bioRxiv Channel: University of Chinese Academy of Sciences https://biorxiv.org This feed contains articles for bioRxiv Channel "University of Chinese Academy of Sciences" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ DISC1 regulates astrogenesis in the embryonic brain via modulation of RAS/MEK/ERK signaling through RASSF7 ]]> https://biorxiv.org/content/10.1101/032243v1?rss=1 Shukun Wang Qingli Liang Huimin Qiao Hong Li Tianjin Shen Fen Ji Jianwei Jiao 2015-11-19 doi:10.1101/032243 Cold Spring Harbor Laboratory Press 2015-11-19 <![CDATA[ Local-Global Parcellation of the Human Cerebral Cortex From Intrinsic Functional Connectivity MRI ]]> https://biorxiv.org/content/10.1101/135632v1?rss=1 Schaefer, A. Kong, R. Gordon, E. M. Laumann, T. O. Zuo, X.-N. Holmes, A. Eickhoff, S. B. Yeo, B. T. T. 2017-06-06 doi:10.1101/135632 Cold Spring Harbor Laboratory Press 2017-06-06 <![CDATA[ Identity-By-Descent Refines Mapping Of Candidate Regions For Preaxial Polydactyly In A Large Chinese Pedigree ]]> https://biorxiv.org/content/10.1101/139428v1?rss=1 Yang, X. Shen, Q. Sulaiman, X. Liu, H. Peng, M. Zhang, Y. 2017-05-22 doi:10.1101/139428 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ Single cell atlas of domestic pig brain illuminates the conservation and divergence of cell types at spatial and species levels ]]> https://biorxiv.org/content/10.1101/2019.12.11.872721v1?rss=1 Chen, D. Zhu, J. Zhong, J. Chen, F. Lin, X. Dai, J. Chen, Y. Wang, S. Ding, X. Wang, H. Qiu, J. Wang, F. Wu, W. Liu, P. Tang, G. Qiu, X. Ruan, Y. Li, J. Zhu, S. Xu, X. Li, F. Liu, Z. Cao, G. 2019-12-12 doi:10.1101/2019.12.11.872721 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Single cell atlas of trisomy 21 cerebral cortex ]]> https://biorxiv.org/content/10.1101/2020.01.01.892398v1?rss=1 Zhang, J. wang, S. Xu, Z. Ding, X. Li, C. Zhang, Y. Chen, Y. Zhong, J. Liang, L. Chai, C. Wang, X. Xiang, R. Zhu, J. Lin, X. Ding, P. Zhang, Q. Wang, M. Feng, Q. Zhang, Z. Guo, G. Xue, S. Jin, L. He, Z. Yan, L. Xiao, B. Zhang, C. Xu, Y. Li, W. Zhang, Y. Wu, W. Jiang, S. Xia, J. Gao, Y. Wang, L. Dong, S. Liu, S. Zhu, S. Chen, F. Chen, D. Xu, X. 2020-01-02 doi:10.1101/2020.01.01.892398 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Accucopy: accurate and fast inference of allele-specific copy number alterations for heterogeneous tumor samples from high-throughput sequencing data ]]> https://biorxiv.org/content/10.1101/2020.01.02.892364v1?rss=1 Fan, X. Chen, L. Liu, F. Huang, Y. 2020-01-03 doi:10.1101/2020.01.02.892364 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ A general role of zinc binding domain revealed by structures of σ28-dependent transcribing complexes ]]> https://biorxiv.org/content/10.1101/2020.01.02.893370v1?rss=1 Shi, W. Zhou, W. Zhang, B. Huang, S. Jiang, Y. Schammel, A. Hu, Y. Liu, B. 2020-01-03 doi:10.1101/2020.01.02.893370 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ Separation or Integration of Sequential Arrays in VWM Depends On the interval Between Them ]]> https://biorxiv.org/content/10.1101/2020.01.08.814889v1?rss=1 Li, Z. Zhang, J. Liang, T. Ye, C. Liu, Q. 2020-01-09 doi:10.1101/2020.01.08.814889 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ DREAM: A Toolbox to Decode Rhythms of the Brain System ]]> https://biorxiv.org/content/10.1101/2020.01.29.926204v1?rss=1 Gong, Z.-Q. Gao, P. Xing, X.-X. Jiang, C. White, T. H. Castellanos, F. X. Li, H.-F. Zuo, X.-N. 2020-01-31 doi:10.1101/2020.01.29.926204 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Integrated profiling of single cell epigenomic and transcriptomic landscape of Parkinson's disease mouse brain ]]> https://biorxiv.org/content/10.1101/2020.02.04.933259v1?rss=1 Zhong, J. Tang, G. Zhu, J. Qiu, X. Wu, W. Li, G. Lin, X. Liang, L. Chai, C. Zeng, Y. Wang, F. Luo, L. Li, J. Chen, F. Huang, Z. Xu, X. Tang, S. Zhu, S. Chen, D. 2020-02-04 doi:10.1101/2020.02.04.933259 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ A Comprehensive Survey of Genomic Mutations in Breast Cancer Reveals Recurrent Neoantigens as Potential Therapeutic Targets ]]> https://biorxiv.org/content/10.1101/2020.02.11.943258v1?rss=1 Liu, S. Chen, C. Zhang, X. 2020-02-12 doi:10.1101/2020.02.11.943258 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ The intriguing dynamics of chromatin folding and assembly ]]> https://biorxiv.org/content/10.1101/2020.02.18.953398v1?rss=1 Yang, Z. Miao, W. Mofrad, M. R. K. 2020-02-19 doi:10.1101/2020.02.18.953398 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Reconstruction and dynamics of human intestinal microbiome observed in situ ]]> https://biorxiv.org/content/10.1101/2020.02.25.964148v1?rss=1 Liu, X. Dai, M. Ma, Y. Zhao, N. Zhang, H. Xiang, L. Tian, H. Shui, G. Zhang, F. Wang, J. 2020-02-26 doi:10.1101/2020.02.25.964148 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Amorphous nickel titanium alloy film: a new choice for cryo electron microscopy sample preparation ]]> https://biorxiv.org/content/10.1101/2020.03.02.963959v1?rss=1 Huang, X. Zhang, L. Wen, Z. Chen, H. Li, S. Ji, G. Yin, C.-c. Sun, F. 2020-03-02 doi:10.1101/2020.03.02.963959 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Multiple-biological matrices metabolomics identified new metabolite biomarkers for the precise diagnosis of pancreatic cancer and associated tissue metastasis ]]> https://biorxiv.org/content/10.1101/2020.03.09.983239v1?rss=1 Luo, X. Liu, J. Wang, H. Lu, H. 2020-03-09 doi:10.1101/2020.03.09.983239 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Multiple approaches for massively parallel sequencing of HCoV-19 genomes directly from clinical samples ]]> https://biorxiv.org/content/10.1101/2020.03.16.993584v1?rss=1 Xiao, M. Liu, X. Ji, J. Li, M. Li, J. Yang, L. Sun, W. Ren, P. Yang, G. Zhao, J. Liang, T. Ren, H. Chen, T. Zhong, H. Song, W. Wang, Y. Deng, Z. Zhao, Y. Ou, Z. Wang, D. Cai, J. Cheng, X. Feng, T. Wu, H. Gong, Y. Yang, H. Wang, J. Xu, X. Zhu, S. Chen, F. Zhang, Y. Chen, W. Li, Y. Li, J. 2020-03-17 doi:10.1101/2020.03.16.993584 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ Convergence within divergence: insights of wheat adaptation from Triticum population sequencing ]]> https://biorxiv.org/content/10.1101/2020.03.21.001362v1?rss=1 Zhou, Y. Zhao, X. Li, Y. Xu, J. Bi, A. Kang, L. Chen, H. Wang, Y. Wang, Y.-g. Liu, S. Jiao, C. Lu, H. Wang, J. Yin, C. Jiao, Y. Lu, F. 2020-03-23 doi:10.1101/2020.03.21.001362 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells ]]> https://biorxiv.org/content/10.1101/2020.03.22.002766v1?rss=1 Liu, S. Zhou, B. Wu, L. Sun, Y. Chen, J. Liu, S. 2020-03-25 doi:10.1101/2020.03.22.002766 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Single-cell RNA-Seq reveals the link between CD45 isoforms and tumor-infiltrating T cells heterogeneity in liver cancer ]]> https://biorxiv.org/content/10.1101/2020.03.22.002824v1?rss=1 Zhou, B. Liu, S. Wu, L. Sun, Y. Chen, J. Liu, S. 2020-03-25 doi:10.1101/2020.03.22.002824 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Reusable and Sensitive Detection Method for Exonuclease III Activity by DNB Nanoarrays Based on cPAS Sequencing Technology ]]> https://biorxiv.org/content/10.1101/2020.03.24.002956v1?rss=1 Chen, Y. Wang, H. Yang, J. Yang, H. Drmanac, R. Xu, C. Zhang, W. 2020-03-25 doi:10.1101/2020.03.24.002956 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ A Comprehensive Survey of Mutations in Oesophageal Carcinoma Reveals Recurrent Neoantigens as Potential Immunotherapy Targets ]]> https://biorxiv.org/content/10.1101/2020.03.28.013201v1?rss=1 Chen, C. Liu, S. Xiong, H. Zhang, X. Li, B. 2020-03-30 doi:10.1101/2020.03.28.013201 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ Isolation and characterization of two bacterial strains from textile effluents having Malachite Green dye degradation ability ]]> https://biorxiv.org/content/10.1101/2020.03.29.014274v1?rss=1 Roy, D. C. Sheam, M. M. Hasan, M. R. Saha, A. K. Roy, A. K. Haque, M. E. Rahman, M. M. Swee-Seong, T. Biswas, S. K. 2020-03-30 doi:10.1101/2020.03.29.014274 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ ERG orchestrates chromatin interactions to drive prostate cell fate reprogramming ]]> https://biorxiv.org/content/10.1101/2020.04.03.024349v1?rss=1 Li, F. Yuan, Q. Di, W. Xia, X. Liu, Z. Mao, N. Li, L. Li, C. He, J. Li, Y. Guo, W. Zhang, X. Zhu, Y. Aji, R. Wang, S. Chi, P. Carver, B. Wang, Y. Chen, Y. Gao, D. 2020-04-05 doi:10.1101/2020.04.03.024349 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ SARS-CoV-2 detection with CRISPR diagnostics ]]> https://biorxiv.org/content/10.1101/2020.04.10.023358v1?rss=1 Guo, L. Sun, X. Wang, X. Liang, C. Jiang, H. Gao, Q. Dai, M. Qu, B. Fang, S. Mao, Y. Chen, Y. Feng, G. Gu, Q. Wang, L. Wang, R. R. Zhou, Q. Li, W. 2020-04-11 doi:10.1101/2020.04.10.023358 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Proteogenomics analysis of non-coding region encoded peptides in normal tissues and five cancer types ]]> https://biorxiv.org/content/10.1101/2020.04.10.029306v1?rss=1 Xiang, R. Ma, L. Yang, M. Zheng, Z. Chen, X. Jia, F. Xie, F. Li, F. Wu, K. Zhu, Y. 2020-04-13 doi:10.1101/2020.04.10.029306 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Role of short-chain fatty acids in the gut-brain axis in schizophrenia: contribution to immune activation and pathophysiology in humans and mice ]]> https://biorxiv.org/content/10.1101/2020.04.11.021915v1?rss=1 Zhu, F. Wang, W. Ma, Q. Yang, Z. Ju, Y. Fan, Y. Guo, R. Wang, Q. Mu, X. Zhao, B. Gao, Y. He, X. Gao, F. Qian, L. Chen, C. Chen, Y. Gao, C. Ma, X.-c. 2020-04-13 doi:10.1101/2020.04.11.021915 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Long Noncoding RNA Derived from LncRNA-mRNA Co-expression Networks Modulates the Locust Phase Change ]]> https://biorxiv.org/content/10.1101/2020.04.11.036848v1?rss=1 Li, T. Chen, B. Yang, P. Wang, D. Du, B. Kang, L. 2020-04-13 doi:10.1101/2020.04.11.036848 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ CNV-PG: a machine-learning framework for accurate copy number variation predicting and genotyping ]]> https://biorxiv.org/content/10.1101/2020.04.13.039016v1?rss=1 Wang, T. Sun, J. Zhang, X. Wang, W.-J. Zhou, Q. 2020-04-14 doi:10.1101/2020.04.13.039016 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Parkinson's disease-related phosphorylation at Tyr39 rearranges α-synuclein amyloid fibril structure revealed by cryo-EM ]]> https://biorxiv.org/content/10.1101/2020.04.13.040261v1?rss=1 Zhao, K. Lim, Y.-J. Liu, Z. Long, H. Sun, Y. Hu, J.-J. Zhao, C. Tao, Y. Zhang, X. Li, D. Li, Y.-M. Liu, C. 2020-04-14 doi:10.1101/2020.04.13.040261 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Effect of storage conditions on peripheral leukocytes transcriptome ]]> https://biorxiv.org/content/10.1101/2020.04.21.054296v1?rss=1 Xing, Y. Yang, X. Chen, X. Zhu, S. Xu, J. Chen, Y. Zeng, J. Chen, F. Johnson, M. Jiang, H. Wang, W.-J. 2020-04-24 doi:10.1101/2020.04.21.054296 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta) ]]> https://biorxiv.org/content/10.1101/2020.04.29.069583v1?rss=1 Yu, J. Li, L. Wang, S. Dong, S. Chen, Z. Patel, N. Goffinet, B. Liu, H. Liu, Y. 2020-04-30 doi:10.1101/2020.04.29.069583 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Potent antiviral effect of protoporphyrin IX and verteporfin on SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2020.04.30.071290v1?rss=1 Gu, C. Wu, Y. Guo, H. Zhu, Y. Xu, W. Wang, Y. Sun, Z. Cai, X. Li, Y. Liu, J. Yuan, Z. Zhang, R. Deng, Q. Qu, D. Xie, Y. 2020-05-01 doi:10.1101/2020.04.30.071290 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ SLE non-coding Genetic Risk Variant Determines the Epigenetic Dysfunction of an Immune Cell Specific Enhancer that Controls Disease-critical microRNA Expression ]]> https://biorxiv.org/content/10.1101/2020.05.13.092932v1?rss=1 Hou, G. Harley, I. T. W. Lu, X. Zhou, T. Xu, N. Yao, C. Qin, Y. Ouyang, Y. Ma, J. Zhu, X. Yu, X. Dai, D. Xu, H. Ding, H. Tang, Y. Namjou, B. Weirauch, M. T. Kottyan, L. C. Harley, J. B. Shen, N. 2020-05-15 doi:10.1101/2020.05.13.092932 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Electronic blood vessel ]]> https://biorxiv.org/content/10.1101/2020.05.19.103457v1?rss=1 Cheng, S. Hang, C. Ding, L. Jia, L. Tang, L. Mou, L. Qi, J. Dong, R. Zheng, W. Zhang, Y. Jiang, X. 2020-05-21 doi:10.1101/2020.05.19.103457 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ Lipidomic profiling of plasma extracellular vesicles as an effective means to evaluate the risk of preterm birth ]]> https://biorxiv.org/content/10.1101/2020.06.07.135764v1?rss=1 Zhao, Q. Ma, Z. Wang, X. Liang, M. Wang, W. Su, F. Yang, H. Gao, Y. Ren, Y. 2020-06-08 doi:10.1101/2020.06.07.135764 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Structure Basis for Inhibition of SARS-CoV-2 by the Feline Drug GC376 ]]> https://biorxiv.org/content/10.1101/2020.06.07.138677v1?rss=1 Luan, X. Shang, W. Wang, Y. Yin, W. Jiang, Y. Feng, S. Wang, Y. Liu, M. Zhou, R. Zhang, Z. Wang, F. Wang, C. Gao, M. Wang, H. Wu, W. Tian, R. Tian, Z. Jin, Y. Jiang, H. Zhang, L. Xu, H. E. Zhang, S. 2020-06-08 doi:10.1101/2020.06.07.138677 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Parabrachial neuron types categorically encode thermoregulation variables during heat defense ]]> https://biorxiv.org/content/10.1101/2020.06.11.138370v1?rss=1 Yang, W. Z. Du, X. Zhang, W. Gao, C. Xie, H. Xiao, Y. Jia, X. Liu, J. Xu, J. Fu, X. Tu, H. Fu, X. Ni, X. He, M. Yang, J. Wang, H. Yang, H. Xu, X.-H. Shen, W. 2020-06-12 doi:10.1101/2020.06.11.138370 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Mapping Connectional Differences between Humans and Macaques in the Nucleus Accumbens Shell-Core Architecture ]]> https://biorxiv.org/content/10.1101/2020.06.12.147546v1?rss=1 Xia, X. Fan, L. Cheng, C. Cheng, L. Cao, L. He, B. Chen, J. Li, H. Jiang, T. 2020-06-12 doi:10.1101/2020.06.12.147546 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ A path towards SARS-CoV-2 attenuation: metabolic pressure on CTP synthesis rules the virus evolution ]]> https://biorxiv.org/content/10.1101/2020.06.20.162933v1?rss=1 Ou, Z. Ouzounis, C. Wang, D. Sun, W. Li, J. Chen, W. Marliere, P. Danchin, A. 2020-06-21 doi:10.1101/2020.06.20.162933 Cold Spring Harbor Laboratory Press 2020-06-21 <![CDATA[ Integration of Machine Learning Improves the Prediction Accuracy of Molecular Modelling for M. jannaschii Tyrosyl-tRNA Synthetase Substrate Specificity ]]> https://biorxiv.org/content/10.1101/2020.06.26.174524v1?rss=1 Duan, B. Sun, Y. 2020-06-28 doi:10.1101/2020.06.26.174524 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM ]]> https://biorxiv.org/content/10.1101/2020.06.30.177097v1?rss=1 Xu, C. Wang, Y. Liu, C. Zhang, C. Han, W. Hong, X. Wang, Y. Hong, Q. Wang, S. Zhao, Q. Wang, Y. Yang, Y. Chen, K. Zheng, W. Kong, L. Wang, F. Zuo, Q. Huang, Z. Cong, Y. 2020-06-30 doi:10.1101/2020.06.30.177097 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Phosphoproteomics Reveals AMPK Substrate Network in Response to DNA Damage and Histone Acetylation ]]> https://biorxiv.org/content/10.1101/2020.07.02.182121v1?rss=1 Jiang, Y. Cong, X. Jiang, S. Dong, Y. Zhao, L. Zang, Y. Tan, M. Li, J. 2020-07-02 doi:10.1101/2020.07.02.182121 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Regeneration of Functional Retinal Ganglion Cells by Neuronal Identity Reprogramming ]]> https://biorxiv.org/content/10.1101/2020.07.16.203497v1?rss=1 Liu, H. Wei, X. Zhang, Z. Zeng, H.-h. Wang, X.-F. Zhan, W. Qiao, N. Chang, Z. Liu, L. Fan, C. Yang, Z. Li, X. Yang, Y. 2020-07-17 doi:10.1101/2020.07.16.203497 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ A single-cell transcriptome atlas of the aging human and macaque retina ]]> https://biorxiv.org/content/10.1101/2020.07.17.207977v1?rss=1 Xue, T. Yi, W. Lu, y. Zhong, S. zhang, m. Sun, L. Dong, H. Wang, M. Wei, M. Xie, H. Qu, H. Peng, R. Hong, J. Yao, Z. Tong, Y. Wang, W. Ma, Q. Liu, z. Ma, Y. Li, S. Yin, C. Liu, J. Ma, C. Wang, X. Wu, Q. 2020-07-17 doi:10.1101/2020.07.17.207977 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Single-cell transcriptome analysis of the immunosuppressive effect of differential expression of tumor PD-L1 on responding TCR-T cells ]]> https://biorxiv.org/content/10.1101/2020.07.23.217059v1?rss=1 Ding, R. Liu, S. Wang, S. Chen, H. Wang, F. Xu, Q. Zhu, L. Dong, X. Gu, Y. Chao, C.-C. Gao, Q. 2020-07-24 doi:10.1101/2020.07.23.217059 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[ Screening of Botanical Drugs Against Lassa Virus Entry ]]> https://biorxiv.org/content/10.1101/2020.07.24.220749v1?rss=1 Liu, Y. Guo, J. Cao, J. Zhang, G. Jia, X. Wang, P. Xiao, G. Wang, W. 2020-07-25 doi:10.1101/2020.07.24.220749 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Genome-Wide Mapping of Cisplatin Damaged Gene Loci ]]> https://biorxiv.org/content/10.1101/2020.07.27.222752v1?rss=1 12, where EFG refers to the ratio of total read counts of a gene detected in cells with and without cisplatin treatment, are sperm motility, cancer and hepatotoxicity with association P values of < 1x10-22. Among 616 kinase genes damaged by cisplatin, 427 are protein kinases which account for 82% of putative protein kinases, suggesting that cisplatin may act as broad-spectrum protein kinase inhibitor. Western Blot assays verified that expression of 8 important protein kinase genes was significantly reduced due to cisplatin damage. SPAG9 is closely related to 147 of 361 cancer diseases which the cisplatin damaged genes are associated with and was severely damaged by cisplatin. Given SPAG9 abundantly expresses JIP-4, a upstream mediator of protein kinase signaling, in testis, it may be responsible for the high sensitivity of testicular cancer to cisplatin, thus being a potential therapeutic target for precise treatment of testicular cancer. These findings provide novel insights into better understanding in molecular mechanism of anticancer activity and toxicity of cisplatin, more importantly inspire further studies in prioritizing gene targets for precise treatment of cancers. ]]> Qi, L. Luo, Q. Xu, Y. Yu, W. Liu, X. Zhang, Y. Jia, F. Fang, T. Wang, S. Li, X. Zhao, Y. Wang, F. 2020-07-28 doi:10.1101/2020.07.27.222752 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Regulation of specific cell clusters in TCR-T cells responding to differential expression of tumor PD-L1 ]]> https://biorxiv.org/content/10.1101/2020.07.28.224816v1?rss=1 Renpeng, D. Liu, S. Chen, H. Kang, B. Drmanac, R. Gu, Y. Dong, X. Gao, Q. 2020-07-29 doi:10.1101/2020.07.28.224816 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ The molecular taxonomy of primate amygdala via single-nucleus RNA-sequencing analysis ]]> https://biorxiv.org/content/10.1101/2020.07.29.226829v1?rss=1 Zhang, L. Cheng, Y. Wu, S. Lu, Y. Xue, Z. Chen, D. Zhang, B. Qiu, Z. Jiang, H. 2020-07-30 doi:10.1101/2020.07.29.226829 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ A dynamic regulatory interface on SARS-CoV-2 RNA polymerase ]]> https://biorxiv.org/content/10.1101/2020.07.30.229187v1?rss=1 Shi, W. Chen, M. Yang, Y. Zhou, W. Chen, S. Hu, Y. Liu, B. 2020-07-30 doi:10.1101/2020.07.30.229187 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Photosynthetic resistance and resilience under drought and rewatering in maize plants ]]> https://biorxiv.org/content/10.1101/2020.08.03.234542v1?rss=1 Qi, M. Liu, X. Li, Y. Song, H. Zhang, F. Xu, Z. Zhou, G. 2020-08-04 doi:10.1101/2020.08.03.234542 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Prime editing primarily induces undesired outcomes in mice ]]> https://biorxiv.org/content/10.1101/2020.08.06.239723v1?rss=1 Aida, T. Wilde, J. J. Yang, L. Hou, Y. Li, M. Xu, D. Lin, J. Qi, P. Lu, Z. Feng, G. 2020-08-06 doi:10.1101/2020.08.06.239723 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency ]]> https://biorxiv.org/content/10.1101/2020.08.16.252668v1?rss=1 Li, Y. Xue, B. Zhang, L. Su, Q. P. Zhang, M. Long, H. Wang, Y. Jin, Y. Hou, Y. Cao, Y. Li, G. sun, y. 2020-08-17 doi:10.1101/2020.08.16.252668 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ A novel copper-sensing two-component system for activating Dsb genes in bacteria ]]> https://biorxiv.org/content/10.1101/2020.08.17.255257v1?rss=1 Yu, L. Cao, Q. Chen, W. Yang, N. Yang, C.-G. Ji, Q. Wu, M. Bae, T. Lan, L. 2020-08-18 doi:10.1101/2020.08.17.255257 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ The SARS-CoV-2 Envelope and Membrane proteins modulate maturation and retention of the Spike protein, allowing optimal formation of VLPs in presence of Nucleoprotein ]]> https://biorxiv.org/content/10.1101/2020.08.24.260901v1?rss=1 Boson, B. Legros, V. Zhou, B. Mathieu, C. Cosset, F.-L. Lavillette, D. Denolly, S. 2020-08-24 doi:10.1101/2020.08.24.260901 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Human Olfactory Perception is Sensitive to Temporal Information within a Single Sniff ]]> https://biorxiv.org/content/10.1101/2020.08.29.271254v1?rss=1 Wu, Y. Chen, K. Zhao, K. Zhou, W. 2020-08-31 doi:10.1101/2020.08.29.271254 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Dissecting the landscape of activated CMV-stimulated CD4+ T cells in human by linking single-cell RNA-seq with T-cell receptor sequencing ]]> https://biorxiv.org/content/10.1101/2020.08.30.268433v1?rss=1 Lyu, M. Wang, S. Gao, K. Wang, L. Li, B. Tian, L. 2020-08-31 doi:10.1101/2020.08.30.268433 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Small molecules inhibit SARS-COV-2 induced aberrant inflammation and viral replication in mice by targeting S100A8/A9-TLR4 axis ]]> https://biorxiv.org/content/10.1101/2020.09.09.288704v1?rss=1 Guo, Q. Zhao, Y. Li, J. Liu, J. Qin, C. Wang, X. You, F. Guo, X. Zhang, Z. Cao, L. Luo, Y. Wang, X. Wei, X. Chen, L. Bao, L. Deng, W. Zhu, H. Gao, R. 2020-09-09 doi:10.1101/2020.09.09.288704 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ ERWR: Predicting Efficacious Drug Combinations in Cancer Based on Random Walk with Restart ]]> https://biorxiv.org/content/10.1101/2020.09.13.295063v1?rss=1 Wang, Q. Yan, G. 2020-09-13 doi:10.1101/2020.09.13.295063 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Mapping Mouse Behavior with an Unsupervised Spatio-temporal Sequence Decomposition Framework ]]> https://biorxiv.org/content/10.1101/2020.09.14.295808v1?rss=1 Huang, K. Han, Y. Chen, K. Pan, H. Yi, W. Li, X. Liu, S. Wei, P. Wang, L. 2020-09-14 doi:10.1101/2020.09.14.295808 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex ]]> https://biorxiv.org/content/10.1101/2020.09.20.305029v1?rss=1 Tian, C. Du, Q. Xu, M. Du, F. Jiao, Y. 2020-09-20 doi:10.1101/2020.09.20.305029 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Regulation of lipid accumulation-induced ROS in myeloid-derived suppressor cells via targeting fatty-acid transport protein 2 enhanced anti-PD-L1 tumor immunotherapy ]]> https://biorxiv.org/content/10.1101/2020.09.28.316091v1?rss=1 Adeshakin, A. O. Liu, W. Adeshakin, F. O. Afolabi, L. O. Zhang, M. Zhang, G. Wang, L. Li, Z. Lin, L. Yan, D. Wan, X. 2020-09-28 doi:10.1101/2020.09.28.316091 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Effects of N-linked glycan of Lassa Virus Envelope Glycoprotein on the Immune Response ]]> https://biorxiv.org/content/10.1101/2020.09.29.319855v1?rss=1 Zhu, X. Liu, Y. Guo, J. Wang, Z. Cao, J. Xiao, G. Wang, W. 2020-09-30 doi:10.1101/2020.09.29.319855 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ ATF6 aggravates angiogenesis-osteogenesis coupling during ankylosing spondylitis by mediating FGF2 expression in chondrocytes ]]> https://biorxiv.org/content/10.1101/2020.10.08.332379v1?rss=1 Ma, M. Li, H. Wang, P. Yang, W. Mi, R. Jiang, Y. Lu, Y. Shen, X. Sui, P. Wu, Y. Shen, H. 2020-10-08 doi:10.1101/2020.10.08.332379 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Construction of a third NAD+ de novo biosynthesis pathway ]]> https://biorxiv.org/content/10.1101/2020.10.18.342451v1?rss=1 Ding, Y. Li, X. Horsman, G. P. Li, P. Wang, M. Li, J. Zhang, Z. Liu, W. Wu, B. Tao, Y. Chen, Y. 2020-10-18 doi:10.1101/2020.10.18.342451 Cold Spring Harbor Laboratory Press 2020-10-18 <![CDATA[ Proteomics study of colorectal cancer and adenomatous polyps identifies TFR1, SAHH, and HV307 as potential biomarkers for screening ]]> https://biorxiv.org/content/10.1101/2020.10.19.344887v1?rss=1 Tang, M. Zeng, L. Zeng, Z. Liu, J. Yuan, J. Wu, D. Lu, Y. Zi, J. Ye, M. 2020-10-20 doi:10.1101/2020.10.19.344887 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Genetic determinants of COVID-19 drug efficacy revealed by genome-wide CRISPR screens ]]> https://biorxiv.org/content/10.1101/2020.10.26.356279v1?rss=1 Jiang, W. Yang, A. Ma, J. Lv, D. Liu, M. Xu, L. Wang, C. He, Z. Chen, S. Zhao, J. Chen, S. Jiang, Q. Chu, Y. Shan, L. Zhou, Z. Zhao, Y. Long, G. Jiang, H. 2020-10-27 doi:10.1101/2020.10.26.356279 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Single-cell Multi-omics reveal heterogeneity and metastasis potential in different liver cancer cell lines ]]> https://biorxiv.org/content/10.1101/2020.11.03.367532v1?rss=1 Wu, L. Xie, J. Wang, S. Zou, X. Pan, T. Zhuang, Z. Wang, Z. Yuan, Y. Liu, L. Liu, S. 2020-11-05 doi:10.1101/2020.11.03.367532 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Potent SARS-CoV-2 neutralizing antibodies selected from a human antibody library constructed decades ago ]]> https://biorxiv.org/content/10.1101/2020.11.06.370676v1?rss=1 Qiang, M. Ma, P. Li, Y. Liu, H. Harding, A. Min, C. Liu, L. Yuan, M. Ji, Q. Tao, P. Shi, X. Li, Z. Wang, F. Zhang, Y. Wu, N. C. Lee, C.-C. D. Zhu, X. Gilbert-Jaramillo, J. Saxena, A. Huang, X. Wang, H. James, W. Dwek, R. A. Wilson, I. A. Yang, G. Lerner, R. A. 2020-11-06 doi:10.1101/2020.11.06.370676 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Resuscitation of soil microbiota after > 70-years of desiccation ]]> https://biorxiv.org/content/10.1101/2020.11.06.371641v1?rss=1 1000-fold average increase) following rewetting. Additionally, some Actinobacteria and Proteobacteria genera showed relatively high activity following rewetting, suggesting that the resilience to long-term desiccation and rewetting is a common trait across phylogenetically divergent microbes. The present study thus demonstrated that diversified groups of microbes are present and potentially active in historically desiccated soils, which might be of importance in the context of microbial ecology. ]]> Zhao, J. Chen, D. Gao, W. Guo, Z. Jia, Z. Hernandez, M. 2020-11-07 doi:10.1101/2020.11.06.371641 70-years of desiccation]]> Cold Spring Harbor Laboratory Press 2020-11-07 <![CDATA[ The expression of PDCD1 and CD274 in T cells and macrophages correlated positively with COVID-19 severity ]]> https://biorxiv.org/content/10.1101/2020.11.17.378992v1?rss=1 Gao, Q. Liu, S. Ding, R. Chen, H. Dong, X. Xie, J. Li, Y. Chen, L. Liu, H. Mu, F. 2020-11-18 doi:10.1101/2020.11.17.378992 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Human fecal microbiota is associated with colorectal cancer ]]> https://biorxiv.org/content/10.1101/2020.11.17.387647v1?rss=1 Yao, Q. Tang, M. Zeng, L. Chu, Z. Sheng, H. Zhang, Y. Zhou, Y. Zhang, H. Jiang, H. Ye, M. 2020-11-18 doi:10.1101/2020.11.17.387647 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage ]]> https://biorxiv.org/content/10.1101/2020.11.24.395426v1?rss=1 Ge, W. Liang, X. Zhang, F. Xu, L. Xiang, N. Sun, R. Liu, W. Xue, Z. Yi, X. Wang, B. Zhu, J. Lu, C. Zhan, X. Chen, L. Wu, Y. Zheng, Z. Gong, W. Wu, Q. Yu, J. Ye, Z. Teng, X. Huang, S. Zheng, S. Liu, T. Yuan, C. Guo, T. 2020-11-25 doi:10.1101/2020.11.24.395426 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Predicting Brain Regions Related to Alzheimer's Disease Based on Global Feature ]]> https://biorxiv.org/content/10.1101/2020.11.27.401950v1?rss=1 Wang, Q. Chen, S. Wang, H. Chen, L. Sun, Y. Yan, G. 2020-11-28 doi:10.1101/2020.11.27.401950 Cold Spring Harbor Laboratory Press 2020-11-28 <![CDATA[ Caerulomycin and Collismycin Antibiotics Share a trans Flavin-Dependent Assembly Line for 2,2-Bipyridine Formation and Sulfur Fate Differentiation ]]> https://biorxiv.org/content/10.1101/2020.12.07.415471v1?rss=1 pang, b. liao, r. tang, z. guo, s. wu, z. liu, w. 2020-12-08 doi:10.1101/2020.12.07.415471 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ High-throughput Single-cell CNV Detection Reveals Clonal Evolution During Hepatocellular Carcinoma Recurrence ]]> https://biorxiv.org/content/10.1101/2020.12.09.417626v1?rss=1 Wu, L. Wang, Y. Jiang, M. Zhou, B. Sun, Y. Zhou, K. Xie, J. Zhong, Y. Zhao, Z. Dean, M. Hou, Y. Liu, S. 2020-12-09 doi:10.1101/2020.12.09.417626 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ HRWR: Predicting Potential Efficacious Drug Combination Based on Hypergraph Random Walk with Restart ]]> https://biorxiv.org/content/10.1101/2020.12.10.420760v1?rss=1 Wang, Q. Yan, G. 2020-12-11 doi:10.1101/2020.12.10.420760 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Mechanism through which retrocyclin targets flavivirus multiplication ]]> https://biorxiv.org/content/10.1101/2020.12.15.422996v1?rss=1 Jia, X. Guo, J. yuan, W. Sun, L. Liu, Y. Zhou, M. Xiao, G. Lu, W. Garzino-Demo, A. Wang, W. 2020-12-16 doi:10.1101/2020.12.15.422996 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Identification of inhibitors of SARS-CoV-2 3CL-Pro enzymatic activity using a small molecule in-vitro repurposing screen ]]> https://biorxiv.org/content/10.1101/2020.12.16.422677v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@17ca2aeorg.highwire.dtl.DTLVardef@19c5159org.highwire.dtl.DTLVardef@1a0adf6org.highwire.dtl.DTLVardef@1fd05cd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOAbstract Figure.C_FLOATNO Workflow for identification and profiling of inhibitors of SARS-CoV-2 3CL-Pro using a large scale repurposing and bioactive compound collection (rhs). Primary assay principle based on quenched FRET peptide substrate of SARS-CoV-2 3CL-Pro (lhs). Inhibiting compounds reduce fluorescence signal relative to DMSO controls. Hit profiling using X-ray. C_FIG ]]> Kuzikov, M. Costanzi, E. Reinshagen, J. Esposito, F. Vangeel, L. Wolf, M. Ellinger, B. Claussen, C. Geisslinger, G. Corona, A. Iaconis, D. Talarico, C. Manelfi, C. Cannalire, R. Rossetti, G. Gossen, J. Albani, S. Musiani, F. Herzog, K. Ye, Y. Giabbai, B. Demitri, N. Jochmans, D. De Jonghe, S. Rymenants, J. Summa, V. Tramontano, E. Beccari, A. R. Leyssen, P. Storici, P. Neyts, J. Gribbon, P. Zaliani, A. 2020-12-16 doi:10.1101/2020.12.16.422677 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ SARS-CoV-2 spike protein interacts with and activates TLR4 ]]> https://biorxiv.org/content/10.1101/2020.12.18.423427v1?rss=1 Zhao, Y. Kuang, M. Wang, X. You, F. 2020-12-18 doi:10.1101/2020.12.18.423427 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ High-resolution Cell Atlas of Pig Lung and Online Platform Exploring for Lung Single Cell ]]> https://biorxiv.org/content/10.1101/2020.12.20.423716v1?rss=1 Zhang, L. Zhu, J. Wang, H. Xia, J. Liu, P. Chen, F. Jiang, H. Wu, W. Luo, L. Chen, D. Zhang, X. 2020-12-22 doi:10.1101/2020.12.20.423716 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence ]]> https://biorxiv.org/content/10.1101/2020.12.22.424042v1?rss=1 Wang, J. Wang, L. Wei, C. Wang, J. Teng, J. Shen, S. Xiao, Q. Bao, S. Feng, Y. Zhang, Y. Li, Y. Sun, S. Yue, Y. Wu, C. Wang, Y. Zhou, T. Xu, W. Yu, J. 2020-12-22 doi:10.1101/2020.12.22.424042 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Functional Characterization of a Lassa Virus Fusion Inhibitors Adaptive Mutant ]]> https://biorxiv.org/content/10.1101/2020.12.23.424274v1?rss=1 Guo, J. Zhang, G. Liu, Y. Cao, J. Zhang, M. Lan, X. Zhang, Y. Liu, C. Xiao, G. Wang, W. 2020-12-24 doi:10.1101/2020.12.23.424274 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Sequencing of clinical samples reveals that adaptation keeps establishing during H7N9 virus infection in humans ]]> https://biorxiv.org/content/10.1101/2020.12.30.424890v1?rss=1 Li, L. Ma, J. Li, J. Yuan, J. Su, W. Jin, T. Wang, X. Zhang, R. Zou, R. Li, L. Li, J. Fang, S. Yuan, J. Yang, C. Qi, Y. Gao, Q. Ji, J. Ma, K. Fan, G. Pei, N. Deng, Y. Zhou, Y. Lin, D. Li, F. Ouyang, W. Jia, H. Liu, X. Jiang, H. Yang, H. Xu, X. Wang, H. Liu, Y. 2020-12-31 doi:10.1101/2020.12.30.424890 Cold Spring Harbor Laboratory Press 2020-12-31 <![CDATA[ RNAi screening reveals requirement for PDGFRβ in JEV infection. ]]> https://biorxiv.org/content/10.1101/2021.01.21.427722v1?rss=1 Zhou, M. Wang, S. Guo, J. Liu, Y. Cao, J. Lan, X. Jia, X. Zhang, B. Xiao, G. Wang, W. 2021-01-22 doi:10.1101/2021.01.21.427722 Cold Spring Harbor Laboratory Press 2021-01-22 <![CDATA[ Genome-wide analysis of mobile element insertions in human genomes ]]> https://biorxiv.org/content/10.1101/2021.01.22.427873v1?rss=1 Niu, Y. Teng, X. Shi, Y. Li, Y. Tang, Y. Zhang, P. Luo, H. Kang, Q. The Han100K Initiative, Xu, T. He, S. 2021-01-24 doi:10.1101/2021.01.22.427873 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ Recombinant chimpanzee adenovirus AdC7 expressing dimeric tandem-repeat RBD of SARS-CoV-2 spike protein protects mice against COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.02.05.429860v1?rss=1 Xu, K. An, Y. Li, Q. Huang, W. Han, Y. Zheng, T. Fang, F. Liu, H. Liu, C. Gao, P. Xu, S. Liu, W. J. Bi, Y. Wang, Y. Zhou, D. Wang, Q. Hou, W. Xia, Q. Gao, G. F. Dai, L. 2021-02-08 doi:10.1101/2021.02.05.429860 Cold Spring Harbor Laboratory Press 2021-02-08 <![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[ The possible fidelity-speed-proofreading cost trade-offs in DNA replication due to the exonuclease proofreading ]]> https://biorxiv.org/content/10.1101/2021.02.18.431768v1?rss=1 Li, Q. Shu, Y. Fu, W. Ouyang, Z. Li, M. 2021-02-19 doi:10.1101/2021.02.18.431768 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Familial prion disease-related mutation E196K displays a novel amyloid fibril structure revealed by cryo-EM ]]> https://biorxiv.org/content/10.1101/2021.02.18.431846v1?rss=1 Wang, L.-Q. Zhao, K. Yuan, H.-Y. Li, X.-N. Dang, H.-B. Ma, Y. Wang, Q. Wang, C. Sun, Y. Chen, J. Li, D. Zhang, D. Yin, P. Liu, C. Liang, Y. 2021-02-18 doi:10.1101/2021.02.18.431846 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ A recombinant selective drug-resistant M. bovis BCG enhances the bactericidal activity of a second-line tuberculosis regimen ]]> https://biorxiv.org/content/10.1101/2021.03.04.434024v1?rss=1 Chiwala, G. Liu, Z. Mugweru, J. N. Wang, B. Khan, S. A. Bate, P. N. N. Yusuf, B. Hameed, H. M. A. Fang, C. Tan, Y. Guan, P. Hu, J. Tan, S.-Y. Liu, J. Zhong, N. Zhang, T. 2021-03-05 doi:10.1101/2021.03.04.434024 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ A tandem-repeat dimeric RBD protein-based COVID-19 vaccine ZF2001 protects mice and nonhuman primates ]]> https://biorxiv.org/content/10.1101/2021.03.11.434928v1?rss=1 An, Y. Li, S. Jin, X. Han, J.-B. Xu, K. Xu, S. Han, Y. Liu, C. Zheng, T. Liu, M. Yang, M. Song, T.-z. Huang, B. Zhao, L. Wang, W. A, R. Cheng, Y. Wu, C. Huang, E. Yang, S. Wang, G. Bi, Y. Ke, C. Tan, W. Yan, J. Zheng, Y.-T. Dai, L. Gao, G. F. 2021-03-11 doi:10.1101/2021.03.11.434928 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells ]]> https://biorxiv.org/content/10.1101/2021.03.17.435782v1?rss=1 Li, G.-W. Nan, F. Yuan, G.-H. Tian, B. Yang, L. 2021-03-19 doi:10.1101/2021.03.17.435782 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ A novel method for generating 3D constructs with branched vascular networks using multi-materials bioprinting and direct surgical anastomosis ]]> https://biorxiv.org/content/10.1101/2021.03.21.436268v1?rss=1 Liu, X. Wang, X. Zhang, L. Sun, L. Wang, H. Zhao, H. Zhang, Z. Huang, Y. Zhang, J. Song, B. Li, C. Zhang, H. Li, S. Wang, S. Zheng, X. Gu, Q. 2021-03-22 doi:10.1101/2021.03.21.436268 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Bayesian metamodeling of complex biological systems across varying representations ]]> https://biorxiv.org/content/10.1101/2021.03.29.437574v1?rss=1 Raveh, B. Sun, L. White, K. L. Sanyal, T. Tempkin, J. Zheng, D. Bharath Pilla, K. Singla, J. Wang, C. Zha, J. Li, A. Graham, N. A. Kesselman, C. Stevens, R. C. Sali, A. 2021-03-29 doi:10.1101/2021.03.29.437574 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Impact of blood storage conditions on the transcript profile of plasma cell-free RNA ]]> https://biorxiv.org/content/10.1101/2021.03.30.437637v1?rss=1 Sun, J. Yang, X. Wang, T. Xing, Y. Chen, H. Zhu, S. Zeng, J. Zhou, Q. Chen, F. Zhang, X. Wang, W.-J. 2021-03-30 doi:10.1101/2021.03.30.437637 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ A recombinant receptor-binding domain in trimeric form generates completely protective immunity against SARS-CoV-2 infection in nonhuman primates ]]> https://biorxiv.org/content/10.1101/2021.03.30.437647v1?rss=1 Yang, L. Tian, D. Han, J.-b. Fan, W. Zhang, Y. Li, Y. Sun, W. Wei, Y. Tian, X. Yu, D.-d. Feng, X.-l. Cheng, G. Zheng, Y.-t. Bi, Y. Liu, W. 2021-03-30 doi:10.1101/2021.03.30.437647 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Dynamic functional connectivity links with treatment response of electroconvulsive therapy in major depressive disorder ]]> https://biorxiv.org/content/10.1101/2021.03.31.437958v1?rss=1 Sendi, M. S. E. Dini, H. Sui, J. Fu, Z. Espinoza, R. Narr, K. Qi, S. Abbott, C. C. van Rooij, S. Riva-Posse, P. Mayberg, H. S. Calhoun, V. D. 2021-04-02 doi:10.1101/2021.03.31.437958 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ CDCA-seq resolve the different chromatin structure on integral circular DNAs ]]> https://biorxiv.org/content/10.1101/2021.03.31.437970v1?rss=1 Chen, W. Weng, Z. Xie, Z. Xie, Y. Zhang, C. Chen, Z. Ruan, F. Wang, J. Sun, Y. Guo, M. Fang, Y. Tong, Y. Li, Y. Tang, C. 2021-04-02 doi:10.1101/2021.03.31.437970 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ The PD-L1 and TLR7 dual-targeting nanobody-drug conjugate exerts potent antitumor efficacy by orchestrating innate and adaptive immune responses ]]> https://biorxiv.org/content/10.1101/2021.04.11.439388v1?rss=1 Yu, X. Long, Y. Chen, B. Tong, Y. Jia, X. Zhou, J. Tang, F. Xu, P. Cao, Y. Huang, W. Ren, J. Wan, Y. Sun, J. Jin, G. Gong, L. 2021-04-12 doi:10.1101/2021.04.11.439388 Cold Spring Harbor Laboratory Press 2021-04-12 <![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[ Endothelial SIRPα signaling controls thymic progenitor homing for T cell regeneration and antitumor immunity ]]> https://biorxiv.org/content/10.1101/2021.04.19.440464v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@d53edorg.highwire.dtl.DTLVardef@100f2c9org.highwire.dtl.DTLVardef@1438a6forg.highwire.dtl.DTLVardef@135aa2b_HPS_FORMAT_FIGEXP M_FIG C_FIG Thymic homing of hematopoietic progenitor cells is fundamental to the T cell-based adaptive immunity, yet the molecular basis of this process is less clear. We discovered that endothelial SIRP signaling, engaged by migrating cell derived CD47 ligand, regulates thymic homing of hematopoietic progenitor cells for T cell regeneration and antitumor immunity. O_LISIRP is preferentially expressed on thymic portal endothelial cells. C_LIO_LIEndothelial SIRP regulates thymic homing of hematopoietic progenitor cells. C_LIO_LICD47-SIRP downstream signaling induces VE-cadherin endocytosis. C_LIO_LICD47-SIRP signaling blockade impairs thymic T cell regeneration and antitumor immunity. C_LI ]]> Ren, B. Xia, H. Liao, Y. Zhou, H. Wang, Z. Shi, Y. Zhu, M. 2021-04-20 doi:10.1101/2021.04.19.440464 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Urgent Brain Vascular Regeneration Occurs via Lymphatic Transdifferentiation ]]> https://biorxiv.org/content/10.1101/2021.04.23.441119v1?rss=1 Luo, L. Chen, J. Li, X. Ni, R. Chen, Q. Yang, Q. He, J. 2021-04-23 doi:10.1101/2021.04.23.441119 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ SmProt: a reliable repository with comprehensive annotation of small proteins identified from ribosome profiling ]]> https://biorxiv.org/content/10.1101/2021.04.29.441405v1?rss=1 Li, Y. Zhou, H. Chen, X. Zheng, Y. Kang, Q. Hao, D. Zhang, L. Song, T. Luo, H. Hao, Y. Chen, Y. Chen, R. Zhang, P. He, S. 2021-04-30 doi:10.1101/2021.04.29.441405 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Identification of residues in Lassa virus glycoprotein 1 involved in receptor switch ]]> https://biorxiv.org/content/10.1101/2021.04.30.442226v1?rss=1 L107F > K88E > H170S. IMPORTANCELassa virus requires pH-dependent receptor switch to infect host cells; however, the underlying molecular mechanisms of this process are not well known. Here, we identify four residues, L84, K88, L107, and H170 that contribute to the interaction with the second receptor lysosome-associated membrane protein 1 (LAMP1). Mutant any of the four residues would impair the binding affinity to LAMP1, decrease the glycoprotein mediated membrane fusion, and reduce the pseudovirus infectivity. ]]> Guo, J. Jia, X. Liu, Y. Cao, J. Xiao, G. Wang, W. 2021-05-01 doi:10.1101/2021.04.30.442226 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ Homogeneous environmental selection overturns distance-decay relationship of soil prokaryotic community ]]> https://biorxiv.org/content/10.1101/2021.05.13.443991v1?rss=1 Zhang, B. Xue, K. Zhou, S. Wang, K. Liu, W. Xu, C. Cui, L. Li, L. Ran, Q. Hu, R. Hao, Y. Cui, X. Wang, Y. 2021-05-14 doi:10.1101/2021.05.13.443991 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ High-throughput mapping of single-cell molecular and projection architecture of neurons by retrograde barcoded labelling ]]> https://biorxiv.org/content/10.1101/2021.05.16.444258v1?rss=1 Xu, P. Peng, J. Yuan, T. Chen, Z. Wu, Z. Li, T. Li, X. Wang, L. Wei, W. Li, C. T. Luo, Z.-G. Chen, Y. 2021-05-17 doi:10.1101/2021.05.16.444258 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Screening of Botanical Drugs against SARS-CoV-2 Entry ]]> https://biorxiv.org/content/10.1101/2021.06.03.447021v1?rss=1 Cao, J. Liu, Y. Zhou, M. Dong, S. Jia, X. Lan, X. Zhang, Y. Guo, J. Xiao, G. Wang, W. 2021-06-04 doi:10.1101/2021.06.03.447021 Cold Spring Harbor Laboratory Press 2021-06-04 <![CDATA[ Complexin-1 regulated transition in the assembly of single neuronal SNARE complex ]]> https://biorxiv.org/content/10.1101/2021.06.07.447331v1?rss=1 Tongrui, H. Nan, F. Fan, G. Jiaquan, L. Ma, L. Yu-Xuan, R. 2021-06-07 doi:10.1101/2021.06.07.447331 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Molecular insights into differentiated ligand recognition of the human parathyroid hormone receptor 2 ]]> https://biorxiv.org/content/10.1101/2021.06.09.447485v1?rss=1 Wang, X. Cheng, X. Zhao, L. Wang, Y. Ye, C. Zou, X. Dai, A. Cong, Z. Chen, J. Zhou, Q. Xia, T. Jiang, H. Xu, H. E. Yang, D. Wang, M.-W. 2021-06-10 doi:10.1101/2021.06.09.447485 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[ Uncovering the Genetic Profiles Underlying the Intrinsic Organization of the Human Cerebellum ]]> https://biorxiv.org/content/10.1101/2021.06.23.448673v1?rss=1 Wang, Y. Chai, L. Li, D. Gao, C. Chu, C. Yang, Z. Zhang, Y. Xu, J. Nyengaard, J. R. Liu, B. Madsen, K. H. Jiang, T. Fan, L. 2021-06-24 doi:10.1101/2021.06.23.448673 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface ]]> https://biorxiv.org/content/10.1101/2021.06.27.450103v1?rss=1 Yang, B. Yao, H. Li, D. Liu, Z. 2021-06-28 doi:10.1101/2021.06.27.450103 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ ERp44 is Required for Endocardial Cushion Development by Regulating VEGFA Secretion in Myocardium ]]> https://biorxiv.org/content/10.1101/2021.07.02.450976v1?rss=1 Bi, Y. Yang, Z. Jin, M. Zhai, K. Wang, J. Mao, Y. Liu, Y. Ding, M. Wang, H. Wang, F. Ji, G. 2021-07-03 doi:10.1101/2021.07.02.450976 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Long-range single-molecule mapping of chromatin modification in eukaryotes ]]> https://biorxiv.org/content/10.1101/2021.07.08.451578v1?rss=1 Weng, Z. Ruan, F. Chen, W. Xie, Z. Xie, Y. Zhang, C. Chen, Z. Wang, J. Sun, Y. Fang, Y. Guo, M. Tong, Y. Li, Y. Tang, C. 2021-07-09 doi:10.1101/2021.07.08.451578 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ A recombinant protein containing influenza viral conserved epitopes and superantigen induces broad-spectrum protection ]]> https://biorxiv.org/content/10.1101/2021.07.08.451596v1?rss=1 Li, Y. Xu, M. Li, Y. Gu, W. Halimu, G. Li, Y. Zhang, Z. Zhou, L. Liao, H. Yao, S. Zhang, H. Zhang, C. 2021-07-10 doi:10.1101/2021.07.08.451596 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Screening and Identification of Lassa Virus Endonuclease-targeting Inhibitors from a Fragment-based Drug Development Library ]]> https://biorxiv.org/content/10.1101/2021.07.09.451867v1?rss=1 Lan, X. Zhang, Y. Liu, Y. Guo, J. Jia, X. Zhang, M. Cao, J. Xiao, G. Guo, Y. Wang, W. 2021-07-10 doi:10.1101/2021.07.09.451867 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Unconventional tonicity-regulated nuclear trafficking of NFAT5 mediated by KPNB1, XPOT and RUVBL2 ]]> https://biorxiv.org/content/10.1101/2021.07.11.451941v1?rss=1 Cheung, C. Y. Huang, T.-T. Chow, N. Zhang, S. Zhao, Y. Wong, C. C. Boassa, D. Phan, S. Ellisman, M. H. Yates, J. R. Xu, S. Yu, Z. Zhang, Y. Zhang, R. Ng, L. L. Ko, B. C. B. 2021-07-11 doi:10.1101/2021.07.11.451941 Cold Spring Harbor Laboratory Press 2021-07-11 <![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[ BAI-Net: Individualized Human Cerebral Cartography using Graph Convolutional Network ]]> https://biorxiv.org/content/10.1101/2021.07.15.452577v1?rss=1 Ma, L. Zhang, Y. Zhang, H. Cheng, L. Zhuo, J. Shi, W. Lu, Y. Li, W. Wang, J. Yang, Z. Fan, L. Jiang, T. 2021-07-16 doi:10.1101/2021.07.15.452577 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Viral receptor profiles of masked palm civet revealed by single-cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2021.07.20.452903v1?rss=1 Chen, D. Ou, Z. Wang, H. Zhang, Y. Zhu, J. An, F. Xu, J. Ding, X. Ding, P. Luo, L. Wu, W. Qin, Q. Wei, Y. Zhao, W. Lv, Z. Lan, T. Li, M. Zhang, W. Liu, H. Hua, Y. 2021-07-21 doi:10.1101/2021.07.20.452903 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ The transcription factor Zeb2 drives differentiation of age-associated B cells ]]> https://biorxiv.org/content/10.1101/2021.07.24.453633v1?rss=1 Gu, S. Han, X. Yao, C. Ding, H. Zhang, J. Hou, G. Qu, B. Zhou, H. Ying, Z. Ye, Z. Qian, J. Guo, Q. Chen, S. Vinuesa, C. G. Dai, D. Shen, N. 2021-07-24 doi:10.1101/2021.07.24.453633 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Characterizing enterotypes in human metagenomics: a viral perspective ]]> https://biorxiv.org/content/10.1101/2021.07.26.453761v1?rss=1 song, l. Zhang, L. Fang, X. 2021-07-26 doi:10.1101/2021.07.26.453761 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ New insights into the earlier evolutionary history of epiphytic macrolichens ]]> https://biorxiv.org/content/10.1101/2021.08.02.454570v1?rss=1 Yang, Q. Wang, Y. Lucking, R. Lumbsch, H. T. Wang, X. Du, Z. Chen, Y. Bai, M. Ren, D. Wei, J. Li, H. Wang, Y. Wei, X. 2021-08-03 doi:10.1101/2021.08.02.454570 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ IntroSpect: motif-guided immunopeptidome database building tool to improve the sensitivity of HLA binding peptide identification ]]> https://biorxiv.org/content/10.1101/2021.08.02.454768v1?rss=1 Zhang, L. Liu, G. Hou, G. Xiang, H. Zhang, X. Huang, Y. Zhang, X. Li, B. Lee, L. J. 2021-08-04 doi:10.1101/2021.08.02.454768 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Synaptic and mitochondrial plasticity associated with fear memory revealed by deep learning-based 3D reconstruction ]]> https://biorxiv.org/content/10.1101/2021.08.05.455246v1?rss=1 Liu, J. Qi, J. Chen, X. Li, Z. Hong, B. Ma, H. Li, G. Shen, L. Liu, D. Kong, Y. Xie, Q. Han, H. Yang, Y. 2021-08-06 doi:10.1101/2021.08.05.455246 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Screening of cell-virus, cell-cell, gene-gene interactions among kingdoms of life at single cell resolution ]]> https://biorxiv.org/content/10.1101/2021.08.13.456190v1?rss=1 Chen, D. Ou, Z. Zhu, J. Ding, P. Wang, H. Luo, L. Ding, X. Lan, T. Wu, W. Yuan, Y. Wu, W. Qiu, J. Zhu, Y. Jia, Y. Wei, Y. Qin, Q. Li, R. Sun, C. Zhao, W. Lv, Z. Pu, M. Yang, S. Chang, A. Wei, X. Chen, F. Yang, T. Wei, Z. Yang, F. Li, Y. Hua, Y. Liu, H. 2021-08-13 doi:10.1101/2021.08.13.456190 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ CDCP: a visualization and analyzing platform for single-cell datasets ]]> https://biorxiv.org/content/10.1101/2021.08.24.457455v1?rss=1 Li, Y. Yang, T. Lai, T. You, L. Yang, F. Qiu, J. Wang, L. Du, W. Hua, C. Xu, Z. Cai, J. Li, Z. Liu, Y. Li, L. Zhang, M. Chen, J. Zhang, L. Chen, D. Liu, S. Wu, L. Zeng, W. Wang, B. Liu, L. Chen, F. Wei, X. 2021-08-25 doi:10.1101/2021.08.24.457455 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Programmable RNA base editing with a single gRNA-free enzyme ]]> https://biorxiv.org/content/10.1101/2021.08.31.458316v1?rss=1 Han, W. Huang, W. Mao, M. Wei, T. Ye, Y. Wang, Z. 2021-08-31 doi:10.1101/2021.08.31.458316 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ RNA secondary structure regulates fragments' adsorption onto flat substrates ]]> https://biorxiv.org/content/10.1101/2021.08.31.458432v1?rss=1 Poblete, S. Bozic, A. Kanduc, M. Podgornik, R. V. Guzman, H. 2021-09-01 doi:10.1101/2021.08.31.458432 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Screening and Identification of Lujo Virus Entry Inhibitors from an FDA-Approved Drugs Library ]]> https://biorxiv.org/content/10.1101/2021.09.01.458657v1?rss=1 Cao, J. Liu, Y. Dong, S. Zhou, M. Guo, J. Jia, X. Zhang, Y. Hou, Y. Xiao, G. Wang, W. 2021-09-02 doi:10.1101/2021.09.01.458657 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling ]]> https://biorxiv.org/content/10.1101/2021.09.08.459391v1?rss=1 Liu, F. Ding, Y. Li, Y. Cliff Zhang, Q. 2021-09-09 doi:10.1101/2021.09.08.459391 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ A Comparison of Methods to Harmonize Cortical Thickness Measurements Across Scanners and Sites ]]> https://biorxiv.org/content/10.1101/2021.09.22.461242v1?rss=1 Sun, D. Rakesh, G. Clarke-Rubright, E. K. Haswell, C. C. Logue, M. O'Leary, B. M. Cotton, A. S. Xie, H. Dennis, E. L. Jahanshad, N. Salminen, L. E. Thomopolous, S. I. Rashid, F. Ching, C. R. K. Koch, S. B. J. Frijling, J. L. Nawijn, L. van Zuiden, M. Zhu, X. Suarez-Jimenez, B. Sierk, A. Walter, H. Manthey, A. Stevens, J. S. Fani, N. van Rooij, S. J. H. Stein, M. Bomyea, J. Koerte, I. K. Choi, K. van der Werff, S. J. A. Vermeiren, R. R. J. M. Herzog, J. Lebois, L. A. M. Baker, J. T. Ressler, K. J. Olson, E. A. Straube, T. Korgaonkar, M. S. Andrew, E. Zhu, 2021-09-24 doi:10.1101/2021.09.22.461242 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Comprehensive simulation and interpretation of single nucleotide substitutions in GJB2 reveals the genetic and phenotypic landscape of GJB2-related hearing loss ]]> https://biorxiv.org/content/10.1101/2021.09.30.462500v1?rss=1 Xiang, J. Sun, X. Song, N. Chen, L. Ramaswamy, S. Tayoun, A. A. Peng, Z. 2021-10-01 doi:10.1101/2021.09.30.462500 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use ]]> https://biorxiv.org/content/10.1101/2021.10.07.463401v1?rss=1 Hegarty, B. E. Dai, Z. Raskin, L. Pinto, A. J. Wigginton, K. Duhaime, M. B. 2021-10-08 doi:10.1101/2021.10.07.463401 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Remarkable Adsorption Performance of Rutile TiO2 (110) Nanosheet for DNA Nucleobases: A First-Principles Study ]]> https://biorxiv.org/content/10.1101/2021.10.15.464499v1?rss=1 Yang, J. Liu, W. Hu, Q. Hu, S. Chi, Z. Han, Y. Meng, F. 2021-10-16 doi:10.1101/2021.10.15.464499 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Single-cell Stereo-seq enables cell type-specific spatial transcriptome characterization in Arabidopsis leaves ]]> https://biorxiv.org/content/10.1101/2021.10.20.465066v1?rss=1 Xia, K. Sun, H.-X. Li, J. Li, J. Zhao, Y. Chen, R. Liu, G. Chen, Z. Yin, R. Hao, S. Wang, J. Xie, Q. Xu, J. Li, Y. Chen, A. Liu, L. Yin, Y. Yang, H. Wang, J. Gu, Y. Xu, X. 2021-10-21 doi:10.1101/2021.10.20.465066 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Spatially-resolved transcriptomics analyses of invasive fronts in solid tumors ]]> https://biorxiv.org/content/10.1101/2021.10.21.465135v1?rss=1 Wu, L. Yan, J. Bai, Y. Chen, F. Xu, J. Zou, X. Huang, A. Hou, L. Zhong, Y. Jing, Z. Zhou, X. Sun, H. Cheng, M. Ji, Y. Luo, R. Li, Q. Wu, L. Wang, P. Guo, D. Huang, W. Lei, J. Liao, S. Li, Y. Jiang, Z. Yao, N. Yu, Y. Li, Y. Liu, F. Zhang, M. Yang, H. Yang, S. Xu, X. Liu, L. Wang, X. Wang, J. Fan, J. Liu, S. Yang, X. Chen, A. Zhou, J. 2021-10-22 doi:10.1101/2021.10.21.465135 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis ]]> https://biorxiv.org/content/10.1101/2021.10.21.465298v1?rss=1 Liu, C. Li, R. Li, Y. Lin, X. Wang, S. Liu, Q. Zhao, K. Yang, X. Shi, X. Ma, Y. Pei, C. Wang, H. Bao, W. Hui, J. Berberoglu, M. A. Sahu, S. K. Esteban, M. Ma, K. Fan, G. Li, Y. Liu, S. Chen, A. Xu, X. Dong, Z. Liu, L. 2021-10-22 doi:10.1101/2021.10.21.465298 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ A low-resource reliable pipeline to democratize multi-modal connectome estimation and analysis ]]> https://biorxiv.org/content/10.1101/2021.11.01.466686v1?rss=1 Lawrence, R. Loftus, A. Kiar, G. Bridgeford, E. Consortium for Reliability and Reproducibility, Chandrashekhar, V. Mhembere, D. Ryman, S. Zuo, X.-N. Margulies, D. Craddock, R. C. Priebe, C. E. Jung, R. Calhoun, V. D. Caffo, B. Burns, R. Milham, M. P. Vogelstein, J. 2021-11-03 doi:10.1101/2021.11.01.466686 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Inactivation effect and damage of multi-irradiance by UVCLED on Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/2021.11.19.469185v1?rss=1 Li, M. Zhao, B. Han, L. Wang, Z. 2021-11-19 doi:10.1101/2021.11.19.469185 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Visual Attention in The Fovea and The Periphery during Visual Search ]]> https://biorxiv.org/content/10.1101/2021.11.22.469359v1?rss=1 Zhang, J. Zhu, X. Wang, S. Esteky, H. Tian, Y. Desimone, R. Zhou, H. 2021-11-23 doi:10.1101/2021.11.22.469359 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Delta variant with P681R critical mutation revealed by ultra-large atomic-scale ab initio simulation: Implications for the fundamentals of biomolecular interactions ]]> https://biorxiv.org/content/10.1101/2021.12.01.470802v1?rss=1 Adhikari, P. Jawad, B. Rao, P. Podgornik, R. Ching, W.-Y. 2021-12-03 doi:10.1101/2021.12.01.470802 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ]]> https://biorxiv.org/content/10.1101/2021.12.07.470215v1?rss=1 Ramdas, S. Judd, J. Graham, S. E. Kanoni, S. Wang, Y. Surakka, I. Wenz, B. Clarke, S. L. Chesi, A. Wells, A. Bhatti, K. F. Vedantam, S. Winkler, T. W. Locke, A. E. Marouli, E. Zajac, G. J. Wu, K.-H. H. Ntalla, I. Hui, Q. Klarin, D. Hilliard, A. T. Wang, Z. Xue, C. Thorleifsson, G. Helgadottir, A. Gudbjartsson, D. F. Holm, H. Olafsson, I. Hwang, M. Y. Han, S. Akiyama, M. Sakaue, S. Terao, C. Kanai, M. Zhou, W. Brumpton, B. M. Rasheed, H. Havulinna, A. S. Veturi, Y. Pacheco, J. A. Rosenthal, E. A. Lingren, T. Feng, Q. Kullo, I. J. Narita, A. Takayama, 2021-12-08 doi:10.1101/2021.12.07.470215 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Molecular mechanisms governing circulating immune cell heterogeneity across different species revealed by single cell sequencing ]]> https://biorxiv.org/content/10.1101/2021.12.17.472326v1?rss=1 Li, Z. Sun, c. Wang, F. Wang, X. Zhu, J. Luo, L. Ding, X. Zhang, Y. Ding, P. wang, H. Pu, M. Li, Y. wang, S. Qin, Q. Wei, Y. Sun, J. Wang, X. Luo, Y. Chen, D. Qiu, W. 2021-12-17 doi:10.1101/2021.12.17.472326 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Transcriptomic Profiling Reveals Cancer-Associated Fibroblasts as Potential Targets for the Prognosis and Treatment of Cervical Squamous Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2021.12.23.473944v1?rss=1 Ou, Z. Lin, S. Qiu, J. Ding, W. Ren, P. Chen, D. Wang, J. Tong, Y. Wu, D. Chen, A. Deng, Y. Cheng, M. Peng, T. Lu, H. Yang, H. Wang, J. Jin, X. Ma, D. Xu, X. Wang, Y. Li, J. Wu, P. 2021-12-23 doi:10.1101/2021.12.23.473944 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Comparative analysis of single cell lung atlas of bat, cat, tiger and pangolin ]]> https://biorxiv.org/content/10.1101/2021.12.26.473325v1?rss=1 Wang, X. Ou, Z. Ding, P. Sun, C. Wang, D. Zhu, J. Wu, W. Wei, Y. Ding, X. Luo, L. Li, M. Zhang, W. Jin, X. Sun, J. Liu, H. Chen, D. 2021-12-27 doi:10.1101/2021.12.26.473325 Cold Spring Harbor Laboratory Press 2021-12-27 <![CDATA[ Ccdc38 is required for sperm flagellum biogenesis and male fertility in mouse ]]> https://biorxiv.org/content/10.1101/2022.01.10.475757v1?rss=1 Zhang, R. Li, W. Yuan, L. Gao, F. Wu, B. Liu, C. Wang, X. Wang, L. Xiao, S. Chen, Y. Wei, H. 2022-01-11 doi:10.1101/2022.01.10.475757 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Comparison of double-stranded and single-stranded cfDNA library construction methods for targeted genome and methylation sequencing ]]> https://biorxiv.org/content/10.1101/2022.01.12.475986v1?rss=1 Zheng, J. Li, Z. Zhang, X. Zhang, H. Zhu, S. Sun, J. Wang, Y. 2022-01-12 doi:10.1101/2022.01.12.475986 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ AAV11 permits efficient retrograde targeting of projection neurons ]]> https://biorxiv.org/content/10.1101/2022.01.13.476170v1?rss=1 Han, Z. Luo, N. Kou, J. Li, L. Ma, W. Peng, S. Xu, Z. Zhang, W. Qiu, Y. Wu, Y. Wang, J. Ye, C. Lin, K. Xu, F. 2022-01-13 doi:10.1101/2022.01.13.476170 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells ]]> https://biorxiv.org/content/10.1101/2022.01.20.476705v1?rss=1 Zhao, L. Zhao, Q. An, Y. Gao, H. Zhang, W. Gong, Z. Liu, X. Zhao, B. Liang, Z. Tang, C. Zhang, L. Zhang, Y. 2022-01-20 doi:10.1101/2022.01.20.476705 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Mutations of Omicron variant at the interface of the receptor domain motif and human angiotensin-converting enzyme-2 ]]> https://biorxiv.org/content/10.1101/2022.02.04.479136v1?rss=1 Adhikari, P. Jawad, B. Podgornik, R. Ching, W.-Y. 2022-02-07 doi:10.1101/2022.02.04.479136 Cold Spring Harbor Laboratory Press 2022-02-07 <![CDATA[ Binding Interactions between RBD of Spike-Protein and Human ACE2 in Omicron variant ]]> https://biorxiv.org/content/10.1101/2022.02.10.480009v1?rss=1 View larger version (102K): org.highwire.dtl.DTLVardef@88f654org.highwire.dtl.DTLVardef@1e42d14org.highwire.dtl.DTLVardef@14b7d04org.highwire.dtl.DTLVardef@fca7d0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jawad, B. Adhikari, P. Podgornik, R. Ching, W.-Y. 2022-02-11 doi:10.1101/2022.02.10.480009 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Single-cell transcriptional profiling reveals cellular and molecular divergence in human maternal-fetal interface ]]> https://biorxiv.org/content/10.1101/2022.02.15.479798v1?rss=1 Wang, Q. Li, J. Wang, S. Deng, Q. An, Y. Xing, Y. Dai, X. Li, Z. Ma, Q. Wang, K. Liu, C. Yuan, Y. Dong, G. Zhang, T. Yang, H. Du, Y. Hou, Y. Ke, W. Shang, Z. 2022-02-16 doi:10.1101/2022.02.15.479798 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Improved fluorescent proteins for dual-color post-embedding CLEM ]]> https://biorxiv.org/content/10.1101/2022.02.16.480633v1?rss=1 Peng, D. Li, N. He, W. Kim, D. R. Xu, T. Zhang, M. Xu, P. 2022-02-16 doi:10.1101/2022.02.16.480633 Cold Spring Harbor Laboratory Press 2022-02-16 <![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[ Cohesin mutation sensitizes cancer cells to anti-PD-1 therapy through endogenous retrovirus-mediated PD-L1 upregulation ]]> https://biorxiv.org/content/10.1101/2022.02.19.481125v1?rss=1 Han, Y. Peng, F. Chang, Y. Liu, T. Shen, J. Chen, Z. Zhou, P. Jiang, F. Xiang, H. Zhu, H. Qing, C. Kong, X. Ding, J. Lang, J.-Y. 2022-02-19 doi:10.1101/2022.02.19.481125 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Single-cell RNA Sequencing of Pediatric Ependymoma Unravels Subclonal Heterogeneity Associated with Patient Survival ]]> https://biorxiv.org/content/10.1101/2022.02.26.482082v1?rss=1 Wu, H. Jin, W. Zhang, Y.-H. Liu, Z. Chen, Z. Xu, J. Tian, Y. Jin, W. Wong, S. Z. H. Wu, Q.-F. 2022-03-01 doi:10.1101/2022.02.26.482082 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Oxidative phosphorylation pathway disruption is an alternative pathological mechanism leading to Diamond-Blackfan anemia ]]> https://biorxiv.org/content/10.1101/2022.03.14.484221v1?rss=1 Xiao, R. Zhang, L. Xin, Z. Zhu, J. Zhang, Q. Chu, S. Wu, J. Zhang, L. Wan, Y. Chen, X. Yuan, W. Zhang, Z. Zhu, X. Fang, X. 2022-03-14 doi:10.1101/2022.03.14.484221 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Non-ribosomal peptide synthetase domain boundary identification and new motifs discovery based on motif-intermotifs standardized architecture ]]> https://biorxiv.org/content/10.1101/2022.03.14.484258v1?rss=1 He, R. Zhang, J. Gu, S. Yin, W.-B. Li, Z. 2022-03-17 doi:10.1101/2022.03.14.484258 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Structural connectivity gradient associated with a dichotomy reveals the topographic organization of the macaque insular cortex ]]> https://biorxiv.org/content/10.1101/2022.03.18.484254v1?rss=1 Cao, L. Du, Z. Cui, Y. Zhang, Y. Lu, Y. Zhang, B. Liu, Y. Hou, X. Liu, X. Cheng, L. Li, K. Yang, Z. Fan, L. Jiang, T. 2022-03-20 doi:10.1101/2022.03.18.484254 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Simultaneously spatiotemporal gene expression and chromatin accessibility for mouse brain development ]]> https://biorxiv.org/content/10.1101/2022.03.22.485333v1?rss=1 Peng, G. Jiang, F. Zhou, X. Qian, Y. Wang, L. Shen, Q. Qu, F. Cui, G. Chen, K. 2022-03-23 doi:10.1101/2022.03.22.485333 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Drug design and repurposing with a sequence-to-drug paradigm ]]> https://biorxiv.org/content/10.1101/2022.03.26.485909v1?rss=1 Chen, L. C. Fan, Z. Chang, J. Yang, R. Guo, H. Zhang, Y. Yang, T. Zhou, C. Chen, Z. Zheng, C. Hao, X. Zhang, K. Cui, R. Ding, Y. Zhang, N. Luo, X. Jiang, H. Zhang, S. Zheng, M. 2022-03-26 doi:10.1101/2022.03.26.485909 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Identification of C270 as a novel site for allosteric modulators of SARS-CoV-2 papain-like protease ]]> https://biorxiv.org/content/10.1101/2022.03.30.486313v1?rss=1 Hu, H. Wang, Q. Su, H. Shao, Q. Zhao, W. Chen, G. Li, M. Xu, Y. 2022-03-31 doi:10.1101/2022.03.30.486313 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource ]]> https://biorxiv.org/content/10.1101/2022.04.10.487568v1?rss=1 chen, z. Luo, Z. Zhang, D. Li, H. Liu, X. Zhu, K. Zhang, H. Wang, Z. Zhou, P. Ren, J. Zhao, A. Zuo, Z. 2022-04-10 doi:10.1101/2022.04.10.487568 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ A landscape of differentiated biological processes involved in the initiation of sex differentiation in zebrafish ]]> https://biorxiv.org/content/10.1101/2022.04.14.488425v1?rss=1 Ye, D. Tu, Y.-X. Wang, H. He, M. Wang, Y. Chen, Z. Chen, Z.-X. Sun, Y. 2022-04-15 doi:10.1101/2022.04.14.488425 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ Spatial chromatin accessibility sequencing resolves next-generation genome architecture ]]> https://biorxiv.org/content/10.1101/2022.04.21.489011v1?rss=1 Xie, Y. Li, Y. Ruan, F. Zhang, C. Chen, Z. Xie, Z. Weng, Z. Chen, W. Chen, W. Fang, Y. Sun, Y. Guo, M. Wang, J. Wang, H. Tang, C. 2022-04-21 doi:10.1101/2022.04.21.489011 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ A cocktail containing two synergetic antibodies broadly neutralizes SARS-CoV-2 and its variants including Omicron BA.1 and BA.2 ]]> https://biorxiv.org/content/10.1101/2022.04.26.489529v1?rss=1 Zhang, X. Luo, F. Zhang, H. Guo, H. Zhou, J. Li, T. Chen, S. Song, S. Shen, M. Wu, Y. Gao, Y. Han, X. Wang, Y. Hu, C. Lu, Y. Wang, W. Wang, K. Tang, N. Jin, T. Yang, C. Cheng, G. Yang, H. Jin, A. Ji, X. Gong, R. Chiu, S. Huang, A. 2022-04-26 doi:10.1101/2022.04.26.489529 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Reversible and gain modulation of neuronal responses and sensorimotor behavior by mid-infrared stimulation ]]> https://biorxiv.org/content/10.1101/2022.04.27.489693v1?rss=1 Xiao, T. Wu, K. Ding, Y. Yang, X. Chang, C. Yang, Y. 2022-04-28 doi:10.1101/2022.04.27.489693 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Suppression of tumor/host intrinsic CMTM6 drives anti-tumor cytotoxicity in a PD-L1 independent manner ]]> https://biorxiv.org/content/10.1101/2022.05.06.490847v1?rss=1 Long, Y. Chen, R. Yu, X. Tong, Y. Peng, X. Li, F. Hu, C. Sun, J. Gong, L. 2022-05-06 doi:10.1101/2022.05.06.490847 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Machine learning enables accurate prediction of breast cancer five-year survival using somatic genomic variants ]]> https://biorxiv.org/content/10.1101/2022.05.22.492994v1?rss=1 Jiang, X. Zhang, L. Cao, G. Li, J. Bai, Y. 2022-05-24 doi:10.1101/2022.05.22.492994 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Sex differences in the nasal microbiome of healthy young adults ]]> https://biorxiv.org/content/10.1101/2022.05.23.493011v1?rss=1 Ju, Y. Zhang, Z. Liu, M. Lin, S. Sun, Q. Song, Z. Liang, W. Tong, X. Jie, Z. Lu, H. Cai, K. Chen, P. Jin, X. Xu, X. Yang, H. Wang, J. Hou, Y. Xiao, L. Jia, H. Zhang, T. Guo, R. 2022-05-24 doi:10.1101/2022.05.23.493011 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ A flexible, efficient, and scalable platform to produce circular RNAs as new therapeutics ]]> https://biorxiv.org/content/10.1101/2022.05.31.494115v1?rss=1 Chen, C. Wei, H. Zhang, K. Li, Z. Wei, T. Tang, C. Yang, Y. Wang, Z. 2022-05-31 doi:10.1101/2022.05.31.494115 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Increased α-ketoglutarate as a missing link from the C3-C4 intermediate state to C4 photosynthesis in the genus Flaveria ]]> https://biorxiv.org/content/10.1101/2022.06.01.494409v1?rss=1 Tang, Q. Huang, Y. Ni, X. Lyu, M.-J. A. Chen, G. Sage, R. F. Zhu, X. 2022-06-03 doi:10.1101/2022.06.01.494409 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Atomic-scale Quantum Chemical Calculation of Omicron Mutations Near Cleavage Sites of the Spike Protein ]]> https://biorxiv.org/content/10.1101/2022.06.03.494698v1?rss=1 Adhikari, P. Jawad, B. Podgornik, R. Ching, W.-Y. 2022-06-03 doi:10.1101/2022.06.03.494698 Cold Spring Harbor Laboratory Press 2022-06-03 <![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[ Prior-guided Individualized Thalamic Parcellation based on Local Diffusion Characteristics using Deep Learning ]]> https://biorxiv.org/content/10.1101/2022.07.19.500596v1?rss=1 Gao, C. Wu, X. Wang, Y. Li, G. Chu, C. Madsen, K. H. Fan, L. 2022-07-20 doi:10.1101/2022.07.19.500596 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Effect of Delta and Omicron mutations on the RBD-SD1 do-main of the Spike protein in SARS-CoV-2 and the Omicron mutations on RBD-ACE2 interface complex ]]> https://biorxiv.org/content/10.1101/2022.07.28.501901v1?rss=1 Ching, W.-Y. Adhikari, P. Jawad, B. Podgornik, R. 2022-07-28 doi:10.1101/2022.07.28.501901 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Pathway and mechanism of tubulin folding mediated by TRiC/CCT conjugated with its ATPase cycle revealed by cryo-EM ]]> https://biorxiv.org/content/10.1101/2022.08.08.503128v1?rss=1 Cong, Y. Liu, C. Jin, M. Wang, S. Han, W. Zhao, Q. Wang, Y. Xu, C. Diao, L. Yin, Y. Peng, C. Bao, L. Wang, Y. 2022-08-08 doi:10.1101/2022.08.08.503128 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ Recovery of structural integrity of epithelial monolayer in response to massive apoptosis-induced defects ]]> https://biorxiv.org/content/10.1101/2022.08.08.503238v1?rss=1 Yuan, Y. Han, Y. L. Xia, J. Li, H. Tang, C. Ye, F. Weitz, D. Guo, M. 2022-08-08 doi:10.1101/2022.08.08.503238 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model ]]> https://biorxiv.org/content/10.1101/2022.08.18.504370v1?rss=1 Li, Y. Li, L. Xu, Y. Yu, Y. 2022-08-19 doi:10.1101/2022.08.18.504370 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Dear-DIAXMBD: deep autoencoder for data-independent acquisition proteomics ]]> https://biorxiv.org/content/10.1101/2022.08.27.505516v1?rss=1 He, Q. Zhong, C. Li, X. 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Han, Z. Liu, C. Wang, Z.-B. Qian, W.-P. 2022-09-21 doi:10.1101/2022.09.20.508723 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Reconstruct a eukaryotic chromosome arm by de novo design and synthesis ]]> https://biorxiv.org/content/10.1101/2022.10.04.509869v1?rss=1 Jiang, S. Luo, Z. Yu, K. Zhao, S. Cai, Z. Yu, W. Wang, H. Cheng, L. Liang, Z. Gao, H. Monti, M. Schindler, D. Huang, L. Zeng, C. Zhang, W. Zhou, C. Tang, Y. Li, T. Ma, Y. Cai, Y. Boeke, J. D. Dai, J. 2022-10-05 doi:10.1101/2022.10.04.509869 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Molecular recognition of two endogenous hormones by the human parathyroid hormone receptor-1 ]]> https://biorxiv.org/content/10.1101/2022.10.09.511452v1?rss=1 Zhao, L.-h. Yuan, Q. Dai, A. Chen, C.-W. He, X. Zhang, C. Xu, Y. Zhou, Y. Wang, M.-W. Yang, D. Xu, H. 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Pei, W. 2022-11-08 doi:10.1101/2022.11.07.515530 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Default But Not Rest: Topological Discrimination Defines the Default Mode Network ]]> https://biorxiv.org/content/10.1101/2022.11.10.516071v1?rss=1 Wang, B. Zhou, T. He, S. Chen, L. 2022-11-13 doi:10.1101/2022.11.10.516071 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Cell-type annotation with accurate unseen cell-type identification using multiple references ]]> https://biorxiv.org/content/10.1101/2022.11.17.516980v1?rss=1 Yixuan, X. Mengguo, W. Luonan, C. Xiaofei, Z. 2022-11-18 doi:10.1101/2022.11.17.516980 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Architecture of chloroplast TOC-TIC translocon supercomplex ]]> https://biorxiv.org/content/10.1101/2022.11.20.517165v1?rss=1 Liu, H. Li, A. Rochaix, J.-D. Liu, Z. 2022-11-20 doi:10.1101/2022.11.20.517165 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Bioinformatics techniques for efficient structure prediction of SARS-CoV-2 protein ORF7a via structure prediction approaches ]]> https://biorxiv.org/content/10.1101/2022.12.03.518956v1?rss=1 Kazmi, A. Kazim, M. Aslam, F. Kazmi, S. M.-u.-H. Wahab, A. Mikhlef, R. M. Khizar, C. Kazmi, A. Wazir, N. U. Mainali, R. P. 2022-12-05 doi:10.1101/2022.12.03.518956 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision ]]> https://biorxiv.org/content/10.1101/2022.12.06.519083v1?rss=1 Vromman, M. Anckaert, J. Bortoluzzi, S. Buratin, A. Chen, C.-Y. Chu, Q. Chuang, T.-J. Dehghannasiri, R. Dieterich, C. Dong, X. Flicek, P. Gaffo, E. Gu, W. He, C. Hoffmann, S. Izuogu, O. Jackson, M. S. Jakobi, T. Lai, E. C. Nuytens, J. Salzman, J. Santibanez-Koref, M. Stadler, P. Thas, O. Vanden Eynde, E. Verniers, K. Wen, G. Westholm, J. Yang, L. Ye, C.-Y. Yigit, N. Yuan, G.-H. Zhang, J. Zhao, F. Vandesompele, J. Volders, P.-J. 2022-12-06 doi:10.1101/2022.12.06.519083 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation ]]> https://biorxiv.org/content/10.1101/2022.12.06.519249v1?rss=1 Yu, J. Tang, J. WEI, R. Lan, M. Xiang, R. Xiang, Q.-P. Zhang, X.-C. 2022-12-08 doi:10.1101/2022.12.06.519249 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ From whole genome to probiotic candidates: a study of potential Lactobacillus strain selection for vaginitis treatment ]]> https://biorxiv.org/content/10.1101/2022.12.11.519948v1?rss=1 Lyu, J. Gao, M. Zhao, S. Lyu, X. Zhao, X. Zou, Y. Zhong, Y. Ge, L. Zhang, H. Xiao, L. Zhang, X. 2022-12-11 doi:10.1101/2022.12.11.519948 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Multimodal Imaging-Based Classification of PTSD Using Data-Driven Computational Approaches: A Multisite Big Data Study from the ENIGMA-PGC PTSD Consortium ]]> https://biorxiv.org/content/10.1101/2022.12.12.519838v1?rss=1 Zhu, X. Kim, Y. Ravid, O. He, X. Suarez-Jimenez, B. Zilcha-Mano, S. Lazarov, A. Lee, S. Abdallah, C. G. Angstadt, M. Averill, C. L. Baird, C. L. Baugh, L. A. Blackford, J. U. Bomyea, J. Bruce, S. E. Bryant, R. A. Cao, Z. Choi, K. Cisler, J. Cotton, A. S. Daniels, J. K. Davenport, N. D. Davidson, R. J. DeBellis, M. D. Dennis, E. L. Densmore, M. deRoon-Cassini, T. Disner, S. G. El Hage, W. Etkin, A. Fani, N. Fercho, K. A. Fitzgerald, J. Forster, G. L. Frijling, J. L. Geuze, E. Gonenc, A. Gordon, E. M. Gruber, S. Grupe, D. W. Guenette, J. P. Haswell, C. 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Dai, X. Yue, L. Li, L. Pham, T. V. Piersma, S. R. Xiao, Q. Luo, M. Lu, C. Zhu, J. Zhao, Y. Wang, G. Xiao, J. Liu, T. Liu, Z. He, Y. Wu, Q. Gong, T. Zhu, J. Zheng, Z. Ye, J. Li, Y. Jimenez, C. R. A, J. Guo, T. 2023-01-08 doi:10.1101/2023.01.07.523067 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Topological design principle for the robustness of necroptosis biphasic, emergent, and coexistent (BEC) dynamics ]]> https://biorxiv.org/content/10.1101/2023.01.23.525173v1?rss=1 Xu, F. Li, X. Wu, R. Qi, H. Jin, J. Liu, Z. Wu, Y. Lin, H. Shen, C. Shuai, J. 2023-01-24 doi:10.1101/2023.01.23.525173 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ IMPACT: a web server for exploring immunotherapeutic predictive and cancer prognostic biomarkers ]]> https://biorxiv.org/content/10.1101/2023.01.31.526401v1?rss=1 Liu, Y. Zhang, Y. Xie, W. Zhao, J. Dong, Y. Xu, C. Wang, Y. Li, M. Wang, G. Zhu, X. Wang, W. Lin, K. Lu, H. Han, Y. Li, L. Duan, J. Cai, S. Wang, J. Wang, Z. 2023-02-03 doi:10.1101/2023.01.31.526401 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Single-cell RNA sequencing to explore the immune process difference between Kawasaki disease and febrile patients ]]> https://biorxiv.org/content/10.1101/2023.02.21.529340v1?rss=1 Lin, Q. Xie, L. Li, G. Liu, R. Wang, Z. 2023-02-21 doi:10.1101/2023.02.21.529340 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Angiopoietin-like 4 promotes the proliferation and migration of epidermal stem cells and contributes to the re-epithelialization of cutaneous wounds ]]> https://biorxiv.org/content/10.1101/2023.02.23.529672v1?rss=1 Yang, Y. Yu, C. Le, Y. Gong, W. Ju, J. Zhang, G. Ji, P. Zuo, R. Liu, Z. Zhang, P. Hou, R. Fu, Y. 2023-02-23 doi:10.1101/2023.02.23.529672 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ A cataract-causing Y204X mutation of CRYβB1 promotes C-terminal degradation and higher-order oligomerization ]]> https://biorxiv.org/content/10.1101/2023.02.24.529791v1?rss=1 Jing, X. Lu, X. Zhu, M. Shi, L. Wei, P. Zhang, B.-Y. Xu, Y. Xiang, D. Tang, Y.-P. Gong, P. 2023-02-25 doi:10.1101/2023.02.24.529791 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ Excessive apoptosis of naïve T cells resulting hyperactivation as a cause of mammalian aging ]]> https://biorxiv.org/content/10.1101/2023.02.24.529806v1?rss=1 Wang, L. Zhang, X. Zhang, H. Lu, K. Li, M. Li, X. Ouyang, J. Zhao, X. Wu, X. Wu, X. Liu, J. Xing, M. Liu, H. Zhang, Y. Tan, Y. Li, F. Deng, J. Zhang, X. Li, J. Zhao, Y. Wang, X. Luo, Y. Zhou, B. Zhang, H. 2023-02-26 doi:10.1101/2023.02.24.529806 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2023.03.12.532219v1?rss=1 Bozic, A. Podgornik, R. 2023-03-13 doi:10.1101/2023.03.12.532219 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ A meta-analysis of immune cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes ]]> https://biorxiv.org/content/10.1101/2023.03.20.533349v1?rss=1 Luo, Q. Dwaraka, V. B. Chen, Q. Tong, H. Zhu, T. Seale, K. Raffaele, J. M. Zheng, S. C. Mendez, T. L. Chen, Y. Begum, S. Mendez, K. Voisin, S. Eynon, N. Lasky-Su, J. A. Smith, R. Teschendorff, A. 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Lifespan Brain Chart Consortium, Chinese Color Nest Consortium, Zuo, X.-N. 2023-04-08 doi:10.1101/2023.04.07.535977 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Shin in the eye: Au-CS@FNDs as contact lens additives for blocking UV irradiation, bacterial keratitis, and corneal neovascularizationtherapies ]]> https://biorxiv.org/content/10.1101/2023.04.11.536356v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1b94b65org.highwire.dtl.DTLVardef@4f598org.highwire.dtl.DTLVardef@198058forg.highwire.dtl.DTLVardef@1950cd3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nie, L. Hu, X. Zhao, Y. Wang, Y. Chen, L. Wang, Y. Liu, Y. Wu, F. 2023-04-12 doi:10.1101/2023.04.11.536356 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Transcriptomic profiling of nuclei from PFA-fixed and FFPE brain tissues ]]> https://biorxiv.org/content/10.1101/2023.04.13.536693v1?rss=1 Guo, Y. Ma, J. Dang, K. Li, Z. Ge, Q. Huang, Y. Wang, G.-Z. Zhao, X. 2023-04-13 doi:10.1101/2023.04.13.536693 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae) ]]> https://biorxiv.org/content/10.1101/2023.04.25.538215v1?rss=1 Liu, S. Yang, Y. Tian, Q. Yang, Z. Li, S. Valdes, P. J. Farnsworth, A. Kates, H. R. Siniscalchi, C. M. Guralnick, R. P. Soltis, D. E. Soltis, P. S. Stull, G. W. Folk, R. A. Yi, T. 2023-04-28 doi:10.1101/2023.04.25.538215 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Intermediate basal cell population in prostate homeostasis and cancer initiation ]]> https://biorxiv.org/content/10.1101/2023.05.12.540502v1?rss=1 Guo, W. Zhang, X. Li, L. Shao, P. Zhang, H. Liu, K. Liang, C. Wang, S. Peng, Y. Ju, Y. Yu, C. Chen, L. Zhou, B. Gao, D. 2023-05-13 doi:10.1101/2023.05.12.540502 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ Genetic evidence for functions of Chloroplast CA in Pyropia yezoensis: decreased CCM but increased starch accumulation ]]> https://biorxiv.org/content/10.1101/2023.05.22.541789v1?rss=1 Zhang, B. Liu, X. Xie, X. Huan, L. Wang, H. Shao, Z. Wang, G. 2023-05-23 doi:10.1101/2023.05.22.541789 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Associative memory neurons of encoding multi-modal signals are recruited by neuroligin-3 mediated new synapse formation ]]> https://biorxiv.org/content/10.1101/2023.06.01.543188v1?rss=1 Xu, Y. Cui, T. Li, J. Chen, B. Wang, J.-H. 2023-06-01 doi:10.1101/2023.06.01.543188 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ A pseudovirus-based method to dynamically mimic SARS-CoV-2-associated cell-to-cell fusion and transmission ]]> https://biorxiv.org/content/10.1101/2023.06.26.546514v1?rss=1 Sheng, X. Yang, Y. Zhu, F. Yang, F. Wang, H. Hu, R. 2023-06-26 doi:10.1101/2023.06.26.546514 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Augmented Super-Resolution Radial Fluctuations (aSRRF) Pushing the Limits of Structured Illumination Microscopy ]]> https://biorxiv.org/content/10.1101/2023.07.05.547885v1?rss=1 Zhang, H. Wang, J. Jin, L. Zhu, Y. Guo, Y. Zhang, M. Zhang, Y. Wang, Z. Su, Y. Wu, Y. Ji, B. Toomre, D. Liu, X. Xu, Y. 2023-07-06 doi:10.1101/2023.07.05.547885 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ A Motion Transformer for Single Particle Tracking in Fluorescence Microscopy Images ]]> https://biorxiv.org/content/10.1101/2023.07.20.549804v1?rss=1 Zhang, Y. Yang, G. 2023-07-22 doi:10.1101/2023.07.20.549804 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Correlation of a pan-tissue epigenetic mitotic clock with tumor cell-of-origin ]]> https://biorxiv.org/content/10.1101/2023.07.27.549809v1?rss=1 Zhu, T. Tong, H. Du, Z. Teschendorff, A. 2023-07-29 doi:10.1101/2023.07.27.549809 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Microbiome Analysis of the Eastern Oyster As a Function of Ploidy and Seasons ]]> https://biorxiv.org/content/10.1101/2023.08.10.552804v1?rss=1 Pathak, A. Marquez, M. Stothard, P. Chukwujindu, C. Su, J.-Q. Zhou, Y. Zhou, X.-Y. Jagoe, C. H. Chauhan, A. 2023-08-10 doi:10.1101/2023.08.10.552804 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Phylogenomic analyses support a new infrageneric classification of Pourthiaea (Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling ]]> https://biorxiv.org/content/10.1101/2023.08.13.552906v1?rss=1 Liu, G.-N. Ma, D.-K. Zhang, Y. Hodel, R. G. J. Xie, S.-Y. Wang, H. Jin, Z.-T. Li, F.-X. Jin, S.-H. Zhao, L. Xu, C. Wei, Y. Liu, B.-B. 2023-08-14 doi:10.1101/2023.08.13.552906 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Longer mandible or nose? Co-evolution of feeding organs in early elephantiforms ]]> https://biorxiv.org/content/10.1101/2023.08.15.553347v1?rss=1 Li, C. Deng, T. Wang, Y. Sun, F. Wolff, B. Jiangzuo, Q. Ma, J. Xing, L. Fu, J. Zhang, J. Wang, S. 2023-08-16 doi:10.1101/2023.08.15.553347 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ The translation of a short open reading frame product within the human TUBA1B gene regulates cancer cell proliferation by importin-β ]]> https://biorxiv.org/content/10.1101/2023.08.26.554759v1?rss=1 Tao, Y. Bai, X. Zhou, Y. Zhao, Y. Yang, L. Zhang, S. Yan, S. Huang, X. Schneider, E. Zampetaki, A. Margariti, A. Giacca, M. Arnold, J. N. Zeng, L. Cai, T. 2023-08-27 doi:10.1101/2023.08.26.554759 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Enhancement of Protein Stability by Quenching Millisecond Conformational Dynamics ]]> https://biorxiv.org/content/10.1101/2023.08.30.555640v1?rss=1 Hou, X.-N. Zhao, C. Song, B. Ruan, M.-X. Dong, X. Gong, Z. Weng, X.-X. Zheng, J. Tang, C. 2023-09-01 doi:10.1101/2023.08.30.555640 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ SIDERITE: Unveiling Hidden Siderophore Diversity in the Chemical Space Through Digital Exploration ]]> https://biorxiv.org/content/10.1101/2023.08.31.555687v1?rss=1 He, R. Gu, S. Xu, J. Li, X. Chen, H. Shao, Z. Wang, H. Shao, J. Yin, W.-B. Qian, L. Wei, Z. Li, Z. 2023-09-01 doi:10.1101/2023.08.31.555687 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Neutralization of SARS-CoV-2 EG.5/EG.5.1 by sera from ZF2001 RBD-dimer and its next-generation vaccines ]]> https://biorxiv.org/content/10.1101/2023.09.02.556038v1?rss=1 An, Y. Zhou, X. Tao, L. Xie, H. Yang, C. Li, D. Wang, R. Hu, H. Liu, K. Dai, L. Xu, K. Gao, G. F. 2023-09-04 doi:10.1101/2023.09.02.556038 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ Inferring cell trajectories of spatial transcriptomics via optimal transport analysis ]]> https://biorxiv.org/content/10.1101/2023.09.04.556175v1?rss=1 Shen, X. Huang, K. Zuo, L. Ye, Z. Li, Z. Yu, Q. Zou, X. Wei, X. Xu, P. Jin, X. Xu, X. Wu, L. Zhu, H. Qin, P. 2023-09-05 doi:10.1101/2023.09.04.556175 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Converging Topographic Axes of Connectivity and Genetic Architectures Scaffold Cortical Patterning ]]> https://biorxiv.org/content/10.1101/2023.09.06.556618v1?rss=1 Li, D. Ma, L. Wang, Y. Lu, Y. Wang, H. Wang, Y. Gao, C. Cheng, L. Zhang, Y. Yang, Z. Eickhoff, S. Chen, C.-h. Chu, C. Fan, L. 2023-09-09 doi:10.1101/2023.09.06.556618 Cold Spring Harbor Laboratory Press 2023-09-09 <![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[ Controlling for Intra-Subject and Inter-Subject Variability in Individual-Specific Cortical Network Parcellations ]]> https://biorxiv.org/content/10.1101/213041v1?rss=1 Kong, R. Li, J. Sun, N. Sabuncu, M. R. Schaefer, A. Zuo, X.-N. Holmes, A. Eickhoff, S. B. Yeo, B. T. T. 2017-11-02 doi:10.1101/213041 Cold Spring Harbor Laboratory Press 2017-11-02 <![CDATA[ Recovered and dead outcome patients caused by influenza A (H7N9) virus infection show different pro-inflammatory cytokine dynamics during disease progress and its application in real-time prognosis ]]> https://biorxiv.org/content/10.1101/339333v1?rss=1 Liu, Y. Wang, X. Zhu, H. Ma, J. Lu, Z. Yuan, J. Li, J. Li, J. Ren, Y. Wen, B. Ouyang, W. Zheng, H. Zou, R. Bi, Y. Yin, C. Guo, Z. Sun, W. Pei, N. Li, J. Zhu, S. Yang, H. Liu, L. Xu, X. Liu, S. Wang, H. Li, L. 2018-06-07 doi:10.1101/339333 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ How do wind speed, release height, seed morphology interact to determine seed dispersal trajectory of Calligonum (Polygonaceae) species ]]> https://biorxiv.org/content/10.1101/362434v1?rss=1 Zhou, Q. Liu, Z. Xin, Z. Qian, J. Wang, Y. Liang, W. Qin, X. Zhao, Y. Li, X. Cui, X. Liu, M. 2018-07-04 doi:10.1101/362434 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ Non-canonical role of E3 ligase RIPLET in innate immunity as a co-receptor for RIG-I ]]> https://biorxiv.org/content/10.1101/367656v1?rss=1 Cadena, C. Ahmad, S. Xavier, A. Park, J. W. Oh, S.-W. Fujita, T. Hou, F. Hur, S. 2018-07-11 doi:10.1101/367656 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ A Reptilian Endogenous Foamy Virus Sheds Light on the Early Evolution of Retroviruses ]]> https://biorxiv.org/content/10.1101/426585v1?rss=1 Wei, X. Chen, Y. Holmes, E. C. Cui, J. 2018-09-26 doi:10.1101/426585 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Group ICA for Identifying Biomarkers in Schizophrenia: ‘Adaptive’ Networks via Spatially Constrained ICA Show More Sensitivity to Group Differences than Spatio-temporal Regression ]]> https://biorxiv.org/content/10.1101/429837v1?rss=1 Salman, M. S. Du, Y. Lin, D. Fu, Z. Damaraju, E. Sui, J. Chen, J. Yu, Q. Mayer, A. R. Posse, S. Mathalon, D. H. Ford, J. M. Erp, T. V. Calhoun, V. D. 2018-09-29 doi:10.1101/429837 Cold Spring Harbor Laboratory Press 2018-09-29 <![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[ Bacterial strain displacement in inflammatory bowel diseases after fecal microbiota transplantation ]]> https://biorxiv.org/content/10.1101/439687v1?rss=1 80%) could be properly predicted (AUC > 85%) using a random forest classification model, with the gut microbiota composition and clinical parameters of pre-FMT recipients acting as the most contributive factors for prediction accuracy. ]]> Zou, M. Jie, Z. Cui, B. Wang, H. Feng, Q. Zou, Y. Zhang, X. Yang, H. Wang, J. Zhang, F. Jia, H. 2018-10-11 doi:10.1101/439687 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ The mitochondrial DNA content can not predict the embryo viability ]]> https://biorxiv.org/content/10.1101/445940v1?rss=1 Qiu, Y. Chen, S. Chen, D. Liu, P. Xia, J. Yang, L. Song, Z. Shi, Q. Xie, L. Zhu, Z. Du, Y. Jiang, H. Wang, J. Yang, H. Xu, C. Chen, F. 2018-10-17 doi:10.1101/445940 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Molecular profiles and mutation burden analysis in Chinese patients with gastric carcinoma ]]> https://biorxiv.org/content/10.1101/449736v1?rss=1 = 60). Furthermore, we found a list of 18 genes and two genomic regions (1p36.21 and Xq26.3) were associated with peritoneal metastasis (PM) of GC, and patients with amplification of 1p36.21 and Xq26.3 have a worse prognosis (p=0.002, 0.01, respectively). Our analysis provides GC patients with potential markers for single and combination therapies. ]]> Chen, C. Shi, C. Huang, X. Zheng, J. Zhu, Z. Li, Q. Qiu, S. Huang, Z. Zhuang, Z. Wu, R. Liu, P. Wu, F. Lin, S. Li, B. Zhang, X. Chen, Q. 2018-10-23 doi:10.1101/449736 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ A Whole-Genome Association Approach for Large-scaled Inter-species Trait ]]> https://biorxiv.org/content/10.1101/454363v1?rss=1 Wu, Q. Fan, H. Chen, L. Hu, Y. Wei, F. 2018-10-26 doi:10.1101/454363 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Genetic effect of type 2 Diabetes to the progression of Neurological Diseases ]]> https://biorxiv.org/content/10.1101/480400v1?rss=1 Rahman, M. H. Peng, S. Chen, C. Lio, P. Moni, M. A. 2018-11-29 doi:10.1101/480400 Cold Spring Harbor Laboratory Press 2018-11-29 <![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[ Nonobese subjects of Bacteroides and Prevotella enterotypes responded differentially to calorie restriction intervention ]]> https://biorxiv.org/content/10.1101/514596v1?rss=1 Zou, H. Wang, D. Ren, H. Fang, C. Shi, Z. Zhang, P. Chen, P. Wang, J. Yang, H. Cai, K. Zhong, H. 2019-01-09 doi:10.1101/514596 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Comparative Population Genomics of Bread Wheat (Triticum aestivum) Reveals Its Cultivation and Breeding History in China ]]> https://biorxiv.org/content/10.1101/519587v1?rss=1 Chen, H. Jiao, C. Wang, Y. Wang, Y. Tian, C. Yu, H. Wang, J. Wang, X. Lu, F. Fu, X. Xue, Y. Jiang, W. Ling, H. Lu, H. Jiao, Y. 2019-01-14 doi:10.1101/519587 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ High-quality genome assembly and high-density genetic map of asparagus bean ]]> https://biorxiv.org/content/10.1101/521179v1?rss=1 Xia, Q. Zhang, R. Ni, X. Pan, L. Wang, Y. Dong, X. Gao, Y. Zhang, Z. Kui, L. Li, Y. Wang, W. Yang, H. Chen, C. Miao, J. Chen, W. Dong, Y. 2019-01-16 doi:10.1101/521179 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ FabriEVEs: A dedicated platform for endogenous viral elements in fishes, amphibians, birds, reptiles and invertebrates ]]> https://biorxiv.org/content/10.1101/529354v1?rss=1 Zhong, J. Zhu, J. Xu, Z. Zou, G. Zhao, J. Jiang, S. Zhang, W. Xia, J. Yang, L. Li, F. Gao, Y. Chen, F. Wu, Y. Chen, D. 2019-01-24 doi:10.1101/529354 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Gene pathogenicity prediction of Mendelian diseases via the Random Forest algorithm ]]> https://biorxiv.org/content/10.1101/553362v1?rss=1 He, S. Chen, W. Liu, H. Li, S. Lei, D. Dang, X. Chen, Y. Zhang, X. Zhang, J. 2019-02-18 doi:10.1101/553362 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Molecular subtyping and prognostic assessment based on tumor mutation burden in patients with lung adenocarcinomas ]]> https://biorxiv.org/content/10.1101/553461v1?rss=1 Wang, C. Li, F. Xie, G. Qiao, S. Shi, X. Deng, J. Liang, H. Lin, C. Zhao, X. Wu, K. Zhang, X. 2019-02-25 doi:10.1101/553461 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ A Single-Cell Immune Atlas of Triple Negative Breast Cancer Reveals Novel Immune Cell Subsets ]]> https://biorxiv.org/content/10.1101/566968v1?rss=1 Qiu, S. Hong, R. Zhuang, Z. Li, Y. Zhu, L. Lin, X. Zheng, Q. Liu, S. Zhang, K. Huang, M. Lee, K. Lu, Q. Xia, W. Xu, F. Wang, X. Tang, J. Xiao, X. Wei, W. Yuan, Z. Shi, Y. Hou, Y. Zhang, X. Wang, J. Yang, H. Zhan, Q. Li, B. Wang, S. 2019-07-05 doi:10.1101/566968 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ An ATAC-seq atlas of chromatin accessibility in mouse tissues ]]> https://biorxiv.org/content/10.1101/582171v1?rss=1 Liu, C. Wang, M. Wei, X. Wu, L. Xu, J. Dai, X. Xia, J. Cheng, M. Yuan, Y. Zhang, P. Li, J. Feng, T. Chen, A. Zhang, W. Chen, F. Shang, Z. Zhang, X. Peters, B. A. Liu, L. 2019-03-19 doi:10.1101/582171 Cold Spring Harbor Laboratory Press 2019-03-19 <![CDATA[ Parallel Group ICA + ICA: Joint Estimation of Linked Functional Network Variability and Structural Covariation with Application to Schizophrenia ]]> https://biorxiv.org/content/10.1101/595017v1?rss=1 Qi, S. Sui, J. Chen, J. Liu, J. Jiang, R. Silva, R. Iraji, A. Damaraju, E. Salman, M. Lin, D. Fu, Z. Zhi, D. Turner, J. A. Bustillo, J. Ford, J. M. Mathalon, D. H. Voyvodic, J. McEwen, S. Preda, A. Belger, A. Potkin, S. G. Mueller, B. A. Adali, T. Calhoun, V. D. 2019-04-01 doi:10.1101/595017 Cold Spring Harbor Laboratory Press 2019-04-01 <![CDATA[ Identification of a basal stem cell subpopulation in the prostate via functional, lineage tracing and single-cell RNA-seq analyses ]]> https://biorxiv.org/content/10.1101/601872v1?rss=1 Wang, X. Xu, H. Cheng, C. Ji, Z. Zhao, H. Sheng, Y. Li, X. Wang, J. Shu, Y. He, Y. Fan, L. Dong, B. Xue, W. Chua, C. W. Wu, D. Gao, W.-Q. Zhu, H. H. 2019-04-08 doi:10.1101/601872 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ CRISPR-GNL: an improved model for predicting CRISPR activity by machine learning and featurization ]]> https://biorxiv.org/content/10.1101/605790v1?rss=1 Zhang, X. Wang, J. Luo, Y. Xi, X. LiXin, C. 2019-04-11 doi:10.1101/605790 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Single cell RNA sequencing reveals cellular diversity of trisomy 21 retina ]]> https://biorxiv.org/content/10.1101/614149v1?rss=1 Chen, F. Sun, X. Chen, D. Wu, J. Ding, X. Hu, F. Xu, Z. Zhang, S. Liang, L. Chai, C. Zhong, J. Wang, S. Zhu, J. Lin, X. Chen, Y. Feng, Q. Jiang, S. Li, W. Li, J. Xia, J. Gao, Y. Zhang, J. He, Z. Xue, S. Guo, G. Xu, P. Gao, F. Wang, D. Zhang, D. 2019-04-20 doi:10.1101/614149 Cold Spring Harbor Laboratory Press 2019-04-20 <![CDATA[ Germline-encoded TCR-MHC contacts promote TCR V gene bias in umbilical cord blood T cell repertoire ]]> https://biorxiv.org/content/10.1101/621821v1?rss=1 Tian, L. Liu, X. Qiu, X. Gao, K. Chen, L. Zhang, Y. Zhao, Y. Wan, Z. Wu, J. Lin, L. Kuang, Y. Lu, J. Zhang, X. 2019-04-29 doi:10.1101/621821 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Metagenomic Next-generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Central Nervous System Infections: A Multicentre Prospective Study ]]> https://biorxiv.org/content/10.1101/658047v1?rss=1 Fan, S. Wang, X. Hu, Y. Shi, J. Zou, Y. Zhao, W. Qiao, X. Wang, C. Chin, J. H. Liu, L. Qin, L. Wang, S. Li, H. Yue, W. Zhang, W. Li, X. Ge, Y. Wu, H. Chen, W. Li, Y. Guan, T. Li, S. Wu, Y. Zhou, G. Liu, Z. Piao, Y. Zhang, J. Ren, C. Cui, L. Liu, C. Ren, H. Zhao, Y. Feng, S. Jiang, H. Wang, J. Bu, H. Guo, S. Peng, B. Cui, L. Li, W. Guan, H. 2019-06-10 doi:10.1101/658047 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Dosage effect of multiple genes accounts for multisystem disorder of myotonic dystrophy type 1 ]]> https://biorxiv.org/content/10.1101/658526v1?rss=1 Yin, Q. Wang, H. Xie, Z. Jin, L. Ding, Y. Li, N. Li, Y. Wang, Q. Liu, X. Wang, K. Xu, L. Cheng, Y. Chang, B. Zhong, C. Yu, Q. Tang, W. Yang, W. Zhang, F. Ding, C. Bao, L. Zhou, B. Hu, P. Li, J. 2019-06-03 doi:10.1101/658526 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Phylogenomics provides new insights into gains and losses of selenoproteins among Archaeplastida ]]> https://biorxiv.org/content/10.1101/674895v1?rss=1 Liu, H. Wang, S. B. Liang, P. H. Wei, T. Xu, Y. Li, Z. L. Sahu, S. K. Wang, L. H. Li, Y. H. Fu, X. Zhang, Y. G. Melkonian, M. Liu, X. 2019-07-01 doi:10.1101/674895 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Assessment of the gene expression profiles of leukocytes from different isolations ]]> https://biorxiv.org/content/10.1101/678904v1?rss=1 Xing, Y. Yang, X. Chen, H. Zhu, S. Xu, J. Chen, Y. Zeng, J. Chen, F. Jiang, H. Wang, W.-J. 2019-06-24 doi:10.1101/678904 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss ]]> https://biorxiv.org/content/10.1101/679985v1?rss=1 Wang, Q. Zhao, H. Sun, Q. Li, X. Chen, J. Wang, Z. Ju, Y. Jie, Z. Guo, R. Liang, Y. Sun, X. Zheng, H. Zhang, T. Xiao, L. Xu, X. Yang, H. Peng, S. Jia, H. 2019-06-23 doi:10.1101/679985 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ Novel genetic loci affecting facial shape variation in humans ]]> https://biorxiv.org/content/10.1101/693002v1?rss=1 Xiong, Z. Dankova, G. Howe, L. H. Lee, M. Hysi, P. de Jong, M. Zhu, G. Adhikari, K. Li, D. Li, Y. Pan, B. Feingold, E. Marazita, M. Shaffer, J. McAloney, K. Xu, S. Jin, L. Wang, S. Vrij, F. Lendemeijer, B. Richmond, S. Zhurov, A. Lewis, S. Sharp, G. Paternoster, L. Thompson, H. Gonzales-Jose, R. Bortolini, M. C. Canizales-Quinteros, S. Gallo, C. Poletti, G. Bedoya, G. Rothhammer, F. Uitterlinden, A. Ikram, M. A. Wolvius, E. Kushner, S. Nijsten, T. Palstra, R.-J. Boehringer, S. Medland, S. Tang, K. Ruiz-Linares, A. Martin, N. Spector, T. Stergiakouli 2019-07-04 doi:10.1101/693002 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era ]]> https://biorxiv.org/content/10.1101/730531v1?rss=1 Armstrong, J. Hickey, G. Diekhans, M. Deran, A. Fang, Q. Xie, D. Feng, S. Stiller, J. Genereux, D. Johnson, J. Marinescu, V. D. Haussler, D. Alföldi, J. Lindblad-Toh, K. Karlsson, E. Zhang, G. Paten, B. 2019-08-09 doi:10.1101/730531 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Gut Microbiome Biomarkers in Adolescent Obesity：a Regional Study ]]> https://biorxiv.org/content/10.1101/745489v1?rss=1 Gao, X. Wu, B. Pan, Y. Zhou, S. Zhang, M. Cai, Y. Liang, Y. 2019-08-24 doi:10.1101/745489 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Generating Templates and Growth Charts for School-Aged Brain Development ]]> https://biorxiv.org/content/10.1101/747352v1?rss=1 Dong, H.-M. Castellanos, F. X. Yang, N. Zhang, Z. He, Y. Zhang, L. Xu, T. Holmes, A. Yeo, B. T. T. Chen, F. Wang, B. Beckmann, C. F. White, T. H. Sporns, O. Qiu, J. Feng, T. Chen, A. Liu, X. Chen, X. Weng, X. Milham, M. Zuo, X.-N. 2019-08-28 doi:10.1101/747352 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ The co-stimulation of anti-CD28 and IL-2 enhances the sensitivity of ELISPOT assays for detection of neoantigen-specific T cells in PBMC ]]> https://biorxiv.org/content/10.1101/760355v1?rss=1 Lee, L. J. Li, B. zhang, x. tang, y. Zhu, L. 2019-09-08 doi:10.1101/760355 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme ]]> https://biorxiv.org/content/10.1101/762385v1?rss=1 Deng, L. Guo, L. Xu, M. Wang, W. Gu, S. Zhao, X. Chen, F. Wang, O. Xu, X. Fan, G. Liu, X. 2019-09-08 doi:10.1101/762385 Cold Spring Harbor Laboratory Press 2019-09-08 <![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[ Satellite Imaging of Global Urbanicity relate to Adolescent Brain Development and Behavior ]]> https://biorxiv.org/content/10.1101/781674v1?rss=1 Xu, J. Liu, X. Ing, A. Li, Q. Qin, W. Guo, L. Huang, C. Cheng, J. Wang, M. Geng, Z. Zhu, W. Zhang, B. Liao, W. Qiu, S. Zhang, H. Xu, X. Yu, Y. Gao, B. Han, T. Cui, G. Chen, F. Xian, J. Li, J. Zhang, J. Zuo, X. Wang, D. Shen, W. Miao, Y. Yuan, F. Lui, S. Zhang, X. Xu, K. Zhang, L. Ye, Z. Banaschewski, T. Barker, G. J. Bokde, A. L. W. Quinlan, E. B. Desrivieres, S. Flor, H. Grigis, A. Garavan, H. Gowland, P. Heinz, A. Bruhl, R. Martinot, J.-L. Artiges, E. Nees, F. Orfanos, D. P. Lemaitre, H. Paus, T. Poustka, L. Hohmann, S. Frohner, J. H. Smo 2019-09-25 doi:10.1101/781674 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Defining relative mutational difficulty to understand cancer formation and prevention ]]> https://biorxiv.org/content/10.1101/789313v1?rss=1 Jiang, H. Shan, L. Yu, J. He, J. Z. Chen, S. S. Liu, X. M. Ding, Y. H. Xu, L. Zhao, J. Yang, L. A. 2019-10-01 doi:10.1101/789313 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Optimal Experimental Design for Big Data: Applications in Brain Imaging ]]> https://biorxiv.org/content/10.1101/802629v1?rss=1 Bridgeford, E. W. Wang, S. Yang, Z. Wang, Z. Xu, T. Craddock, C. Kiar, G. Gray-Roncal, W. Priebe, C. E. Caffo, B. Milham, M. Zuo, X.-N. Consortium for Reliability and Reproducibility, Vogelstein, J. T. 2019-10-13 doi:10.1101/802629 Cold Spring Harbor Laboratory Press 2019-10-13 <![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[ Low-disturbance farming regenerates healthy critical zone towards sustainable agriculture ]]> https://biorxiv.org/content/10.1101/828673v1?rss=1 Deng, F. Wang, H. Xie, H. Bao, X. He, H. Zhang, X. Liang, C. 2019-11-02 doi:10.1101/828673 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Recurrent Neoantigens in Colorectal Cancer as Potential Immunotherapy Targets ]]> https://biorxiv.org/content/10.1101/840918v1?rss=1 Chen, C. Liu, S. Li, B. 2019-11-13 doi:10.1101/840918 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Functional connectome analyses reveal a highly optimized human olfactory network ]]> https://biorxiv.org/content/10.1101/843532v1?rss=1 Arnold, T. C. You, Y. Ding, M. Zuo, X.-N. de Araujo, I. E. Li, W. 2019-11-16 doi:10.1101/843532 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Characterization of Isoforms of the Ovine Granulocyte Colony Stimulating Factor ]]> https://biorxiv.org/content/10.1101/849166v1?rss=1 Li, R. Chen, L. Wang, Y. Zhang, L. Liu, T. Nie, X. He, H. Wang, Y. Wang, K. Yang, R. Duan, C. Liu, Y. Ma, R. Z. Zhang, Y. 2019-11-21 doi:10.1101/849166 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Parkinson's disease associated mutation E46K of α-synuclein triggers the formation of a novel fibril structure ]]> https://biorxiv.org/content/10.1101/870758v1?rss=1 Liu, C. Li, X. Zhao, K. Li, Y. Liu, Z. Long, H. Zhao, C. Luo, F. Sun, Y. Tao, Y. Su, X.-d. Li, D. 2019-12-10 doi:10.1101/870758 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ A novel method for large-scale identification of polymorphic microsatellites through comparative transcriptome analysis ]]> https://biorxiv.org/content/10.1101/114645v1?rss=1 90%) that were indicated as putatively polymorphic by this method were indeed polymorphic. The frequency of polymorphic SSRs was significantly higher (P < 0.05) but the cost and running time were much lower than those of traditional and HTS approaches. The method has a practical value for polymorphic SSRs development and might be widely used for genetic analyses in any species. ]]> Luo, W. Qu, H. Wang, X. Zhan, Q. Lin, Q. 2017-03-07 doi:10.1101/114645 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ Inferring Disease-Associated Piwi-Interacting RNAs via Graph Attention Networks ]]> https://biorxiv.org/content/10.1101/2020.01.08.898155v1?rss=1 Zheng, K. You, Z.-H. wang, l. Wong, L. Chen, Z.-H. Jiang, H.-J. 2020-01-09 doi:10.1101/2020.01.08.898155 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Genome wide sequencing provides evidence of adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales) ]]> https://biorxiv.org/content/10.1101/2020.01.14.902643v1?rss=1 Zhang, X. Sun, Y. Landis, J. B. Zhang, J. Yang, L. Lin, N. Zhang, H. Guo, R. Li, L. Zhang, Y. Deng, T. Sun, H. Wang, H. 2020-01-15 doi:10.1101/2020.01.14.902643 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin ]]> https://biorxiv.org/content/10.1101/2020.01.22.914952v1?rss=1 Shi, Z.-L. Zhou, P. Yang, X.-L. Wang, X.-G. Hu, B. Zhang, L. Zhang, W. Si, H.-R. Zhu, Y. Li, B. Huang, C.-L. Chen, H.-D. Chen, J. Luo, Y. Guo, H. Jiang, R.-D. Liu, M.-Q. Chen, Y. Shen, X.-R. Wang, X. Zheng, X.-S. Zhao, K. Chen, Q.-J. Deng, F. Liu, L.-L. Yan, B. Zhan, F.-X. Wang, Y.-Y. Xiao, G. 2020-01-23 doi:10.1101/2020.01.22.914952 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Single-cell transcriptome analyses recapitulate the cellular and developmental responses to abiotic stresses in rice ]]> https://biorxiv.org/content/10.1101/2020.01.30.926329v1?rss=1 Wang, Y. Huan, Q. Chu, X. Li, K. Qian, W. 2020-01-31 doi:10.1101/2020.01.30.926329 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ TWIRLS, an automated topic-wise inference method based on massive literature, suggests a possible mechanism via ACE2 for the pathological changes in the human host after coronavirus infection ]]> https://biorxiv.org/content/10.1101/2020.02.27.967588v1?rss=1 Ji, X. Zhang, C. Zhai, Y. Zhang, Z. Zhang, C. Xue, Y. Tan, G. Niu, G. 2020-03-02 doi:10.1101/2020.02.27.967588 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Transcriptome analysis of the Nematode Caenorhabditis elegans in acidic stress environments ]]> https://biorxiv.org/content/10.1101/2020.03.06.980102v1?rss=1 Cong, Y. Yang, H. Zhang, P. Xie, Y. Cao, X. Zhang, L. 2020-03-08 doi:10.1101/2020.03.06.980102 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Single cell chromatin accessibility of the developmental cephalochordate ]]> https://biorxiv.org/content/10.1101/2020.03.17.994954v1?rss=1 Chen, D. Xu, X. wang, x. 2020-03-19 doi:10.1101/2020.03.17.994954 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ Structure-Based Design, Synthesis and Biological Evaluation of Peptidomimetic Aldehydes as a Novel Series of Antiviral Drug Candidates Targeting the SARS-CoV-2 Main Protease ]]> https://biorxiv.org/content/10.1101/2020.03.25.996348v1?rss=1 Dai, W. Zhang, B. Jiang, X.-M. Su, H. Li, J. Zhao, Y. Xie, X. Jin, Z. Peng, J. Liu, F. Li, C. Li, Y. Bai, F. Wang, H. Cheng, X. Cen, X. Hu, S. Yang, X. Wang, J. Liu, X. Xiao, G. Jiang, H. Rao, Z. Zhang, L. Xu, Y. Yang, H. Liu, H. 2020-03-28 doi:10.1101/2020.03.25.996348 Cold Spring Harbor Laboratory Press 2020-03-28 <![CDATA[ Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes ]]> https://biorxiv.org/content/10.1101/2020.04.02.021840v1?rss=1 Zhang, X. Sun, Y. Landis, J. B. Lv, Z. Shen, J. Zhang, H. Lin, N. Li, L. Sun, J. Deng, T. Sun, H. Wang, H. 2020-04-03 doi:10.1101/2020.04.02.021840 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Immunoglobulin fragment F(ab')2 against RBD potently neutralizes SARS-CoV-2 in vitro ]]> https://biorxiv.org/content/10.1101/2020.04.07.029884v1?rss=1 Pan, X. Zhou, P. Fan, T. Wu, Y. Zhang, J. Shi, X. Shang, W. Fang, L. Jiang, X. Shi, J. Sun, Y. Zhao, S. Gong, R. Chen, Z. Xiao, G. 2020-04-09 doi:10.1101/2020.04.07.029884 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Structural basis for the inhibition of COVID-19 virus main protease by carmofur, an antineoplastic drug ]]> https://biorxiv.org/content/10.1101/2020.04.09.033233v1?rss=1 Jin, Z. Zhao, Y. Sun, Y. Zhang, B. Wang, H. Wu, Y. Zhu, Y. Zhu, C. Hu, T. Du, X. Duan, Y. Yu, J. Yang, X. Yang, X. Liu, X. Guddat, L. W. Xiao, G. Zhang, L. Yang, H. Rao, Z. 2020-04-09 doi:10.1101/2020.04.09.033233 Cold Spring Harbor Laboratory Press 2020-04-09 <![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[ Broad-spectrum antivirals of protoporphyrins inhibit the entry of highly pathogenic emerging viruses ]]> https://biorxiv.org/content/10.1101/2020.05.09.085811v1?rss=1 Lu, S. Pan, X. Chen, D. Xie, X. Wu, Y. Shang, W. Jiang, X. Sun, Y. Fan, S. He, J. 2020-05-10 doi:10.1101/2020.05.09.085811 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Dynamic dopaminergic activity controls the timing of self-timed movement ]]> https://biorxiv.org/content/10.1101/2020.05.13.094904v1?rss=1 Hamilos, A. E. Spedicato, G. Hong, Y. Sun, F. Li, Y. Assad, J. A. 2020-05-14 doi:10.1101/2020.05.13.094904 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Ultra-sensitive nanozyme-based chemiluminescence paper test for rapid diagnosis of SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2020.06.05.131748v1?rss=1 Liu, D. Ju, C. Han, C. Shi, R. Chen, X. Duan, D. Yan, J. Yan, X. 2020-06-05 doi:10.1101/2020.06.05.131748 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ SARS-CoV-2 envelope protein causes acute respiratory distress syndrome (ARDS)-like pathological damage and constitutes an antiviral target ]]> https://biorxiv.org/content/10.1101/2020.06.27.174953v1?rss=1 Gao, Z. Xia, B. Shen, X. He, Y. Pan, X. Wang, Y. Yang, F. Fang, S. Wu, Y. Zuo, X. Xie, Z. Jiang, X. Chi, H. Meng, Q. Zhou, H. Zhou, Y. Cheng, X. Cheng, T. Xin, X. Jiang, H. Xiao, G. Zhao, Q. Zhang, L.-K. Shen, J. Li, J. 2020-06-29 doi:10.1101/2020.06.27.174953 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[ CGMTSA: An R package for continuous glucose monitoring time series data analysis ]]> https://biorxiv.org/content/10.1101/2020.07.06.174748v1?rss=1 Jian, S. Tao, X. Xin, Z. K. 2020-07-07 doi:10.1101/2020.07.06.174748 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Single-cell landscape of immunological responses in COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.07.23.217703v1?rss=1 Wang, F.-S. Zhang, J.-Y. Wang, X. Xing, X. Xu, Z. Zhang, C. Song, J.-W. Fan, X. Xia, P. Fu, J.-L. Wang, S.-Y. Xu, R.-N. Dai, X.-P. Shi, L. Huang, L. Jiang, T.-J. Shi, M. Zhang, Y. Zumla, A. Maeurer, M. Bai, F. 2020-07-24 doi:10.1101/2020.07.23.217703 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Induction of core symptoms of autism spectrum disorders by in vivo CRISPR/Cas9-based gene editing in the brain of adolescent rhesus monkeys ]]> https://biorxiv.org/content/10.1101/2020.08.03.233437v1?rss=1 Shihao, W. Xiao, L. Dongdong, Q. Linheng, Z. Tian-Lin, C. Zhifang, C. Binbin, N. Xiaofeng, R. Jing, W. Wenchao, W. Yingzhou, H. Yilin, G. Longbao, L. Yong, Y. Xintian, H. Zilong, Q. 2020-08-04 doi:10.1101/2020.08.03.233437 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ An Industrial-Grade Brain Imaging-Based Deep Learning Classifier ]]> https://biorxiv.org/content/10.1101/2020.08.18.256594v1?rss=1 Lu, B. Li, H.-X. Chang, Z.-K. Li, L. Chen, N.-X. Zhu, Z.-C. Zhou, H.-X. Fan, Z. Yang, H. Chen, X. Yan, C.-G. 2020-08-20 doi:10.1101/2020.08.18.256594 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ A novel oxidase from Alcaligenes sp. 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You, E. Liu, M. Wang, Q. Wang, Q. Jiang, Y. Jiang, H. Xiao, G. Yu, X. Zhang, S. Xu, H. E. 2020-10-06 doi:10.1101/2020.10.06.328336 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Increased light availability enhances tolerance against ocean acidification stress in Halimeda opuntia ]]> https://biorxiv.org/content/10.1101/2020.10.09.333799v1?rss=1 Wei, Z. Long, C. Zhang, Y. Huo, Y. Yang, F. Long, L. 2020-10-10 doi:10.1101/2020.10.09.333799 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Structural basis for repurpose and design of nucleoside drugs for treating COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.11.01.363812v1?rss=1 Yin, W. Luan, X. Li, Z. Xie, Y. Zhou, Z. Liu, J. Gao, M. Wang, X. Zhou, F. Wang, Q. Wang, Q. Shen, D. Zhang, Y. Tian, G. Aisa, H. A. Hu, T. Wei, D. Jiang, Y. Xiao, G. Jiang, H. Zhang, L. Yu, X. Shen, J. Zhang, S. Xu, H. E. 2020-11-02 doi:10.1101/2020.11.01.363812 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ NyuWa Genome Resource: Deep Whole Genome Sequencing Based Chinese Population Variation Profile and Reference Panel ]]> https://biorxiv.org/content/10.1101/2020.11.10.376574v1?rss=1 Zhang, P. Luo, H. Li, Y. Wang, Y. Wang, J. Zheng, Y. Niu, Y. Shi, Y. Zhou, H. Song, T. Kang, Q. Xu, T. He, S. 2020-11-11 doi:10.1101/2020.11.10.376574 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Characterization of the first cultured free-living representative of Candidatus Izimaplasma uncovers its unique biology ]]> https://biorxiv.org/content/10.1101/2020.11.18.388454v1?rss=1 Zheng, R. liu, R. Shan, Y. Cai, R. Liu, G. Sun, C. 2020-11-19 doi:10.1101/2020.11.18.388454 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Rigorous anterograde trans-monosynaptic tracing of genetic defined neurons with retargeted HSV1 H129 ]]> https://biorxiv.org/content/10.1101/2020.12.01.407312v1?rss=1 su, p. ying, m. xia, j. li, y. wu, y. wang, h. xu, f. 2020-12-02 doi:10.1101/2020.12.01.407312 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Body site-specific and disease-specific virulome in the human microbiome ]]> https://biorxiv.org/content/10.1101/2020.12.13.403006v1?rss=1 Liu, F. Dong, W. Guo, Y. Xiong, Q. Lu, N. Song, X. Xue, Y. Cao, D. Fan, X. Fang, Y. Li, Z. Cao, J. Wang, Y. Yang, G. Gao, G. F. Zhao, F. Zhu, B. 2020-12-14 doi:10.1101/2020.12.13.403006 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling ]]> https://biorxiv.org/content/10.1101/2021.01.05.425403v1?rss=1 Zheng, R. Cai, R. liu, r. Shan, Y. Liu, G. Sun, C. 2021-01-05 doi:10.1101/2021.01.05.425403 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1 ]]> https://biorxiv.org/content/10.1101/2021.02.07.430097v1?rss=1 Wang, Y.-Y. Zhang, J. Liu, X.-M. Dong, M.-Q. Ye, K. Du, L.-L. 2021-02-07 doi:10.1101/2021.02.07.430097 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Sulfur limitation increases duckweed starch accumulation without compromising growth ]]> https://biorxiv.org/content/10.1101/2021.02.22.432231v1?rss=1 Sun, Z. Guo, W. Zhao, X. Yang, J. Duan, P. Xu, S. Hou, H. 2021-02-23 doi:10.1101/2021.02.22.432231 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Resurrection of human endogenous retroviruses during aging reinforces senescence ]]> https://biorxiv.org/content/10.1101/2021.02.22.432260v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@31d384org.highwire.dtl.DTLVardef@13594c0org.highwire.dtl.DTLVardef@b8e070org.highwire.dtl.DTLVardef@196e5be_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Liu, X. Liu, Z. Sun, L. Ren, J. Wu, Z. Jiang, X. Ji, Q. Wang, Q. Fan, Y. Cai, Y. Wang, S. Li, W. Cao, G. Song, M. Lu, F. Zhang, W. Qu, J. liu, g. 2021-02-22 doi:10.1101/2021.02.22.432260 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ The dynamic interactive network of long non-coding RNAs and chromatin accessibility facilitates erythroid differentiation ]]> https://biorxiv.org/content/10.1101/2021.03.02.433076v1?rss=1 Ren, Y. Zhu, J. Han, Y. Li, P. Qu, H. Zhang, Z. Fang, X. 2021-03-02 doi:10.1101/2021.03.02.433076 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses ]]> https://biorxiv.org/content/10.1101/2021.03.08.434390v1?rss=1 Zhou, H. Ji, J. Chen, X. Bi, Y. Li, J. Hu, T. Song, H. Chen, Y. Cui, M. Zhang, Y. Hughes, A. C. Holmes, E. C. Shi, W. 2021-03-08 doi:10.1101/2021.03.08.434390 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Butyryl/Caproyl-CoA:Acetate CoA-Transferase: Cloning, Expression and Characterization of the Key Enzyme Involved in Medium-Chain Fatty Acid Biosynthesis ]]> https://biorxiv.org/content/10.1101/2021.03.10.434813v1?rss=1 Yang, Q. Guo, S. Lu, Q. Tao, Y. Zheng, D. Zhou, Q. Liu, J. 2021-03-10 doi:10.1101/2021.03.10.434813 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Insights into the drivers of radiating diversification in biodiversity hotspots using Saussurea (Asteraceae) as a case ]]> https://biorxiv.org/content/10.1101/2021.03.15.435394v1?rss=1 Zhang, X. Landis, J. B. Sun, Y. Zhang, H. Feng, T. Lin, N. Tiamiyu, B. B. Huang, X. Deng, T. Wang, H. Sun, H. 2021-03-16 doi:10.1101/2021.03.15.435394 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Structure of SOQ1 lumenal domains identifies potential disulfide exchange for negative regulation of photoprotection, qH ]]> https://biorxiv.org/content/10.1101/2021.03.16.435614v1?rss=1 Yu, G. Pan, X. Hao, J. Shi, L. Zhang, Y. Wang, J. Xiao, Y. Yang, F. Lou, J. Chang, W. Malnoe, A. Li, M. 2021-03-17 doi:10.1101/2021.03.16.435614 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation ]]> https://biorxiv.org/content/10.1101/2021.03.23.436689v1?rss=1 Liu, R. Shan, Y. Xi, S. Zhang, X. Sun, C. 2021-03-23 doi:10.1101/2021.03.23.436689 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ A Chromosome-level Assembly of a Wild Castor Genome Provides New Insights into the Adaptive Evolution in a Tropical Desert ]]> https://biorxiv.org/content/10.1101/2021.03.31.437884v1?rss=1 Lu, J. Pan, C. Fan, W. Liu, W. Zhao, H. Li, D. Wang, S. Hu, L. He, B. Qian, K. Qin, R. Ruan, J. Lin, Q. Lu, S. Cui, P. 2021-04-02 doi:10.1101/2021.03.31.437884 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ PRMT5 regulates ovarian follicle development by facilitating Wt1 translation ]]> https://biorxiv.org/content/10.1101/2021.04.04.438394v1?rss=1 Chen, M. Dong, F. Chen, M. Shen, Z. Wu, H. Cen, C. Cui, X. Bao, S. Gao, F. 2021-04-04 doi:10.1101/2021.04.04.438394 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Surrogate production of genome edited sperm from a different subfamily by spermatogonial stem cell transplantation ]]> https://biorxiv.org/content/10.1101/2021.04.20.440715v1?rss=1 Zhang, F. Li, X. Hao, Y. Li, Y. Ye, D. He, M. Wang, H. Zhu, Z. Sun, Y. 2021-04-21 doi:10.1101/2021.04.20.440715 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Transcriptomic encoding of sensorimotor transformation in the midbrain ]]> https://biorxiv.org/content/10.1101/2021.04.27.441692v1?rss=1 Xie, Z. Wang, M. Liu, Z. Shang, C. Zhang, C. Sun, L. Gu, H. Ran, G. Pei, Q. Ma, Q. Huang, M. Zhang, J. Zhang, J. Zhao, M. Wu, Q. Cao, P. Wang, X. 2021-04-28 doi:10.1101/2021.04.27.441692 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Noise-Transfer2Clean: Denoising cryo-EM images based on noise modeling and transfer ]]> https://biorxiv.org/content/10.1101/2021.05.10.443396v1?rss=1 Li, H. Zhang, H. Wan, X. Yang, Z. Li, C. Li, J. Han, R. Zhu, P. Zhang, F. 2021-05-10 doi:10.1101/2021.05.10.443396 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ The First High-Quality Reference Genome of Sika Deer Provides Insights for High-Tannin Adaptation ]]> https://biorxiv.org/content/10.1101/2021.05.13.443962v1?rss=1 Xing, X. Ai, C. Wang, T. LI, Y. Liu, H. Hu, P. Wang, G. Liu, H. Wang, H. Zhang, R. Zheng, J. Wang, X. Wang, L. Chang, Y. Qian, Q. Yu, J. Tang, L. Wu, S. Shao, X. Li, A. Cui, P. Zhan, W. Zhao, S. Wu, Z. Shao, X. Dong, Y. Rong, M. Tan, Y. Cui, X. Chang, S. Song, X. Yang, T. Sun, L. Ju, Y. Zhao, P. Fan, H. Liu, Y. Wang, X. Yang, W. Yang, M. Wei, T. Song, S. Xu, J. Yue, Z. Liang, Q. Li, C. Ruan, J. Yang, F. 2021-05-14 doi:10.1101/2021.05.13.443962 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ A multiple-causal-gene-cluster model underlying GWAS signals of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2021.05.14.444131v1?rss=1 Xu, M. Liu, Q. Bi, R. Li, Y. Zeng, C. Yan, Z. Zheng, Q. Li, X. Sun, C. Ye, M. Luo, X.-J. Li, M. Zhang, D.-F. Yao, Y.-G. 2021-05-17 doi:10.1101/2021.05.14.444131 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor ]]> https://biorxiv.org/content/10.1101/2021.05.21.445091v1?rss=1 Guo, H. Hu, B. Si, H.-r. Zhu, Y. Zhang, W. Li, B. Li, A. Geng, R. Lin, H.-F. Yang, X.-L. Zhou, P. Shi, Z. 2021-05-21 doi:10.1101/2021.05.21.445091 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Single-cell RNA-sequencing reveals thoracolumbar vertebra heterogeneity and rib-genesis in pigs ]]> https://biorxiv.org/content/10.1101/2021.05.25.445704v1?rss=1 Li, J. Wang, L. Yu, D. Hao, J. Zhang, L. Adeola, A. C. Mao, B. Gao, Y. Wu, S. Zhu, C. Zhang, Y. Ren, J. Mu, C. Irwin, D. M. Wang, L. Hai, T. Xie, H. Zhang, Y.-p. 2021-05-26 doi:10.1101/2021.05.25.445704 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Neutralization of recombinant RBD-subunit vaccine ZF2001-elicited antisera to SARS-CoV-2 variants including Delta ]]> https://biorxiv.org/content/10.1101/2021.07.15.452504v1?rss=1 Zhao, X. Zheng, A. Li, D. Zhang, R. Sun, H. Wang, Q. Gao, G. F. Han, P. Dai, L. 2021-07-16 doi:10.1101/2021.07.15.452504 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020. ]]> https://biorxiv.org/content/10.1101/2021.07.17.452774v1?rss=1 Ren, N. Wang, S. Shi, C. Yu, P. Zhao, L. Huang, D. Ma, H. Xiao, S. Wang, F. Yuan, Z. Xia, H. 2021-07-18 doi:10.1101/2021.07.17.452774 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ Opposite effects of nutrient enrichment and herbivory by an alien snail on growth of an invasive macrophyte and native macrophytes ]]> https://biorxiv.org/content/10.1101/2021.08.03.455002v1?rss=1 Yan, Y. Oduor, A. M. O. Li, F. Xie, Y. Liu, Y. 2021-08-05 doi:10.1101/2021.08.03.455002 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Deciphering spatial domains from spatially resolved transcriptomics with adaptive graph attention auto-encoder ]]> https://biorxiv.org/content/10.1101/2021.08.21.457240v1?rss=1 Dong, K. Zhang, S. 2021-08-23 doi:10.1101/2021.08.21.457240 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ A universal microfluidic approach for quantitative study of bacterial biofilms ]]> https://biorxiv.org/content/10.1101/2021.08.24.457583v1?rss=1 Zhang, Y. Zeng, L. Cai, Y. Chen, Z. Liu, P. Ma, L. Liu, J. 2021-08-25 doi:10.1101/2021.08.24.457583 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Molecular basis for the R-type anion channel QUAC1 activity in guard cells ]]> https://biorxiv.org/content/10.1101/2021.09.09.459598v1?rss=1 Qin, L. Tang, L.-h. Xu, J.-s. Zhang, X.-h. Zhu, Y. Zhang, C.-r. Liu, X.-l. Wang, M.-h. Li, F. Sun, F. Su, M. Zhai, Y.-J. Chen, Y.-h. 2021-09-10 doi:10.1101/2021.09.09.459598 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Deactivation of SARS-CoV-2 surrogate porcine epidemic diarrhea virus with electron beam irradiation under the cold chain transportation condition ]]> https://biorxiv.org/content/10.1101/2021.09.25.461766v1?rss=1 Liu, Y. Shao, Y. Wang, L. Lu, W. Li, S. Xu, D. Fu, Y. V. 2021-09-26 doi:10.1101/2021.09.25.461766 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Cross-species cell-type assignment of single-cell RNA-seq by a heterogeneous graph neural network ]]> https://biorxiv.org/content/10.1101/2021.09.25.461790v1?rss=1 Liu, X. Shen, Q. Zhang, S. 2021-09-26 doi:10.1101/2021.09.25.461790 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ A genetic bottleneck of mitochondrial DNA during human lymphocyte development ]]> https://biorxiv.org/content/10.1101/2021.09.28.462268v1?rss=1 Tang, Z. Lu, Z. Chen, B. Zhang, W. Chang, H. Hu, Z. Xu, J. 2021-09-30 doi:10.1101/2021.09.28.462268 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Drought stress delays photosynthetic induction and accelerates photoinhibition of photosystem I under fluctuating light ]]> https://biorxiv.org/content/10.1101/2021.10.07.463522v1?rss=1 Sun, H. Shi, Q. Liu, N.-Y. Zhang, S.-B. Huang, W. 2021-10-09 doi:10.1101/2021.10.07.463522 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Severe fever with thrombocytopenia syndrome virus and parthenogenetic Asian longhorned tick Haemaphysalis longicornis (Acari: Ixodidae) ]]> https://biorxiv.org/content/10.1101/2021.10.20.465214v1?rss=1 Zheng, A. Zhang, Z. Zhang, G. Zhan, X. Z. Zhang, X. Zhao, C. Cheng, C. Li, H. Yu, T. Lawrence, K. L. Sun, J. Yang, Z. Ye, L. Chu, H. C. Wang, Y. W. Han, X. Jia, Y. Fan, S. Kanuka, H. Tanaka, T. Jenkins, C. Gedye, K. Chandra, S. Price, D. C. Liu, Q. Choi, Y. 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Zhang, C. 2021-11-11 doi:10.1101/2021.11.10.468004 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Integrative Omics Analysis Reveals the Immunomodulatory Effects of the Parasitic Dinoflagellate Hematodinium on Crustacean Immunity ]]> https://biorxiv.org/content/10.1101/2021.11.17.468922v1?rss=1 Li, M. Huang, Q. Lv, X. Small, H. J. Li, C. 2021-11-19 doi:10.1101/2021.11.17.468922 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Cell free extrachromosomal circular DNA is common in human urine ]]> https://biorxiv.org/content/10.1101/2021.12.02.471038v1?rss=1 Lv, W. Pan, X. Han, P. Wang, Z. Yuan, H. Feng, W. Wang, Q. Qu, K. Xu, Z. Li, Y. Zheng, T. Lin, L. Liu, C. Liu, X. Li, H. Henriksen, R. H. A. Bolund, L. Lin, L. Jin, X. Yang, H. Zhang, X. Regenberg, B. Luo, Y. 2021-12-05 doi:10.1101/2021.12.02.471038 Cold Spring Harbor Laboratory Press 2021-12-05 <![CDATA[ Structure and dynamics of human disease-complication network ]]> https://biorxiv.org/content/10.1101/2021.12.13.472342v1?rss=1 Jiang, X. Xiong, L. Bai, L. Lin, J. Zhang, J.-F. Yan, K. Zhu, J.-Z. Zheng, B. Zheng, J.-J. 2021-12-14 doi:10.1101/2021.12.13.472342 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Evidence for a mouse origin of the SARS-CoV-2 Omicron variant ]]> https://biorxiv.org/content/10.1101/2021.12.14.472632v1?rss=1 Wei, C. Shan, K.-J. Wang, W. Zhang, S. Huan, Q. Qian, W. 2021-12-15 doi:10.1101/2021.12.14.472632 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ Reduced sera neutralization to Omicron SARS-CoV-2 by bothinactivated and protein subunit vaccines and the convalescents ]]> https://biorxiv.org/content/10.1101/2021.12.16.472391v1?rss=1 Zhao, X. Li, D. Ruan, W. Zhang, R. Zheng, A. Qiao, S. Zheng, X. Zhao, Y. Chen, Z. Dai, L. Han, P. Gao, G. F. 2021-12-20 doi:10.1101/2021.12.16.472391 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Replication is the key barrier during the dual-host adaption of mosquito-borne flaviviruses ]]> https://biorxiv.org/content/10.1101/2021.12.21.473591v1?rss=1 Zheng, A. Wang, X. Zhang, Y. Liang, D. Yuan, F. Yan, Y. Wang, Z. Liu, P. Qu, Q. Zhang, X. 2021-12-21 doi:10.1101/2021.12.21.473591 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant ]]> https://biorxiv.org/content/10.1101/2021.12.29.474402v1?rss=1 Cui, Z. Liu, P. Wang, N. Wang, L. Fan, K. Zhu, Q. Wang, K. Chen, R. Feng, R. Jia, Z. Yang, M. Zhu, B. Fu, W. Chu, T. Feng, L. Wang, Y. Pei, X. Yang, P. Xie, X. S. Cao, L. Cao, Y. R. Wang, X. 2021-12-30 doi:10.1101/2021.12.29.474402 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Parasite defensive limb movements enhance signal attraction in male little torrent frogs: insight into the evolution of multimodal signals ]]> https://biorxiv.org/content/10.1101/2021.12.31.474622v1?rss=1 Zhao, L. Wang, J. Zhang, H. Wang, T. Yang, Y. Tang, Y. Halfwerk, W. Cui, J. 2022-01-01 doi:10.1101/2021.12.31.474622 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ Impact of various vaccine boosters on neutralization against Omicron following prime vaccinations with inactivated or adenovirus-vectored vaccine ]]> https://biorxiv.org/content/10.1101/2022.01.25.476850v1?rss=1 Huang, Q. Zeng, J. Lang, Q. Gao, F. Liu, D. Tian, S. Shi, R. Luo, L. Wang, H. Hu, L. Jiang, L. Liu, Y. Li, K. Wu, Y. Xu, J. Jiang, W. Guo, N. Chen, Z. Hao, X. Jin, R. Yan, J. Sun, Y. 2022-01-27 doi:10.1101/2022.01.25.476850 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Transcriptome Analysis of the Nematode Caenorhabditis elegans and Litoditis marina in a Chemically Defined Food Environment ]]> https://biorxiv.org/content/10.1101/2022.01.28.478261v1?rss=1 Sun, P. Cao, X. Zhang, L. 2022-01-29 doi:10.1101/2022.01.28.478261 Cold Spring Harbor Laboratory Press 2022-01-29 <![CDATA[ Hedgehogs are the major amplifying hosts of severe fever with thrombocytopenia syndrome virus ]]> https://biorxiv.org/content/10.1101/2022.01.30.478379v1?rss=1 Zheng, A. Jiang, J. Zhao, C. Zhang, X. Hao, J. Ye, L. Lawrence, K. Lu, Y. Du, C. Si, X. Xu, H. Yang, Q. Xia, Q. Yu, G. Yuan, F. 2022-01-30 doi:10.1101/2022.01.30.478379 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Cilia regulate meiotic recombination in zebrafish ]]> https://biorxiv.org/content/10.1101/2022.03.05.482955v1?rss=1 Xie, H. Wang, X. Jin, M. Li, L. Zhu, J. Kang, Y. Chen, Z. Sun, Y. Zhao, C. 2022-03-06 doi:10.1101/2022.03.05.482955 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ Evolutionary Principles of Bacterial Signaling Capacity and Complexity ]]> https://biorxiv.org/content/10.1101/2022.03.11.484041v1?rss=1 Mo, R. Liu, Y. Chen, Y. Mao, Y. Gao, B. 2022-03-12 doi:10.1101/2022.03.11.484041 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Minor differences in peptide presentation between chicken MHC class I molecules can explain differences in disease susceptibility ]]> https://biorxiv.org/content/10.1101/2022.03.11.484051v1?rss=1 Han, L. Wu, S. Peng, W. Zhao, M. Yue, C. Wen, W. Cai, W. Zhang, T. Wallny, H. J. Avila, D. W. Mwangi, W. Nair, V. Ternette, N. Guo, Y. Zhao, Y. Chai, Y. Qi, J. Liang, H. Gao, G. F. Kaufman, J. Liu, W. J. 2022-03-13 doi:10.1101/2022.03.11.484051 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ LANTSA: Landmark-based transferable subspace analysis for single-cell and spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.03.13.484116v1?rss=1 Zhang, C. Wang, L. Li, X. Guo, W.-F. Shi, Q. Chen, L. 2022-03-14 doi:10.1101/2022.03.13.484116 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Maternal separation induces autism spectrum disorder in young rhesus monkeys ]]> https://biorxiv.org/content/10.1101/2022.03.17.484827v1?rss=1 Ren, X.-F. Wu, S.-H. Zhou, H. Lv, L.-B. Qiu, Z.-L. Feng, X.-L. Hu, X.-T. 2022-03-19 doi:10.1101/2022.03.17.484827 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Ralstonia solanacearum effector RipAF1 ADP-ribosylates host FBN1 to induce resistance against bacterial wilt ]]> https://biorxiv.org/content/10.1101/2022.04.04.487053v1?rss=1 Wu, W. Luo, X. Chen, X. Wang, L. Wang, K. Tian, S. Tong, Z. Zhao, T. Fan, X. Zhuo, T. Hu, X. Zou, H. 2022-04-05 doi:10.1101/2022.04.04.487053 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ FliL has a conserved function in diverse microbes to negatively modulate motor output via its N-terminal region ]]> https://biorxiv.org/content/10.1101/2022.05.17.492383v1?rss=1 Liu, X. Roujeinikova, A. Ottemann, K. M. 2022-05-18 doi:10.1101/2022.05.17.492383 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ The largest haplotype-phased and chromosome-scale genome assembly of the fungal pathogen, Puccinia polysora, by HiFi reads and Hi-C data ]]> https://biorxiv.org/content/10.1101/2022.05.18.492400v1?rss=1 Liang, j. Li, y. Dodds, P. N. Figueroa, M. Sperschneider, J. Han, S. Tsui, C. K. M. Zhang, K. Li, L. Ma, Z. Cai, L. 2022-05-19 doi:10.1101/2022.05.18.492400 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Genomic analyses provide new insights into the evolutionary history and reproduction of the Paleogene relictual Kingdonia (Circaeasteraceae, Ranunculales) ]]> https://biorxiv.org/content/10.1101/2022.06.07.495209v1?rss=1 Sun, Y. Zhang, X. Zhang, A. Landis, J. B. Zhang, H. Sun, H. Xiang, J. Wang, H. 2022-06-12 doi:10.1101/2022.06.07.495209 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ An improved graph representation learning method for drug-target interaction prediction over heterogeneous biological information graph ]]> https://biorxiv.org/content/10.1101/2022.06.30.498357v1?rss=1 Zhao, B.-W. Su, X. You, Z.-H. Hu, P.-W. Hu, L. 2022-07-02 doi:10.1101/2022.06.30.498357 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ A geometric deep learning framework for drug repositioning over heterogeneous information networks ]]> https://biorxiv.org/content/10.1101/2022.07.16.500310v1?rss=1 Zhao, B.-W. Su, X. Hu, P.-W. Ma, Y.-P. Zhou, X. Hu, L. 2022-07-18 doi:10.1101/2022.07.16.500310 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Osteocytes regulate organismal senescence of bone and bone marrow ]]> https://biorxiv.org/content/10.1101/2022.07.17.500353v1?rss=1 Ding, P. Gao, C. Gao, Y. Liu, D. Li, H. Xu, J. Chen, X. Huang, Y. Zhang, C. Zheng, M. H. Gao, J. 2022-07-18 doi:10.1101/2022.07.17.500353 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Neutralizing antibody evasion and receptor binding features of SARS-CoV-2 Omicron BA.2.75 ]]> https://biorxiv.org/content/10.1101/2022.07.18.500332v1?rss=1 Cao, Y. Yu, Y. Song, W. Jian, F. Yisimayi, A. Yue, C. Feng, R. Wang, P. Yu, L. Zhang, N. Wang, J. Xiao, T. An, R. Wang, Y. Wang, J. Liu, L. Yang, S. Niu, X. Gu, Q. Shao, F. Hao, X. Jin, R. Wang, X. Wang, Y. Xie, X. S. 2022-07-19 doi:10.1101/2022.07.18.500332 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Pore-forming protein βγ-CAT drives extracellular nutrient scavenging under cell starvation ]]> https://biorxiv.org/content/10.1101/2022.07.20.500773v1?rss=1 Liu, L.-Z. Liu, L. Shi, Z.-H. Bian, X.-L. Wang, Q.-Q. Xiang, Y. Zhang, Y. 2022-07-21 doi:10.1101/2022.07.20.500773 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ A unique peptide recognition mechanism by the human relaxin family peptide receptor 4 (RXFP4) ]]> https://biorxiv.org/content/10.1101/2022.07.28.501832v1?rss=1 Chen, Y. Zhou, Q. Wang, J. Xu, Y. Wang, Y. Yan, J. Wang, Y. Zhu, Q. Zhao, F. Li, C. Chen, C.-W. Cai, X. Bathgate, R. A. D. Shen, C. Xu, H. E. Yang, D. Liu, H. Wang, M.-W. 2022-07-28 doi:10.1101/2022.07.28.501832 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ CRIC-seq reveals positional rule of PTBP1-mediated long-range RNA looping in splicing regulation ]]> https://biorxiv.org/content/10.1101/2022.08.09.503273v1?rss=1 Ye, R. Hu, N. Cao, C. Su, R. Yang, C. Xu, S. Xue, Y. 2022-08-11 doi:10.1101/2022.08.09.503273 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Stability of SARS-CoV-2 in cold-chain transportation environments and the efficacy of disinfection measures ]]> https://biorxiv.org/content/10.1101/2022.08.09.503429v1?rss=1 Peng, S. Li, G. Pathak, J. L. Guo, X. Lin, Y. Xu, H. Qiu, W. Zheng, J. Sun, W. Hu, X. Zhang, G. Li, B. Bi, X. Dai, J. 2022-08-10 doi:10.1101/2022.08.09.503429 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ ELI trifocal microscope: A precise cryogenic fabrication system to prepare target cryo-lamellae of cells for in situ cryo-ET study ]]> https://biorxiv.org/content/10.1101/2022.08.15.503951v1?rss=1 Li, S. Wang, Z. Jia, X. Niu, T. Zhang, J. Yin, G. Zhang, X. Zhu, Y. Ji, G. Sun, F. 2022-08-15 doi:10.1101/2022.08.15.503951 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Targeted genome editing in grape using multiple CRISPR-guided editing systems ]]> https://biorxiv.org/content/10.1101/2022.08.22.504768v1?rss=1 Ren, C. Lin, Y. Li, H. Li, S. Liang, Z. 2022-08-23 doi:10.1101/2022.08.22.504768 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Heritability enrichment in context-specific regulatory networks improves phenotype-relevant tissue identification ]]> https://biorxiv.org/content/10.1101/2022.09.06.506769v1?rss=1 Feng, Z. Duren, Z. Xin, J. Yuan, Q. He, Y. Su, B. Wong, W. H. Wang, Y. 2022-09-07 doi:10.1101/2022.09.06.506769 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Global mosquito virome profiling and mosquito spatial diffusion pathways revealed by marker-viruses ]]> https://biorxiv.org/content/10.1101/2022.09.24.509300v1?rss=1 Zhao, L. Yu, P. Shi, C. Jia, L. Evans, A. Wang, X. Wu, Q. Xiong, G. Ming, Z. Salazar, F. Agwanda, B. Bente, D. Wang, F. Liu, D. Yuan, Z. Xia, H. 2022-09-24 doi:10.1101/2022.09.24.509300 Cold Spring Harbor Laboratory Press 2022-09-24 <![CDATA[ SmartGate is a spatial metabolomics tool for resolving tissue structures ]]> https://biorxiv.org/content/10.1101/2022.09.25.509375v1?rss=1 Xiao, K. Wang, Y. Dong, K. Zhang, S. 2022-09-27 doi:10.1101/2022.09.25.509375 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Genomic underpinnings of convergent adaptation to high altitudes for alpine plants ]]> https://biorxiv.org/content/10.1101/2022.10.20.508685v1?rss=1 Zhang, X. Kuang, T. Dong, W. Qian, Z. Zhang, H. Landis, J. B. Feng, T. Li, L. Sun, Y. Huang, J. Deng, T. Wang, H. Sun, H. 2022-10-21 doi:10.1101/2022.10.20.508685 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Heavy metal pollution characteristics of soil around a copper-nickel mine tailings pond in the northwest arid area of China and evaluation of desert phytoremediation potential ]]> https://biorxiv.org/content/10.1101/2022.10.24.513495v1?rss=1 Shi, J. Jin, Z. Zhou, Z. Wang, X. Yang, X. Qian, W. 2022-10-25 doi:10.1101/2022.10.24.513495 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ The endogenous modulation of visual plasticity in human adults ]]> https://biorxiv.org/content/10.1101/2022.10.27.513994v1?rss=1 Chen, Y. Gao, Y. He, Z. Sun, Z. Mao, Y. Hess, R. F. Zhang, P. Zhou, J. 2022-10-28 doi:10.1101/2022.10.27.513994 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Network Occlusion Sensitivity Analysis Identifies Regional Contributions to Brain Age Prediction ]]> https://biorxiv.org/content/10.1101/2022.10.31.514506v1?rss=1 He, L. Chen, C. Wang, Y. Fan, Q. Chu, C. Xu, J. Fan, L. 2022-11-03 doi:10.1101/2022.10.31.514506 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ STAMarker: Determining spatial domain-specific variable genes with saliency maps in deep learning ]]> https://biorxiv.org/content/10.1101/2022.11.07.515535v1?rss=1 Zhang, C. Dong, K. Aihara, K. Chen, L. Zhang, S. 2022-11-08 doi:10.1101/2022.11.07.515535 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ The more synthetic polymer types pollute the soil, the stronger the growth suppression of invasive alien and native plants ]]> https://biorxiv.org/content/10.1101/2022.12.08.519663v1?rss=1 Fu, Y. van Kleunen, M. Ma, K. Liu, Y. 2022-12-12 doi:10.1101/2022.12.08.519663 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Causal network inference based on cross-validation predictability ]]> https://biorxiv.org/content/10.1101/2022.12.11.519942v1?rss=1 Zhang, Y. Li, Q. Chang, X. Chen, L. Liu, X. 2022-12-13 doi:10.1101/2022.12.11.519942 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Integrating spatial transcriptomics data across different conditions, technologies, and developmental stages ]]> https://biorxiv.org/content/10.1101/2022.12.26.521888v1?rss=1 Zhou, X. Dong, K. Zhang, S. 2022-12-26 doi:10.1101/2022.12.26.521888 Cold Spring Harbor Laboratory Press 2022-12-26 <![CDATA[ Forces driving transposable element load variation during Arabidopsis range expansion ]]> https://biorxiv.org/content/10.1101/2022.12.28.522087v1?rss=1 Jiang, J. Xu, Y.-C. Zhang, Z.-Q. Chen, J.-F. Niu, X.-M. Hou, X.-H. Li, X.-T. Wang, L. Zhang, Y. Ge, S. Guo, Y. 2022-12-30 doi:10.1101/2022.12.28.522087 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Biphasic curvature-dependence of cell migration inside microcylinders: persistent randomness versus directionality ]]> https://biorxiv.org/content/10.1101/2022.12.30.522287v1?rss=1 Yu, X. Wang, H. Ye, F. Wang, X. Fan, Q. Xu, X. 2022-12-30 doi:10.1101/2022.12.30.522287 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ A simple and efficient in planta transformation method based on the active regeneration capacity of plants ]]> https://biorxiv.org/content/10.1101/2023.01.02.522521v1?rss=1 Mei, G. Chen, A. Wang, Y. Li, S. Wu, M. Liu, X. Hou, X. 2023-01-03 doi:10.1101/2023.01.02.522521 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Enhanced transmissibility of XBB.1.5 is contributed by both strong ACE2 binding and antibody evasion ]]> https://biorxiv.org/content/10.1101/2023.01.03.522427v1?rss=1 Yue, C. Song, W. Wang, L. Jian, F. Chen, X. Gao, F. Shen, Z. Wang, Y. Wang, X. Cao, Y. R. 2023-01-03 doi:10.1101/2023.01.03.522427 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Anti-CRISPR AcrIIC5 is a dsDNA mimic that inhibits type II-C Cas9 effectors by blocking PAM recognition ]]> https://biorxiv.org/content/10.1101/2023.01.17.524369v1?rss=1 Sun, W. Zhao, X. Wang, J. Yang, X. Cheng, Z. Liu, S. Wang, J. Sheng, G. Wang, Y. 2023-01-17 doi:10.1101/2023.01.17.524369 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Lhcb9-dependent photosystem I structure in moss reveals evolutionary adaptation to changing light conditions during aquatic-terrestrial transition ]]> https://biorxiv.org/content/10.1101/2023.01.18.524345v1?rss=1 Sun, H. Shang, H. Pan, X. Li, M. 2023-01-20 doi:10.1101/2023.01.18.524345 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Structure of human NaV1.6 channel reveals Na+ selectivity and pore blockade by 4,9-anhydro-tetrodotoxin ]]> https://biorxiv.org/content/10.1101/2023.01.26.525614v1?rss=1 Li, Y. Yuan, T. Huang, B. Zhou, F. Peng, C. Li, X. Qiu, Y. Yang, B. Zhao, Y. Huang, Z. Jiang, D. 2023-01-27 doi:10.1101/2023.01.26.525614 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Zero-shot learning enables instant denoising and super-resolution in optical fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2023.02.24.529803v1?rss=1 Qiao, C. Zeng, Y. Meng, Q. Chen, X. Chen, H. Jiang, T. Wei, R. Guo, J. Fu, W. Lu, H. Li, D. wang, Y. Qiao, H. Wu, J. Li, D. Dai, Q. 2023-02-27 doi:10.1101/2023.02.24.529803 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Isolation of ACE2-dependent and -independent sarbecoviruses from Chinese horseshoe bats ]]> https://biorxiv.org/content/10.1101/2023.03.02.530738v1?rss=1 Guo, H. Li, A. Dong, T.-Y. Si, H.-R. Ben, H. Li, B. Zhu, Y. Shi, Z. Letko, M. C. 2023-03-02 doi:10.1101/2023.03.02.530738 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ The Complexity of Functional Connectivity Profiles of the Subgenual Anterior Cingulate Cortex and Dorsal Lateral Prefrontal Cortex in Major Depressive Disorder: a DIRECT Consortium Study ]]> https://biorxiv.org/content/10.1101/2023.03.09.531726v1?rss=1 Chen, X. Lu, B. Wang, Y.-W. Li, X.-Y. Wang, Z.-H. Li, H.-X. Liao, Y.-F. Blumberger, D. M. Castellanos, F. X. Cao, L.-P. Chen, G.-M. Chen, J.-S. Chen, T. Chen, T.-L. Cheng, Y.-Q. Chu, Z.-S. Cui, S.-X. Cui, X.-L. Deng, Z.-Y. Gong, Q.-Y. Guo, W.-B. He, C.-C. Hu, Z.-J.-Y. Huang, Q. Ji, X.-L. Jia, F.-N. Kuang, L. Li, B.-J. Li, F. Li, T. Lian, T. Liu, X.-Y. Liu, Y.-S. Liu, Z.-N. Long, Y.-C. Lu, J.-P. Qiu, J. Shan, X.-X. Si, T.-M. Sun, P.-F. Wang, C.-Y. Wang, H.-N. Wang, X. Wang, Y. Wu, X.-P. Wu, X.-R. Wu, Y.-K. Xie, C.-M. Xie, G.-R. Xie, P. Xu, X.-F. 2023-03-11 doi:10.1101/2023.03.09.531726 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification ]]> https://biorxiv.org/content/10.1101/2023.03.13.532390v1?rss=1 Zhang, C. Li, X. Huang, W. Wang, L. Shi, Q. 2023-03-14 doi:10.1101/2023.03.13.532390 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Substrate specificity and functional conservation of SWEET10 transporter in pineapple ]]> https://biorxiv.org/content/10.1101/2023.04.06.535793v1?rss=1 Fakher, B. Ashraf, M. A. Wang, L. Wang, X. Zheng, P. Aslam, M. Qin, Y. 2023-04-06 doi:10.1101/2023.04.06.535793 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Apolipoprotein B and Interleukin 1 Receptor Antagonist: Reversing the Risk of Coronary Heart Disease ]]> https://biorxiv.org/content/10.1101/2023.04.19.537591v1?rss=1 Yang, F. Huangfu, N. Shen, J. Su, P. Zhu, L. Cui, H. Yuan, S. 2023-04-21 doi:10.1101/2023.04.19.537591 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Pathogen protein modularity enables elaborate mimicry of a host phosphatase ]]> https://biorxiv.org/content/10.1101/2023.05.05.539533v1?rss=1 Li, H. Wang, J. Kuan, T. Tang, B. Feng, L. Wang, J. Cheng, Z. Sklenar, J. Derbyshire, P. Hulin, M. Li, Y. Zhai, Y. Hou, Y. Menke, F. Wang, Y. Ma, W. 2023-05-05 doi:10.1101/2023.05.05.539533 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors ]]> https://biorxiv.org/content/10.1101/2023.05.13.540645v1?rss=1 View larger version (5K): org.highwire.dtl.DTLVardef@1272a3corg.highwire.dtl.DTLVardef@45e25aorg.highwire.dtl.DTLVardef@f83e0org.highwire.dtl.DTLVardef@9b04e7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tarn, C. Wu, Y.-Z. Wang, K.-F. 2023-05-14 doi:10.1101/2023.05.13.540645 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Telomere-to-telomere genome of the model plant Physcomitrium patens ]]> https://biorxiv.org/content/10.1101/2023.05.19.541548v1?rss=1 Bi, G. Zhao, S. Yao, J. Wang, H. Zhao, M. Sun, Y. Hou, X. Jiao, Y. Ma, Y. Yan, J. Dai, J. 2023-05-22 doi:10.1101/2023.05.19.541548 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ In-cell structural insight into the stability of sperm microtubule doublet ]]> https://biorxiv.org/content/10.1101/2023.05.30.542832v1?rss=1 Tai, L. Yin, G. Huang, X. Zhu, Y. Sun, F. 2023-05-31 doi:10.1101/2023.05.30.542832 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ EquiScore: A generic protein-ligand interaction scoring method integrating physical prior knowledge with data augmentation modeling ]]> https://biorxiv.org/content/10.1101/2023.06.18.545464v1?rss=1 Cao, D. Chen, G. Jiang, J. Yu, J. Zhang, R. Chen, M. Zhang, W. Chen, L. Zhong, F. Zhang, Y. Lu, C. Li, X. Luo, X. Zhang, S. Zheng, M. 2023-06-21 doi:10.1101/2023.06.18.545464 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Natural Circulation of Tick-borne Severe Fever with Thrombocytopenia Syndrome Virus in the City Ecosystem, China ]]> https://biorxiv.org/content/10.1101/2023.07.02.547301v1?rss=1 Zheng, A. Zhang, X. Zhao, C. Si, X. Hu, Q. 2023-07-03 doi:10.1101/2023.07.02.547301 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Visualizing translating dynamics in situ at high spatial and temporal resolution in eukaryotic cells ]]> https://biorxiv.org/content/10.1101/2023.07.12.548775v1?rss=1 Zhang, X. Cheng, J. Chunling, W. Junxi, L. Qi, Y. 2023-07-13 doi:10.1101/2023.07.12.548775 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Atypical Biological Motion Perception in Children with Attention Deficit Hyperactivity Disorder: Dissociating the Roles of Local Motion and Global Configuration Processing ]]> https://biorxiv.org/content/10.1101/2023.07.25.550597v1?rss=1 Tian, J. Yang, F. Wang, Y. Wang, L. Wang, N. Jiang, Y. Yang, L. 2023-07-28 doi:10.1101/2023.07.25.550597 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ The longitudinal single-cell panorama of cynomolgus monkey ovary throughout lifespan revealed a conserved ovarian clock between primates ]]> https://biorxiv.org/content/10.1101/2023.08.14.553309v1?rss=1 Yan, L. Long, X. Zhao, Y. Zhao, F. Tu, W. Yang, Q. Qian, J. Zhai, J. Wang, M. Hu, Y. He, B. Su, Y. Jiang, X. Gao, F. Wang, H. Guo, F. 2023-08-16 doi:10.1101/2023.08.14.553309 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Structural insights into DNA Topoisomerase II of African Swine Fever Virus ]]> https://biorxiv.org/content/10.1101/2023.08.21.554066v1?rss=1 Cong, J. Xin, Y. Kang, H. Yang, Y. Wang, C. Li, X. Rao, Z. Chen, Y. 2023-08-22 doi:10.1101/2023.08.21.554066 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ In situ structural insights into the excitation contraction coupling mechanism of skeletal muscle ]]> https://biorxiv.org/content/10.1101/2023.08.26.554922v1?rss=1 Xu, J. Liao, C. Yin, C.-c. Li, G. Zhu, Y. Sun, F. 2023-08-28 doi:10.1101/2023.08.26.554922 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Ennet: exert enhaner-only somatic mutations to discover potential cancer-driving biological networks ]]> https://biorxiv.org/content/10.1101/216226v1?rss=1 Cui, Y. Niu, Y. Teng, X. Wang, D. Luo, H. Zhang, P. Wu, W. He, S. Luo, J. Chen, R. 2017-11-08 doi:10.1101/216226 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis ]]> https://biorxiv.org/content/10.1101/285593v1?rss=1 Sun, G. Xu, Y. Liu, H. Sun, T. Zhang, J. Hettenhausen, C. Shen, G. Qi, J. Qin, Y. Li, J. Wang, L. Chang, W. Guo, Z. Baldwin, I. T. Wu, J. 2018-03-20 doi:10.1101/285593 Cold Spring Harbor Laboratory Press 2018-03-20 <![CDATA[ Dietary lysozyme supplement alters serum biochemical makers and milk metabolite profile of sows via gut microbiota ]]> https://biorxiv.org/content/10.1101/444778v1?rss=1 Zhou, J. Xiong, X. Zou, L. Yin, J. Wang, K. Shao, Y. Yin, Y. 2018-10-16 doi:10.1101/444778 Cold Spring Harbor Laboratory Press 2018-10-16 <![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[ RobustClone: A robust PCA method of tumor clone and evolution inference from single-cell sequencing data ]]> https://biorxiv.org/content/10.1101/666271v1?rss=1 Chen, Z. Gong, F. Ma, L. Wan, L. 2019-06-10 doi:10.1101/666271 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Construct a molecular associations network to systematically understand intermolecular associations in Human cells ]]> https://biorxiv.org/content/10.1101/693051v1?rss=1 Yi, H.-C. You, Z.-H. Guo, Z.-H. 2019-07-04 doi:10.1101/693051 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data ]]> https://biorxiv.org/content/10.1101/721290v1?rss=1 Dong, K. Zhang, S. 2019-07-31 doi:10.1101/721290 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Dynamic response of RNA editing to temperature in Grape by RNA deep-sequencing ]]> https://biorxiv.org/content/10.1101/745364v1?rss=1 Zhang, a. jiang, x. zhang, x. 2019-08-24 doi:10.1101/745364 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Admistration of Exogenous Melatonin Improves the Diurnal Rhythms of Gut Microbiota in High Fat Diet-Fed Mice ]]> https://biorxiv.org/content/10.1101/760421v1?rss=1 Yin, J. Han, H. Li, Y. Liu, G. Wu, X. Huang, X. Fang, R. Baba, K. Bin, P. Zhu, G. Ren, W. Tan, B. Tosini, G. He, X. Li, T. Yin, Y. 2019-09-08 doi:10.1101/760421 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ In Vivo Neuroregeneration to Treat Ischemic Stroke in Adult Non-Human Primate Brains through NeuroD1 AAV-based Gene Therapy ]]> https://biorxiv.org/content/10.1101/816066v1?rss=1 Ge, L. Yang, F. Feng, J. Chen, N. Jiang, M. Wang, J. Hu, X. Chen, G. 2019-11-01 doi:10.1101/816066 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Increasing vitrification temperature improves the cryo-electron microscopy reconstruction ]]> https://biorxiv.org/content/10.1101/824698v1?rss=1 Shi, H. Wu, C. Zhu, D. Zhang, X. 2019-10-30 doi:10.1101/824698 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ MeSHHeading2vec: A new method for representing MeSH headings as feature vectors based on graph embedding algorithm ]]> https://biorxiv.org/content/10.1101/835637v1?rss=1 Guo, Z.-H. You, Z.-H. Yi, H.-C. Zheng, K. Yanbin, W. 2019-11-14 doi:10.1101/835637 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ GNMFLMI: Graph Regularized Nonnegative Matrix Factorization for Predicting LncRNA-MiRNA Interactions ]]> https://biorxiv.org/content/10.1101/835934v1?rss=1 wang, m. You, Z.-H. li, l. wong, L. chen, z. gan, c. 2019-11-09 doi:10.1101/835934 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Prediction of liquid-liquid phase separation proteins using machine learning ]]> https://biorxiv.org/content/10.1101/842336v1?rss=1 Sun, T. Li, Q. Xu, Y. Zhang, Z. Lai, L. Pei, J. 2019-11-15 doi:10.1101/842336 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Biomarker2vec: Attribute- and Behavior-driven Representation for Multi-type Relationship Prediction between Various Biomarkers ]]> https://biorxiv.org/content/10.1101/849760v1?rss=1 Guo, Z.-H. You, Z.-H. Yanbin, W. Yi, H.-C. 2019-11-21 doi:10.1101/849760 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ A muscle hypertrophy-derived myokine reprograms the stromal vascular fractions differentiation towards thermogenic adipocytes in subcutaneous adipose tissue ]]> https://biorxiv.org/content/10.1101/2023.09.20.558627v1?rss=1 View larger version (63K): org.highwire.dtl.DTLVardef@1178e6org.highwire.dtl.DTLVardef@1184d4eorg.highwire.dtl.DTLVardef@7b592aorg.highwire.dtl.DTLVardef@1b0b03_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBambi, a direct target gene of HIF2 in skeletal muscle, when deleted, triggers muscle hypertrophy and the transformation of white into beige adipocytes, improving systemic energy metabolism. C_LIO_LIThe metabolic reprogramming of stromal vascular fractions (SVFs) contributes to the observed improvements in energy metabolism and adipocyte hyperplasia. C_LIO_LIThbs4, a novel myokine produced in skeletal muscle during hypertrophy and aerobic exercise, plays a key role in the transformation of white into beige adipocytes. C_LIO_LIOverexpression of Thbs4 provides enduring protection against high-fat diet (HFD)-induced metabolic disorders, demonstrating its potential as a therapeutic target. C_LIO_LIThbs4 deletion abrogates the beneficial metabolic reprogramming of SVFs and exacerbates HFD-induced metabolic syndromes, further underlining its crucial role in metabolic regulation. C_LI ]]> Yao, X. Mai, X. Tian, Y. Liu, Y. Jin, G. Li, Z. Chen, S. Dai, X. Jin, X. Huang, L. Han, M. Fan, Z. Xiao, L. Pan, G. Pan, X. Lin, Z. Li, X. Sun, J. Ou, J. Chen, H. Xie, L. 2023-09-22 doi:10.1101/2023.09.20.558627 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ ER mediates spatial regulation of lysosome-endosome interactions via motion switch at junction sites ]]> https://biorxiv.org/content/10.1101/2023.09.23.558934v1?rss=1 Li, W. Qiu, M. Zhang, Y. Guo, Y. Yang, Y. Hu, J. Yang, G. 2023-09-23 doi:10.1101/2023.09.23.558934 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Genome-wide characterization of MLO family genes in bread wheat shed light on their role in powdery mildew, rusts, blight, abiotic stresses, and development ]]> https://biorxiv.org/content/10.1101/2023.09.22.559087v1?rss=1 Hussain, B. Ramzan, H. Raza, Q. Atif, R. M. Budak, H. Ghazy, A.-H. I. 2023-09-24 doi:10.1101/2023.09.22.559087 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity ]]> https://biorxiv.org/content/10.1101/2023.09.25.559159v1?rss=1 Zheng, L. Yang, T. Guo, H. Qi, C. Lu, Y. Xiao, H. Gao, Y. Liu, Y. Yang, Y. Zhou, M. Nguyen, H. Zhu, Y. Sun, F. Zhang, C.-Y. Ji, X. 2023-09-26 doi:10.1101/2023.09.25.559159 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ High plasticity of ribosomal DNA organization in budding yeast ]]> https://biorxiv.org/content/10.1101/2023.09.26.559284v1?rss=1 Jiang, S. Cai, Z. Wang, Y. Zeng, C. Zhang, J. Yu, W. Su, C. Zhao, S. Chen, Y. Shen, Y. Ma, Y. Cai, Y. Dai, J. 2023-09-26 doi:10.1101/2023.09.26.559284 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ SARS-CoV-2 Omicron BA.2.86: less neutralization evasion compared to XBB sub-variants ]]> https://biorxiv.org/content/10.1101/2023.09.26.559580v1?rss=1 30 additional mutations on S protein. Compared to XBB sub-variants, BA.2.86 does not display more resistance to the neutralizing responses induced by ZF2001-vaccination, BF.7/BA.5.2 breakthrough infection or a booster dose of ZF2202-A-vaccination. In addition, the mouse experiment results showed that BQ.1.1-XBB.1.5 RBD-heterodimer and XBB.1.5 RBD-homodimer induced high neutralizing responses against XBB sub-variants and BA.2.86, indicating that next-generation COVID-19 vaccine should be developed to enhance the protection efficacy against the circulating strains in the future. ]]> An, Y. Zhou, X. Tao, L. Xie, H. Li, D. Wang, R. Hu, H. Xu, Z. Dai, L. Xu, K. Gao, G. F. 2023-09-27 doi:10.1101/2023.09.26.559580 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Light management by algal aggregates in living photosynthetic hydrogels. ]]> https://biorxiv.org/content/10.1101/2023.09.28.559714v1?rss=1 Chua, S. T. Smith, A. Murthy, S. Murace, M. Yang, H. Kuhl, M. Cicuta, P. Smith, A. G. Wangpraseurt, D. Vignolini, S. 2023-09-28 doi:10.1101/2023.09.28.559714 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Efficient inhibition of fusion inhibitor HY3000 peptide to SARS-CoV-2 emerging EG.5, EG.5.1 and BA.2.86 variants ]]> https://biorxiv.org/content/10.1101/2023.09.28.559747v1?rss=1 Wu, L. Zheng, A. Tang, Y. Wang, X. Gao, Y. Lei, W. Wu, G. Wang, Q. Gao, G. F. 2023-09-28 doi:10.1101/2023.09.28.559747 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Novel Epidermal Oxysterols Function as Alarm Substances in Zebrafish ]]> https://biorxiv.org/content/10.1101/2023.09.26.559639v1?rss=1 Li, Y. Yan, Z. Lin, A. Yang, X. Li, X. Yin, X. Li, W. Li, K. 2023-09-29 doi:10.1101/2023.09.26.559639 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Spatially Resolved Gene Expression is Not Necessary for Identifying Spatial Domains ]]> https://biorxiv.org/content/10.1101/2023.10.15.562443v1?rss=1 Lin, S. Zhao, Y. Yuan, Z. 2023-10-18 doi:10.1101/2023.10.15.562443 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ A peptide-centric local stability assay to unveil protein targets of diverse ligands ]]> https://biorxiv.org/content/10.1101/2023.10.17.562693v1?rss=1 Li, K. Chen, S. Wang, K. Wang, Y. Fang, Z. Lyu, J. Zhu, H. Li, Y. Yu, T. Yang, F. Zhang, X. Guo, S. Ruan, C. Zhou, J. Wang, Q. Luo, C. Ye, M. 2023-10-19 doi:10.1101/2023.10.17.562693 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ A deep learning model embedded framework to distinguish DNA and RNA mutations directly from RNA-seq ]]> https://biorxiv.org/content/10.1101/2023.10.17.562625v1?rss=1 Fu, Z.-C. Gao, B.-Q. Nan, F. Ma, X.-K. Yang, L. 2023-10-20 doi:10.1101/2023.10.17.562625 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages ]]> https://biorxiv.org/content/10.1101/2023.10.21.563433v1?rss=1 Bozic, A. Podgornik, R. 2023-10-23 doi:10.1101/2023.10.21.563433 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Spatiotemporal Profiling Unveiling the Cellular Organization Patterns and Local Protumoral Immune Microenvironment Remodeling in Early Lung Adenocarcinoma Progression ]]> https://biorxiv.org/content/10.1101/2023.10.29.564580v1?rss=1 Chen, H. Peng, Y. Li, Y. Zheng, Q. Zhao, Y. Liu, P. Wu, Z. Wo, Y. Hong, H. Sun, Y. Shao, Z. 2023-11-01 doi:10.1101/2023.10.29.564580 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Targeted Deletion of All Known Thyroid Hormone Receptors Causes Maturation Retardation and Early-onset Degeneration of Cochlear Outer Sulcus ]]> https://biorxiv.org/content/10.1101/2023.10.31.565054v1?rss=1 Ma, X. Jiang, F. Han, S. Zhang, Y. Sun, L. Qu, J. Yin, H. Chen, Y. Tang, J. He, D. Z. Z. Zhang, W. J. Xie, Z. 2023-11-02 doi:10.1101/2023.10.31.565054 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ FFCM-MRF: An accurate and generalizable cerebrovascular segmentation pipeline for humans and rhesus monkeys based on TOF-MRA ]]> https://biorxiv.org/content/10.1101/2023.11.07.566142v1?rss=1 Cui, Y. Huang, H. Liu, J. Zhao, M. Li, C. Han, X. Luo, N. Gao, J. Yan, D. Zhang, C. Jiang, T. Yu, S. 2023-11-11 doi:10.1101/2023.11.07.566142 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Fusion dynamics and size-dependent droplet microstructure in ssDNA mediated protein phase separation ]]> https://biorxiv.org/content/10.1101/2023.11.13.566798v1?rss=1 Bian, Y. Li, W. 2023-11-13 doi:10.1101/2023.11.13.566798 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ TranSiGen: Deep representation learning of chemical-induced transcriptional profile ]]> https://biorxiv.org/content/10.1101/2023.11.12.566777v1?rss=1 Tong, X. Qu, N. Kong, X. Ni, S. Wang, K. Zhang, L. Wen, Y. Zhang, S. Li, X. Zheng, M. 2023-11-15 doi:10.1101/2023.11.12.566777 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ SCC3 acts as the cohesin and inhibits inter-sister chromatids repair during rice meiosis ]]> https://biorxiv.org/content/10.1101/2023.11.22.568373v1?rss=1 Zhao, Y. Ren, L. Zhao, T. You, H. Miao, Y. Liu, H. Cao, L. Wang, B. Shen, Y. Li, Y. Tang, D. Cheng, Z. 2023-11-23 doi:10.1101/2023.11.22.568373 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ De novo design and optimization of aptamers with AptaDiff ]]> https://biorxiv.org/content/10.1101/2023.11.25.568693v1?rss=1 Wang, Z. Liu, Z. Zhang, W. Li, Y. Feng, Y. Lv, S. Diao, H. Luo, Z. Yan, P. He, M. Li, X. 2023-11-26 doi:10.1101/2023.11.25.568693 Cold Spring Harbor Laboratory Press 2023-11-26 <![CDATA[ The receptor VLDLR binds East Equine Encephalitis virus through multiple distinct modes ]]> https://biorxiv.org/content/10.1101/2023.11.30.569340v1?rss=1 Cao, D. Ma, B. Cao, Z. Xu, X. Zhang, X. Xiang, Y. 2023-11-30 doi:10.1101/2023.11.30.569340 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ CpG Island Definition and Methylation Mapping of the T2T-YAO Genome ]]> https://biorxiv.org/content/10.1101/2023.12.02.568720v1?rss=1 Xiao, M. Wei, R. Yu, J. Gao, C. Yang, F. Zhang, L. 2023-12-02 doi:10.1101/2023.12.02.568720 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ Spatially resolved molecular and cellular atlas of the mouse brain ]]> https://biorxiv.org/content/10.1101/2023.12.03.569501v1?rss=1 Han, L. Liu, Z. Jing, Z. Liu, Y. Chang, H. Lei, J. Peng, Y. Wang, K. Xu, Y. Liu, W. Wu, Z. Li, Q. Shi, X. Zheng, M. Wang, H. Deng, J. Zhong, Y. Pan, H. Lin, J. Zhang, R. Chen, Y. Wu, J. Xu, M. Ren, B. Cheng, M. Yu, Q. Song, X. Lu, Y. Tang, Y. Yuan, N. Sun, S. An, Y. Ding, W. Sun, X. Wei, Y. Zhang, S. Dou, Y. Zhao, Y. Han, L. Zhu, Q. Xu, J. Wang, S. Chen, H. Wang, D. Bai, Y. Liang, Y. Liu, Y. Chen, M. Xie, C. Bo, B. Li, M. Zhang, X. Ting, W. Chen, Z. Fang, J. Li, S. Jiang, Y. Tan, X. Zuo, G. Xie, Y. Li, H. Tao, Q. Li, Y. Liu, J. Li 2023-12-05 doi:10.1101/2023.12.03.569501 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ A novel nested gene Aff3ir participates in vascular remodelling by enhancing endothelial cell differentiation in mice ]]> https://biorxiv.org/content/10.1101/2023.12.09.570916v1?rss=1 Zhao, Y. Ehteramyan, M. Li, Y. Bai, X. Huang, L. Gao, Y. Angbohang, A. Yang, X. Lynham, S. Margariti, A. Shah, A. Tao, Y. Cai, T. Li, T. Zhang, M. Zeng, L. 2023-12-10 doi:10.1101/2023.12.09.570916 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ Structure basis for recognition of 26RFa by the pyroglutamylated RFamide peptide receptor ]]> https://biorxiv.org/content/10.1101/2023.12.09.570933v1?rss=1 Jin, S. Li, X. Xu, Y. Guo, S. Wu, C. Pan, B. Xin, W. Zhang, H. Hu, W. Yin, Y. Zhang, T. Wu, K. Yuan, Q. Xu, H. E. Xie, X. Jiang, Y. 2023-12-10 doi:10.1101/2023.12.09.570933 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ Cytochrome P450 Enzyme Design by Constraining Catalytic Pocket in Diffusion model ]]> https://biorxiv.org/content/10.1101/2024.01.08.574609v1?rss=1 Wang, Q. Liu, X. Zhang, H. Chu, H. Shi, C. Chang, Z. Cheng, J. Jiang, H. 2024-01-08 doi:10.1101/2024.01.08.574609 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ The stability of lower genital tract microbiota correlates with reproductive system function and in vitro fertilization and frozen embryo transfer outcomes in women with polycystic ovarian syndrome ]]> https://biorxiv.org/content/10.1101/2024.01.18.576212v1?rss=1 Tu, Y. Huang, H. Jin, L. Zhang, Y. Chen, H. Wei, B. Ge, Y. Ding, G. Dong, X. Sheng, J. 2024-01-22 doi:10.1101/2024.01.18.576212 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Engineered minimal type I CRISPR-Cas system for transcriptional activation and base editing in human cells ]]> https://biorxiv.org/content/10.1101/2024.01.26.577312v1?rss=1 Guo, J. Gong, L. Yu, H. Li, M. Liu, Z. Fan, S. Yang, C. Zhao, D. Han, J. Xiang, H. 2024-01-26 doi:10.1101/2024.01.26.577312 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[ Architecture of the spinach plastid-encoded RNA polymerase ]]> https://biorxiv.org/content/10.1101/2024.02.16.580782v1?rss=1 Wang, T. Wang, G. Fang, Y. Zhang, Y. Peng, W. Zhou, Y. Zhang, A. Yu, L.-J. Lu, C. 2024-02-17 doi:10.1101/2024.02.16.580782 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ The ZmHSF20-ZmHSF4-ZmCesA2 module regulates heat stress tolerance in maize ]]> https://biorxiv.org/content/10.1101/2024.02.21.581499v1?rss=1 Li, Z. Li, Z. Ji, Y. Wang, C. Wang, S. Shi, Y. Le, J. Zhang, M. 2024-02-23 doi:10.1101/2024.02.21.581499 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Platinum drug reprogramming of protein phosphorylation ]]> https://biorxiv.org/content/10.1101/2024.02.28.582513v1?rss=1 1.5. Surprisingly, bioinformatics analysis demonstrates that cisplatin targets the majority of human protein kinase and phosphatase genes and involved in 300 core signalling pathways (-log p >4). The most associated key signalling pathways are sperm motility and protein kinase A. The highest related disease is cancer, and tissue toxicities related to CDGs are about hepato- and nephro- toxicities. Notably, cisplatin damaged 85% (440) of human protein kinase genes and 81% (110) of human protein phosphatase genes. This suggests that cisplatin acts as a multi-targeting protein-phosphorylation regulator, confirmed by a significant decrease in expression of a series of key protein kinase genes. These results reveal that cisplatin disrupts protein phosphorylation signalling genome-wide. Key points summarising the key messages of your articleA total of 16216 genes damaged by the clinical drug cisplatin in human lung cancer cells were identified using a forward chemical genetics method. Bioinformatics analysis revealed that cisplatin targets 85% of protein kinase and 81% of phosphatase genes. Cisplatin acts as a multi-targeting protein-phosphorylation regulator, disrupting protein phosphorylation signalling genome-wide. The disturbance of protein phosphorylation by cisplatin can be related to anticancer activity and tissue toxicities of the drug. These findings suggests novel strategies for rational design of next-generation anticancer metallodrugs involving specific targeting of protein phosphorylation. ]]> Qi, L. Hou, Y. Luo, Q. Liu, X. Zhang, Y. Jia, F. Fang, T. Zhao, Y. Wang, F. Xu, Y. Li, X. Yu, W. Wang, S. Xin, B. Sadler, P. 2024-03-02 doi:10.1101/2024.02.28.582513 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ CMTM6 maintains B cell intrinsic CD40 expression to regulate anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2024.03.05.583639v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@7639cdorg.highwire.dtl.DTLVardef@1ccddaaorg.highwire.dtl.DTLVardef@ecc9f3org.highwire.dtl.DTLVardef@1be8cb0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic AbstractsC_FLOATNO C_FIG The essential role of B cells and B cell intrinsic molecules in tumor immunity is beginning to be recognized. Tumor cell CMTM6 is a novel tumor immunoregulator involved in maintaining membrane levels of several important molecules, such as PD-L1 and CD58. Host CMTM6 may also play a function in the tumor microenvironment. Here, we found that CMTM6 was highly expressed in splenic B cells and tumor-infiltrating B cells. CMTM6 deficiency resulted in impaired splenic development, germinal center B cell differentiation, memory B cell differentiation, T/B cell interaction and B cell anti-tumor immune responses. Through multi-omics data mining and B-cell agonist screening, we identified that CMTM6 interacted with CD40 and maintained CD40 membrane levels in B cells. CMTM6 cis-interacts with CD40 and inhibits ubiquitin/proteasome-mediated CD40 degradation. CMTM6 deficiency led to impaired CD40 signaling-mediated B cell activation, survival, proliferation, differentiation and T/B cell interaction. In vivo, CMTM6 deficiency leads to a significant decrease in the anti-tumor activity of ICB therapy and B cell-dependent CD40 agonists. Collectively, B-cell intrinsic CMTM6 maintains B cell CD40 levels and signaling to promote B cell function and anti-tumor immunity. ]]> Long, Y. Chen, R. Chang, W. Luo, H. Li, F. Sun, J. Chen, J. Gong, L. 2024-03-10 doi:10.1101/2024.03.05.583639 Cold Spring Harbor Laboratory Press 2024-03-10 <![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[ Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA ]]> https://biorxiv.org/content/10.1101/2024.03.11.584023v1?rss=1 33-fold decreases in runtime of PAS computation and further identified reliable and interpretable multicellular pathway modules that capture the transcriptomic features of CRC tumor status and transcriptional abnormalities in lupus patients, respectively. ]]> Huang, Z. Zheng, Y. Wang, W. Zhou, W. Wei, C. Zhang, X. Jin, X. Yin, J. 2024-03-13 doi:10.1101/2024.03.11.584023 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Soil viruses reduce greenhouse gas emissions and promote microbial necromass accrual ]]> https://biorxiv.org/content/10.1101/2024.03.13.584929v1?rss=1 Liang, X. Sun, S. Zhong, Y. Zhang, Y. Wang, S. Wang, Y. Xie, N. Yang, L. Radosevich, M. 2024-03-14 doi:10.1101/2024.03.13.584929 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ LncRNA-Snhg3 Aggravates Hepatic Steatosis by Regulating PPARγ via SND1/H3K27me3 ]]> https://biorxiv.org/content/10.1101/2024.03.22.586335v1?rss=1 Xie, X. Gao, M. Zhao, W. Li, C. Zhang, W. Yang, J. Zhang, Y. Chen, E. Guo, Y. Guo, Z. Zhang, M. Ngowi, E. E. Wang, H. Wang, X. Zhu, Y. Wang, Y. Li, X. Yao, H. Yan, L. Fang, F. Li, M. Qiao, A. Liu, X. 2024-03-23 doi:10.1101/2024.03.22.586335 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ Proteome analysis provides insights into sex differences in Holothuria Scabra ]]> https://biorxiv.org/content/10.1101/2024.03.26.586852v1?rss=1 Cheng, C. Wu, F. Xu, Y. Ren, C. Chen, T. Li, S. Shen, P. Jiang, F. 2024-03-27 doi:10.1101/2024.03.26.586852 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Extracellular electron transfer drives efficient H2-independent methylotrophic methanogenesis by Methanomassiliicoccus, a seventh order methanogen ]]> https://biorxiv.org/content/10.1101/2024.03.29.587405v1?rss=1 Li, L. Tian, X. Wang, X. Chen, C. Qi, L. Zhou, Q. Li, J. Xue, K. Zhao, F. Wang, Y. Dong, X. 2024-04-02 doi:10.1101/2024.03.29.587405 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ An interpretable integration model improving disease-free survival prediction for gastric cancer based on CT images and clinical parameters ]]> https://biorxiv.org/content/10.1101/2024.04.01.587508v1?rss=1 Cen, X. Hu, C. Yuan, L. Yang, H. Cheng, X. Dong, W. Tong, Y. 2024-04-02 doi:10.1101/2024.04.01.587508 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Tonotopic organization of auditory cortex in awake marmosets revealed by multi-modal wide-field optical imaging ]]> https://biorxiv.org/content/10.1101/2024.04.05.588237v1?rss=1 Song, X. Guo, Y. Chen, C. Lee, J. H. Wang, X. 2024-04-10 doi:10.1101/2024.04.05.588237 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ AncestryPainter 2.0: Visualizing ancestry composition and admixture history graph ]]> https://biorxiv.org/content/10.1101/2024.04.08.588394v1?rss=1 Chen, S. Lei, C. Zhao, X. Pan, Y. Lu, D. Xu, S. 2024-04-09 doi:10.1101/2024.04.08.588394 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ PAMPHLET: A Robust Toolkit for Precise PAM Prediction and Unveiling PAM Consistency in Highly Co-occurrence CRISPR-Cas Systems ]]> https://biorxiv.org/content/10.1101/2024.04.09.587696v1?rss=1 Qi, C. Shen, X. Li, B. Liu, C. Huang, L. Lan, H. Chen, D. Jiang, Y. Wang, D. 2024-04-09 doi:10.1101/2024.04.09.587696 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ A generalized framework to identify SARS-CoV-2 broadly neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2024.04.16.589454v1?rss=1 Jian, F. Wec, A. Z. Feng, L. Yu, Y. Wang, L. Wang, P. Yu, L. Wang, J. Hou, J. Berrueta, D. M. Lee, D. Speidel, T. Ma, L. Kim, T. Yisimayi, A. Song, W. Wang, J. Liu, L. Yang, S. Niu, X. Xiao, T. An, R. Wang, Y. Shao, F. Wang, Y. Pecetta, S. Wang, X. Walker, L. M. Cao, Y. 2024-04-18 doi:10.1101/2024.04.16.589454 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Knowledge Graph-based Thought: a knowledge graph enhanced LLMs framework for pan-cancer question answering ]]> https://biorxiv.org/content/10.1101/2024.04.17.589873v1?rss=1 Feng, Y. Zhou, L. Zheng, Y. He, R. Ma, C. Li, Y. 2024-04-20 doi:10.1101/2024.04.17.589873 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Amblyopic deficits in monocular processing and binocular interactions revealed by submillimeter 7T fMRI and EEG frequency tagging ]]> https://biorxiv.org/content/10.1101/2024.04.25.591076v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@c174d8org.highwire.dtl.DTLVardef@de51eborg.highwire.dtl.DTLVardef@1d443c0org.highwire.dtl.DTLVardef@ac267a_HPS_FORMAT_FIGEXP M_FIG C_FIG This figure illustrates the precise neural deficits of amblyopia in monocular processing and binocular interactions based on the main findings of the current study. Attenuated and delayed neural activity arises from V1 cortical layers receiving thalamic input in monocular processing, followed by imbalanced binocular suppression and weakened binocular integration in the superficial layers, further reducing visual signal strength and processing speed. ]]> Wang, Y. Qian, C. Gao, Y. Zhou, Y. Zhang, X. Wen, W. Zhang, P. 2024-04-28 doi:10.1101/2024.04.25.591076 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ The under-recognized dominance of magnetosome gene cluster-containing bacteria in oxygen-stratified freshwater ecosystems ]]> https://biorxiv.org/content/10.1101/2024.04.27.591411v1?rss=1 Ji, R. Wan, J. Goswami, P. Shen, J. Pan, Y. Lin, W. 2024-04-27 doi:10.1101/2024.04.27.591411 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Haplotype-resolved genomes and population genetics to analyze glandular secretory trichome formation mechanism in oregano ]]> https://biorxiv.org/content/10.1101/2024.04.30.591903v1?rss=1 Sun, M. Miao, J. Liu, N. Zhang, Y. Zhang, J. Wang, D. Xia, F. Bai, H. Li, H. Shi, L. 2024-05-03 doi:10.1101/2024.04.30.591903 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Multi-omics Reveals Immune Response and Metabolic Profiles during High-Altitude Mountaineering ]]> https://biorxiv.org/content/10.1101/2024.05.03.592361v1?rss=1 Yin, J. Lv, J. Yang, S. Wang, Y. Huang, Z. Wang, X. Hou, G. Zhou, W. Liu, Y. Wang, W. Lin, X. Huang, Y. Zheng, Y. Wei, C. Yuan, Y. Huang, Y. Liu, C. Tao, H. Liu, H. Liu, R. Zhang, Y. Zeng, G. Gao, P. Liu, L. Cao, J. Liu, C. Jin, X. Wang, J. 2024-05-07 doi:10.1101/2024.05.03.592361 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Non-structural Proteins Inhibitors ]]> https://biorxiv.org/content/10.1101/2024.05.08.593105v1?rss=1 Lu, X. Hu, H. Mei, L. Wang, X. Xiong, L. Zhu, Y. Liu, S. Zhao, W. Mengnisa, S. Li, L. Lin, X. Liu, J. Wang, X. Duan, Z. Lu, W. Suo, Y. Wu, X. Cui, M. Yue, J. Xu, Y. 2024-05-08 doi:10.1101/2024.05.08.593105 Cold Spring Harbor Laboratory Press 2024-05-08 <![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[ Interleukin-1 prevents SARS-CoV-2-induced membrane fusion to restrict viral transmission via induction of actin bundles ]]> https://biorxiv.org/content/10.1101/2024.05.16.594569v1?rss=1 Zheng, X. Yu, S. Zhou, Y. Yu, K. Gao, Y. Chen, M. Duan, D. Li, Y. Cui, X. Mou, J. Yang, Y. Wang, X. Chen, M. Jiu, Y. Zhao, J. Meng, G. 2024-05-17 doi:10.1101/2024.05.16.594569 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ RNADiffFold: Generative RNA Secondary Structure Prediction using Discrete Diffusion Models ]]> https://biorxiv.org/content/10.1101/2024.05.28.596177v1?rss=1 Feng, Y. Wang, Z. Tian, Q. Liu, Z. Yan, P. Li, X. 2024-06-02 doi:10.1101/2024.05.28.596177 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Structures of PSI-FCPI from Thalassiosira pseudonana in high light provide convergent evolution and light-adaptive strategies in diatom FCPIs ]]> https://biorxiv.org/content/10.1101/2024.05.30.596378v1?rss=1 Feng, Y. Li, Z. Yang, Y. Shen, L. Li, X. Liu, X. Zhang, X. Zhang, J. Ren, F. Wang, Y. Liu, C. Han, G. Wang, X. Kuang, T. Shen, J.-R. Wang, W. 2024-06-02 doi:10.1101/2024.05.30.596378 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Comparative Analysis of Human-Chimpanzee Divergence in Brain Connectivity and its Genetic Underpinnings ]]> https://biorxiv.org/content/10.1101/2024.06.03.597252v1?rss=1 Wang, Y. Cheng, L. Li, D. Lu, Y. Wang, C. Wang, Y. Gao, C. Wang, H. Vanduffel, W. Hopkins, W. Sherwood, C. Jiang, T. Chu, C. Fan, L. 2024-06-04 doi:10.1101/2024.06.03.597252 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ A nanobody-enzyme fusion protein targeting PD-L1 and sialic acid exerts anti-tumor effects by affecting tumor associated macrophages ]]> https://biorxiv.org/content/10.1101/2024.06.05.597674v1?rss=1 Tong, Y. Lu, X. Chen, R. Chen, C. Sun, G. Yu, X. Lyu, S. Feng, M. Long, Y. Gong, L. CHEN, L. 2024-06-09 doi:10.1101/2024.06.05.597674 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Viral diversiy within marine biofilms and their potential roles in microbially influenced corrosion ]]> https://biorxiv.org/content/10.1101/2024.06.11.598143v1?rss=1 Li, C. Zhang, Y. Jiang, S. Shi, W. Peng, Y. Han, Y. Dong, X. Zhang, R. 2024-06-11 doi:10.1101/2024.06.11.598143 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Uncovering topologically associating domains from three-dimensional genome maps with TADGATE ]]> https://biorxiv.org/content/10.1101/2024.06.12.598668v1?rss=1 Dang, D. Zhang, S.-W. Dong, K. Duan, R. Zhang, S. 2024-06-14 doi:10.1101/2024.06.12.598668 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Dopamine D1 receptor expression in dlPFC inhibitory parvalbumin neurons may contribute to higher visuospatial distractibility in marmosets versus macaques ]]> https://biorxiv.org/content/10.1101/2024.06.15.599163v1?rss=1 Joyce, M. K. P. Ivanov, T. G. Krienen, F. Mitchell, J. Ma, S. Inoue, W. Nandy, A. P. Datta, D. Duque, A. Arellano, J. I. Gupta, R. Gonzalez-Burgos, G. Lewis, D. A. Sestan, N. McCarroll, S. A. Martinez-Trujillo, J. C. Froudist-Walsh, S. Arnsten, A. F. 2024-06-16 doi:10.1101/2024.06.15.599163 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Decoding the anti-aging effect of retinol in reshaping the human skin microbiome niches ]]> https://biorxiv.org/content/10.1101/2024.06.26.600860v1?rss=1 Gui, M. Cheng, J. Lin, X. Guo, D. Zhou, Q. Ma, W. Yang, H. Chen, X. Liu, Z. Ma, L. Xing, X. Shu, P. Liu, X. 2024-06-27 doi:10.1101/2024.06.26.600860 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Cost-effective DNA storage with DNA movable type ]]> https://biorxiv.org/content/10.1101/2024.07.17.603163v1?rss=1 Wang, C. Wei, D. Wei, Z. Yang, D. Xing, J. Wang, Y. Wang, X. Wang, P. Ma, G. Zhang, X. Li, H. Tang, C. Hou, P. Wang, J. Gao, R. Xie, G. Li, C. Ju, Y. Wang, P. Yue, L. Zhao, Y. Sheng, Y. Xiao, J. Niu, H. Xu, S. Duan, B. Bu, D. Tan, G. Chen, F. 2024-07-19 doi:10.1101/2024.07.17.603163 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Stiffness-tunable neurotentacles for minimally invasive implantation and long-term neural activity recordings ]]> https://biorxiv.org/content/10.1101/2024.07.21.604464v1?rss=1 Wang, Y. Xu, X. Yang, X. Tang, R. Chen, Y. Wang, Y. Liang, J. Pei, W. 2024-07-23 doi:10.1101/2024.07.21.604464 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Segmentation and Feature Extraction of Fingernail Plate and Lunula Based on Deep Learning ]]> https://biorxiv.org/content/10.1101/2024.07.26.605289v1?rss=1 Fan, Y. You, M. Ge, J. Zhai, G. Wang, S. 2024-07-26 doi:10.1101/2024.07.26.605289 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Unraveling the Web of Life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species ]]> https://biorxiv.org/content/10.1101/2024.07.29.605463v1?rss=1 Jin, Z. Lin, X. Ma, D. Hodel, R. G. J. Zhao, L. Ren, C. Duan, L. Xu, C. Wu, J. Liu, B. 2024-07-30 doi:10.1101/2024.07.29.605463 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Intraperitoneal programming of tailored CAR macrophages via mRNA-LNP to boost cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.07.30.605730v1?rss=1 Gu, K. Liang, T. Hu, L. Zhao, Y. Ying, W. Zhang, M. Chen, Y. Liang, B. Lin, X. Zhang, Y. Wu, H. Wang, M. Zhu, Y. Wang, W. Zhang, Y. Zuo, C. Du, Z. Zhang, P. Song, J. Liu, X. Xie, S. Tan, W. 2024-07-30 doi:10.1101/2024.07.30.605730 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ GageTracker: a tool for dating gene age by micro- and macro-synteny with high speed and accuracy ]]> https://biorxiv.org/content/10.1101/2024.08.28.610050v1?rss=1 Fang, C. Dong, C. Wang, C. Xiong, F. Lu, S. Fang, W. Li, T. Gan, X. Yang, L. Zeng, H. He, S. 2024-08-29 doi:10.1101/2024.08.28.610050 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL ]]> https://biorxiv.org/content/10.1101/2024.09.02.610893v1?rss=1 Shang, H. Jia, K. Zhou, M. Yang, H. Ma, Y. Zhang, R. 2024-09-03 doi:10.1101/2024.09.02.610893 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2 ]]> https://biorxiv.org/content/10.1101/2024.09.03.610799v1?rss=1 Feng, L. Sun, Z. Zhang, Y. Jian, F. Yang, S. Yu, L. Wang, J. Shao, F. Wang, X. Cao, Y. 2024-09-04 doi:10.1101/2024.09.03.610799 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Contrasting patterns of specificity and transfer in human odor discrimination learning ]]> https://biorxiv.org/content/10.1101/2024.09.10.612215v1?rss=1 Chang, X. Tan, H. Niu, J. Yuan, K. Chen, R. Zhou, W. 2024-09-14 doi:10.1101/2024.09.10.612215 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Intra-hypothalamic circuit orchestrates β-endorphin release following coital ejaculation in male mice ]]> https://biorxiv.org/content/10.1101/2024.09.18.613624v1?rss=1 Zha, X. Jiao, Z. Li, S.-S. Liu, X.-Y. Li, X.-Y. Sun, Y.-Z. Ding, X.-J. Gao, M.-T. Gao, S.-C. Chen, A.-X. Lin, J.-K. Zhang, W. Cao, X.-Z. Zhang, Y.-L. Yang, R.-R. Xu, C. Xu, X.-H. 2024-09-19 doi:10.1101/2024.09.18.613624 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ DNFE: Directed-network flow entropy for detecting the tipping points during biological processes ]]> https://biorxiv.org/content/10.1101/2024.09.18.613673v1?rss=1 Peng, X. Li, P. Chen, L. 2024-09-19 doi:10.1101/2024.09.18.613673 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Tetanizing wakeful consolidation: ten-hertz repetitive visual stimulation enhances the offline gain of visual learning ]]> https://biorxiv.org/content/10.1101/2024.09.20.614122v1?rss=1 Yang, X.-Y. Zhao, C. Zuo, Z. Li, A. Luo, H. He, Q. Fang, F. 2024-09-20 doi:10.1101/2024.09.20.614122 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ IgGM: A Generative Model for Functional Antibody and Nanobody Design ]]> https://biorxiv.org/content/10.1101/2024.09.19.613838v1?rss=1 Wang, R. Wu, F. Gao, X. Wu, J. Zhao, P. Yao, J. 2024-09-22 doi:10.1101/2024.09.19.613838 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Adaptive immunity shapes innate and epithelial cell landscapes by silencing tonic IFN-gamma in innate lymphoid cells during homeostasis. ]]> https://biorxiv.org/content/10.1101/2024.09.19.613869v1?rss=1 Mejri, O. Ma, L. Aoudi, A. Labiad, O. Mondot, S. IGALOUZENE, R. Codan, C. Hernandez-Vargas, H. Rousseaux, N. Lapaque, N. Paul, S. Walzer, T. Marie, J. C. Soudja, S. 2024-09-22 doi:10.1101/2024.09.19.613869 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ snCED-seq: High-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues ]]> https://biorxiv.org/content/10.1101/2024.09.20.614201v1?rss=1 yunxia, G. Junjie, M. Ruicheng, Q. Wang, G.-Z. Zhao, X. 2024-09-24 doi:10.1101/2024.09.20.614201 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Exploring the Biological Mechanisms of Severe COVID-19 in the Elderly: Insights from an Aged Mouse Model ]]> https://biorxiv.org/content/10.1101/2024.09.24.614691v1?rss=1 Ma, L. Lin, X. Xu, M. Ke, X. Di, L. Chen, Q. 2024-09-25 doi:10.1101/2024.09.24.614691 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Diverse defense systems synergistically drive the microbe-virus arms race in deep sea cold seeps ]]> https://biorxiv.org/content/10.1101/2024.09.26.614923v1?rss=1 Han, Y. Liao, J. Li, C. Xing, F. Peng, J. Liu, X. Xie, W. Wu, F. Jian, H. Cheng, R. Dong, X. 2024-09-26 doi:10.1101/2024.09.26.614923 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ FishCODE: a web-based information platform for comprehensive omics data exploration in fish research ]]> https://biorxiv.org/content/10.1101/2024.09.25.614839v1?rss=1 Li, H. Zhang, W. Ren, K. Yang, H. Zhang, L. Younas, W. Cheng, Y. Wang, Y. Shi, M. Xia, X.-Q. 2024-09-27 doi:10.1101/2024.09.25.614839 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ C-Reactive Protein Drives Potent Clearance of Blood Bacteria in the Liver by Activating the Complement System ]]> https://biorxiv.org/content/10.1101/2024.10.05.616753v1?rss=1 Chen, D. Hu, J. Zhu, M. Xie, Y. Yao, H. An, H. Meng, Y. Wang, J. Huang, X. Shao, Z. Xiang, Y. Qi, J. Gao, G. F. Zhang, J.-R. 2024-10-05 doi:10.1101/2024.10.05.616753 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Mechanical control of germ cell specification in Arabidopsis anthers ]]> https://biorxiv.org/content/10.1101/2024.10.17.618875v1?rss=1 Liu, C. Shi, H. Han, Y. Wang, P. Li, K. Zhang, Z. Liu, J. Zheng, Y. Li, L. Lin, L. Liang, C. Qin, B. Han, H. Bai, S. Liu, X. Chen, W. Zhao, F. 2024-10-19 doi:10.1101/2024.10.17.618875 Cold Spring Harbor Laboratory Press 2024-10-19 <![CDATA[ Phage CRISPR-like regulatory RNAs silence bacterial adaptive and innate immunity ]]> https://biorxiv.org/content/10.1101/2024.10.29.618823v1?rss=1 Liu, C. Wang, R. Li, Z. Wang, W. Yao, J. Cheng, F. Du, X. Guan, L. Mestre, M. R. Xue, Q. Du, J. Xu, J. Zhou, T. Shu, X. Zhao, H. Feng, Y. Pinilla-Redondo, R. Li, M. 2024-10-30 doi:10.1101/2024.10.29.618823 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Differential destinations, dynamics, and functions of high- and low-order features in the feedback signal during object processing ]]> https://biorxiv.org/content/10.1101/2024.11.01.621525v1?rss=1 Hou, W. He, S. Zhang, J. 2024-11-01 doi:10.1101/2024.11.01.621525 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Deep generative model for protein subcellular localization prediction ]]> https://biorxiv.org/content/10.1101/2024.10.29.620765v1?rss=1 Yang, L. Yuan, G.-H. Li, J. Yang, Z. Chen, Y.-Q. Yuan, Z. Chen, T. Ouyang, W. Dong, N. 2024-11-03 doi:10.1101/2024.10.29.620765 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ PreDigs: a Database of Context-specific Cell-type Markers and Precise cell subtypes for Digestive Cell Annotation ]]> https://biorxiv.org/content/10.1101/2024.10.29.620788v1?rss=1 Meng, J. Han, M. Huang, Y. Li, L. Ju, Y. Lv, D. Chen, X. Yuan, L. Zhang, G. 2024-11-03 doi:10.1101/2024.10.29.620788 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Multi-dimensional social relationships shape social attention in monkeys ]]> https://biorxiv.org/content/10.1101/2024.11.06.622326v1?rss=1 Liu, S. Huang, J. Chen, S. Platt, M. L. Yang, Y. 2024-11-08 doi:10.1101/2024.11.06.622326 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Language model generates cis-regulatory elements across prokaryotes ]]> https://biorxiv.org/content/10.1101/2024.11.07.622410v1?rss=1 Xia, Y. Sun, J. Du, X. Liang, Z. Shi, W. Guo, S. Huo, Y.-X. 2024-11-09 doi:10.1101/2024.11.07.622410 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Increased preference for lysine over arginine in spike proteins of SARS-CoV-2 BA.2.86 variant and its sublineages ]]> https://biorxiv.org/content/10.1101/2024.11.11.622903v1?rss=1 Bozic, A. Podgornik, R. 2024-11-11 doi:10.1101/2024.11.11.622903 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Beta burst characteristics and coupling within the sensorimotor cortical-subthalamic nucleus circuit in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2024.11.19.624397v1?rss=1 200ms) in both structures displayed temporal overlap (>30%), with an estimated cortico-STN conduction delay of 8ms. Furthermore, approximately 27% of all STN bursts were preceded by a cortical burst. ConclusionCortical beta bursts tend to precede STN beta bursts, with short delays. However, subcortical mechanisms are also likely to contribute to STN burst initiation and propagation. ]]> Yao, P. Abdi-Sargezeh, B. Sharma, A. Liu, T. Tan, H. Hahn, A. Starr, P. Little, S. Oswal, A. 2024-11-21 doi:10.1101/2024.11.19.624397 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Chaperonin TRiC bridges radial spokes for folding proteins locally translated in mammalian sperm flagella ]]> https://biorxiv.org/content/10.1101/2024.11.19.624414v1?rss=1 Cong, Y. Meng, X. Li, L. Lin, C. Zhu, Y. Feng, Y. Zhou, X. Tong, Y. Wang, S. Yin, G. Liu, R. Sun, F. Yan, X. Zhu, X. 2024-11-21 doi:10.1101/2024.11.19.624414 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Exploring the Hypothetical Role of Bacteroides Species in Depression Progression: Insights from Metagenomic Analysis ]]> https://biorxiv.org/content/10.1101/2024.11.20.624524v1?rss=1 Li, Z. Sun, J. Long, J. Han, P. Min, L. Cheng, Y. Zou, Y. Liu, Z. 2024-11-21 doi:10.1101/2024.11.20.624524 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Cardiolipin-mimic lipid nanoparticles without antibody modification delivered senolytic in-vivo CAR-T therapy for inflamm-aging ]]> https://biorxiv.org/content/10.1101/2024.11.21.624667v1?rss=1 Zhang, Z. Ma, B. Li, B. Li, Z. Gao, M. Zhao, H. Peng, R. Hu, J. Wang, Y. You, W. Gui, X. Wang, R. Hu, X. Chen, B. Zhang, Y. Hao, Y. Zhou, D. Yang, Y. Deng, M. Miao, L. 2024-11-22 doi:10.1101/2024.11.21.624667 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ BioLLM: A Standardized Framework for Integrating and Benchmarking Single-Cell Foundation Models ]]> https://biorxiv.org/content/10.1101/2024.11.22.624786v1?rss=1 Qiu, P. Chen, Q. Q. Qin, H. Fang, S. Zhang, Y. Xia, T. Cao, L. Zhang, Y. Fang, X. Li, Y. Hu, L. 2024-11-22 doi:10.1101/2024.11.22.624786 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ In situ Membrane Protein Expression by Efficient Recruitment of mRNA to the Membranes of Synthetic Cells ]]> https://biorxiv.org/content/10.1101/2024.11.23.624830v1?rss=1 Fu, H. Ma, L. Xu, C. Li, J. Sun, Y. Tao, Y. Wang, H. Hu, S. Fu, M. Zheng, H. Liu, C. Ye, F. Qiao, Y. Li, M. Lu, Y. 2024-11-23 doi:10.1101/2024.11.23.624830 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Identification and genomic characterization of a novel bisegmented coronavirus in the lesser panda ]]> https://biorxiv.org/content/10.1101/2024.11.26.625429v1?rss=1 chen, x. Guo, H. Zhou, N. Shi, Z. Cui, X. Dong, T. Qin, M. Liang, X. Shan, F. Wang, H. Zuo, Q. Peng, S. You, W. Irwin, D. M. Chen, W. Zeng, L. Ding, C. Shen, Y. 2024-11-27 doi:10.1101/2024.11.26.625429 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Env from EIAV vaccine delicately regulates NLRP3 activation via attenuating NLRP3-NEK7 interaction ]]> https://biorxiv.org/content/10.1101/2024.11.26.625355v1?rss=1 Guo, x. Liu, c. Wang, y. Li, h. Ma, s. Na, l. Ren, h. Lin, y. Wang, X. 2024-11-29 doi:10.1101/2024.11.26.625355 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Deep-learning-enabled generative prevalent mutation prediction through host-to-herd in silico virus evolution ]]> https://biorxiv.org/content/10.1101/2024.11.28.625962v1?rss=1 Liu, X. Nie, Z. Si, H. Shen, X. Liu, Y. Huang, X. Dong, T. Xu, F. Chen, J. Zhou, P. Tian, Y. 2024-12-03 doi:10.1101/2024.11.28.625962 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ The comprehensive detection of hemoglobinopathy variants via long-read sequencing ]]> https://biorxiv.org/content/10.1101/2024.12.03.626522v1?rss=1 Xiang, J. Peng, J. Sun, X. Jiang, C. Zhao, H. Guo, Y. Xu, H. Gu, S. Ye, H. You, L. Huang, X. Chen, S. Zhu, B. Peng, Z. 2024-12-06 doi:10.1101/2024.12.03.626522 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ ANKRD5: a key component of the axoneme required for spermmotility and male fertility ]]> https://biorxiv.org/content/10.1101/2024.12.03.626701v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@1ca36eforg.highwire.dtl.DTLVardef@dcafe3org.highwire.dtl.DTLVardef@9f6086org.highwire.dtl.DTLVardef@17a0a0b_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementMale infertility affects approximately 8%-12% of men globally, with defects in sperm motility accounting for over 80% of these cases. The axoneme, which functions as the motor apparatus of the sperm, adopts a canonical "9+2" microtubule arrangement, where the nexin-dynein regulatory complex (N-DRC) plays a critical role in providing structural support between adjacent outer microtubule doublets. Elucidating the interplay between the structural organization and protein composition of the N-DRC is essential for advancing the understanding of male reproductive biology. In this study, we identify ANKRD5 as a new component of N-DRC that is essential for maintaining normal sperm motility. These findings contribute to the molecular understanding of sperm motility and highlight ANKRD5 as a potential target for the development of novel male contraceptives. ]]> Yu, S. Yin, G. Jin, P. Zhang, W. Tian, Y. Xu, X. Shao, T. Li, Y. Sun, F. Zhu, Y. Wang, F. 2024-12-07 doi:10.1101/2024.12.03.626701 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Radiation damage behavior of soft matter in ultrafast cryo-electron microscopy (cryo-UEM) ]]> https://biorxiv.org/content/10.1101/2024.12.20.629524v1?rss=1 Zhao, Y. Qi, C. Zhu, C. Zhu, Y. Zhang, Y. Gu, T. Tian, H. Wang, W. Huang, S. Yang, H. Li, J. Sun, F. 2024-12-20 doi:10.1101/2024.12.20.629524 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ A Palette of Bridged Bicycle-Strengthened Fluorophores ]]> https://biorxiv.org/content/10.1101/2024.12.20.629585v1?rss=1 Zhang, J. Zhang, K. Wang, K. Wang, B. Zhu, S. Qian, H. Ma, Y. Zhang, M. Liu, T. Chen, P. Shen, Y. Fu, Y. Fang, S. Zhang, X. Zou, P. Deng, W. Mu, Y. Chen, Z. 2024-12-22 doi:10.1101/2024.12.20.629585 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[ ISCO: Intelligent Framework for Accurate Segmentation and Comparative Analysis of Organoids ]]> https://biorxiv.org/content/10.1101/2024.12.24.630244v1?rss=1 ZHOU, J. Fu, Z. Ni, X. Luo, Q. Yang, G. 2024-12-24 doi:10.1101/2024.12.24.630244 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Ether Rhodamines with Enhanced Hydrophilicity, Fluorogenicity, and Brightness for Super-Resolution Imaging ]]> https://biorxiv.org/content/10.1101/2025.01.02.631033v1?rss=1 Fang, X. Qiao, Q. Li, Z. Li, H.-K. Chen, J. Xu, N. An, K. Jiang, W. Tao, Y. Bao, P. Zhang, Y. Wu, Z. Liu, X. Xu, Z. 2025-01-02 doi:10.1101/2025.01.02.631033 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Comprehensive Infectome Analysis Reveals Diverse Infectious Agents with Zoonotic Potential in Wildlife ]]> https://biorxiv.org/content/10.1101/2025.01.09.632079v1?rss=1 Hou, X. Wang, J. Wang, D.-X. Chen, Y. Li, X.-X. Wu, W.-C. Le, S.-J. Mei, S.-Q. Liu, H.-L. Feng, Y. Yang, L.-F. Shi, P.-B. Ren, Z.-R. Yang, L. He, H.-J. Song, W.-J. Chen, J. Zhu, M.-M. Jiang, Z.-W. Li, X.-M. Guo, D. Holmes, E. C. Deng, Z.-Q. Shi, M. Su, S. 2025-01-10 doi:10.1101/2025.01.09.632079 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Lower spatial turnover of rare fungal taxa dominantly shaped by stochastic processes in grassland soils ]]> https://biorxiv.org/content/10.1101/2025.01.20.633927v1?rss=1 0.1%, 2.73% of entire OTUs) and 5,779 rare OTUs (relative abundance < 0.01%, 75.85% of entire OTUs) were identified. Both abundant and rare fungal taxa showed significant distance-decay relationships (P < 0.001), but the turnover rate for rare taxa (0.0024 per 100 km) was nearly half that of abundant taxa (0.0054 per 100 km) based on the binary Bray-Curtis distance. The lower turnover of rare fungal taxa was likely due to their community assembly mechanism dominated by stochastic processes, which were less influenced by environmental gradients. In contrast, abundant taxa assembly was dominated by deterministic factors like soil variables and plant traits, which varied significantly along the geographic distance. Consistently, rare fungal taxa were also less sensitive to environmental changes, with a lower turnover rate by environmental distance (0.0027 vs. 0.0099) than abundant taxa. In summary, our findings revealed that rare fungal taxa, shaped mainly by stochastic processes, had lower spatial turnover compared to abundant taxa, dominated by deterministic processes, enhancing our understanding of rare microbial biogeography. ]]> Zhang, B. Zhou, S. Xue, K. Liu, W. Chen, S. Tang, L. Li, L. Du, J. Hao, Y. Cui, X. Wang, Y. 2025-01-22 doi:10.1101/2025.01.20.633927 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Single-cell spatial transcriptome reveals pathological features of human hippocampus with sclerosis ]]> https://biorxiv.org/content/10.1101/2025.01.21.633854v1?rss=1 Wang, L. Li, X. Liu, Y. Jin, B. Wei, Y. He, Y. Ma, Y. Wu, Z. Gong, X. An, Y. Kong, X. Xing, Y. Ye, R. Tao, Q. Li, A. Chang, M. Pu, L. Li, J. Pang, L. Zhou, D. Song, C. Liu, S. Xu, X. Liu, L. Han, L. Hong, Z. 2025-01-22 doi:10.1101/2025.01.21.633854 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ A versatile miniature two-photon microscope enabling multicolor deep-brain imaging ]]> https://biorxiv.org/content/10.1101/2025.02.13.635171v1?rss=1 Wu, R. Zhao, C. Qiu, S. Zhu, Y. Zhang, L. Fu, Q. Hu, Y. Wu, D. Yu, F. Zhou, F. Huang, H. Zhang, Y. Wang, X. Wang, A. Cheng, H. 2025-02-14 doi:10.1101/2025.02.13.635171 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ The distinct role of human PIT in attention control ]]> https://biorxiv.org/content/10.1101/2025.03.07.641975v1?rss=1 Huang, S. He, S. Wang, L. 2025-03-10 doi:10.1101/2025.03.07.641975 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning ]]> https://biorxiv.org/content/10.1101/2025.03.06.641773v1?rss=1 He, K. LI, A. Martinez, Q. Wang, X. Chen, Z. He, S. Xie, S. Zeng, Z. Wang, K. Ye, Z. Ruan, H. Liu, S. Lu, Q. Zheng, X. Luo, J. Song, W. Schwermann, A. Yu, H. Yu, W. Springer, M. Liu, S. Li, S. Tu, F. Cao, Z. Campbell, K. L. 2025-03-11 doi:10.1101/2025.03.06.641773 Cold Spring Harbor Laboratory Press 2025-03-11 <![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[ Energy inefficiency underpinning brain state dysregulation in individuals with major depressive disorder ]]> https://biorxiv.org/content/10.1101/2025.03.11.642725v1?rss=1 Liu, Q. Xiong, H. Shi, W. Di, S. Cheng, X. Liu, N. Luo, N. Zhang, Y. Jiang, T. 2025-03-13 doi:10.1101/2025.03.11.642725 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ SMART: an approach for accurate formula assignment in spatially-resolved metabolomics ]]> https://biorxiv.org/content/10.1101/2025.03.12.642824v1?rss=1 Cao, Y. Li, S. Liu, Z. Jia, Z. Zhuang, W. Pan, X. Zhou, J. Yang, L. Wang, L. 2025-03-14 doi:10.1101/2025.03.12.642824 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Methylome and transcriptome analysis reveals the impact of psychological stress on the skin ]]> https://biorxiv.org/content/10.1101/2025.03.14.643220v1?rss=1 Li, B. Zou, Y. Tian, S. Gonda, L. Mahns, A. Huang, T. Kolbe, L. Shi, Y. Wang, S. 2025-03-17 doi:10.1101/2025.03.14.643220 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ MAIS: an in-vitro sandbox enables adaptive neuromodulation via scalable neural interfaces ]]> https://biorxiv.org/content/10.1101/2025.03.15.641656v1?rss=1 Chen, H. Chen, F. Chen, X. Liu, Y. Xu, J. Li, J. Bao, X. Chen, Y. Sun, H. Jiang, J. Ye, F. Su, J. Gen, Y. Ye, F. Wang, Z. Liu, L. Hexige, S. Li, X. Ma, L. Shuai, J. 2025-03-17 doi:10.1101/2025.03.15.641656 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ High-efficiency likelihood inference of shared proteomic architectures across 50 complex human traits ]]> https://biorxiv.org/content/10.1101/2025.03.16.643065v1?rss=1 Sun, X. Yang, S. Peng, Q. Zhang, X. Qian, Y. Sun, R. Zhang, G. Wang, S. Jin, L. Zhang, M. 2025-03-17 doi:10.1101/2025.03.16.643065 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ CDK12 condensation in nuclear speckles confers sensitivity to cyclin K molecular glue degraders ]]> https://biorxiv.org/content/10.1101/2025.03.31.646293v1?rss=1 Ye, K. He, Q. Cheng, Y. Zhang, M. Mu, H. Cai, M.-C. Zhou, S. Xiang, H. Hou, Y. Li, Y. Zang, Y. Lv, J. Cheng, L. Xiang, L. Zhao, D. Zhang, Y. Li, Y. Yin, X. Di, W. Shen, P. Zhuang, G. Tan, L. 2025-04-01 doi:10.1101/2025.03.31.646293 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Reshaping epistatic network modules enhances wheat yield potential ]]> https://biorxiv.org/content/10.1101/2025.04.01.646715v1?rss=1 Yin, M. Han, H. Liu, W. Kong, L. Li, X. Ji, W. Wu, J. Deng, G. Dong, H. Zhang, J. Zhou, S. Zhang, Z. Hou, Y. Wang, H. Zhao, C. Li, X. Luo, Q. Guo, X. Yang, X. Ling, H.-Q. He, F. Li, L. 2025-04-08 doi:10.1101/2025.04.01.646715 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ Dynamic Pathway of Guanidine-III Riboswitch Folding Revealed by Single-Molecule FRET: Mg2+-Assisted Preorganization and Ligand-Induced Kinetic Trapping ]]> https://biorxiv.org/content/10.1101/2025.04.15.648854v1?rss=1 Jiang, M. Bian, Y. Zou, L. Liu, T. Ji, Z. Ren, W. Guo, Z. Cao, Y. Jiao, Y. Pan, H. 2025-04-20 doi:10.1101/2025.04.15.648854 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Saccades orchestrate intraocular glucose to shape visual responses in birds ]]> https://biorxiv.org/content/10.1101/2025.04.17.649318v1?rss=1 Xu, X. Xiao, T. Chen, Y. Song, L. Wu, C. Wang, Q. Zhang, T. Yang, Y. 2025-04-23 doi:10.1101/2025.04.17.649318 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ BioMedTools: a language model-powered community for biomedical computational tools ]]> https://biorxiv.org/content/10.1101/2025.05.02.651919v1?rss=1 Liu, S. Xing, H. Han, M. Zhang, D. Gong, L. Liu, D. Chen, J. Cai, P. Hu, Q.-N. 2025-05-08 doi:10.1101/2025.05.02.651919 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Locus-specific Convergent Evolution and Interchromosomal Rearrangements Contribute Type I Interferon Diversification in Amniotes ]]> https://biorxiv.org/content/10.1101/2025.05.08.652797v1?rss=1 Zhang, L. Ma, F. Liu, J. Yu, Y. Ma, J. Zhang, L. Li, B. Li, C. Liu, P. Zhang, L. 2025-05-13 doi:10.1101/2025.05.08.652797 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ A synergistic generative-ranking framework for tailored design of therapeutic single-domain antibodies ]]> https://biorxiv.org/content/10.1101/2025.05.09.653014v1?rss=1 Kong, Y. Shi, J. Wu, F. Zhao, T. Wang, R. Zhu, X. Xu, Q. Song, Y. Li, Q. Wang, Y. Gao, X. Yang, Y. Wu, Y. Yang, Z. Yao, J. Ying, T. 2025-05-14 doi:10.1101/2025.05.09.653014 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Universal Transformer-Based Tracker for Accurate Tracking of Particles and Cells in Microscopy ]]> https://biorxiv.org/content/10.1101/2025.05.09.653028v1?rss=1 Zhang, Y. Liu, D. Yang, G. 2025-05-14 doi:10.1101/2025.05.09.653028 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Adaptive Evolution of Gene Regulatory Networks in Mammalian Neocortical Neurons ]]> https://biorxiv.org/content/10.1101/2025.05.20.652233v1?rss=1 Li, Z. Kaur, N. Santpere, G. Muchnik, S. K. Sindhu, S. K. Qi, C. Shibata, M. Clement, O. Klaric, T. S. Martin, X. d. Luria, V. Cho, H. Li, M. Shibata, A. Tebbenkamp, A. T. N. Ma, S. Han, W. Kim, S. K. Pochareddy, S. Phan, D. Q. Xing, X. Bao, Y. Xu, X. Gladwyn-Ng, I. E. Cullen, H. D. Paolino, A. Fenlon, L. R. Kozulin, P. Suarez, R. Risgaard, R. D. Gulden, F. O. Karger, A. Suzuki, I. K. Hirata, T. Gobeske, K. T. Richards, L. J. Sousa, A. M. M. Heng, J. I. Sestan, N. 2025-05-21 doi:10.1101/2025.05.20.652233 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ TRiC-assisted folding of class I HDAC family proteins regulated by distinct co-chaperone and cofactor networks ]]> https://biorxiv.org/content/10.1101/2025.05.21.655272v1?rss=1 li, z. Zhao, Q. jiang, w. song, q. zhou, x. shi, x. zhang, q. wang, y. lin, y. Yin, Y. pan, c. Cong, Y. 2025-05-21 doi:10.1101/2025.05.21.655272 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ TIP-seq: A Single-cell Multiomics Approach for Simultaneous Transcriptome and Intracellular Protein Profiling ]]> https://biorxiv.org/content/10.1101/2025.05.26.653374v1?rss=1 Xue, Y. Qi, J. Xie, G. Wang, M. Xu, W. Ma, C. Xu, X. Yang, Y. He, Y. Guo, Y. Chen, S. Chen, Z. Qiu, M. Feng, C. Liu, J. Wu, H. Liu, Y. Xu, T. Cao, X. 2025-05-28 doi:10.1101/2025.05.26.653374 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Rational design of respiratory syncytial virus dimeric F-subunit vaccines in protein and mRNA forms ]]> https://biorxiv.org/content/10.1101/2025.05.31.655981v1?rss=1 Li, J. Ma, X. Xu, Z. Guo, W. Peng, R. zhang, Y. Meng, Y. Wang, Q. Li, S. Chen, J. Guo, Y. Lu, X. Wang, Q. Guo, Y. Jia, M.-a. Li, Y. Zhang, Y. Li, S. Du, P. Wang, Q. Gao, G. F. Qi, J. 2025-06-01 doi:10.1101/2025.05.31.655981 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Cryo-EM structure of DNA-unbound human MCM2-7 complex reveals new disease-relevant regulation ]]> https://biorxiv.org/content/10.1101/2025.05.31.656953v1?rss=1 Liu, Y. Yang, M. Lu, P. Gao, H. He, M. Wang, Y. Qi, A. Cao, T. Zhang, Q. Qi, S. Shi, Y. Yu, H. 2025-06-03 doi:10.1101/2025.05.31.656953 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Single-cell spatial map of cis-regulatory elements for disease-related genes in the macaque cortex ]]> https://biorxiv.org/content/10.1101/2025.06.03.657577v1?rss=1 Meng, J. Lei, Y. Chen, C. Zhu, Z. Sun, Y. Huang, Y. Hu, K. Bai, Y. Fei, T. Liu, Z. Li, C. Shen, Z. Liu, L. Li, C. Song, T. Liu, C. Poo, M. Liu, S. Sun, Y. 2025-06-03 doi:10.1101/2025.06.03.657577 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Macrophage-derived reactive oxygen species promote Salmonella aggresome formation contributing to bacterial antibiotic persistence ]]> https://biorxiv.org/content/10.1101/2025.06.03.657582v1?rss=1 View larger version (55K): org.highwire.dtl.DTLVardef@7e5f1forg.highwire.dtl.DTLVardef@970a39org.highwire.dtl.DTLVardef@204449org.highwire.dtl.DTLVardef@632c47_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, X. Fang, K. Li, B. Li, Y. Ke, Y. Ke, W. Tian, T. Zhao, Y. Wang, L. Geng, J. Leake, M. C. Bai, F. C. 2025-06-05 doi:10.1101/2025.06.03.657582 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Designing a broad-spectrum four-helix bundle targeting different strains of SARS-CoV-2 Spike Receptor Binding Domains with ACE2-like binding interface ]]> https://biorxiv.org/content/10.1101/2025.06.04.657798v1?rss=1 Nie, Q. Zhou, Y. Yin, H. Chen, K. Tang, J. Zhang, J. Z. H. Zhan, J. Qi, J. Li, W. Zhang, C. 2025-06-06 doi:10.1101/2025.06.04.657798 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Pathogen effector forms a hexameric phosphatase holoenzyme with host core enzyme to promote disease ]]> https://biorxiv.org/content/10.1101/2025.06.14.659724v1?rss=1 Wang, J. Li, H. Sun, W. Wang, J. Fang, X. Yang, X. Liu, C. Sheng, G. Ma, W. Wang, Y. 2025-06-18 doi:10.1101/2025.06.14.659724 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ UniCure: A Foundation Model for Predicting Personalized Cancer Therapy Response ]]> https://biorxiv.org/content/10.1101/2025.06.14.658531v1?rss=1 Chen, Z. Tian, S. Pei, J. Gu, R. Li, Y. Ding, S. Xu, Y. Zheng, X. Liu, M. Du, X. Zhu, J. Zou, J. Xu, J. Jiang, W. Chen, Y. Dong, B. Zhang, Q. Ren, S. Wang, S. Wen, H. Zhang, W. Chen, L. 2025-06-19 doi:10.1101/2025.06.14.658531 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Predicting the Evolutionary and Functional Landscapes of Viruses with a Unified Nucleotide-Protein Language Model: LucaVirus ]]> https://biorxiv.org/content/10.1101/2025.06.14.659722v1?rss=1 Pan, Y.-F. He, Y. Liu, Y.-Q. Shan, Y.-T. Liu, S.-N. Liu, X. Pan, X. Bai, Y. Xu, Z. Wang, Z. Ye, J. Holmes, E. C. Li, B. Chen, Y.-Q. Li, Z.-R. Shi, M. 2025-06-20 doi:10.1101/2025.06.14.659722 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Competing Programs Shape Cortical Sensorimotor-Association Axis Development ]]> https://biorxiv.org/content/10.1101/2025.06.26.660775v1?rss=1 Tsyporin, J. Zhang, M. Qi, C. Segal, A. Finn, T. Kim, H. Choi, S.-H. Li, X. Bandiera, S. Pavlovic, I. Kim, S. K. K. Shibata, A. Onishi, K. Zhang, Z. Hammarlund, E. Su, G. Salla, N. Kachko, J. Hawley, C. Li, S. Doyle, D. Z. Peng, X. Nottoli, T. Ruiz-Reig, N. Tissir, F. Nakagawa, Y. Herzog, E. Ma, S. Gobeske, K. Pattabiraman, K. Shimogori, T. Duque, A. Fornito, A. Huang, H. Shibata, M. Chen, B. Sestan, N. 2025-06-27 doi:10.1101/2025.06.26.660775 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ ODFormer: a Virtual Organoid for Predicting Personalized Therapeutic Responses in Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/2025.07.08.663664v1?rss=1 0.9 in predicting standardized drug response. Multi-cohort retrospective analyses further demonstrated that ODFormer-guided personalized therapy significantly improves clinical outcomes, without requiring physical organoid assays. Furthermore, ODFormer identified novel clinico-biological PC subtypes and revealed therapy resistance biomarkers by stratifying predicted responders and non-responders. These were validated using independent datasets including TCGA-PDAC. Notably, ODFormer-guided treatment efficacy showed high concordance with prospective clinical responses by CA19-9. ]]> Xu, J. Yang, X. LI, Y. Wang, H. Li, Y. Tang, S. Guo, S. Zou, J. Shi, X. Chen, Z. Zhong, C. Li, P. Jing, W. Zheng, K. Wu, X. Gao, D. Chen, L. Jin, G. 2025-07-10 doi:10.1101/2025.07.08.663664 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ BrainBeacon: A Cross-Species Foundation Model for Single-cell Resolved Brain Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.07.08.663729v1?rss=1 Zhang, C. Yang, Y. Jiao, Y. Yang, Q. Guo, X. Xu, J. Li, J. Zhou, Y. Liu, Z. Wu, Y. Zhang, Y. Jiang, C. Ma, J. Liu, Y. Zhang, Y. Xiao, K. Sun, Y. Liu, C. Han, L. Qi, Y. Aihara, K. Li, C. Cheng, Y. Chen, L. Wei, W. 2025-07-10 doi:10.1101/2025.07.08.663729 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Pluripotent stem cell-derived siTNK cells attack tumors via a synthetic CD8-CD28 TCR complex ]]> https://biorxiv.org/content/10.1101/2025.07.11.663392v1?rss=1 Zheng, X. Zhang, F. Lin, Y. Hu, F. Weng, Q. Liu, P. Wang, Z. Zhang, C. Liu, Y. Liu, L. Zhu, Y. Xiao, Z. Wang, Y. Zhang, L. Qi, H. Shen, Y. Chen, Y. Wu, J. Xu, J. Zhao, Y. Wang, T. Huang, D. Xia, C. Wang, J. Zhang, M. 2025-07-12 doi:10.1101/2025.07.11.663392 Cold Spring Harbor Laboratory Press 2025-07-12 <![CDATA[ Vascularized Bioengineered Kidney Using Decellularized Scaffold Recellularized with human Placenta-Derived Angiogenic stem Cells and Kidney Organoids ]]> https://biorxiv.org/content/10.1101/2025.07.10.664023v1?rss=1 Liu, H. Wen, X. Shi, Y. Zhou, Y. Chen, X. Song, W. Zhang, X. Wang, Y. Hao, J. Ma, Y. Zhang, J. Cai, Y. Gong, Y. Lin, F. Du, X. XU, J. 2025-07-15 doi:10.1101/2025.07.10.664023 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ A Paracrine-to-Autocrine Shunt of GREM1 Fuels Colorectal Cancer Metastasis via ACVR1C ]]> https://biorxiv.org/content/10.1101/2025.07.11.664267v1?rss=1 Zhou, H. Jin, Q. Fu, Z. Yang, Y. Gao, Y. Wang, N. Zhao, B. Gui, L. Li, J. Zhu, Z. Zhang, Y. He, Y. Zhang, Y. Luo, S. Fu, L. Wu, X. Zhang, J. Shen, X. Wang, T. Jiang, Y. Li, N. 2025-07-16 doi:10.1101/2025.07.11.664267 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ An Unexpected Role of Molecular Chaperones in Regulating the Excited States and Activities of Folded Enzymes ]]> https://biorxiv.org/content/10.1101/2025.07.15.664663v1?rss=1 Wang, G. Bin, Y. Chen, Y. Ding, R. Qi, S. Zhao, X. Zhou, G. Zhang, X. Hiller, S. Liu, M. He, L. 2025-07-17 doi:10.1101/2025.07.15.664663 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Real-time visualization of ligand-specific conformational dynamics of GPCR C-terminal domain in living cells ]]> https://biorxiv.org/content/10.1101/2025.07.17.665247v1?rss=1 Lin, Z. Chen, X. Ma, L. Fu, H. Wang, H. Yang, K. Li, Z. Ye, F. Lu, Y. Hu, S. Li, M. 2025-07-21 doi:10.1101/2025.07.17.665247 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Overcoming breeding constraints in polyploid oat from evolutionary insights ]]> https://biorxiv.org/content/10.1101/2025.07.18.665467v1?rss=1 Bai, X. Sun, M. Zhang, Y. Yin, H. Cui, X. Liu, X. Bao, Z. Zhang, Z. Dong, Z. Liu, Z. Wu, Y. Wang, D. Zou, Z. He, J. Li, M. Zheng, L. Liu, Y. Zhou, Y. 2025-07-23 doi:10.1101/2025.07.18.665467 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ AlphaGEM Enables Precise Genome-Scale Metabolic Modelling by Integrating Protein Structure Alignment with deep-learning-based Dark Metabolism Mining ]]> https://biorxiv.org/content/10.1101/2025.07.21.665674v1?rss=1 Han, W. Xiao, L. Sun, H. Xiang, G. Jia, Q. Wang, H. Ji, B. Zhang, C. Kerkhoven, E. J. Nielsen, J. Lu, H. 2025-07-24 doi:10.1101/2025.07.21.665674 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ An AI-based and coding-free protocol for forests Leaf Area Index (LAI) calculation ]]> https://biorxiv.org/content/10.1101/2025.07.24.666563v1?rss=1 Ma, T. Tang, M. Liu, F. Duah-Gyamfi, A. Adu-Bredu, S. Naive, M. A. K. Oliveras Menor, I. Moore, S. Zhang, Z. Malhi, Y. Dahlsjo, C. A. L. Zhang-Zheng, H. 2025-07-30 doi:10.1101/2025.07.24.666563 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ KiF1a-regulated neuronal infrastructures in sensory and prefrontal cortices essential for fear memory and anxiety ]]> https://biorxiv.org/content/10.1101/2025.07.29.667346v1?rss=1 Li, J.-y. Chen, B.-c. Zhang, Y. Xu, Y. Wang, L. Wang, J.-H. 2025-08-01 doi:10.1101/2025.07.29.667346 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Quantifying spatiotemporal decoupling of GDGT-temperature relationships in a deep alpine lake ]]> https://biorxiv.org/content/10.1101/2025.08.01.668065v1?rss=1 Li, J. Meng, F. Wang, Q. Naafs, D. Peterse, F. Wang, R. Yang, H. Yang, X. Wang, J. Xie, S. 2025-08-02 doi:10.1101/2025.08.01.668065 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Spatiotemporal lineage mapping of tumor immune escape with eTRACER ]]> https://biorxiv.org/content/10.1101/2025.08.06.668639v1?rss=1 Yang, J. Hou, L. Wang, X. Zhang, N. Bian, Y. Lu, Z. Chen, Y. Xie, D. Fang, Y. Wang, K. Wan, R. Jin, Y. Chen, Y. Cai, X. Lee, L. T. O. Hu, Z. Ji, H. 2025-08-09 doi:10.1101/2025.08.06.668639 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ CLM-access: A Specialized Foundation Model for High-dimensional Single-cell ATAC-seq analysis ]]> https://biorxiv.org/content/10.1101/2025.08.10.669570v1?rss=1 Liu, Z. Li, B. Xu, Z. Li, Y. Zhang, J. Sha, C. Li, X. 2025-08-12 doi:10.1101/2025.08.10.669570 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ DeepHalo: Deep Learning-Powered Exploration of Halogenated Metabolites Uncovering Antibacterial Depsipeptides ]]> https://biorxiv.org/content/10.1101/2025.08.11.669588v1?rss=1 Chang, S. Qi, X. Wang, M. Huang, X. He, N. Chen, M. Wang, J. Du, Y. Wang, S. Li, Y. Gao, Q. Chen, X. Lv, Q. Li, X. Hong, B. Xie, Y. 2025-08-12 doi:10.1101/2025.08.11.669588 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Spatial transcriptomics identifies distinct domains regulating yield-related traits of the wheat ear ]]> https://biorxiv.org/content/10.1101/2025.08.12.670006v1?rss=1 Qu, Y. Tan, C. Yang, L. Pasquariello, M. Alabdullah, A. K. Sun, S. Iqbal, M. Salamon, J. Boden, S. 2025-08-13 doi:10.1101/2025.08.12.670006 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ KICDB: A Causality-Oriented Multi-Omics Database for Kinase Inhibitor-Induced Cardiotoxicity ]]> https://biorxiv.org/content/10.1101/2025.08.20.671397v1?rss=1 Wei, J. Liu, Y. Wu, M. Li, G. Zheng, X. Fu, H. ZHANG, J. Lin, J. 2025-08-24 doi:10.1101/2025.08.20.671397 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ An activated wheat CCG10-NLR immune receptor forms an octameric resistosome ]]> https://biorxiv.org/content/10.1101/2025.08.26.672026v1?rss=1 Guo, G. Zhao, H. Bai, K. Wu, Q. Dong, L. Lu, L. Chen, Y. Hou, Y. Lu, J. Lu, P. Li, M. Zhang, H. Wang, G. Zhu, K. Huang, B. Cui, X. Fu, H. Hu, C. Chu, Z. Lyu, X. Kamoun, S. Wang, C. Liu, Z. Selvaraj, M. Jones, J. D. 2025-08-27 doi:10.1101/2025.08.26.672026 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Instruction-tuned extraction of virus-host interactions from integrated scientific evidence ]]> https://biorxiv.org/content/10.1101/2025.09.02.673691v1?rss=1 4, 000 training examples), ChatMed-VHI maintained the highest overall performance, while PubMedBERT achieved slightly higher precision (92.3% vs. 91.3%). Notably, ChatMed-VHI improved F1 and recall by 2.79% but precision dropped by 4.20% with more training data, whereas PubMedBERT improved consistently across all metrics. These results demonstrate the effectiveness of instruction-tuned LLMs for full-text biomedical extraction tasks, and position ChatMed-VHI as a scalable, domain-adaptable solution for VHI mining. ]]> Zhang, Z. Li, W. Ren, J. Chen, Y. He, B. Sun, Q. Wang, H. 2025-09-06 doi:10.1101/2025.09.02.673691 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Hypoimmunogenic human motor neurons induced from iPSCs in vivo substantially ameliorate ALS disease in large animal models ]]> https://biorxiv.org/content/10.1101/2025.09.03.673895v1?rss=1 Zhang, N. Yang, Y. Chen, M. Zou, Q. Quan, L. Huang, J. Zhang, Q. Zhao, Y. Ouyang, Z. Zhang, Z. Song, Y. Chen, M. Zhang, K. Sharma, A. D. Ott, M. Li, X. Li, Z. Xie, W. Dai, Z. Lai, L. 2025-09-07 doi:10.1101/2025.09.03.673895 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Abnormal shear stress induces ferroptosis in endothelial cells via KLF6 downregulation ]]> https://biorxiv.org/content/10.1101/2025.09.10.675441v1?rss=1 Cui, J. Fan, Z. Ding, S. Zhang, J. Shen, H. Zaidi, S. A. Ding, Y. 2025-09-16 doi:10.1101/2025.09.10.675441 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ A Generative Foundation Model for Antibody Design ]]> https://biorxiv.org/content/10.1101/2025.09.12.675771v1?rss=1 Wang, R. Wu, F. Shi, J. Song, Y. Kong, Y. Ma, J. He, B. Yan, Q. Ying, T. Gao, X. Zhao, P. Yao, J. 2025-09-16 doi:10.1101/2025.09.12.675771 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ The Genetic Immune Basis of Gout: Identification, Functional Characterization, and Therapeutic Implications ]]> https://biorxiv.org/content/10.1101/2025.09.12.675974v1?rss=1 Syed, A. A. S. Memon, A. A. Fahira, A. Yang, Q. Jian, X. Zhang, M. Shi, Y. 2025-09-17 doi:10.1101/2025.09.12.675974 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ DynPerturb:Dynamic Perturbation Modeling for Spatiotemporal Single-Cell Systems ]]> https://biorxiv.org/content/10.1101/2025.09.15.676236v1?rss=1 QIN, H. Zhang, Y. Guo, Z. Hu, L. Li, Q. Cao, L. Xia, T. Deng, Z. Zhang, Y. Li, Y. Fang, S. 2025-09-18 doi:10.1101/2025.09.15.676236 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Cryo-EM structure of influenza polymerase bound to the cRNA promoter provides insights into the mechanism of virus replication ]]> https://biorxiv.org/content/10.1101/2025.09.23.677976v1?rss=1 Liang, H. Liu, Y. Huang, S. Wu, Y. Li, M. Li, H. Sun, T. Bai, Y. 2025-09-24 doi:10.1101/2025.09.23.677976 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Accurate and efficient phylogenetic inference through end-to-end deep learning ]]> https://biorxiv.org/content/10.1101/2025.09.30.679045v1?rss=1 Zhang, X. Ding, S. Yu, C. Zhao, J. Bu, D. 2025-10-02 doi:10.1101/2025.09.30.679045 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ LINE1 RNA dysregulation impairs chromatin accessibility in C9ORF72- and TDP-43-linked ALS/FTD ]]> https://biorxiv.org/content/10.1101/2025.09.30.679260v1?rss=1 Li, Y. Dou, X. Xiao, Y. Zhang, Z. Ye, Y. Wright, N. Chang, K. Liu, C. Troncoso, J. C. He, C. Sun, S. 2025-10-02 doi:10.1101/2025.09.30.679260 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Autonomous liquid-handling robotics scripting through large language models enables accessible and safe protein engineering workflows ]]> https://biorxiv.org/content/10.1101/2025.09.30.679666v1?rss=1 Yuan, G. Luo, L. Lan, Y. Jiang, H. Fu, L. Si, T. 2025-10-02 doi:10.1101/2025.09.30.679666 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Finding the perfect promoter: Correlating single-cell transcriptome data with gene drive performance ]]> https://biorxiv.org/content/10.1101/2025.10.08.681126v1?rss=1 Wu, Y. Xia, Y. Yao, Z. Chen, W. Jia, X. Liang, N. Champer, J. 2025-10-08 doi:10.1101/2025.10.08.681126 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Joint analysis of expression and variation at single cell resolution by scVar ]]> https://biorxiv.org/content/10.1101/2025.10.12.681753v1?rss=1 Zhao, W. Yang, F. Zong, W. Zheng, X. Bao, Y. 2025-10-14 doi:10.1101/2025.10.12.681753 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex ]]> https://biorxiv.org/content/10.1101/2025.10.13.681959v1?rss=1 Han, L. Liu, Z. Wang, L. Liu, Y. Wei, Y. Ma, J. He, Y. Zuo, Y. Fang, J. Yang, H. Zou, X. Wu, Z. Wang, M. Liu, W. Gao, L. Liu, Y. Song, X. Zhang, Y. S. Lei, J. Li, H. Li, L. An, Y. Jin, B. Zhong, Y. Chai, Q. Tao, Q. Tan, X. Lin, Y. Zhang, R. Wang, S. Chang, M. Yang, B. Chen, M. Mi, L. Zhuang, L. Yuan, N. Li, C. Huang, T. Li, X. Liu, C. Sun, Y. Chen, L. Liu, L. Xu, X. Li, C. Guo, H. Li, H. Poo, M. Gan, W.-B. Yao, J. Yuan, W. Liu, S. Shen, Z. Mao, Y. Wei, W. 2025-10-14 doi:10.1101/2025.10.13.681959 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Engineering Treg-mediated immune tolerance via foxp3a overexpression to evade allograft transplantation barriers in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.10.15.682525v1?rss=1 Zhu, J. Hao, Y. Zhang, F. Gao, X. Wang, H. Wang, X. Sun, Y. 2025-10-16 doi:10.1101/2025.10.15.682525 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Integrating theory and machine learning to reveal determinants of plasmid copy number ]]> https://biorxiv.org/content/10.1101/2025.10.23.684078v1?rss=1 10,000 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct the first comprehensive analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, uncovering niche specific taxonomic PCN hotspots and ecological adaptations. These results provide critical insights into plasmid ecology, ARG surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome. ]]> Shahzadi, I. Wang, T. Ullah, H. U. Maddamsetti, R. You, L. 2025-10-23 doi:10.1101/2025.10.23.684078 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Structure and function of the nairovirus cap-snatching endonuclease ]]> https://biorxiv.org/content/10.1101/2025.10.28.684947v1?rss=1 Kuang, W. Tian, Z. Zhang, G. Wu, F. Li, J. Tang, J. Zhang, H. Zhuo, X. Hu, Z. Wang, M. Zhao, H. Deng, Z. 2025-10-28 doi:10.1101/2025.10.28.684947 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ DomDiff: protein family and domain annotation via diffusion model and ESM2 embedding ]]> https://biorxiv.org/content/10.1101/2025.10.28.685005v1?rss=1 Zhang, C. Xia, H. Yin, P. 2025-10-28 doi:10.1101/2025.10.28.685005 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ DNA Framework Nanoreactor for Programmable Membrane Fusion ]]> https://biorxiv.org/content/10.1101/2025.10.28.685246v1?rss=1 Shi, Q. Yang, Q. Li, F. Bao, M. Wang, S. Huang, K. Liu, J. Wang, Y. Chen, Y. Yang, Y. R. Bian, X. Wu, Z. Yang, Y. 2025-10-30 doi:10.1101/2025.10.28.685246 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Captamer: A Novel Quantitative Protein Detecting Method Depending on Aptamer-activated Molecular Switches and RPA Signal Amplification ]]> https://biorxiv.org/content/10.1101/2025.11.02.686180v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@1e38ffaorg.highwire.dtl.DTLVardef@1019e72org.highwire.dtl.DTLVardef@1498b68org.highwire.dtl.DTLVardef@15f5ea2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cao, Y. Li, M. Xu, G. Xia, S. Wu, X. Shi, K. Xue, R. Wang, H. Ye, R. Han, Z. Xu, J. Hong, J. 2025-11-04 doi:10.1101/2025.11.02.686180 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Identification and Development of Functional Markers Associated with Triple Pistil Phenotype in Wheat ]]> https://biorxiv.org/content/10.1101/2025.11.09.687415v1?rss=1 Raza, Q. Song, Q. Rehman, S. u. Ali, Z. 2025-11-10 doi:10.1101/2025.11.09.687415 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Tumor cell-specific loss of GPX4 reprograms triacylglycerol metabolism to escape ferroptosis and impair antitumor immunity in NSCLC ]]> https://biorxiv.org/content/10.1101/2025.11.12.687999v1?rss=1 Wang, P. Zhang, S. Chen, X. Yang, X.-D. Huang, S. Yin, H. Duan, H.-Y. Zhou, F. Yu, J. Zhong, B. Lin, D. 2025-11-13 doi:10.1101/2025.11.12.687999 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Global Mapping of circRNA-Target RNA Interactions Reveals P-Body-Mediated Translational Repression ]]> https://biorxiv.org/content/10.1101/2025.11.16.688748v1?rss=1 Li, P. Zhang, H. Cai, Z. Zhang, Y. Yang, R. Ye, R. Li, J. Zhao, H. Liu, B. Yuan, Z. Li, X. Wang, X. Zhu, P. Xue, Y. 2025-11-17 doi:10.1101/2025.11.16.688748 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ AI-HEAD: Auto-indexing for Helical assembles' diffraction and fast dynamic structure determination ]]> https://biorxiv.org/content/10.1101/2025.11.17.688965v1?rss=1 Pei, T. Yu, M. Li, S. Zhang, D. Sun, F. Zhang, Y. 2025-11-18 doi:10.1101/2025.11.17.688965 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ MAAD: Multidimensional Antiviral Antibody Database ]]> https://biorxiv.org/content/10.1101/2025.11.18.688681v1?rss=1 Li, Y. Wang, J. Zhang, C. Zhang, Y. Deng, J. Zhang, H. Li, M. Wang, F. Wang, X. 2025-11-18 doi:10.1101/2025.11.18.688681 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ OSM-11 modulates salinity-stress tolerance in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.11.20.689412v1?rss=1 Zhang, P. Xue, B. Xie, Y. Li, K. Yang, H. Sun, P. Zhang, L. 2025-11-20 doi:10.1101/2025.11.20.689412 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ β-Nicotinamide mononucleotide: a novel broad-spectrum CRISPR inhibitor ]]> https://biorxiv.org/content/10.1101/2025.11.22.685598v1?rss=1 Wei, T. Shen, W. Li, W. Song, Y. Fa, Y. An, J. Sun, Y. Li, H. 2025-11-26 doi:10.1101/2025.11.22.685598 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing ]]> https://biorxiv.org/content/10.1101/2025.11.25.690617v1?rss=1 Liu, Y. Su, Z. Yang, W. Li, D. Zhang, J. Zhang, Y. Zeng, T. Zhang, Y. Li, Y. Fan, G. Ma, K. Liu, S. Xu, X. Dong, Y. Wang, Z. 2025-11-28 doi:10.1101/2025.11.25.690617 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Normative modeling of brain morphology reveals neuroanatomical heterogeneity and biological subtypes in major depressive disorder ]]> https://biorxiv.org/content/10.64898/2025.12.07.692810v1?rss=1 Fan, Q. Gao, J. Wu, Y. Wang, Y. Zhang, L. Zhou, J. Feng, Y. Lu, Y. Wang, G. Zhou, Y. 2025-12-10 doi:10.64898/2025.12.07.692810 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ A division-associated envelope protein, MAB_2363, drives intrinsic resistance and virulence in Mycobacterium abscessus ]]> https://biorxiv.org/content/10.64898/2025.12.18.695127v1?rss=1 Li, L. Alam, M. S. Li, C. Hameed, H. M. A. Yusuf, B. BELACHEW, A. M. Tian, X. Malik, A. Fang, C. Ju, Y. Zhang, J. Feng, L. Yu, W. Wang, S. Zhang, T. 2025-12-18 doi:10.64898/2025.12.18.695127 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ Ultrahigh-Throughput Forster Resonance Energy Transfer-Activated Droplet Sorting for Terminator Polymerase Engineering ]]> https://biorxiv.org/content/10.64898/2025.12.18.695305v1?rss=1 Zhang, H. Xie, Q. Xu, H. Li, W. Li, C. Shen, L. Wang, P. Yan, X. Li, X. Zhou, S. Zhuo, S. Liu, C. Teng, B. Dong, Y. Shen, M. Zheng, Y. Xu, X. 2025-12-20 doi:10.64898/2025.12.18.695305 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ tBid mediated genetic ablation of connective tissue cells reveal their key regulatory function during limb regeneration in axolotls ]]> https://biorxiv.org/content/10.64898/2025.12.19.695438v1?rss=1 Hu, Y. Feng, W. He, Z. Zeng, J. Tang, J. Li, S. Yu, T. Fu, S. Ma, H. Lu, B. Liu, Y. Fei, J. 2025-12-21 doi:10.64898/2025.12.19.695438 Cold Spring Harbor Laboratory Press 2025-12-21 <![CDATA[ LDscore: a scalable, Python 3-powered web platform for LD score regression analysis ]]> https://biorxiv.org/content/10.64898/2025.12.19.695639v1?rss=1 Breeze, C. E. Yao, X. Park, B. Kanigicherla, M. Lan, Q. Rothman, N. Teschendorff, A. E. Franceschini, N. Berndt, S. I. Machiela, M. J. 2025-12-23 doi:10.64898/2025.12.19.695639 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Structural Mechanism of Specific Nucleobase Recognition by a Monoclonal Antibody in CoolMPSTM Sequencing ]]> https://biorxiv.org/content/10.64898/2025.12.22.696117v1?rss=1 Yang, L. Wang, Q. Liao, H. Li, W. Xu, C. Qi, J. Zhang, H. Fu, L. Yang, M. 2025-12-23 doi:10.64898/2025.12.22.696117 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Structural Insights into Single-Stranded DNA Recognition and Modified Substrate Tolerance in an Engineered Terminal Deoxynucleotidyl Transferase ]]> https://biorxiv.org/content/10.64898/2025.12.25.696546v1?rss=1 Yang, L. Liao, H. Wang, Q. Li, W. Xu, C. Qi, J. Zhang, H. Fu, L. Yang, M. 2025-12-26 doi:10.64898/2025.12.25.696546 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Ultra-fast genetic recovery of dead fish through cross-family germline stem cell transplantation ]]> https://biorxiv.org/content/10.64898/2026.01.05.697817v1?rss=1 Wang, C. Ma, H. Wang, X. Hao, Y. Zhu, J. Wang, H. Wang, Y. Gao, X. He, M. Chen, S. Sun, Y. 2026-01-06 doi:10.64898/2026.01.05.697817 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[ resolveS: An ultra-fast, memory-efficient and reference-free tool for RNA-seq Strandedness Detection ]]> https://biorxiv.org/content/10.64898/2026.01.08.698333v1?rss=1 Yu, D. Zhao, T. Xi, L. 2026-01-08 doi:10.64898/2026.01.08.698333 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ AutoPELSA: an automated sample preparation system for proteome-wide identification of target proteins of diverse ligands ]]> https://biorxiv.org/content/10.64898/2026.01.08.697612v1?rss=1 Xue, L. Wang, X. Yang, H. Zhou, J. Zhu, H. Shen, J. Gao, W. Tian, R. Wang, Y. Ye, M. 2026-01-09 doi:10.64898/2026.01.08.697612 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Unifying constraints linking protein folding and native dynamics decoded from AlphaFold ]]> https://biorxiv.org/content/10.64898/2026.01.08.698426v1?rss=1 Zhang, Z. Ren, W. Xie, L. Zheng, Y. Guan, X. Wang, J. Li, W. Tang, Q.-Y. 2026-01-09 doi:10.64898/2026.01.08.698426 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Automating the Construction of Contextualized Biomedical Knowledge Graphs for Scientific Inference ]]> https://biorxiv.org/content/10.64898/2026.01.14.699420v1?rss=1 Zheng, Y. Liu, W. Zeng, B. Feng, Y. Du, X. Zhou, L. Li, Y. 2026-01-14 doi:10.64898/2026.01.14.699420 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ The overall and sequence-specific degradation of soil extracellular 16S rRNA genes across China: rates and influential factors ]]> https://biorxiv.org/content/10.64898/2026.01.14.699460v1?rss=1 Li, T. Zhang, S. Wang, Z. Huang, W. Zhang, Z. Wang, F. Liu, D. Cui, X. Che, R. 2026-01-14 doi:10.64898/2026.01.14.699460 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ CTLA-4 inhibitors drive colitis through metabolic reprogramming-mediated Treg/Th17 imbalance ]]> https://biorxiv.org/content/10.64898/2026.01.20.700699v1?rss=1 Li, Z. Wu, S. Liu, R. Chen, R. Li, F. Zhang, R. Wang, Y. Chen, C. Zheng, X. Qiu, F. Chen, L. Zhao, Y. Du, F. Gong, L. Long, Y. 2026-01-21 doi:10.64898/2026.01.20.700699 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Disrupted TRiC allostery and conformational equilibrium by LCA-linked mutations: structural and functional insights ]]> https://biorxiv.org/content/10.64898/2026.01.22.701072v1?rss=1 Zhao, Q. Liu, C. Zhang, Q. Li, Z. Wang, Y. Zhou, X. Ye, X. Wang, S. Wang, Y. Jiang, W. Song, Q. Cong, Y. 2026-01-23 doi:10.64898/2026.01.22.701072 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Endothelial MRG15 Is a Mechanosensitive Suppressor of Atherosclerosis ]]> https://biorxiv.org/content/10.64898/2026.01.28.702256v1?rss=1 Li, Y. Lin, X. Ma, J. Jiang, Q. Lin, J. Qu, L. Ding, Q. Wei, X. Zhi, X. Zhang, P. Shyy, J. Y.- J. Osto, E. Dai, Y. Guo, J. Meng, D. 2026-01-30 doi:10.64898/2026.01.28.702256 Cold Spring Harbor Laboratory Press 2026-01-30 <![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[ Ultra-flexible PINE arrays for month-long, continuous intracellular ion flux monitoring in plants with nanomolar accuracy ]]> https://biorxiv.org/content/10.64898/2026.01.30.702757v1?rss=1 Yang, Z. Shu, M. Ma, H. Zhu, G. Sun, H. Xu, M. Wei, X. Tsang, W.-M. Chao, D. Li, R. He, F. 2026-02-02 doi:10.64898/2026.01.30.702757 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ SPCoral: diagonal integration of spatial multi-omics across diverse modalities and technologies ]]> https://biorxiv.org/content/10.64898/2026.02.02.703207v1?rss=1 Wang, H. Yuan, J. Li, K. Chen, X. Yan, X. Lin, P. Tang, Z. Wu, B. Nan, H. Lai, Y. Lv, Y. Esteban, M. A. Xie, L. Wang, G. Hui, L. Li, H. 2026-02-04 doi:10.64898/2026.02.02.703207 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ The genetic repertoire of the deep sea: from sequence to structure and function ]]> https://biorxiv.org/content/10.64898/2026.02.03.703410v1?rss=1 Guo, Y. Wang, Z. Li, D. Wang, L. Lan, H. Guo, F. Zhao, Z. Liu, Z. Meng, L. Shen, X. Wang, M. Zhao, W. Zhang, W. Kong, C. Shi, L. Sun, Y. Seim, I. Jiang, A. Ma, K. Su, Z. Zhang, N. Ji, Q. Chen, J. Chen, K. Qi, C. Li, B. He, B. Liu, Y. Zhou, J. Zheng, Y. Zhang, H. Wang, Y. Han, M. Yang, T. Tong, J. Zhang, Y. Wang, Z. Xu, X. Chen, J. Liu, Y. Chen, H. Zeng, T. Wei, X. Li, C. Yang, H. Wang, B. Liu, X. Shao, C. Zhang, W. Gu, Y. Xiao, X. Xu, X. Wang, J. Mock, T. Fan, G. Li, Y. Liu, S. Dong, Y. 2026-02-05 doi:10.64898/2026.02.03.703410 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Decomposing multi-scale dynamic regulation from single-cell multiomics with scMagnify ]]> https://biorxiv.org/content/10.64898/2026.02.03.703669v1?rss=1 Chen, X. Yan, X. Shen, B. Wang, H. Tang, Z. Zang, Y. Lin, P. Zhang, H. Li, Y. Li, H. 2026-02-06 doi:10.64898/2026.02.03.703669 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Circadian-Modulated Thresholds as a Mechanistic Basis for Sleep-Wake Transitions, Recovery, and Sleepiness ]]> https://biorxiv.org/content/10.64898/2026.02.04.703688v1?rss=1 Yao, C. Jiang, J. Gu, C. Shuai, J. Yang, D. 2026-02-06 doi:10.64898/2026.02.04.703688 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Identification and characterization of ethR and ethA genes impacting the sensitivity of Mycobacterium abscessus to ethionamide ]]> https://biorxiv.org/content/10.64898/2026.02.08.704650v1?rss=1 Zhang, X. Li, L. Lu, Z. Duan, Z. Hameed, H. M. A. BELACHEW, A. M. Fang, C. Tian, X. Wang, X. Chen, H. Feng, L. McNeil, M. Liu, D. Wang, S. Zhang, T. 2026-02-09 doi:10.64898/2026.02.08.704650 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Metabolism-driven, high-efficiency mining of ethanol-tolerant microorganisms from pit mud microbiota using Raman flow cytometry ]]> https://biorxiv.org/content/10.64898/2026.02.13.705682v1?rss=1 teng, X. qing, S. chao, J. G. ming, D. Y. hang, W. X. yun, Y. X. le, W. C. zi, Z. H. Jian, X. wei, Z. X. xian, W. X. jia, Z. 2026-02-14 doi:10.64898/2026.02.13.705682 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ ProteinConformers: large-scale and energetically profiled descriptions of protein conformational landscapes ]]> https://biorxiv.org/content/10.64898/2026.02.20.707011v1?rss=1 Zhou, Y. Wei, C. Sun, M. Wang, L. Song, J. Xu, F. Li, Y. Zheng, W. Zhang, Y. 2026-02-20 doi:10.64898/2026.02.20.707011 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination ]]> https://biorxiv.org/content/10.64898/2026.02.21.707213v1?rss=1 300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range. ]]> Yuan, L. Qin, Y. West-Roberts, J. Anantharaman, K. Wang, H. Zou, Y. Duan, Y. Camargo, A. P. Koonin, E. V. Chen, L. 2026-02-22 doi:10.64898/2026.02.21.707213 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ Sampling protein structural token space enables accurate prediction of multiple conformations ]]> https://biorxiv.org/content/10.64898/2026.03.03.708411v1?rss=1 Wang, Z. Yu, Y. Yu, C. Bu, D. 2026-03-04 doi:10.64898/2026.03.03.708411 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Decoupling Lineage and Intrinsic Information in Single-Cell Lineage Tracing Data with Deep Disentangled Representation Learning ]]> https://biorxiv.org/content/10.64898/2026.03.10.710716v1?rss=1 Wen, Y. Xiong, J. Gong, F. Ma, L. Wan, L. 2026-03-11 doi:10.64898/2026.03.10.710716 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ STING agonist-mediated endothelial cell activation drives NK cells and neutrophils-dependent pulmonary inflammation ]]> https://biorxiv.org/content/10.64898/2026.03.10.710764v1?rss=1 Chen, C. Zhao, Y. Du, F. Liu, R. Zheng, X. Wu, S. Wang, Y. Qiu, F. Chen, L. Chen, R. Li, F. Gong, L. Long, Y. 2026-03-12 doi:10.64898/2026.03.10.710764 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Ultra-low-illumination, high-fidelity longitudinal monitoring of cerebral perfusion via deep learning-enhanced laser speckle contrast imaging ]]> https://biorxiv.org/content/10.64898/2026.03.10.710928v1?rss=1 1{square}hr)--can induce sublethal neural stress and cause signal drift, compromising physiological relevance and raising ethical concerns. To mitigate these limitations, we introduce TunLSCI--a TransUNet-based recovery network designed to reconstruct high-fidelity mouse cerebral blood flow (CBF) indices from ultra-low-illumination LSCI. We train our network on paired ultra-low-illumination (1.27 {micro}W/mm2) and conventional LSCI data ([~]200 {micro}W/mm2 illumination, the latter as reference), and demonstrate that it outperforms the conventional standard analytical LSCI processing pipeline based on stLASCA, particularly in reconstructing fine vasculature from few frames, suppressing speckle noise, and maintaining robustness against exposure variations. We validate that the proposed TunLSCI reduces illumination power density by [~]157-fold compared with conventional stLASCA, well below the safety threshold for cortical exposure in mice and markedly improves stability during a 2-hour continuous mouse CBF monitoring. Our method significantly minimizes the phototoxic burden of LSCI while preserving spatiotemporal fidelity and quantitative accuracy, thus enabling longitudinal, high-biosafety cerebral perfusion tracking in vivo over multi-hours. ]]> Xu, M. Li, F. Zhu, G. Ma, H. He, F. 2026-03-13 doi:10.64898/2026.03.10.710928 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ A generalized life-motion mechanism supports invariant directional coding of local biological kinematics in humans ]]> https://biorxiv.org/content/10.64898/2026.03.12.705481v1?rss=1 Gao, Z. Xing, L. Wang, R. Jiang, Y. 2026-03-16 doi:10.64898/2026.03.12.705481 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Opening the Black Box of Neural Computation from Neural Recordings with Gain-Modulated Linear Dynamical System ]]> https://biorxiv.org/content/10.64898/2026.03.12.711252v1?rss=1 Zhang, Y. Wang, Z. Li, X. Min, B. 2026-03-16 doi:10.64898/2026.03.12.711252 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Nanosecond laser-driven proton FLASH spares normal tissue cells by sustaining mitochondrial homeostasis and attenuating ferroptosis ]]> https://biorxiv.org/content/10.64898/2026.03.13.711531v1?rss=1 Shao, C. Zhang, Y. He, P. Yu, X. Peng, W. Chen, J. Hu, H. Wang, Y. Xiao, M. Liu, C. Sui, L. Dai, T. Mu, X. Jia, X. Bin, J. Huang, Q. 2026-03-16 doi:10.64898/2026.03.13.711531 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ TracePheno Enables Function-First Inference of Trace-ElementPhenotypes from Microbiome Profiles ]]> https://biorxiv.org/content/10.64898/2026.03.15.711888v1?rss=1 ZHOU, J. 2026-03-16 doi:10.64898/2026.03.15.711888 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Exploration of Orally Disintegrating Tablet for Sublingual Vaccination against Mucosal Bacterial Infection ]]> https://biorxiv.org/content/10.64898/2026.03.14.711758v1?rss=1 Liu, Y. Cai, Q. Hu, X. Liu, X. Guo, P. Zhang, Y. Liu, H. Wang, W. Zheng, D. Pan, C. Guo, L. Yu, X. Zhang, Q. Wang, D. Qiu, Y. Wang, D. Li, W. Du, Y. Ma, G. Xu, J. Wang, S. Liu, Y. Wei, W. 2026-03-17 doi:10.64898/2026.03.14.711758 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ MetaReact: A Reaction-Aware Transformer for End-to-End Prediction of Drug Metabolism ]]> https://biorxiv.org/content/10.64898/2026.03.14.711529v1?rss=1 Wang, Y. Rao, J. Zhang, W. Shi, Y. Zeng, C. Cui, R. Wang, Y. Xiong, J. Li, X. Zheng, M. 2026-03-18 doi:10.64898/2026.03.14.711529 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ A circRNA-based uricase replacement therapy for sustained treatment of hyperuricemia ]]> https://biorxiv.org/content/10.64898/2026.03.19.712815v1?rss=1 Zhang, Z. Zhong, J. Zhang, K. Hu, J. Yang, Y. Wang, Z. 2026-03-19 doi:10.64898/2026.03.19.712815 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ DNA-triggered AIM2 condensation orchestrates immune activation and regulation ]]> https://biorxiv.org/content/10.64898/2026.03.18.712789v1?rss=1 Li, Q. Geng, X. Yan, H. Li, Z. Shi, M. Zhu, Z. Niu, T. Zhao, C. Shu, K. Gao, Y. Feng, H. Liu, S. Jiang, Q. Bu, P. Li, D. Gao, P. 2026-03-20 doi:10.64898/2026.03.18.712789 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Rapid and robust sex determination from ancient enamel proteomes using protSexInferer ]]> https://biorxiv.org/content/10.64898/2026.03.23.713598v1?rss=1 Bai, F. Wu, Z. Xing, S. Fu, Q. 2026-03-25 doi:10.64898/2026.03.23.713598 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ CombinGym: a benchmark platform for machine learning-assisted design of combinatorial protein variants ]]> https://biorxiv.org/content/10.64898/2026.03.24.714074v1?rss=1 Chen, Y. Fu, L. Lu, X. Li, W. Gao, Y. Wang, Y. Ruan, Z. Si, T. 2026-03-25 doi:10.64898/2026.03.24.714074 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ A Conserved Metabolic Oxidative Axis Underlies Immune Cell Cryo-vulnerability ]]> https://biorxiv.org/content/10.64898/2026.03.26.714376v1?rss=1 Mo, Z. Yang, H. Zhang, M. Cao, H. Wang, L. Tao, K. Chen, X. Tian, C. Han, C. Bustamante, C. Liu, Z. 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