, Z. Bentley, S. A. Li, J. Wan, K. Y. Tsang, A. C. H. 2025-08-12 doi:10.1101/2025.08.08.669292 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Mediator Subunit MED16 Collaborates with UBP1-TFCP2 to Control Transcriptional Activation or Repression via Promoter Positional Specificity ]]> https://biorxiv.org/content/10.1101/2025.08.12.669905v1?rss=1 Zheng, Y. Zhao, X. Yang, M. Yang, X. Zhu, H. Zhou, Q. Yu, X. Wang, G. 2025-08-13 doi:10.1101/2025.08.12.669905 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ SFTSV NSs protein is a novel tick antiviral RNAi response suppressor ]]> https://biorxiv.org/content/10.1101/2025.08.14.670292v1?rss=1 Fares, M. McFarlane, M. Parry, R. Arif, R. Clarke, A. T. Kamel, W. Davies, K. Bell-Sakyi, L. Petit, M. J. Schnettler, E. Castello, A. Kohl, A. Brennan, B. 2025-08-14 doi:10.1101/2025.08.14.670292 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Foraminiferal environmental DNA reveals late Holocene sea-level changes ]]> https://biorxiv.org/content/10.1101/2025.08.12.669806v1?rss=1 Liu, Z. Khan, N. S. Yu, H. K. Y. Chung, A. Schweizer, M. Schunter, C. 2025-08-15 doi:10.1101/2025.08.12.669806 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Molecular insights into ligand recognition and signaling of GPR99/OXGR1 ]]> https://biorxiv.org/content/10.1101/2025.08.16.670657v1?rss=1 Liu, A. Liu, Y. Long, Y. Ye, R. D. 2025-08-16 doi:10.1101/2025.08.16.670657 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ Phosphate limitation triggers Fe3+-dependent polymyxin resistance in Enterobacteriaceae ]]> https://biorxiv.org/content/10.1101/2025.08.18.670855v1?rss=1 ZHANG, G. Deng, Z. JIANG, J. WANG, M. Wang, X. Liu, X. Yan, A. 2025-08-19 doi:10.1101/2025.08.18.670855 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ High-salt diet modulates endocrine regulation between cortisol and FGF23 ]]> https://biorxiv.org/content/10.1101/2025.08.14.670453v1?rss=1 Moor, M. Kopper, K. Pechere-Bertschi, A. Sagmeister, M. S. Hardy, R. Feraille, E. Fuster, D. G. Loffing, J. Pathare, G. 2025-08-20 doi:10.1101/2025.08.14.670453 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Multi-omics reveals lipid metabolism, mitochondrial and extracellular matrix dysregulation of diabetic cardiomyopathy in the human heart ]]> https://biorxiv.org/content/10.1101/2025.08.21.671651v1?rss=1 Lu, Q. Tang, S. Wu, Y. Chen, L. Liang, M. Fang, S. Chen, J. Wen, P. Jin, L. Yu, J. Jiao, F. Wu, Y. Jiang, G. 2025-08-22 doi:10.1101/2025.08.21.671651 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Mapping antigenic evolution of influenza A virus using deep learning-based prediction of hemagglutination inhibition titers ]]> https://biorxiv.org/content/10.1101/2025.08.22.670987v1?rss=1 Yang, B. Yin, Y. Wang, L. Tsang, K. L. T. Wu, N. C. Salje, H. 2025-08-23 doi:10.1101/2025.08.22.670987 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ NicheScope: Identifying Multicellular Niches and Niche-Regulated Cell States in Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.08.21.671426v1?rss=1 Yu, X. Wan, X. Tian, L. Chen, Y. Liu, Y. Yu, T. Yang, C. Xiao, J. 2025-08-25 doi:10.1101/2025.08.21.671426 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Endogenous flow and dialytaxis govern aging of Adenosine 5'-triphosphate (ATP) condensates ]]> https://biorxiv.org/content/10.1101/2025.08.23.671873v1?rss=1 Chen, F. Dear, A. J. Kow, P. D. Wang, Y. Michaels, T. Shum, H. C. 2025-08-28 doi:10.1101/2025.08.23.671873 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Avoidance Of Rejuvenation: A Stress Test For Evolutionary Theories Of Aging ]]> https://biorxiv.org/content/10.1101/2025.08.24.671987v1?rss=1 Aisin, S. I. Lidskii, B. V. Lidsky, P. V. 2025-08-28 doi:10.1101/2025.08.24.671987 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ A Multi-Disciplinary Framework for Decoding S1PR1-Selective Agonism ]]> https://biorxiv.org/content/10.1101/2025.08.27.672536v1?rss=1 Yu, L. Jiao, H. Pang, B. Ti, R. Gan, B. Qin, Z. Wang, J. Zhu, L. Hu, H. Ren, R. 2025-08-29 doi:10.1101/2025.08.27.672536 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Disgust propensity, not disgust sensitivity, shapes the reactivity of a subjective disgust circuit in humans ]]> https://biorxiv.org/content/10.1101/2025.08.27.672493v1?rss=1 Gan, X. Zheng, Z. Zhang, R. Zhou, F. Xu, T. Qiu, N. Wang, J. Jiang, H. Gao, S. Wu, Y. Klugah-Brown, B. Yao, D. Becker, B. 2025-09-01 doi:10.1101/2025.08.27.672493 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Temporal and spatial variability of mudflat and mangrove foraminiferal eDNA assemblages and its implication for sea-level reconstruction ]]> https://biorxiv.org/content/10.1101/2025.08.28.672876v1?rss=1 Liu, Z. Khan, N. S. Yu, H. K. Y. Schweizer, M. Walker, J. S. Schunter, C. 2025-09-02 doi:10.1101/2025.08.28.672876 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Therapeutic Salmonella induces long-term protective trained immunity in NK cells against cancer metastasis ]]> https://biorxiv.org/content/10.1101/2025.08.29.673007v1?rss=1 Rong, L. Hu, J. Jin, W. Li, R. Wu, Y. Zhou, N. zhou, z. Shakhawat, H. Wang, X. Han, S. Gong, H. Lin, X. Li, W. He, Y. Kim, S. Zhao, X. Lin, Q. Huang, J.-D. 2025-09-03 doi:10.1101/2025.08.29.673007 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Guess till correct: Gungnir codec enabling high error-tolerance and low-redundancy DNA storage through substantial computing power ]]> https://biorxiv.org/content/10.1101/2025.08.29.673174v1?rss=1 Zhang, J. Chen, L. Sun, J. Li, S. Zhou, Y. Wu, Z. Li, C. Zheng, Z. Luo, R. 2025-09-04 doi:10.1101/2025.08.29.673174 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ RNA helicase Ddx21 safeguards fetal HSPC expansion by recruiting Kdm5a to epigenetically sustain ribosomal and hematopoietic gene transcription ]]> https://biorxiv.org/content/10.1101/2025.09.04.674186v1?rss=1 Leung, A. O.-W. Li, C. Huang, X. Fan, Z. Chen, Y. Liu, J. Lin, H.-M. Cui, X. Zhang, F. Niu, R. Leung, K.-T. Cheung, H. H. 2025-09-06 doi:10.1101/2025.09.04.674186 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ UCHL3 regulates subgenomic flaviviral RNA condensates to promote virus propagation ]]> https://biorxiv.org/content/10.1101/2025.09.05.674517v1?rss=1 Trejo-Cerro, O. Beekmayer-Dhillon, A. Teo, Q. W. Siu, L. Li, M. Sanyal, S. 2025-09-07 doi:10.1101/2025.09.05.674517 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Knowledge-Driven Interpretable Neural Networks for Mechanistic Insight ]]> https://biorxiv.org/content/10.1101/2025.09.08.674894v1?rss=1 Ke, Y. Yu, T. 2025-09-08 doi:10.1101/2025.09.08.674894 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Localized Space Coding and Phase Coding Complement Each Other to Achieve Robust and Efficient Spatial Representation ]]> https://biorxiv.org/content/10.1101/2025.09.07.674775v1?rss=1 Chu, T. Wu, Y. Qiu, W. Jiang, Z. Burgess, N. HONG, B. WU, S. 2025-09-12 doi:10.1101/2025.09.07.674775 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Total variation of quantitative phase map reveals cellular Young's modulus ]]> https://biorxiv.org/content/10.1101/2025.09.08.674874v1?rss=1 Wang, Z. Wang, Z. Sun, D. Li, Y. Nie, Y. Shi, J. Zhou, R. Liu, L. Long, M. Yang, Y. 2025-09-12 doi:10.1101/2025.09.08.674874 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Neurophysiological Sensitivity to Envelope and Pulse Timing Interaural Time Differences in Cochlear Implanted Rats with Different Hearing Experiences ]]> https://biorxiv.org/content/10.1101/2025.09.11.675523v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@1874d3borg.highwire.dtl.DTLVardef@1df79feorg.highwire.dtl.DTLVardef@c244e5org.highwire.dtl.DTLVardef@39220f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fang, S. Fleiner, T. Peng, F. Buchholz, S. Zeeshan, M. Rosskothen-Kuhl, N. Schnupp, J. 2025-09-15 doi:10.1101/2025.09.11.675523 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Modification of RNAs in natural rG4 (MoRNiNG), A Database of RNA Modification Sites Associated with the Dynamics of RNA Secondary Structures ]]> https://biorxiv.org/content/10.1101/2025.09.11.675469v1?rss=1 Zhou, Y. Lyu, S. Liew, S. W. Mou, X. Hoffecker, I. Yan, J. Li, Y. Kwok, C. K. Zhang, J. 2025-09-16 doi:10.1101/2025.09.11.675469 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Excitatory cholecystokinin neurons in CA3 area regulate the navigation learning and neuroplasticity ]]> https://biorxiv.org/content/10.1101/2025.09.13.676045v1?rss=1 Huang, F. Baset, A. Bello, S. T. 2025-09-17 doi:10.1101/2025.09.13.676045 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Distinct neural moderators of resilience and vulnerability confer heterogeneous outcomes following early-life adversity ]]> https://biorxiv.org/content/10.1101/2025.09.16.676492v1?rss=1 Fan, H. Becker, B. Zhang, J. 2025-09-17 doi:10.1101/2025.09.16.676492 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Synaptic and neural pathway redundancy enables the robustness of a sensory-motor reflex and promotes predation escape in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.09.18.677212v1?rss=1 He, H. Fong, E. K. H. Kumar, S. Lee, H. M. T. Leifer, A. M. Chalfie, M. Zheng, C. 2025-09-19 doi:10.1101/2025.09.18.677212 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Re-evaluating the Impact of Biological Sex on Atherosclerosis in Apoe-/- and Ldlr-/- mice ]]> https://biorxiv.org/content/10.1101/2025.09.19.677480v1?rss=1 Zhao, Y. Wang, L. Berk, B. C. Strijdom, H. Huang, Y. Weng, J. Xu, S. 2025-09-21 doi:10.1101/2025.09.19.677480 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ BCKDK, a novel hypoxia-responsive kinase that exacerbates cerebral ischemia injury ]]> https://biorxiv.org/content/10.1101/2025.09.22.677943v1?rss=1 Liao, B. Zhang, F. Yi, X. Zhang, Z. Jin, L. Hoo, R. L. C. Geng, L. Jia, W. 2025-09-23 doi:10.1101/2025.09.22.677943 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Redirection of SARS-CoV-2 to phagocytes by intranasal sACE2-Fc as a universal decoy confers complete prophylactic protection ]]> https://biorxiv.org/content/10.1101/2025.09.23.677998v1?rss=1 Wang, J. Li, J. Chin, A. W. Luo, B. Wei, J. Qiu, J. Ren, J. Xia, Y. Braun, T. L M Poon, L. L. M. Feng, B. 2025-09-23 doi:10.1101/2025.09.23.677998 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Unraveling the Molecular and Physiological Roles of Signal Peptide Peptidase A (SppA) in Flavobacterium columnare ]]> https://biorxiv.org/content/10.1101/2025.09.26.678728v1?rss=1 Zhu, R. Zhong, L. Xun, Y. Zheng, s. Zhu, Y. Cai, W. 2025-09-29 doi:10.1101/2025.09.26.678728 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Dynamic Meta-Networking Identifies Distinct Network Correlates of Positive and Negative Formal Thought Disorder in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.09.29.679140v1?rss=1 Hu, Z. Chen, J. Yang, J. Xie, H. Liu, J. Zhang, P. Wu, Q. Doosti, M.-H. Rong, C. Wang, J. Song, X. Tang, X. Yuan, B. Cao, L. 2025-10-01 doi:10.1101/2025.09.29.679140 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Evolutionarily Conserved and Divergent Mechanisms of Dual Ca2+ Sensors in Synaptic Vesicle Exocytosis ]]> https://biorxiv.org/content/10.1101/2025.09.30.679486v1?rss=1 Li, L. Xia, J. Wang, J. Yu, X. Hu, J. Richmond, J. Liu, H. Hu, Z. 2025-10-01 doi:10.1101/2025.09.30.679486 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ The genetic architecture of trabecular bone score and association with fracture: a genome-wide association and meta-analysis ]]> https://biorxiv.org/content/10.1101/2025.10.01.678241v1?rss=1 Lu, H. Tibbitts, G. LI, G. H.-Y. Frysz, M. Lary, C. W. Trajanoska, K. Das, N. R. de Groot, L. Cheung, C.-L. van Schoor, N. M. Uitterlinden, A. G. van der Velde, N. Tobias, J. H. Rivadeneira, F. Evans, D. M. Kiel, D. P. Kemp, J. P. Medina-Gomez, C. 2025-10-03 doi:10.1101/2025.10.01.678241 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ A knowledge-guided approach to recovering important rare signals from high-dimensional single-cell data ]]> https://biorxiv.org/content/10.1101/2025.10.01.679835v1?rss=1 Zhang, Z. Chen, J. Wu, H. Li, K. Y. Adams, P. D. Itkin-Ansari, P. Yip, K. Y. 2025-10-03 doi:10.1101/2025.10.01.679835 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Magnesium isoglycyrrhizinate alleviates alcohol-associated liver disease through targeting HSD11B1 ]]> https://biorxiv.org/content/10.1101/2025.10.02.679991v1?rss=1 Xiao, L. Li, L. Wu, S. Che, Z. Du, Y. Zheng, J. Yan, J. Wang, H. Zhang, H. Li, Y. Xiao, J. 2025-10-03 doi:10.1101/2025.10.02.679991 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Lysine-R2HGylation identified as a post-translational modification in R2HG-elevated cancers ]]> https://biorxiv.org/content/10.1101/2025.10.03.680013v1?rss=1 Zhao, Q. Huang, P. Yuan, C. Xia, P. Gu, Q. Yang, T. Li, X. D. Tian, R. Yang, D. 2025-10-04 doi:10.1101/2025.10.03.680013 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Sociality and nesting strategy shape the bimodal diversity gradient in bees ]]> https://biorxiv.org/content/10.1101/2025.10.03.680340v1?rss=1 Heinrich, L. R. Martins, A. C. Bossert, S. Hughes, A. C. Orr, M. C. Seltmann, K. C. Swain, A. Vasconcelos, T. 2025-10-04 doi:10.1101/2025.10.03.680340 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Environmental DNA Metabarcoding Effectively Detects Invasive Species, Pests, and Community Changes in Taiwan Rice Fields ]]> https://biorxiv.org/content/10.1101/2025.10.03.680395v1?rss=1 Banerjee, P. Dey, G. Stewart, K. A. Barnes, M. A. Taharia, M. Seymour, M. Wang, C.-W. Sharma, R. K. Maity, J. P. Chen, C.-Y. 2025-10-04 doi:10.1101/2025.10.03.680395 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Engineering magnetically guided bacteriophages for precision antimicrobial therapy and targeted biofilm eradication ]]> https://biorxiv.org/content/10.1101/2025.10.05.680512v1?rss=1 Ma, Y. Liu, S. Y. Hu, M. Wei, W. Ma, K. Zhu, B. Li, S. Khoo, B. L. Chua, S. L. 2025-10-06 doi:10.1101/2025.10.05.680512 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ ceQTL: A co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation ]]> https://biorxiv.org/content/10.1101/2025.10.06.680553v1?rss=1 Wang, P. Liu, L. Wang, J. Yang, P. Sun, Z. 2025-10-06 doi:10.1101/2025.10.06.680553 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ hpGRISZ: a high-performance fluorescent biosensor for in vivo imaging of synaptic zinc dynamics ]]> https://biorxiv.org/content/10.1101/2025.10.06.680726v1?rss=1 Zhang, H. Kumar, M. Correia, R. Yang, S. Huang, W. Soares-Cunha, C. Cody, P. A. Zhang, Y. Tian, X. Zhao, S. Drobizhev, M. Rodrigues, A. J. Tzounopoulos, T. Ai, H. 2025-10-07 doi:10.1101/2025.10.06.680726 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Area-Based Selection of Binding Interfaces for Structural Prediction of Protein-Protein Complexes ]]> https://biorxiv.org/content/10.1101/2025.10.07.680849v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@fc8db3org.highwire.dtl.DTLVardef@bb0f62org.highwire.dtl.DTLVardef@ef1b84org.highwire.dtl.DTLVardef@1f79d8b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, Y. X. Zhu, B. T. 2025-10-07 doi:10.1101/2025.10.07.680849 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Improving the Accuracy of Distance-Based Protein-Ligand Binding Affinity Prediction Using Linear Regression and Artificial Neural Network ]]> https://biorxiv.org/content/10.1101/2025.10.07.680851v1?rss=1 View larger version (50K): org.highwire.dtl.DTLVardef@10e86e4org.highwire.dtl.DTLVardef@b9ec82org.highwire.dtl.DTLVardef@565a90org.highwire.dtl.DTLVardef@153c4ef_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIBy using the newest data in PDBbind (v.2024) to train the linear, neural network and mixed models, the quantitative distance-energy relationships are further explored and improved to predict the binding affinity of protein-ligand complexes. C_LIO_LIThe power exponents of distance in the traditional energy terms are expanded to characterize the distance-energy relationships accurately at atom level for protein-ligand interactions. C_LIO_LIThe best models are superior to the sophisticated machine learning-based scoring functions developed before. C_LI ]]> Yang, Y. X. Zhu, B. T. 2025-10-08 doi:10.1101/2025.10.07.680851 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Optogenetic construction of de novo integrin-adhesion complexes reveals role for biocondensation in adhesion nucleation ]]> https://biorxiv.org/content/10.1101/2025.10.08.681107v1?rss=1 Xiong, M. Leong, T. L. Chen, M. Chen, J. Lee, T. C. Yu, C.-H. Efremov, A. K. Johnson, H. E. 2025-10-08 doi:10.1101/2025.10.08.681107 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Sourdough starter-inspired living materials grown from probiotic consortia with engineered division-of-labor ]]> https://biorxiv.org/content/10.1101/2025.10.09.681537v1?rss=1 Wang, S. Xu, Y. Zhan, Y. Echavarria Galindo, M. Chau, S. C. Y. Cui, L. Shaw, W. M. Xie, W. J. Tan, H. Y. Lin, C. Jiang, X. Bian, Z. Dedon, P. Church, G. M. Lu, T. K. Tang, T.-C. LAI, Y. 2025-10-10 doi:10.1101/2025.10.09.681537 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ CoxMDS: Multiple Data Splitting for High-dimensional Mediation Analysis with Survival Outcomes in Epigenome-wide Studies ]]> https://biorxiv.org/content/10.1101/2025.10.11.681836v1?rss=1 Yao, M. Tian, P. Li, X. Bian, S. Wang, G. Gu, Y. Navas-Acien, A. Vardarajan, B. N. Belsky, D. W. Miller, G. W. Baccarelli, A. A. Liu, Z. 2025-10-13 doi:10.1101/2025.10.11.681836 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ An ultra-long acting insulin enables glucose-synchronised release ]]> https://biorxiv.org/content/10.1101/2025.10.12.681846v1?rss=1 Zhang, Y. Zhang, J. Ji, K. Mei, S. Su, C. Wang, Y. Xu, G. Zhang, H. Lin, J. Huang, X. Zhang, X. Xu, K. Xu, J. Lu, L. Zhou, M. Huang, W. Yao, J. Jiang, C. Yan, J. Liu, X. Liu, P. Buse, J. B. Zhang, S. Wang, J. Gu, Z. 2025-10-14 doi:10.1101/2025.10.12.681846 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Auditory Stimulus Information Entropy Modulates Inter-Brain Synchronization: Evidence from Wireless EEG Hyperscanning ]]> https://biorxiv.org/content/10.1101/2025.10.14.681560v1?rss=1 MMN {approx} ASSR > Resting State); Alpha band had highest PLV in Resting State. Critically, PLVs differed significantly between any two conditions, and each experimental conditions PLV was also significantly different from that of the Resting State. Findings confirm a 6 Hz-specific positive association between auditory uncertainty and IBS, suggesting musical elements may facilitate social interaction by modulating entropy, with entropy-IBS relations showing frequency dependence. ]]> Liao, J. Huang, G. Zhao, W. Li, C. X. Cheng, P. W. C. Sun, R. Yuan, H.-Y. Gao, J. Ho, R. T. H. 2025-10-15 doi:10.1101/2025.10.14.681560 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ An EEG Investigation of Neural Dynamics of Empathy Influenced by Congruent and Incongruent Pain Expressions in Autistic and Neurotypical Adults ]]> https://biorxiv.org/content/10.1101/2025.10.14.681876v1?rss=1 Wang, X. Tong, S. X. 2025-10-15 doi:10.1101/2025.10.14.681876 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Human Organoids Reveal PTEN-driven Mesendoderm Specification via Retinoic Acid Signaling Suppression ]]> https://biorxiv.org/content/10.1101/2025.10.17.682808v1?rss=1 Wang, W. He, Q. Zhang, H. Chan, S.-W. Xiong, Z. Tang, H. Lv, Y. Su, X. Guo, Y. Fan, Y. Liu, X. Bian, X. Chan, A. M. Liu, H. Lu, G. Chan, W.-Y. 2025-10-17 doi:10.1101/2025.10.17.682808 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Cancer-specific sialylation of insulin-like growth factor 1 receptor impairs therapeutic antibody binding and efficacy ]]> https://biorxiv.org/content/10.1101/2025.10.17.682592v1?rss=1 View larger version (14K): org.highwire.dtl.DTLVardef@17c6d5corg.highwire.dtl.DTLVardef@1efe2f7org.highwire.dtl.DTLVardef@1dd05aorg.highwire.dtl.DTLVardef@159fb23_HPS_FORMAT_FIGEXP M_FIG C_FIG Synopsis2-6 sialylation of IGF1R Asn-607 by ST6GAL1 is prevalent in cancer. This modification disrupts the interaction of IGF1R with therapeutic mAb ganitumab. Removal of sialylation augments ganitumab efficacy. ]]> Hassan, A. A. Chen, Q. Fung, K. S. W. To, S. K. Y. Cheung, L. W. T. Zhang, C. Liu, N. Lok, C. N. Che, C.-M. Ip, P. P. C. Li, X. Wong, A. S.-T. 2025-10-19 doi:10.1101/2025.10.17.682592 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Lipid Metabolism Remodeling in Human Cardiomyocyte Differentiation and Maturation ]]> https://biorxiv.org/content/10.1101/2025.10.21.682321v1?rss=1 Tang, H. Liu, R. Xiong, Z. He, Q. Lu, G. Chan, W.-Y. WANG, W. 2025-10-22 doi:10.1101/2025.10.21.682321 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ On-The-Fly Live-Cell Intrinsic Morphological Drug and Genetic Screens by Gigapixel-per-second Spinning Arrayed Disk Imaging ]]> https://biorxiv.org/content/10.1101/2025.10.21.683625v1?rss=1 Siu, D. M. D. Wong, V. M. L. Wang, B. Wong, J. S. J. Wong, A. S. L. Tsia, K. K. 2025-10-22 doi:10.1101/2025.10.21.683625 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Structural basis of the π-stacking network governing cofactor-substrate cooperativity of SbSOMT ]]> https://biorxiv.org/content/10.1101/2025.10.22.683835v1?rss=1 Pow, K. C. Zhang, N. Yan, M. Wang, X. Lui, A. C. W. Lo, C. Hao, Q. 2025-10-22 doi:10.1101/2025.10.22.683835 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Abnormally increased intrinsic neural timescales in sensory and default mode networks in cocaine use disorder ]]> https://biorxiv.org/content/10.1101/2025.10.22.683885v1?rss=1 Tang, X. Di, T. Sheng, J. Sun, Y. Luo, W. Zhang, M. 2025-10-23 doi:10.1101/2025.10.22.683885 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Astrocytes control the Neuroinflammation and ILC2 response through IL-33/ST2 signaling, during protection against Cerebral Malaria in Toxoplasma-P. berghei coinfected Mice ]]> https://biorxiv.org/content/10.1101/2025.10.24.684259v1?rss=1 leleu, i. Keswani, T. Herbert, F. Picavet, C. Arnaud, M. Marion, S. glineur, c. PIED, S. 2025-10-25 doi:10.1101/2025.10.24.684259 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Web engine for tumor pathology image retrievals on massive scales ]]> https://biorxiv.org/content/10.1101/2025.10.25.684566v1?rss=1 Zhong, Z. Huang, J. Li, X. Song, L. Gong, L. Ru, B. Paul, R. Levine, J. Zhang, Y. Aldape, K. Jiang, P. 2025-10-26 doi:10.1101/2025.10.25.684566 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Stand age drives changes in the biodiversity and microclimate of oil palm plantations ]]> https://biorxiv.org/content/10.1101/2025.10.31.682997v1?rss=1 de Lorm, T. A. Barclay, M. Bernard, H. Bush, E. Carbone, C. Hardwick, S. R. Milne, S. Parrett, J. M. Pfeifer, M. Rowcliffe, J. M. Sharp, A. Slade, E. Wearn, O. Ewers, R. M. 2025-10-31 doi:10.1101/2025.10.31.682997 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Clair-Mosaic: A deep-learning method for long-read mosaic small variant calling ]]> https://biorxiv.org/content/10.1101/2025.10.31.685831v1?rss=1 Chen, L. Zheng, Z. He, M. Wong, A. O. K. Yu, X. Li, J. Zhang, J. Zhou, Y. Luo, R. 2025-11-02 doi:10.1101/2025.10.31.685831 Cold Spring Harbor Laboratory Press 2025-11-02 <![CDATA[ Dangling Ends of Third Strand and Duplex Drive Nucleic Acid Triplex Stabilization through Bimodal Association ]]> https://biorxiv.org/content/10.1101/2025.11.02.686076v1?rss=1 DNA*DNA-DNA > RNA*RNA-RNA, with no DNA*RNA-RNA triplex forming, is known, the kinetic roles of terminal residues remain poorly understood. Here, we employ bio-layer interferometry (BLI) and circular dichroism (CD) spectroscopy to demonstrate that dangling ends from both the third strand (triplex-forming oligonucleotide, TFO) and the duplex dramatically enhance triplex stability. Kinetic analysis reveals this stabilization is primarily driven by a marked increase in the association rate (k{square}{square}). Crucially, creating a single-base-pair dangling end at either terminus of the duplex enhanced triplex stability more effectively than blunt ends. For example, DNA TFO dTFO5 binding to d(HP5+TA) was enhanced compared to dHP5, and similarly RNA TFO rTFO5 binding to RNA duplex r(HP5+UA) and DNA duplex d(HP5+TA) showed stronger affinity and faster association than to blunt-ended rHP5 and dHP5. Interestingly, removal of a terminal base pair from the blunt-end duplex, generating a TFO dangling end, also enhances binding affinity and association rate. This indicates that both duplex and TFO dangling ends provide critical nucleation platforms, while blunt-ended terminal triples are dynamic and contribute minimally to stability. Thus, our work establishes that optimal triplex formation requires strategic optimization of both TFO and duplex terminal structures through a fundamental kinetic principle (bimodal nucleation). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/686076v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1dc6950org.highwire.dtl.DTLVardef@1861387org.highwire.dtl.DTLVardef@16c24a5org.highwire.dtl.DTLVardef@da0bf0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDangling ends at both third strand and duplex termini enhance triplex stability by accelerating association C_LIO_LITriplex formation can be nucleated from either end with a bimodal association mechanism C_LIO_LITerminal blunt-end base triples are dynamic and contribute minimally to stability compared to tailored overhangs C_LI ]]> Zhou, F. Liu, Y. Shu, Z. Wang, Y. Chen, G. 2025-11-03 doi:10.1101/2025.11.02.686076 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Bio-synthesis of 15N-Labeled G-Quadruplexes to Investigate the Structure and Interactions in the Cell Lysate using Nuclear Magnetic Resonance ]]> https://biorxiv.org/content/10.1101/2025.11.03.685478v1?rss=1 Zou, M. Tian, F. Zheng, W. Jiang, M. Zhang, S. Liu, X. Ma, C. Zhao, M. Dai, L. Li, C. Wang, S. 2025-11-04 doi:10.1101/2025.11.03.685478 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Associations Between Gut Microbiome and 24-Hour Blood Pressure Variability: A Cross-sectional Study Highlighting Sex Differences and Potential Therapeutic Targets ]]> https://biorxiv.org/content/10.1101/2025.11.03.685706v1?rss=1 Virwani, P. D. Qian, G. Cheung, C. N.-M. Pijarnvanit, T. K. K. T. S. Hsu, M. S. S. Chow, Y. H. Tang, L. K. Tse, Y.-H. Xian, J.-W. Lam, S. S.-W. Lee, C. P. I. Lo, C. C. W. Liu, R. K. C. Ho, T. L. Chow, B. Y. Leung, K. S. Lo, E. K. K. Yuen, M.-F. Leung, S. Y. Hung, I. F.-N. Louie, J. C. Y. Teo, K.-C. El-Nezami, H. Ho, J. W. K. Lau, K. K. 2025-11-04 doi:10.1101/2025.11.03.685706 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ High-throughput functional characterization of enhancers in totipotent-like cells ]]> https://biorxiv.org/content/10.1101/2025.11.03.686172v1?rss=1 Yang, L. Peng, T. Zhu, Y. Zhai, X. Huang, B. Li, L. Zhang, T. Chen, J. Liang, D. He, J. Zhang, M. 2025-11-04 doi:10.1101/2025.11.03.686172 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Distinctive Functionality of Semantic Hubs: Evidence from Semantic Dementia ]]> https://biorxiv.org/content/10.1101/2025.11.06.686766v1?rss=1 Cui, Z. Liu, D. Dai, Z. Zhang, X. Zeng, J. Guo, Q. Han, Z. Huang, L. 2025-11-07 doi:10.1101/2025.11.06.686766 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Blood originates in hypoblasts during embryonic development ]]> https://biorxiv.org/content/10.1101/2025.11.07.687183v1?rss=1 Chao, Y. Li, H. Liu, L. Tay, Z. Zhang, S. Xu, X. Xu, S. Xiang, Y. Ruan, D. Huang, Y. Lan, G. Liu, P. Sugimura, R. 2025-11-07 doi:10.1101/2025.11.07.687183 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Structure basis for distinct protective mechanisms of IGHV3-23 antibodies targeting influenza hemagglutinin stem ]]> https://biorxiv.org/content/10.1101/2025.11.06.687086v1?rss=1 Lv, H. Huan, Y. W. Pholcharee, T. Teo, Q. W. Liu, W. Gopal, A. B. Choi, D. Ardagh, M. R. Tan, T. J. C. Sun, Y. Mehta, A. Li, J. Szlembarski, M. Huang, J. J. Ma, E. X. Wittenborn, L. E. Kasture, P. Mok, C. K. P. Wu, N. C. 2025-11-08 doi:10.1101/2025.11.06.687086 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Leveraging Disease Association Degree for High-Accuracy MicroRNA Target Prediction ]]> https://biorxiv.org/content/10.1101/2025.11.06.686936v1?rss=1 Chen, B. 2025-11-11 doi:10.1101/2025.11.06.686936 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ A Study on the Pharmacokinetic/Pharmacodynamic Profiles of the Novel PPAR Pan Agonist Chiglitazar Sodium in Rats with Hypoalbuminemia ]]> https://biorxiv.org/content/10.1101/2025.11.09.687466v1?rss=1 Liu, X. He, W. Zhang, X. Li, M. Chen, B. Tian, Y. Sun, Q. Zhao, X. Zhao, Y. Li, D. 2025-11-11 doi:10.1101/2025.11.09.687466 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ LEM-3/ANKLE1 nuclease prevents the formation of syncytium between postmitotic sister cells and safeguards neuronal differentiation ]]> https://biorxiv.org/content/10.1101/2025.11.13.688214v1?rss=1 Deng, S. Zheng, C. 2025-11-14 doi:10.1101/2025.11.13.688214 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ A wild genome of the underutilized legume lablab (Lablab purpureus) reveals the genetic basis of domestication ]]> https://biorxiv.org/content/10.1101/2025.11.13.688277v1?rss=1 Cheung, T.-Y. Almerick Tan Boncan, D. Yuan, Y. Zhang, Y. Somta, P. Chapman, M. A. Chan, T.-F. 2025-11-14 doi:10.1101/2025.11.13.688277 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ A CRP-Mediated Coherent Type 4 Feed-Forward Loop Involving Glucose-Regulated LacI in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2025.11.14.688166v1?rss=1 Lin, Y.-C.-D. 2025-11-14 doi:10.1101/2025.11.14.688166 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Epithelial FOXP3 Drives Pancreatic Fibrosis through O-glycosylated IL-6 ]]> https://biorxiv.org/content/10.1101/2025.11.19.689208v1?rss=1 Gong, R. Ren, M. Wang, J. Zhang, W. Ping, S. Ke, L. Qian, Y. Ma, L. Gao, C. Zhao, C. Fu, S. Xue, J. Wang, J. Sun, H. Chen, J. Zhang, S. Liu, M. Zhao, T. Saluja, A. Yang, Z. Ren, H. 2025-11-19 doi:10.1101/2025.11.19.689208 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Engineering Apical Integrin-binding Cellular Patches to Directed Cell Reprogramming via Mechanical Remodeling ]]> https://biorxiv.org/content/10.1101/2025.11.21.689608v1?rss=1 Zhi, J. Zhao, T. Hou, W. Zhang, Q. Gao, Z. Yu, J. Wu, K. Xu, C. Hu, X. Zhang, Y. 2025-11-22 doi:10.1101/2025.11.21.689608 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ LongPhase-S: purity estimation and variant recalibration with somatic haplotying for long-read sequencing ]]> https://biorxiv.org/content/10.1101/2025.11.20.689492v1?rss=1 Ho, M.-E. Zheng, Z. Luo, R. Chiang, H.-H. Huang, Y.-T. 2025-11-24 doi:10.1101/2025.11.20.689492 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Nomenclature updates to the hemagglutinin gene clade designations resulting from the continued evolution of high pathogenicity avian influenza A(H5) virus clades 2.3.2.1c and 2.3.4.4 ]]> https://biorxiv.org/content/10.1101/2025.11.23.690055v1?rss=1 Lam, T. T.-Y. Davis, T. 2025-11-24 doi:10.1101/2025.11.23.690055 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ A programmable mRNA platform for miRNA detection via miRNA-mRNA2 triplex-mediated ribosomal frameshifting ]]> https://biorxiv.org/content/10.1101/2025.11.24.690164v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@1d6d9f7org.highwire.dtl.DTLVardef@8008e6org.highwire.dtl.DTLVardef@1c8344borg.highwire.dtl.DTLVardef@e153ec_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, Y. Zhao, W. Chen, H. Zhou, H. Fan, S. Duan, H. Dai, Y. Lu, R. Li, C. Jiang, C. Chan, E. Chen, G. 2025-11-24 doi:10.1101/2025.11.24.690164 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ RoBep: A Region-Oriented Deep Learning Model for B-Cell Epitope Prediction ]]> https://biorxiv.org/content/10.1101/2025.11.22.689912v1?rss=1 Xu, Y. Wei, G. Zhou, J. Huang, Y. Yu, W. Lin, Z. LIU, R. Fan, X. 2025-11-25 doi:10.1101/2025.11.22.689912 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ sept-1/zina-1 is an Ancient Toxin-Antidote System in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.11.28.691152v1?rss=1 Liu, D. Zheng, C. 2025-11-29 doi:10.1101/2025.11.28.691152 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Associations Between Age, Heart Rate Variability, and BOLD fMRI Signal Variability ]]> https://biorxiv.org/content/10.1101/2025.11.26.690332v1?rss=1 Morris, J. Schaefer, S. M. Zhu, Y. Recchio, J. Gresham, L. Skinner, S. Al-Khalil, K. Krishna, B. S. 2025-12-01 doi:10.1101/2025.11.26.690332 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Learning Invariant Graph Representations for Cox Survival Modeling under Distribution Shifts ]]> https://biorxiv.org/content/10.64898/2025.11.30.691365v1?rss=1 Ng, K. H. Lyu, C. Jiang, A. Chen, L. 2025-12-02 doi:10.64898/2025.11.30.691365 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Pseudodynamics+: Reconstructing Population Dynamics from Time-Resolved Single Cell Landscapes with Physics Informed Neural Networks ]]> https://biorxiv.org/content/10.64898/2025.11.30.691399v1?rss=1 Zheng, W. Barile, M. Wilson, N. K. Huang, Y. Theis, F. J. Gottgens, B. 2025-12-02 doi:10.64898/2025.11.30.691399 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Representation, Alignment, and Generation: A Comprehensive Survey of Foundation Models for Non-Invasive Brain Decoding ]]> https://biorxiv.org/content/10.64898/2025.11.30.691403v1?rss=1 Wang, Y. Wang, S. Zhang, Y. Du, C. Fan, C. Li, D. Zhou, H. Zhang, H. Li, J. Liu, Q. Huang, W. Lu, Y. Chen, Z. Sun, J. 2025-12-02 doi:10.64898/2025.11.30.691403 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Acoustoluminescence in Transition Metal and Rare Earth Oxides Beyond 1800 nm for In Vivo Imaging ]]> https://biorxiv.org/content/10.64898/2025.12.03.692246v1?rss=1 Xiong, P. Xu, S. Liu, Z. XU, D. Yu, H. Dai, Z. Wu, Z. Qu, L. Wang, F. 2025-12-07 doi:10.64898/2025.12.03.692246 Cold Spring Harbor Laboratory Press 2025-12-07 <![CDATA[ Redox-controlled dimerisation regulates ethylene biosynthesis ]]> https://biorxiv.org/content/10.64898/2025.12.04.692314v1?rss=1 Gunawardana, D. M. Kuang, F. Kaur, S. McIvor, J. A. P. Chen, X. Yosaatmadja, Y. Sethi, A. Tang, H. Y. H. Middleditch, M. J. Mercadante, D. Haydon, M. J. Squire, C. J. Leung, I. K. H. 2025-12-08 doi:10.64898/2025.12.04.692314 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Structural insights into how metallochaperones UreE and UreG interact to deliver a toxic metal to urease ]]> https://biorxiv.org/content/10.64898/2025.12.08.692910v1?rss=1 Chan, C.-L. Pang, L. T. H. Choi, T. Chan, K.-C. Tsang, K. L. Lee, K.-M. Wong, K.-B. 2025-12-08 doi:10.64898/2025.12.08.692910 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Domestic goats can follow the direction of human voices to solve a hidden-object task ]]> https://biorxiv.org/content/10.64898/2025.12.08.692563v1?rss=1 Watson, S. K. Nawroth, C. McElligott, A. G. Rossano, F. Townsend, S. W. 2025-12-10 doi:10.64898/2025.12.08.692563 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ From genomic decay to functional advantage: Trait-based evidence for long-term host residency of a next-generation coral probiotic ]]> https://biorxiv.org/content/10.64898/2025.12.10.693533v1?rss=1 Xie, M. Xu, C. Xiang, N. Liao, T. Liu, X. Liu, Z. Feng, X. He, Q. Liang, Z. Wang, W. Dai, Y. Yan, L. Pogoreutz, C. Barra, L. Au, S. W. N. Jiang, L. Voolstra, C. R. Luo, H. 2025-12-10 doi:10.64898/2025.12.10.693533 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Modeling patient tissues at molecular resolution with Eva ]]> https://biorxiv.org/content/10.64898/2025.12.10.693553v1?rss=1 Liu, Y. Sharma, R. Bieniosek, M. Kang, A. Wu, E. Chou, P. Li, I. Rahim, M. Bauer, E. Ji, R. Duan, W. Qian, L. Luo, R. Sharma, P. Dhanasekaran, R. Schürch, C. M. Charville, G. Mayer, A. Zou, J. Trevino, A. E. Wu, Z. 2025-12-12 doi:10.64898/2025.12.10.693553 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Whole-brain connectomics of Drosophila reveals a robust, distributed architecture for the suppression of feeding during escape ]]> https://biorxiv.org/content/10.64898/2025.12.14.694122v1?rss=1 XI, W. Chen, W. 2025-12-16 doi:10.64898/2025.12.14.694122 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Revealing the Drivers Underlying Distinct Evolutionary Trajectories in Lung Adenocarcinoma ]]> https://biorxiv.org/content/10.64898/2025.12.19.695410v1?rss=1 Wirth, C. Zhang, T. Diaz-Gay, M. Steele, C. D. Hoang, P. H. Yang, Y. Khandekar, A. Zhao, W. Sang, J. Leduc, C. Baine, M. K. Travis, W. D. Sholl, L. M. Joubert, P. Homer, R. Yang, S.-R. Tran, T.-V.-T. McElderry, J. P. Hartman, C. Miraftab, M. Lee, O. W. Jones, K. M. Zhu, B. Santamaria, J. M. Schabath, M. B. Yendamuri, S. S. Manczuk, M. Lissowska, J. Swiatkowska, B. Mukeria, A. Shangina, O. Zaridze, D. Holcatova, I. Janout, V. Mates, D. Ognjanovic, S. Savic, M. Kontic, M. Bosse, Y. Rothberg, B. E. G. Christiani, D. C. Gaborieau, V. Brennan, P. Liu, G. 2025-12-23 doi:10.64898/2025.12.19.695410 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Modulation of signal response by small RNAs through feed-forward loops ]]> https://biorxiv.org/content/10.64898/2025.12.22.696124v1?rss=1 LIN, Y.-C.-D. CHEN, Y. LIN, T.-S. Cai, X.-X. HUANG, S. NI, J. LI, L. HUANG, H.-Y. HUANG, H.-D. 2025-12-23 doi:10.64898/2025.12.22.696124 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Real-time functional connectivity-based neurofeedback of the DLPFC-amygdala pathway during threat-exposure attenuates anxiety ]]> https://biorxiv.org/content/10.64898/2025.12.22.695740v1?rss=1 dong, w. Ferraro, S. Liu, D. Zhang, Y. Han, M. Mi, Y. Wang, J. Fu, K. Zhao, Z. Kendrick, K. M. Yao, D. Yao, S. Becker, B. 2025-12-24 doi:10.64898/2025.12.22.695740 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Microbiome-host interactions drive a trade-off between sleep quality and lifespan in Drosophila ]]> https://biorxiv.org/content/10.64898/2025.12.24.696379v1?rss=1 BHARGAVA, P. Chen, S. Lee, J. Yoshinari, Y. Nishimura, T. Ushio, M. Sugiura, Y. Cheng, K. F. Fung, Y. S. Hase, K. Nakamura, H. Enomoto, M. Kim, J. Johnson, H. E. Liao, Y. Hirano, Y. 2025-12-26 doi:10.64898/2025.12.24.696379 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Integrative multiomic analysis on single-nucleotide variants identifies candidate genes for human craniofacial malformation ]]> https://biorxiv.org/content/10.64898/2025.12.29.696805v1?rss=1 Yam, M. H. So, K. K. H. Tong, K. K. Choy, K. W. Sham, M. H. 2025-12-29 doi:10.64898/2025.12.29.696805 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ MusTer: A Generalizable Microfluidic Platform Combining Multi-Parametric Droplet Sorting and Multi-Droplet Merging in Single-Cell Sequencing ]]> https://biorxiv.org/content/10.64898/2025.12.29.696950v1?rss=1 Li, L. Liu, W. Cheng, G. Qu, F. zhong, s. Ho, Y.-P. 2025-12-30 doi:10.64898/2025.12.29.696950 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Focused ultrasound programmed characteristic NIR-IIb lanthanide mechanoluminescence for high sensitivity bioimaging in vivo ]]> https://biorxiv.org/content/10.64898/2025.12.30.696464v1?rss=1 Zhang, M. Zhang, J. Meng, L. Li, X. Xu, S. Zhu, X. 2025-12-31 doi:10.64898/2025.12.30.696464 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Autistic Children Show Reduced Activity in Left Superior Temporal Cortex in Response to Social-emotional Meaning in Language ]]> https://biorxiv.org/content/10.64898/2026.01.02.697285v1?rss=1 Wu, H. Shi, M. G. Chan, P. W.-Y. Song, P. Lau, S.-F. Lam, G. Y.-H. Kang, X. Wong, P. C. M. Geng, X. 2026-01-02 doi:10.64898/2026.01.02.697285 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Spatial transcriptomic analysis of myositis muscles reveals novel molecular insights of MDA5+ dermatomyositis ]]> https://biorxiv.org/content/10.64898/2026.01.04.696800v1?rss=1 Wang, H. So, H. Sun, H. Ong, M. T.-Y. QIAO, Y. Liu, G. 2026-01-05 doi:10.64898/2026.01.04.696800 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Mechanistic insights into chromatin modulation by the orphan remodeler ATRX ]]> https://biorxiv.org/content/10.64898/2026.01.04.697590v1?rss=1 Duan, S. Wong, T.-F. Yang, X. Xi, H. Zhao, Y. Yao, Z.-P. Zhai, Y. Liao, J. Ni, T. Zhou, K. Liu, Y. 2026-01-05 doi:10.64898/2026.01.04.697590 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Ultrashort optical-pin excitation for scattering brain imaging ]]> https://biorxiv.org/content/10.64898/2026.01.04.697592v1?rss=1 Weng, X. Song, Q. Kong, C. Dong, X. Zhao, Q. Dong, J. He, H. 2026-01-05 doi:10.64898/2026.01.04.697592 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ NORAD orchestrates KLC1-mediated SFPQ transport via liquid-liquid phase separation ]]> https://biorxiv.org/content/10.64898/2026.01.06.697853v1?rss=1 Lian, Q. Han, S. Chen, H. Liu, J. Wang, Y. Chen, S. Sun, P. Jiang, J. Zhao, R. Chen, R. Zhang, X. Duan, F. Rong, L. Yi, W. Kinghorn, A. B. Yan, J. Li, R. Xia, J. Qi, Z. Menasche, G. Lai, K.-O. Lai, C. S. W. Zhou, P. Huang, J.-D. 2026-01-06 doi:10.64898/2026.01.06.697853 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Delta PSA: A New Metric for Conformational Dynamics Underlying Macrocyclic Peptide Permeability ]]> https://biorxiv.org/content/10.64898/2026.01.06.697862v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@18fc9e4org.highwire.dtl.DTLVardef@10fbc70org.highwire.dtl.DTLVardef@1c763aorg.highwire.dtl.DTLVardef@95d9e4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yu, Y. Wu, Q. Chem, J. She, Y. Zhu, L. Guo, Z. 2026-01-06 doi:10.64898/2026.01.06.697862 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ TSTScope Unifies Single-Cell Multi-Omics to Identify Functional T Cell States Predictive of Immunotherapy Response ]]> https://biorxiv.org/content/10.64898/2026.01.08.698283v1?rss=1 Cao, S. Cheng, J. Wang, F. Yi, C. Chen, J. Wang, K. Liu, L. Liu, J. Li, Y. 2026-01-08 doi:10.64898/2026.01.08.698283 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ The Red Rice Bran Extract (RRBE) Mitigates Photoaging by Targeting Mitochondrial Oxidative Stress and Regulating Thermal Damage Responses ]]> https://biorxiv.org/content/10.64898/2026.01.08.698301v1?rss=1 Lin, T.-S. Chen, Y. Li, X. Ji, X. Huang, S. Lyu, J. Li, L. Zuo, H. Li, S. Li, J. Huang, H.-Y. Zhuo, H. Zhang, X. Wang, Y.-F. Ning, S. Zhang, Z. Gu, Y. Zhang, T. Lin, Y.-C.-D. Huang, H.-D. 2026-01-08 doi:10.64898/2026.01.08.698301 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Linkage-aware inference of fitness from short-read time-series genomic data ]]> https://biorxiv.org/content/10.64898/2026.01.08.698347v1?rss=1 Abdullah, S. M. U. Sohail, M. S. Louie, R. H. Y. Sun, Y. Barton, J. P. McKay, M. R. 2026-01-08 doi:10.64898/2026.01.08.698347 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ caRBP-Pred: Deep Learning-based Prediction of Chromatin-Associated RNA-Binding Proteins Using Short Peptide Sequences ]]> https://biorxiv.org/content/10.64898/2026.01.12.698323v1?rss=1 SUN, Q. Wang, H. Sun, H. Chen, X. Yang, F. 2026-01-13 doi:10.64898/2026.01.12.698323 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Universal nucleic acid preservation in biological fluids with boron clusters ]]> https://biorxiv.org/content/10.64898/2026.01.13.697153v1?rss=1 Pang, B. P. S. Zhang, L. Wong, B. T. Y. Williamson, M. P. Lai, H. M. 2026-01-14 doi:10.64898/2026.01.13.697153 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Plasma proteomics reveal heterogeneous subtypes of depression linked to inflammation and aging ]]> https://biorxiv.org/content/10.64898/2026.01.14.699397v1?rss=1 Lian, Z. Palaniyappan, L. Liu, Z. Kuang, N. Liu, Y. Jiang, Y. Sahakian, B. J. Robbins, T. W. Feng, J. Becker, B. Cheng, W. Wu, X. Zhang, J. Bullmore, E. 2026-01-15 doi:10.64898/2026.01.14.699397 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ When CycloneSEQ meets Oxford Nanopore Technologies: a performance comparison of contemporary nanopore DNA sequencing platforms ]]> https://biorxiv.org/content/10.64898/2026.01.14.699587v1?rss=1 Liu, X. Ding, Q. Shao, Y. GUO, Z. Ni, Y. Fan, L. Yang, Y. Yang, M. Li, R. 2026-01-15 doi:10.64898/2026.01.14.699587 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Transcriptomic profiling of human γδ T cells reveals non-linear immune aging characterized by childhood transitions and relative stability in adulthood ]]> https://biorxiv.org/content/10.64898/2026.01.15.699622v1?rss=1 Yang, T. Leon-Lara, X. Almeida, V. Wang, Z. Abu, Y. E. Janssen, A. Kleine-wechelmann, C. Hassan, A. Song, Z. Dempsey, M. Tan, L. Boehne, M. Kaisenberg, C. v. Prinz, I. Förster, R. Ravens, S. 2026-01-16 doi:10.64898/2026.01.15.699622 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Microbial Antioxidants Reduce ROS In Human Skin Cells Under Oxidative Stress ]]> https://biorxiv.org/content/10.64898/2026.01.15.699165v1?rss=1 Huang, S. Dong, D. Wan, J. Lin, Y.-C.-D. Huang, H.-D. 2026-01-18 doi:10.64898/2026.01.15.699165 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ PCRD-seq: Proximity Crosslinking-induced RNA Depletion for Low-Input Subcellular Transcriptome Profiling ]]> https://biorxiv.org/content/10.64898/2026.01.17.700046v1?rss=1 Han, J. Li, L. Kong, X. Zhao, K. Leung, Y. T. Wong, A. S.-T. Li, Y. 2026-01-20 doi:10.64898/2026.01.17.700046 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Coacervate Droplets as a Liquefier for the Solid-to-Liquid Transition of RNA Aggregates ]]> https://biorxiv.org/content/10.64898/2026.01.18.700211v1?rss=1 Guo, W. Luo, R. Shen, Y. Zeng, X. Liu, Z. Shum, H. C. 2026-01-20 doi:10.64898/2026.01.18.700211 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Shared and distinct default mode systems in mental time travel and affective experience over time ]]> https://biorxiv.org/content/10.64898/2026.01.20.700521v1?rss=1 Zhang, Y. Dong, W. Fu, K. Zhou, M. Qing, Y. Chan, R. C. K. Kendrick, K. M. Yao, D. Yao, S. Becker, B. 2026-01-21 doi:10.64898/2026.01.20.700521 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Dysregulated RNA G-quadruplex binding proteins reveal shifted stress responses in Alzheimer's Disease ]]> https://biorxiv.org/content/10.64898/2026.01.20.700564v1?rss=1 Zhou, X. Zhang, Y. Sun, L. Kwok, C. K. Zhang, J. 2026-01-23 doi:10.64898/2026.01.20.700564 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ SparseAEH: Scalable autoregressive expression histology discovery in spatial transcriptomics via sparse Gaussian kernels ]]> https://biorxiv.org/content/10.64898/2026.01.22.701193v1?rss=1 Wang, T. Li, L. Huang, Y. 2026-01-23 doi:10.64898/2026.01.22.701193 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Quantitative Optimization of Sensitivity and Specificity in Targeted and Whole-Exome Sequencing Using Reference-Standard DNA Mixtures ]]> https://biorxiv.org/content/10.64898/2026.01.25.701479v1?rss=1 3-fold and reduced FP rates >96% versus suboptimal pipelines. Notably, VAF thresholds flattened sensitivity differences across platforms, obscuring key performance disparities--challenging assumptions that T-NGS is inherently more sensitive than WES. In-house and conventional pipelines undercalled up to 10% of true variants. Restricting reporting of 1-4% VAF variants to [~]1,000 predefined actionable sites enabled recovery of clinically relevant mutations while reducing FP risk >99%. ConclusionsThis study provides a quantitative framework for optimizing NGS performance. Our findings support actionable strategies to improve diagnostic accuracy in clinical genomics through tailored pipeline selection, VAF thresholding, and artifact filtering. ]]> Moon, Y.-B. Hong, C. H. Kim, J.-K. Kang, E.-K. Choi, H. W. Hwang, D.-W. Ko, J.-H. Kim, H.-S. Lee, D.-e. Park, S.-y. Wang, C. C. Kim, Y.-H. Kim, T. Heo, S. G. Han, N. Hong, K.-M. 2026-01-27 doi:10.64898/2026.01.25.701479 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Light-inducible proximity labelling in vivo captures sex-specific RNA at excitatory synapses ]]> https://biorxiv.org/content/10.64898/2026.01.28.702434v1?rss=1 Davies, J. Suhinin, V. Brueckner, A. M. Araneta, G. J. A. Leighton, L. J. Walsh, A. Madugalle, S. U. Young, T. Gong, H. Musgrove, M. R. B. Ren, H. Kielar, M. Lin, J. Y.-l. Li, Y. Bredy, T. Marshall, P. 2026-01-29 doi:10.64898/2026.01.28.702434 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Analysis of the assembly, stabilization and maturation of the multiphasic TAZ biomolecular condensates ]]> https://biorxiv.org/content/10.64898/2026.01.29.702607v1?rss=1 Shapira, K. E. Zhu, Q. Grig, E. Chen, X. Jing, Y. Li, X. D. Wolfenson, H. Henis, Y. I. Luo, K. 2026-02-02 doi:10.64898/2026.01.29.702607 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Integrative Multi-Omics Analysis Identifies a Functional Enhancer Driving Tumorigenesis in Head and Neck Squamous Cell Carcinoma ]]> https://biorxiv.org/content/10.64898/2026.02.03.703438v1?rss=1 Xu, P. Liu, X. Yang, P. Tran, N. L. Pu, J. Lu, X. Lee, V. Wang, Y. E. Jiang, Q. Yu, D. Song, J. Zhong, Q. Guan, X. Su, Y.-X. Wang, J. 2026-02-05 doi:10.64898/2026.02.03.703438 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Acoustic Modulation of Ion-Solvent Interactions: Microscopic Insights into Acoustoelectric Effect Modelling ]]> https://biorxiv.org/content/10.64898/2026.02.04.703740v1?rss=1 Tang, Y. Oon, W. Y. Lee, W.-N. 2026-02-07 doi:10.64898/2026.02.04.703740 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Rapid and Quantitative Phage Susceptibility Test by Ramanome ]]> https://biorxiv.org/content/10.64898/2026.02.07.704537v1?rss=1 Han, X. Wan, X. Zhou, Y. Fu, X. Zheng, X. Gao, B. Huang, S. Ge, A. Huang, J. Lu, H. Xu, J. 2026-02-08 doi:10.64898/2026.02.07.704537 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ AI-driven discovery and engineering of human endogenous nanocage proteins for mRNA delivery ]]> https://biorxiv.org/content/10.64898/2026.02.07.704552v1?rss=1 Xun, D. Li, L. Liu, Y. Yang, Z. Zou, J. Liang, Q. Li, K. Zhu, Z. Zhang, J. Lang, L. Liu, K. Wang, X. Tian, M. Chen, G. An, B. Heng, P.-A. Zhong, C. 2026-02-09 doi:10.64898/2026.02.07.704552 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Leveraging ONT move table values for signal aware variant calling ]]> https://biorxiv.org/content/10.64898/2026.02.13.705285v1?rss=1 Yu, X. Zheng, Z. Chen, L. Qin, Z. He, M. Luo, R. 2026-02-16 doi:10.64898/2026.02.13.705285 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Heterogeneous and specific localization of mRNAs at dendritic spine and its dependence on microtubule entry and kinesin motor ]]> https://biorxiv.org/content/10.64898/2026.02.13.705666v1?rss=1 Wang, X. Song, J. Lin, J. Tian, T. Lui, A. T. L. Lee, C. Y. Zhang, L. Lai, K.-O. 2026-02-16 doi:10.64898/2026.02.13.705666 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Learning sculpts orthogonal task manifolds for continual skill learning in recurrent networks ]]> https://biorxiv.org/content/10.64898/2026.02.15.705283v1?rss=1 Liu, Z. Kurth, A. Osako, Y. Asabuki, T. 2026-02-16 doi:10.64898/2026.02.15.705283 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ MicrowellMicrofluidicsMiner (M3): Leverage Large Language Model Agents for Knowledge Mining of Microwell Microfluidics ]]> https://biorxiv.org/content/10.64898/2026.02.14.705953v1?rss=1 Nguyen, D.-N. Shakil, S. Tong, R. K. Y. Dinh, N.-D. 2026-02-17 doi:10.64898/2026.02.14.705953 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection ]]> https://biorxiv.org/content/10.64898/2026.02.18.706711v1?rss=1 Kikawa, C. Huddleston, J. Turner, S. A. Loes, A. N. Liu, J. Gang, S. Griffiths, T. Drapeau, E. M. Cowling, B. J. Ho, F. Leung, N. H. Englund, J. A. Lacombe, K. Watanabe, S. Hasegawa, H. Busch, M. Lanteri, M. Stone, M. Spencer, B. Neher, R. A. Smith, D. J. Bedford, T. Hensley, S. E. Bloom, J. D. 2026-02-19 doi:10.64898/2026.02.18.706711 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Functional and sensitivity profiling of theKITMutation Landscape in Melanoma ]]> https://biorxiv.org/content/10.64898/2026.02.18.706482v1?rss=1 Yeung, S. F. Chan, M. S. M. Law, C. T. Y. Law, A. C. H. Lee, C. Leung, A. M. F. Chau, M. P. K. Chan, H. H. Y. Chen, J. X. Ko, B. C. B. Chan, K. K. L. Cho, W. C. Tsui, S. K. W. 2026-02-20 doi:10.64898/2026.02.18.706482 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Volumetric montaging of optical coherence tomography in human retinas ]]> https://biorxiv.org/content/10.64898/2026.02.21.706699v1?rss=1 Fang, R. Xu, F. Kim, D. Zambrano, R. Lam, A. Tinio, R. Leung, C. K. S. Sun, C. Schuman, J. Mirza, R. G. Zhang, H. F. 2026-02-23 doi:10.64898/2026.02.21.706699 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines ]]> https://biorxiv.org/content/10.64898/2026.02.23.707528v1?rss=1 Loes, A. N. Tarabi, R. A. Li, S. H. Atkinson, R. K. Huddleston, J. Kikawa, C. Griffths, T. Drapeau, E. M. Wong, S.-S. Cheng, S. M. Leung, N. H. Cobey, S. Cowling, B. J. Bedford, T. Hensley, S. E. Bloom, J. D. 2026-02-23 doi:10.64898/2026.02.23.707528 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Gut Microbiota Dysbiosis-Mediated Gut NLRP3 Inflammasome Activation Exacerbates Corticospinal Tract Injury After Intracerebral Hemorrhage ]]> https://biorxiv.org/content/10.64898/2026.02.23.707330v1?rss=1 Zeng, M. Peng, M. Tian, H. He, C. Zhang, L. Yuan, W. Huang, J.-D. Sun, H. 2026-02-24 doi:10.64898/2026.02.23.707330 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Integrative Multi-Scale Sequence-Structure Modeling for Antimicrobial Peptide Prediction and Design ]]> https://biorxiv.org/content/10.64898/2026.02.24.707610v1?rss=1 Li, J. Shao, Y. Li, Y. Yu, Q. 2026-02-25 doi:10.64898/2026.02.24.707610 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Propagule and Juvenile-derived Foraminiferal eDNA across intertidal habitats and its implications for accurate sea-level reconstruction ]]> https://biorxiv.org/content/10.64898/2026.02.24.707652v1?rss=1 Liu, Z. Khan, N. S. Schweizer, M. Schunter, C. 2026-02-25 doi:10.64898/2026.02.24.707652 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ SpaMOAL: A spatial multi-omics graph contrastive learning method for spatial domains identification ]]> https://biorxiv.org/content/10.64898/2026.02.23.707433v1?rss=1 Wang, J. Huo, Y. Zhao, R. Pan, Y. Wang, H. Li, X. 2026-02-26 doi:10.64898/2026.02.23.707433 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Exploring differences across pangenome-graph representations using Escherichia coli O157:H7 as a model ]]> https://biorxiv.org/content/10.64898/2026.02.25.707890v1?rss=1 Liu, P. Hu, K. Mughini-Gras, L. Zomer, A. L. Brouwer, M. S. M. Dallman, T. J. Paganini, J. A. 2026-02-26 doi:10.64898/2026.02.25.707890 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Computational Analysis of Microtubule-Mediated Saltatory Neuroelectrical Transmission ]]> https://biorxiv.org/content/10.64898/2026.02.25.708076v1?rss=1 Yang, Y. X. Zhu, B. T. 2026-02-27 doi:10.64898/2026.02.25.708076 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Minimal biophysical rules are sufficient for the emergence of computational intelligence at the neuronal scale ]]> https://biorxiv.org/content/10.64898/2026.03.01.708921v1?rss=1 Wang, G. Qi, L. Li, K. Tang, C. Chen, X. Mao, Y. Occhipinti, L. G. Nathan, A. Wang, N. Pan, Y. Smielewski, P. Wang, Y. Han, H. Guo, X. Gao, S. 2026-03-03 doi:10.64898/2026.03.01.708921 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ gSV: a general structural variant detector using the third-generation sequencing data ]]> https://biorxiv.org/content/10.64898/2026.03.02.703663v1?rss=1 HAO, J. Shi, J. Lian, S. Zhang, Z. Luo, Y. Hu, T. Ishibashi, T. Wang, D. Wang, S. Fan, X. Yu, W. 2026-03-04 doi:10.64898/2026.03.02.703663 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles ]]> https://biorxiv.org/content/10.64898/2026.03.02.708991v1?rss=1 Ni, Z. Li, Y. Qiu, Z. Schölkopf, B. Guo, H. Liu, W. Liu, S. 2026-03-04 doi:10.64898/2026.03.02.708991 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ A Resolution-Agnostic Geometric Transformer for Chromosome Modeling Using Inertial Frame ]]> https://biorxiv.org/content/10.64898/2026.03.02.709187v1?rss=1 Zhou, Y. Li, H. Liu, S. 2026-03-05 doi:10.64898/2026.03.02.709187 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ MetaSAG: A Tool for Multi-level Exploration and Taxonomic Analysis of Microbial Single-Amplified Genomes ]]> https://biorxiv.org/content/10.64898/2026.03.04.709444v1?rss=1 Zhang, S. Du, M. He, G. Qian, K. Li, K. Li, B. Wang, P. Lu, M. Wu, X. Wang, C. Han, H. Yuan, S. Zhang, X. Cheng, L. 2026-03-06 doi:10.64898/2026.03.04.709444 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Prophase Chromosomes Relocalizes to Nuclear Periphery for Protection in Depletion of Nucleoporin NPP-3/NUP205 Through the Spindle Assembly Checkpoint Activity, Centromere-Kinetochore Proteins and BAF-1-LEM-2 ]]> https://biorxiv.org/content/10.64898/2026.03.04.709728v1?rss=1 Jiang, L. Tse, Y. C. Yuen, K. W. Y. 2026-03-06 doi:10.64898/2026.03.04.709728 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Neurocognitive deficits in controlling aversive memory among insomnia disorders ]]> https://biorxiv.org/content/10.64898/2026.03.04.709020v1?rss=1 Zuo, X. Lin, X. Yao, Z. Chen, D. Liu, J. Guo, S. Yue, W. Y. W. Yang, Y. Wang, W. Feng, H. Zhang, J. Anderson, M. Li, S. X. Hu, X. 2026-03-07 doi:10.64898/2026.03.04.709020 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Synergistic Inhibition of Notch Signaling and Forced Cell Cycle Re-entry Drive Müller Glia Reprogramming in Uninjured Mouse Retina ]]> https://biorxiv.org/content/10.64898/2026.03.09.710684v1?rss=1 Liao, B. Lyu, C. Jiang, Y. Liu, S. Wong, W. Zhang, J. Tsang, H. Xie, J. Chen, L. Zhang, Q. Xiong, W. 2026-03-12 doi:10.64898/2026.03.09.710684 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Ubiquitination-mediated mitochondrial protein degradation ensures seedling emergence by regulating ER-mitochondrial interaction and mitophagy ]]> https://biorxiv.org/content/10.64898/2026.03.10.710782v1?rss=1 tian, z. Huo, Y. Li, C. Zheng, Q. Hu, F. Li, J. Ma, J. Qu, X. Cheng, Y. Kang, B.-H. Duckney, P. Wang, P. 2026-03-13 doi:10.64898/2026.03.10.710782 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ STEVE: Single-cell Transcriptomics Expression Visualization and Evaluation ]]> https://biorxiv.org/content/10.64898/2026.03.10.710898v1?rss=1 Torbenson, E. J. Ma, X. Lin, J.-R. Garry, D. Jameson, S. C. Zhang, Z. Niedernhofer, L. J. Zhang, L. Li, M. Dong, X. 2026-03-13 doi:10.64898/2026.03.10.710898 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Reactivating conflicting evaluative memories during sleep reduces decision ambivalence ]]> https://biorxiv.org/content/10.64898/2026.03.11.710434v1?rss=1 Chen, D. Xia, T. Liu, J. Zhang, Y. Zuo, X. Wu, H. Lai, C. S. W. Hu, X. 2026-03-13 doi:10.64898/2026.03.11.710434 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ CAPZ, but not canonical autophagy, regulates the endosomal-exosomal trafficking of plasma membrane PD-L1 ]]> https://biorxiv.org/content/10.64898/2026.03.12.711228v1?rss=1 Xu, P. Ye, Z. Zhu, Y. Lin, N. Chan, C.-F. Zhu, C. Zhang, X. Wang, Y. Sun, W. Peng, M. Lu, Y. Yue, J. 2026-03-13 doi:10.64898/2026.03.12.711228 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Single cell multiomics reveal clonal and functional dynamics of MDS stem/progenitor cells during hypomethylating therapy ]]> https://biorxiv.org/content/10.64898/2026.03.13.711488v1?rss=1 Thoms, J. A. I. Hampton, H. R. Boon, P. L. S. Stonehouse, O. Zou, X. Chung, H. M. Koch, F. C. Yan, F. Joshi, S. Nguyen, M. N. T. Hung, D. Wright, D. C. Vafaee, F. Polizzotto, M. N. Swarbrick, A. Huang, Y. Jolly, C. J. Zanini, F. Pimanda, J. E. 2026-03-13 doi:10.64898/2026.03.13.711488 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Ancient metapopulations and extreme sex-biased demography revealed by ABC inference and X-Chromosome diversity in Indo-Pacific reef sharks ]]> https://biorxiv.org/content/10.64898/2026.03.13.711537v1?rss=1 Dahms, C. Momigliano, P. 2026-03-13 doi:10.64898/2026.03.13.711537 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ TRIM21 is a molecular rheostat for influenza A virus replication ]]> https://biorxiv.org/content/10.64898/2026.03.16.711963v1?rss=1 Teo, Q. W. Lv, H. Pholcharee, T. Chen, X. Ramadin, V. Mao, K. J. Huang, J. J. Rivera-Cardona, J. Zhu, J. Huan, Y. W. Shao, E. K. Tun, H. M. brooke, c. Radoshevich, L. Sanyal, S. Wu, N. C. 2026-03-17 doi:10.64898/2026.03.16.711963 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Quinone reductase 2 reads H3 serotonylation to support neuronal maturation ]]> https://biorxiv.org/content/10.64898/2026.03.17.712426v1?rss=1 Chen, M. Yang, C. Li, X. Kong, L. Weekley, B. H. Wei, X. O'Chan, J. C. Vinson, D. A. Cetin, B. Ramakrishnan, A. Shen, L. Zeng, R. Liu, Z. Zhang, J. Cappuccio, K. M. Sokol, J. R. Baljinnyam, E. Hu, R. Rosenblum, K. Molina, H. Zheng, Q. David, Y. Marro, S. G. Muir, T. W. Li, X. D. Li, H. Maze, I. 2026-03-18 doi:10.64898/2026.03.17.712426 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Spatio-temporal mapping of immune cell dynamics during human sequential lymph node metastasis ]]> https://biorxiv.org/content/10.64898/2026.03.17.712495v1?rss=1 Zhao, Q. Lu, Y. Shi, Z. Zhang, H. Li, C. S. Zhao, R. Ling, Y. Gao, Y. Zhang, Z. Sun, X. Qian, Y. Wang, X. Wang, C. Cong, B. Ni, X. Liu, Y. Zhao, M. Wang, Y. Mahata, B. Qiu, P. 2026-03-19 doi:10.64898/2026.03.17.712495 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ RNAGAN: Train One and Get Four, Multipurpose Human RNA-Seq Analysis Tool with Enhanced Interpretability and Small Data Size Capability ]]> https://biorxiv.org/content/10.64898/2026.03.17.712527v1?rss=1 HOU, Z. Lee, V. H.-F. Kwong, D. L.-W. Guan, X. Liu, Z. Dai, W. 2026-03-20 doi:10.64898/2026.03.17.712527 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Enhancing non-local interaction modeling for ab initio biomolecular calculations and simulations with ViSNet-PIMA ]]> https://biorxiv.org/content/10.64898/2026.03.18.712561v1?rss=1 Cui, T. Wang, Z. Wang, T. 2026-03-20 doi:10.64898/2026.03.18.712561 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Recombination rate and efficiency of linked selection in small and large stickleback populations ]]> https://biorxiv.org/content/10.64898/2026.03.18.712813v1?rss=1 Wang, H. Zhang, C. Reid, K. Merila, J. 2026-03-20 doi:10.64898/2026.03.18.712813 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Defining influenza-specific B cells in vaccine responders, non-responders and influenza breakthrough infections ]]> https://biorxiv.org/content/10.64898/2026.03.19.710321v1?rss=1 Kedzierska, K. Kedzierski, L. Holloway, A. Habel, J. Rowntree, L. Li, S. McQuilten, H. James, F. Murdiyarso, L. Tarasova, I. Leung, N. Chen, Y. Ip, D. Kent, S. J. Peiris, J. S. M. Tong, S. Cheng, A. C. Kotsimbos, T. Trubiano, J. Schroeder, J. Wheatley, A. K. Cowling, B. J. Valkenburg, S. Nguyen, T. H. O. 2026-03-22 doi:10.64898/2026.03.19.710321 Cold Spring Harbor Laboratory Press 2026-03-22 <![CDATA[ Adenosine 5'-triphosphate (ATP) forms protein-free and responsive condensates in crowded environments ]]> https://biorxiv.org/content/10.64898/2026.03.22.713448v1?rss=1 Wang, Y. Chen, F. Dang Kow, P. Shum, H. C. 2026-03-24 doi:10.64898/2026.03.22.713448 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Somatic evolution of a cross-reactive germline antibody that expands its breadth to neutralize new SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.64898/2026.03.20.713312v1?rss=1 Lv, H. Feng, Z. Teo, Q. W. Chen, C. Gopal, A. B. Choi, D. Tan, T. J. C. Tang, Y. S. Siu, L. Nourmohammad, A. Bruzzone, R. Wilson, I. A. Yuan, M. Wu, N. C. Mok, C. K.-P. 2026-03-25 doi:10.64898/2026.03.20.713312 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ EvoRMD: Integrating Biological Context and Evolutionary RNA Language Models for Interpretable Prediction of RNA Modifications ]]> https://biorxiv.org/content/10.64898/2026.03.22.713386v1?rss=1 Wang, B. Zhang, H. Cui, T. Wang, X. Song, J. Xu, H. 2026-03-25 doi:10.64898/2026.03.22.713386 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Starvation-induced autophagy occurs independently of the ATG1 complex in Chlamydomonas ]]> https://biorxiv.org/content/10.64898/2026.03.23.713624v1?rss=1 Zou, Y. Wu, Y. Stael, S. Moschou, P. N. Zhuang, X. Minina, A. E. A. Bozhkov, P. 2026-03-25 doi:10.64898/2026.03.23.713624 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Study comparing characteristics of ademetionine-containing tablets from different countries ]]> https://biorxiv.org/content/10.64898/2026.03.27.714742v1?rss=1 Mato, J. M. Wong, G. L. Gooijer, Y. Safaei, A. 2026-03-30 doi:10.64898/2026.03.27.714742 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Natural and breeding selection converge on overlapping haplotypes with divergent directions and outcomes in wheat ]]> https://biorxiv.org/content/10.64898/2026.03.28.714077v1?rss=1 Wang, X. Quiroz-Chavez, J. Ramirez Gonzalez, R. H. Xiong, Z. Xu, S. Przewieslik Allen, S. Cheng, S. Adamski, N. Uauy, C. 2026-03-31 doi:10.64898/2026.03.28.714077 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Using Light to Establish Habits in Laboratory Mice ]]> https://biorxiv.org/content/10.64898/2026.03.28.714966v1?rss=1 Tam, S. K. E. Xiao, X. Cheng, X. Kwok, S. C. Becker, B. 2026-03-31 doi:10.64898/2026.03.28.714966 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Increased diffusion in livers with advanced fibrosis: pre-clinical and clinical observations with diffusion MRI ]]> https://biorxiv.org/content/10.64898/2026.03.30.715426v1?rss=1 Xu, F.-Y. Wang, Y.-X. 2026-04-01 doi:10.64898/2026.03.30.715426 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ nELAVL phosphorylation by CDKL5 regulates inter-condensates composition and communication to promote experience-dependent maturation of the visual cortex ]]> https://biorxiv.org/content/10.64898/2026.04.03.716270v1?rss=1 Yuan, S. Zhu, Y. Zheng, Z. Yip, H. M. Chan, M. S. W. Zhang, Z. Chai, Y. Jenks, K. R. Tsimring, K. Heller, G. R. Zepeda, J. C. Celotto, M. Hung, H. K. Duan, Y. Lau, S.-F. Ho, C. W. Y. Tsang, H. W. S. Fu, A. K. Y. Lai, H. M. Kwok, A. J. Ko, H. Gu, C. Ng, B. W.-L. Liao, J. Fung, S. H. Cao, Q. Tsui, S. K.-W. Ku, T. Tan, L. Colarusso, A. Lasker, K. Wan, Y. Zhu, J. Ip, J. P. K. 2026-04-04 doi:10.64898/2026.04.03.716270 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ CellBench-LS: Benchmark Evaluation of Single-cell Foundation Models for Low-supervision Scenarios ]]> https://biorxiv.org/content/10.64898/2026.04.01.714123v1?rss=1 Xu, Y. Li, Y. Yuan, Y. Yu, C. Zang, Z. 2026-04-05 doi:10.64898/2026.04.01.714123 Cold Spring Harbor Laboratory Press 2026-04-05 <![CDATA[ Breast cancer interactions with osteoclasts generate osteoclast tumor hybrid like cells through dynamic non-canonical cell fusion and cell-in-cell processes ]]> https://biorxiv.org/content/10.64898/2026.04.05.716538v1?rss=1 Lim, K. H. Siriwanna, D. Li, X. Dotse, E. Wang, M. Mun, C. Li, Y. Wang, X. Chow, K. T. 2026-04-07 doi:10.64898/2026.04.05.716538 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Geometry-enhanced protein language modeling enables discovery of novel antibiotic resistance genes ]]> https://biorxiv.org/content/10.64898/2026.04.05.716581v1?rss=1 Lin, X. Guan, J. Hong, Y. Guo, Y. Yang, Y. Xie, P. Zhao, Z. Liu, X. Huang, Y. Ye, Y. Tang, Y. Lee, T.-Y. Chiang, Y.-C. Wei, L. Liu, X. Wang, J. Pan, Y. Tang, J. Pei, Y. Yao, L. 2026-04-08 doi:10.64898/2026.04.05.716581 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ Hippocampal and Midbrain Function in Superagers Relates to Memory for Novelty and Expectation Violation ]]> https://biorxiv.org/content/10.64898/2026.04.16.718970v1?rss=1 Garcia Huescar, M. Zhang, L. Strange, B. Frank, D. 2026-04-17 doi:10.64898/2026.04.16.718970 Cold Spring Harbor Laboratory Press 2026-04-17 <![CDATA[ LagCI Enables Inference of Temporal Causal Relationships from Dense Multi-Omic Time Series ]]> https://biorxiv.org/content/10.64898/2026.04.15.718654v1?rss=1 Ge, Y. Bai, S. Qiang, Z. Liu, Y. Wu, Y. Shen, X. 2026-04-18 doi:10.64898/2026.04.15.718654 Cold Spring Harbor Laboratory Press 2026-04-18