bioRxiv Channel: National Taiwan University https://biorxiv.org This feed contains articles for bioRxiv Channel "National Taiwan University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ R2d2 drives selfish sweeps in the house mouse ]]> https://biorxiv.org/content/10.1101/024851v1?rss=1 John P Didion Andrew Parker Morgan Liran Yadgary Timothy A Bell Rachel Clara McMullan Lydia Ortiz de Solorzano Janice Britton-Davidian Carol J Bult Karl J Campbell Riccardo Castiglia Yung-Hao Ching Amanda J Chunco James J Crowley Elissa J Chesler John E French Sofia I Gabriel Daniel M Gatti Theodore Garland Eva B Giagia-Athanasopoulou Mabel D Giménez Sofia A Grize İslam Gündüz Andrew Holmes Heidi C Hauffe Jeremy S Herman James M Holt Kunji Hua Wesley J Jolley Anna K Lindholm María J López-Fuster George Mitsainas Maria Mathias Leonard McMillan M Graça Ramalhinho Barbara Rehermann Stephan P Ross 2015-08-20 doi:10.1101/024851 Cold Spring Harbor Laboratory Press 2015-08-20 <![CDATA[ Further genetic diversification in multiple tumors and an evolutionary perspective on therapeutics ]]> https://biorxiv.org/content/10.1101/025429v1?rss=1 Yong Tao Zheng Hu Shaoping Ling Shiou-Hwie Yeh Weiwei Zhai Ke Chen Chunyan Li Yu Wang Kaile Wang Hurng-Yi Wang Eric A Hungate Kenan Onel Jiang Liu Changqing Zeng Richard R Hudson Pei-Jer Chen Xuemei Lu Chung-I Wu 2015-08-25 doi:10.1101/025429 Cold Spring Harbor Laboratory Press 2015-08-25 <![CDATA[ Quantifying Differences and Similarities in Whole-brain White Matter Architecture Using Local Connectome Fingerprints ]]> https://biorxiv.org/content/10.1101/043778v1?rss=1 Fang-Cheng Yeh Jean Vettel Aarti Singh Barnabas Poczos Scott Grafton Kirk Erickson Wen-Yih Isaac Tseng Timothy Verstynen 2016-03-15 doi:10.1101/043778 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ An atypical role for the myeloid receptor Mincle in CNS injury ]]> https://biorxiv.org/content/10.1101/044602v1?rss=1 Thiruma Arumugam Silvia Manzanero Milena Furtado Patrick Biggins Yu-Hsuan Hsieh Mathias Gelderblom Kelli MacDonald Ekaterina Salimova Yu-I Li Othmar Korn Deborah Dewar I Mhairi Macrae Robert Ashman Sung-Chun Tang Nadia Rosenthal Marc Ruitenberg Tim Magnus Christine Wells 2016-03-19 doi:10.1101/044602 Cold Spring Harbor Laboratory Press 2016-03-19 <![CDATA[ Bias in community-weighted mean analysis relating species attributes to sample attributes: justification and remedy ]]> https://biorxiv.org/content/10.1101/046946v1?rss=1 David Zeleny 2016-04-05 doi:10.1101/046946 Cold Spring Harbor Laboratory Press 2016-04-05 <![CDATA[ Elevated nonlinearity as indicator of transition to overexploitation in fish stocks ]]> https://biorxiv.org/content/10.1101/051532v1?rss=1 Vasilis Dakos Sarah Glaser Chih-hao Hsieh George Sugihara 2016-05-03 doi:10.1101/051532 Cold Spring Harbor Laboratory Press 2016-05-03 <![CDATA[ Actomyosin Contractility Drives Bile Regurgitation as an Early Homeostatic Response to Increased Biliary Pressure in Obstructive Cholestasis ]]> https://biorxiv.org/content/10.1101/077792v1?rss=1 Kapish Gupta Qiushi Li Junjun Fan Eliza Li Shan Fong Ziwei Song Shupei Mo Haoyu Tang Inn Chuan Ng Chan Way Ng Pornteera Pawijit Shuangmu Zhuo Chen-Yuan Dong Boon Chuan Low Aileen Wee Yock Young Dan Pakorn Kanchanawong Peter So Virgile Viasnoff Hanry Yu 2016-09-28 doi:10.1101/077792 Cold Spring Harbor Laboratory Press 2016-09-28 <![CDATA[ Logic Synthesis of Recombinase-Based Genetic Circuits ]]> https://biorxiv.org/content/10.1101/088930v1?rss=1 Chiu, T.-Y. Jiang, J.-H. R. 2016-11-21 doi:10.1101/088930 Cold Spring Harbor Laboratory Press 2016-11-21 <![CDATA[ Biocuration as an undergraduate training experience: Improving the annotation of the insect vector of Citrus greening disease ]]> https://biorxiv.org/content/10.1101/099168v1?rss=1 Saha, S. Hosmani, P. S. Villalobos-Ayala, K. Miller, S. Shippy, T. Rosendale, A. Cordola, C. Bell, T. Mann, H. DeAvila, G. DeAvila, D. Moore, Z. Buller, K. Ciolkevich, K. Nandyal, S. Mahoney, R. Voorhis, J. V. Dunlevy, M. Farrow, D. Hunter, D. Morgan, T. Shore, K. Guzman, V. Izsak, A. Dixon, D. E. Cano, L. Cridge, A. Johnson, S. Cantarel, B. L. Richardson, S. English, A. Leng, N. Cao, X. Jiang, H. Childers, C. Chen, M.-J. Flores, M. Hunter, W. Cilia, M. Mueller, L. A. Munoz-Torres, M. Nelson, D. Poelchau, M. F. Benoit, J. Wiersma-Koch, H. D'elia, T. 2017-01-09 doi:10.1101/099168 Cold Spring Harbor Laboratory Press 2017-01-09 <![CDATA[ Fragile dynamics enable diverse genomic determinants to influence arrhythmia propensity ]]> https://biorxiv.org/content/10.1101/101162v1?rss=1 Kamerzell, T. J. Sobie, E. A. Yang, K.-C. Nerbonne, J. M. MacRae, C. A. Iyengar, R. 2017-01-18 doi:10.1101/101162 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ The Genomic Landscape Of Tree Rot In Phellinus noxius And Its Hymenochaetales Members ]]> https://biorxiv.org/content/10.1101/132712v1?rss=1 Chung, C.-L. Lee, J. T. Akiba, M. Lee, H.-H. Kuo, T.-H. Liu, D. Ke, H.-M. Yokoi, T. Roa, M. B. Lu, M. J. Chang, Y.-Y. Ann, P.-J. Tsai, J.-N. Chen, C.-Y. Tzean, S.-S. Ota, Y. Hattori, T. Sahashi, N. Liou, R.-F. Kikuchi, T. Tsai, I. J. 2017-05-07 doi:10.1101/132712 Cold Spring Harbor Laboratory Press 2017-05-07 <![CDATA[ NINJA-Associated ERF19 Negatively Regulates Arabidopsis Pattern-Triggered Immunity ]]> https://biorxiv.org/content/10.1101/180059v1?rss=1 Huang, P.-Y. Zhang, J. Jiang, B. Yu, J.-H. Lu, Y.-P. Chung, K. Zimmerli, L. 2017-08-23 doi:10.1101/180059 Cold Spring Harbor Laboratory Press 2017-08-23 <![CDATA[ A New Evidence of Lubrication Hypothesis on Nephila pilipes Spider Silk Spinning ]]> https://biorxiv.org/content/10.1101/188771v1?rss=1 Wu, H.-C. Wu, S.-R. Yang, J.-C. 2017-09-15 doi:10.1101/188771 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Brain-behavior patterns define a dimensional biotype in medication-naïve adults with attention-deficit hyperactivity disorder ]]> https://biorxiv.org/content/10.1101/190660v1?rss=1 Lin, H.-Y. Cocchi, L. Zalesky, A. Lv, J. Perry, A. Tseng, W.-Y. I. Kundu, P. Breakspear, M. Gau, S. S.-F. 2017-09-19 doi:10.1101/190660 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ Genetic load and mutational meltdown in cancer cell populations ]]> https://biorxiv.org/content/10.1101/193482v1?rss=1 Zhang, Y. Li, Y. Zhu, T. Shen, X. Tao, Y. Li, T. Li, X. Wang, D. Ma, Q. Hu, Z. Liu, J. Zheng, C. Ruan, J. Cai, J. Wu, C.-I. Wang, H.-Y. Lu, X. 2017-10-05 doi:10.1101/193482 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Response to Qian et al (2017): Daily and seasonal climate variations are both critical in the evolution of species’ elevational range size ]]> https://biorxiv.org/content/10.1101/195248v1?rss=1 Chan, W.-P. Chen, I.-C. Colwell, R. K. Liu, W.-C. Huang, C.-y. Shen, S.-F. 2017-09-30 doi:10.1101/195248 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome ]]> https://biorxiv.org/content/10.1101/201731v1?rss=1 Panfilio, K. A. Vargas Jentzsch, I. M. Benoit, J. B. Erezyilmaz, D. Suzuki, Y. Colella, S. Robertson, H. M. Poelchau, M. F. Waterhouse, R. M. Ioannidis, P. Weirauch, M. T. Hughes, D. S. T. Murali, S. C. Werren, J. H. Jacobs, C. G. C. Duncan, E. J. Armisen, D. Vreede, B. M. I. Baa-Puyoulet, P. Berger, C. S. Chang, C.-c. Chao, H. Chen, M.-J. M. Chen, Y.-T. Childers, C. P. Chipman, A. D. Cridge, A. G. Crumiere, A. J. J. Dearden, P. K. Didion, E. M. Dinh, H. doddapaneni, h. Dolan, A. Dugan-Perez, S. Extavour, C. G. Febvvay, G. Friedrich, M. Ginzburg, N. Han, Y 2017-10-11 doi:10.1101/201731 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Landscape structured by physical settings and benthic polychaete and avifauna habitat uses in a mangrove-vegetated estuary ]]> https://biorxiv.org/content/10.1101/2019.12.12.874008v1?rss=1 Shih, S.-S. Ding, T.-S. Chen, C.-P. Huang, S.-C. Hsieh, H.-L. 2019-12-12 doi:10.1101/2019.12.12.874008 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Thermal cycling protects SH-SY5Y cells against hydrogen peroxide and -amyloid-induced cell injury through stress response mechanisms involving Akt pathway ]]> https://biorxiv.org/content/10.1101/2019.12.19.877373v1?rss=1 Chen, W.-T. Kuo, Y.-Y. Lin, G.-B. Lu, C.-H. Hsu, H.-P. Sun, Y.-K. Chao, C.-Y. 2019-12-19 doi:10.1101/2019.12.19.877373 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ A genomic view of coral-associated Prosthecochloris and a companion sulfate-reducing bacterium ]]> https://biorxiv.org/content/10.1101/2019.12.20.883736v1?rss=1 Chen, Y.-H. Yang, S.-H. Tandon, K. Lu, C.-Y. Chen, H.-J. Shih, C.-J. Tang, S.-L. 2019-12-20 doi:10.1101/2019.12.20.883736 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Effect of high frequency and low intensity pulsed electric field on protecting SH-SY5Y cells against hydrogen peroxide and β-amyloid-induced cell injury via ERK pathway ]]> https://biorxiv.org/content/10.1101/2019.12.30.891499v1?rss=1 Chen, W.-T. Lin, G.-B. Kuo, Y.-Y. Hsieh, C.-H. Lu, C.-H. Sun, Y.-K. Chao, C.-Y. 2019-12-31 doi:10.1101/2019.12.30.891499 Cold Spring Harbor Laboratory Press 2019-12-31 <![CDATA[ Hyaluronic Acid on the Urokinase Sustained Release with a Hydrogel System Composed of Poloxamer 407: Enhanced Stability of Intracellular Interaction by Adding HA. ]]> https://biorxiv.org/content/10.1101/2019.12.31.891614v1?rss=1 Hsieh, H. Y. Lin, W. Y. Lee, A. L. Li, Y. C. Chen, Y. J. Chen, K. C. Young, T.-H. 2020-01-01 doi:10.1101/2019.12.31.891614 Cold Spring Harbor Laboratory Press 2020-01-01 <![CDATA[ Long-term warming weakens stabilizing effects of biodiversity in aquatic ecosystems ]]> https://biorxiv.org/content/10.1101/2020.01.06.896746v1?rss=1 Chang, C.-W. Ye, H. Miki, T. Deyle, E. R. Souissi, S. Anneville, O. Adrian, R. Chiang, Y.-R. Ichise, S. Kumagai, M. Matsuzaki, S.-i. S. Shiah, F.-K. Wu, J.-T. Hsieh, C.-h. Sugihara, G. 2020-01-07 doi:10.1101/2020.01.06.896746 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ The fate of standing variation and new mutation under climate change ]]> https://biorxiv.org/content/10.1101/2020.01.12.903427v1?rss=1 Lu, C.-Y. Lee, C.-R. 2020-01-14 doi:10.1101/2020.01.12.903427 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Macrofaunal Diversity and Community Structure of the DeSoto Canyon and Adjacent Slope ]]> https://biorxiv.org/content/10.1101/2020.01.15.908194v1?rss=1 2000 m. Abundance differed between depth groups. Species richness was lowest for the deepest group and evenness was lowest for the shallowest. Community structure within the canyon most related to fluorometry and oxygen saturation, combined with any of salinity, particulate organic carbon, sediment organic carbon, or slope. Canyon wall abundances were higher than the canyon axis or adjacent slope. Community structure differed between all three habitat types. Ordination of community structure suggests a longitudinal pattern that potentially tracks with increasing sea-surface chlorophyll that occurs in the eastward direction across the northern GOM. Canyon and slope differences may result from seasonal water masses entrained by canyon topography characterized by high salinity, oxygen saturation, fluorometry, and turbidity. Higher fluorescence and turbidity in the canyon did not translate into higher sediment organic matter. Flushing along canyon wall channels and the canyon axis may explain the low organic matter. Differences in abundance and structure between the canyon wall and axis may result from microhabitat heterogeneity due to potential hydrocarbon seepage, organically enriched sediment deposits along channels, or remnant influence from the Deepwater Horizon blowout. ]]> Shantharam, A. K. Wei, C.-L. Silva, M. Baco, A. R. 2020-01-16 doi:10.1101/2020.01.15.908194 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ The effects of seasonal climate variability on dengueannual incidence in Hong Kong: A modellingstudy ]]> https://biorxiv.org/content/10.1101/2020.01.20.912097v1?rss=1 Yuan, H.-Y. Liang, J. Lin, P.-S. Sucipto, K. Tsegaye, M. M. Wen, T.-H. Pfeiffer, S. Pfeiffer, D. P. 2020-01-21 doi:10.1101/2020.01.20.912097 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Dietary supplementation with PUFAs rescues the eggshell defects caused by seipin mutations in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.01.23.916718v1?rss=1 Bai, X. Huang, L.-J. Chen, S.-W. Nebenfuehr, B. Wysolmerski, B. Wu, J.-C. Olson, S. K. Golden, A. Wang, C.-W. 2020-01-23 doi:10.1101/2020.01.23.916718 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ An allometric scaling approach to estimate epiphytic bryophyte biomass in tropical montane cloud forests ]]> https://biorxiv.org/content/10.1101/2020.02.01.928515v1?rss=1 Lai, G.-Y. Liu, H.-C. Kuo, A. J. Huang, C.-y. 2020-02-02 doi:10.1101/2020.02.01.928515 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Reciprocal transplant experiment in lakes with disparate trophic states show resolution dependent partial functional redundancy ]]> https://biorxiv.org/content/10.1101/2020.02.01.930198v1?rss=1 Tandon, K. Wan, M.-T. Yang, C.-C. Yang, S.-H. Baatar, B. Chiu, C.-Y. Tsai, J.-W. Liu, W.-C. Ng, C. S. Tang, S.-L. 2020-02-02 doi:10.1101/2020.02.01.930198 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Non-canonical regulation of glycogenolysis and the Warburg phenotype by soluble adenylyl cyclase ]]> https://biorxiv.org/content/10.1101/2020.02.02.929901v1?rss=1 Chang, J.-C. Go, S. Gilglioni, E. H. Li, H. L. Huang, H.-L. Levin, L. R. Buck, J. Verhoeven, A. J. Oude Elferink, R. P. J. 2020-02-02 doi:10.1101/2020.02.02.929901 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Categorizing SHR and WKY rats by chi2 algorithm and decision tree ]]> https://biorxiv.org/content/10.1101/2020.02.03.931899v1?rss=1 Tsai, P.-R. Chen, K.-H. Hong, T.-M. Wang, F.-N. Huang, T.-Y. 2020-02-03 doi:10.1101/2020.02.03.931899 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Excessive O-GlcNAcylation causes heart failure and sudden death ]]> https://biorxiv.org/content/10.1101/2020.02.11.943910v1?rss=1 Umapathi, P. Banerjee, P. Zachara, N. E. Abrol, N. Wang, Q. Mesubi, O. O. Luczak, E. D. Wu, Y. Granger, J. M. Wei, A.-C. Reyes Gaido, O. E. Florea, L. D. Talbot, C. C. Hart, G. W. Anderson, M. E. 2020-02-12 doi:10.1101/2020.02.11.943910 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Predicting molecular subtypes of breast cancer using pathological images by deep convolutional neural network from public dataset ]]> https://biorxiv.org/content/10.1101/2020.02.12.946723v1?rss=1 Phan, N. N. Huang, C.-C. Chuang, E. Y. 2020-02-13 doi:10.1101/2020.02.12.946723 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Mitochondrial CaMKII causes metabolic reprogramming, energetic insufficiency, and dilated cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2020.02.13.947564v1?rss=1 Luczak, E. D. Wu, Y. Granger, J. M. Joiner, M.-l. A. Wilson, N. R. Gupta, A. Umapathi, P. Murphy, K. R. Reyes Gaido, O. E. Sabet, A. Corradini, E. Wang, Y. Heck, A. J. Wei, A.-C. Weiss, R. G. Anderson, M. E. 2020-02-14 doi:10.1101/2020.02.13.947564 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ G protein-Coupled Receptor Distribution Impacts the Effectiveness of Signal Transmission. ]]> https://biorxiv.org/content/10.1101/2020.02.18.953554v1?rss=1 Chou, M.-Y. Hu, Y.-Y. Chuang, H.-h. 2020-02-18 doi:10.1101/2020.02.18.953554 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Systematic functional analysis of Rab GTPasesreveals limits of neuronal robustness in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.02.21.959452v1?rss=1 Kohrs, F. E. Daumann, I.-M. Pavlovic, B. Jin, E. J. Lin, S.-C. Port, F. Kiral, F. R. Wolfenberg, H. Mathejczyk, T. F. Chan, C.-C. Boutros, M. Hiesinger, P. R. 2020-02-22 doi:10.1101/2020.02.21.959452 Cold Spring Harbor Laboratory Press 2020-02-22 <![CDATA[ Heteroplasmy variability in individuals with biparentally inherited mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/2020.02.26.939405v1?rss=1 Slone, J. Zou, W. Luo, S. Schmitt, E. S. Chen, S. M. Wang, X. Brown, J. Bromwell, M. Chien, Y.-H. Hwu, W.-L. Fan, P.-C. Lee, N.-C. Wong, L.-J. Zhang, J. Huang, T. 2020-02-26 doi:10.1101/2020.02.26.939405 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Redirected tropisms of extracellular vesicles and exomeres yield distinct biodistribution profiles ]]> https://biorxiv.org/content/10.1101/2020.03.27.012625v1?rss=1 200 nm) EVs. PalmGRET emits robust, sustained signals and allows the visualization, tracking and quantification of the EPs from whole-animal to nanoscopic resolutions under different imaging modalities, including bioluminescence, BRET and fluorescence. Using PalmGRET, we show that EPs released by lung metastatic hepatocellular carcinoma (HCC) exhibit lung tropism with varying distributions to other major organs in immunocompetent mice. We further demonstrate that gene knockdown of lung-tropic membrane proteins, solute carrier organic anion transporter family member 2A1 (Slco2a1), alanine aminopeptidase (Cd13) and chloride intracellular channel (Clic1) decreases HCC-EP distribution to the lungs and yields distinct biodistribution profiles. We anticipate that EP-specific imaging, quantitative assays and detailed in vivo characterization to be a starting point for more accurate and comprehensive in vivo models of EP biology and therapeutic design. ]]> Wu, A. Y.-T. Sung, Y.-C. Chou, S. T.-Y. Guo, V. Chien, J. C.-Y. Ko, J. J.-S. Yang, A. L. Chuang, J.-C. Huang, H.-C. Wu, Y. Ho, M.-R. Ericsson, M. Lin, W.-W. Cheung, C. H. Y. Juan, H.-F. Ueda, K. Chen, Y. Lai, C. P.-K. 2020-03-28 doi:10.1101/2020.03.27.012625 Cold Spring Harbor Laboratory Press 2020-03-28 <![CDATA[ A multiplexed bioluminescent reporter for sensitive and non-invasive tracking of DNA double strand break repair dynamics in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2020.03.30.015271v1?rss=1 Chien, J. C. Tabet, E. Pinkham, K. da Hora, C. C. Chang, J. C. Lin, S. Badr, C. E. Lai, C. P. 2020-03-31 doi:10.1101/2020.03.30.015271 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Prediction and discrimination of skeletal muscle function by bioelectrical impedance vector analysis using a standing impedance analyzer in healthy Taiwanese adults ]]> https://biorxiv.org/content/10.1101/2020.03.30.016196v1?rss=1 Lee, L.-W. Lu, H.-K. Chen, Y.-Y. Lai, C.-L. Chu, L.-P. Hsieh, M.-C. Hsieh, K.-C. 2020-03-30 doi:10.1101/2020.03.30.016196 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ The origin and underlying driving forces of the SARS-CoV-2 outbreak ]]> https://biorxiv.org/content/10.1101/2020.04.12.038554v1?rss=1 Chaw, S.-M. Tai, J.-H. Chen, S.-L. Hsieh, C.-H. Chang, S.-Y. Yeh, S.-H. Yang, W.-S. Chen, P.-J. Wang, H.-Y. 2020-04-14 doi:10.1101/2020.04.12.038554 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Identification of a Novel Picorna-like Virus in Coconut Rhinoceros Beetles (Oryctes rhinoceros). ]]> https://biorxiv.org/content/10.1101/2020.04.15.042309v1?rss=1 Etebari, K. Shelomi, M. Furlong, M. J. 2020-04-17 doi:10.1101/2020.04.15.042309 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Zinc oxide nanoparticles modulate the gene expression of ZnT1 and ZIP8 to manipulate zinc homeostasis and stress-induced cytotoxicity in human neuroblastoma SH-SY5Y cells ]]> https://biorxiv.org/content/10.1101/2020.04.22.055152v1?rss=1 Pan, C.-Y. Lin, F.-Y. Kao, L.-S. Huang, C.-C. Liu, P.-S. 2020-04-22 doi:10.1101/2020.04.22.055152 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Circulating microRNA-762 upregulates colorectal cancer might through Wnt-1/b-catenin signaling ]]> https://biorxiv.org/content/10.1101/2020.04.22.056796v1?rss=1 Lai, P.-S. Chang, W.-M. Chen, Y.-Y. Lin, Y.-F. Liao, H.-F. Chen, C.-Y. 2020-04-24 doi:10.1101/2020.04.22.056796 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Mind Wandering in Sensory Cortices ]]> https://biorxiv.org/content/10.1101/2020.04.27.064360v1?rss=1 Hung, S.-M. Hsieh, P.-J. 2020-04-28 doi:10.1101/2020.04.27.064360 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Toward the pathogenicity of the SLC26A4 p.C565Y variant using a genetically driven mouse model ]]> https://biorxiv.org/content/10.1101/2020.04.29.067918v1?rss=1 G/C565Y) for this variant. Subsequent phenotypic characterization revealed that mice segregating these genotypes demonstrated normal auditory and vestibular functions and normal inner ear morphology and expression of pendrin. These findings indicate that the p.C565Y variant is non-pathogenic for mice and that a single p.C565Y allele is sufficient to maintain normal inner ear physiology in mice. Our results highlight the differences in the pathogenicity associated with certain SLC26A4 variants between transgenic mice and humans, which should be taken into consideration while interpreting the results of animal studies for SLC26A4-related deafness. ]]> Hu, C.-J. Lu, Y.-C. Yang, T.-H. Chan, Y.-H. Tsai, C.-Y. Yu, I.-S. Lin, S.-W. Liu, T.-C. Cheng, Y.-F. Wu, C.-C. Hsu, C.-J. 2020-04-29 doi:10.1101/2020.04.29.067918 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Epigenetic therapy remodels the immune synaptic cytoskeleton to potentiate cancer susceptibility to γδ T cells ]]> https://biorxiv.org/content/10.1101/2020.04.30.069955v1?rss=1 Weng, R. R. Lu, H.-H. Lin, C.-T. Fan, C.-C. Lin, R.-S. Huang, T.-C. Lin, S.-Y. Huang, Y.-J. Juan, Y.-H. Wu, Y.-C. Hung, Z.-C. Liu, C. Lin, X.-H. Hsieh, W.-C. Chiu, T.-Y. Liao, J.-C. Chiu, Y.-L. Chen, S.-Y. Yu, C.-J. Tsai, H.-C. 2020-05-02 doi:10.1101/2020.04.30.069955 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Distinct Inductions of and Responses to Type I and Type III Interferons PromoteInfections in Two SARS-CoV-2 Isolates ]]> https://biorxiv.org/content/10.1101/2020.04.30.071357v1?rss=1 Hsin, F. Chao, T.-L. Chan, Y.-R. Kao, H.-C. Liu, W.-D. Wang, J.-T. Pang, Y.-H. Lin, C.-H. Tsai, Y.-M. Lin, J.-Y. Chang, S.-Y. Liu, H. M. 2020-05-01 doi:10.1101/2020.04.30.071357 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Benefit of Drought on an Herbivore of Herbaceous Plants: Enemy Free Space and Reduced Competition ]]> https://biorxiv.org/content/10.1101/2020.05.25.115519v1?rss=1 Lin, P.-A. Liu, C.-M. Ou, J.-A. Sun, C.-H. Chuang, W.-P. Ho, C.-K. Kinoshita, N. Felton, G. W. 2020-05-28 doi:10.1101/2020.05.25.115519 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Dynamin-2 regulates synaptic podosome maturation to facilitate neuromuscular junction development ]]> https://biorxiv.org/content/10.1101/2020.05.30.125062v1?rss=1 Lin, S.-S. Hsieh, T.-L. Liou, G.-G. Li, T.-N. Lin, H.-C. Chang, C.-W. Wu, H.-Y. Yao, C.-K. Liu, Y.-W. 2020-05-31 doi:10.1101/2020.05.30.125062 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Dihydroceramide desaturase regulates the compartmentalization of Rac1 for neuronal oxidative stress ]]> https://biorxiv.org/content/10.1101/2020.06.01.128579v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@174c3b0org.highwire.dtl.DTLVardef@db65e5org.highwire.dtl.DTLVardef@1fea501org.highwire.dtl.DTLVardef@10318f7_HPS_FORMAT_FIGEXP M_FIG A DEGS1/ifc converts dihydroceramide to ceramide in neuronal cells, and the endolysosomal NOX complex is not activated. B Dihydroceramide accumulates without functional DEGS1/ifc and causes alterations in membrane microdomains and recruits active Rac1 to endolysosomes. The activation of endolysosomal Rac1-NOX complex elevates cytosolic ROS levels, causing neurodegeneration. C_FIG In Brief (eTOC blurb)Deficiency in dihydroceramide desaturase causes oxidative stress-mediated neurological disorders. Tzou and Su et al. show that increased dihydroceramide causes the relocalization of active Rac1, whilst inhibition of the Rac1-NOX ameliorates the oxidative stress and neuronal defects. NOX inhibitor apocynin may provide new direction of treatments for patients with DEGS1 variants. HighlightsO_LIDeficiency in dihydroceramide (dhCer) desaturase induces cytoplasmic ROS elevation C_LIO_LIdhCer alters the binding of active Rac1 to reconstituted organelle membranes C_LIO_LIActive Rac1 is enriched in endolysosomes in ifc-KO neurons for ROS genesis C_LIO_LIRac1-NADPH oxidase elicits ROS, degenerating leukodystrophy-related neuronal cells C_LI ]]> Tzou, F.-Y. Su, T.-Y. Yu, Y.-L. Yeh, Y.-H. Liu, C.-C. Huang, S.-Y. Chan, C.-C. 2020-06-02 doi:10.1101/2020.06.01.128579 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ DNMT3b Dysfunction Promotes DNA cleavages at Centromeric R-loops to Increase Centromere Instability ]]> https://biorxiv.org/content/10.1101/2020.06.04.133272v1?rss=1 Shih, H.-T. Chen, W.-Y. Wang, H.-Y. Huang, H.-D. Chou, C.-H. Chang, Z.-F. 2020-06-04 doi:10.1101/2020.06.04.133272 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Temporal expectation modulates the neural dynamics of delayed responses to working memory representations ]]> https://biorxiv.org/content/10.1101/2020.06.08.137539v1?rss=1 Chen, F.-W. Li, C.-H. Kuo, B.-C. 2020-06-09 doi:10.1101/2020.06.08.137539 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Three Dimensional Multi-gene Expression Maps Reveal Cell Fate Changes Associated with Laterality Reversal of Zebrafish Habenula ]]> https://biorxiv.org/content/10.1101/2020.07.03.182949v1?rss=1 Wang, G.-T. Pan, H.-Y. Lang, W.-H. Yu, Y.-D. Hsieh, C.-H. Kuan, Y.-S. 2020-07-05 doi:10.1101/2020.07.03.182949 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ A Strategy to Treat COVID-19 Disease with Targeted Delivery of Inhalable Liposomal Hydroxychloroquine: A Non-clinical Pharmacokinetic Study ]]> https://biorxiv.org/content/10.1101/2020.07.09.196618v1?rss=1 Tien-Tzu Tai Tzung-Ju Wu Huey-Dong Wu Yi-Chen Tsai Hui-Ting Wang An-Min Wang Sheue-Fang Shih Yee-Chun Chen 2020-07-10 doi:10.1101/2020.07.09.196618 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ ASIC1a is required for neuronal activation via low-intensity ultrasound stimulation in mouse brain ]]> https://biorxiv.org/content/10.1101/2020.07.10.196634v1?rss=1 30 mW/cm2). Using micropipette ultrasound in calcium imaging, we show the reactions of CNS neurons to ultrasound is through ASIC1a channels, pointing to the molecular basis for direct ultrasound neuromodulation at low intensity. Furthermore, we also show evidence of neurogenesis with the same ultrasound stimulation, suggesting potential therapeutic translation. ]]> Jormay Lim Ya-Cherng Chu Chen-Ming Hao Wei-Hao Liao Shao-Shien Lin Sherry Hsu Hsiao-Hsin Tai Ya-Chih Chien Dar-Ming Lai Wen-Shiang Chen Chih-Cheng Chen Jaw-Lin Wang 2020-07-10 doi:10.1101/2020.07.10.196634 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ A Statistical Framework for QTL Hotspot Detection ]]> https://biorxiv.org/content/10.1101/2020.08.13.249342v1?rss=1 Kao, C.-H. Wu, P.-Y. Yang, M.-H. 2020-08-14 doi:10.1101/2020.08.13.249342 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Inhibition of Severe Acute Respiratory Syndrome Coronavirus 2 main protease by tafenoquine in vitro ]]> https://biorxiv.org/content/10.1101/2020.08.14.250258v1?rss=1 Chen, Y. Yang, W.-H. Huang, L.-M. Wang, Y.-C. Yang, C.-S. Liu, Y.-L. Hou, M.-H. Tsai, C.-L. Chou, Y.-Z. Huang, B.-Y. Hung, C.-F. Hung, Y.-L. Chen, J.-S. Chiang, Y.-P. Cho, D.-Y. Jeng, L.-B. Tsai, C.-H. Hung, M.-C. 2020-08-15 doi:10.1101/2020.08.14.250258 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Evaluation of Compatibility of 16S rRNA V3V4 and V4 Amplicon Libraries for Clinical Microbiome Profiling ]]> https://biorxiv.org/content/10.1101/2020.08.18.256818v1?rss=1 Liu, P.-Y. Wu, W.-K. Chen, C.-C. Panyod, S. Sheen, L.-Y. Wu, M.-S. 2020-08-20 doi:10.1101/2020.08.18.256818 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Segmentation boosting with compensation methods in optical coherence tomography angiography images ]]> https://biorxiv.org/content/10.1101/2020.08.20.258905v1?rss=1 Lee, Y.-C. Ding, J.-J. Yeung, L. Lee, T.-W. Chang, C.-J. Lin, Y.-T. Chang, R. Y. 2020-08-20 doi:10.1101/2020.08.20.258905 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Identifications of novel avian and mammalian deltaviruses filled the large evolutionally gaps and revealed inter-family transmission of deltaviruses ]]> https://biorxiv.org/content/10.1101/2020.08.30.274571v1?rss=1 Iwamoto, M. Shibata, Y. Kawasaki, J. Kojima, S. Li, Y.-T. Iwami, S. Wu, H.-L. Wada, K. Tomonaga, K. Watashi, K. Horie, M. 2020-08-31 doi:10.1101/2020.08.30.274571 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Schizophrenia, autism spectrum disorders and developmental disorders share specific disruptive coding mutations ]]> https://biorxiv.org/content/10.1101/2020.09.02.279265v1?rss=1 Rees, E. Creeth, H. Hwu, H.-G. Chen, W. J. Tsuang, M. Glatt, S. Rey, R. Kirov, G. Walters, J. Holmans, P. Owen, M. O'Donovan, M. 2020-09-02 doi:10.1101/2020.09.02.279265 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Dual GRIN lens two-photon endoscopy for high-speed volumetric and deep brain imaging ]]> https://biorxiv.org/content/10.1101/2020.09.19.304675v1?rss=1 Chien, Y.-F. Lin, J.-Y. Yeh, P.-T. Hsu, K.-J. Tsai, Y.-H. Chen, S.-K. Chu, S.-W. 2020-09-20 doi:10.1101/2020.09.19.304675 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ A new species of subgenus Typhlodromus (Anthoseius) De Leon (Acari: Phytoseiidae), and phytoseiid mites intercepted in samples imported from 12 different countries to Taiwan ]]> https://biorxiv.org/content/10.1101/2020.09.20.305656v1?rss=1 Liao, J.-R. Ho, C.-C. Ko, C.-C. 2020-09-21 doi:10.1101/2020.09.20.305656 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Multimodal Brain Age Gap as a Mediating Indicator in the Relation between Modifiable Dementia Risk Factors and Cognitive Functioning ]]> https://biorxiv.org/content/10.1101/2020.09.23.309369v1?rss=1 Chen, C.-L. Chen, P.-Y. Tung, Y.-H. Hsu, Y.-C. Tseng, W.-Y. I. 2020-09-23 doi:10.1101/2020.09.23.309369 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ MAP kinase Slt2p attenuates cell wall mRNA decay by downregulating the RNA-binding protein Rbp1p in response to stress ]]> https://biorxiv.org/content/10.1101/2020.09.30.319939v1?rss=1 Chang, L.-C. Wu, Y.-C. Chang, Y.-Y. Lee, F.-J. S. 2020-10-01 doi:10.1101/2020.09.30.319939 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ ezGeno: An Automatic Model Selection Package for Genomic Data Analysis ]]> https://biorxiv.org/content/10.1101/2020.09.30.319996v1?rss=1 Lin, J.-L. Hsieh, T.-T. Tung, Y.-A. Chen, X.-J. Hsiao, Y.-C. Yang, C.-L. Liu, T.-L. Chen, C.-Y. 2020-10-02 doi:10.1101/2020.09.30.319996 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ COVID-19: Variant screening, an important step towards precision epidemiology ]]> https://biorxiv.org/content/10.1101/2020.10.19.345140v1?rss=1 Chattopadhyay, A. Lu, T.-P. Shih, C.-Y. Lai, L.-C. Tsai, M.-H. Chuang, E. Y. 2020-10-19 doi:10.1101/2020.10.19.345140 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Two-photon microscopy at >500 volumes/second ]]> https://biorxiv.org/content/10.1101/2020.10.21.349712v1?rss=1 500-volumes/second imaging speed over ~200x200x200-m3. ]]> Tsai, Y.-H. Liu, C.-W. Lin, W.-K. Wang, C.-S. Chiang, C.-H. Singh, V. R. So, P. T. C. Chou, C.-F. Chu, S.-W. 2020-10-22 doi:10.1101/2020.10.21.349712 500 volumes/second]]> Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ External light dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/2020.10.23.351650v1?rss=1 Lee, C.-C. Lu, T.-H. Lee, I.-C. Zou, Y.-F. Yu, H.-T. Chen, S.-K. 2020-10-23 doi:10.1101/2020.10.23.351650 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Mitochondrial ATP Synthase Trafficking along Microtubules to Cell Surface Depends on KIF5B and DRP1 ]]> https://biorxiv.org/content/10.1101/2020.10.23.352385v1?rss=1 Chang, Y.-W. Yang, T. T. Chen, M.-C. Liaw, Y.-g. Yin, C.-F. Huang, T.-Y. Hou, J.-T. Hung, Y.-H. Hsu, C.-L. Huang, H.-C. Juan, H.-F. 2020-10-23 doi:10.1101/2020.10.23.352385 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ EGF-Activated Grb7 Confers to STAT3-Mediated EPHA4 Gene Expression in Regulating Lung Cancer Progression ]]> https://biorxiv.org/content/10.1101/2020.10.24.353268v1?rss=1 Chu, P.-Y. Tai, Y.-L. Wang, M.-Y. Lee, H. Kuo, W. H. Shen, T.-L. 2020-10-24 doi:10.1101/2020.10.24.353268 Cold Spring Harbor Laboratory Press 2020-10-24 <![CDATA[ A novel equilibrative nucleoside transporter 1 inhibitor alleviates Tau-mediated neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.10.25.334201v1?rss=1 Chang, C.-P. Chang, Y.-G. Chuang, P.-Y. Nguyen, A. T. N. Chou, F.-Y. Cheng, S.-J. Chen, H.-M. Jin, L.-W. Carvalho, K. Huin, V. Buee, L. Blum, D. Liao, Y.-F. Lin, C.-J. Chern, Y. 2020-10-26 doi:10.1101/2020.10.25.334201 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Canopy micrometeorology monitoring in diverse climates innovatively improves the evaluation heat-induced sterility of rice under climate change ]]> https://biorxiv.org/content/10.1101/2020.11.01.363143v1?rss=1 Yoshimoto, M. Fukuoka, M. Tsujimoto, Y. Matsui, T. Kobayasi, K. Saito, K. van Oort, P. A. J. Inusah, B. I. Y. Vijayalakshmi, C. Vijayalakshmi, D. Weerakoon, W. M. W. Chandradasa, S. Myint Daw, T. T. Phyo Daw, Z. C. Tian, X. Lur, H.-S. Yang, C.-M. Tarpley, L. Manigbas, N. L. Hasegawa, T. 2020-11-02 doi:10.1101/2020.11.01.363143 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ accuEnhancer: Accurate enhancer prediction by integration of multiple cell type data with deep learning ]]> https://biorxiv.org/content/10.1101/2020.11.10.375717v1?rss=1 Tung, Y.-A. Yang, W.-T. Hsieh, T.-T. Chang, Y.-C. Wu, J.-T. Oyang, Y.-J. Chen, C.-Y. 2020-11-11 doi:10.1101/2020.11.10.375717 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron retention of ABA-responsive genes ]]> https://biorxiv.org/content/10.1101/2020.11.17.386672v1?rss=1 Tu, Y.-T. Chen, C.-Y. Huang, Y.-S. Yen, M.-R. Hsieh, J.-W. A. Chen, P.-Y. Wu, K. 2020-11-17 doi:10.1101/2020.11.17.386672 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains ]]> https://biorxiv.org/content/10.1101/2020.11.19.389437v1?rss=1 Hung, P.-H. Liao, C.-W. Ko, F.-H. Tsai, H.-K. Leu, J.-Y. 2020-11-20 doi:10.1101/2020.11.19.389437 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ phiC31 integrase for recombination mediated single copy insertion and genome manipulation in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.11.25.398784v1?rss=1 Yang, F.-J. Chen, C.-N. Chang, T. Cheng, T.-W. Chang, N.-C. Kao, C.-Y. Lee, C.-C. Huang, Y.-C. Chan, S.-P. Wang, J. 2020-11-25 doi:10.1101/2020.11.25.398784 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite ]]> https://biorxiv.org/content/10.1101/2020.11.27.399857v1?rss=1 Lin, M.-J. Lin, Y.-C. Chen, N.-C. Luo, A. C.-L. Lai, S.-K. Hsu, C.-L. Hsu, J. S. Chen, C.-Y. Yang, W.-S. Chen, P.-L. 2020-11-27 doi:10.1101/2020.11.27.399857 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Detection of Deformed wing virus (DWV) in the Vietnamese Walking Stick Medauroidea extradentata (Phasmatodea) ]]> https://biorxiv.org/content/10.1101/2020.12.06.413948v1?rss=1 Shelomi, M. Lin, W. Johnson, B. R. Furlong, M. J. Etebari, K. 2020-12-07 doi:10.1101/2020.12.06.413948 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Molecular insights into substrate recognition and discrimination by the N-terminal domain of Lon AAA+ protease ]]> https://biorxiv.org/content/10.1101/2020.12.17.423354v1?rss=1 Tzeng, S.-R. Tseng, Y.-C. Lin, C.-C. Hsu, C.-Y. Huang, S.-J. Kuo, Y.-T. Chang, C.-I. 2020-12-18 doi:10.1101/2020.12.17.423354 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ INPP5E regulates CD3ζ enrichment at the immune synapse by phosphoinositide distribution control ]]> https://biorxiv.org/content/10.1101/2021.01.06.425541v1?rss=1 Chiu, T.-Y. Yang, F.-H. Chong, W. M. Tsai, H.-C. Wang, W.-J. Liao, J.-C. 2021-01-07 doi:10.1101/2021.01.06.425541 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Azithromycin Plus Zinc Sulfate Rapidly and Synergistically Suppresses IκBα-Mediated In Vitro Human Airway Cell ACE2 Expression for SARS-CoV-2 Entry ]]> https://biorxiv.org/content/10.1101/2021.01.19.427206v1?rss=1 Chen, Y.-K. Huang, T.-T. Chang, C.-W. Lee, M.-C. Lin, B.-R. Lu, Y.-P. Hsu, Y.-J. Chuang, C.-Y. 2021-01-19 doi:10.1101/2021.01.19.427206 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ An all-solid-state heterojunction oxide transistor for the rapid detection of biomolecules and SARS-CoV-2 spike S1 protein ]]> https://biorxiv.org/content/10.1101/2021.01.19.427256v1?rss=1 Lin, Y.-H. Han, Y. Sharma, A. AlGhamdi, W. S. Liu, C.-H. Chang, T.-H. Xiao, X.-W. Seitkhan, A. Mottram, A. D. Pattanasattayavong, P. Faber, H. Heeney, M. Anthopoulos, T. D. 2021-01-19 doi:10.1101/2021.01.19.427256 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Zinc supplement augments the suppressive effects of repurposed drugs of NF-kappa B inhibitor on ACE2 expression in human lung cell lines in vitro. ]]> https://biorxiv.org/content/10.1101/2021.01.27.428372v1?rss=1 Lee, M. C. Chen, Y.-K. Hsu, Y.-J. Lin, B.-R. 2021-01-27 doi:10.1101/2021.01.27.428372 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Viral Transmission via Enhanced Furin-mediated Spike Cleavage ]]> https://biorxiv.org/content/10.1101/2021.01.27.428541v1?rss=1 Cheng, Y.-W. Chao, T.-L. Li, C.-L. Wang, S.-H. Kao, H.-C. Tsai, Y.-M. Wang, H.-Y. Hsieh, C.-L. Chen, P.-J. Chang, S.-Y. Yeh, S.-H. 2021-01-28 doi:10.1101/2021.01.27.428541 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ DRDOCK: A Drug Repurposing platform integrating automated docking, simulations and a log-odds-based drug ranking scheme ]]> https://biorxiv.org/content/10.1101/2021.01.31.429052v1?rss=1 Tsai, K.-L. Yang, L.-W. 2021-02-02 doi:10.1101/2021.01.31.429052 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Consequences of the Nyquist-Shannon sampling criterion in Mesoscopic Multiphoton Microscopy to avail full-field sub-micron resolution resolvability ]]> https://biorxiv.org/content/10.1101/2021.01.31.429063v1?rss=1 3800 FOV-resolution ratio while not compromising the imaging speed as well as the photon-budget. ]]> Borah, B. J. Lee, J.-C. Chi, H.-H. Hsiao, Y.-T. Yen, C.-T. Sun, C.-K. 2021-02-02 doi:10.1101/2021.01.31.429063 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ The impact of distributional assumptions in gene-set and pathway analysis: how far can it go wrong? ]]> https://biorxiv.org/content/10.1101/2021.02.01.429279v1?rss=1 Ho, C.-H. Huang, Y.-J. Lai, Y.-J. Mukherjee, R. Hsiao, C. K. 2021-02-02 doi:10.1101/2021.02.01.429279 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Synthetic dysmobility screen unveils an integrated STK40-YAP-MAPK system driving cell migration ]]> https://biorxiv.org/content/10.1101/2021.02.15.431287v1?rss=1 Yu, L.-Y. Tseng, T.-J. Lin, H.-C. Lu, T.-X. Tsai, C.-J. Lin, Y.-C. Hsu, C.-L. Tsai, F.-C. 2021-02-16 doi:10.1101/2021.02.15.431287 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Revisiting the early evolution of Cyanobacteria with a new thylakoid-less and deeply diverged isolate from a hornwort ]]> https://biorxiv.org/content/10.1101/2021.02.18.431691v1?rss=1 Rahmatpour, N. Hauser, D. A. Nelson, J. M. Chen, P. Y. Villarreal, J. C. Ho, M.-Y. Li, F.-W. 2021-02-18 doi:10.1101/2021.02.18.431691 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Climate fluctuations drive the recruitment and growth of temperate grassland plants ]]> https://biorxiv.org/content/10.1101/2021.03.08.434383v1?rss=1 Dolezal, J. Altman, J. Jandova, V. Chytry, M. Conti, L. Mendez-Castro, F. Klimesova, J. Zeleny, D. Ottaviani, G. 2021-03-09 doi:10.1101/2021.03.08.434383 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Complete genome sequence of Xylella taiwanensis and comparative analysis of virulence gene content with Xylella fastidiosa ]]> https://biorxiv.org/content/10.1101/2021.03.08.434500v1?rss=1 Weng, L.-W. Lin, Y.-C. Su, C.-C. Huang, C.-T. Cho, S.-T. Chen, A.-P. Chou, S.-J. Tsai, C.-W. Kuo, C.-H. 2021-03-09 doi:10.1101/2021.03.08.434500 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan ]]> https://biorxiv.org/content/10.1101/2021.03.24.436723v1?rss=1 Castillo, A. I. Tsai, C.-W. Su, C.-C. Weng, L.-W. Lin, Y.-C. Cho, S.-T. Almeida, R. P. P. Kuo, C.-H. 2021-03-24 doi:10.1101/2021.03.24.436723 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer di-(2-ethylhexyl) phthalate from estuarine sediments ]]> https://biorxiv.org/content/10.1101/2021.03.24.436900v1?rss=1 Wei, S. T.-S. Chen, Y.-L. Wu, Y.-W. Wu, T.-Y. Lai, Y.-L. Wang, P.-H. Ismail, W. Lee, T.-H. Chiang, Y.-R. 2021-03-25 doi:10.1101/2021.03.24.436900 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Mathematical Model for the Study of Mitochondrial Retrograde Signaling Dynamics ]]> https://biorxiv.org/content/10.1101/2021.03.27.437239v1?rss=1 Chiu, S.-T. Tseng, W.-W. Wei, A.-C. 2021-03-29 doi:10.1101/2021.03.27.437239 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ COVID-19 dominant D614G mutation in the SARS-CoV-2 spike protein desensitizes its temperature-dependent denaturation ]]> https://biorxiv.org/content/10.1101/2021.03.28.437426v1?rss=1 Yang, T.-J. Yu, P.-Y. Chang, Y.-C. Kuo, C.-W. Khoo, K.-H. Hsu, S.-T. D. 2021-03-29 doi:10.1101/2021.03.28.437426 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ A Positive Regulatory Feedback Loop Between 1 EKLF/ KLF1 and TAL1/SCL2 Sustaining the Erythropoiesis ]]> https://biorxiv.org/content/10.1101/2021.04.08.439008v1?rss=1 Hung, C.-H. Huang, Y.-S. Lee, T.-L. Yang, K.-C. Shyu, Y.-C. Wen, S.-C. Lu, M.-J. Yuan, S. Shen, C.-K. J. 2021-04-08 doi:10.1101/2021.04.08.439008 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Connecting MHC-I-binding motifs with HLA alleles via deep learning ]]> https://biorxiv.org/content/10.1101/2021.04.18.440359v1?rss=1 Lee, K.-H. Chang, Y.-C. Chen, T.-F. Juan, H.-F. Tsai, H.-K. Chen, C.-Y. 2021-04-20 doi:10.1101/2021.04.18.440359 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Positive modulation of cerebellar α6GABAA receptors for treating essential tremor: a proof-of-concept study in harmaline-treated mice ]]> https://biorxiv.org/content/10.1101/2021.04.19.440397v1?rss=1 Huang, Y.-H. Lee, M. T. Sieghart, W. Knutson, D. E. Wimmer, L. R. Sharmin, D. Cook, J. Mihovilovic, M. D. Chiou, L.-C. 2021-04-20 doi:10.1101/2021.04.19.440397 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Identification of essential β-oxidation genes and corresponding metabolites for estrogen degradation by actinobacteria ]]> https://biorxiv.org/content/10.1101/2021.04.22.440886v1?rss=1 Hsiao, T.-H. Lee, T.-H. Chuang, M.-R. Wang, P.-H. Meng, M. Horinouchi, M. Hayashi, T. Chen, Y.-L. Chiang, Y.-R. 2021-04-22 doi:10.1101/2021.04.22.440886 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Misregulation of MYB16 causes stomatal cluster formation by disrupting polarity in asymmetric cell division ]]> https://biorxiv.org/content/10.1101/2021.05.03.442461v1?rss=1 Yang, S.-L. Tran, N. Tsai, M.-Y. Ho, C.-M. K. 2021-05-03 doi:10.1101/2021.05.03.442461 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ Endothelial restoration of CAD GWAS gene PLPP3 by nanomedicine suppresses YAP/TAZ activity and reduces atherosclerosis in vivo ]]> https://biorxiv.org/content/10.1101/2021.05.06.443006v1?rss=1 Zhu, J. Yeh, C.-F. Huang, R.-T. Lee, T.-H. Shentu, T.-P. Wu, D. Yang, K.-C. Fang, Y. 2021-05-07 doi:10.1101/2021.05.06.443006 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ The polar flagellar transcriptional regulatory network in Vibrio campbellii deviates from canonical Vibrio species ]]> https://biorxiv.org/content/10.1101/2021.05.10.443453v1?rss=1 Petersen, B. D. Liu, M. S. Podicheti, R. Yang, A. Y.-P. Simpson, C. A. Hemmerich, C. Rusch, D. B. van Kessel, J. 2021-05-10 doi:10.1101/2021.05.10.443453 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Insularity forcing on plant persistence strategies in edaphic island systems ]]> https://biorxiv.org/content/10.1101/2021.05.13.444066v1?rss=1 Conti, L. Mendez-Castro, F. E. Chytry, M. Goetzenberger, L. Hajek, M. Horsak, M. Jimenez-Alfaro, B. Klimesova, J. Zeleny, D. Ottaviani, G. 2021-05-15 doi:10.1101/2021.05.13.444066 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ C. elegans DSB-3 Reveals Conservation and Divergence among Protein Complexes Promoting Meiotic Double-Strand Breaks ]]> https://biorxiv.org/content/10.1101/2021.05.14.444243v1?rss=1 Hinman, A. W. Yeh, H.-Y. Roelens, B. Yamaya, K. Woglar, A. Bourbon, H.-M. Chi, P. Villeneuve, A. M. 2021-05-16 doi:10.1101/2021.05.14.444243 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Impact of Glycosylation on SARS-CoV-2 Infection and Broadly Protective Vaccine Design ]]> https://biorxiv.org/content/10.1101/2021.05.25.445523v1?rss=1 Liao, H.-Y. Huang, H.-Y. Chen, X. Cheng, C.-W. Wang, S.-W. Shahed-Al-Mahmud, M. Chen, T.-H. Lo, J. M. Liu, Y.-M. Ma, H.-H. Chang, Y.-H. Tsai, C.-Y. Huang, P.-Y. Chang, S.-Y. Chao, T.-L. Kao, H.-C. Tsai, Y.-M. Chen, Y.-H. Chen, C.-Y. Lee, K.-C. Wu, C.-Y. Jan, J.-T. Lin, K.-I. Cheng, T.-J. R. Ma, C. Wong, C.-H. 2021-05-25 doi:10.1101/2021.05.25.445523 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Case study: Digital spatial profiling of metastatic clear cell carcinoma reveals intra-tumor heterogeneity in epithelial-mesenchymal gradient. ]]> https://biorxiv.org/content/10.1101/2021.05.27.445912v1?rss=1 Wang, D. Y.-T. Tan, T. Z. Tai, Y.-T. Ye, J. Lin, W.-C. Wei, L.-H. Huang, R. Y.-J. 2021-05-28 doi:10.1101/2021.05.27.445912 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Apical Actin-myosin Network Regulates the Tight Junction of Polarized Madin-Darby Canine Kidney Cells ]]> https://biorxiv.org/content/10.1101/2021.05.30.446323v1?rss=1 Lu, C.-h. Wen, F.-l. Hsueh, S. C.-C. Wu, W.-h. Lin, Y.-F. Prouveur, M. Boudier, T. Lin, K.-h. 2021-05-30 doi:10.1101/2021.05.30.446323 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Sticking around: plant persistence strategies on edaphic islands ]]> https://biorxiv.org/content/10.1101/2021.06.15.448516v1?rss=1 Ottaviani, G. Mendez Castro, F. E. Conti, L. Zeleny, D. Chytry, M. Dolezal, J. Jandova, V. Altman, J. Klimesova, J. 2021-06-16 doi:10.1101/2021.06.15.448516 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ One viral sequence for each host? - The neglected within-host diversity as the main stage of SARS-CoV-2 evolution ]]> https://biorxiv.org/content/10.1101/2021.06.21.449205v1?rss=1 Ruan, Y. Hou, M. Li, J. Song, Y. Wang, H.-Y. Zeng, H. Lu, J. Wen, H. Chen, C. Wu, C.-I. 2021-06-21 doi:10.1101/2021.06.21.449205 Cold Spring Harbor Laboratory Press 2021-06-21 <![CDATA[ Towards a Neurometric-based Construct Validity of Trust ]]> https://biorxiv.org/content/10.1101/2021.07.04.451074v1?rss=1 Chen, P.-H. A. Fareri, D. Guroglu, B. Delgado, M. R. Chang, L. J. 2021-07-05 doi:10.1101/2021.07.04.451074 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Dietary Exposure to Antibiotic Residues Facilitates Metabolic Disorder by Altering the Gut Microbiota and Bile Acid Composition ]]> https://biorxiv.org/content/10.1101/2021.07.06.451284v1?rss=1 Chen, R.-A. Wu, W.-K. Panyod, S. Liu, P.-Y. Chuang, H.-L. Chen, Y.-H. Lyu, Q. Hsu, H.-C. Lin, T.-L. Shen, T.-C. D. Yang, Y.-T. Zou, H.-B. Huang, H.-S. Lin, Y.-E. Chen, C.-C. Ho, C.-T. Lai, H.-C. Wu, M.-S. Hsu, C.-C. Sheen, L.-Y. 2021-07-06 doi:10.1101/2021.07.06.451284 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants ]]> https://biorxiv.org/content/10.1101/2021.07.21.453140v1?rss=1 Kuo, C.-W. Yang, T.-J. Chien, Y.-C. Yu, P.-Y. Hsu, S.-T. D. Khoo, K.-H. 2021-07-21 doi:10.1101/2021.07.21.453140 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Typhoid toxin sorting and exocytic transport from Salmonella Typhi infected cells ]]> https://biorxiv.org/content/10.1101/2021.08.10.455839v1?rss=1 Chang, S.-J. Lin, Y.-Y. Lara-Tejero, M. Galan, J. E. 2021-08-10 doi:10.1101/2021.08.10.455839 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Insulin Signaling Attenuates GLUT4 Endocytosis in Muscle Cells via GSK3a-Dyn2-Bin1 Interplay ]]> https://biorxiv.org/content/10.1101/2021.08.23.457303v1?rss=1 Liu, Y.-W. Laiman, J. Loh, J. Tang, W.-C. Chuang, M.-C. Chen, B.-C. Chang, Y.-C. Chuang, L.-M. 2021-08-24 doi:10.1101/2021.08.23.457303 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Gastrodia elata Blume prevents dopaminergic neuron degeneration via glial Nrf2 signaling in Lrrk2-G2019S Parkinson's disease models ]]> https://biorxiv.org/content/10.1101/2021.08.25.457612v1?rss=1 Lin, Y.-E. Lin, C.-H. Ho, E.-P. Ke, Y.-C. Petridi, S. Elliott, C. J. H. Sheen, L.-Y. Chien, C.-T. 2021-08-27 doi:10.1101/2021.08.25.457612 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Do forest over- and understory respond to the same environmental variables when viewed at the taxonomic and trait level? ]]> https://biorxiv.org/content/10.1101/2021.09.06.459058v1?rss=1 Helsen, K. Shen, Y.-C. Lin, T.-Y. Chen, C.-F. Huang, C.-M. Li, C.-F. Zeleny, D. 2021-09-06 doi:10.1101/2021.09.06.459058 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Comparing trait syndromes between Taiwanese subtropical terrestrial and epiphytic ferns and lycophytes at the species and community level ]]> https://biorxiv.org/content/10.1101/2021.09.06.459074v1?rss=1 Helsen, K. Lin, T.-Y. Zeleny, D. 2021-09-06 doi:10.1101/2021.09.06.459074 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Extending the CWM approach to intraspecific trait variation: how to deal with overly optimistic standard tests? ]]> https://biorxiv.org/content/10.1101/2021.09.09.459685v1?rss=1 Zeleny, D. Helsen, K. Lee, Y.-N. 2021-09-11 doi:10.1101/2021.09.09.459685 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Structure-activity relationships of B.1.617 and other SARS-CoV-2 spike variants ]]> https://biorxiv.org/content/10.1101/2021.09.12.459978v1?rss=1 Yang, T.-J. Yu, P.-Y. Chang, Y.-C. Chang, N.-E. Tsai, Y.-X. Liang, K.-H. Draczkowski, P. Lin, B. Wang, Y.-S. Chien, Y.-C. Khoo, K.-H. Wu, H.-C. Hsu, S.-T. D. 2021-09-13 doi:10.1101/2021.09.12.459978 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Signatures of adaptive evolution during human to mink SARS CoV2 cross species transmission inform estimates of the COVID19 pandemic timing ]]> https://biorxiv.org/content/10.1101/2021.09.15.459215v1?rss=1 Tai, J.-H. Chaw, S.-M. Sun, H.-Y. Tseng, Y.-C. Li, G. Chang, S.-Y. Yeh, S.-H. Chen, P.-J. Wang, H.-Y. 2021-09-16 doi:10.1101/2021.09.15.459215 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Intrinsic neural activity predisposes susceptibility to a body illusion ]]> https://biorxiv.org/content/10.1101/2021.09.18.460883v1?rss=1 Hsu, T.-Y. Zhou, J.-F. Northoff, G. Yeh, S.-L. Lane, T. J. 2021-09-20 doi:10.1101/2021.09.18.460883 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Different methods for niche and fitness differences computation offer contrasting explanations of species coexistence ]]> https://biorxiv.org/content/10.1101/2021.09.28.462166v1?rss=1 Spaak, J. W. Ke, P.-J. Letten, A. W. De Laender, F. 2021-09-30 doi:10.1101/2021.09.28.462166 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Real-time Noise-suppressed Wide-Dynamic-Range Compression in Ultrahigh-Resolution Neuronal Imaging ]]> https://biorxiv.org/content/10.1101/2021.09.29.462090v1?rss=1 Borah, B. J. Sun, C.-K. 2021-10-01 doi:10.1101/2021.09.29.462090 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Metabolic Regulation of Mitochondrial Morphologies in Pancreatic Beta Cells: Bioenergetics-Mitochondrial Dynamics Coupling ]]> https://biorxiv.org/content/10.1101/2021.10.04.462897v1?rss=1 Tseng, W.-W. Chu, C.-H. Chang, C. Lee, Y.-J. Zhao, S. Ho, Y.-P. Wei, A.-C. 2021-10-04 doi:10.1101/2021.10.04.462897 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Trade-off between competition ability and invulnerability to predation in marine microbes; protist grazing versus viral lysis effects ]]> https://biorxiv.org/content/10.1101/2021.10.09.463787v1?rss=1 Yang, J. W. Chang, F.-H. Yeh, Y.-C. Tsai, A.-Y. Chiang, K.-P. Shiah, F.-K. Gong, G.-C. Hsieh, C.-h. 2021-10-09 doi:10.1101/2021.10.09.463787 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Whole genome sequence analysis of blood lipid levels in >66,000 individuals ]]> https://biorxiv.org/content/10.1101/2021.10.11.463514v1?rss=1 Selvaraj, M. S. Li, X. Li, Z. Pampana, A. Zhang, D. Y. Park, J. Aslibekyan, S. Bis, J. C. Brody, J. A. Cade, B. E. Chuang, L.-M. Chung, R.-H. Curran, J. E. de las Fuentes, L. de Vries, P. S. Duggirala, R. Freedman, B. I. Graff, M. Guo, X. Heard-Costa, N. Hidalgo, B. Hwu, C.-M. Irvin, M. R. Kelly, T. N. Kral, B. G. Lange, L. Li, X. Lisa, M. Lubitz, S. A. Manichaikul, A. W. Michael, P. Montasser, M. E. Morrison, A. C. Naseri, T. O'Connell, J. R. Palmer, N. D. Peyser, P. A. Reupena, M. S. Smith, J. A. Sun, X. Taylor, K. D. Tracy, R. P. Tsai, M. Y. Wang, 2021-10-12 doi:10.1101/2021.10.11.463514 66,000 individuals]]> Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Dynamin-2 Phosphorylation as A Critical Regulatory Target of Bin1 and GSK3α for Endocytosis in Muscle ]]> https://biorxiv.org/content/10.1101/2021.10.11.463889v1?rss=1 Laiman, J. Loh, J. Tang, W.-C. Chuang, M.-C. Liu, H.-K. Chen, B.-C. Chang, Y.-C. Chuang, L.-M. Liu, Y.-W. 2021-10-11 doi:10.1101/2021.10.11.463889 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ White matter microstructural and morphometric alterations in autism: Implications for intellectual and verbal capabilities ]]> https://biorxiv.org/content/10.1101/2021.10.11.464005v1?rss=1 Yeh, C.-H. Tseng, R.-Y. Ni, H.-C. Cocchi, L. Chang, J.-C. Hsu, M.-Y. Tu, E.-N. Wu, Y.-Y. Chou, T.-L. Gau, S. S.-F. Lin, H.-Y. 2021-10-13 doi:10.1101/2021.10.11.464005 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Functional single cell proteomic profiling of cells with abnormal DNA damage response dynamics ]]> https://biorxiv.org/content/10.1101/2021.10.13.464241v1?rss=1 1000 proteins per cell. However, a method to link single cell proteomes with cellular behaviors is needed to advance this type of profiling technique. Here, we developed a microscopy-based functional single cell proteomic profiling technology, called FUNpro, to link the proteome of individual cells with phenotypes of interest, even if the phenotypes are dynamic or the cells of interest are sparse. FUNpro enables one i) to screen thousands of cells with subcellular resolution and monitor (intra)cellular dynamics using a custom-built microscope, ii) to real-time analyze (intra)cellular dynamics of individual cells using an integrated cell tracking algorithm, iii) to promptly isolate the cells displaying phenotypes of interest, and iv) to single cell proteomically profile the isolated cells. We applied FUNpro to proteomically profile a newly identified small subpopulation of U2OS osteosarcoma cells displaying an abnormal, prolonged DNA damage response (DDR) after ionizing radiation (IR). With this, we identified PDS5A and PGAM5 proteins contributing to the abnormal DDR dynamics and helping the cells survive after IR. ]]> Su, P.-R. You, L. Beerens, C. Bezstarosti, K. Demmers, J. Pabst, M. Kanaar, R. Hsu, C.-C. Chien, M.-P. 2021-10-14 doi:10.1101/2021.10.13.464241 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Single-cell transcriptomics unveils xylem cell development and evolution ]]> https://biorxiv.org/content/10.1101/2021.10.16.464627v1?rss=1 Tung, C.-C. Kuo, S.-C. Yang, C.-L. Huang, C.-E. Yu, J.-H. Sun, Y.-H. Shuai, P. Su, J.-C. Ku, C. Lin, Y.-C. J. 2021-10-16 doi:10.1101/2021.10.16.464627 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Different mycorrhizal nutrient acquisition strategies shape tree species competition and coexistence dynamics ]]> https://biorxiv.org/content/10.1101/2021.10.26.465925v1?rss=1 Van Nuland, M. E. Ke, P.-J. Wan, J. Peay, K. G. 2021-10-28 doi:10.1101/2021.10.26.465925 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ DNA-free CRISPR-Cas9 gene editing of tetraploid tomatoes using protoplast regeneration ]]> https://biorxiv.org/content/10.1101/2021.11.02.466947v1?rss=1 Hsu, C.-T. Yuan, Y.-H. Zheng, P.-X. Wu, F.-H. Cheng, Q.-W. Wu, Y.-L. Lin, S. Yue, J.-J. Cheng, Y.-H. Lin, S.-I. L. Shih, M.-C. Sheen, J. Lin, Y.-C. Lin, C.-S. 2021-11-02 doi:10.1101/2021.11.02.466947 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ AMPK promotes Arf6 activation in a kinase-independent manner upon energy deprivation ]]> https://biorxiv.org/content/10.1101/2021.11.18.469188v1?rss=1 Chen, K. J. S. Hsu, J.-W. Lee, F.-J. S. 2021-11-19 doi:10.1101/2021.11.18.469188 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Study on the effect of a triple cancer treatment of propolis, thermal cycling-hyperthermia, and low-intensity ultrasound on PANC-1 cells ]]> https://biorxiv.org/content/10.1101/2021.11.19.469215v1?rss=1 Kuo, Y.-Y. Chen, W.-T. Lin, G.-B. Lu, C.-H. Chao, C.-Y. 2021-11-20 doi:10.1101/2021.11.19.469215 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Discovering Novel Antimicrobial Peptides in Generative Adversarial Network ]]> https://biorxiv.org/content/10.1101/2021.11.22.469634v1?rss=1 Lin, T.-T. Yang, L.-Y. Wang, C.-T. Lai, G.-W. Ko, C.-F. Shih, Y.-H. Chen, S.-H. Lin, C.-Y. 2021-11-23 doi:10.1101/2021.11.22.469634 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Developing an Antiviral Peptides Predictor with Generative Adversarial Network Data Augmentation ]]> https://biorxiv.org/content/10.1101/2021.11.29.470292v1?rss=1 Lin, T.-T. Sun, Y.-Y. Cheng, W.-C. Lu, I.-H. Chen, S.-H. Lin, C.-Y. 2021-11-30 doi:10.1101/2021.11.29.470292 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Structural basis for the peptidoglycan editing activity of YfiH ]]> https://biorxiv.org/content/10.1101/2021.12.07.471703v1?rss=1 Lee, M.-S. Hsieh, K.-Y. Kuo, C.-I. Lee, S.-H. Chang, C.-I. 2021-12-08 doi:10.1101/2021.12.07.471703 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ MSRCall: A Multi-scale Deep Neural Network to Basecall Oxford Nanopore Sequences ]]> https://biorxiv.org/content/10.1101/2021.12.20.471615v1?rss=1 Yeh, Y.-M. Lu, Y.-C. 2021-12-21 doi:10.1101/2021.12.20.471615 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Macrophages break interneuromast cell quiescence by intervening the inhibition of Schwann cells in zebrafish lateral line ]]> https://biorxiv.org/content/10.1101/2021.12.29.474498v1?rss=1 Lin, M.-J. Lee, C.-M. Hsu, W.-L. Chen, B.-C. Lee, S.-J. 2021-12-30 doi:10.1101/2021.12.29.474498 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ The 24-chain core-shell nanostructure of wood cellulose microfibrils in seed plants ]]> https://biorxiv.org/content/10.1101/2021.12.31.474620v1?rss=1 Chang, C.-H. Cai, W. Lin, J.-H. Huang, S.-J. Lin, Y.-C. J. Tsao, C.-S. Tai, H.-C. 2022-01-01 doi:10.1101/2021.12.31.474620 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ HLJ1 amplifies endotoxin-induced sepsis severity by promoting IL-12 heterodimerization in macrophages ]]> https://biorxiv.org/content/10.1101/2022.01.05.475083v1?rss=1 Luo, W.-J. Yu, S.-L. Chang, C.-C. Chien, M.-H. Liao, K.-M. Chang, Y.-L. Chuang, Y.-H. Chen, J. J. W. Yang, P.-C. Su, K.-Y. 2022-01-06 doi:10.1101/2022.01.05.475083 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Phosphate transporter PHT1;1 as a key determinant of phosphorus acquisition in Arabidopsis natural accessions ]]> https://biorxiv.org/content/10.1101/2022.01.05.475091v1?rss=1 Chien, P.-S. Chao, Y.-T. Chou, C.-H. Hsu, Y.-Y. Chiang, S.-F. Tung, C.-W. Chiou, T.-J. 2022-01-06 doi:10.1101/2022.01.05.475091 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Increased academic performance and prolonged career duration among Taiwanese academic faculty in ecology and evolutionary biology ]]> https://biorxiv.org/content/10.1101/2022.01.31.478501v1?rss=1 Hsu, G.-C. Lin, W.-J. Sun, S.-J. 2022-02-02 doi:10.1101/2022.01.31.478501 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Peptide-based drug predictions for cancer therapy using deep learning ]]> https://biorxiv.org/content/10.1101/2022.02.01.478580v1?rss=1 Sun, Y.-Y. Lin, T.-T. Cheng, W.-C. Lu, I.-H. Chen, S.-H. Lin, C.-Y. 2022-02-04 doi:10.1101/2022.02.01.478580 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2 ]]> https://biorxiv.org/content/10.1101/2022.02.23.481647v1?rss=1 Hung, F.-Y. Feng, Y.-R. Shih, Y.-H. Lai, Y.-C. Wu, K. 2022-02-25 doi:10.1101/2022.02.23.481647 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ Niche-based deterministic assembly processes strengthen the effects of β-diversity on metacommunity functioning of marine bacterioplankton ]]> https://biorxiv.org/content/10.1101/2022.03.09.483723v1?rss=1 Chang, F.-H. Yang, J. W. Liu, A. C.-H. Lu, H.-P. Gong, G.-C. Shiah, F.-K. Hsieh, C.-h. 2022-03-11 doi:10.1101/2022.03.09.483723 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Tension anisotropy drives phenotypic transitions of cells via two-way cell-ECM feedback ]]> https://biorxiv.org/content/10.1101/2022.03.13.484154v1?rss=1 Alisafaei, F. Shakiba, D. Iannucci, L. Davidson, M. Pryse, K. Chao, P.-h. G. Burdick, J. Lake, S. Elson, E. Shenoy, V. Genin, G. 2022-03-14 doi:10.1101/2022.03.13.484154 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Molecular Crowding Facilitates Bundling of IMPDH Polymers and Cytoophidium Formation ]]> https://biorxiv.org/content/10.1101/2022.03.15.484061v1?rss=1 Chang, C.-C. Peng, M. Zhong, J. Zhang, Z. Keppeke, G. D. Sung, L.-Y. Liu, J.-L. 2022-03-16 doi:10.1101/2022.03.15.484061 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Targeting Reductive Metabolic Shifts by T315I Mutation in BCR-ABL Myeloid Leukemia for Therapy ]]> https://biorxiv.org/content/10.1101/2022.03.22.485260v1?rss=1 Huang, C. Y. Chung, Y.-H. Wu, S.-Y. Wang, H.-Y. Lin, Z.-Y. Yang, T.-J. Feng, J.-M. Hu, C.-M. Chang, Z.-F. 2022-03-23 doi:10.1101/2022.03.22.485260 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Fusarium solani species complex genomes reveal bases of compartmentalisation and animal pathogenesis ]]> https://biorxiv.org/content/10.1101/2022.03.22.485422v1?rss=1 Hoh, D. Z. Lee, H.-H. Wada, N. Liu, W.-A. Lu, M. R. Lai, C.-K. Ke, H.-M. Sun, P. F. Tang, S.-L. Chung, W.-H. Chen, Y.-L. Chung, C.-L. Tsai, I. J. 2022-03-23 doi:10.1101/2022.03.22.485422 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Antimicrobial Susceptibility Test by Surface-enhanced Raman Scattering of Bacterial Metabolites directly from Positive Blood Cultures ]]> https://biorxiv.org/content/10.1101/2022.03.23.485571v1?rss=1 HAN, Y.-Y. Wang, J.-T. Cheng, W.-C. Chen, K.-L. Chi, Y. Teng, L.-J. Wang, J.-K. Wang, Y.-L. 2022-03-24 doi:10.1101/2022.03.23.485571 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Genome structures resolve the early diversification of teleost fishes ]]> https://biorxiv.org/content/10.1101/2022.04.07.487469v1?rss=1 Parey, E. Louis, A. Montfort, J. Bouchez, O. Roques, C. Iampietro, C. Lluch, J. Castinel, A. Donnadieu, C. Desvignes, T. Bucao, C. F. Jouanno, E. Wen, M. Mejri, S. Dirks, R. P. Jansen, H. J. Henkel, C. V. Chen, W.-J. Zahm, M. Cabau, C. Klopp, C. Thompson, A. W. Robinson-Rechavi, M. Braasch, I. Lecointre, G. Bobe, J. Postlethwait, J. H. Berthelot, C. Roest Crollius, H. Guiguen, Y. 2022-04-10 doi:10.1101/2022.04.07.487469 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ The climatic constrains of the historical global spread of mungbean ]]> https://biorxiv.org/content/10.1101/2022.04.27.489711v1?rss=1 Ong, P.-W. Lin, Y.-P. Chen, H.-W. Lo, C.-Y. Burlyaeva, M. Noble, T. Nair, R. M. Schafleitner, R. Vishnyakova, M. von Wettberg, E. Samsonova, M. G. Nuzhdin, S. Ting, C.-T. Lee, C.-R. 2022-04-28 doi:10.1101/2022.04.27.489711 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Equilibrative Nucleoside Transporter 3 is an IFN-stimulated Gene that Facilitates Viral Genome Release ]]> https://biorxiv.org/content/10.1101/2022.04.27.489746v1?rss=1 Hsieh, Y.-T. Tsai, T.-L. Tu, C.-C. Huang, S.-Y. Heng, J.-W. Tsai, P.-Y. Chao, T.-L. Tsai, Y.-M. Chang, P.-C. Lee, C.-K. Yu, G.-Y. Chang, S.-Y. Dzhagalov, I. Hsu, C.-L. 2022-04-28 doi:10.1101/2022.04.27.489746 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Computer simulations reveal pathogenicity and inheritance modes of hearing loss-causing germinal variants ]]> https://biorxiv.org/content/10.1101/2022.05.02.490275v1?rss=1 Tsai, C.-Y. Lu, Y.-C. Chan, Y.-H. Chang, Y.-Y. Lin, S.-W. Liu, T.-C. Hsu, C.-J. Chen, P.-L. Yang, L.-W. Wu, C.-C. 2022-05-04 doi:10.1101/2022.05.02.490275 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Thermal cycling hyperthermia sensitizes non-small cell lung cancer A549 cells to EGFR-tyrosine kinase inhibitor Erlotinib ]]> https://biorxiv.org/content/10.1101/2022.05.03.490542v1?rss=1 Chen, W.-T. Lin, G.-B. Liu, H.-H. Chen, Y.-M. Kuo, Y.-Y. Chao, C.-Y. 2022-05-04 doi:10.1101/2022.05.03.490542 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ The soil microbiome may offer solutions to ginger cultivation ]]> https://biorxiv.org/content/10.1101/2022.05.03.490558v1?rss=1 Wang, C.-W. Michelle Wong, J.-W. Yeh, S.-S. Eric Hsieh, Y. Tseng, C.-H. Yang, S.-H. Tang, S.-L. 2022-05-04 doi:10.1101/2022.05.03.490558 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Quantification of hypoxic regions distant from occlusions in cerebral penetrating arteriole trees ]]> https://biorxiv.org/content/10.1101/2022.05.06.490869v1?rss=1 Xue, Y. Georgakopoulou, T. van der Wijk, A.-E. Jozsa, T. I. van Bavel, E. Payne, S. J. 2022-05-06 doi:10.1101/2022.05.06.490869 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Protection of high-frequency low-intensity pulsed electric fields and brain-derived neurotrophic factor for SH-SY5Y cells against hydrogen peroxide-induced cell damage ]]> https://biorxiv.org/content/10.1101/2022.05.10.491265v1?rss=1 Lin, G.-B. Chen, W.-T. Kuo, Y.-Y. Chen, Y.-M. Liu, H.-H. Chao, C.-Y. 2022-05-10 doi:10.1101/2022.05.10.491265 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology ]]> https://biorxiv.org/content/10.1101/2022.05.10.491406v1?rss=1 Manubens-Gil, L. Zhou, Z. Chen, H. Ramanathan, A. Liu, X. Liu, Y. Bria, A. Gillette, T. Ruan, Z. Yang, J. Radojevic, M. Zhao, T. Cheng, L. Qu, L. Liu, S. Bouchard, K. E. Gu, L. Cai, W. Ji, S. Roysam, B. Wang, C.-W. Yu, H. Sironi, A. Iascone, D. M. Zhou, J. Bas, E. Conde-Sousa, E. Aguiar, P. Li, X. Li, Y. Nanda, S. Wang, Y. Muresan, L. Fua, P. Ye, B. He, H.-y. Staiger, J. F. Peter, M. Cox, D. N. Simonneau, M. Oberlaender, M. Jefferis, G. Ito, K. Gonzalez-Bellido, P. Kim, J. Rubel, E. Cline, H. T. Zeng, H. Nern, A. Chiang, A.-S. Yao, J. Roskams, 2022-05-11 doi:10.1101/2022.05.10.491406 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ The time course of categorical and perceptual similarity effects in visual search ]]> https://biorxiv.org/content/10.1101/2022.05.16.492133v1?rss=1 Yeh, L.-C. Peelen, M. V. 2022-05-16 doi:10.1101/2022.05.16.492133 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Multilevel selection leads to divergent coadaptation of care-giving parents during pre-hatching parental care ]]> https://biorxiv.org/content/10.1101/2022.05.23.493134v1?rss=1 Jarrett, B. J. M. Mashoodh, R. Issar, S. Pascoal, S. Rebar, D. Sun, S.-J. Schrader, M. Kilner, R. M. 2022-05-24 doi:10.1101/2022.05.23.493134 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Cancer Cells in all EMT States Lack Rigidity Sensing Depletion of Different Tumor Suppressors Causes Loss of Rigidity Sensing in Cancer Cells ]]> https://biorxiv.org/content/10.1101/2022.06.06.495045v1?rss=1 Simpson, C. M. Sundararajan, V. Tan, T. Z. Huang, R. Sheetz, M. 2022-06-07 doi:10.1101/2022.06.06.495045 Cold Spring Harbor Laboratory Press 2022-06-07 <![CDATA[ An atypical F-actin capping protein modulates cytoskeleton behaviors crucial to colonization of Trichomonas vaginalis ]]> https://biorxiv.org/content/10.1101/2022.06.09.495492v1?rss=1 Wang, K.-H. Chang, J.-Y. Li, F.-A. Chen, Y.-J. Wu, K.-Y. Chu, T.-L. Lin, J. Hsu, H.-M. 2022-06-09 doi:10.1101/2022.06.09.495492 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Nuclear receptor interaction protein (NRIP) as a novel actin-binding protein involved in invadosome formation for myoblast fusion ]]> https://biorxiv.org/content/10.1101/2022.06.14.496213v1?rss=1 Chen, H.-H. Han, Y.-J. Wu, T.-C. Yen, W.-S. Lai, T.-Y. Wei, P.-H. Tsai, L.-K. Lai, H.-J. Tsao, Y.-P. Chen, S.-L. 2022-06-15 doi:10.1101/2022.06.14.496213 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Spatial and temporal origin of the third SARS-CoV-2 Outbreak in Taiwan ]]> https://biorxiv.org/content/10.1101/2022.07.04.498645v1?rss=1 Tai, J.-H. Low, Y. K. Lin, H.-F. Wang, T.-Y. Lin, Y.-Y. Foster, C. Lai, Y.-Y. Yeh, S.-H. Chen, P.-J. Wang, H.-Y. 2022-07-05 doi:10.1101/2022.07.04.498645 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Multi-ancestry GWAS of major depression aids locus discovery, fine-mapping, gene prioritisation, and causal inference ]]> https://biorxiv.org/content/10.1101/2022.07.20.500802v1?rss=1 Meng, X. Navoly, G. Giannakopoulou, O. DL, D. Koller, D. Pathak, G. Koen, N. Lin, K. Renteria, M. Feng, Y. Gaziano, J. M. Stein, D. Zar, H. Campbell, M. van Heel, D. Trivedi, B. Finer, S. McQuillin, A. Bass, N. Chundru, V. K. Martin, H. Huang, Q. Q. Valkovskaya, M. Kuo, P.-H. Chen, H.-C. Tsai, S.-J. Liu, Y.-L. Kendler, K. Peterson, R. Cai, N. Fang, Y. Sen, S. Scott, L. Burmeister, M. Loos, R. Preuss, M. Actkins, K. Davis, L. Uddin, M. Wani, A. Wildman, D. Ursano, R. Kessler, R. Kanai, M. Okada, Y. Sakaue, S. Rabinowitz, J. Maher, B. Uhl, G. Eato 2022-07-21 doi:10.1101/2022.07.20.500802 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Circulating androgen regulation by androgen-catabolizing gut bacteria in male mouse gut ]]> https://biorxiv.org/content/10.1101/2022.07.20.500890v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@515126org.highwire.dtl.DTLVardef@a696faorg.highwire.dtl.DTLVardef@1020beforg.highwire.dtl.DTLVardef@15da175_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefHsiao et al. found that oral administration of androgen-catabolizing Thauera species regulated mouse serum androgen level. They characterized the gut microbe-mediated androgen catabolism through genetic and biochemical analyses. Their discovery portends a possibility of harnessing androgen-catabolic gut bacteria as functional probiotics to treat hyperandrogenism. ]]> Hsiao, T.-H. Chou, C.-H. Chen, Y.-L. Wang, P.-H. Mong, G.-J. B. Lee, T.-H. Wu, T.-Y. Li, P.-T. Li, C.-W. Lai, Y.-L. Tseng, Y.-L. Shih, C.-J. Chen, M.-J. Chiang, Y.-R. 2022-07-20 doi:10.1101/2022.07.20.500890 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Single-molecule localization microscopy reveals the ultrastructural root constitution of distal appendages in expanded mammalian centrioles ]]> https://biorxiv.org/content/10.1101/2022.07.21.500782v1?rss=1 Chang, T.-J. B. Hsu, J. C.-C. Yang, T. T. 2022-07-22 doi:10.1101/2022.07.21.500782 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Thermal cycling-hyperthermia ameliorates cognitive impairment of intracerebroventricular Aβ25-35-induced Alzheimer's disease in C57BL/6 mice ]]> https://biorxiv.org/content/10.1101/2022.07.22.500895v1?rss=1 Kuo, Y.-Y. Chen, W.-T. Lin, G.-B. Chen, Y.-M. Liu, H.-H. Chao, C.-Y. 2022-07-23 doi:10.1101/2022.07.22.500895 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Probabilistic Edge Inference of Gene Networks with Bayesian Markov Random Field Modelling ]]> https://biorxiv.org/content/10.1101/2022.07.30.501645v1?rss=1 Huang, Y.-J. Mukherjee, R. Hsiao, C. K. 2022-08-01 doi:10.1101/2022.07.30.501645 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ A single dose of intravenous human amniotic membrane-derived mesenchymal stem cells limits transmural infarction, reduces fibrosis size, and improves left ventricular systolic function in the myocardial ischemic/reperfusion model of rats ]]> https://biorxiv.org/content/10.1101/2022.07.30.501939v1?rss=1 Sung, J.-W. Yeh, Y.-T. Peng, F.-S. Chen, Y.-C. Li, A.-H. Wu, S.-C. 2022-07-31 doi:10.1101/2022.07.30.501939 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75 ]]> https://biorxiv.org/content/10.1101/2022.07.31.502235v1?rss=1 Wang, Q. Iketani, S. Li, Z. Guo, Y. Yeh, A. Y. Liu, M. Yu, J. Sheng, Z. Huang, Y. Liu, L. Ho, D. D. 2022-08-01 doi:10.1101/2022.07.31.502235 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Chemoenzymatic Synthesis of Genetically-Encoded Multivalent Liquid N-glycan Arrays ]]> https://biorxiv.org/content/10.1101/2022.08.05.503005v1?rss=1 Lin, C.-L. Sojitra, M. Carpenter, E. J. Hayhoe, E. S. Sarkar, S. Volker, E. A. Atrazhev, A. Lowary, T. L. Macauley, M. S. Derda, R. 2022-08-06 doi:10.1101/2022.08.05.503005 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ A neural signature of reward ]]> https://biorxiv.org/content/10.1101/2022.08.23.504939v1?rss=1 Chang, L. J. Li, X. Nguyen, K. Ranger, M. S. Begunova, Y. Chen, P.-H. A. Castrellon, j. Samanez-Larkin, G. R. Zald, D. Fareri, D. Delgado, M. Tomova, L. 2022-08-24 doi:10.1101/2022.08.23.504939 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Multiple climate change factors jointly increased the competitiveness of a C4 grass against its C3 competitor ]]> https://biorxiv.org/content/10.1101/2022.09.01.506280v1?rss=1 Hsu, G.-C. Ke, P.-J. Ho, C.-K. 2022-09-03 doi:10.1101/2022.09.01.506280 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization ]]> https://biorxiv.org/content/10.1101/2022.09.05.506628v1?rss=1 Wang, Q. Li, Z. Ho, J. Guo, Y. Yeh, A. Y. Liu, M. Wang, M. Yu, J. Sheng, Z. Liu, L. Ho, D. D. 2022-09-06 doi:10.1101/2022.09.05.506628 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ MRI-based computational model generation for cerebral perfusion simulations in health and ischaemic stroke ]]> https://biorxiv.org/content/10.1101/2022.09.07.506940v1?rss=1 Jozsa, T. I. Petr, J. Barkhof, F. Payne, S. J. Mutsaerts, H. J. 2022-09-08 doi:10.1101/2022.09.07.506940 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Distinct selection signatures during domestication and improvement in crops: a tale of two genes in mungbean ]]> https://biorxiv.org/content/10.1101/2022.09.08.506689v1?rss=1 Lin, Y.-P. Chen, H.-W. Yeh, P.-M. Lin, J. Anand, S. Li, J. Noble, T. Nair, R. M. Schafleitner, R. Samsonova, M. Bishop-von-Wettberg, E. Nuzhdin, S. Ting, C.-T. Lawn, R. Lee, C.-R. 2022-09-09 doi:10.1101/2022.09.08.506689 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Antigenic characterisation of human monoclonal antibodies for therapeutic use against H7N9 avian influenza virus ]]> https://biorxiv.org/content/10.1101/2022.09.16.508351v1?rss=1 Chang, P. Lukosaityte, D. Sealy, J. E. Rijal, P. Sadeyen, J.-R. Bhat, S. Crossley, S. Daines, R. Huang, K.-Y. A. Townsend, A. Iqbal, M. 2022-09-17 doi:10.1101/2022.09.16.508351 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ SUBTLE DIFFERENCES IN FINE POLYSACCHARIDE STRUCTURES GOVERN SELECTION AND SUCCESSION OF HUMAN GUT MICROBIOTA ]]> https://biorxiv.org/content/10.1101/2022.10.04.510853v1?rss=1 Yao, T. Deemer, D. G. Chen, M.-H. Reuhs, B. L. Hamaker, B. R. Lindemann, S. R. 2022-10-04 doi:10.1101/2022.10.04.510853 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Baculovirus Surface Display of Hemagglutinin and Neuraminidase for Monoclonal Antibody Production ]]> https://biorxiv.org/content/10.1101/2022.10.16.512416v1?rss=1 Lo, H.-R. Wu, C.-P. Jan, J.-T. Chao, Y.-C. Tsai, C.-H. 2022-10-18 doi:10.1101/2022.10.16.512416 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ The role of the cerebellum in learning to predict reward: evidence from cerebellar ataxia ]]> https://biorxiv.org/content/10.1101/2022.11.04.515251v1?rss=1 Nicholas, J. Amlang, C. Lin, C.-Y. Montaser-Kouhsari, L. Desai, N. Pan, M.-K. Kuo, S.-H. Shohamy, D. 2022-11-06 doi:10.1101/2022.11.04.515251 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Environmental luminance impairs socio-sexual recognition memory through a succinct retina to supraoptic nucleus circuit ]]> https://biorxiv.org/content/10.1101/2022.11.08.515735v1?rss=1 Huang, Y.-F. Liao, P.-Y. Yu, J.-H. Chen, S.-K. 2022-11-09 doi:10.1101/2022.11.08.515735 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Evaluating the analytical validity of mutation calling pipeline for tumor whole exome sequencing ]]> https://biorxiv.org/content/10.1101/2022.11.17.516840v1?rss=1 Cheng, C. Huang, J.-H. Hsu, J. S. 2022-11-18 doi:10.1101/2022.11.17.516840 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration ]]> https://biorxiv.org/content/10.1101/2022.11.22.517520v1?rss=1 Wei, K.-H. Lin, I.-T. Chowdhury, K. Liu, K.-T. Ko, T.-M. Chang, Y.-M. Yang, K.-C. Lai, S.-L. 2022-11-22 doi:10.1101/2022.11.22.517520 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Prostaglandin E2 prevents radiotherapy-induced alopecia by attenuating transit amplifying cell apoptosis through promoting G1 arrest ]]> https://biorxiv.org/content/10.1101/2022.11.24.517788v1?rss=1 Lai, S.-f. Huang, W.-Y. Wang, W.-H. Hong, J.-B. Kuo, S.-H. Lin, S.-J. 2022-11-24 doi:10.1101/2022.11.24.517788 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ A versatile method to archive and delipidate brain tissues for ensuing multiplexed immunolabeling and organ-level imaging ]]> https://biorxiv.org/content/10.1101/2022.11.28.518189v1?rss=1 Lin, Y.-H. Wang, L.-W. Chen, Y.-H. Chan, Y.-C. Hu, S.-H. Wu, S.-Y. Chiang, C.-S. Huang, G.-J. Yang, S.-D. Chu, S.-W. Wang, K.-C. Lin, C.-H. Huang, P.-H. Cheng, H.-J. Chen, B.-C. Chu, L.-A. 2022-12-02 doi:10.1101/2022.11.28.518189 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Ecological and genetic trade-offs drive Arabidopsis thaliana range expansion in Europe ]]> https://biorxiv.org/content/10.1101/2022.11.29.518298v1?rss=1 Bastias, C. C. Estarague, A. Vile, D. Lee, C.-R. Exposito-Alonso, M. Violle, C. Vasseur, F. 2022-12-02 doi:10.1101/2022.11.29.518298 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ TWAS coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.12.07.519424v1?rss=1 Chien, P.-S. Chen, P.-H. Lee, C.-R. Chiou, T.-J. 2022-12-10 doi:10.1101/2022.12.07.519424 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ A Noninvasive Skin Biopsy of Free Nerve Endings via Realtime Third-Harmonic Microscopy ]]> https://biorxiv.org/content/10.1101/2022.12.14.520369v1?rss=1 Wu, P. J. Tseng, H.-C. Chao, C.-C. Liao, Y.-H. Yen, C.-T. Lin, W.-Y. Hsieh, S.-T. Sun, W.-Z. Sun, C.-K. 2022-12-16 doi:10.1101/2022.12.14.520369 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Effect of flavonoids hydroxygenkwanin on vascular smooth muscle cell proliferation, migration, and neointimal formation ]]> https://biorxiv.org/content/10.1101/2022.12.20.521220v1?rss=1 Chen, C.-C. Lin, M.-S. Chen, P.-Y. Leu, Y.-L. Wang, S.-H. 2022-12-20 doi:10.1101/2022.12.20.521220 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Thermal cycling-hyperthermia down-regulates liposaccharide-induced inflammatory response in human whole-blood and helps clear herpes simplex virus type 1 by U-937 macrophages ]]> https://biorxiv.org/content/10.1101/2022.12.20.521318v1?rss=1 Kuo, Y.-Y. Chen, W.-T. Lin, G.-B. Chen, Y.-M. Liu, H.-H. Chao, C.-Y. 2022-12-21 doi:10.1101/2022.12.20.521318 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Multiphoton imaging of glucose, galactose, and fructose-induced formation of fluorescent advanced glycation end products in tissues ]]> https://biorxiv.org/content/10.1101/2023.01.04.522782v1?rss=1 Lin, C.-J. Mondal, S. I. Lee, S.-L. Kang, J.-W. So, P. T. Dong, C.-Y. 2023-01-04 doi:10.1101/2023.01.04.522782 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14 ]]> https://biorxiv.org/content/10.1101/2023.01.10.523456v1?rss=1 Wang, M. Zhong, Z. Gallego-Bartolome, J. Feng, S. Shih, Y.-H. Liu, M. Zhou, J. Richey, J. C. Ng, C. Jami-Alahmadi, Y. Wohlschlegel, J. Wu, K. Jacobsen, S. E. 2023-01-10 doi:10.1101/2023.01.10.523456 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Enhancing glymphatic function with very low-intensity ultrasound via the transient receptor potential vanilloid-4-aquaporin-4 pathway ]]> https://biorxiv.org/content/10.1101/2023.01.13.523878v1?rss=1 Liao, W.-H. Wu, C.-H. Chu, Y.-C. Hsiao, M.-Y. Kung, Y. Wang, J.-L. Chen, W.-S. 2023-01-13 doi:10.1101/2023.01.13.523878 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature ]]> https://biorxiv.org/content/10.1101/2023.01.20.524893v1?rss=1 Stylianou, N. Sebina, I. Matigian, N. Deohler, H. Monkman, J. Rohl, J. Allenby, M. Nam, A. Pan, L. Rockstroh, A. Sadeghirad, H. Chung, K. Sobanski, T. O'Byrne, K. Rebutini, P. Z. Machado-Souza, C. Stonoga, E. T. S. Warkiani, M. E. Salomon, C. Short, K. R. McClements, L. de Noronha, L. Huang, R. Y.-J. Belz, G. Guimaraes, F. Clifton, V. Kulasinghe, A. 2023-01-21 doi:10.1101/2023.01.20.524893 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Antagonistic pleiotropy plays an important role in governing the evolution and genetic diversity of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.02.10.527437v1?rss=1 Lee, D.-C. Tai, J.-H. Lin, H.-F. Chao, T.-L. Ruan, Y. Cheng, Y.-W. Chou, Y.-C. Lin, Y.-Y. Chang, S.-Y. Chen, P.-J. Yeh, S.-H. Wang, H.-Y. 2023-02-10 doi:10.1101/2023.02.10.527437 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Evolution of horn length and lifting strength in the Japanese rhinoceros beetle Trypoxylus dichotomus ]]> https://biorxiv.org/content/10.1101/2023.02.16.528888v1?rss=1 Weber, J. N. Kojima, W. Boisseau, R. Niimi, T. Morita, S. Shigenobu, S. Gotoh, H. Araya, K. Lin, C.-P. Thomas-Bulle, C. Allen, C. E. Tong, W. Lavine, L. C. Swanson, B. O. Emlen, D. J. 2023-02-17 doi:10.1101/2023.02.16.528888 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ A Suspension Trapping-Based Sample Preparation Workflow for Sensitive Plant Phosphoproteomics ]]> https://biorxiv.org/content/10.1101/2023.02.23.529696v1?rss=1 Chen, C.-W. Tsai, C.-F. Lin, M.-H. Lin, S.-Y. Hsu, C.-C. 2023-02-23 doi:10.1101/2023.02.23.529696 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Single-cell analysis of CX3CR1+ cells reveal a pathogenic role for BIRC5+ myeloid proliferating cells driven by Staphylococcus aureus leukotoxins ]]> https://biorxiv.org/content/10.1101/2023.02.27.529760v1?rss=1 Loredan, D. G. Devlin, J. C. Lacey, K. A. Howard, N. Chen, Z. Zwack, E. E. Lin, J.-D. Ruggles, K. V. Khanna, K. M. Torres, V. J. Loke, P. 2023-02-27 doi:10.1101/2023.02.27.529760 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Impaired potency of neutralizing antibodies against cell-cell fusion mediated by SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.03.09.531948v1?rss=1 Wang, Q. Yeh, A. Y. Guo, Y. Yu, J. Ho, D. D. Liu, L. 2023-03-10 doi:10.1101/2023.03.09.531948 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Gut microbial community in proboscis monkeys: implications for effects of geographical and social factors ]]> https://biorxiv.org/content/10.1101/2023.03.14.532648v1?rss=1 Jose, L. Lee, W. Hanya, G. Tuuga, A. Goossens, B. Tangah, J. Matsuda, I. Subbiah, V. K. 2023-03-14 doi:10.1101/2023.03.14.532648 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Video-rate three-photon imaging in deep Drosophila brain based on a single Cr:forsterite oscillator ]]> https://biorxiv.org/content/10.1101/2023.03.23.533955v1?rss=1 Chou, L.-T. Wu, S.-H. Hung, H.-H. Jang, J.-C. Chen, C.-M. Chang, T.-C. Lin, W.-Z. Chu, L.-A. Sun, C.-K. Kartner, F. X. Ivanov, A. A. Chu, S.-W. Chia, S.-H. 2023-03-25 doi:10.1101/2023.03.23.533955 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Self-Healable Spider Dragline Silk Materials ]]> https://biorxiv.org/content/10.1101/2023.04.01.535237v1?rss=1 Chen, W.-C. Wang, R.-C. Yu, S.-K. Chen, J.-L. Kao, Y.-H. Wang, T.-Y. Chang, P.-Y. Sheu, H.-S. Chen, S. C. C. Liu, W.-R. Yang, T.-I. Wu, H.-C. 2023-04-04 doi:10.1101/2023.04.01.535237 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ PGSbuilder: An end-to-end platform for human genome association analysis and polygenic risk score predictions ]]> https://biorxiv.org/content/10.1101/2023.04.12.536584v1?rss=1 Lee, K.-H. Lee, Y.-L. Hsieh, T.-T. Chang, Y.-C. Wang, S.-S. Fann, G.-Z. Lin, W.-C. Chen, T.-F. Li, P.-H. Kuo, Y.-L. Chen, P.-L. Juan, H.-F. Tsai, H.-K. Chen, C.-Y. Huang, J.-H. 2023-04-13 doi:10.1101/2023.04.12.536584 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ High-throughput Automated Muropeptide Analysis (HAMA) Reveals Peptidoglycan Composition of Gut Microbial Cell Walls ]]> https://biorxiv.org/content/10.1101/2023.04.17.537164v1?rss=1 Hsu, Y.-C. Su, P.-R. Huang, L.-J. Cheng, K.-Y. Chen, C.-h. Hsu, C.-C. 2023-04-17 doi:10.1101/2023.04.17.537164 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Can motional dynamics account for the cytotoxicity of beta amyloid oligomers? ]]> https://biorxiv.org/content/10.1101/2023.05.04.539338v1?rss=1 Yeh, C.-T. Chang, H.-W. Hsu, W.-H. Huang, S.-J. Wu, M.-H. Tu, L.-H. Lee, M.-C. Chan, C. C. J. 2023-05-05 doi:10.1101/2023.05.04.539338 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Identification of Pain-Associated Effusion-Synovitis from Knee Magnetic Resonance Imaging by Deep Generative Networks ]]> https://biorxiv.org/content/10.1101/2023.05.04.539501v1?rss=1 Lian, P.-h. Chuang, T.-I. Yen, Y.-H. Chang, G. 2023-05-07 doi:10.1101/2023.05.04.539501 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ The ecological characteristics of the safe sites for early-stage establishment of Chamaecyparis obtusa var. formosana seedlings in Taiwan ]]> https://biorxiv.org/content/10.1101/2023.05.15.540728v1?rss=1 Wei, S. Tseng, Y.-P. Zeleny, D. 2023-05-15 doi:10.1101/2023.05.15.540728 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet ]]> https://biorxiv.org/content/10.1101/2023.05.16.541011v1?rss=1 Yang, Y. Lin, Y.-T. Li, G. Zhong, Y. Xu, Q. Cai, J. 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Ashley-Koch, A. 2023-07-14 doi:10.1101/2023.07.12.548702 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ A Novel Genome Optimization Tool for Chromosome-Level Assembly across Diverse Sequencing Techniques ]]> https://biorxiv.org/content/10.1101/2023.07.20.549842v1?rss=1 Chuang, W. H. Cheng, H.-C. Chang, Y.-J. Huang, Y.-C. Fu, P.-Y. Hsieh, P.-H. Chen, S.-H. Kwok, P.-Y. Lin, C.-Y. Ho, J.-M. 2023-07-24 doi:10.1101/2023.07.20.549842 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Matrix stiffness modulates 3D spheroid sorting and burst-like collective migration ]]> https://biorxiv.org/content/10.1101/2023.07.23.549940v1?rss=1 Cai, G. Li, X. Lin, S.-S. Chen, S. J. Koning, K. Bi, D. Liu, A. P. 2023-07-25 doi:10.1101/2023.07.23.549940 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Spatial profiling of ovarian clear cell carcinoma reveals immune-hot features ]]> https://biorxiv.org/content/10.1101/2023.07.27.550775v1?rss=1 Tai, Y.-T. Lin, W.-C. Wang, D. Y.-T. Ye, J. Tan, T. Z. Wei, L.-H. Huang, R. Y.-J. 2023-07-29 doi:10.1101/2023.07.27.550775 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ ISRSA uncovers the impact of state anxiety on multivariate activation patterns in the human extrastriate cortex ]]> https://biorxiv.org/content/10.1101/2023.07.29.551128v1?rss=1 Hsiao, P.-Y. A. Kim, M. J. Chou, F.-C. B. Chen, P.-H. A. 2023-07-31 doi:10.1101/2023.07.29.551128 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Interdependence of a kinase and its cognate substrate plasma membrane nanoscale dynamics underlies Arabidopsis response to viral infection ]]> https://biorxiv.org/content/10.1101/2023.07.31.551174v1?rss=1 JOLIVET, M.-D. Deroubaix, A.-F. Boudsocq, M. Abel, N. B. Rocher, M. Robbe, T. Wattelet, V. Huard, J. Lefebvre, D. Lu, Y.-J. Day, B. Saias, G. Ahmed, J. Cotelle, V. Giovinazzo, N. Gallois, J.-L. Yamaji, Y. German-Retana, S. Gronnier, J. Ott, T. MONGRAND, S. Germain, V. 2023-08-01 doi:10.1101/2023.07.31.551174 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Plasmodium falciparum Raf kinase inhibitor is a lipid binding protein that interacts with CDPK1 and regulates its activity in asexual blood stage. ]]> https://biorxiv.org/content/10.1101/2023.08.23.554426v1?rss=1 Sharma, M. Krishnan, D. Negi, P. Rani, K. Revikumar, A. Munde, M. Bansal, A. 2023-08-23 doi:10.1101/2023.08.23.554426 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ Characterizing Subcortical Structural Heterogeneity in Autism ]]> https://biorxiv.org/content/10.1101/2023.08.28.554882v1?rss=1 MacDonald, D. N. Bedford, S. A. Olafson, E. Park, M. T. M. Devenyi, G. A. Tullo, S. Patel, R. Anagnostou, E. Baron-Cohen, S. Bullmore, E. T. Chura, L. R. Craig, M. C. Ecker, C. Floris, D. L. Holt, R. J. Lenroot, R. Lerch, J. P. Lombardo, M. V. Murphy, D. G. M. Raznahan, A. Ruigrok, A. N. V. Smith, E. Shinohara, R. T. Spencer, M. D. Suckling, J. Taylor, M. J. Thurm, A. MRC AIMS Consortium, Lai, M.-C. Chakravarty, M. M. 2023-08-29 doi:10.1101/2023.08.28.554882 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Structural and functional analyses of viral H2 protein of the vaccinia virus entry fusion complex ]]> https://biorxiv.org/content/10.1101/2023.08.28.555102v1?rss=1 Kao, C.-F. Liu, C.-Y. Hsieh, C.-L. Carillo, K. J. D. Tzou, D.-L. M. Wang, H.-C. Chang, W. 2023-08-28 doi:10.1101/2023.08.28.555102 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Non-invasive detection of upper tract urothelial carcinomas through the analysis of driver gene mutations and aneuploidy in urine ]]> https://biorxiv.org/content/10.1101/203968v1?rss=1 Springer, S. U. Chen, C.-H. Li, L. Douville, C. Wang, Y. Cohen, J. Afsari, B. Danilova, L. Silliman, N. Schaeffer, J. Ptak, J. Dobbyn, L. Papoli, M. Kinde, I. Huang, C.-Y. Shun, C.-T. Karchin, R. Netto, G. J. Turesky, R. J. Yun, B. H. Rosenquist, T. A. Hruban, R. H. Pu, Y.-S. Grollman, A. P. Tomasetti, C. Papadopoulos, N. Kinzler, K. W. Vogelstein, B. Dickman, K. G. 2017-10-16 doi:10.1101/203968 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ Identification of Cell States Using Super-Enhancer RNA ]]> https://biorxiv.org/content/10.1101/209387v1?rss=1 Tu, Y.-H. Juan, H.-F. Huang, H.-C. 2017-10-26 doi:10.1101/209387 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Temporal neural mechanisms underlying conscious access to different levels of facial stimulus contents ]]> https://biorxiv.org/content/10.1101/220426v1?rss=1 Hsu, S.-M. Yang, Y.-f. 2017-11-16 doi:10.1101/220426 Cold Spring Harbor Laboratory Press 2017-11-16 <![CDATA[ SeqsLab: an integrated platform for cohort-based annotation and interpretation of genetic variants on Spark ]]> https://biorxiv.org/content/10.1101/239962v1?rss=1 Chang, M.-T. Tung, Y.-A. Chung, J.-M. Yao, H.-F. Li, Y.-L. Lin, Y.-H. Wang, Y.-T. Chen, C.-Y. Su, C.-T. 2017-12-27 doi:10.1101/239962 Cold Spring Harbor Laboratory Press 2017-12-27 <![CDATA[ Naa10p promotes metastasis by stabilizing matrix metalloproteinase-2 protein in human osteosarcomas ]]> https://biorxiv.org/content/10.1101/243592v1?rss=1 Chien, M.-H. Lee, W.-J. Yang, Y.-C. Tan, P. Pan, K.-F. Tsai, H.-C. Hsu, C.-H. Hsiao, M. Hua, K.-T. 2018-01-05 doi:10.1101/243592 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Hemicellulose Degradation and Utilization by a Synthetic Saccharomyces cerevisiae Consortium ]]> https://biorxiv.org/content/10.1101/244244v1?rss=1 Tabanag, I. D. Tsai, S.-L. 2018-01-07 doi:10.1101/244244 Cold Spring Harbor Laboratory Press 2018-01-07 <![CDATA[ Identify and predict environmental change effects on tiger mosquitos, Aedes polynesiensis ]]> https://biorxiv.org/content/10.1101/284174v1?rss=1 Grziwotz, F. Strauss, J. F. Hsieh, C.-h. Telschow, A. 2018-03-18 doi:10.1101/284174 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ Emergence of mosaic plasmids harboring Tn1546-ermB element in Staphylococcus aureus isolates ]]> https://biorxiv.org/content/10.1101/294348v1?rss=1 Wan, T.-W. Lin, Y.-T. Hung, W.-C. Tsai, J.-C. Liu, Y.-J. Hsueh, P.-R. Teng, L.-J. 2018-04-04 doi:10.1101/294348 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Structural insights into DNA sequence recognition by Arabidopsis ETHYLENE RESPONSE FACTOR 96 ]]> https://biorxiv.org/content/10.1101/302299v1?rss=1 Chen, C.-Y. Lin, P.-H. Chen, K.-H. Cheng, Y.-S. 2018-04-16 doi:10.1101/302299 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Dlk1-Dio3 Locus-Derived LncRNAs Perpetuate Postmitotic Motor Neuron Cell Fate and Subtype Identity ]]> https://biorxiv.org/content/10.1101/320135v1?rss=1 Yen, Y.-P. Hsieh, W.-F. Lu, Y.-L. Liau, E. S. Hsu, H.-C. Chen, Y.-C. Liu, T.-C. Chang, M. Li, J. Lin, S.-P. Hung, J.-H. Chen, J.-A. 2018-05-11 doi:10.1101/320135 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Whole-brain imaging and characterization of Drosophila brains based on one-, two-, and three-photon excitations ]]> https://biorxiv.org/content/10.1101/339531v1?rss=1 Chu, S.-W. Lin, Y.-Y. Chiang, A.-S. Hsu, K.-J. 2018-06-05 doi:10.1101/339531 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Which results of the standard test in community weighted mean approach are too optimistic? ]]> https://biorxiv.org/content/10.1101/349589v1?rss=1 Zeleny, D. 2018-06-18 doi:10.1101/349589 Cold Spring Harbor Laboratory Press 2018-06-18 <![CDATA[ Three-dimensional culture of chicken primordial germ cells in chemically defined media containing the functional polymer FP003 ]]> https://biorxiv.org/content/10.1101/358952v1?rss=1 Pain, B. Jean, C. Chen, Y.-C. CHANG, W.-C. Lin, S.-P. Rival-Gervier, S. MINAMI, M. HAYASHI, H. KANAKI, T. WU, S.-C. 2018-06-29 doi:10.1101/358952 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Integrated Disease Surveillance and Response (IDSR) in Malawi: Implementation Gaps and Challenges for Timely Alert ]]> https://biorxiv.org/content/10.1101/363713v1?rss=1 Wu, T.-S. J. Kagoli, M. Kaasboll, J. J. Bjune, G. A. 2018-07-06 doi:10.1101/363713 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Glucose intake hampers PKA-regulated HSP90 chaperone activity ]]> https://biorxiv.org/content/10.1101/376186v1?rss=1 Chen, Y.-C. Jiang, P.-H. Chen, H.-M. Chen, C.-H. Wang, Y.-T. Chen, Y.-J. Yu, C.-J. Teng, S.-C. 2018-07-24 doi:10.1101/376186 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Effect of de novo transcriptome assembly on transcript quantification ]]> https://biorxiv.org/content/10.1101/380998v1?rss=1 Hsieh, P.-H. Oyang, Y.-J. Chen, C.-Y. 2018-07-31 doi:10.1101/380998 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ An efficient timer and sizer of protein motions reveals the time scales of functional dynamics in the ribosome ]]> https://biorxiv.org/content/10.1101/384511v1?rss=1 Chan, J. Lin, H.-R. Takemura, K. Chang, K.-C. Chang, Y.-Y. Joti, Y. Kitao, A. Yang, L.-W. 2018-08-03 doi:10.1101/384511 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Mating system of Ustilago esculenta and its polymorphism ]]> https://biorxiv.org/content/10.1101/384727v1?rss=1 Liang, S. Huang, Y.-H. Chiu, J.-Y. Tseng, H.-W. Haung, J.-H. Shen, W.-C. 2018-08-04 doi:10.1101/384727 Cold Spring Harbor Laboratory Press 2018-08-04 <![CDATA[ Assessment of population differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers ]]> https://biorxiv.org/content/10.1101/402420v1?rss=1 Lin, Y.-P. Liu, C.-Y. Chen, K. 2018-08-28 doi:10.1101/402420 Cold Spring Harbor Laboratory Press 2018-08-28 <![CDATA[ Mutant p53 triggers a dynamin-1/APPL1 endosome feedback loop that regulates β1 integrin recycling and migration ]]> https://biorxiv.org/content/10.1101/408815v1?rss=1 Lakoduk, A. M. Roudot, P. Mettlen, M. Grossman, H. M. Chen, P.-H. Schmid, S. L. 2018-09-05 doi:10.1101/408815 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ On the post-glacial spread of human commensal Arabidopsis thaliana: journey to the east ]]> https://biorxiv.org/content/10.1101/411108v1?rss=1 Hsu, C.-W. Lo, C.-Y. Lee, C.-R. 2018-09-07 doi:10.1101/411108 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Active Transport of Membrane Components by Self-Organization of the Min Proteins ]]> https://biorxiv.org/content/10.1101/418384v1?rss=1 Shih, Y.-L. Huang, L.-T. Tu, Y.-M. Lee, B.-F. Bau, Y.-C. Hong, C. Y. Lee, H.-l. Shih, Y.-P. Hsu, M.-F. Chen, J.-S. Lu, Z.-X. Chao, L. 2018-09-14 doi:10.1101/418384 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ GenEpi: Gene-based Epistasis Discovery Using Machine Learning ]]> https://biorxiv.org/content/10.1101/421719v1?rss=1 Chang, Y.-C. Wu, J.-T. Hong, M.-Y. Tung, Y.-A. Hsieh, P.-H. Yee, S. W. Giacomini, K. M. Oyang, Y.-J. Chen, C.-Y. Alzheimer's Disease Neuroimaging Initiative, 2018-09-20 doi:10.1101/421719 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ Analysis of contributory gut microbiota and lauric acid against necrotic enteritis in Clostridium perfringens and Eimeria side-by-side challenge model ]]> https://biorxiv.org/content/10.1101/434449v1?rss=1 Wang, C. Yang, W.-Y. Lee, Y. Lu, H. Chou, C.-H. Wen-Yuan Yang, Yuejia Lee, Hsinyi Lu, Chung-Hsi Chou, 2018-10-03 doi:10.1101/434449 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Comparative genetic architectures of schizophrenia in East Asian and European populations ]]> https://biorxiv.org/content/10.1101/445874v1?rss=1 Lam, M. Chen, C.-Y. Li, Z. Martin, A. Bryois, J. Ma, X. Gaspar, H. Ikeda, M. Benyamin, B. Brown, B. Liu, R. Zhou, W. Huan, L. Kamatani, Y. Kim, S.-W. Kubo, M. Kusumawardhani, A. Liu, C.-M. Ma, H. Periyasamy, S. Takahashi, A. Wang, Q. Xu, Z. Yu, H. Zhu, F. Psychiatric Genomics Consortium - Schizophrenia Working Group, Indonesia Schizophrenia Consortium, Genetic REsearch on schizophreniA neTwork-China and Netherland (GREAT-CN), Chen, W. Faraone, S. Glatt, S. He, L. Hyman, S. Hwu, H.-G. Li, T. McCarroll, S. Neale, B. Sklar, P. Wildenauer, D. Yu, X. Zh 2018-10-17 doi:10.1101/445874 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ The distinct biochemical property enables thymidylate kinase as a drug target and participates in pyrimidine drug sensitivity in Candida albicans ]]> https://biorxiv.org/content/10.1101/466938v1?rss=1 Huang, C. Y. Chen, Y.-C. Wu-Hsieh, B. A. Fang, J.-M. Chang, Z.-F. Chang-Yu Huang, Yee-Chun Chen, Betty A. Wu-Hsieh, Jim-Min Fang and Zee-Fen Chang, 2018-11-09 doi:10.1101/466938 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ AICAR induces apoptosis and inhibits migration of prostate cancer cells through an AMPK/mTOR-dependent pathway ]]> https://biorxiv.org/content/10.1101/474197v1?rss=1 Su, C.-C. Hsieh, K.-L. Wang, S.-C. Yeh, H.-C. Huang, S.-P. Liu, P.-L. Fang, S.-H. Cheng, W.-C. Huang, K.-H. Chiu, F.-Y. Lin, I.-L. Huang, M.-Y. Li, C.-Y. 2018-11-19 doi:10.1101/474197 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Schizophrenia risk conferred by protein-coding de novo mutations ]]> https://biorxiv.org/content/10.1101/495036v1?rss=1 Howrigan, D. Rose, S. A. Samocha, K. E. Fromer, M. Cerrato, F. Chen, W. J. Churchhouse, C. Chambert, K. Chandler, S. D. Daly, M. J. Dumont, A. Genovese, G. Hwu, H.-G. Laird, N. Kosmicki, J. A. Moran, J. Roe, C. Singh, T. Wang, S.-H. Faraone, S. Glatt, S. McCarroll, S. Tsuang, M. Neale, B. 2018-12-13 doi:10.1101/495036 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ The integrated stress response mediates type I interferon driven necrosis in Mycobacterium tuberculosis granulomas ]]> https://biorxiv.org/content/10.1101/499467v1?rss=1 Bhattacharya, B. Xiao, S. Chatterjee, S. Urbanowski, M. Ordonez, A. Ihms, E. A. Agrahari, G. Lun, S. Berland, R. Pichugin, A. Gao, Y. Connor, J. Ivanov, A. Yan, B.-S. Kobzik, L. Jain, S. Bishai, W. Kramnik, I. 2018-12-19 doi:10.1101/499467 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Mitochondrial cristae biogenesis coordinates with ETC complex IV assembly during Drosophila maturation ]]> https://biorxiv.org/content/10.1101/503474v1?rss=1 Jiang, Y.-f. Lin, H.-l. Wang, L.-j. Hsu, T. Fu, C. 2018-12-21 doi:10.1101/503474 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Structure-guided design of a pure orthosteric antagonist of integrin αIIbβ3 that inhibits thrombosis but not clot retraction ]]> https://biorxiv.org/content/10.1101/509299v1?rss=1 Adair, B. D. Alonso, J. L. van Agthoven, J. Hayes, V. Ahn, H. S. Xiong, J.-P. Poncz, M. Arnaout, M. A. 2018-12-31 doi:10.1101/509299 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Dominant coral bacterium Endozoicomonas acroporae metabolizes DMSP ]]> https://biorxiv.org/content/10.1101/519546v1?rss=1 95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase--a dddD gene homolog found in all E. acroporae strains--and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle. ]]> Tandon, K. Chiang, P.-W. Lu, C.-Y. Yang, S.-H. Chen, Y.-F. Wada, N. Chen, P.-Y. Chang, H.-Y. Chou, M.-S. Chen, W.-M. Tang, S.-L. 2019-01-17 doi:10.1101/519546 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Thermal cycling-hyperthermia in combination with polyphenols, epigallocatechin gallate and chlorogenic acid, exerts synergistic anticancer effect against human pancreatic cancer PANC-1 cells ]]> https://biorxiv.org/content/10.1101/548552v1?rss=1 Lu, C.-H. Chen, W.-T. Hsieh, C.-H. Kuo, Y.-Y. Chao, C.-Y. 2019-02-14 doi:10.1101/548552 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Extracellular Pgk1 enhances neurite outgrowth of motoneurons through Nogo66-independent targeting of NogoA ]]> https://biorxiv.org/content/10.1101/550921v1?rss=1 Lin, C. Y. Wu, C. L. Lee, K. Z. Chen, Y. J. Zhang, P. H. Chang, C. Y. Han, H. J. Lin, S. Z. Tsai, H. J. 2019-02-15 doi:10.1101/550921 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Divergence in Thermostability of Arabidopsis Mitochondrial Nucleotide Exchange Factors Encoded by Duplicate Genes, MGE1 and MGE2 ]]> https://biorxiv.org/content/10.1101/553503v1?rss=1 Chen, Z.-t. Hung, M.-J. Yu, S.-J. Liao, T.-Y. Lin, Y.-P. Chen, R. P.- Y. Yang, C.-C. Charng, Y.-y. 2019-02-18 doi:10.1101/553503 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Sterol-O acyltransferase 1 is inhibited by gga-miR-181a-5p and gga-miR-429-3p through the TGFβ pathway in endodermal epithelial cells of Japanese quail ]]> https://biorxiv.org/content/10.1101/569806v1?rss=1 Lin, H.-J. Lin, C.-W. Mersmann, H. J. Ding, S.-T. 2019-03-07 doi:10.1101/569806 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Selection of a Malignant Subpopulation from a Colorectal Cancer Cell Line ]]> https://biorxiv.org/content/10.1101/578823v1?rss=1 Lai, P.-L. Chen, T.-C. Feng, C.-Y. Lin, H. Wu, N. Chen, Y. Hsiao, M. Lu, J. Huang, H.-C. 2019-03-15 doi:10.1101/578823 Cold Spring Harbor Laboratory Press 2019-03-15 <![CDATA[ Evidence of extensive intraspecific noncoding reshuffling in a 169-kb mitochondrial genome of a basidiomycetous fungus ]]> https://biorxiv.org/content/10.1101/579870v1?rss=1 Lee, H.-H. Ke, H.-M. Lin, C.-Y. I. Lee, J. J. Chung, C.-L. Tsai, I. J. 2019-03-16 doi:10.1101/579870 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ variant2literature: full text literature search for genetic variants ]]> https://biorxiv.org/content/10.1101/583450v1?rss=1 Lin, Y.-H. Lu, Y.-C. Hsu, J. S. Lee, K.-H. Cheng, Y.-W. Chen, Y.-C. Chen, T.-F. Tu, C.-T. Hsu, C.-M. Chou, C.-C. Chen, P.-L. Tu, Y.-C. E. Chen, C.-Y. 2019-03-21 doi:10.1101/583450 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ A normative study of modified spatial context memory test in middle and older individuals ]]> https://biorxiv.org/content/10.1101/584136v1?rss=1 Kuo, H.-C. Wang, H.-M. Huang, Y.-P. Kuo, H.-Y. 2019-03-20 doi:10.1101/584136 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Acute decrease in plasma membrane tension induces macropinocytosis via PLD2 activation ]]> https://biorxiv.org/content/10.1101/594416v1?rss=1 Loh, J. Joseph, J. Chuang, M.-C. Lin, S.-S. Chang, Y.-C. Su, Y.-A. Liu, A. P. Liu, Y.-W. 2019-03-31 doi:10.1101/594416 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Bone regeneration in Ds-Red pig calvarial defect using allogenic transplantation of EGFP-pMSCs - a comparison of host cells and seeding cells in the scaffold ]]> https://biorxiv.org/content/10.1101/599670v1?rss=1 Hsieh, M.-k. Wu, C.-J. Su, X.-C. Chen, Y.-C. Tsai, T.-T. Niu, C.-C. Lai, P.-L. Wu, S.-C. 2019-04-04 doi:10.1101/599670 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ ADHD symptoms map onto noise-driven structure-function decoupling between hub and peripheral brain regions ]]> https://biorxiv.org/content/10.1101/606228v1?rss=1 Hearne, L. Lin, H.-Y. Sanz-Leon, P. Tseng, W.-Y. I. Gau, S. S.-F. Roberts, J. Cocchi, L. 2019-04-11 doi:10.1101/606228 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Plant A20/AN1 proteins coordinate different immune responses including RNAi pathway for antiviral immunity ]]> https://biorxiv.org/content/10.1101/622696v1?rss=1 Chang, L. Chang, H.-H. Chiu, Y.-S. Chang, J.-C. Hsu, D.-W. Tzean, Y. Cheng, A.-P. Lu, H.-C. Yeh, H.-H. 2019-04-29 doi:10.1101/622696 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Stable species boundaries despite ten million years of hybridization in tropical eels ]]> https://biorxiv.org/content/10.1101/635631v1?rss=1 Barth, J. M. I. Gubili, C. Matschiner, M. Torresen, O. K. Watanabe, S. Egger, B. Han, Y.-S. Feunteun, E. Sommaruga, R. Jehle, R. Schabetsberger, R. 2019-05-13 doi:10.1101/635631 Cold Spring Harbor Laboratory Press 2019-05-13 <![CDATA[ RNASeqR: an R package for automated two-group RNA-Seq analysis workflow ]]> https://biorxiv.org/content/10.1101/641324v1?rss=1 Chao, K.-H. Hsiao, Y.-W. Lee, Y.-F. Lee, C.-Y. Lai, L.-C. Tsai, M.-H. Lu, T.-P. Chuang, E. Y. 2019-05-27 doi:10.1101/641324 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Structural Lipidomics and Molecular Imaging of C=C Positional Isomers Enabled by mCPBA Epoxidation with Tandem Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/649103v1?rss=1 Kuo, T.-H. Chung, H.-H. Chang, H.-Y. Wang, M.-Y. Shen, T.-L. Hsu, C.-C. 2019-05-24 doi:10.1101/649103 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ High Spatial Resolution Ambient Ionization Mass Spectrometry Imaging Using Microscopy Image Fusion ]]> https://biorxiv.org/content/10.1101/657494v1?rss=1 Chen, C.-L. Lin, L.-E. Huang, Y.-C. Chung, H.-H. Chen, K.-C. Peng, Y.-J. Lin, C.-W. Ding, S.-T. Shen, T.-L. Hsu, C.-C. 2019-06-02 doi:10.1101/657494 Cold Spring Harbor Laboratory Press 2019-06-02 <![CDATA[ Association Tests Using Copy Number Profile Curves (CONCUR) Enhances Power in Rare Copy Number Variant Analysis ]]> https://biorxiv.org/content/10.1101/666875v1?rss=1 Brucker, A. R. Lu, W. Marceau West, R. Yu, Q.-Y. Hsiao, C. K. Hsiao, T.-H. Lin, C.-H. Magnusson, P. K. E. Sullivan, P. F. Szatkiewicz, J. Lu, T.-P. Tzeng, J.-Y. 2019-06-10 doi:10.1101/666875 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Identification of type 2 diabetes loci in 433,540 East Asian individuals ]]> https://biorxiv.org/content/10.1101/685172v1?rss=1 240 loci associated with type 2 diabetes (T2D), however most loci have been identified in analyses of European-ancestry individuals. To examine T2D risk in East Asian individuals, we meta-analyzed GWAS data in 77,418 cases and 356,122 controls. In the main analysis, we identified 298 distinct association signals at 178 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 56 loci newly implicated in T2D predisposition. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. New associations include signals in/near GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect muscle and adipose differentiation. At another locus, eQTLs at two overlapping T2D signals act through two genes, NKX6-3 and ANK1, in different tissues. Association studies in diverse populations identify additional loci and elucidate disease genes, biology, and pathways.nnType 2 diabetes (T2D) is a common metabolic disease primarily caused by insufficient insulin production and/or secretion by the pancreatic {beta} cells and insulin resistance in peripheral tissues1. Most genetic loci associated with T2D have been identified in populations of European (EUR) ancestry, including a recent meta-analysis of genome-wide association studies (GWAS) of nearly 900,000 individuals of European ancestry that identified >240 loci influencing the risk of T2D2. Differences in allele frequency between ancestries affect the power to detect associations within a population, particularly among variants rare or monomorphic in one population but more frequent in another3,4. Although smaller than studies in European populations, a recent T2D meta-analysis in almost 200,000 Japanese individuals identified 28 additional loci4. The relative contributions of different pathways to the pathophysiology of T2D may also differ between ancestry groups. For example, in East Asian (EAS) populations, T2D prevalence is greater than in European populations among people of similar body mass index (BMI) or waist circumference5. We performed the largest meta-analysis of East Asian individuals to identify new genetic associations and provide insight into T2D pathogenesis. ]]> Spracklen, C. N. Horikoshi, M. Kim, Y. J. Lin, K. Bragg, F. Moon, S. Suzuki, K. Tam, C. Tabara, Y. Kwak, S.-H. Takeuchi, F. Long, J. Lim, V. Chai, J.-F. Chen, C.-H. Nakatochi, M. Yao, J. Choi, H. S. Iyengar, A. K. Perrin, H. J. Brotman, S. M. van de Bunt, M. Gloyn, A. L. Below, J. L. Boehnke, M. Bowden, D. W. Chambers, J. C. Mahajan, A. McCarthy, M. I. Ng, M. C. Petty, L. E. Zhang, W. Morris, A. P. Adair, L. S. Bian, Z. Chan, J. Chang, L.-C. Chee, M.-L. Chen, Y.-D. I. Chen, Y.-T. Chen, Z. Chuang, L.-M. Du, S. Gordon-Larsen, P. Gross, M. Guo, X. Guo 2019-06-28 doi:10.1101/685172 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation ]]> https://biorxiv.org/content/10.1101/714501v1?rss=1 Wang, P.-H. Chen, Y.-L. Wei, S. T.-S. Wu, K. Lee, T.-H. Wu, T.-Y. Chiang, Y.-R. 2019-07-25 doi:10.1101/714501 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences ]]> https://biorxiv.org/content/10.1101/714907v1?rss=1 Ereful, N. C. Liu, L.-y. Kao, S.-M. Tsai, E. Laurena, A. Thomson, M. Greenland, A. Powell, W. Mackay, I. Leung, H. 2019-07-25 doi:10.1101/714907 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Identification of Escherichia coli ClpAP in regulating susceptibility to type VI secretion system-mediated attack by Agrobacterium tumefaciens ]]> https://biorxiv.org/content/10.1101/734046v1?rss=1 Lin, H.-H. Yu, M. Sriramoju, M. K. Hsu, S.-T. D. Liu, C.-T. Lai, E.-M. 2019-08-14 doi:10.1101/734046 Cold Spring Harbor Laboratory Press 2019-08-14 <![CDATA[ Massive parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity ]]> https://biorxiv.org/content/10.1101/740837v1?rss=1 Suiter, C. C. Moriyama, T. Matreyek, K. A. Yang, W. Scaletti, E. R. Nishii, R. Yang, W. Hoshitsuki, K. Singh, M. Trehan, A. Parish, C. Smith, C. Bhojwani, D. Yuen, L. Y. Li, C.-k. Li, C.-h. Yang, Y.-l. Walker, G. J. Goodhand, J. R. Kennedy, N. A. Klussmann, F. A. Bhatia, S. Relling, M. V. Kato, M. Hori, H. Bhatia, P. Ahmad, T. Yoeh, A. E. J. Stenmark, P. Fowler, D. M. Yang, J. J. 2019-08-20 doi:10.1101/740837 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Application of non-invasive low-intensity pulsed electric field with thermal cycling-hyperthermia for synergistically enhanced anticancer effect of chlorogenic acid on PANC-1 cells ]]> https://biorxiv.org/content/10.1101/745562v1?rss=1 Lu, C.-H. Kuo, Y.-Y. Lin, G.-B. Chen, W.-T. Chao, C.-Y. 2019-08-23 doi:10.1101/745562 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Fucosyltransferase 4 shapes oncogenic glycoproteome to drive metastasis of lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/752519v1?rss=1 Lu, H.-H. Lin, S.-Y. Weng, R. R. Juan, Y.-H. Chen, Y.-W. Hou, H.-H. Hung, Z.-C. Oswita, G. A. Huang, Y.-J. Shih, J.-Y. Yu, C.-J. Tsai, H.-C. 2019-09-02 doi:10.1101/752519 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ CaMKII oxidation is a performance/disease trade-off in vertebrate evolution ]]> https://biorxiv.org/content/10.1101/767525v1?rss=1 Wang, Q. Hernandez-Ochoa, E. O. Viswanathan, M. C. Blum, I. D. Granger, J. M. Murphy, K. R. Wei, A.-C. Aja, S. Liu, N. Antonescu, C. M. Florea, L. D. Talbot, C. C. Mohr, D. Wagner, K. R. Regot, S. Lovering, R. M. Wu, M. N. Cammarato, A. Schneider, M. F. Bever, G. S. Anderson, M. E. 2019-09-12 doi:10.1101/767525 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ The Trend of Suicide Reporting in the Media: an Effectiveness Study of Daily Surveillance over Nine Years ]]> https://biorxiv.org/content/10.1101/768945v1?rss=1 Wu, C.-Y. Lee, M.-B. Liao, S.-C. Chan, C.-T. Chen, C.-Y. 2019-09-13 doi:10.1101/768945 Cold Spring Harbor Laboratory Press 2019-09-13 <![CDATA[ Coconut inflorescence sap mediated synthesis of silver nanoparticles and its diverse antimicrobial properties ]]> https://biorxiv.org/content/10.1101/775940v1?rss=1 nView larger version (64K):norg.highwire.dtl.DTLVardef@3c3f1forg.highwire.dtl.DTLVardef@1540f6borg.highwire.dtl.DTLVardef@1c069aborg.highwire.dtl.DTLVardef@159772c_HPS_FORMAT_FIGEXP M_FIG Graphical abstractnnC_FIG ]]> MK, R. K.S., M. Nair, S. S. B, K. K. TM, S. KP, S. K, S. Hallur, S. Prasad, K. Chandran, N. KB, H. Karun, A. 2019-09-23 doi:10.1101/775940 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Interplay between Desmoglein2 and hypoxia controls intravasation and circulating tumor cell clustering in breast cancer metastasis ]]> https://biorxiv.org/content/10.1101/790519v1?rss=1 Chang, P.-H. Chen, M.-C. Tsai, Y.-P. Hsu, P.-H. Jeng, Y.-M. Hwang-Verslues, W. W. 2019-10-02 doi:10.1101/790519 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Human CST complex protects replication fork stability by directly blocking MRE11 degradation of nascent strand DNA ]]> https://biorxiv.org/content/10.1101/797647v1?rss=1 Lyu, X. Lei, K.-H. Shiva, O. Chastain, M. Chi, P. Chai, W. 2019-10-08 doi:10.1101/797647 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Diversification of metazoan Kexin-like proprotein convertases: insights from the leech Helobdella ]]> https://biorxiv.org/content/10.1101/802215v1?rss=1 Tao, W.-Y. Cheng, Y.-C. Song, M. H. Weisblat, D. A. Kuo, D.-H. 2019-10-13 doi:10.1101/802215 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Heterochronically expressed midline netrin was recruited to guide mesoderm migration in epibolic gastrulation of the leech ]]> https://biorxiv.org/content/10.1101/803353v1?rss=1 Lee, J.-R. Kuo, D.-H. 2019-10-13 doi:10.1101/803353 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Characterizing the Cancer-Associated Microbiome with Small RNA Sequencing Data ]]> https://biorxiv.org/content/10.1101/807586v1?rss=1 1000 genera among 630 colorectal samples and clustered these samples into three distinctive colorectal enterotypes. Each cluster has its own distinctive microbial composition and interactions. Furthermore, we found 12 genera from these clusters that are associated with cancer stages and revealed their putative functions. Our results indicate that the proposed analytical approach can effectively determine the cancer-associated microbiome. It may be readily applied to explore other types of cancer, in which specimens of the microbiome are difficult to collect. ]]> Lee, W.-H. Chen, K.-P. Wang, K. Huang, H.-C. Juan, H.-F. 2019-10-17 doi:10.1101/807586 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction ]]> https://biorxiv.org/content/10.1101/810176v1?rss=1 Cheng, L.-H. Lin, C. 2019-10-18 doi:10.1101/810176 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of domestication ]]> https://biorxiv.org/content/10.1101/822411v1?rss=1 Matsumura, H. Hsiao, M.-C. Toyoda, A. Taniai, N. Tarora, K. Urasaki, N. Anand, S. S. Dhillon, N. P. Schafleitner, R. Lee, C.-R. 2019-10-29 doi:10.1101/822411 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Chromatin organization in early land plants reveals an ancestral association between H3K27me3, transposons, and constitutive heterochromatin ]]> https://biorxiv.org/content/10.1101/827881v1?rss=1 Montgomery, S. A. Tanizawa, Y. Galik, B. Wang, N. Ito, T. A. Mochizuki, T. Akimcheva, S. Bowman, J. Cognat, V. Drouard, L. Ekker, H. Houng, S.-F. Kohchi, T. Lin, S.-S. Liu, L.-Y. D. Nakamura, Y. Valeeva, L. R. Shakirov, E. V. Shippen, D. E. Wei, W.-L. Yagura, M. Yamaoka, S. Yamato, K. T. Liu, C. Berger, F. 2019-11-01 doi:10.1101/827881 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Sustained modulation of emotion-related fibers after 8 weeks of mindfulness-based stress reduction training ]]> https://biorxiv.org/content/10.1101/855551v1?rss=1 Chen, C.-L. Shih, Y.-C. Hsu, Y.-C. Wen, T.-K. Fang, S.-C. Tang, D.-L. Lee, S.-C. Tseng, W.-Y. I. 2019-11-26 doi:10.1101/855551 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Contrasting species functional trait structuring of subarctic versus subtropical copepod communities ]]> https://biorxiv.org/content/10.1101/2020.01.31.928705v1?rss=1 Garcia-Comas, C. Hsieh, C.-h. Chiba, S. Sugisaki, H. Hashioka, T. Smith, S. L. 2020-02-01 doi:10.1101/2020.01.31.928705 Cold Spring Harbor Laboratory Press 2020-02-01 <![CDATA[ Canonical Wnt signaling Is Involved in Anterior Regeneration of the Annelid Aeolosoma viride ]]> https://biorxiv.org/content/10.1101/2020.03.01.972448v1?rss=1 Chen, C.-Y. Yueh, W.-T. Chen, J.-H. 2020-03-02 doi:10.1101/2020.03.01.972448 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ The potential SARS-CoV-2 entry inhibitor ]]> https://biorxiv.org/content/10.1101/2020.03.26.009803v1?rss=1 Lung, J. Lin, Y.-S. Yang, Y.-H. Chou, Y.-L. Chang, G.-H. Tsai, M.-S. Hsu, C.-M. Yeh, R.-A. Shu, L.-H. Cheng, Y.-C. Te Liu, H. Wu, C.-Y. 2020-03-26 doi:10.1101/2020.03.26.009803 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ A Method to sort heterogenous cell populations based on migration in 2D and 3D environments ]]> https://biorxiv.org/content/10.1101/2020.05.06.080234v1?rss=1 Arora, A. Galeano, J. L. Myaing, M. Z. Arasi, B. Huang, R. Y.-J. DasGupta, R. Biro, M. Viasnoff, V. 2020-05-07 doi:10.1101/2020.05.06.080234 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ sangeranalyseR: simple and interactive analysis of Sanger sequencing data in R ]]> https://biorxiv.org/content/10.1101/2020.05.18.102459v1?rss=1 Chao, K.-H. Barton, K. Palmer, S. Lanfear, R. 2020-05-21 doi:10.1101/2020.05.18.102459 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ NLRP3 inflammasome contributes to host defense against Talaromyces marneffei infection ]]> https://biorxiv.org/content/10.1101/2020.08.17.253518v1?rss=1 Ma, H. Chan, J. F.-W. Tan, Y. P. Kui, L. Tsang, C.-C. Pei, S. L. Lau, Y.-L. Woo, P. C. Lee, P. P. 2020-08-23 doi:10.1101/2020.08.17.253518 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Assessing the cognitive status of Drosophila by the value-based feeding decision ]]> https://biorxiv.org/content/10.1101/2020.08.27.267955v1?rss=1 Kao, C.-F. Yu, C.-C. Chang, F.-C. Hong, Y.-H. Li, J.-C. Chen, P.-L. Chen, C.-H. Chiu, T.-W. Lu, T.-T. Wang, Y.-M. 2020-08-27 doi:10.1101/2020.08.27.267955 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ A Novel DNA Chromatography Method to Distinguish M. abscessus Subspecies and Macrolide Susceptibility ]]> https://biorxiv.org/content/10.1101/2020.09.17.292417v1?rss=1 Yoshida, M. Sano, S. Chien, J.-Y. Fukano, H. Suzuki, M. Asakura, T. Morimoto, K. Murase, Y. Miyamoto, S. Kurashima, A. Hasegawa, N. Hsueh, P.-R. Mitarai, S. Ato, M. Hoshino, Y. 2020-09-18 doi:10.1101/2020.09.17.292417 Cold Spring Harbor Laboratory Press 2020-09-18 <![CDATA[ IFN-{lambda}4 may contribute to HCV persistence by increasing ER stress and enhancing IRF1 signaling ]]> https://biorxiv.org/content/10.1101/2020.10.28.359398v1?rss=1 Onabajo, O. O. Wang, F. Lee, M.-H. Florez-Vargas, O. Obajemu, A. Castro, M. A. A. Tanikawa, C. Vargas, J. Liao, S.-F. Song, C. Huang, Y.-H. Shen, C.-Y. Banday, A. R. O'Brien, T. R. Hu, Z. Matsuda, K. Robertson, A. G. Prokunina-Olsson, L. 2020-10-29 doi:10.1101/2020.10.28.359398 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Rare coding variants in 35 genes associate with circulating lipid levels: a multi-ancestry analysis of 170,000 exomes ]]> https://biorxiv.org/content/10.1101/2020.12.22.423783v1?rss=1 170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels. Ten of these: ALB, SRSF2, JAK2, CREB3L3, TMEM136, VARS, NR1H3, PLA2G12A, PPARG and STAB1 have not been implicated for lipid levels using rare coding variation in population-based samples. We prioritize 32 genes identified in array-based genome-wide association study (GWAS) loci based on gene-based associations, of which three: EVI5, SH2B3, and PLIN1, had no prior evidence of rare coding variant associations. Most of the associated genes showed evidence of association in multiple ancestries. Also, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes, and for genes closest to GWAS index single nucleotide polymorphisms (SNP). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels. ]]> Hindy, G. Dornbos, P. Chaffin, M. D. Liu, D. J. Wang, M. X. Aguilar-Salinas, C. A. Antonacci-Fulton, L. Ardissino, D. Arnett, D. K. Aslibekyan, S. Atzmon, G. Ballantyne, C. M. Barajas-Olmos, F. Barzilai, N. Becker, L. C. Bielak, L. F. Bis, J. C. Blangero, J. Boerwinkle, E. Bonnycastle, L. L. Bottinger, E. Bowden, D. W. Bown, M. J. Brody, J. A. Broome, J. G. Burtt, N. P. Cade, B. E. Centeno-Cruz, F. Chan, E. Chang, Y.-C. Chen, Y.-D. I. Cheng, C.-Y. Choi, W. J. Chowdhury, R. Contreras-Cubas, C. Cordova, E. J. Correa, A. Cupples, L. A. Curran, J. E. Danesh, 2020-12-23 doi:10.1101/2020.12.22.423783 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Myocardial BDNF regulates cardiac bioenergetics through the transcription factor Yin Yang 1 ]]> https://biorxiv.org/content/10.1101/2021.01.19.427213v1?rss=1 Yang, X. Zhang, M. Zimmerman, R. J. Wang, Q. Wei, A.-c. Zhu, G. Bedja, D. Jiang, H. Shiva, S. S. Scott, I. O'Rourke, B. Kass, D. A. Paolocci, N. Feng, N. 2021-01-21 doi:10.1101/2021.01.19.427213 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Modulated TRPC1 expression predicts sensitivity of breast cancer to doxorubicin and magnetic field therapy: segue towards a precision medicine approach. ]]> https://biorxiv.org/content/10.1101/2021.04.30.442085v1?rss=1 Tai, Y. K. Chan, K. K. W. Fong, C. H. H. Ramanan, S. Yap, J. L. Y. Yin, J. N. Yip, Y. S. Tan, W. R. Koh, A. P. F. Tan, N. S. Chan, C. W. Huang, R. Y. J. Franco-Obregon, A. 2021-04-30 doi:10.1101/2021.04.30.442085 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Cell-specific expression buffering promotes cell survival and cancer robustness ]]> https://biorxiv.org/content/10.1101/2021.07.26.453775v1?rss=1 Lin, H.-K. Cheng, J.-H. Wu, C.-C. Hsieh, F.-S. Dunlap, C. A. Chen, S.-h. 2021-07-27 doi:10.1101/2021.07.26.453775 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ The In Vivo Source of Type I and Type III IFNs is Pathogen Dependent ]]> https://biorxiv.org/content/10.1101/2021.10.05.463160v1?rss=1 Sandoval, M. J. Tseng, H.-C. Risman, H. P. Smirnov, S. Li, Q. Lin, J.-D. Rivera, A. Durbin, R. K. Kotenko, S. V. Durbin, J. 2021-10-05 doi:10.1101/2021.10.05.463160 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Omicron-specific mRNA vaccine induced potent neutralizing antibody against Omicron but not other SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2022.01.31.478406v1?rss=1 Lee, I.-J. Sun, C.-P. Wu, P.-Y. Lan, Y.-H. Wang, I.-H. Liu, W.-C. Tseng, S.-C. Tsung, S.-I. Chou, Y.-C. Kumari, M. Chang, Y.-W. Chen, H.-F. Lin, Y.-S. Chen, T. -Y. Chiu, C.-W. Hsieh, C.-H. Chuang, C.-Y. Lin, C.-C. Cheng, C.-M. Lin, H.-T. Chen, W.-Y. Chiang, P.-C. Lee, C.-C. Liao, J. C. Wu, H.-C. Tao, M.-H. 2022-01-31 doi:10.1101/2022.01.31.478406 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Insertion of YFP at the Arabidopsis AFL1 and P5CS1 loci shows the potential, and potential limitations, of gene targeting for functional analysis of stress-related genes ]]> https://biorxiv.org/content/10.1101/2022.03.08.483394v1?rss=1 Longkumer, T. Grillet, L. Chen, C.-Y. Putra, H. Schmidt, W. Verslues, P. E. 2022-03-08 doi:10.1101/2022.03.08.483394 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Niche hypervolume analysis revealed that water pollution reduces reproductive success of endangered landlocked salmon but does not directly impact their population density ]]> https://biorxiv.org/content/10.1101/2022.03.21.485106v1?rss=1 Yi-An, C. Liu, M. Tzu-Man, H. Lin-Yan, L. Shen, S.-F. 2022-03-22 doi:10.1101/2022.03.21.485106 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Enhanced expression of 4-Cl-IAA and 6-Cl-IAA by touch stimulus for rapid and differential growths of the Madeira vine ]]> https://biorxiv.org/content/10.1101/2022.04.13.488269v1?rss=1 Ma, M.-H. Batsaikhan, E. Wu, C.-M. Lee, H.-H. Luo, C.-I. Chen, N.-J. Chung, J.-D. Chien, C.-T. Tsai, Y.-H. Li, W.-H. 2022-04-14 doi:10.1101/2022.04.13.488269 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Broadly neutralizing antibodies against Omicron variants of SARS-CoV-2 derived from mRNA-lipid nanoparticle-immunized mice ]]> https://biorxiv.org/content/10.1101/2022.04.19.488843v1?rss=1 Lu, R.-M. Liang, K.-H. Chiang, H.-L. Hsu, F.-F. Lin, H.-T. Chen, W.-Y. Ke, F.-Y. Kumari, M. Chou, Y.-C. Wu, H.-C. 2022-04-20 doi:10.1101/2022.04.19.488843 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Allosteric inhibition of PRPS is moderated by filamentous polymerization ]]> https://biorxiv.org/content/10.1101/2022.04.28.489849v1?rss=1 Hu, H. Lu, G.-M. Chang, C.-C. Li, Y. Zhong, J. Guo, C.-J. Zhou, X. Yin, B. Zhang, T. Liu, J.-L. 2022-04-28 doi:10.1101/2022.04.28.489849 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Predicting FDA approvability of small-molecule drugs ]]> https://biorxiv.org/content/10.1101/2022.10.15.512330v1?rss=1 Huang, C.-H. Hsu, J. Yang, L.-y. CHEN, T.-M. Shih, E. S. C. Hwang, M.-J. 2022-10-18 doi:10.1101/2022.10.15.512330 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Mechanical transmission of Dengue Virus by Aedes aegypti may influence disease transmission dynamics during outbreaks ]]> https://biorxiv.org/content/10.1101/2023.03.07.531453v1?rss=1 Li, H.-H. Su, M. P. Wu, S.-C. Tsou, H.-H. Chang, M.-C. Cheng, Y.-C. Tsai, K.-N. Wang, H.-W. Chen, G.-H. Tang, C.-K. Chung, P.-J. Tsai, W.-T. Huang, L.-R. Yueh, Y. A. Chen, H.-W. Pan, C.-Y. Akbari, O. Chang, H.-H. Yu, G.-Y. Marshall, J. M. CHEN, C.-H. 2023-03-07 doi:10.1101/2023.03.07.531453 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ The NPH3-domain protein NRL5 is a plant specific type of GTPase essential for drought resistance ]]> https://biorxiv.org/content/10.1101/2023.05.10.540297v1?rss=1 UPADHYAY-TIWARI, N. Huang, X.-J. Lee, Y.-C. Singh, S. K. Hsu, C.-C. Huang, S.-S. Verslues, P. E. 2023-05-11 doi:10.1101/2023.05.10.540297 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Correlation between plant cell wall stiffening and root extension arrest phenotype in the combined abiotic stress of Fe and Al ]]> https://biorxiv.org/content/10.1101/2023.06.20.545659v1?rss=1 Kaur, H. Teulon, J.-M. Godon, C. Desnos, T. Chen, S.-w. W. Pellequer, J.-L. 2023-06-20 doi:10.1101/2023.06.20.545659 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Multifaceted roles of rice ABA/stress-induced intrinsically disordered proteins in augmenting drought resistance ]]> https://biorxiv.org/content/10.1101/2023.06.22.546131v1?rss=1 Lin, M.-C. Tseng, I.-C. Wang, C.-L. Hsiao, W.-R. Shih, Y.-J. Lin, W.-D. Yu, S.-M. Ho, T.-h. D. 2023-06-23 doi:10.1101/2023.06.22.546131 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Four-dimensional omics data reveals ribosome heterogeneity, regulation of translation efficacy, and nonsense-mediated decay in the differentiation of spermatocyte to round spermatid. ]]> https://biorxiv.org/content/10.1101/2023.07.13.548784v1?rss=1 Lee, S. S. Kung, Y.-C. Jou, Y.-S. 2023-07-13 doi:10.1101/2023.07.13.548784 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Macrophage resilience and control of intracellular bacteria requires sst1-dependent integration of c-Myc, stress response and type I IFN pathways ]]> https://biorxiv.org/content/10.1101/238873v1?rss=1 Bhattacharya, B. Chatterjee, S. Berland, R. Pichugin, A. Ivanov, A. Connor, J. H. Yan, B.-S. Kobzik, L. Kramnik, I. 2017-12-22 doi:10.1101/238873 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Arabidopsis inositol phosphate kinases, IPK1 and ITPK1, constitute a metabolic pathway in maintaining phosphate homeostasis ]]> https://biorxiv.org/content/10.1101/270355v1?rss=1 Kuo, H.-F. Hsu, Y.-Y. Lin, W.-C. Chen, K.-Y. Munnik, T. Brearley, C. Chiou, T.-J. 2018-02-24 doi:10.1101/270355 Cold Spring Harbor Laboratory Press 2018-02-24 <![CDATA[ Electron microscopy 3-dimensional segmentation and quantification of axonal dispersion and diameter distribution in mouse brain corpus callosum ]]> https://biorxiv.org/content/10.1101/357491v1?rss=1 Lee, H.-H. Yaros, K. Veraart, J. Pathan, J. Liang, F.-X. Kim, S. G. Novikov, D. S. Fieremans, E. 2018-06-27 doi:10.1101/357491 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ General characterization of regeneration in Aeolosoma viride ]]> https://biorxiv.org/content/10.1101/493304v1?rss=1 Chen, C.-P. Fok, S. K.-W. Hsieh, Y.-W. Chen, C.-Y. Hsu, F.-M. Chen, J.-H. 2018-12-11 doi:10.1101/493304 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Glia-derived exosomal miR-274 targets Sprouty in trachea and synaptic boutons to modulate growth and responses to hypoxia ]]> https://biorxiv.org/content/10.1101/547554v1?rss=1 Tsai, Y.-W. Sung, H.-H. Li, J.-C. Yeh, C.-Y. Chen, P.-Y. Cheng, Y.-J. Chen, C.-H. Tsai, Y.-C. Chien, C.-T. 2019-02-12 doi:10.1101/547554 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Effector loading onto VgrG spike proteins is critical for the assembly of the type VI secretion system in Agrobacterium tumefaciens ]]> https://biorxiv.org/content/10.1101/556712v1?rss=1 Lien, Y.-W. Wu, C.-F. Bondage, D. Lin, J.-S. Shih, Y.-L. Chang, J. Lai, E.-M. 2019-02-21 doi:10.1101/556712 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Seasonal Change of Microbial Diversity and Its Relation with Soil Chemical Properties in Orchard ]]> https://biorxiv.org/content/10.1101/600668v1?rss=1 Luo, X. Wang, M. Hu, G. Weng, B. 2019-04-06 doi:10.1101/600668 Cold Spring Harbor Laboratory Press 2019-04-06 <![CDATA[ Detection and Classification of Cardiac Arrhythmias by a Challenge-Best Deep Learning Neural Network Model ]]> https://biorxiv.org/content/10.1101/766022v1?rss=1 Chen, T.-M. Huang, C.-H. Shih, E. S. C. Hu, Y.-F. Hwang, M.-J. 2019-09-19 doi:10.1101/766022 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ A prospective, observational study on conversion of Clinically Isolated Syndrome to Multiple Sclerosis during 4-year period (MS NEO study) in Taiwan ]]> https://biorxiv.org/content/10.1101/385898v1?rss=1 Ro, L.-S. Yang, C.-C. Lyu, R.-K. Lin, K.-P. Tsai, T.-C. Lu, S.-R. Huang, L.-C. Tsai, C.-P. Chang, K.-H. 2018-08-06 doi:10.1101/385898 Cold Spring Harbor Laboratory Press 2018-08-06 <![CDATA[ The HOMEODOMAIN-Like protein HDL mediates chromatin organization and rewires leaf epidermal patterning ]]> https://biorxiv.org/content/10.1101/2023.09.13.557516v1?rss=1 Ali, A. Kuan, C. Hung, F.-Y. Chen, T.-C. Lee, H.-C. Yang, S.-L. Feng, Y.-R. Wu, K. Ho, C.-M. K. 2023-09-15 doi:10.1101/2023.09.13.557516 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Automatic vocalisation detection delivers reliable, multi-faceted, and global avian biodiversity monitoring ]]> https://biorxiv.org/content/10.1101/2023.09.14.557670v1?rss=1 Sethi, S. S. Bick, A. Chen, M.-Y. Crouzeilles, R. Hillier, B. V. Lawson, J. Lee, C.-Y. Liu, S.-H. Parruco, C. H. d. F. Rosten, C. Somveille, M. Tuanmu, M.-N. Banks-Leite, C. 2023-09-17 doi:10.1101/2023.09.14.557670 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Larval thermosensitivity shapes adult population dynamics in Anopheles mosquitoes ]]> https://biorxiv.org/content/10.1101/2023.09.19.558414v1?rss=1 Estupinan, J. Weyrich, A. M. Schloesser, P. Naujoks, C. Gildenhard, M. Diarra, A. Diallo, M. Sangare, D. Telschow, A. Hsieh, C.-h. Levashina, E. A. Carrillo-Bustamante, P. 2023-09-20 doi:10.1101/2023.09.19.558414 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Successive responses of three coral holobiont components (coral hosts, symbiotic algae, and bacteria) to daily temperature fluctuations ]]> https://biorxiv.org/content/10.1101/2023.09.30.560297v1?rss=1 Hsieh, Y. E. Lu, C.-Y. Liu, P.-Y. Kao, J.-M. Yang, S.-Y. Wu, C.-Y. Wong, J.-W. M. Shikina, S. Fan, T.-Y. Yang, S.-H. 2023-09-30 doi:10.1101/2023.09.30.560297 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ The genetic evolution of acral melanoma ]]> https://biorxiv.org/content/10.1101/2023.10.18.562802v1?rss=1 Wang, M. Fukushima, S. Sheen, Y.-S. Ramelyte, E. Cruz Pacheco, N. Shi, C. Liu, S. Banik, I. Aquino, J. D. Sangueza Acosta, M. Levesque, M. Dummer, R. Liau, J.-Y. Chu, C.-Y. Shain, A. H. Yeh, I. Bastian, B. C. 2023-10-19 doi:10.1101/2023.10.18.562802 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Growth inhibitory factor/metallothionein-3 is a sulfane sulfur-binding protein ]]> https://biorxiv.org/content/10.1101/2023.10.19.563042v1?rss=1 Shinkai, Y. Ding, Y. Matsui, T. Devitt, G. Akiyama, M. Shen, T.-L. Nishida, M. Ida, T. Akaike, T. Mahajan, S. Fukuto, J. M. Shigeta, Y. Kumagai, Y. 2023-10-19 doi:10.1101/2023.10.19.563042 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Feasibility of intranasal delivery of thin-film freeze-dried monoclonal antibodies ]]> https://biorxiv.org/content/10.1101/2023.10.23.563139v1?rss=1 Yu, Y.-S. Xu, H. AboulFotouh, K. Williams, G. Suman, J. Sahakijpijarn, S. Cano, C. Warnken, Z. Wu, K. C.- W. Williams, R. O. Cui, Z. 2023-10-24 doi:10.1101/2023.10.23.563139 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Somatic mutation detection workflow validity distinctly influences clinical decision. ]]> https://biorxiv.org/content/10.1101/2023.10.26.562640v1?rss=1 Chien, P.-M. Cheng, C. Yuan, T.-H. Wang, Y.-B. Chen, P.-L. Chen, C.-Y. Huang, J.-H. Hsu, J. S. 2023-10-30 doi:10.1101/2023.10.26.562640 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Transcriptome and Mutant Analysis of Neuronal Genes for Memory Formation and Retrieval in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.10.31.564890v1?rss=1 Chen, Y.-J. Wu, S.-J. Tang, Y.-C. Wu, Y.-C. Chiang, Y.-C. Pan, C.-L. 2023-11-02 doi:10.1101/2023.10.31.564890 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Vegetation of Chamaecyparis montane cloud forest in Lalashan Forest Dynamics Plot ]]> https://biorxiv.org/content/10.1101/2023.11.04.565604v1?rss=1 Chen, T. Lee, Y.-N. Lin, P.-Y. Wu, K.-S. Zeleny, D. 2023-11-05 doi:10.1101/2023.11.04.565604 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ An acidophilic fungus is integral to prey digestion in a carnivorous plant ]]> https://biorxiv.org/content/10.1101/2023.11.07.566145v1?rss=1 Sun, P.-F. Lu, M. R. Liu, Y.-C. Lin, Y.-f. Hoh, D. Z. Ke, H.-M. Wang, I.-F. Lu, M.-Y. J. Kirschner, R. Lin, Y.-C. J. Chen, Y.-L. Tsai, I. J. 2023-11-08 doi:10.1101/2023.11.07.566145 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ MiR-221/222-enriched ADSC-exosome mitigates PM exposure-exacerbated cardiac ischemia/reperfusion injury through the modulation of the BNIP3/LC3B/PUMA pathway ]]> https://biorxiv.org/content/10.1101/2023.11.10.566671v1?rss=1 Lee, T.-L. Shen, W.-C. Chen, Y.-C. Lai, T.-C. Lin, S.-R. Lin, S.-W. Yu, I.-S. Yeh, Y.-H. Li, T.-K. Lee, I.-T. Lee, C.-W. Chen, Y.-L. 2023-11-12 doi:10.1101/2023.11.10.566671 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Annotation-Free Deep Learning for Predicting Gene Mutations from Whole Slide Images of Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2023.11.13.563550v1?rss=1 Wei, B.-H. Tsai, X. C.-H. Lo, M.-Y. Hung, S.-Y. Chou, W.-C. Tien, H.-F. Hou, H.-A. Chen, C.-Y. 2023-11-13 doi:10.1101/2023.11.13.563550 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Genetic Diversity and Structural Complexity of the Killer-Cell Immunoglobulin-Like Receptor Gene Complex: A Comprehensive Analysis using Human Pangenome Assemblies ]]> https://biorxiv.org/content/10.1101/2023.11.12.566753v1?rss=1 Hung, T.-K. Liu, W.-C. Lai, S.-K. Chuang, H.-W. Lee, Y.-C. Lin, H.-Y. Hsu, C.-L. Chen, C.-Y. Yang, Y.-C. Hsu, J. S. Chen, P.-L. 2023-11-15 doi:10.1101/2023.11.12.566753 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Proteomic Features of Adolescents and Young Adults with Soft Tissue Tumours ]]> https://biorxiv.org/content/10.1101/2023.11.18.567667v1?rss=1 Tam, Y. B. Low, K. PS, H. Chadha, M. Burns, J. Wilding, C. Arthur, A. Chen, T. Thway, K. Sadanandam, A. Jones, R. Huang, P. H. 2023-11-20 doi:10.1101/2023.11.18.567667 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Crossmodal Hierarchical Predictive Coding for Audiovisual Sequences in Human Brain ]]> https://biorxiv.org/content/10.1101/2023.11.19.567767v1?rss=1 Huang, Y. T. Wu, C.-T. Fang, Y.-X. M. Fu, C.-K. Koike, S. Chao, Z. C. 2023-11-20 doi:10.1101/2023.11.19.567767 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Evaluating the performance of protein structure prediction in detecting structural changes of pathogenic nonsynonymous single nucleotide variants ]]> https://biorxiv.org/content/10.1101/2023.11.25.568523v1?rss=1 Lai, H.-S. Chen, C.-Y. 2023-11-25 doi:10.1101/2023.11.25.568523 Cold Spring Harbor Laboratory Press 2023-11-25 <![CDATA[ Colonization of Bacillus altitudinis on the Compatible Soybean Varieties to Provide Seed Rot Resistance ]]> https://biorxiv.org/content/10.1101/2023.11.27.568843v1?rss=1 Wu, P.-H. Chang, H.-X. 2023-11-27 doi:10.1101/2023.11.27.568843 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Graph-KIR: Graph-based KIR Copy Number Estimation and Allele Calling Using Short-read Sequencing Data ]]> https://biorxiv.org/content/10.1101/2023.11.29.568665v1?rss=1 Lin, H.-Y. Chuang, H.-W. Hung, T.-K. Wang, T.-J. Lin, C.-J. Hsu, J. S. Hsu, C.-L. Yang, Y.-C. Chen, P.-L. Chen, C.-Y. 2023-12-01 doi:10.1101/2023.11.29.568665 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Individual variability in neural representations of mind-wandering ]]> https://biorxiv.org/content/10.1101/2024.01.20.576471v1?rss=1 Kucyi, A. Anderson, N. Bounyarith, T. Braun, D. Shareef-Trudeau, L. Treves, I. Braga, R. M. Hsieh, P.-J. Hung, S.-M. 2024-01-22 doi:10.1101/2024.01.20.576471 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Fusion, fission, and scrambling of the bilaterian genome in Bryozoa ]]> https://biorxiv.org/content/10.1101/2024.02.15.580425v1?rss=1 Lewin, T. D. Liao, I. J.-Y. Chen, M.-E. Bishop, J. D. D. Holland, P. W. H. Luo, Y.-J. 2024-02-16 doi:10.1101/2024.02.15.580425 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Expansion microscopy for super-resolution imaging of collagen-abundant tissues ]]> https://biorxiv.org/content/10.1101/2024.02.28.582497v1?rss=1 Chuang, Y.-H. Wu, Y.-F. Lin, Y.-H. Zhou, Y.-X. Hsu, S.-C. Lin, S.-J. Chu, L.-A. 2024-03-02 doi:10.1101/2024.02.28.582497 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Spectroscopic assessment of flavor-related chemical compounds in fresh tea shoots using deep learning ]]> https://biorxiv.org/content/10.1101/2024.03.05.583504v1?rss=1 Denaro, L. G. Lin, S.-Y. Huang, C.-y. 2024-03-08 doi:10.1101/2024.03.05.583504 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Detection of oat crown rust disease in Taiwan (2019-2021) ]]> https://biorxiv.org/content/10.1101/2024.03.12.584714v1?rss=1 Ho, C.-Y. Henningsen, E. Chen, S.-T. Ariyawansa, H. A. Nazareno, E. C. Sperschneider, J. Dodds, P. Riddle, J. M. Kianian, S. F. Figueroa, M. Huang, Y.-F. 2024-03-13 doi:10.1101/2024.03.12.584714 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Advancing marker-gene-based methods for prokaryote-mediated multifunctional redundancy: exploring random and nonrandom extinctions in a watershed ]]> https://biorxiv.org/content/10.1101/2024.03.14.584931v1?rss=1 Cheng, W.-H. Miki, T. Ido, M. Yoneya, K. Matsui, K. Yokokawa, T. Yamanaka, H. Nakano, S.-i. 2024-03-16 doi:10.1101/2024.03.14.584931 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Clostridium innocuum, an opportunistic gut pathogen, inactivates host gut progesterone and arrests ovarian follicular development ]]> https://biorxiv.org/content/10.1101/2024.03.15.585140v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@14cceaborg.highwire.dtl.DTLVardef@1946432org.highwire.dtl.DTLVardef@13e46d2org.highwire.dtl.DTLVardef@19b9a25_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG In briefChen et al. identified Clostridium innocuum as a major species involved in gut progesterone metabolism, with epipregnanolone as the main product, and elucidated the molecular mechanisms. C. innocuum inactivates gut progesterone in female mice, leading to decreased circulating progesterone levels. C. innocuum is also a causal factor of follicular arrest. Levels of progesterone, an endogenous female hormone, increase after ovulation; progesterone is crucial in the luteal phase to maintain successful pregnancy and prevent early miscarriage. Both endogenous and exogenous progesterone are recycled between the liver and gut; thus, the gut microbiota regulate host progesterone levels by inhibiting enterohepatic progesterone circulation. Our data indicated Clostridium innocuum as a major species involved in gut progesterone metabolism in women with infertility. C. innocuum converts progesterone into the neurosteroid epipregnanolone (with negligible progestogenic activity). We purified and characterized the corresponding enzyme, namely NADPH-dependent 5{beta}-dihydroprogesterone reductase, which is highly oxygen sensitive and whose corresponding genes are prevalent in C. innocuum. Moreover, C. innocuum-administered female C57BL/6 mice (aged 7 weeks) exhibited decreased serum progesterone levels ([~]35%). Clostridium-specific antibiotics (metronidazole) restored low serum progesterone levels in these mice. Furthermore, prolonged C. innocuum administration (12 weeks) arrested ovarian follicular development in female mice. Cytological and histological analyses indicated that C. innocuum may cause luteal phase insufficiency and affect menstrual regularity. Our findings suggest C. innocuum as a causal factor of progesterone resistance in women taking progesterone. ]]> Chen, M.-J. Chou, C.-H. Hsiao, T.-H. Wu, T.-Y. Li, C.-Y. Chen, Y.-L. Chao, K.-H. Lee, T.-H. Gicana, R. Shih, C.-J. Brandon-Mong, G.-J. Lai, Y.-L. Li, P.-T. Tseng, Y.-L. Wang, P.-H. Chiang, Y.-R. 2024-03-15 doi:10.1101/2024.03.15.585140 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ Development of a tightly regulated copper-inducible transient gene expression system in Nicotiana benthamiana incorporating suicide exon and Cre recombinase ]]> https://biorxiv.org/content/10.1101/2024.03.23.586378v1?rss=1 Chiang, B.-J. Lin, K.-Y. Chen, Y.-F. Huang, C.-Y. Goh, F.-J. Huang, L.-T. Chen, L.-H. Wu, C.-H. 2024-03-27 doi:10.1101/2024.03.23.586378 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ MOS4-Associated Complex subunits 3A and 3B modulate FLM splicing to repress photoperiod-dependent floral transition ]]> https://biorxiv.org/content/10.1101/2024.03.26.586198v1?rss=1 Huang, Y.-W. Tseng, C.-Y. Tu, Y.-T. Hsieh, H.-Y. Wang, Y.-S. Chen, Y.-Z. Ly, Y.-T. Tu, S.-L. Lee, C.-M. 2024-03-27 doi:10.1101/2024.03.26.586198 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Novel synthetic ecteinascidins exhibit potent anti-melanoma activity by suppressing super-enhancer-driven oncogenic transcription ]]> https://biorxiv.org/content/10.1101/2024.03.26.586754v1?rss=1 Coin, F. 2024-03-28 doi:10.1101/2024.03.26.586754 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ A high-resolution haplotype pangenome uncovers somatic hybridization, recombination and intercontinental migration in oat crown rust ]]> https://biorxiv.org/content/10.1101/2024.03.27.583983v1?rss=1 Henningsen, E. Lewis, D. Nazareno, E. Huang, Y.-F. Steffenson, B. J. Boesen, B. Kianian, S. F. Stone, E. Dodds, P. Sperschneider, J. Figueroa, M. 2024-03-27 doi:10.1101/2024.03.27.583983 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Can social media serve as a potential citizen science source for bird-window collision (BWC) data? A study using a decadal data set in Taiwan ]]> https://biorxiv.org/content/10.1101/2024.03.29.587372v1?rss=1 Hsieh, C.-H. Hsu, G.-C. Wang, L.-M. 2024-04-01 doi:10.1101/2024.03.29.587372 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Chromosome-level genome assembly of the loach goby, Rhyacichthys aspro, reveals mechanisms underlying Gobioidei diversification ]]> https://biorxiv.org/content/10.1101/2024.04.02.587698v1?rss=1 Wang, T.-Y. Lu, H.-J. Wu, Y.-W. Liao, T.-Y. Huang, S.-P. Wang, F.-Y. Ting, C.-T. Chaw, S.-M. Wang, H.-Y. 2024-04-03 doi:10.1101/2024.04.02.587698 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ A robust platform for BaEVRless-lentiviral synthesis and primary natural killer cell transduction ]]> https://biorxiv.org/content/10.1101/2024.04.03.587896v1?rss=1 Lan, Y.-J. Nguyen, Q. V. Chao, T.-L. Yeh, K.-L. Lin, S. 2024-04-04 doi:10.1101/2024.04.03.587896 Cold Spring Harbor Laboratory Press 2024-04-04 <![CDATA[ Zebrafish Foxl2l suppresses stemness and directs feminization of germline progenitors ]]> https://biorxiv.org/content/10.1101/2024.04.03.587938v1?rss=1 Hsu, C.-w. Ho, H. Yang, C.-H. Wang, Y.-W. Li, K.-C. Chung, B.-c. 2024-04-04 doi:10.1101/2024.04.03.587938 Cold Spring Harbor Laboratory Press 2024-04-04 <![CDATA[ Multiplexed Assays of Human Disease-relevant Mutations Reveal UTR Dinucleotide Composition as a Major Determinant of RNA Stability ]]> https://biorxiv.org/content/10.1101/2024.04.10.588845v1?rss=1 Su, J.-Y. Wang, Y.-L. Hsieh, Y.-T. Chang, Y.-C. Yang, C.-H. Kang, Y. Huang, Y.-T. Lin, C.-L. 2024-04-10 doi:10.1101/2024.04.10.588845 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Discrete photoentrainment of mammalian central clock is regulated by bi-stable dynamic network in the suprachiasmatic nucleus. ]]> https://biorxiv.org/content/10.1101/2024.04.10.588949v1?rss=1 Yeh, P.-T. Jhan, K.-C. Chua, E.-P. Chen, W.-C. Chu, S.-W. Wu, S.-C. Chen, S.-K. 2024-04-14 doi:10.1101/2024.04.10.588949 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Massively Parallel Polyribosome Profiling Reveals Translation Defects of Human Disease-Relevant UTR Mutations ]]> https://biorxiv.org/content/10.1101/2024.04.11.589132v1?rss=1 0.8) in predicting polysome-shifting mutations in the test dataset. Additionally, several lines of evidence indicate that changes in uORF usage underlie the translation deficiency arising from these mutations. Illustrating this, we demonstrate that a pathogenic mutation in the IRF6 5 UTR suppresses translation of the primary open reading frame by creating a uORF. Remarkably, site- directed ADAR editing of the mutant mRNA rescued this translation deficiency. Overall, our study provides insights into the molecular mechanisms of UTR mutations and their links to clinical impacts through translation defects. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/589132v2_ufig1.gif" ALT="Figure 1000"> View larger version (50K): org.highwire.dtl.DTLVardef@57217corg.highwire.dtl.DTLVardef@575410org.highwire.dtl.DTLVardef@15013bforg.highwire.dtl.DTLVardef@408840_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, W.-P. Su, J.-Y. Chang, Y.-C. Wang, Y.-L. Chiang, H.-L. Hsieh, Y.-T. Chiang, Y.-H. Ko, Y.-L. Chiang, B.-J. Yang, C.-H. Huang, Y.-T. Lin, C.-L. 2024-04-13 doi:10.1101/2024.04.11.589132 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Parameter quantification for oxygen transport in the human brain ]]> https://biorxiv.org/content/10.1101/2024.04.13.589308v1?rss=1 Bing, Y. Jozsa, T. I. Payne, S. J. 2024-04-15 doi:10.1101/2024.04.13.589308 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ A Libra in the Brain: Neural Correlates of Error Awareness Predict Moral Wrongness and Guilt Proneness ]]> https://biorxiv.org/content/10.1101/2024.04.17.589679v1?rss=1 Chen, C. Kao, S. S.- C. Fan, Y.-T. Chen, Y.-C. Cheng, Y. 2024-04-21 doi:10.1101/2024.04.17.589679 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Effects of Age on Cross-Cultural Differences in the Neural Correlates of Memory Retrieval ]]> https://biorxiv.org/content/10.1101/2024.04.25.591227v1?rss=1 Cho, I. Leger, K. R. Valoumas, I. Mair, R. W. Goh, J. O. S. Gutchess, A. 2024-04-28 doi:10.1101/2024.04.25.591227 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ How weedy Arabidopsis thaliana dominated the world: ancestral variation and polygenic adaptation ]]> https://biorxiv.org/content/10.1101/2024.04.28.591542v1?rss=1 Lo, C.-Y. Chien, C.-C. Lin, Y.-P. Yeh, P.-M. Lee, C.-R. 2024-04-30 doi:10.1101/2024.04.28.591542 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Functional coexistence theory: a mechanistic framework linking biodiversity to ecosystem function ]]> https://biorxiv.org/content/10.1101/2024.05.05.591902v1?rss=1 Wan, J. Ke, P.-J. Hordijk, I. Bialic-Murphy, L. Crowther, T. W. 2024-05-05 doi:10.1101/2024.05.05.591902 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Acceleration of genome rearrangement in clitellate annelids ]]> https://biorxiv.org/content/10.1101/2024.05.12.593736v1?rss=1 Schultz, D. T. Heath-Heckman, E. A. C. Winchell, C. J. Kuo, D.-H. T. Yu, Y.-s. Oberauer, F. Kocot, K. Cho, S.-J. Simakov, O. Weisblat, D. A. 2024-05-14 doi:10.1101/2024.05.12.593736 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ A Sap Peptide Conserved across Flowering Plants Positively Regulates Lignin Biosynthesis, Biomass and Immunity ]]> https://biorxiv.org/content/10.1101/2024.05.20.594799v1?rss=1 Chen, C.-H. Liou, P.-C. Hsu, Y.-F. Wang, I.-F. Kuo, C.-Y. Huang, K.-H. Yu, J.-H. Chen, C.-W. Wu, C.-C. Lin, D.-G. Li, C.-B. Tu, Y.-K. Hsu, C.-C. Su, J.-C. Xia, K. Tsai, I. J. Lin, Y.-C. J. Chen, Y.-L. 2024-05-21 doi:10.1101/2024.05.20.594799 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Evolutionary Insights into Muscle Fiber Distribution in the Twin Tails of Ornamental Goldfish ]]> https://biorxiv.org/content/10.1101/2024.06.03.597082v1?rss=1 Ota, K. Abe, G. Wang, C.-Y. Li, I.-J. Sanchez, P. G. L. Chi, T.-C. 2024-06-04 doi:10.1101/2024.06.03.597082 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Agricultural landscapes with high compositional heterogeneity support both forest and farmland birds in Taiwan ]]> https://biorxiv.org/content/10.1101/2024.07.16.603643v1?rss=1 Lin, D.-L. Amano, T. Fuller, R. Ding, T.-S. Maron, M. 2024-07-18 doi:10.1101/2024.07.16.603643 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ Programmable Editing of Primary MicroRNA Switches Stem Cell Differentiation and Improves Tissue Regeneration ]]> https://biorxiv.org/content/10.1101/2024.07.19.604260v1?rss=1 Truong, V. A. Chang, Y.-H. Tu, Y. Nguyen, N. T. K. Pham, N. N. Chang, C.-W. Chang, Y.-H. Ngo, D. T. K. Pham, D. H. Tu, J. Dang, Q. T. Truong, V. A. Hu, Y.-C. 2024-07-22 doi:10.1101/2024.07.19.604260 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ AI-assisted In-silico Trial for the Optimization of Osmotherapy following Ischaemic Stroke ]]> https://biorxiv.org/content/10.1101/2024.07.20.604439v1?rss=1 chen, x. Lu, L. Jozsa, T. I. Clifton, D. Payne, S. 2024-07-23 doi:10.1101/2024.07.20.604439 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Synthetic dysmobility screening reveals a phosphorylation-independent facet of the SLK-Ezrin-F-actin signaling cascade. ]]> https://biorxiv.org/content/10.1101/2024.07.23.604488v1?rss=1 LIN, H. C. LIN, Y. Y. WEI, L. Y. ZHANG, J. M. TSAI, P. J. LIN, Y. C. CHIA, J. S. TSAI, F. C. 2024-07-24 doi:10.1101/2024.07.23.604488 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ ChromBERT: Uncovering Chromatin State Motifs in the Human Genome Using a BERT-based Approach ]]> https://biorxiv.org/content/10.1101/2024.07.25.605219v1?rss=1 Lee, S. Lin, C. Chen, C.-Y. Nakato, R. 2024-07-26 doi:10.1101/2024.07.25.605219 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Zebrafish Foxl2l functions in proliferating germ cells for female meiotic entry ]]> https://biorxiv.org/content/10.1101/2024.07.30.605757v1?rss=1 Yang, C.-H. Wang, Y.-W. Hsu, C.-w. Pan, Y.-J. Chung, B.-c. 2024-07-31 doi:10.1101/2024.07.30.605757 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Guard-cell phytosterol homeostasis is critical for proper stomatal development ]]> https://biorxiv.org/content/10.1101/2024.08.29.610202v1?rss=1 Yen, C.-C. Hsu, Y.-W. Leu, K.-C. Chen, S.-S. Chen, T.-Y. Juan, C.-T. Kuan, C. Shaw, J.-F. Ho, C.-M. K. Jauh, G.-Y. 2024-08-30 doi:10.1101/2024.08.29.610202 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Combination of cycling hyperthermia and Echinacoside creates synergistic curing effect on pancreatic cancer PANC-1 cells ]]> https://biorxiv.org/content/10.1101/2024.09.04.611320v1?rss=1 Chen, W.-T. Chen, Y.-M. Lin, G.-B. Kuo, Y.-Y. Liu, H.-H. Chao, C.-Y. 2024-09-08 doi:10.1101/2024.09.04.611320 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Inter- and intra-tumor heterogeneous immune presentation in primary uterine carcinosarcoma determined by digital spatial profiling ]]> https://biorxiv.org/content/10.1101/2024.09.05.611350v1?rss=1 Li, Y. Lin, W.-C. Chen, K.-C. Chang, W.-C. Wu, C.-J. Wei, L.-H. Huang, R. Y.-J. Sheu, B.-C. 2024-09-10 doi:10.1101/2024.09.05.611350 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Structural insights into terminal arabinosylation biosynthesis of the mycobacterial cell wall arabinan ]]> https://biorxiv.org/content/10.1101/2024.09.17.613533v1?rss=1 Liu, Y. Brown, C. M. Erramilli, S. Su, Y.-C. Tseng, P.-S. Wang, Y.-J. Duong, N. H. Tokarz, P. Kloss, B. Han, C.-R. Chen, H.-Y. Rodrigues, J. Archer, M. Lowary, T. L. Kossiakoff, A. A. Stansfeld, P. J. Nygaard, R. Mancia, F. 2024-09-18 doi:10.1101/2024.09.17.613533 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Early Prediction of Ischaemic Stroke Outcomes: A Novel Computational Approach ]]> https://biorxiv.org/content/10.1101/2024.09.25.615002v1?rss=1 Chen, X. El-Bouri, W. Payne, S. Lu, L. 2024-09-26 doi:10.1101/2024.09.25.615002 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2024.09.25.614736v1?rss=1 Wassenaar, E. C. Gorelick, A. N. Hung, W.-T. Cheek, D. M. Kucukkose, E. Lee, I.-H. Blohmer, M. Degner, S. Giunta, P. Wiezer, R. M. Raicu, M. G. Ubink, I. Klaasen, S. J. Lansu, N. Watson, E. V. Corcoran, R. B. Boland, G. Getz, G. Kops, G. J. Juric, D. Lennerz, J. K. Boerma, D. Kranenburg, O. Naxerova, K. 2024-09-27 doi:10.1101/2024.09.25.614736 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ A multi-omics census reveals obesity-associated microRNA miR-let-7 as novel instigator of adipose mitochondrial dysfunction and of intergenerational metabolic decline. ]]> https://biorxiv.org/content/10.1101/2024.10.03.615866v1?rss=1 Huang, C. Park, J.-H. Altintas, A. Stanic, N. Batarlar, H. T. Malmros, R. V. Havelund, J. Faergeman, N. J. Marcher Larsen, B. D. Szczepanowska, K. Lackmann, J.-W. Trifunovic, A. Hejbol, E. K. Detlefsen, S. Jepsen, I. E. Kolstrup, S. H. Laguna Barraza, R. A. Gonzalez, J.-M. Khodosevich, K. Barres, R. Kornfeld, J.-W. 2024-10-04 doi:10.1101/2024.10.03.615866 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Evolutionary conserved sap peptides derived from xylem-specific peptide precursors in woody angiosperms ]]> https://biorxiv.org/content/10.1101/2024.10.08.617308v1?rss=1 Chen, C.-H. Liou, P.-C. Lin, C.-C. Kuo, S.-C. Wu, C.-C. Lin, Y.-C. J. Chen, Y.-L. 2024-10-12 doi:10.1101/2024.10.08.617308 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Toward Automatic Variant Interpretation: Discordant Genetic Interpretation Across Variant Annotations for ClinVar Pathogenic Variants ]]> https://biorxiv.org/content/10.1101/2024.10.11.617756v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@9f6378org.highwire.dtl.DTLVardef@3b9a2corg.highwire.dtl.DTLVardef@106fb58org.highwire.dtl.DTLVardef@15f70c8_HPS_FORMAT_FIGEXP M_FIG This study examined the consistency of variant annotations produced by three widely used open-source toolsANNOVAR, SnpEff, and VEPagainst 164,549 ClinVar two starts variants. The investigation covers HGVS-based transcript, protein nomenclature and coding impact annotation. The results showed that none of the tools were fully consistent with ClinVar across all coding impact categories, particularly in the LoF category, which exhibited the poorest consistency. This inconsistency may lead to discrepancies in PVS1 interpretation, affecting the final pathogenicity assessment. PVS1 loss resulted in a significant downgrading of PLP variants, potentially leading to the omission of clinically relevant variants in reports. C_FIG ]]> Chen, A. Y.-A. Yuan, T.-H. Huang, J.-H. Wang, Y.-B. Hung, T.-M. Chen, C.-Y. Hsu, J. S. Chen, P.-L. 2024-10-15 doi:10.1101/2024.10.11.617756 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Loop Grafting Improves Neuraminidase Protein Vaccine Production ]]> https://biorxiv.org/content/10.1101/2024.10.11.617814v1?rss=1 View larger version (57K): org.highwire.dtl.DTLVardef@14d4b4eorg.highwire.dtl.DTLVardef@18af09aorg.highwire.dtl.DTLVardef@ba1982org.highwire.dtl.DTLVardef@1e0d143_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rijal, P. Wei, L. Paesen, G. C. Stuart, D. I. Howarth, M. R. Huang, K.-Y. A. Bowden, T. A. Townsend, A. R. 2024-10-15 doi:10.1101/2024.10.11.617814 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Diversity of ancestral brainstem noradrenergic neurons across species and multiple biological factors ]]> https://biorxiv.org/content/10.1101/2024.10.14.618224v1?rss=1 Kelberman, M. A. Rodberg, E. Arabzadeh, E. Bair-Marshall, C. J. Berridge, C. W. Berrocoso, E. Breton-Provencher, V. Chandler, D. J. Che, A. Davy, O. Devilbiss, D. M. Downs, A. M. Drummond, G. Dvorkin, R. Fazlali, Z. Froemke, R. C. Glennon, E. Gold, J. I. Ito, H. Jiang, X. Johansen, J. P. Kaye, A. P. Kim, J. R. Kuo, C.-c. Liu, R.-j. Liu, Y. Llorca-Torralba, M. McCall, J. G. McElligott, Z. A. McKinney, A. M. Miguelez, C. Min, M.-Y. Nowlan, A. C. Omrani, M. Pickering, A. E. Poe, G. R. Ranjbar-Slamloo, Y. Razquin, J. Rodenkirch, C. Sales, A. C. Satyasambit, 2024-10-16 doi:10.1101/2024.10.14.618224 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ The Taiwan Precision Medicine Initiative: A Cohort for Large-Scale Studies ]]> https://biorxiv.org/content/10.1101/2024.10.14.616932v1?rss=1 1.4 billion people around the world and serve as a model for developing population-based precision medicine. ]]> Yang, H.-C. Kwok, P.-Y. Li, L.-H. Liu, Y.-M. Jong, Y.-J. Lee, K.-Y. Wang, D.-W. Tsai, M.-F. Yang, J.-H. Chen, C.-H. Yeh, E.-C. Wei, C.-y. Fann, C. S.- J. Huang, Y.-T. Chen, C.-W. Lee, Y.-J. Chu, S.-K. Ho, C.-h. Yang, C.-S. Lee, Y. L. Chen, H.-H. Hou, M.-C. Chiou, J.-F. Yang, S.-F. Wang, C.-H. Huang, C.-Y. Chiu, K.-M. Chen, M. Chiang, F.-T. Lee, S.-L. Chen, S.-S. Yao, W.-J. Chien, C.-C. Lin, S.-Y. Chang, F.-P. Ho, H.-L. Yeh, Y.-C. Tseng, W.-C. Lin, M.-H. Chang, H.-T. Tseng, L.-M. Liang, W.-Y. Chen, P. C.-H. Hang, J.-F. Lin, S.-C. Chan, Y.-J. Kuo, Y. 2024-10-17 doi:10.1101/2024.10.14.616932 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Stabilization of HSA32, an aggregation-prone protein, by the protein disaggregase HSP101 plays a critical role in maintaining acquired thermotolerance in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2024.10.15.618377v1?rss=1 Mitra, S. Yu, S.-J. Liu, N.-Y. Hsu, C.-C. Li, H.-Y. Borah, A. Shen, Y.-Y. Hsu, Y.-H. Fu, H. Charng, Y.-y. 2024-10-17 doi:10.1101/2024.10.15.618377 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Spatial Transcriptomic Profiling Of Advanced Ovarian Clear Cell Carcinoma Reveals Intra-Tumor Heterogeneity In Epithelial-Mesenchymal Gradient ]]> https://biorxiv.org/content/10.1101/2024.10.19.619181v1?rss=1 Truong Le, T. Chen, K.-C. Yi-Te Wan, D. Yan, S. R.-G. Chu, P.-Y. Tan, T. Z. Chiu, Y.-C. Sheu, J.-Y. Huang, C.-H. Ye, J. Tai, Y.-T. Juan, H.-F. Tsai, F.-C. Lin, W.-C. Wei, L.-H. Huang, R. Y.-J. 2024-10-22 doi:10.1101/2024.10.19.619181 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Genomes of Wiebesia fig wasps reveal the adaptation and codiversification in fig-fig wasp mutualism ]]> https://biorxiv.org/content/10.1101/2024.10.22.619299v1?rss=1 Lo, B.-W. Lin, H.-F. Kong, S.-W. Wu, W.-J. Wang, S. C.-L. Lu, X. Wang, H.-Y. 2024-10-25 doi:10.1101/2024.10.22.619299 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Structure and evolution of Photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis ]]> https://biorxiv.org/content/10.1101/2024.10.31.621444v1?rss=1 Jiang, H.-W. Gisriel, C. J. Cardona, T. Flesher, D. A. Brudvig, G. W. Ho, M.-Y. 2024-11-02 doi:10.1101/2024.10.31.621444 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Living xylem cells encode a large number of conserved gene families responsible for vascular sap peptides ]]> https://biorxiv.org/content/10.1101/2024.11.10.622827v1?rss=1 Lu, M. R. Tung, C.-C. Huang, C.-E. Chen, C.-H. Liou, P.-C. Lin, C.-Y. I. Yu, J.-H. Chen, Y.-L. Lin, Y.-C. J. Tsai, I. J. 2024-11-11 doi:10.1101/2024.11.10.622827 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Salinity impacted microbial carbonate precipitation mechanisms of modern microbialites in peritidal zone ]]> https://biorxiv.org/content/10.1101/2024.11.11.623098v1?rss=1 Hsieh, Y. E. Yang, S.-Y. Liu, S.-L. Wang, S.-W. Wang, W.-L. Tang, S.-L. Yang, S.-H. 2024-11-12 doi:10.1101/2024.11.11.623098 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Telomeric Repeat-Containing RNA Increases in Aged Human Cells ]]> https://biorxiv.org/content/10.1101/2024.11.14.623513v1?rss=1 Chu, H.-P. C. Hsieh, Y.-H. Tai, C.-H. Yeh, M.-T. Yang, P.-C. Chen, Y.-C. Yen, C.-P. Han, D.-S. 2024-11-15 doi:10.1101/2024.11.14.623513 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ CNV-Finder: Streamlining Copy Number Variation Discovery ]]> https://biorxiv.org/content/10.1101/2024.11.22.624040v1?rss=1 Kuznetsov, N. Daida, K. Makarious, M. B. Al-Mubarak, B. Atterling Brolin, K. Malik, L. Kouam, C. Baker, B. Ostrozovicova, M. Andersh, K. M. Kung, P.-J. Mecheri, Y. Tay, Y.-W. Soundous Malek, B. Al Tassan, N. Teresa Perinan, M. Hong, S. Koretsky, M. Sargeant, L. Levine, K. Blauwendraat, C. Billingsley, K. J. Bandres-Ciga, S. Leonard, H. L. Morris, H. R. Singleton, A. B. Nalls, M. A. Vitale, D. The Global Parkinson's Genetics Program, 2024-11-23 doi:10.1101/2024.11.22.624040 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Rhizobium rhizogenes A4-derived strains mediate hyper-efficient transient gene expression in Nicotiana benthamiana and other solanaceous plants ]]> https://biorxiv.org/content/10.1101/2024.11.30.626145v1?rss=1 Lopez-Agudelo, J. C. Goh, F.-J. Tchabashvili, S. Huang, Y.-S. Huang, C.-Y. Lee, K.-T. Wang, Y.-C. Wu, Y. Chang, H.-X. Kuo, C.-H. Lai, E.-M. Wu, C.-H. 2024-12-03 doi:10.1101/2024.11.30.626145 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Arabidopsis EID1 E3 ubiquitin ligase regulates acquired thermotolerance by modulating HSBP translocation ]]> https://biorxiv.org/content/10.1101/2024.12.22.627358v1?rss=1 Tu, Y.-T. Yen, T.-C. Chuo, G.-L. Wu, Z.-Q. Jinn, T.-L. Lee, C.-M. 2024-12-22 doi:10.1101/2024.12.22.627358 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Ganoderma formosanum polysaccharides enhance antitumor immune responses by downregulating the differentiation of myeloid-derived suppressor cells and tumor-associated macrophages ]]> https://biorxiv.org/content/10.1101/2024.12.23.630057v1?rss=1 Yang, J.-Y. Chen, K.-L. Lin, Y.-C. Chiu, H.-C. Hsieh, H.-T. Chen, C.-J. 2024-12-23 doi:10.1101/2024.12.23.630057 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Enolase-1 is essential for neutrophil recruitment during acute inflammation ]]> https://biorxiv.org/content/10.1101/2024.12.26.630451v1?rss=1 Lu, H.-Y. Huang, P.-H. Lee, T.-W. Chang, H.-W. Chen, N.-Y. Zhuang, Y.-J. Yuan, T.-T. Chen, C.-J. 2024-12-27 doi:10.1101/2024.12.26.630451 Cold Spring Harbor Laboratory Press 2024-12-27 <![CDATA[ Tracking changes in stability of North Sea Atlantic cod in 40 years ]]> https://biorxiv.org/content/10.1101/2025.01.06.631473v1?rss=1 Tao, H.-H. Hsieh, C.-h. Hidalgo, M. Dakos, V. 2025-01-07 doi:10.1101/2025.01.06.631473 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ Plasma membrane mediated GLUT10 mitochondrial targeting regulates intracellular ascorbic acid homeostasis ]]> https://biorxiv.org/content/10.1101/2025.01.09.632083v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@17ac1d1org.highwire.dtl.DTLVardef@4aa2f3org.highwire.dtl.DTLVardef@101849org.highwire.dtl.DTLVardef@aa9c26_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jose, A. C. Syu, Y.-W. Lai, H.-W. Tsai, M.-Y. Jiang, Y.-F. Hsu, S.-C. Lin, P.-Y. Huang, W.-C. Chu, W.-C. Fu, C.-Y. Lee, Y.-C. 2025-01-13 doi:10.1101/2025.01.09.632083 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Mitochondrial Ca2+ flickers on endoplasmic reticulum (ER)-mitochondrial contact sites to suppress store-operated Ca2+ entry ]]> https://biorxiv.org/content/10.1101/2025.01.17.633482v1?rss=1 Lin, Y.-C. Tsai, F.-C. 2025-01-18 doi:10.1101/2025.01.17.633482 Cold Spring Harbor Laboratory Press 2025-01-18 <![CDATA[ Unravel the start element and promoter architecture across the domain Bacteria ]]> https://biorxiv.org/content/10.1101/2025.01.23.634641v1?rss=1 Kuo, S.-T. Chang, J. K. Chang, C. Shen, W.-Y. Hsu, C. Lai, S.-W. Chou, H.-H. D. 2025-01-24 doi:10.1101/2025.01.23.634641 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Ancient origin of an urban underground mosquito ]]> https://biorxiv.org/content/10.1101/2025.01.26.634793v1?rss=1 1000 years, likely in concert with the rise of agricultural civilizations. Our results highlight the role of early human society in priming taxa for contemporary urban evolution and have important implications for understanding arbovirus transmission. ]]> Haba, Y. Aardema, M. L. Afonso, M. O. Agramonte, N. M. Albright, J. Alho, A. M. Almeida, A. P. G. Alout, H. Alten, B. Altinli, M. Amara Korba, R. Andreadis, S. S. Anghel, V. Arich, S. Arsenault-Benoit, A. Atyame, C. Aubry, F. Avila, F. W. Ayala, D. Azrag, R. S. Babayan, L. Bear, A. Becker, N. Bega, A. G. Bejarano, S. Ben-Avi, I. Benoit, J. B. Boubidi, S. C. Bradshaw, W. E. Bravo-Barriga, D. Bueno-Mari, R. Busic, N. Cabanova, V. Cabeje, B. Caputo, B. Cardo, M. V. Carpenter, S. Carreton, E. Chouaibou, M. S. Christian, M. Coetzee, M. Conner, W. R. Cornel, 2025-01-28 doi:10.1101/2025.01.26.634793 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Axon collateral pattern of a sparse locus coeruleus norepinephrine neuron in mouse cerebral cortex. ]]> https://biorxiv.org/content/10.1101/2025.02.04.636453v1?rss=1 Wu, Y.-M. Hung, W.-C. Chang, Y. Min, M.-Y. Yang, H.-W. 2025-02-04 doi:10.1101/2025.02.04.636453 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Neutron crystallography of the covalent intermediate of β-glucosidase reveals remodeling of the catalytic center ]]> https://biorxiv.org/content/10.1101/2025.02.06.636774v1?rss=1 Yano, N. Arakawa, H. Lin, C.-C. Ishiwata, A. Tanaka, K. Kusaka, K. Fushinobu, S. 2025-02-06 doi:10.1101/2025.02.06.636774 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Muscle Activation of Upper Body in Different-Angle Suspension Push-Ups: An Analysis of Angle-Specific Muscle Engagement ]]> https://biorxiv.org/content/10.1101/2025.02.19.638473v1?rss=1 Lin, Y.-C. Lin, K.-F. Chen, C. Chan, S.-H. Lee, P.-C. Hsu, C.-H. CHIANG, T.-L. 2025-02-26 doi:10.1101/2025.02.19.638473 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ Thermal cycling-hyperthermia attenuates rotenone-induced cell injury in SH-SY5Y cells through heat-activated mechanisms ]]> https://biorxiv.org/content/10.1101/2025.03.12.642756v1?rss=1 Kuo, Y.-Y. Lin, G.-B. Chen, Y.-M. Liu, H.-H. Hsu, F.-T. Kung, Y. Chao, C.-Y. 2025-03-13 doi:10.1101/2025.03.12.642756 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Phylogenomic inference suggests differential deep time phylogenetic signals from nuclear and organellar genomes in gymnosperms ]]> https://biorxiv.org/content/10.1101/2025.03.16.643507v1?rss=1 Lin, Y.-E. Chaw, S.-M. Wu, C.-S. Wu, Y.-W. 2025-03-17 doi:10.1101/2025.03.16.643507 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ The PXBAR-domain protein SNX9 selectively sequesters PI(3,4)P2 lipid and protects it from hydrolysis at the plasma membrane ]]> https://biorxiv.org/content/10.1101/2025.03.26.645564v1?rss=1 Beiter, J. Sung, C.-J. Lin, S.-S. DeVuono, N. Arumugam, S. Manzi, J. Bertin, A. Bassereau, P. Liu, Y.-W. Voth, G. A. Tsai, F.-C. 2025-03-29 doi:10.1101/2025.03.26.645564 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Targeting Wnt Signaling and DNAJB6/MRJ-L as a Dual Anti-RSV Strategy: Insights into a Positive Regulatory Loop ]]> https://biorxiv.org/content/10.1101/2025.03.27.645670v1?rss=1 Lu, C.-Y. Lai, P.-Y. Huang, J.-M. Chang, L.-Y. Yen, T.-Y. Tarn, W.-Y. Huang, L.-M. 2025-04-01 doi:10.1101/2025.03.27.645670 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Tracking White Matter Changes After Stereotaxic Radiosurgery inMiniature Pigs Using structural MRI, DTI, and FDG-PET ]]> https://biorxiv.org/content/10.1101/2025.05.04.652148v1?rss=1 Chen, K.-H. Yeh, C.-I. Xiao, F. Cheng, M.-F. Yen, R.-F. Ju, Y.-T. Chen, Y. Alder, J. R. Barbosa, D. Schneider, M. B. 2025-05-09 doi:10.1101/2025.05.04.652148 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Thermal cycling stimulation via nasal inhalation attenuates Aβ25-35-induced cognitive deficits in C57BL/6 mice ]]> https://biorxiv.org/content/10.1101/2025.05.08.652792v1?rss=1 Lin, G.-B. LIU, H.-H. Kuo, Y.-Y. CHEN, Y.-M. Hsu, F.-T. Wang, Y.-W. Kung, Y. Ching, C. Chao, C.-Y. 2025-05-13 doi:10.1101/2025.05.08.652792 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ DNA2 and FANCM function in two distinctive pathways in disrupting TERRA R-loops and suppressing replication stress at ALT telomeres ]]> https://biorxiv.org/content/10.1101/2025.05.22.655602v1?rss=1 Ragupathi, A. Abid, H. Z. Chen, Y. Zhao, R. Kosiyatrakul, S. T. Yetil, D. I. Neiswander, J. Feltman, R. Thomas, S. Yusupov, B. Singh, M. Zheng, L. Shen, B. Zhang, H. Chu, H.-P. C. Schildkraut, C. L. Xiao, M. Zhang, D. 2025-05-24 doi:10.1101/2025.05.22.655602 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Cell type specific CaMKII activation patterns revealed by CaMKAR, a bioactivity reporter deployable in living cells ]]> https://biorxiv.org/content/10.1101/2025.06.11.658946v1?rss=1 Severino, A. Reyes Gaido, O. E. Liu, B. Lopez-Cecetaite, G. A. Wei, A.-C. Rosales-Soto, G. Hernandez-Ochoa, E. O. Luczak, E. D. 2025-06-15 doi:10.1101/2025.06.11.658946 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Molecular and Phenotypic Characterization of Telomere Repeat Binding (TRBs) Proteins in Moss: Evolutionary and Functional Perspectives ]]> https://biorxiv.org/content/10.1101/2025.06.11.659030v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@1fea36dorg.highwire.dtl.DTLVardef@9b5569org.highwire.dtl.DTLVardef@488d0org.highwire.dtl.DTLVardef@1b22c6b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kusova, A. Hola, M. Goffova Petrova, I. Rudolf, J. Zachova, D. Skalak, J. Hejatko, J. Klodova, B. Prerovska, T. Lycka, M. Sykorova, E. Bertrand, Y. J. K. Fajkus, J. Honys, D. Prochazkova Schrumpfova, P. 2025-06-17 doi:10.1101/2025.06.11.659030 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Orphan nuclear receptors recruit TRIM28 to promote telomeric H3K9me3 for the alternative lengthening of telomeres pathway ]]> https://biorxiv.org/content/10.1101/2025.06.16.658187v1?rss=1 Tsai, C.-T. Gaela, V. M. Hsia, H.-Y. Huang, Y.-C. Chen, L.-Y. 2025-06-19 doi:10.1101/2025.06.16.658187 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Stay or Stray: Lpar1 regulates neutrophil retention and epidermal homeostasis in early zebrafish development ]]> https://biorxiv.org/content/10.1101/2025.06.22.660980v1?rss=1 Li, S.-C. Lin, Y.-C. Hsiao, C.-D. Lee, S.-J. 2025-06-25 doi:10.1101/2025.06.22.660980 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Airway microbiome-host transcriptome networks link microbial dysbiosis to survival outcomes and therapeutic opportunities in severe COVID-19 ]]> https://biorxiv.org/content/10.1101/2025.06.24.661228v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@2fc879org.highwire.dtl.DTLVardef@1128d5dorg.highwire.dtl.DTLVardef@fef0eaorg.highwire.dtl.DTLVardef@17aa499_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, K.-P. Huang, C.-H. Chen, K.-Y. Hsu, C.-L. Huang, H.-C. Juan, H.-F. 2025-06-25 doi:10.1101/2025.06.24.661228 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Development and In Vivo Evaluation of a Novel Bioabsorbable Polylactic Acid Middle Ear Ventilation Tube ]]> https://biorxiv.org/content/10.1101/2025.06.25.661110v1?rss=1 Lu, Y.-C. Chang, C.-C. Teng, P.-T. Wu, C.-H. Wu, H.-H. Lin, C.-J. Chan, Y.-H. Wu, C.-C. 2025-06-27 doi:10.1101/2025.06.25.661110 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Centriole biogenesis is seeded by CEP152-CEP63-PCNT aggregates propagating outside the centriole through the Alstrom syndrome protein ALMS1 ]]> https://biorxiv.org/content/10.1101/2025.06.26.661604v1?rss=1 Ozaki, K. Chang, T.-J. B. Yang, W.-Q. Shulman, A. Izquierdo, D. Jane, W.-N. Wang, W.-J. Stearns, T. Luders, J. Yang, T. T. Tsou, M.-F. B. 2025-06-27 doi:10.1101/2025.06.26.661604 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Genetic Network Shaping Kenyon Cell Identity and Function in Drosophila Mushroom Bodies ]]> https://biorxiv.org/content/10.1101/2025.07.07.663451v1?rss=1 Chung, P.-C. Ku, K.-Y. Chu, S.-Y. Chen, C. Yu, H.-H. 2025-07-09 doi:10.1101/2025.07.07.663451 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ Spatiotemporal Dynamics of fMRI Signal Changes Induced by High Concentration Normobaric Oxygen Inhalation ]]> https://biorxiv.org/content/10.1101/2025.07.29.667573v1?rss=1 Su, Y.-S. Wu, C.-T. Goh, J. O. S. Sanes, J. N. Chao, Z. C. 2025-08-01 doi:10.1101/2025.07.29.667573 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ CASTLE: a training-free foundation-model pipeline for cross-species behavioral classification ]]> https://biorxiv.org/content/10.1101/2025.08.22.671685v1?rss=1 90%), reveals disease-relevant phenotypes in Parkinsonian mouse models. By eliminating purpose-specific model training and providing a raw-image-informed accessible workflow, CASTLE offers a scalable framework for interpretable, cross-species behavioral phenotyping. ]]> Liu, Y.-S. R. Yeh, H.-Y. Hu, Y.-T. Wu, B.-S. Chen, Y.-F. Yang, J.-B. Jasmin, S. Hsu, C.-L. Lin, S. Chen, C.-H. Wu, Y.-W. 2025-08-27 doi:10.1101/2025.08.22.671685 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Utilization of Arabidopsis E3 ubiquitin decoys high-throughput yeast screen platform to dissect the ubiquitin-mediated circadian clock regulation ]]> https://biorxiv.org/content/10.1101/2025.08.31.673341v1?rss=1 Tu, Y.-T. Chen, C.-A. Gendron, J. Lee, C.-M. 2025-09-01 doi:10.1101/2025.08.31.673341 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ MAESTRO uncovers tandem paralog dynamics as a core driver of fungal stress adaptation ]]> https://biorxiv.org/content/10.1101/2025.08.29.673034v1?rss=1 Hsieh, P.-H. Sasaki, Y. Yang, C.-I. Wu, Z.-Y. Steindorff, A. S. Haridas, S. Ke, J. Fatma, Z. Zhao, Z. Opulente, D. A. Deng, S. Hittinger, C. T. Grigoriev, I. V. Dien, B. Zhao, H. Li, Y.-P. Yoshikuni, Y. 2025-09-04 doi:10.1101/2025.08.29.673034 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2025.09.03.673934v1?rss=1 Bourguet, P. Lorkovic, Z. J. Casado, D. K. Bapteste, V. Cho, C. H. Igolkina, A. Lee, C.-R. Nordborg, M. Berger, F. Sasaki, E. 2025-09-07 doi:10.1101/2025.09.03.673934 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Neural coding for tactile motion: Scanning speed or temporal frequency? ]]> https://biorxiv.org/content/10.1101/2025.09.06.674674v1?rss=1 Cheng, Y.-P. Huang, J.-J. Yeh, C.-I. Pei, Y.-C. 2025-09-11 doi:10.1101/2025.09.06.674674 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ High-frequency, low-intensity pulsed electric field and N-acetylcysteine synergistically protect SH-SY5Y cells against hydrogen peroxide-induced cell damage in vitro ]]> https://biorxiv.org/content/10.1101/2025.09.11.675733v1?rss=1 Hsu, F.-T. Kuo, Y.-Y. Chao, C.-Y. 2025-09-15 doi:10.1101/2025.09.11.675733 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Algebraic and Generative Design of DNA Origami via Origami Monoids ]]> https://biorxiv.org/content/10.1101/2025.09.13.675984v1?rss=1 Lin, Z. 2025-09-17 doi:10.1101/2025.09.13.675984 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ TypeAssembly: Copy number estimation and allele typing for haplotype assemblies ]]> https://biorxiv.org/content/10.1101/2025.09.13.675996v1?rss=1 Lai, H.-S. Liu, Y.-S. Chiu, H.-C. Chang, T.-Y. Lin, H.-F. Tseng, Y.-H. Hung, T.-K. Lai, S.-K. Hsu, J. S. Hsu, C.-L. Yang, Y.-C. Chen, P.-L. Chen, C.-Y. 2025-09-17 doi:10.1101/2025.09.13.675996 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Pan-cancer analysis of patient-specific gene regulatory landscapes identifies recurrent PD-1 pathway dysregulation linked to outcome ]]> https://biorxiv.org/content/10.1101/2025.10.03.680219v1?rss=1 Belova, T. Hsieh, P.-H. Hovan, L. Osorio, D. Kuijjer, M. L. 2025-10-06 doi:10.1101/2025.10.03.680219 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Plant-soil feedback persists beyond host death to shape density-dependent plant competition ]]> https://biorxiv.org/content/10.1101/2025.10.04.680482v1?rss=1 Huang, C.-L. Wan, J. Wei, S. Chang-Yang, C.-H. Ke, P.-J. 2025-10-06 doi:10.1101/2025.10.04.680482 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ gAIRR-wgs: An Algorithm to Genotype T Cell Receptor Alleles Using Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/2025.10.11.681280v1?rss=1 Huang, K.-T. Yang, Y.-H. Lin, M.-J. Lai, S.-K. Chou, T.-H. Lee, C.-Y. Hung, T.-K. Hsu, C.-L. Yang, Y.-C. Chen, C.-Y. Chen, P.-L. Hsu, J. S. 2025-10-13 doi:10.1101/2025.10.11.681280 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ deCYPher: Star Allele-Resolution Computational Framework of Pharmacogenes for Haplotype-Resolved Long-Read Assemblies ]]> https://biorxiv.org/content/10.1101/2025.10.13.681303v1?rss=1 Chang, T.-Y. Liu, Y.-S. Lai, H.-S. Hung, T.-K. Lin, H.-F. Lin, Y.-H. Hsu, C.-L. Yang, Y.-C. Chen, C.-Y. Chen, P.-L. Hsu, J. S. 2025-10-14 doi:10.1101/2025.10.13.681303 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ The Fallacy and Bias of Averages on Vegetation Indices based Plant Phenotyping ]]> https://biorxiv.org/content/10.1101/2025.10.14.682309v1?rss=1 Lee, C.-H. Tseng, C.-C. Liu, L.-y. D. Chen, T.-W. 2025-10-15 doi:10.1101/2025.10.14.682309 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Predator decision-making shapes the dynamics and stability of mimicry systems ]]> https://biorxiv.org/content/10.1101/2025.10.15.670298v1?rss=1 Sun, Y. Ke, P.-J. 2025-10-16 doi:10.1101/2025.10.15.670298 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ The demographic history, genomic variation, and transcontinental genotype-phenotype-environment map of mungbean ]]> https://biorxiv.org/content/10.1101/2025.10.16.682767v1?rss=1 Lin, Y.-P. Chen, H.-W. Chien, C.-C. Lien, Y.-H. Ong, P.-W. Yeh, C.-M. Yeh, P.-M. Chai, M.-W. Douglas, C. A. Alam, A. M. Win, M. M. Pratap, A. Boddepalli, V. N. Karimi, R. Zohoungbogbo, H. P. F. Tignegre, J. B. D. L. S. Asibuo, J. Y. Binagwa, P. H. Mbeyagala, E. K. Malik, S. R. Samsonova, M. G. Chu, J. H. Yen, J.-Y. von Wettberg, E. B. Naito, K. Schafleitner, R. Nair, R. M. Lee, C.-R. 2025-10-16 doi:10.1101/2025.10.16.682767 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Comparative genomics of a poinsettia-associated phytoplasma and functional validation of its SAP11-homologous effectors that induce plant branching ]]> https://biorxiv.org/content/10.1101/2025.10.17.683024v1?rss=1 Pei, S.-C. Li, N.-P. Li, T.-T. Yang, Y.-C. Hung, T.-H. Kuo, C.-H. 2025-10-17 doi:10.1101/2025.10.17.683024 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ BMAL2 is a druggable target for ARID1A-wildtype ovarian clear cell carcinoma (OCCC) ]]> https://biorxiv.org/content/10.1101/2025.10.21.683700v1?rss=1 Tan, G. Y. T. Lin, P.-Y. Cheng, L.-T. Tsai Yuan, Y.-S. Huang, S.-H. Yu, C.-H. Chen, C.-T. Chi, P. Hwang-Verslues, W. W. 2025-10-22 doi:10.1101/2025.10.21.683700 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ TRIB2 couples UCP1 degradation to thermogenic adaptation and metabolic health ]]> https://biorxiv.org/content/10.1101/2025.10.26.684708v1?rss=1 Lee, J. H. Chueh, L.-Y. Tien, S.-C. Lee, H.-l. Lin, K.-R. Lee, T.-Y. Che, T. P.-H. Yen, J. J. Y. Hu, C.-M. Chang, Y.-C. 2025-10-27 doi:10.1101/2025.10.26.684708 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ A topologically conserved unstructured region helps positioning the evolutionarily conserved Prp40 WW domains to promote non-canonical intron splicing ]]> https://biorxiv.org/content/10.1101/2025.10.29.685309v1?rss=1 Tung, L. Yeh, C.-S. Lin, H.-H. Tsai, H.-Y. Chang, S.-L. Larson, A. Wang, H.-K. Yeh, F.-L. Hsu, C.-L. Kao, C.-F. Pleiss, J. Chang, W.-H. Chang, T.-H. 2025-10-30 doi:10.1101/2025.10.29.685309 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Phosphoglycerate kinase 1 cooperates with AP-2 complex to promote endocytosis ]]> https://biorxiv.org/content/10.1101/2025.10.29.685329v1?rss=1 Hsu, J.-W. Chu, S.-L. Chang, Y.-T. Hung, C.-Y. Yu, C.-J. 2025-10-30 doi:10.1101/2025.10.29.685329 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Comprehensive Atlas of Cancer-Type-Specific Molecular Features from Comparative Analysis of TCGA Data ]]> https://biorxiv.org/content/10.1101/2025.10.26.684620v1?rss=1 Tung, Y.-G. 2025-11-04 doi:10.1101/2025.10.26.684620 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Pharmacological and Physiological Characteristics of Synaptic Transmissions from the Medial Prefrontal Cortex onto Noradrenergic Neurons and Their Presynaptic Neurons in the Mouse Locus Coeruleus ]]> https://biorxiv.org/content/10.1101/2025.11.07.687181v1?rss=1 Lai, P.-H. Hung, W.-C. Min, M.-Y. Yang, H.-W. 2025-11-10 doi:10.1101/2025.11.07.687181 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Structured Neural Variability from Repeated Naturalistic Video Watching Experiences ]]> https://biorxiv.org/content/10.1101/2025.11.07.687258v1?rss=1 Yang, M. Chen, P.-h. A. Brandt, A. M. Sadhukha, S. Farrens, M. Jolly, E. Chang, L. J. 2025-11-10 doi:10.1101/2025.11.07.687258 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ A Single-Aliquot, Enrichment-Free Workflow for High-Throughput Plasma Proteome and N-Glycoproteome Profiling ]]> https://biorxiv.org/content/10.1101/2025.11.11.687106v1?rss=1 10-20 fold) profiling speed to achieve 113 PGs/min and high protein abundance reproducibility (Pearson r > 0.9), confirming cross-instrument transferability. Application to a 300-participant lung cohort (cancer, LDCT-detected non-cancer nodules, and controls) revealed differential expression of S100 and annexin family proteins between cancer and nodules. Paired glycoproteomic analysis (n=30) identified site-specific N-glycosylation alterations in FN1, IGHG2, C3, and MET independent of total protein abundance, uncovering additional biomarker candidates for early lung cancer detection. Together, this dual-omics strategy enables deep, scalable, and reproducible plasma analysis, supporting longitudinal biomarker discovery and validation across instruments and laboratories. ]]> Chang, K.-H. Deyarmin, J. Pradita, T. Chen, Y.-J. Samra, S. Chang, G.-C. Yu, C.-J. Chuang, Y.-S. Arrey, T. Hsu, H.-E. Xuan, Y. Huang, P.-R. Lin, K.-T. Yen, K.-H. Tsai, H.-j. Hermanson, D. Chang, Y. Yu, S.-L. Yang, P.-C. Chen, Y.-J. 2025-11-12 doi:10.1101/2025.11.11.687106 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ scDock: Streamlining drug discovery targeting cell-cell communication via scRNA-seq analy-sis and molecular docking ]]> https://biorxiv.org/content/10.1101/2025.11.20.689638v1?rss=1 Huang, C.-H. Oyang, Y.-J. Huang, H.-C. Juan, H.-F. 2025-11-21 doi:10.1101/2025.11.20.689638 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ TXNDC5 Governs Extracellular Matrix Homeostasis in Pulmonary Hypertension ]]> https://biorxiv.org/content/10.1101/2025.11.21.689856v1?rss=1 Chen, Z. Kong, F. Huang, L. Wu, W. Wang, Z. Chen, H. Zhang, J. Deng, L. Cao, C. Zhang, X. Liu, Z. Yang, K.-C. Chang, W.-T. Bian, J.-S. Nie, X. 2025-11-23 doi:10.1101/2025.11.21.689856 Cold Spring Harbor Laboratory Press 2025-11-23 <![CDATA[ Antimetastatic Sulfonate-Functionalized Mesoporous Silica Nanoparticles Enhance Irinotecan Stability and Delivery for Colorectal Cancer Treatment ]]> https://biorxiv.org/content/10.1101/2025.11.25.690433v1?rss=1 Wu, C.-H. Chen, Z.-A. Zhang, R.-L. Sun, T. C. Li, D.-W. Lin, C. K. Wu, S.-H. Chen, P. Mou, C.-Y. Chen, Y.-P. 2025-11-28 doi:10.1101/2025.11.25.690433 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Host-derived lipid transfer and metabolic reprogramming in a ciliate-algal symbiosis ]]> https://biorxiv.org/content/10.1101/2025.11.27.690892v1?rss=1 Chen, Y.-J. Wei, C.-Y. Kamal, M. M. Hsu, C.-W. Hsiao, S.-Y. Lee, D.-C. Wang, P.-L. Leu, J.-Y. 2025-11-28 doi:10.1101/2025.11.27.690892 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Sperm-specific fertility factors SMZ-1/2 promote FB-MO biogenesis and MSP filament assembly in C. elegans ]]> https://biorxiv.org/content/10.64898/2025.12.01.691703v1?rss=1 Peng, H.-F. Liu, C.-L. Jane, W.-N. Chen, C.-S. Wang, C.-W. Wu, J.-c. 2025-12-03 doi:10.64898/2025.12.01.691703 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Core elements play distinct roles in promoter birth and transcriptional regulation ]]> https://biorxiv.org/content/10.64898/2025.12.02.691827v1?rss=1 Kuo, S.-T. Shen, W.-Y. Lai, S.-W. Ni, C.-W. Chang, C.-C. Palmai, Z. Yang, L.-W. Chan, N.-L. Lee, I.-R. Chou, H.-H. D. 2025-12-04 doi:10.64898/2025.12.02.691827 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ S100A8/A9 Inhibition Reduces Splenic Myelopoiesis and Improves Outcomes After Stroke ]]> https://biorxiv.org/content/10.64898/2025.12.03.692236v1?rss=1 Kim, H. A. Al-Sharea, A. Chu, H. Tang, S.-C. Rupasinghe, S. A. Zhang, S. R. Nagareddy, P. R. Drummond, G. R. Arumugam, T. V. Murphy, A. J. Sobey, C. G. Lee, M. K. 2025-12-07 doi:10.64898/2025.12.03.692236 Cold Spring Harbor Laboratory Press 2025-12-07 <![CDATA[ White eye-rings coevolved with diurnal behaviors as a trait enhancing visual appeal in rodents ]]> https://biorxiv.org/content/10.64898/2025.12.07.692862v1?rss=1 Le, N. H. K. Li, S.-H. Chiu, C.-C. Weng, M.-P. Chen, S.-K. Liao, B.-Y. 2025-12-10 doi:10.64898/2025.12.07.692862 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Tissue-guided multi-omics profiling identifies extracellular vesicle biomarkers indicative of lung pathology in acute respiratory distress syndrome ]]> https://biorxiv.org/content/10.64898/2025.12.09.693331v1?rss=1 Chen, P.-T. Chang, C.-Y. Chung, C.-L. Lee, C.-H. Suk, C.-W. Lin, C.-F. Fan, Y.-J. Lu, Y.-W. Hsu, Y.-C. Chang, T. Huang, C.-J. Tsai, I.-L. 2025-12-12 doi:10.64898/2025.12.09.693331 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Reduction of Aβ25-35-Induced Cognitive Impairments in C57BL/6 Mice Through Focused Ultrasound Thermal-Cycling Stimulation ]]> https://biorxiv.org/content/10.64898/2025.12.10.693347v1?rss=1 Lin, G.-B. Liu, H.-H. Kuo, Y.-Y. Chen, Y.-M. Hsu, F.-T. Wang, Y.-W. Kung, Y. Ching, C. Chao, C.-Y. 2025-12-12 doi:10.64898/2025.12.10.693347 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Nanodisc-Mediated Visualization of Crowding-Induced Condensation and Membrane Reorganization in Two-Dimensional Membrane Environments ]]> https://biorxiv.org/content/10.64898/2026.01.02.697448v1?rss=1 Bai, R.-H. Tien, H.-Y. Cheng, C.-C. Tsai, H.-J. Lin, C.-K. Kuo, C.-J. Wong, W.-T. Jiang, C.-M. Chiang, Y.-W. Lin, C.-W. 2026-01-03 doi:10.64898/2026.01.02.697448 Cold Spring Harbor Laboratory Press 2026-01-03 <![CDATA[ Dopaminergic Modulation of Mushroom Body Output Neurons Mediates Nociception-Induced Escape in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.01.04.697536v1?rss=1 Yang, C.-L. Feng, K.-L. Peng, H.-C. Wu, M.-C. Charng, C.-C. Chu, L.-A. Chen, C.-W. Wen, Y.-R. Chiang, A.-S. 2026-01-04 doi:10.64898/2026.01.04.697536 Cold Spring Harbor Laboratory Press 2026-01-04 <![CDATA[ Organelle biogenesis on a synthetic bead ]]> https://biorxiv.org/content/10.64898/2026.01.09.698636v1?rss=1 Chang, C.-C. Peng, M. Blaya-Martinez, L. Wong, S.-S. Mohamad, N. Xiao, B. Monteiro, J. M. Harrison, T. Raff, J. W. 2026-01-12 doi:10.64898/2026.01.09.698636 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Rice Annotation Project Database (RAP-DB): literature-curated gene annotation and integrated omics resources for rice functional genomics and molecular breeding ]]> https://biorxiv.org/content/10.64898/2026.01.16.699882v1?rss=1 Kawahara, Y. Kishikawa, T. H. Hirata, R. Wang, X. Tamagaki, Y. Kumagai, M. Tabei, N. Sakai, H. Itoh, T. 2026-01-21 doi:10.64898/2026.01.16.699882 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Engineering a performance-improved, axon-targeted kalium channelrhodopsin for optogenetic neuropathway inhibition ]]> https://biorxiv.org/content/10.64898/2026.01.17.700073v1?rss=1 Lopez, S. M. M. Wang, H.-Y. Lee, I.-C. Chen, W.-H. Chen, Y.-C. Lin, Y.-J. Chen, C.-C. Pan, M.-K. Hsu, C.-L. Lin, W.-C. 2026-01-21 doi:10.64898/2026.01.17.700073 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Deficiency of miR130a leads to fat hypertrophy, hepatic steatosis, insulin resistance and glucose intolerance in mice ]]> https://biorxiv.org/content/10.64898/2026.01.24.701468v1?rss=1 Chang, Y.-C. Chuang, C.-H. Chou, S.-F. Huang, J.-Y. Shih, C.-h. 2026-01-24 doi:10.64898/2026.01.24.701468 Cold Spring Harbor Laboratory Press 2026-01-24 <![CDATA[ Time perception follows Weber's law in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.02.04.703894v1?rss=1 Lo, T.-N. Huang, C.-Y. Lin, S. 2026-02-07 doi:10.64898/2026.02.04.703894 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ HSPB8 regulates CTP synthase filaments to couple nucleotide metabolism and autophagy in tumors ]]> https://biorxiv.org/content/10.64898/2026.02.10.704981v1?rss=1 Lin, W.-C. Wang, C.-Y. Huang, K.-J. Chakraborty, A. Lin, Y.-T. Hsieh, Y.-J. Chien, K.-Y. Ke, P.-Y. Huang, W.-H. Cheng, C.-Y. Chang, I. Y.-F. Tang, H.-Y. Yang, C.-H. Cheng, M.-L. Chang, Y.-C. Yeh, C.-T. Lee, C.-K. Yu, J.-S. Chang, Y.-S. Grosshans, J. Pai, L.-M. 2026-02-11 doi:10.64898/2026.02.10.704981 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Tuning metaplasticity in the adult visual cortex using flickering light ]]> https://biorxiv.org/content/10.64898/2026.02.16.706197v1?rss=1 Reilly-Andujar, F. Cramer, T. M. L. Wang, E. Y. Chang, D. Chang, N.-W. Heynen, A. J. Bear, M. F. 2026-02-18 doi:10.64898/2026.02.16.706197 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ STRATA: Spatial Regulon Field Theory Reveals Coupling Architecture of Human Skin and Its Homogenization in Melanoma ]]> https://biorxiv.org/content/10.64898/2026.02.24.707661v1?rss=1 Tjiu, J.-W. 2026-02-25 doi:10.64898/2026.02.24.707661 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Robust volumetric multiplex staining of centimeter-scale FFPE tissues guided by neural network-based optimization ]]> https://biorxiv.org/content/10.64898/2026.03.09.710440v1?rss=1 Lin, Y.-H. Huang, C.-Y. Chen, Y.-H. Chen, Y.-H. Xu, Z.-W. Ko, P.-L. Hsu, H.-H. Tung, Y.-C. Chen, Y.-F. Chen, H.-C. Chiang, A.-S. Fiock, K. L. Wang, K.-C. Lin, C.-H. Hu, S.-H. Chen, B.-C. Chu, L.-A. 2026-03-11 doi:10.64898/2026.03.09.710440 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Improved Protein Encapsulation and Delivery by Lipid Nanoparticles with Refined Ionizable Lipid Content ]]> https://biorxiv.org/content/10.64898/2026.03.10.710763v1?rss=1 Dirvelyte-Valauske, E. Mazerimas, M. Pavliukeviciene, B. Daugelaviciene, N. Kutanovas, S. Kao, C.-Y. Chen, Y.-T. Neniskyte, U. Budvytyte, R. 2026-03-12 doi:10.64898/2026.03.10.710763 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ A Distinct Layer 1 Astrocyte Program Shapes Perisynaptic Structure and Calcium Signaling in Mouse Motor Cortex ]]> https://biorxiv.org/content/10.64898/2026.03.16.712002v1?rss=1 View larger version (65K): org.highwire.dtl.DTLVardef@89c916org.highwire.dtl.DTLVardef@1f0d71eorg.highwire.dtl.DTLVardef@bb02f3org.highwire.dtl.DTLVardef@1bedf7e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LILayer 1 astrocytes in mouse motor cortex have compact, loop-rich nanoarchitecture C_LIO_LILayer 1 astrocytes show fast, frequent, widespread calcium events C_LIO_LISingle-cell data define a superficial astrocyte state enriched for Id1 and Id3 C_LIO_LIAdult Id1/Id3 loss selectively disrupts Layer 1 astrocyte structure and calcium C_LI In BriefBhattacharjee et al., identify a specialized Layer 1 astrocyte state in mouse motor cortex, defined by compact, loop-rich nanoarchitecture and unusually high calcium signaling. Id1/Id3 deletion selectively disrupts this superficial program, linking layer-specific astrocyte form and function to adult transcriptional control. ]]> Bhattacharjee, S. Yeh, K.-H. Wu, P.-Y. Pan, M.-X. Liu, T.-H. Tsai, Z.-B. Tong, S.-K. Zhuang, Z.-H. Huang, Y.-M. Chou, S.-J. Chiu, S.-L. Chou, M.-Y. Yu, C.-H. Wu, Y.-W. 2026-03-17 doi:10.64898/2026.03.16.712002 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ De Novo Regeneration of Rete Ridges during Cetacean skin wound healing ]]> https://biorxiv.org/content/10.64898/2026.03.16.711258v1?rss=1 Liu, T.-Y. Wang, H.-V. Yang, W.-C. Yang, C.-C. Su, C.-Y. Chiou, Y.-T. Chiou, T.-H. Shieh, S.-J. Tang, M.-J. Chuong, C. M. Hughes, M. W. 2026-03-19 doi:10.64898/2026.03.16.711258 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Extending island biogeography theory to biotic islands: Microbial communities in epiphytic bird's nest fern Asplenium nidus ]]> https://biorxiv.org/content/10.64898/2026.03.30.715435v1?rss=1 Tseng, Y.-P. Wei, S. Ke, P.-J. 2026-04-01 doi:10.64898/2026.03.30.715435 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography ]]> https://biorxiv.org/content/10.64898/2026.04.05.716573v1?rss=1 Wang, B. Moya, N. D. Tanny, R. E. Sauria, M. E. G. O Connor, L. M. Khorshidian, A. McKeown, R. Stevens, L. Buchanan, C. Crombie, T. A. Dilks, C. M. Evans, K. S. Cook, D. E. Zhang, G. Stinson, L. A. Roberto, N. M. Lee, D. Zdraljevic, S. Gosse, C. Gimond, C. Chen, M.-E. Dang, V. D. Wang, J. Cutter, A. D. Rockman, M. V. Felix, M.-A. Braendle, C. Andersen, E. C. 2026-04-08 doi:10.64898/2026.04.05.716573 Cold Spring Harbor Laboratory Press 2026-04-08