bioRxiv Channel: Academia Sinica https://biorxiv.org This feed contains articles for bioRxiv Channel "Academia Sinica" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ High-throughput functional annotation of influenza A virus genome at single-nucleotide resolution ]]> https://biorxiv.org/content/10.1101/005702v1?rss=1 Nicholas C. Wu Arthur P. Young Laith Q. Al-Mawsawi C. Anders Olson Jun Feng Hangfei Qi Shu-Hwa Chen I-Hsuan Lu Chung-Yen Lin Robert G. Chin Harding H. Luan Nguyen Nguyen Stanley F. Nelson Xinmin Li Ting-Ting Wu Ren Sun 2014-05-31 doi:10.1101/005702 Cold Spring Harbor Laboratory Press 2014-05-31 <![CDATA[ The impacts of historical barriers on floristic patterns of plant groups with different dispersal abilities in the Ryukyu Archipelago, Japan ]]> https://biorxiv.org/content/10.1101/007617v1?rss=1 Koh Nakamura Rempei Suwa Tetsuo Denda Masatsugu Yokota 2014-08-01 doi:10.1101/007617 Cold Spring Harbor Laboratory Press 2014-08-01 <![CDATA[ The architectural stratification and woody species diversity in subtropical evergreen broadleaf forests along a latitudinal thermal gradient of the Ryukyu Archipelago, Japan ]]> https://biorxiv.org/content/10.1101/007625v1?rss=1 Sm Feroz Rempei Suwa Koh Nakamura Akio Hagihara Masatsugu Yokota 2014-08-03 doi:10.1101/007625 Cold Spring Harbor Laboratory Press 2014-08-03 <![CDATA[ The genetic basis of natural variation in C. elegans telomere length ]]> https://biorxiv.org/content/10.1101/051276v1?rss=1 Daniel E Cook Stefan Zdraljevic Robyn E Tanny Beomseok Seo David Riccardi Luke M Noble Matthew V Rockman Mark Alkema Christian Braendle Jan Kammenga John Wang Leonid Kruglyak Marie-Anne Felix Junho Lee Erik Andersen 2016-05-02 doi:10.1101/051276 Cold Spring Harbor Laboratory Press 2016-05-02 <![CDATA[ Antibiotic Stress Selects against Cooperation in a Pathogenic Bacterium ]]> https://biorxiv.org/content/10.1101/053066v1?rss=1 Marie Vasse Robert Noble Andrei R Akhmetzhanov Clara Torres-Barceló James Gurney Simon Benateau Claire Gougat-Barbera Oliver Kaltz Michael E Hochberg 2016-05-12 doi:10.1101/053066 Cold Spring Harbor Laboratory Press 2016-05-12 <![CDATA[ Familial Mutations and Post-translational Modifications of UCH-L1 in Parkinson’s Disease and Neurodegenerative Disorders ]]> https://biorxiv.org/content/10.1101/094953v1?rss=1 Lee, Y.-T. C. Hsu, S.-T. D. 2016-12-17 doi:10.1101/094953 Cold Spring Harbor Laboratory Press 2016-12-17 <![CDATA[ Allopatric divergence, local adaptation, and multiple Quaternary refugia in a long-lived tree (Quercus spinosa) from subtropical China ]]> https://biorxiv.org/content/10.1101/112375v1?rss=1 Feng, L. Zhang, Y.-P. Chen, X.-D. Yang, J. Zhou, T. Bai, G.-Q. Yang, J. Li, Z.-H. Peng, C.-I. Zhao, G.-F. 2017-02-28 doi:10.1101/112375 Cold Spring Harbor Laboratory Press 2017-02-28 <![CDATA[ Molecular Basis Underlying Male Sterility In bHLH142 Overexpressing Rice ]]> https://biorxiv.org/content/10.1101/116996v1?rss=1 Ko, S.-S. Li, M.-J. Lin, Y.-J. Hsing, H.-X. Yang, T.-T. Chen, T.-K. Jhong, C.-M. Ku, M. S.-B. 2017-03-15 doi:10.1101/116996 Cold Spring Harbor Laboratory Press 2017-03-15 <![CDATA[ Trichoderma reesei Complete Genome Sequence, Repeat-Induced Point Mutation And Partitioning Of CAZyme Gene Clusters ]]> https://biorxiv.org/content/10.1101/120071v1?rss=1 1.5 Mb of new sequences. Most new sequences are located on AT-rich blocks, including 7 centromeres, 14 subtelomeres and 2329 interspersed AT-rich blocks. The seven QM6a centromeres separately consist of 24 conserved repeats and 37 putative centromere-encoded genes. These findings open up a new perspective for future centromere and chromosome architecture studies. Next, we demonstrate that sexual crossing readily induced cytosine-to-thymine point mutations on both tandem and unlinked duplicated sequences. We also show by bioinformatic analysis that Trichoderma reesei has evolved a robust repeat-induced point mutation (RIP) system to accumulate AT-rich sequences, with longer AT-rich blocks having more RIP mutations. The widespread distribution of AT-rich blocks correlates genome-wide partitions with gene clusters, explaining why clustering of genes has been reported to not influence gene expression in Trichoderma reesei. Compartmentation of ancestral gene clusters by AT-rich blocks might promote flexibilities that are evolutionarily advantageous in this fungus soil habitats and other natural environments. Our analyses, together with the complete genome sequence, provide a better blueprint for biotechnological and industrial applications. ]]> Li, W.-C. Huang, C.-H. Chen, C.-L. Chuang, Y.-C. Tung, S.-Y. Wang, T.-F. 2017-03-24 doi:10.1101/120071 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ Three-dimensional actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes ]]> https://biorxiv.org/content/10.1101/120444v1?rss=1 Fritz-Laylin, L. K. Riel-Mehan, M. Chen, B.-C. Lord, S. J. Goddard, T. D. Ferrin, T. E. Johnson, G. Betzig, E. Mullins, R. D. 2017-03-24 doi:10.1101/120444 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ Regulatory Divergence In Wound-Responsive Gene Expression In Domesticated And Wild Tomato ]]> https://biorxiv.org/content/10.1101/123992v1?rss=1 Liu, M.-J. Sugimoto, K. Uygun, S. Panchy, N. Campbell, M. S. Yandell, M. Howe, G. A. Shiu, S.-H. 2017-04-04 doi:10.1101/123992 Cold Spring Harbor Laboratory Press 2017-04-04 <![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[ Matryoshka: Ratiometric biosensors from a nested 1 cassette of green- and orange-emitting fluorescent proteins ]]> https://biorxiv.org/content/10.1101/143107v1?rss=1 Ast, C. Foret, J. Oltrogge, L. De Michele, R. Kleist, T. Ho, C.-H. Frommer, W. 2017-06-06 doi:10.1101/143107 Cold Spring Harbor Laboratory Press 2017-06-06 <![CDATA[ Inferring synteny between genome assemblies: a systematic evaluation ]]> https://biorxiv.org/content/10.1101/149989v1?rss=1 Liu, D. Hunt, M. Tsai, I. J. 2017-06-14 doi:10.1101/149989 Cold Spring Harbor Laboratory Press 2017-06-14 <![CDATA[ Fibroblast Growth Factor Signaling Instructs Ensheathing Glia Wrapping of Drosophila Olfactory Glomeruli ]]> https://biorxiv.org/content/10.1101/151662v1?rss=1 Wu, B. Li, J. Chou, Y.-H. Luginbuhl, D. Luo, L. 2017-06-18 doi:10.1101/151662 Cold Spring Harbor Laboratory Press 2017-06-18 <![CDATA[ Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs ]]> https://biorxiv.org/content/10.1101/163626v1?rss=1 Liu, W.-H. Tsai, Z. T.-Y. Tsai, H.-K. 2017-07-17 doi:10.1101/163626 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ SFMetaDB: A Comprehensive Annotation of Mouse RNA Splicing Factor RNA-Seq Datasets ]]> https://biorxiv.org/content/10.1101/177931v1?rss=1 Li, J. Tseng, C.-S. Federico, A. Ivankovic, F. Huang, Y.-S. Ciccodicola, A. Swanson, M. S. Yu, P. 2017-08-18 doi:10.1101/177931 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Architecture of mammalian centriole distal appendages accommodates distinct blade and matrix functional elements ]]> https://biorxiv.org/content/10.1101/193474v1?rss=1 Yang, T. T. Chong, W. M. Wang, W.-J. Mazo, G. Tanos, B. Chen, Z. Tran, M. N. T. Chen, Y.-D. Weng, R. R. Huang, C.-E. Jane, W.-N. Tsou, M.-F. B. Liao, J.-C. 2017-09-25 doi:10.1101/193474 Cold Spring Harbor Laboratory Press 2017-09-25 <![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[ Adenylate kinase-4 modulates oxidative stress and stabilizes HIF-1α to drive lung cancer metastasis ]]> https://biorxiv.org/content/10.1101/196857v1?rss=1 Jan, Y.-H. Lai, T.-C. Yang, C.-J. Lin, Y.-F. Huang, M.-S. Hsiao, M. 2017-10-01 doi:10.1101/196857 Cold Spring Harbor Laboratory Press 2017-10-01 <![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[ 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[ Bmal1 integrates mitochondrial metabolism and macrophage activation ]]> https://biorxiv.org/content/10.1101/2019.12.20.884429v1?rss=1 Lee, C.-H. Alexander, R. Liou, Y.-H. Knudsen, N. Starost, K. Xu, C. Hyde, A. Liu, S. Jacobi, D. Liao, N.-S. 2019-12-20 doi:10.1101/2019.12.20.884429 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Plasma membrane damage removal by F-actin-mediated shedding from repurposed filopodia ]]> https://biorxiv.org/content/10.1101/2019.12.23.887638v1?rss=1 Mageswaran, S. K. Yang, W. Y. Chakrabarty, Y. Oikonomou, C. M. Jensen, G. J. 2019-12-24 doi:10.1101/2019.12.23.887638 Cold Spring Harbor Laboratory Press 2019-12-24 <![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[ Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus ]]> https://biorxiv.org/content/10.1101/2020.01.10.901983v1?rss=1 Langner, T. Harant, A. Gomez-Luciano, L. B. Shrestha, R. K. Win, J. Kamoun, S. 2020-01-11 doi:10.1101/2020.01.10.901983 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ On the origin and evolution of RNA editing in metazoans ]]> https://biorxiv.org/content/10.1101/2020.01.19.911685v1?rss=1 Li, Q. Zhang, P. Li, J. Yu, H. Zhan, X. Zhu, Y. Guo, Q. Tan, H. Lundholm, N. Garcia, L. Martin, M. D. Subirats, M. A. Su, Y.-H. Ruiz-Trillo, I. Martindale, M. Q. Yu, J.-K. Gilbert, M. T. P. Zhang, G. 2020-01-19 doi:10.1101/2020.01.19.911685 Cold Spring Harbor Laboratory Press 2020-01-19 <![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[ Species boundaries and molecular markers for classification among 16SrI phytoplasmas informed by genome analysis ]]> https://biorxiv.org/content/10.1101/2020.01.31.928135v1?rss=1 97% genome-wide average nucleotide identity (ANI) and >78% of their protein-coding genes. In comparison, strains assigned to different OTUs share <94% ANI and <75% of their genes. Reduction in homologous recombination between OTUs is one possible explanation for the discontinuity in genome similarities, and these findings supported the proposal that 95% ANI could serve as a cutoff for distinguishing species in bacteria. Additionally, critical examination of these results and the raw sequencing reads led to the identification of one genome that was presumably mis-assembled by combining two sequencing libraries built from phytoplasmas belonging to different OTUs. This finding provided a cautionary tale for working on uncultivated bacteria. Based on the new understanding of phytoplasma divergence and the current genome availability, we developed five molecular markers that could be used for multilocus sequence analysis (MLSA). By selecting markers that are short yet highly informative, and are distributed evenly across the chromosome, these markers provided a cost-effective system that is robust against recombination. Finally, examination of the effector gene distribution further confirmed the rapid gains and losses of these genes, as well as the involvement of potential mobile units (PMUs) in their molecular evolution. Future improvements on the taxon sampling of phytoplasma genomes will allow further expansions of similar analysis, and thus contribute to phytoplasma taxonomy and diagnostics. ]]> Cho, S.-T. Kung, H.-J. Huang, W. Hogenhout, S. A. Kuo, C.-H. 2020-01-31 doi:10.1101/2020.01.31.928135 Cold Spring Harbor Laboratory Press 2020-01-31 <![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[ EM-net: Deep learning for electron microscopy image segmentation ]]> https://biorxiv.org/content/10.1101/2020.02.03.933127v1?rss=1 Khadangi, A. Boudier, T. Rajagopal, V. 2020-02-04 doi:10.1101/2020.02.03.933127 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Directed effective connectivity and synaptic weights of invitro neuronal cultures revealed from high-density multielectrode array recordings ]]> https://biorxiv.org/content/10.1101/2020.02.06.936781v1?rss=1 Sun, C. Lin, K. C. Huang, Y.-T. Ching, E. S. C. Lai, P.-Y. Chan, C. K. 2020-02-06 doi:10.1101/2020.02.06.936781 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Comparative transcriptomics across nematode life cycles reveal gene expression conservation and correlated evolution in adjacent developmental stages ]]> https://biorxiv.org/content/10.1101/2020.02.07.938399v1?rss=1 Lu, M. R. Lai, C.-K. Liao, B.-Y. Tsai, I. J. 2020-02-07 doi:10.1101/2020.02.07.938399 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Alteration of Power Law Scaling of Spontaneous Brain Activity in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.02.13.946657v1?rss=1 Lee, Y.-J. Huang, S.-Y. Lin, C.-P. Tsai, S.-J. Yang, A. C. 2020-02-13 doi:10.1101/2020.02.13.946657 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ A universal subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish ]]> https://biorxiv.org/content/10.1101/2020.02.13.947093v1?rss=1 Wada, N. Yuasa, H. Kajitani, R. Gotoh, Y. Ogura, Y. Yoshimura, D. Toyoda, A. Tang, S.-L. Higashimura, Y. Sweatman, H. Forsman, Z. H. Bronstein, O. Eyal, G. Thongtham, N. Itoh, T. Hayashi, T. Yasuda, N. 2020-02-14 doi:10.1101/2020.02.13.947093 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[ Basal leakage in oscillation: coupled transcriptional and translational control using feed-forward loops ]]> https://biorxiv.org/content/10.1101/2020.02.24.962415v1?rss=1 Hsu, C.-P. Joanito, I. Sanders, C.-C. Chu, J.-W. Wu, S.-H. 2020-02-24 doi:10.1101/2020.02.24.962415 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Parkin coordinates mitochondrial lipid remodeling to execute mitophagy ]]> https://biorxiv.org/content/10.1101/2020.02.28.970210v1?rss=1 Lin, C.-C. Yan, J. Kapur, M. D. Norris, K. L. Hsieh, C.-W. Lai, C.-H. Vitale, N. Lim, K.-L. Guan, Z. Chi, J.-T. Yang, W.-Y. Yao, T.-P. 2020-02-28 doi:10.1101/2020.02.28.970210 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ PIP3 depletion rescues myoblast fusion defects in human rhabdomyosarcoma cells ]]> https://biorxiv.org/content/10.1101/2020.03.06.980706v1?rss=1 Lian, Y.-L. Chen, K.-W. Chou, Y.-T. Ke, T.-L. Chen, B.-C. Lin, Y.-C. Chen, L. 2020-03-07 doi:10.1101/2020.03.06.980706 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Standardization and Harmonization of Distributed Multi-National Proteotype Analysis supporting Precision Medicine Studies ]]> https://biorxiv.org/content/10.1101/2020.03.12.988089v1?rss=1 Xuan, Y. Bateman, N. W. Gallien, S. Goetze, S. Zhou, Y. Navarro, P. Hu, M. Parikh, N. Hood, B. L. Conrads, K. A. Loosse, C. Kitata, R. B. Piersma, S. R. Chiasserini, D. Zhu, H. Hou, G. Tahir, M. Macklin, A. Khoo, A. Sun, X. Crossett, B. Sickmann, A. Chen, Y.-J. Jimenez, C. R. Zhou, H. Liu, S. Larsen, M. R. Kislinger, T. Chen, Z. Parker, B. L. Cordwell, S. J. Wollscheid, B. Conrads, T. P. 2020-03-12 doi:10.1101/2020.03.12.988089 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ TPX2 activation by GM130 controls astral microtubule formation and spindle orientation ]]> https://biorxiv.org/content/10.1101/2020.03.16.994426v1?rss=1 Guo, H. Wei, J.-H. Seemann, J. 2020-03-17 doi:10.1101/2020.03.16.994426 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity ]]> https://biorxiv.org/content/10.1101/2020.03.18.997080v1?rss=1 Cui, L. Chen, S.-Y. Lerbs, T. Lee, J.-W. Domizi, P. Gordon, S. Kim, Y.-h. Nolan, G. P. Betancur, P. Wernig, G. 2020-03-20 doi:10.1101/2020.03.18.997080 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Medicago truncatula Yellow Stripe-Like7 encodes a peptide transporter required for symbiotic nitrogen fixation ]]> https://biorxiv.org/content/10.1101/2020.03.26.009159v1?rss=1 Castro-Rodriguez, R. Reguera, M. Escudero, V. Gil-Diez, P. Quintana, J. Prieto, R. I. Kumar, R. K. Brear, E. Grillet, L. Wen, J. Mysore, K. S. Walker, E. L. Smith, P. M. Imperial, J. Gonzalez-Guerrero, M. 2020-03-27 doi:10.1101/2020.03.26.009159 Cold Spring Harbor Laboratory Press 2020-03-27 <![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[ 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[ Mitochondrial ROS1 increases mitochondrial fission and respiration in oral squamous cancer carcinoma ]]> https://biorxiv.org/content/10.1101/2020.04.13.038844v1?rss=1 Chang, Y.-J. Chen, K.-W. Chen, L. 2020-04-13 doi:10.1101/2020.04.13.038844 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Genomic, geographic and temporal distributions of SARS-CoV-2 mutations ]]> https://biorxiv.org/content/10.1101/2020.04.22.055863v1?rss=1 Yang, H.-C. Chen, C.-h. Wang, J.-H. Liao, H.-C. Yang, C.-T. Chen, C.-W. Lin, Y.-C. Kao, C.-H. Liao, J. C. 2020-04-24 doi:10.1101/2020.04.22.055863 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Molecular basis for the ATPase-powered substrate translocation by the Lon AAA+ protease ]]> https://biorxiv.org/content/10.1101/2020.04.29.068361v1?rss=1 Zhang, K. Li, S. Hsieh, K.-Y. Su, S.-C. Pintilie, G. D. Chiu, W. Chang, C.-I. 2020-04-30 doi:10.1101/2020.04.29.068361 Cold Spring Harbor Laboratory Press 2020-04-30 <![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[ Antagonistic Effects of Intraspecific Cooperation and Interspecific Competition on Thermal Performance ]]> https://biorxiv.org/content/10.1101/2020.05.03.075325v1?rss=1 Tsai, H.-Y. Rubenstein, D. R. Chen, B.-F. Liu, M. Chan, S.-F. Chen, D.-P. Sun, S.-J. Yuan, T.-N. Shen, S.-F. 2020-05-04 doi:10.1101/2020.05.03.075325 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ Mycena genomes resolve the evolution of fungal bioluminescence ]]> https://biorxiv.org/content/10.1101/2020.05.06.079921v1?rss=1 Ke, H.-M. Lee, H.-H. Lin, C.-Y. I. Liu, Y.-C. Lu, M. R. Hsieh, J.-W. A. Chang, C.-C. Wu, P.-H. Lu, M. J. Li, J.-Y. Shang, G. Lu, R. J.-H. Nagy, L. G. Chen, P.-Y. Kao, H.-W. Tsai, I. J. 2020-05-07 doi:10.1101/2020.05.06.079921 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Cell-extracellular matrix interactions in the fluidic phase direct the topology and polarity of self-organized epithelial structures ]]> https://biorxiv.org/content/10.1101/2020.05.12.090068v1?rss=1 Ouyang, M. Yu, J.-Y. Chen, Y. Deng, L. Guo, C.-L. 2020-05-14 doi:10.1101/2020.05.12.090068 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ A previously uncharacterized gene in SARS-CoV-2 illuminates the functional dynamics and evolutionary origins of the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2020.05.21.109280v1?rss=1 Nelson, C. W. Ardern, Z. Goldberg, T. L. Meng, C. Kuo, C.-H. Ludwig, C. Kolokotronis, S.-O. Wei, X. 2020-05-22 doi:10.1101/2020.05.21.109280 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ pH-Dependent Transcriptional Profile Changes in Iron-Deficient Arabidopsis Roots ]]> https://biorxiv.org/content/10.1101/2020.05.21.109777v1?rss=1 Tsai, H.-H. Schmidt, W. 2020-05-22 doi:10.1101/2020.05.21.109777 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ An updated staging system for cephalochordate development: one table suits them all ]]> https://biorxiv.org/content/10.1101/2020.05.26.112193v1?rss=1 Carvalho, J. E. Lahaye, F. Yong, L. W. Croce, J. C. Escriva, H. Yu, J.-K. Schubert, M. 2020-05-26 doi:10.1101/2020.05.26.112193 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Simeprevir suppresses SARS-CoV-2 replication and synergizes with remdesivir ]]> https://biorxiv.org/content/10.1101/2020.05.26.116020v1?rss=1 Lo, H. S. Hui, K. P. Y. Lai, H.-M. Khan, K. S. Kaur, S. Li, Z. Chan, A. K. N. Cheung, H. H.-Y. Ng, K. C. Ho, J. C. W. Che, Y. W. Ma, B. Cheung, P. M.-H. Shin, D. Wang, K. Wu, K.-P. Dikic, I. Liang, P.-H. Zuo, Z. Chan, F. K. L. Hui, D. S. C. Mok, V. C. T. Wong, K.-B. Ko, H. Aik, W. S. Chan, M. C. W. Ng, W.-L. 2020-05-26 doi:10.1101/2020.05.26.116020 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ 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[ Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient ]]> https://biorxiv.org/content/10.1101/2020.06.12.148387v1?rss=1 Zhou, D. Duyvesteyn, H. M. E. Chen, C.-P. Huang, C.-G. Chen, T.-H. Shih, S.-R. Lin, Y.-C. Cheng, C.-Y. Cheng, S.-H. Huang, Y.-C. Lin, T.-Y. Ma, C. Huo, J. Carrique, L. Malinauskas, T. Ruza, R. R. Shah, P. Tan, T. K. Rijal, P. Donat, R. F. Godwin, K. Buttigieg, K. Tree, J. Radecke, J. Paterson, N. G. Supasa, P. Mongkolsapaya, J. Screaton, G. R. Carroll, M. W. Jaramillo, J. G. Knight, M. James, W. S. Owens, R. J. Naismith, J. H. Townsend, A. Fry, E. E. Zhao, Y. Ren, J. Stuart, D. I. Huang, K.-Y. A. 2020-06-13 doi:10.1101/2020.06.12.148387 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Flower initiates a positive feedback loop upon PIP2 enrichment at periactive zones to control bulk endocytosis ]]> https://biorxiv.org/content/10.1101/2020.06.22.164400v1?rss=1 Yao, C.-K. Li, T.-N. Chen, Y.-J. Wang, Y.-T. Lin, H.-C. 2020-06-22 doi:10.1101/2020.06.22.164400 Cold Spring Harbor Laboratory Press 2020-06-22 <![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[ The Peroxiredoxin 6 gene plays a critical role in the homeostatic regulation of fear response ]]> https://biorxiv.org/content/10.1101/2020.07.10.196477v1?rss=1 Sarayut Phasuk Tanita Pairojana Pavithra Suresh Shun-Ping Huang Narawut Pakaprot Supin Chompoopong Chee-Hing Yang Hsueh-Kai Chang Chien-Chang Chen Ingrid Liu 2020-07-10 doi:10.1101/2020.07.10.196477 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[ EM-stellar: benchmarking deep learning for electron microscopy image segmentation ]]> https://biorxiv.org/content/10.1101/2020.07.15.203836v1?rss=1 Khadangi, A. Boudier, T. Rajagopal, V. 2020-07-15 doi:10.1101/2020.07.15.203836 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Neurodegeneration induces a developmental RNA processing program by calpain-mediated MBNL2 degradation ]]> https://biorxiv.org/content/10.1101/2020.07.24.219121v1?rss=1 Wang, L.-H. Lin, Y.-M. Lin, C.-Y. Chern, Y. Wang, G.-S. 2020-07-25 doi:10.1101/2020.07.24.219121 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ ZmMTOPVIB is essential for double-strand break formation and bipolar spindle assembly in maize meiosis ]]> https://biorxiv.org/content/10.1101/2020.07.28.225250v1?rss=1 Jing, J. Zhang, T. He, Y. Kao, Y.-H. Huang, T.-H. Wang, C.-J. R. 2020-07-28 doi:10.1101/2020.07.28.225250 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Species-specific phototaxis of coral larvae causes variation in vertical positioning during dispersal ]]> https://biorxiv.org/content/10.1101/2020.07.31.230235v1?rss=1 Mulla, A. J. Lin, C.-H. Takahashi, S. Nozawa, Y. 2020-08-02 doi:10.1101/2020.07.31.230235 Cold Spring Harbor Laboratory Press 2020-08-02 <![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[ 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[ Hyperpolyploidization of hepatocyte initiates preneoplastic lesion formation in the liver ]]> https://biorxiv.org/content/10.1101/2020.08.23.258699v1?rss=1 Chao, H.-W. Lin, H. Huang, Y.-S. Fustin, J.-M. Doi, M. Chen, H. Lai, H.-H. Lin, S.-H. Lee, Y.-L. King, P.-C. Hou, H.-S. Chen, H.-W. Young, P.-Y. 2020-08-24 doi:10.1101/2020.08.23.258699 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Plasmablast-derived antibody response to acute SARS-CoV-2 infection in humans ]]> https://biorxiv.org/content/10.1101/2020.08.28.267526v1?rss=1 Huang, K.-Y. A. Tan, T. Chen, T.-H. Huang, C.-G. Harvey, R. Hussain, S. Chen, C.-P. Harding, A. Gilbert-Jaramillo, J. Liu, X. Knight, M. Schimanski, L. Shih, S.-R. Lin, Y.-C. Cheng, C.-Y. Cheng, S.-H. Huang, Y.-C. Lin, T.-Y. Rahikainen, R. Howarth, M. Jan, J.-T. Ma, C. James, W. S. Daniels, R. McCauley, J. Rijal, P. Townsend, A. 2020-08-28 doi:10.1101/2020.08.28.267526 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ A Human Multi-Lineage Hepatic Organoid Model for Liver Fibrosis ]]> https://biorxiv.org/content/10.1101/2020.09.01.278473v1?rss=1 GUAN, Y. Enejder, A. Wang, M. Fang, Z. Cui, L. Chen, S.-Y. Wang, J. Tan, Y. Wu, M. Chen, X. Johansson, P. K. Osman, I. Kunimoto, K. Russo, P. Heilshorn, S. C. Peltz, G. 2020-09-02 doi:10.1101/2020.09.01.278473 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains ]]> https://biorxiv.org/content/10.1101/2020.09.03.281089v1?rss=1 Vidal-Diez de Ulzurrun, G. Lee, Y.-Y. Stajich, J. E. Schwarz, E. M. Hsueh, Y.-P. 2020-09-03 doi:10.1101/2020.09.03.281089 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Genome sequence of the oyster mushroom Pleurotus ostreatus strain PC9 ]]> https://biorxiv.org/content/10.1101/2020.09.03.281683v1?rss=1 Lee, Y.-Y. Vidal-Diez de Ulzurrun, G. Schwarz, E. M. Stajich, J. E. Hsueh, Y.-P. 2020-09-04 doi:10.1101/2020.09.03.281683 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Forward genetic screens identified mutants with defects in trap morphogenesis in the nematode-trapping fungus Arthrobotrys oligospora ]]> https://biorxiv.org/content/10.1101/2020.09.15.298422v1?rss=1 Huang, T.-Y. Lee, Y.-Y. Vidal-Diez de Ulzurrun, G. Hsueh, Y.-P. 2020-09-16 doi:10.1101/2020.09.15.298422 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ A self-assembled protein nanoparticle serving as a one-shot vaccine carrier ]]> https://biorxiv.org/content/10.1101/2020.09.16.299149v1?rss=1 Kan, M.-C. Wong, T.-T. Liou, G.-G. 2020-09-18 doi:10.1101/2020.09.16.299149 Cold Spring Harbor Laboratory Press 2020-09-18 <![CDATA[ Ultra-sensitive measurement of brain penetration mechanics and blood vessel rupture with microscale probes ]]> https://biorxiv.org/content/10.1101/2020.09.21.306498v1?rss=1 Obaid, A. Wu, Y.-W. Hanna, M.-E. Jaidar, O. Nix, W. Ding, J. B. Melosh, N. 2020-09-22 doi:10.1101/2020.09.21.306498 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ GAMYB modulates bHLH142 and is homeostatically regulated by TDR during rice anther tapetal and pollen development ]]> https://biorxiv.org/content/10.1101/2020.09.26.314641v1?rss=1 Ko, S.-S. Li, M.-J. Ho, Y.-C. Yu, C.-P. Yang, T.-T. Lin, Y.-J. Hsing, H.-C. Chen, T.-K. Jhong, C.-M. Li, W.-H. Ku, M. S.-B. 2020-09-26 doi:10.1101/2020.09.26.314641 Cold Spring Harbor Laboratory Press 2020-09-26 <![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[ South Asian patient population genetics reveal strong founder effects and high rates of homozygosity - new resources for precision medicine ]]> https://biorxiv.org/content/10.1101/2020.10.02.323238v1?rss=1 Wall, J. Sathirapongsasuti, J. F. Gupta, R. Barik, A. Rai, R. K. Rasheed, A. Radha, V. Belsare, S. Menon, R. Phalke, S. Mittal, A. Fang, J. Tanneeru, D. Robinson, J. Chaudhary, R. Fuchsberger, C. Forer, L. Schoenherr, S. Bei, Q. Bhangale, T. Tom, J. Gadde, S. G. K. V, P. B. Naik, N. K. Wang, M. Kwok, P.-Y. Khera, A. V. Lakshmi, B. R. Butterworth, A. Danesh, J. Seshagiri, S. Kathiresan, S. Ghosh, A. Mohan, V. Chowdhury, A. Saleheen, D. Stawiski, E. Peterson, A. S. 2020-10-02 doi:10.1101/2020.10.02.323238 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Genetic and metabolite biomarkers reveal actinobacteria-mediated estrogen biodegradation in urban estuarine sediment ]]> https://biorxiv.org/content/10.1101/2020.10.07.329094v1?rss=1 View larger version (93K): org.highwire.dtl.DTLVardef@17e1e23org.highwire.dtl.DTLVardef@ecc60borg.highwire.dtl.DTLVardef@be03d4org.highwire.dtl.DTLVardef@ed81d6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIsolation of an estrogen-degrading actinobacterium Rhodococcus sp. strain B50 and establishment of a strain B50 genetic manipulation system. C_LIO_LIStrain B50 exhibits a two-fold estrogen degradation rate of that of estrogen-degrading alpha-proteobacteria under the same cultivation conditions. C_LIO_LIFunctional characterization of two oxygenase genes, oecB and oecC, involved in estrogenic A-ring cleavage in actinobacteria. C_LIO_LIIdentification of two extracellular estrogenic metabolites, PEA and HIP, in the estrone-fed strain B50 cultures. C_LIO_LIDetection of actinobacterial oecC sequences as well as PEA and HIP in the estrone-spiked urban estuarine sediments. C_LI ]]> Hsiao, T.-H. Chen, Y.-L. Meng, M. Chuang, M.-R. Horinouchi, M. Hayashi, T. Wang, P.-H. Chiang, Y.-R. 2020-10-07 doi:10.1101/2020.10.07.329094 Cold Spring Harbor Laboratory Press 2020-10-07 <![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[ 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[ 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[ Feedback inhibition of AMT1 NH4+-transporters mediated by CIPK15 kinase ]]> https://biorxiv.org/content/10.1101/2020.11.03.367383v1?rss=1 Chen, H.-Y. Chen, Y.-N. Wang, H.-Y. Liu, Z.-T. Frommer, W. B. Ho, C.-H. 2020-11-04 doi:10.1101/2020.11.03.367383 Cold Spring Harbor Laboratory Press 2020-11-04 <![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[ Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells ]]> https://biorxiv.org/content/10.1101/2020.11.24.396713v1?rss=1 Swygert, S. G. Lin, D. Portillo-Ledesma, S. Lin, P.-Y. Hunt, D. R. Kao, C.-F. Schlick, T. Noble, W. S. Tsukiyama, T. 2020-11-24 doi:10.1101/2020.11.24.396713 Cold Spring Harbor Laboratory Press 2020-11-24 <![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[ A Novel SARS-CoV-2 Multitope Protein/Peptide Vaccine Candidate is Highly Immunogenic and Prevents Lung Infection in an Adeno Associated Virus Human Angiotensin-Converting Enzyme 2 (AAV hACE2) Mouse Model ]]> https://biorxiv.org/content/10.1101/2020.11.30.399154v1?rss=1 Guirakhoo, F. Kuo, L. Peng, J. Huang, J. H. Kuo, B. Lin, F. Liu, K. Liu, Z. Wu, G. Ding, S. Hou, L.-L. Cheng, J. Yang, V. Jiang, H. Wang, J. Chen, T. Xia, W. Lin, E. Hung, C. H. Chen, K. Shih, Z. Lin, Y. Schurter, B. T. Hu, M. M. Heppner, G. Malherbe, D. C. Bukreyev, A. Hellerstein, M. Monath, T. Wang, C. Y. 2020-11-30 doi:10.1101/2020.11.30.399154 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Comparative Analysis of Embryo Proper and Suspensor Transcriptomes in Plant Embryos With Different Morphologies ]]> https://biorxiv.org/content/10.1101/2020.11.30.404376v1?rss=1 Goldberg, R. Chen, M. Lin, J.-Y. Wu, X. Apuya, N. R. Henry, K. F. Le, B. H. Bui, A. Q. Pelletier, J. M. Cokus, S. Pellegrini, M. Harada, J. J. 2020-12-01 doi:10.1101/2020.11.30.404376 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ SARS-CoV-2 D614 and G614 spike variants impair neuronal synapses and exhibit differential fusion ability ]]> https://biorxiv.org/content/10.1101/2020.12.03.409763v1?rss=1 Chen, C.-Y. Chou, Y.-C. Hsueh, Y.-P. 2020-12-03 doi:10.1101/2020.12.03.409763 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Intrinsic disorder codes for leaps of protein expression ]]> https://biorxiv.org/content/10.1101/2020.12.08.407247v1?rss=1 Chuang, C.-N. Woo, T.-T. Tsai, S.-Y. Chen, C.-L. Li, W.-C. Liu, H.-C. Chen, C.-Y. Hsueh, Y.-P. Wang, T.-F. 2020-12-08 doi:10.1101/2020.12.08.407247 Cold Spring Harbor Laboratory Press 2020-12-08 <![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[ AI4AMP: Sequence-based antimicrobial peptides predictor using physicochemical properties-based encoding method and deep learning ]]> https://biorxiv.org/content/10.1101/2020.12.17.423359v1?rss=1 Lin, T.-T. Yang, L.-Y. Lu, I.-H. Cheng, W.-C. Hsu, Z.-R. Chen, S.-H. Lin, C.-Y. 2020-12-18 doi:10.1101/2020.12.17.423359 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Human Surfactant Protein D Binds S1 and Receptor Binding Domain of Spike protein and acts as an entry inhibitor of SARS-CoV-2 Pseudotyped viral particles in vitro ]]> https://biorxiv.org/content/10.1101/2020.12.18.423418v1?rss=1 Hsieh, M.-H. Beirag, N. Murugaiah, V. Chou, Y.-C. Kuo, W.-S. Kao, H.-F. Madan, T. Kishore, U. Wang, J.-Y. 2020-12-18 doi:10.1101/2020.12.18.423418 Cold Spring Harbor Laboratory Press 2020-12-18 <![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[ Population Differentiation of Rhodobacteraceae Along Coral Compartments ]]> https://biorxiv.org/content/10.1101/2020.12.31.424895v1?rss=1 Luo, H. Luo, D. Wang, X. Feng, X. Tian, M. Wang, S. Tang, S.-L. Ang, P. O. Yan, A. 2021-01-05 doi:10.1101/2020.12.31.424895 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ 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[ CpG-adjuvanted stable prefusion SARS-CoV-2 spike protein protected hamsters from SARS-CoV-2 challenge ]]> https://biorxiv.org/content/10.1101/2021.01.07.425674v1?rss=1 Lien, C.-E. Lin, Y.-J. Kuo, T.-Y. Campbell, J. D. Traquina, P. Lin, M.-Y. Liu, L. T. C. Chuang, Y.-S. Ku, H.-Y. Liao, C.-C. Chen, Y.-H. Jan, J.-T. Sun, C.-P. Lin, Y.-S. Wu, P.-Y. Wang, Y.-C. Tao, M.-H. Lin, Y.-L. 2021-01-07 doi:10.1101/2021.01.07.425674 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation ]]> https://biorxiv.org/content/10.1101/2021.01.13.426511v1?rss=1 EswarKumar, N. Yang, C.-H. Tewary, S. Yeh, Y.-Q. Yang, H.-C. Ho, M.-C. 2021-01-14 doi:10.1101/2021.01.13.426511 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ The prevalence, predominance, and metabolic potentials of Candidatus Prochlorobium terpiosii in the coral-killing sponge, Terpios hoshinota ]]> https://biorxiv.org/content/10.1101/2021.02.04.429686v1?rss=1 Chen, Y.-H. Chen, H.-J. Yang, C.-Y. Shiu, J.-H. Hoh, D. Z. Chiang, P.-W. Chow, W. S. Chen, C. A. Shih, T.-H. Lin, S.-H. Yang, C.-M. Reimer, J. D. Hirose, E. Iskandar, B. H. Huang, H. Schupp, P. J. Tan, C. H. J. Yamashiro, H. Liao, M.-H. Tang, S.-L. 2021-02-05 doi:10.1101/2021.02.04.429686 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Parasite co-opts a ubiquitin receptor to induce a plethora of developmental changes ]]> https://biorxiv.org/content/10.1101/2021.02.15.430920v1?rss=1 Huang, W. MacLean, A. Sugio, A. Maqbool, A. Busscher, M. Cho, S.-T. Kamoun, S. Kuo, C.-H. Immink, R. G. H. Hogenhout, S. A. 2021-02-15 doi:10.1101/2021.02.15.430920 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ IRONMAN Tunes Responses to Iron Deficiency in Concert with Environmental pH ]]> https://biorxiv.org/content/10.1101/2021.02.16.431461v1?rss=1 Schmidt, W. Tsai, H.-H. Gautam, C. K. 2021-02-17 doi:10.1101/2021.02.16.431461 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Sialic acid-Dependent Binding and Viral Entry of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.03.08.434228v1?rss=1 Nguyen, L. McCord, K. A. Bui, D. T. Bouwman, K. A. Kitova, E. N. Kumawat, D. Daskan, G. C. Tomris, I. Han, L. Chopra, P. Yang, T.-J. Williows, S. D. Lowary, T. L. West, L. J. Hsu, S.-T. D. Tompkins, S. M. Boons, G.-J. Mason, A. L. de Vries, R. P. Macauley, M. S. Klassen, J. S. 2021-03-08 doi:10.1101/2021.03.08.434228 Cold Spring Harbor Laboratory Press 2021-03-08 <![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[ A New Protocol for Targeted insertion using CRISPR-Cas9, Oligo Single-Stranded DNA and Protoplast Regeneration ]]> https://biorxiv.org/content/10.1101/2021.03.09.434087v1?rss=1 Hsu, C.-T. Yuan, Y.-H. Lin, Y.-C. Lin, S. Cheng, Q.-W. Wu, F.-H. Sheen, J. Shih, M.-C. Lin, C.-S. 2021-03-10 doi:10.1101/2021.03.09.434087 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies of Glycopeptide Data ]]> https://biorxiv.org/content/10.1101/2021.03.14.435332v1?rss=1 Kawahara, R. Alagesan, K. Bern, M. Cao, W. Chalkley, R. J. Cheng, K. Choo, M. S. Edwards, N. Goldman, R. Hoffmann, M. Hu, Y. Huang, Y. Kim, J. Y. Kletter, D. Liquet-Weiland, B. Liu, M. Mechref, Y. Meng, B. Neelamegham, S. Nguyen-Khuong, T. Nilsson, J. Pap, A. Park, G. W. Parker, B. L. Pegg, C. L. Penninger, J. M. Phung, T. K. Pioch, M. Rapp, E. Sakalli, E. Sanda, M. Shulz, B. L. Scott, N. E. Sofronov, G. Stadlmann, J. Vakhrushev, S. Y. Woo, C. M. Wu, H.-Y. Yang, P. Ying, W. Zhang, H. Zhang, Y. Zhao, J. Zaia, J. Haslam, S. M. Palmisano, G. Yoo, J. S 2021-03-15 doi:10.1101/2021.03.14.435332 Cold Spring Harbor Laboratory Press 2021-03-15 <![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[ A viral toolbox for conditional and transneuronal gene expression in zebrafish ]]> https://biorxiv.org/content/10.1101/2021.03.25.436574v1?rss=1 Satou, C. Neve, R. L. Oyibo, H. K. Arn Bouldoires, E. Mori, T. Higashijima, S.-i. Keller, G. B. Friedrich, R. W. 2021-03-25 doi:10.1101/2021.03.25.436574 Cold Spring Harbor Laboratory Press 2021-03-25 <![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[ Multi-omics approach to identify bacterial polyynes and unveil their antifungal mechanism against Candida albicans ]]> https://biorxiv.org/content/10.1101/2021.03.30.437786v1?rss=1 Lin, C.-C. Hoo, S. Y. Lin, C. Huang, K.-F. Ho, Y.-N. Sun, C.-H. Lee, H.-J. Chen, P.-Y. Shu, L.-J. Wang, B.-W. Hsu, W.-C. Yang, Y.-L. 2021-03-31 doi:10.1101/2021.03.30.437786 Cold Spring Harbor Laboratory Press 2021-03-31 <![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[ 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[ TIC236 gain-of-function mutations unveil the link between plastid division and plastid protein import ]]> https://biorxiv.org/content/10.1101/2021.04.25.441383v1?rss=1 Kim, C. Fang, J. Li, B. Chen, L.-J. Dogra, V. Luo, S. Wang, P. Hwang, I. Li, H.-m. 2021-04-26 doi:10.1101/2021.04.25.441383 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Ancient gene duplications, rather than polyploidization, facilitate diversification of petal pigmentation patterns in Clarkia gracilis (Onagraceae) ]]> https://biorxiv.org/content/10.1101/2021.04.26.441548v1?rss=1 Lin, R.-C. Rausher, M. D. 2021-04-27 doi:10.1101/2021.04.26.441548 Cold Spring Harbor Laboratory Press 2021-04-27 <![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[ Binocular Mirror-Symmetric Microsaccadic Sampling of Hyperacute 3D-Vision ]]> https://biorxiv.org/content/10.1101/2021.05.03.442473v1?rss=1 Kemppainen, J. Scales, B. Razban Haghighi, K. Takalo, J. Mansour, N. McManus, J. Lego, G. Saari, P. Hurcomb, J. Antohi, A. Suuronen, J.-P. Blanchard, F. Hardie, R. C. song, z. Hampton, M. Eckermann, M. Westermeier, F. Frohn, J. Hoekstra, H. Lee, C.-H. Huttula, M. Mokso, R. Juusola, M. 2021-05-04 doi:10.1101/2021.05.03.442473 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Sex-biased response to and brain cell infection by SARS-CoV-2 in a highly susceptible human ACE2 transgenic model ]]> https://biorxiv.org/content/10.1101/2021.05.04.441029v1?rss=1 Tsai, C.-Y. Chou, Y.-C. Chen, C.-Y. Jan, J.-T. Chang, M.-L. Lu, L.-A. Huang, P.-Y. Hsu, T.-T. Hsueh, Y.-P. 2021-05-04 doi:10.1101/2021.05.04.441029 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Complete and high-quality genomes of novel microbial species from a meromictic lake using a workflow combining long- and short-read sequencing platforms ]]> https://biorxiv.org/content/10.1101/2021.05.07.443067v1?rss=1 Chen, Y.-H. Chiang, P.-W. Rogozin, D. Y. Degermendzhy, A. G. Chiu, H.-H. Tang, S.-L. 2021-05-07 doi:10.1101/2021.05.07.443067 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations ]]> https://biorxiv.org/content/10.1101/2021.05.11.443686v1?rss=1 Yang, T.-J. Yu, P.-Y. Chang, Y.-C. Liang, K.-H. Tso, H.-C. Ho, M.-R. Chen, W.-Y. Lin, H.-T. Wu, H.-C. Hsu, S.-T. D. 2021-05-12 doi:10.1101/2021.05.11.443686 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Species boundaries in the Agrobacterium tumefaciens complex and multi-level modular evolution of their antibacterial type VI secretion system and tumor-inducing plasmids ]]> https://biorxiv.org/content/10.1101/2021.05.20.444927v1?rss=1 Chou, L. Lin, Y.-C. Haryono, M. Santos, M. N. M. Cho, S.-T. Weisberg, A. J. Wu, C.-F. Chang, J. H. Lai, E.-M. Kuo, C.-H. 2021-05-21 doi:10.1101/2021.05.20.444927 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Biomechanics and Myofibrillar Alignment Enhance Contractile Development and Reproducibility in Stem Cell Derived Cardiac Muscle ]]> https://biorxiv.org/content/10.1101/2021.05.23.445330v1?rss=1 Tsan, Y.-C. Zhao, Y.-T. DePalma, S. J. Capilnasiu, A. Wu, Y.-W. Elder, B. Panse, I. Friedline, S. O'Leary, T. S. Wubshet, N. Ho, K. K. Y. Previs, M. J. Nordsletten, D. Baker, B. M. Isom, L. L. Liu, A. P. Helms, A. S. 2021-05-23 doi:10.1101/2021.05.23.445330 Cold Spring Harbor Laboratory Press 2021-05-23 <![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[ 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[ Chromatin enrichment for Proteomics in Plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling ]]> https://biorxiv.org/content/10.1101/2021.06.02.446857v1?rss=1 Velez-Bermudez, I. C. Schmidt, W. 2021-06-03 doi:10.1101/2021.06.02.446857 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ A new method to identify global targets of RNA-binding proteins in plants ]]> https://biorxiv.org/content/10.1101/2021.06.11.448000v1?rss=1 Cheng, Y.-L. Hsieh, H.-Y. Tu, S.-L. 2021-06-11 doi:10.1101/2021.06.11.448000 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.06.14.448173v1?rss=1 Chang, P. Hsieh, H.-Y. Tu, S.-L. 2021-06-14 doi:10.1101/2021.06.14.448173 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Carbohydrate sulfation as a mechanism for fine-tuning Siglec ligands ]]> https://biorxiv.org/content/10.1101/2021.06.27.450109v1?rss=1 Jung, J. Enterina, J. R. Bui, D. T. Mozaneh, F. Lin, P.-H. Nitin, H. Kuo, C.-W. Rodrigues, E. Bhattacherjee, A. Raeisimakiani, P. Daskhan, G. C. St. Laurent, C. D. Khoo, K.-H. Mahal, L. K. Zandberg, W. F. Huang, X. Klassen, J. S. Macauley, M. S. 2021-06-28 doi:10.1101/2021.06.27.450109 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Rapid synaptic plasticity contributes to a learned conjunctive code of position and choice-related information in the hippocampus ]]> https://biorxiv.org/content/10.1101/2021.06.30.450574v1?rss=1 Spruston, N. Zhao, X. Hsu, C.-L. 2021-06-30 doi:10.1101/2021.06.30.450574 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ A cell-sorting-based nano-scale pipeline for cell-type-specific proteomics in plants ]]> https://biorxiv.org/content/10.1101/2021.07.06.451220v1?rss=1 Wang, H. Li, R. Rong, J. Sang, T. Kim, C. Song, C.-P. Dai, S. Hsu, C.-C. Wang, P. 2021-07-08 doi:10.1101/2021.07.06.451220 Cold Spring Harbor Laboratory Press 2021-07-08 <![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[ 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[ Pharmacokinetics and biodistribution of extracellular vesicles administered intravenously and intranasally to Macaca nemestrina ]]> https://biorxiv.org/content/10.1101/2021.07.28.454192v1?rss=1 Driedonks, T. Jiang, L. Carlson, B. Han, Z. Liu, G. Queen, S. E. Shirk, E. N. Gololobova, O. Nyberg, L. Lima, G. Schonvisky, K. Stover, M. Guerrero-Martin, S. Richardson, M. R. Smith, B. Lai, C. P. Izzi, J. M. Hutchinson, E. K. Pate, K. A. Witwer, K. W. 2021-07-29 doi:10.1101/2021.07.28.454192 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Vaccinia virus-based vaccines confer protective immunity against SARS-CoV-2 virus in Syrian hamsters ]]> https://biorxiv.org/content/10.1101/2021.08.03.454910v1?rss=1 Kulkarni, R. Chen, W.-C. Lee, Y. Kao, C.-F. Hu, S.-L. Ma, H.-H. Jan, J.-T. Liao, C.-C. Liang, J.-J. Ko, H.-Y. Sun, C.-P. Lin, Y.-S. Wang, Y.-C. Wei, S.-C. Lin, Y.-L. Ma, C. Chao, Y.-C. Chou, Y.-C. Chang, W. 2021-08-03 doi:10.1101/2021.08.03.454910 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Identification of a developmental switch in information transfer between whisker S1 and S2 cortex in mice ]]> https://biorxiv.org/content/10.1101/2021.08.06.455364v1?rss=1 Karayannis, T. Cai, L. Yang, J.-W. Chou, S.-J. Wang, C.-F. Luhmann, H. J. 2021-08-08 doi:10.1101/2021.08.06.455364 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ BioSANS: A Software Package for Symbolic and Numeric Biological Simulation ]]> https://biorxiv.org/content/10.1101/2021.08.17.456661v1?rss=1 Fajiculay, E. Hsu, C.-P. 2021-08-17 doi:10.1101/2021.08.17.456661 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states ]]> https://biorxiv.org/content/10.1101/2021.08.18.456372v1?rss=1 0.8 and p-value < 0.01), many DELs were co-regulated with DEGs after mating. Furthermore, several remarkable lncRNAs (MSTRG.6523, MSTRG.588, and nc909) that were found to associate with particular coding genes may play important roles in the regulation of brain gene expression in reproductive transition in fire ants. ConclusionThis study provides the first genome-wide identification of S. invicta lncRNAs in the brains in different reproductive states and will contribute to a fuller understanding of the transcriptional regulation underpinning reproductive changes. ]]> Tsai, C.-H. Lin, T.-C. Tsai, H.-K. Chang, Y.-H. Huang, J.-H. 2021-08-18 doi:10.1101/2021.08.18.456372 Cold Spring Harbor Laboratory Press 2021-08-18 <![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[ Genomically hardwired regulation of gene activity orchestrates cellular iron homeostasis in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.09.01.458651v1?rss=1 Hsieh, E.-J. Lin, W. Schmidt, W. 2021-09-02 doi:10.1101/2021.09.01.458651 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis ]]> https://biorxiv.org/content/10.1101/2021.09.02.458763v1?rss=1 Zhang, R. Kuo, R. Coulter, M. Calixto, C. P. G. Entizne, J. C. Guo, W. Marquez, Y. Milne, L. Riegler, S. Matsui, A. Tanaka, M. Harvey, S. Yubang, G. Wiebner-Kroh, T. Crespi, M. Denby, K. Hur, A. b. Huq, E. Jantsch, M. F. Jarmolowski, A. Koester, T. Laubinger, S. Li, Q. Q. Gu, L. Seki, M. Staiger, D. Sunkar, R. Szweykowska-Kulinska, Z. Tu, S.-L. Wachter, A. Waugh, R. Xiong, L. Zhang, X.-N. Reddy, A. S. N. Barta, A. Kalyna, M. Brown, J. W. 2021-09-03 doi:10.1101/2021.09.02.458763 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Comparative genomics of three Colletotrichum scovillei strains and genetic analysis revealed genes involved in fungal growth and virulence on chili pepper ]]> https://biorxiv.org/content/10.1101/2021.09.06.459084v1?rss=1 Hsieh, D.-K. Chuang, S.-C. Chen, C.-Y. Chao, Y.-T. Lu, M.-Y. J. Shih, M.-C. Lee, M.-H. 2021-09-06 doi:10.1101/2021.09.06.459084 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories ]]> https://biorxiv.org/content/10.1101/2021.09.07.459046v1?rss=1 Lee, T. J. Liu, Y.-C. Liu, W.-A. Lin, Y.-F. Lee, H.-H. Ke, H.-M. Huang, J.-P. Lu, M.-Y. J. Hsieh, C.-L. Chung, K.-F. Liti, G. Tsai, I. J. 2021-09-08 doi:10.1101/2021.09.07.459046 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ GABOLA: A Reliable Gap-Filling Strategy for de novo Chromosome-Level Assembly ]]> https://biorxiv.org/content/10.1101/2021.09.07.459217v1?rss=1 Chuang, W.-H. Cheng, H.-C. Chang, Y.-J. Fu, P.-Y. Huang, Y.-C. Hsieh, P.-H. Chen, S.-H. Lin, C.-Y. Ho, J.-M. 2021-09-08 doi:10.1101/2021.09.07.459217 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Phosphatidylglycerol synthesis facilitates plastid gene expression and light induction of nuclear photosynthetic genes ]]> https://biorxiv.org/content/10.1101/2021.09.08.459525v1?rss=1 Fujii, S. Kobayashi, K. Lin, Y.-C. Liu, Y.-c. Nakamura, Y. Wada, H. 2021-09-10 doi:10.1101/2021.09.08.459525 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Comparative Genome Analysis of 'Candidatus Phytoplasma luffae' Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution ]]> https://biorxiv.org/content/10.1101/2021.09.09.459700v1?rss=1 Huang, C.-T. Cho, S.-T. Tan, C.-M. Chiu, Y.-C. Yang, J.-Y. Kuo, C.-H. 2021-09-11 doi:10.1101/2021.09.09.459700 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[ Response of Endozoicomonas montiporae to heat stress and coral host lysates ]]> https://biorxiv.org/content/10.1101/2021.09.27.461970v1?rss=1 Chan, Y. Chen, C.-Y. Lu, C.-Y. Tu, Y.-C. Tandon, K. Shikina, S. Tang, S.-L. 2021-09-27 doi:10.1101/2021.09.27.461970 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ The helper NLR immune protein NRC3 mediates the hypersensitive cell death caused by the cell-surface receptor Cf-4 ]]> https://biorxiv.org/content/10.1101/2021.09.28.461843v1?rss=1 Kourelis, J. Contreras, M. P. Harant, A. Adachi, H. Derevnina, L. Wu, C.-H. Kamoun, S. 2021-09-28 doi:10.1101/2021.09.28.461843 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Single-cell transcriptomic analysis unveils spinal motor neuron subtype diversity underpinning the water-to-land transition in vertebrates ]]> https://biorxiv.org/content/10.1101/2021.09.29.462340v1?rss=1 Liau, E. S. Jin, S. Chen, Y.-C. Liu, W.-S. Yong, L. W. Tsai, C.-T. Calon, M. Yu, J.-K. Su, Y.-H. Nedelec, S. Nie, Q. Chen, J.-A. 2021-09-30 doi:10.1101/2021.09.29.462340 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Exploration of deep-learning based classification with human SNP image graphs ]]> https://biorxiv.org/content/10.1101/2021.10.01.462710v1?rss=1 Chen, C.-H. Tung, K.-F. Lin, W.-c. 2021-10-01 doi:10.1101/2021.10.01.462710 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Allometric scaling of RNA abundance from genes to communities ]]> https://biorxiv.org/content/10.1101/2021.10.03.462954v1?rss=1 Lopez, M. L. D. Lin, Y.-y. Schneider, S. Q. Machida, R. J. 2021-10-04 doi:10.1101/2021.10.03.462954 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Spatial differences in stoichiometry of EGR phosphatase and Microtubule-Associated Stress Protein 1 control root meristem activity during drought stress. ]]> https://biorxiv.org/content/10.1101/2021.10.06.463370v1?rss=1 Longkumer, T. Chen, C.-Y. Biancucci, M. Badiger, B. G. Verslues, P. E. 2021-10-07 doi:10.1101/2021.10.06.463370 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Development of transcriptomics-based eukaryotes growth rate indices ]]> https://biorxiv.org/content/10.1101/2021.10.08.463626v1?rss=1 Kong, W.-L. Machida, R. J. 2021-10-09 doi:10.1101/2021.10.08.463626 Cold Spring Harbor Laboratory Press 2021-10-09 <![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[ 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[ 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[ Cancer malignancy is correlated with up-regulation of PCYT2-mediated glycerol phosphate modification of α-dystroglycan ]]> https://biorxiv.org/content/10.1101/2021.10.25.465649v1?rss=1 Umezawa, F. Natsume, M. Fukusada, S. Nakajima, K. Yamasaki, F. Kawashima, H. Kuo, C.-W. Khoo, K.-H. Shimura, T. Yagi, H. Kato, K. 2021-10-25 doi:10.1101/2021.10.25.465649 Cold Spring Harbor Laboratory Press 2021-10-25 <![CDATA[ Prevalent sex ratio bias in Caenorhabditis nematodes ]]> https://biorxiv.org/content/10.1101/2021.10.26.465869v1?rss=1 Lo, Y.-H. Huang, Y. Le, T. S. Hsu, J.-C. Yang, F.-J. Chang, T. Braendle, C. Wang, J. 2021-10-26 doi:10.1101/2021.10.26.465869 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Microbiome restructuring: dominant coral bacterium Endozoicomonas species display differential adaptive capabilities to environmental changes ]]> https://biorxiv.org/content/10.1101/2021.10.31.466697v1?rss=1 Tandon, K. Chiou, Y.-J. Yu, S.-P. Hsieh, H. J. Lu, C.-Y. Hsu, M.-T. Chiang, P.-W. Chen, H.-J. Wada, N. Tang, S.-L. 2021-11-01 doi:10.1101/2021.10.31.466697 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Maize AFP1 confers antifungal activity by inhibiting chitin deacetylases from a broad range of fungi ]]> https://biorxiv.org/content/10.1101/2021.11.02.466889v1?rss=1 Ma, L.-S. Tsai, W.-L. Kalunke, R. M. Xu, M.-Y. Lin, Y.-H. Damei, F. A. Lee, H.-C. 2021-11-02 doi:10.1101/2021.11.02.466889 Cold Spring Harbor Laboratory Press 2021-11-02 <![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[ Thymic macrophages consist of two populations with distinct localization and origin ]]> https://biorxiv.org/content/10.1101/2021.11.04.467238v1?rss=1 Zhou, T.-A. Hsu, H.-P. Tu, Y.-H. Lin, C.-Y. Chen, N.-J. Tsai, J.-W. Robey, E. A. Huang, H.-C. Hsu, C.-L. Dzhagalov, I. L. 2021-11-04 doi:10.1101/2021.11.04.467238 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ An atypical NLR protein modulates the NRC immune receptor network ]]> https://biorxiv.org/content/10.1101/2021.11.15.468391v1?rss=1 Adachi, H. Sakai, T. Harant, A. Duggan, C. Bozkurt, T. Wu, C.-H. Kamoun, S. 2021-11-15 doi:10.1101/2021.11.15.468391 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Electrochemical biosensors based on peptide-kinase interactions at the kinase docking site ]]> https://biorxiv.org/content/10.1101/2021.11.16.468793v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@277550org.highwire.dtl.DTLVardef@870467org.highwire.dtl.DTLVardef@32098aorg.highwire.dtl.DTLVardef@1104840_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Joshi, P. N. Mervinetsky, E. Solomon, O. Chen, Y.-J. Yitzchaik, S. Friedler, A. 2021-11-16 doi:10.1101/2021.11.16.468793 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Laser Ablation and Fluid Flows Show a Single Force Mechanism Governs Spindle Positioning ]]> https://biorxiv.org/content/10.1101/2021.11.21.469320v1?rss=1 Wu, H.-Y. Kabacaoglu, G. Nazockdast, E. Chang, H.-C. Shelley, M. J. Needleman, D. J. 2021-11-22 doi:10.1101/2021.11.21.469320 Cold Spring Harbor Laboratory Press 2021-11-22 <![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[ A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ]]> https://biorxiv.org/content/10.1101/2021.12.07.470215v1?rss=1 Ramdas, S. Judd, J. Graham, S. E. Kanoni, S. Wang, Y. Surakka, I. Wenz, B. Clarke, S. L. Chesi, A. Wells, A. Bhatti, K. F. Vedantam, S. Winkler, T. W. Locke, A. E. Marouli, E. Zajac, G. J. Wu, K.-H. H. Ntalla, I. Hui, Q. Klarin, D. Hilliard, A. T. Wang, Z. Xue, C. Thorleifsson, G. Helgadottir, A. Gudbjartsson, D. F. Holm, H. Olafsson, I. Hwang, M. Y. Han, S. Akiyama, M. Sakaue, S. Terao, C. Kanai, M. Zhou, W. Brumpton, B. M. Rasheed, H. Havulinna, A. S. Veturi, Y. Pacheco, J. A. Rosenthal, E. A. Lingren, T. Feng, Q. Kullo, I. J. Narita, A. Takayama, 2021-12-08 doi:10.1101/2021.12.07.470215 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ BSImp: imputing partially observed methylation patterns for evaluating methylation heterogeneity ]]> https://biorxiv.org/content/10.1101/2021.12.07.471020v1?rss=1 Chang, Y.-T. Yen, M.-R. Chen, P.-Y. 2021-12-09 doi:10.1101/2021.12.07.471020 Cold Spring Harbor Laboratory Press 2021-12-09 <![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[ NITROGEN LIMITATION ADAPTATION functions as a negative regulator of Arabidopsis immunity ]]> https://biorxiv.org/content/10.1101/2021.12.09.471910v1?rss=1 Val Torregrosa, B. Bundo, M. Chiou, T. J. Flors, V. San Segundo, B. 2021-12-10 doi:10.1101/2021.12.09.471910 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Phosphate-induced resistance to pathogen infection in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.12.09.471930v1?rss=1 Val Torregrosa, B. Bundo, M. Cardoso, H. M. Pages, M. B. Chiou, T. J. Flors, V. San Segundo, B. 2021-12-09 doi:10.1101/2021.12.09.471930 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Analysis of single-cell RNA-sequencing data to identify quiescent and proliferating neural cell populations in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2021.12.09.472030v1?rss=1 Vikram, R. Chou, W.-C. Wu, P.-E. Chen, W.-T. Shen, C.-Y. 2021-12-10 doi:10.1101/2021.12.09.472030 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Nanoscale details of mitochondrial fission revealed by cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2021.12.13.472487v1?rss=1 Mageswaran, S. K. Grotjahn, D. A. Zeng, X. Barad, B. A. Medina, M. A. Hoang, M. H. Dobro, M. J. Chang, Y.-W. Xu, M. Yang, W. Y. Jensen, G. J. 2021-12-14 doi:10.1101/2021.12.13.472487 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Genomes of keystone Mortierella species lead to better in silico prediction of soil mycobiome functions from Taiwan's offshore islands ]]> https://biorxiv.org/content/10.1101/2021.12.20.473467v1?rss=1 Lin, Y.-f. Liu, W.-A. Liu, Y.-C. Lee, H.-H. Lin, Y.-J. Chang, E.-H. Lu, M.-Y. J. Chiu, C.-Y. Tsai, I. J. 2021-12-21 doi:10.1101/2021.12.20.473467 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ The role of the angular gyrus in semantic cognition - A synthesis of five functional neuroimaging studies ]]> https://biorxiv.org/content/10.1101/2021.12.21.473704v1?rss=1 Kuhnke, P. Chapman, C. A. Cheung, V. K. M. Turker, S. Graessner, A. Martin, S. Williams, K. A. Hartwigsen, G. 2021-12-23 doi:10.1101/2021.12.21.473704 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ HSFA1 proteins mediate heat-induced accumulation of CPT7-derived polyprenols affecting thylakoid organization ]]> https://biorxiv.org/content/10.1101/2021.12.22.473876v1?rss=1 Buszewicz, D. Kowalewska, Łucja M. Mazur, R. Zajbt-Łuczniewska, M. Surmacz, L. Sosnowska, K. Welc, R. Jemioła-Rzeminska, M. Link-Lenczowski, P. Onysk, A. Skorupinska-Tudek, K. Liu, H.-C. Charng, Y.-Y. Archacki, R. Gruszecki, W. I. Swiezewska, E. 2021-12-24 doi:10.1101/2021.12.22.473876 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution ]]> https://biorxiv.org/content/10.1101/2021.12.23.474023v1?rss=1 Panibe, J. P. Wang, L. Lee, Y.-C. Wang, C.-S. Li, W.-H. 2021-12-24 doi:10.1101/2021.12.23.474023 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Chromatin state transition underlies the temporal changes in gene expression during cardiomyocyte maturation ]]> https://biorxiv.org/content/10.1101/2021.12.28.474318v1?rss=1 Lin, C.-Y. Chang, Y.-M. Tseng, H.-Y. Shih, Y.-L. Yeh, H.-H. Chen, P.-L. Chen, C.-C. Yan, Y.-T. Kao, C.-F. 2021-12-28 doi:10.1101/2021.12.28.474318 Cold Spring Harbor Laboratory Press 2021-12-28 <![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[ Optogenetic Manipulation of Cell Migration with High Spatiotemporal Resolution Using Lattice Lightsheet Microscopy ]]> https://biorxiv.org/content/10.1101/2022.01.02.474058v1?rss=1 Tang, W.-C. Liu, Y.-T. Yeh, C.-H. Lin, Y.-L. Lin, Y.-C. Hsu, T.-L. Gao, L. Chang, S.-W. Chen, P. Chen, B.-C. 2022-01-02 doi:10.1101/2022.01.02.474058 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Three amphioxus reference genomes reveal gene and chromosome evolution of chordates ]]> https://biorxiv.org/content/10.1101/2022.01.04.475009v1?rss=1 Zhen, H. Xu, L. Cai, C. Zhou, Y. Liu, J. Zhu, Z. Kang, W. Chen, D. Pei, S. Xue, T. Cen, W. Shi, C. Wu, X. Huang, Y. Xu, C. Yan, Y. Yang, Y. He, W. Hu, X. Zhang, Y. Chen, Y. Bi, C. He, C. Xue, L. Xiao, S. Yue, Z. Jiang, Y. Yu, J.-K. Jarvis, E. Li, G. Lin, G. Zhang, Q. Zhou, Q. 2022-01-05 doi:10.1101/2022.01.04.475009 Cold Spring Harbor Laboratory Press 2022-01-05 <![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[ New insights on the role of HCN in root hair elongation through single cell proteomics ]]> https://biorxiv.org/content/10.1101/2022.01.05.475094v1?rss=1 Garcia, I. Arenas-Alfonseca, L. Romero, L. C. Yamada, M. 2022-01-07 doi:10.1101/2022.01.05.475094 Cold Spring Harbor Laboratory Press 2022-01-07 <![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[ 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[ CLEC5A and TLR2 are critical in SARS-CoV-2-induced NET formation and lung inflammation ]]> https://biorxiv.org/content/10.1101/2022.02.01.478701v1?rss=1 Sung, P.-S. Yang, S.-P. Peng, Y.-C. Sun, C.-P. Tao, M.-H. Hsieh, S.-L. 2022-02-02 doi:10.1101/2022.02.01.478701 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Canonical Wnt signaling promotes formation of somatic permeability barrier for proper germ cell differentiation ]]> https://biorxiv.org/content/10.1101/2022.02.15.480616v1?rss=1 Chen, T.-A. Lin, K.-Y. Yang, S.-M. Tseng, C.-Y. Wang, Y.-T. Lin, C.-H. Luo, L. Cai, Y. Hsu, H.-J. 2022-02-16 doi:10.1101/2022.02.15.480616 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ FAM21 is critical for TLR2-CLEC4E-mediated dendritic cell function against Candida albicans ]]> https://biorxiv.org/content/10.1101/2022.02.16.480635v1?rss=1 Kulkarni, R. Kasani, S. K. Tsai, C.-Y. Tung, S.-Y. Yeh, K.-H. Yu, C.-H. A. Chang, W. 2022-02-17 doi:10.1101/2022.02.16.480635 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ The multi-level regulation of clownfish metamorphosis by thyroid hormones ]]> https://biorxiv.org/content/10.1101/2022.03.04.482938v1?rss=1 Roux, N. Miura, S. Dussene, M. Tara, Y. Lee, S. h. de Bernard, S. Reynaud, M. Salis, P. Barua, A. Boulahtouf, A. Balaguer, P. Gauthier, K. Lecchini, D. Gibert, Y. Besseau, L. Laudet, V. C. 2022-03-04 doi:10.1101/2022.03.04.482938 Cold Spring Harbor Laboratory Press 2022-03-04 <![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[ BMAL1 and MEX3A co-regulate intestinal stem cell succession ]]> https://biorxiv.org/content/10.1101/2022.03.08.483537v1?rss=1 Chang, F.-P. Wang, C.-K. Chou, Y.-C. Chen, T.-J. Wu, Y.-W. Sridharan, S. Hsu, P.-H. Hwang-Verslues, W. W. 2022-03-10 doi:10.1101/2022.03.08.483537 Cold Spring Harbor Laboratory Press 2022-03-10 <![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[ 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[ 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[ Nucleic Acid Adductomics - the Next Generation of Adductomics for Assessing Environmental Health Risk ]]> https://biorxiv.org/content/10.1101/2022.03.24.485617v1?rss=1 Cooke, M. S. Chang, Y.-J. Chen, Y.-R. Hu, C.-W. Chao, M.-R. 2022-03-28 doi:10.1101/2022.03.24.485617 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum ]]> https://biorxiv.org/content/10.1101/2022.03.24.485721v1?rss=1 De Vivo, M. Lee, H.-H. Huang, Y.-H. Drever, N. Fong, C.-l. de Mattos, F. M. G. Jain, D. Wen, Y.-H. V. Mwihaki, J. K. Wang, T.-Y. Machida, R. J. Wang, J. Chan, B. K. K. Tsai, I. J. 2022-03-27 doi:10.1101/2022.03.24.485721 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Natural variation identifies new effectors of water use efficiency in Arabidopsis. ]]> https://biorxiv.org/content/10.1101/2022.03.28.486113v1?rss=1 Badiger, B. G. Lasky, J. R. Razzaque, S. Zhang, L. Haque, T. Bonnette, J. E. Civelek, G. Z. Verslues, P. E. Juenger, T. E. 2022-03-29 doi:10.1101/2022.03.28.486113 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Orphan nuclear receptors promote alternative lengthening of telomeres (ALT) through ALT-associated PML bodies ]]> https://biorxiv.org/content/10.1101/2022.03.30.485724v1?rss=1 Gaela, V. M. A. Hsia, H.-Y. Boudier, T. Chen, L.-Y. 2022-03-30 doi:10.1101/2022.03.30.485724 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Subtyping of major SARS-CoV-2 variants reveals different transmission dynamics ]]> https://biorxiv.org/content/10.1101/2022.04.10.486823v1?rss=1 Yang, H.-C. Wang, J.-H. Yang, C.-T. Lin, Y.-C. Hsieh, H.-N. Chen, P.-W. Liao, H.-C. Chen, C.-h. Liao, J. C. 2022-04-11 doi:10.1101/2022.04.10.486823 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics ]]> https://biorxiv.org/content/10.1101/2022.04.12.488038v1?rss=1 3,000 (>9,500) phosphopeptides from 1 (10) {micro}g of cell lysate using the label-free method without a spectral library. It also enabled precise quantification of [~]600 phosphopeptides from 100 cells sorted by FACS (single-cell level input for the enriched phosphopeptides) and [~]700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 {micro}m (equivalent to [~]100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level. ]]> Tsai, C.-F. Wang, Y.-T. Hsu, C.-C. Kitata, R. B. Chu, R. K. Velickovic, M. Zhao, R. Williams, S. M. Chrisler, W. B. Jorgensen, M. L. Moore, R. J. Zhu, Y. Rodland, K. D. Smith, R. D. Wasserfall, C. H. Shi, T. Liu, T. 2022-04-12 doi:10.1101/2022.04.12.488038 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Systems Biology Approach of Understanding Insulin Resistance: Linkage between Type 2 Diabetes and Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.04.13.463890v1?rss=1 Lao, A. R. Villasis, O. B. T. Tan, D. S. Mendoza, E. 2022-04-15 doi:10.1101/2022.04.13.463890 Cold Spring Harbor Laboratory Press 2022-04-15 <![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[ An Efficient Approach for SARS-CoV-2 Monoclonal Antibody Production via Modified mRNA-LNP Immunization ]]> https://biorxiv.org/content/10.1101/2022.04.20.488878v1?rss=1 Hsu, F.-F. Liang, K.-H. Kumari, M. Chen, W. Y. Lin, H. T. Cheng, C. M. Tao, M.-H. Wu, H.-C. 2022-04-22 doi:10.1101/2022.04.20.488878 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Adaptive plasticity in the healthy reading network investigated through combined neurostimulation and neuroimaging ]]> https://biorxiv.org/content/10.1101/2022.04.20.488885v1?rss=1 Turker, S. Kuhnke, P. Schmid, F. R. Cheung, V. K. M. Zeidler, B. Seidel, K. Eckert, L. Hartwigsen, G. 2022-04-21 doi:10.1101/2022.04.20.488885 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis ]]> https://biorxiv.org/content/10.1101/2022.04.21.488980v1?rss=1 Ma, Q. Yang, L. Tolentino, K. Zhao, Y. Lizenburger, U. M. Shi, Q. Zhu, L. Tsai, M.-C. Chen, J.-A. Lai, I. Zeng, H. Li, L. Chang, H. 2022-04-22 doi:10.1101/2022.04.21.488980 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Detecting intragenic trans-splicing events with hybrid transcriptome sequencing in cancer cells ]]> https://biorxiv.org/content/10.1101/2022.04.21.489006v1?rss=1 Chen, Y.-C. Chen, C.-Y. Chiang, T.-W. Chan, M.-H. Hsiao, M. Ke, H.-M. Tsai, I. J. Chuang, T.-J. 2022-04-22 doi:10.1101/2022.04.21.489006 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ The association between working memory precision and the nonlinear dynamics of frontal and parieto-occipital EEG activity. ]]> https://biorxiv.org/content/10.1101/2022.04.24.489284v1?rss=1 Chang, W.-S. Liang, W.-K. Li, D.-H. Muggleton, N. G. Balachandran, P. Huang, N. E. Juan, C.-H. 2022-04-25 doi:10.1101/2022.04.24.489284 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Sensor NLR immune proteins activate oligomerization of their NRC helper ]]> https://biorxiv.org/content/10.1101/2022.04.25.489342v1?rss=1 Contreras, M. P. Pai, H. Tumtas, Y. Duggan, C. Yuen, E. L. H. Vergara Cruces, A. Kourelis, J. Ahn, H.-K. Wu, C.-H. Bozkurt, T. O. Derevnina, L. Kamoun, S. 2022-04-25 doi:10.1101/2022.04.25.489342 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Divergence of trafficking and polarity mechanisms for PIN auxin transporters during land plant evolution ]]> https://biorxiv.org/content/10.1101/2022.04.28.489888v1?rss=1 Tang, H. Lu, K.-J. Cheng, Y.-L. Tu, S.-L. Friml, J. 2022-04-30 doi:10.1101/2022.04.28.489888 Cold Spring Harbor Laboratory Press 2022-04-30 <![CDATA[ Manufacturing highly potent CD20/CD19-targeted iCasp9 regulatable CAR-T cells using the Quantum pBac-based CAR-T (qCART) system for clinical application ]]> https://biorxiv.org/content/10.1101/2022.05.03.490475v1?rss=1 50% of CAR19-treated patients experienced progressive disease mainly due to antigen escape and low persistence. Clinical prognosis is heavily influenced by CAR-T cell function and systemic cytokine toxicities. Furthermore, it remains a challenge to efficiently, cost-effectively, and consistently manufacture clinically relevant number of virally engineered CAR-T cells. MethodsUsing a highly efficient piggyBac transposon-based vector, Quantum pBac, we developed a virus-free cell engineering system, Quantum CART (qCART), for development and production of multiplex CAR-T therapies. ResultsHere, we demonstrated in vitro and in vivo that consistent, robust, and functional CD20/CD19 dual-targeted CAR-T stem cell memory (TSCM) cells can be efficiently manufactured using the qCART system for clinical application. qCART-manufactured CAR-T cells from cancer patients expanded efficiently, rapidly eradicated tumors, and can be safely controlled via an iCasp9 suicide gene-inducing drug. ConclusionsThe qCART system is an elegant system for the manufacturing of CAR-T products having all the desired CAR-T therapy attributes. We believe that the simplicity of manufacturing multiplex CAR-T cells using the qCART system will not only significantly enhance the accessibility of CAR-T therapy but also unlock the full potential of armored CAR-T therapy for the treatment of solid tumors in the future. What is already known on this topicDespite the considerable success which has been achieved with CD19-targeted chimeric antigen receptor therapies (CAR19), >50% of CAR19-treated patients still experienced progressive disease. Therefore, there is a need to further improve CAR19 therapies. Current CAR19 therapies commonly utilize virus-based cell engineering methods. CAR-T production using these methods face multiple hurdles, including difficulties to efficiently, cost-effectively, and consistently manufacture clinically relevant number of CAR-T cells. We have previously used a highly efficient piggyBac transposon-based vector, Quantum pBac, to establish Quantum CART (qCART) which is a virus-free cell engineering system for development and production of multiplex CAR-T therapies. What this study addsIn this report, we further demonstrate in vitro and in vivo that consistent, robust, and functional iCasp9-regulatable, CD20/CD19 dual-targeted CAR-T stem cell memory (TSCM) cells can be efficiently manufactured using the qCART system for clinical application. These cells possess all the desired attributes for ensuring therapeutic efficacy in CAR-T therapy, including high CAR-TSCM, balanced CD8/CD4 ratio, low exhaustion and senescence marker expressions, and high ex vivo and in vivo expansion capacity. Importantly, we show that qCART-manufactured CAR-T cells from hematological cancer patients expanded efficiently, effectively eradicated tumors, and can be safely controlled via an iCasp9 suicide gene-inducing drug. We believe that the simplicity of manufacturing multiplex CAR-T cells using the qCART system will not only significantly enhance the accessibility of CAR-T therapy but also unlock the full potential of armored CAR-T therapy for the treatment of solid tumors in the future. How this study might affect research, practice or policyOur findings demonstrate that qCART is a virus-free CAR-T engineering system for manufacturing CAR-TSCM cells from either healthy donors or hematological cancer patients, that possess all the desired attributes for a successful CAR-T therapy. These cells expanded efficiently, rapidly eradicated tumors, and can be safely controlled via activation of iCasp9. We expect that this simple yet robust system for manufacturing multiplex CAR-T cells will advance the CAR-T field. ]]> Chen, Y.-C. Chang, P. S. Hua, W.-K. Hsu, J. C. Tsai, J.-C. Huang, Y.-W. Kao, Y.-H. Wu, P.-H. Chang, Y.-F. Chang, M. C. Chang, Y. C. Wen, K.-L. K. Wu, S. C.-Y. 2022-05-04 doi:10.1101/2022.05.03.490475 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[ The histone variant H2A.W cooperates with chromatin modifications and linker histone H1 to maintain transcriptional silencing of transposons in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.05.31.493688v1?rss=1 Bourguet, P. Yelagandula, R. To, T. K. Osakabe, A. Alishe, A. Lu, R. J.-H. Kakutani, T. Chen, P.-Y. Berger, F. 2022-05-31 doi:10.1101/2022.05.31.493688 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ ECM-derived biophysical cues mediate interstitial flow-induced sprouting angiogenesis ]]> https://biorxiv.org/content/10.1101/2022.06.04.494804v1?rss=1 Chang, C.-W. Shih, H.-C. Cortes-Medina, M. Beshay, P. E. Avendano, A. Seibel, A. J. Liao, W.-H. Tung, Y.-C. Song, J. W. 2022-06-05 doi:10.1101/2022.06.04.494804 Cold Spring Harbor Laboratory Press 2022-06-05 <![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[ Insights into deuterostome evolution from the biphasic transcriptional programmes of hemichordates ]]> https://biorxiv.org/content/10.1101/2022.06.10.495707v1?rss=1 Perez-Posada, A. Lin, C.-Y. Lin, C.-Y. Chen, Y.-C. Gomez-Skarmeta, J. L. Yu, J.-K. Su, Y.-H. Tena, J. J. 2022-06-12 doi:10.1101/2022.06.10.495707 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Rapid compensatory evolution by secondary perturbation of a primary disrupted transcriptional network ]]> https://biorxiv.org/content/10.1101/2022.06.15.496250v1?rss=1 Hsu, P.-C. Cheng, Y.-H. Liao, C.-W. Jhou, Y.-T. Opoc, F. J. G. Amine, A. A. A. Leu, J.-Y. 2022-06-16 doi:10.1101/2022.06.15.496250 Cold Spring Harbor Laboratory Press 2022-06-16 <![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[ A glycine zipper motif governs translocation of type VI secretion toxic effectors across the cytoplasmic membrane of target cells ]]> https://biorxiv.org/content/10.1101/2022.07.12.499750v1?rss=1 Ali, J. Yu, M. Sung, L.-K. Cheung, Y. W. Lai, E.-M. 2022-07-13 doi:10.1101/2022.07.12.499750 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA ]]> https://biorxiv.org/content/10.1101/2022.07.20.500760v1?rss=1 Lou, Y.-C. Huang, H.-Y. Yeh, H.-H. Chiang, W.-H. Chen, C. Wu, K.-P. 2022-07-21 doi:10.1101/2022.07.20.500760 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[ Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop--Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan ]]> https://biorxiv.org/content/10.1101/2022.07.28.501534v1?rss=1 Chuang, C.-R. Hsieh, C.-L. Chang, C.-S. Wang, C.-M. Tandang, D. N. Gardner, E. M. Audi, L. Zerega, N. J. C. Chung, K.-F. 2022-07-30 doi:10.1101/2022.07.28.501534 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ Central visceral commands formatted as the slow rhythms encoded in the temporal structures of the sympathetic firing originated from the neonatal rat spinal cord in vitro ]]> https://biorxiv.org/content/10.1101/2022.08.01.502255v1?rss=1 1. Along the time course, the dynamic components of Lv (dLv) displayed quasiperiodic oscillations. Continuous wavelet analysis showed that dLv oscillations registered a dominant power rhythm at [~]7 mHz. This slow rhythmicity was heterogeneously altered by application of various antagonists that interrupted endogenous neurotransmitter activities mediated by ionotropic glutamate receptors or GABAA receptors in the spinal cord. Thus, the oscillation of dLv manifested itself as a feature of neural network operation. On the assumption that the total power of the dLv oscillations reflects an activity status of neural network operation, the antagonist-induced change of the power fits well with a concomitant ISI change in a negative sigmoid relationship, which explains the heterogeneity of the antagonist-induced firing responses. In conclusion, dLv oscillations reflect a dynamic status of neural network operation. The slow rhythms embedded in the dLv oscillations are likely acting as an information coder and convey effective central visceral commands that can be followed by their downstream effectors. Author summaryIn what format the information is encoded by the neural activity is relatively unknown. This is especially true for autonomic regulation of visceral functions. We seek to determine the format of the central sympathetic commands, by which it can generate an effective driving force to regulate the operation of their peripheral target organs. Because most visceral organs operate with certain rhythms, we anticipate that the central visceral commands are also formatted in rhythms. Two aspects of techniques were employed. One was the in vitro electrophysiological and pharmacological techniques to acquire and to manipulate the neural signals recorded from sympathetic single-fibers. The other was the computational techniques to extract the information embedded in the timing of the spiking behaviors and to examine how these features were altered by pharmacological manipulations. We found a spontaneous change of sympathetic spiking patterns displaying rhythms with a frequency that could match the rhythmic operation of many visceral organs. Thus, the meaningful information carried by the sympathetic neural circuits for the visceral controls is likely to be encoded in the dynamics of their spiking patterns. In summary, a dynamic change of neural spiking patterns could be used as a simple scheme for neural information coding. ]]> Su, C.-K. Ho, C.-M. 2022-08-03 doi:10.1101/2022.08.01.502255 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Pregnenolone reorganizes cytoskeleton to promote neuron development via CLIP1 ]]> https://biorxiv.org/content/10.1101/2022.08.01.502406v1?rss=1 Kolas, V. Wu, Y.-T. Bandonil, J. Chung, B.-c. 2022-08-03 doi:10.1101/2022.08.01.502406 Cold Spring Harbor Laboratory Press 2022-08-03 <![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[ lncRNA HOTAIRM1 Coordinates with RNA Processing Factors in DNA Damage Repair ]]> https://biorxiv.org/content/10.1101/2022.08.13.503833v1?rss=1 Chuang, T.-W. Wu, P.-Y. Chang, Y.-M. Tarn, W.-Y. 2022-08-13 doi:10.1101/2022.08.13.503833 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Cryo-EM reveals the structure and dynamics of a 723-residue malate synthase G ]]> https://biorxiv.org/content/10.1101/2022.08.19.504428v1?rss=1 Ho, M.-R. Wu, Y.-M. Lu, Y.-C. Ko, T.-P. Wu, K.-P. 2022-08-19 doi:10.1101/2022.08.19.504428 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Structural analyses of the plant PRT6-UBR box in the Cys-Arg/N-degron pathway and insights into the plant submergence response ]]> https://biorxiv.org/content/10.1101/2022.08.19.504472v1?rss=1 Kim, L. Lin, C.-C. Lin, T.-J. Cao, Y.-C. Chen, M.-C. Chou, M.-Y. Lin, W.-H. Kim, M. Wu, J.-L. Shih, M.-C. Song, H. K. Ho, M.-C. 2022-08-19 doi:10.1101/2022.08.19.504472 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ In vivo visualization of nitrate dynamics using a genetically encoded biosensor ]]> https://biorxiv.org/content/10.1101/2022.08.29.505680v1?rss=1 Chen, Y.-N. Cartwright, H. N. Ho, C.-H. 2022-08-29 doi:10.1101/2022.08.29.505680 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ The Aphelenchoides genomes reveal major events of horizontal gene transfers in clade IV nematodes ]]> https://biorxiv.org/content/10.1101/2022.09.13.507733v1?rss=1 Lai, C.-K. Lee, Y. Ke, H.-M. Lu, M. R. Liu, W.-A. Lee, H.-H. Liu, Y.-C. Yoshiga, T. Kikuchi, T. Chen, P. J. Tsai, I. J. 2022-09-15 doi:10.1101/2022.09.13.507733 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Membrane Protein Modification Modulates Big and Small Extracellular Vesicle Biodistribution and Tumorigenic Potential in Breast Cancers In Vivo ]]> https://biorxiv.org/content/10.1101/2022.09.28.510006v1?rss=1 200 nm, microvesicles) are less well explored. Here, we identify bEVs and sEVs as distinct EV populations, and determine that bEVs are released in a greater bEV:sEV ratio in the aggressive human triple-negative breast cancer (TNBC) subtype. PalmGRET, bioluminescence resonance energy transfer (BRET)-based EV reporter, reveals dose- dependent EV biodistribution at non-lethal and physiological EV dosages, as compared to lipophilic fluorescent dyes. Remarkably, the bEVs and sEVs exhibit unique biodistribution profiles, et individually promote in vivo tumor growth in a syngeneic immunocompetent TNBC breast tumor murine model. The bEVs and sEVs share mass spectrometry (MS)- identified tumor progression-associated EV surface membrane proteins (tpEVSurfMEMs), which include SLC29A1, CD9 and CD44. tpEVSurfMEM depletion attenuates EV lung organotropism, alters biodistribution, and reduces protumorigenic potential. This study identifies distinct in vivo property and function of bEVs and sEVs in breast cancer, which suggest the significant role of bEVs in diseases, diagnostic and therapeutic applications. ]]> Magoling, B. J. A. Chen, Y.-J. Wu, A. Y.-T. Wong, W. W.-T. Chuo, S. T.-Y. Huang, H.-C. Sung, Y.-C. Hsieh, H.-T. Huang, P. Lee, K.-Z. Huang, K.-W. Chen, R.-H. Chen, Y. Lai, C. P. 2022-09-30 doi:10.1101/2022.09.28.510006 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Microbial mat compositions and localization patterns explain the virulence of black band disease in corals ]]> https://biorxiv.org/content/10.1101/2022.10.04.510905v1?rss=1 Wada, N. Iguchi, A. Urabe, Y. Yoshioka, Y. Abe, N. Takase, K. Hayashi, S. Kawanabe, S. Sato, Y. Tang, S.-L. Mano, N. 2022-10-05 doi:10.1101/2022.10.04.510905 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ The lectin receptor Clec4F participates in the capture of circulating parasite mucins by Kupffer cells in cystic echinococcosis. ]]> https://biorxiv.org/content/10.1101/2022.10.06.511139v1?rss=1 Barrios, A. A. Mouhape, C. Schreiber, L. Nell, J. Suarez-Martins, M. Schlapp, G. Meikle, M. N. Mulet, A. P. Hsu, T.-L. Hsieh, S.-L. Mourglia-Ettlin, G. Gonzalez, C. Crispo, M. Barth, T. F. E. Casaravilla, C. Jenkins, S. J. Diaz, A. 2022-10-07 doi:10.1101/2022.10.06.511139 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Allee effects mediate the impact of land-use change on the thermal niche of social species ]]> https://biorxiv.org/content/10.1101/2022.10.11.511768v1?rss=1 Chan, S.-F. Rubenstein, D. R. Wang, T.-W. Chen, Y.-Y. Chen, I.-C. Ni, D.-Z. Shih, W.-K. Shen, S.-F. 2022-10-14 doi:10.1101/2022.10.11.511768 Cold Spring Harbor Laboratory Press 2022-10-14 <![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[ Daily turnover of active giant virus infection during algal blooms revealed by single-cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.10.15.512338v1?rss=1 Hevroni, G. Vincent, F. J. Ku, C. Sheyn, U. Vardi, A. 2022-10-15 doi:10.1101/2022.10.15.512338 Cold Spring Harbor Laboratory Press 2022-10-15 <![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[ Assessing the impacts of various factors related to identification, conservation, biogenesis, and function on circular RNA reliability ]]> https://biorxiv.org/content/10.1101/2022.10.28.514164v1?rss=1 full-length circular sequences > supporting BSJ read count > both BSJ donor and acceptor splice sites at the same co-linear transcript isoforms > both BSJ donor and acceptor splice sites at the annotated exon boundaries > BSJs detected by multiple tools > supporting functional features > both BSJ donor and acceptor splice sites undergoing alternative splicing. By extracting RT-independent circRNAs, circRNAs passing multiple experimental validations, and database-specific circRNAs, we showed the additive effects of these important factors in determining circRNA reliability. This study thus provides a useful guideline and an important resource for selecting high-confidence circRNAs for further investigations. ]]> Chuang, T.-J. Chiang, T.-W. Chen, C.-Y. 2022-10-28 doi:10.1101/2022.10.28.514164 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ The antibacterial T6SS of Agrobacterium tumefacien promotes disease occurrence and influences crown gall microbiota composition ]]> https://biorxiv.org/content/10.1101/2022.10.28.514271v1?rss=1 Wang, S.-C. Chen, A.-P. Chou, S.-J. Kuo, C. H. Lai, E.-M. 2022-10-30 doi:10.1101/2022.10.28.514271 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Megacolonies: an alternative social organization in anemonefishes? ]]> https://biorxiv.org/content/10.1101/2022.11.06.515354v1?rss=1 Mercader, M. Zwahlen, J. Hayashi, K. Takamiyagi, H. Tseng, Y.-C. Nguyen, H.-T. Asada, K. Sowinski, J. Rimer, J. Lecchini, D. Laudet, V. 2022-11-07 doi:10.1101/2022.11.06.515354 Cold Spring Harbor Laboratory Press 2022-11-07 <![CDATA[ Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen ]]> https://biorxiv.org/content/10.1101/2022.11.10.515791v1?rss=1 Sahu, N. Indjic, B. Wong-Bajracharya, J. Merenyi, Z. Ke, H.-M. Ahrendt, S. Monk, T.-L. Kocsube, S. Drula, E. Lipzen, A. Balint, B. Henrissat, B. Andreopoulos, B. Martin, F. M. Harder, C. B. Rigling, D. Ford, K. L. Foster, G. D. Pangilinan, J. Papanicolaou, A. Barry, K. LaButti, K. Viragh, M. Koriabine, M. Yan, M. Riley, R. Champramary, S. Plett, K. L. Grigoriev, I. V. Tsai, I. J. Slot, J. Sipos, G. Plett, J. Nagy, L. G. 2022-11-13 doi:10.1101/2022.11.10.515791 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ RE2DC: a robust and efficient 2D classifier with visualization for processing massive and heterogeneous cryo-EM data ]]> https://biorxiv.org/content/10.1101/2022.11.21.517443v1?rss=1 Chung, S.-C. Lin, H.-H. Wu, K.-P. Chen, T.-L. Chang, W.-H. Tu, I.-P. 2022-11-24 doi:10.1101/2022.11.21.517443 Cold Spring Harbor Laboratory Press 2022-11-24 <![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[ 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[ Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision ]]> https://biorxiv.org/content/10.1101/2022.12.06.519083v1?rss=1 Vromman, M. Anckaert, J. Bortoluzzi, S. Buratin, A. Chen, C.-Y. Chu, Q. Chuang, T.-J. Dehghannasiri, R. Dieterich, C. Dong, X. Flicek, P. Gaffo, E. Gu, W. He, C. Hoffmann, S. Izuogu, O. Jackson, M. S. Jakobi, T. Lai, E. C. Nuytens, J. Salzman, J. Santibanez-Koref, M. Stadler, P. Thas, O. Vanden Eynde, E. Verniers, K. Wen, G. Westholm, J. Yang, L. Ye, C.-Y. Yigit, N. Yuan, G.-H. Zhang, J. Zhao, F. Vandesompele, J. Volders, P.-J. 2022-12-06 doi:10.1101/2022.12.06.519083 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ 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[ SARM1 detection in oligodendrocytes but not Schwann cells though sarm1/Sarm1 deletion does not perturb CNS nor PNS myelination in zebrafish and mice. ]]> https://biorxiv.org/content/10.1101/2022.12.08.519209v1?rss=1 Fazal, S. V. Mutschler, C. Chen, C. Turmaine, M. Chen, C.-Y. Hsueh, Y.-P. Loreto, A. Casillas-Bajo, A. Cabedo, H. Franklin, R. J. Barker, R. A. Monk, K. Steventon, B. Coleman, M. Gomez-Sanchez, J. A. Arthur-Farraj, P. 2022-12-09 doi:10.1101/2022.12.08.519209 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Resurrection of plant disease resistance proteins via helper NLR bioengineering ]]> https://biorxiv.org/content/10.1101/2022.12.11.519957v1?rss=1 Contreras, M. P. Pai, H. Selvaraj, M. Toghani, A. Lawson, D. M. Tumtas, Y. Duggan, C. Yuen, E. L. H. Stevenson, C. E. M. Harant, A. Wu, C.-H. Bozkurt, T. O. Kamoun, S. Derevnina, L. 2022-12-11 doi:10.1101/2022.12.11.519957 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Alkalinity modulates a unique suite of genes to recalibrate growth and pH homeostasis ]]> https://biorxiv.org/content/10.1101/2022.12.12.520164v1?rss=1 Bailey, M. Hsieh, E.-J. Tsai, H.-H. Ravindran, A. Schmidt, W. 2022-12-14 doi:10.1101/2022.12.12.520164 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ A GFP splicing reporter in a coilin mutant background reveals links between alternative splicing, siRNAs and coilin function in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2022.12.18.520953v1?rss=1 Matzke, M. Matzke, A. Kanno, T. K. Wu, M.-T. L. Chiou, P. Lin, W. 2022-12-19 doi:10.1101/2022.12.18.520953 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Hybrid-DIA: Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids ]]> https://biorxiv.org/content/10.1101/2022.12.19.520999v1?rss=1 Martinez del Val, A. Fort, K. Koenig, C. van der Hoeven, L. R. Franciosa, G. Moehring, T. Ishihama, Y. Chen, Y.-J. Makarov, A. A. Xuan, Y. Olsen, J. V. 2022-12-20 doi:10.1101/2022.12.19.520999 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Is there an accurate and generalisable way to use soundscapes to monitor biodiversity? ]]> https://biorxiv.org/content/10.1101/2022.12.19.521085v1?rss=1 Sethi, S. S. Bick, A. Ewers, R. M. Klinck, H. Ramesh, V. Tuanmu, M.-N. Coomes, D. A. 2022-12-20 doi:10.1101/2022.12.19.521085 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ A thermally stable protein nanoparticle that stimulates long lasting humoral immune response ]]> https://biorxiv.org/content/10.1101/2022.12.30.522068v1?rss=1 Wong, T.-T. Liou, G.-G. Kan, M.-C. 2022-12-30 doi:10.1101/2022.12.30.522068 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Widespread distribution and evolution of poxviral entry-fusion complex proteins in giant viruses ]]> https://biorxiv.org/content/10.1101/2023.01.19.524718v1?rss=1 Kao, S. Kao, C.-F. Chang, W. Ku, C. 2023-01-19 doi:10.1101/2023.01.19.524718 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Sensory diversity and precise adaptation enable independent bet-hedging strategies for multiple signals at the same time ]]> https://biorxiv.org/content/10.1101/2023.02.08.527720v1?rss=1 Moore, J. P. Kamino, K. Kottou, R. Shimizu, T. S. Emonet, T. 2023-02-09 doi:10.1101/2023.02.08.527720 Cold Spring Harbor Laboratory Press 2023-02-09 <![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[ The thermostability of a VADEX-Pro based protein nanoparticle ]]> https://biorxiv.org/content/10.1101/2023.02.15.528623v1?rss=1 Kan, M.-C. 2023-02-15 doi:10.1101/2023.02.15.528623 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha) ]]> https://biorxiv.org/content/10.1101/2023.02.21.529467v1?rss=1 De Vivo, M. Chen, W.-Y. Huang, J.-P. 2023-02-22 doi:10.1101/2023.02.21.529467 Cold Spring Harbor Laboratory Press 2023-02-22 <![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[ Adjuvant Effects of Amphipathic Helical Peptides ]]> https://biorxiv.org/content/10.1101/2023.03.13.532490v1?rss=1 Kan, M.-C. Liou, G.-G. Lyu, J.-H. Wang, M. 2023-03-15 doi:10.1101/2023.03.13.532490 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Engineering Nanomolar Potent Protein-based Inhibitors for Papain-like Protease Guided by Residue Correlation Network ]]> https://biorxiv.org/content/10.1101/2023.03.15.532709v1?rss=1 Huang, T. I. Hsieh, Y.-J. Lu, W.-L. Wu, K.-P. Chang, C.-e. 2023-03-15 doi:10.1101/2023.03.15.532709 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Protein Phosphorylation Orchestrates Acclimations of Arabidopsis Plants to Environmental pH ]]> https://biorxiv.org/content/10.1101/2023.03.19.533375v1?rss=1 Jain, D. Schmidt, W. 2023-03-20 doi:10.1101/2023.03.19.533375 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Expansion microscopy with trypsin digestion and tyramide signal amplification (TT-ExM) for protein and lipid staining ]]> https://biorxiv.org/content/10.1101/2023.03.20.533392v1?rss=1 Wang, U.-T. T. Tian, X. Liou, Y.-H. Lee, S.-P. Lu, C.-H. Chen, P. Chen, B.-C. 2023-03-21 doi:10.1101/2023.03.20.533392 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Two classes of His-Me finger superfamily nuclease effectors exerting synergy for Agrobacterium T6SS-mediated interbacterial competition ]]> https://biorxiv.org/content/10.1101/2023.03.20.533438v1?rss=1 Santos, M. N. M. Pintor, K. L. Hsieh, P.-Y. Cheung, Y.-W. Sung, L.-K. Shih, Y.-L. Lai, E.-M. 2023-03-20 doi:10.1101/2023.03.20.533438 Cold Spring Harbor Laboratory Press 2023-03-20 <![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[ Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning ]]> https://biorxiv.org/content/10.1101/2023.04.09.536141v1?rss=1 Lin, T.-C. Tsai, C.-H. Shiau, C.-K. Huang, J.-H. Tsai, H.-K. 2023-04-09 doi:10.1101/2023.04.09.536141 Cold Spring Harbor Laboratory Press 2023-04-09 <![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[ Single worm long read sequencing reveals genome diversity in free-living nematodes ]]> https://biorxiv.org/content/10.1101/2023.04.17.537128v1?rss=1 Lee, Y.-C. Lee, H.-H. Ke, H.-M. Liu, Y.-C. Wang, M.-C. Tseng, Y.-C. Kikuchi, T. Tsai, I. J. 2023-04-18 doi:10.1101/2023.04.17.537128 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ AHL10 phosphorylation determines RRP6L1 chromatin association and growth suppression during water stress. ]]> https://biorxiv.org/content/10.1101/2023.04.17.537135v1?rss=1 Wong, M. M. Huang, X.-J. Bau, Y.-C. Verslues, P. 2023-04-18 doi:10.1101/2023.04.17.537135 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Hematopoietic Transfer of the Anti-Cancer and Lifespan-Extending Capabilities of A Genetically Engineered Blood System ]]> https://biorxiv.org/content/10.1101/2023.04.21.537849v1?rss=1 Wang, J.-P. Hung, C.-H. Liou, Y.-H. Liu, C.-C. Yeh, K.-H. Wang, K.-Y. Lai, Z.-S. Hsu, T.-C. Lee, T.-L. Shyu, Y.-C. Hsiao, P.-W. Chen, L.-Y. Chuang, T.-J. Yu, C.-H. A. Liao, N.-S. Shen, C.-K. J. 2023-04-21 doi:10.1101/2023.04.21.537849 Cold Spring Harbor Laboratory Press 2023-04-21 <![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[ Tight junctions regulate lumen morphology via hydrostatic pressure and junctional tension ]]> https://biorxiv.org/content/10.1101/2023.05.23.541893v1?rss=1 Mukenhirn, M. Wang, C.-H. Guyomar, T. Bovyn, M. J. Staddon, M. F. Maraspini, R. Lu, L. Martin-Lemaitre, C. Sano, M. Hiraiwa, T. Riveline, D. Honigmann, A. 2023-05-23 doi:10.1101/2023.05.23.541893 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii ]]> https://biorxiv.org/content/10.1101/2023.05.26.542455v1?rss=1 Pare, L. Bideau, L. Baduel, L. Dalle, C. Benchouaia, M. Schneider, S. Q. Laplane, L. Clement, Y. Vervoort, M. Gazave, E. 2023-05-26 doi:10.1101/2023.05.26.542455 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ OICNet: A Neural Network for Online EEG Source Separation using Independent Component Analysis ]]> https://biorxiv.org/content/10.1101/2023.05.29.542778v1?rss=1 Yeh, P.-T. Tsai, A. C. Hsieh, C.-Y. Yang, C.-C. Wei, C.-S. 2023-06-01 doi:10.1101/2023.05.29.542778 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Structural and functional analysis of vaccinia viral fusion complex component protein A28 through NMR and molecular dynamic simulations ]]> https://biorxiv.org/content/10.1101/2023.06.22.546044v1?rss=1 Kao, C.-F. Tsai, M.-H. Carillo, K. J. Tzou, D.-L. Chang, W. 2023-06-22 doi:10.1101/2023.06.22.546044 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ polo affects cell fate upon ionizing radiation in Drosophila hematopoietic progenitors by negatively regulating lok ]]> https://biorxiv.org/content/10.1101/2023.06.22.546047v1?rss=1 Nguyen, T. T. N. Shim, J. Chen, G.-C. Song, Y.-H. 2023-06-22 doi:10.1101/2023.06.22.546047 Cold Spring Harbor Laboratory Press 2023-06-22 <![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[ The receptor binding domain of SARS-CoV-2 spike protein fused with the type IIb E. coli heat-labile enterotoxin A subunit as an intranasal booster after mRNA vaccination ]]> https://biorxiv.org/content/10.1101/2023.07.05.547781v1?rss=1 Hsieh, H.-C. Chen, C.-C. Chou, P.-H. Liu, W.-C. Wu, S.-C. 2023-07-05 doi:10.1101/2023.07.05.547781 Cold Spring Harbor Laboratory Press 2023-07-05 <![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[ Tbr1 autism mouse model displays altered structural and functional amygdalar connectivity and abnormal whole-brain synchronization ]]> https://biorxiv.org/content/10.1101/2023.07.14.548970v1?rss=1 Hsu, T.-T. Wang, C.-Y. Hsueh, Y.-P. 2023-07-14 doi:10.1101/2023.07.14.548970 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[ Transcriptome and translatome comparison of tissues from Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2023.07.22.550136v1?rss=1 Velez-Bermudez, I. C. Lin, W.-D. Chou, S.-J. Chen, A.-P. Schmidt, W. 2023-07-25 doi:10.1101/2023.07.22.550136 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Overcoming the nutritional immunity by engineering iron scavenging bacteria for cancer therapy ]]> https://biorxiv.org/content/10.1101/2023.07.25.550605v1?rss=1 Huang, S.-W. Lim, S.-K. Yu, Y.-A. Lien, W.-J. Mou, K. Y. 2023-07-27 doi:10.1101/2023.07.25.550605 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Growth-dependent concentration gradient of the oscillating Min system in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.08.01.551406v1?rss=1 Parada, C. Yan, C.-C. Hung, C.-Y. Tu, I.-P. Hsu, C.-P. Shih, Y.-L. 2023-08-02 doi:10.1101/2023.08.01.551406 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ The interplay between lumen pressure and cell proliferation determines organoid morphology in a multicellular phase field model ]]> https://biorxiv.org/content/10.1101/2023.08.17.553655v1?rss=1 Tanida, S. Fuji, K. Lu, L. Guyomar, T. Lee, B. H. Honigmann, A. Grapin-Botton, A. Riveline, D. Nonomura, M. Sano, M. Hiraiwa, T. 2023-08-18 doi:10.1101/2023.08.17.553655 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Insights into RAG evolution from the identification of "missing link" family A RAGL transposons ]]> https://biorxiv.org/content/10.1101/2023.08.20.553239v1?rss=1 Martin, E. C. Le Targa, L. Tsakou-Ngouafo, L. Fan, T.-P. Lin, C.-Y. Xiao, J. Su, Y.-H. Petrescu, A.-J. Pontarotti, P. Schatz, D. G. 2023-08-20 doi:10.1101/2023.08.20.553239 Cold Spring Harbor Laboratory Press 2023-08-20 <![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[ Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest ]]> https://biorxiv.org/content/10.1101/210641v1?rss=1 Thomas, D. Vandegrift, R. Ju, Y.-M. Hsieh, H. M. Roy, B. A. 2017-10-28 doi:10.1101/210641 Cold Spring Harbor Laboratory Press 2017-10-28 <![CDATA[ Intraflagellar transport proteins undergo nonaxonemal staged hindrance between the recruiting distal appendages and the cilium ]]> https://biorxiv.org/content/10.1101/227587v1?rss=1 Yang, T. Tran, M. N. T. Chong, W. M. Huang, C.-E. Liao, J.-C. 2017-12-01 doi:10.1101/227587 Cold Spring Harbor Laboratory Press 2017-12-01 <![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[ UniLoc: A universal protein localization site predictor for eukaryotes and prokaryotes ]]> https://biorxiv.org/content/10.1101/252916v1?rss=1 Lin, H.-N. Chen, C.-T. Sung, T.-Y. Hsu, W.-L. 2018-01-25 doi:10.1101/252916 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Targeting redox regulatory site of protein kinase B impedes neutrophilic inflammation ]]> https://biorxiv.org/content/10.1101/264184v1?rss=1 Hwang, T.-L. Chen, P.-J. Ko, I.-L. Lee, C.-L. Hu, H.-C. Chang, F.-R. Wu, Y.-C. Leu, Y.-L. Wu, C.-C. Tsai, Y.-F. Lin, C.-Y. Pan, C.-Y. 2018-02-13 doi:10.1101/264184 Cold Spring Harbor Laboratory Press 2018-02-13 <![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[ A dengue monovalent vaccine with novel structure provides cross-protection against four serotypes of dengue virus ]]> https://biorxiv.org/content/10.1101/275685v1?rss=1 Chao, D.-Y. Shen, W.-F. Galula, J. U. Liu, J.-H. Liao, M.- Y. Huang, C.-H. Wang, Y.-C. Wu, H.-C. Liang, J.-J. Lin, Y.- L. Whitney, M. T. Chang, G.-J. J. Chen, S.-R. Wu, S.-R. 2018-03-05 doi:10.1101/275685 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Human Puf-A, a Novel Component of 90S Pre-ribosome, Links Ribosome Biogenesis to Cancer Progression ]]> https://biorxiv.org/content/10.1101/281857v1?rss=1 Yu, J. Cho, H.-C. Huang, Y. Hung, J.-T. Lai, L.-C. Wang, S.-H. Liu, Y.-H. Cho, I.-M. Kuo, M.-W. Cheng, P.-Y. Ho, M.-Y. Lin, R.-J. Yu, A. L. 2018-03-13 doi:10.1101/281857 Cold Spring Harbor Laboratory Press 2018-03-13 <![CDATA[ The Organization of Membranes Below 100 nm: Experimental Breakthroughs Occasion a Modeling Manifesto ]]> https://biorxiv.org/content/10.1101/292383v1?rss=1 Lyman, E. Eggeling, C. Hsieh, C.-L. 2018-03-31 doi:10.1101/292383 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ A Con Artist: Phenylphenoxybenzamide is not a Glycosyltransferase Inhibitor ]]> https://biorxiv.org/content/10.1101/292912v1?rss=1 Wybenga, G. G. Wu, W.-S. 2018-04-11 doi:10.1101/292912 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Programmed Variations of Cytokinesis Contribute to Morphogenesis in the C. elegans embryo ]]> https://biorxiv.org/content/10.1101/319657v1?rss=1 Bai, X. Lee, P.-Y. Chen, C.-Y. Simmons, J. R. Nebenfuehr, B. Mitchell, D. Klebanow, L. R. Mattson, N. Turpin, C. Chen, B.-C. Betzig, E. Bembenek, J. N. 2018-05-10 doi:10.1101/319657 Cold Spring Harbor Laboratory Press 2018-05-10 <![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[ Pristionchus nematodes occur frequently in diverse rotting vegetal substrates and are not exclusively necromenic, while Panagrellus redivivoides is found specifically in rotting fruits ]]> https://biorxiv.org/content/10.1101/324996v1?rss=1 Felix, M.-A. Ailion, M. Hsu, J.-C. Richaud, A. Wang, J. 2018-05-18 doi:10.1101/324996 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ RBPMetaDB: A comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins ]]> https://biorxiv.org/content/10.1101/326116v1?rss=1 Li, J. Deng, S.-P. Vieira, J. Thomas, J. Costa, V. Tseng, C.-S. Ivankovic, F. Ciccodicola, A. Yu, P. 2018-05-18 doi:10.1101/326116 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation ]]> https://biorxiv.org/content/10.1101/332569v1?rss=1 Wu, C.-C. Klaesson, A. Buskas, J. Ranefall, P. Mirzazadeh, R. Söderberg, O. Wolf, J. B. W. 2018-05-28 doi:10.1101/332569 Cold Spring Harbor Laboratory Press 2018-05-28 <![CDATA[ Targeting BMI1 and MCL1 for Lung Adenocarcinoma Treatment ]]> https://biorxiv.org/content/10.1101/344275v1?rss=1 Lin, E.-H. Hsu, C.-F. Jan, Y.-H. Lin, T.-H. Chang, H.-Y. Cheng, C.-M. Hsu, H.-J. Chen, W.-W. Chen, B.-H. Tsai, H.-F. Li, J.-J. Huang, C.-Y. Chuang, S.-H. Chang, J.-M. Hsiao, M. Wu, C.-W. 2018-06-12 doi:10.1101/344275 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ IRON MAN, a ubiquitous family of peptides that control iron transport in plants ]]> https://biorxiv.org/content/10.1101/351635v1?rss=1 Grillet, L. Lan, P. Li, W. Mokkapati, G. Schmidt, W. 2018-06-20 doi:10.1101/351635 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ An epitope-resurfaced virus-like particle can induce broad neutralizing antibody against four serotypes of dengue virus ]]> https://biorxiv.org/content/10.1101/351700v1?rss=1 Shen, W.-F. Galula, J. U. Liu, J.-H. Liao, M.-Y. Huang, C.-H. Wang, Y.-C. Wu, H.-C. Liang, J.-J. Lin, Y.-L. Whitney, M. T. Chang, G.-J. J. Chen, S.-R. Wu, S.-R. Chao, D.-Y. 2018-06-20 doi:10.1101/351700 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Long-term blooming filamentous calcareous alga provides substrate for other coral-competitive macroalgae in the degraded lagoon of Dongsha Atoll (Pratas), Taiwan ]]> https://biorxiv.org/content/10.1101/363796v1?rss=1 Nieder, C. Chen, C. A. Liu, S.-L. 2018-07-06 doi:10.1101/363796 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course ]]> https://biorxiv.org/content/10.1101/369892v1?rss=1 Ly, S. Kaun, K. Li, C.-h. Stewart, D. Pulver, S. R. Keene, A. C. 2018-07-16 doi:10.1101/369892 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution ]]> https://biorxiv.org/content/10.1101/371112v1?rss=1 Chaw, S.-M. Liu, Y.-C. Wang, H.-Y. Wu, Y.-W. Lin, C.-Y. I. Wu, C.-S. Ke, H.-M. Chang, L.-Y. Hsu, C.-Y. Yang, H.-T. Sudianto, E. Hsu, M.-H. Wu, K.-P. Wang, N.-N. Leebens-Mack, J. Tsai, I. J. J. 2018-07-18 doi:10.1101/371112 Cold Spring Harbor Laboratory Press 2018-07-18 <![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[ Modelling bistable tumour population dynamics to design effective treatment strategies ]]> https://biorxiv.org/content/10.1101/381418v1?rss=1 Akhmetzhanov, A. R. Kim, J. W. Sullivan, R. Beckman, R. A. Tamayo, P. Yeang, C.-H. 2018-07-31 doi:10.1101/381418 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ The borders of cis-regulatory DNA sequences harbor the divergent transcription factor binding motifs in the human genome ]]> https://biorxiv.org/content/10.1101/383182v1?rss=1 Huang, J.-H. Kwan, R. S.-Y. Tsai, Z. T.-Y. Tsai, H.-K. 2018-08-02 doi:10.1101/383182 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ A Chemically-triggered Transition from Conflict to Cooperation in Burying Beetles ]]> https://biorxiv.org/content/10.1101/389163v1?rss=1 Chen, B.-F. Liu, M. Rubenstein, D. R. Sun, S.-J. Liu, J.-N. Lin, Y.-H. Shen, S.-F. 2018-08-09 doi:10.1101/389163 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ A single-cell level and connectome-derived computational model of the Drosophila brain ]]> https://biorxiv.org/content/10.1101/391474v1?rss=1 Huang, Y.-C. Wang, C.-T. Su, T.-S. Kao, K.-W. Lin, Y.-J. Chiang, A.-S. Lo, C.-C. 2018-08-14 doi:10.1101/391474 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ Enlarged and highly repetitive plastome of Lagarostrobos and plastid phylogenomics of Podocarpaceae ]]> https://biorxiv.org/content/10.1101/392357v1?rss=1 Sudianto, E. Wu, C.-S. Leonhard, L. Martin, W. F. Chaw, S.-M. 2018-08-16 doi:10.1101/392357 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Karyopherin Kap114p regulates TATA-binding protein-mediated transcription ]]> https://biorxiv.org/content/10.1101/411223v1?rss=1 Liao, C.-C. Shankar, S. Ahmed, G. R. Hsia, K.-C. 2018-09-07 doi:10.1101/411223 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Phosphoproteomics of Highly ABA-Induced1 identifies AT Hook Like10 phosphorylation required for growth regulation during stress ]]> https://biorxiv.org/content/10.1101/413013v1?rss=1 Wong, M. M. Bhaskara, G. B. Wen, T.-N. Lin, W.-D. Nguyen, T. T. Chong, G. L. Verslues, P. 2018-09-10 doi:10.1101/413013 Cold Spring Harbor Laboratory Press 2018-09-10 <![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[ Altered Gene Regulatory Networks are Associated with the Transition from C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae) ]]> https://biorxiv.org/content/10.1101/431460v1?rss=1 Heyduk, K. Hwang, M. Albert, V. Silvera, K. Lan, T. Winter, K. Leebens-Mack, J. 2018-10-02 doi:10.1101/431460 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Transcriptional dynamics following freezing stress reveal selection for mechanisms of freeze tolerance at the poleward range margin in the cold water intertidal barnacle Semibalanus balanoides ]]> https://biorxiv.org/content/10.1101/449330v1?rss=1 Marshall, K. E. Dowle, E. J. Petrunina, A. Kolbasov, G. Chan, B. K. K. 2018-10-24 doi:10.1101/449330 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Visualization of axonal protein allocation in Drosophila with whole brain localization microscopy ]]> https://biorxiv.org/content/10.1101/454942v1?rss=1 Chu, L.-A. Lu, C.-H. Yang, S.-M. Feng, K.-L. Liu, Y.-T. Chen, C.-C. Tsai, Y.-C. Chen, P. Lee, T.-K. Hwu, Y.-K. Chen, B.-C. Chiang, A.-S. 2018-10-27 doi:10.1101/454942 Cold Spring Harbor Laboratory Press 2018-10-27 <![CDATA[ Biological adaptation under fluctuating selection ]]> https://biorxiv.org/content/10.1101/457762v1?rss=1 Liu, M. Rubenstein, D. Liu, W.-C. Shen, S.-F. 2018-10-31 doi:10.1101/457762 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Nonsynonymous A-to-I RNA editing contributes to burden of deleterious missense variants in healthy individuals ]]> https://biorxiv.org/content/10.1101/462390v1?rss=1 Mai, T.-L. Chuang, T.-J. 2018-11-05 doi:10.1101/462390 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ A Statistical Procedure for Genome-wide Detection of QTL Hotspots Using Public Databases with Application to Rice ]]> https://biorxiv.org/content/10.1101/479725v1?rss=1 Kao, C.-H. Yang, M.-H. Wu, D.-H. 2018-11-27 doi:10.1101/479725 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ The dynamic association of SPO11-1 with conformational changes of meiotic axial elements in maize ]]> https://biorxiv.org/content/10.1101/489278v1?rss=1 Ronceret, A. Golubovskaya, I. Ku, J.-C. Lee, D. H. Timofejeva, L. Angoa, A. K. G. Kao, Y.-H. Kremling, K. Williams-Carrier, R. Meeley, R. Barkan, A. Cande, W. Z. Wang, C.-J. R. 2018-12-06 doi:10.1101/489278 Cold Spring Harbor Laboratory Press 2018-12-06 <![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[ Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine ]]> https://biorxiv.org/content/10.1101/513408v1?rss=1 Borgers, K. Ou, J.-Y. Zheng, P.-X. Tiels, P. Van Hecke, A. Plets, E. Michielsen, G. Festjens, N. Callewaert, N. Lin, Y.-C. 2019-01-07 doi:10.1101/513408 Cold Spring Harbor Laboratory Press 2019-01-07 <![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[ Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes ]]> https://biorxiv.org/content/10.1101/521054v1?rss=1 Fachal, L. Aschard, H. Beesley, J. Barnes, D. Allen, J. Kar, S. Pooley, K. Dennis, J. Michailidou, K. Turman, C. Soucy, P. Lemacon, A. Lush, M. Tyrer, J. Ghoussaini, M. Moradi Marjaneh, M. Jiang, X. Agata, S. Aittomaki, K. Alonso, M. R. Andrulis, I. Anton-Culver, H. Antonenkova, N. Arason, A. Arndt, V. Aronson, K. Arun, B. Auber, B. Auer, P. Azzollini, J. Balmana, J. Barkardottir, R. Barrowdale, D. Beeghly-Fadiel, A. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Blot, W. Bogdanova, N. Bojesen, S. Bolla, M. Bonanni, B. Borg, A. B 2019-01-15 doi:10.1101/521054 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals ]]> https://biorxiv.org/content/10.1101/523936v1?rss=1 6,000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.nnConclusionsA genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating diversity in corals. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life. ]]> Quattrini, A. M. Wu, T. Soong, K. Jeng, M.-S. Benayahu, Y. McFadden, C. S. 2019-01-17 doi:10.1101/523936 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Assessing chromatin accessibility in maize using ATAC-seq ]]> https://biorxiv.org/content/10.1101/526079v1?rss=1 Lee, Y.-J. Chang, P. Lu, J.-H. Chen, P.-Y. Wang, C.-J. R. 2019-01-22 doi:10.1101/526079 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Glial response to hypoxia in trachealess mutants induces synapse remodeling. ]]> https://biorxiv.org/content/10.1101/527671v1?rss=1 Chien, C.-T. Chen, P.-Y. Tsai, Y.-W. Giangrande, A. 2019-01-22 doi:10.1101/527671 Cold Spring Harbor Laboratory Press 2019-01-22 <![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[ 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[ 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[ Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize ]]> https://biorxiv.org/content/10.1101/574319v1?rss=1 Pecher, P. Moro, G. Canale, M. C. Capdevielle, S. Singh, A. MacLean, A. Sugio, A. Kuo, C.-H. Lopes, J. R. S. Hogenhout, S. A. 2019-03-12 doi:10.1101/574319 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Characterization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus ]]> https://biorxiv.org/content/10.1101/576488v1?rss=1 Wada, N. Ishimochi, M. Matsui, T. Pollock, F. J. Tang, S.-L. Ainsworth, T. D. Willis, B. L. Mano, N. Bourne, D. G. 2019-03-14 doi:10.1101/576488 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Population histories of the United States revealed through fine-scale migration and haplotype analysis ]]> https://biorxiv.org/content/10.1101/577411v1?rss=1 Dai, C. L. Vazifeh, M. M. Yeang, C.-H. Tachet, R. Vilar, M. G. Daly, M. J. Ratti, C. Martin, A. R. 2019-03-14 doi:10.1101/577411 Cold Spring Harbor Laboratory Press 2019-03-14 <![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[ Selection and gene flow shape niche-associated copy-number variation of pheromone receptor genes ]]> https://biorxiv.org/content/10.1101/580803v1?rss=1 Lee, D. Zdraljevic, S. Cook, D. E. Frezal, L. Hsu, J.-C. Sterken, M. G. Riksen, J. A. G. Wang, J. Kammenga, J. E. Braendle, C. Felix, M.-A. Schroeder, F. C. Andersen, E. C. 2019-03-18 doi:10.1101/580803 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Rule-governed Dynamic Stochastic Equilibration of Multicellular Motion In Vivo During Olfactory Neurogenesis ]]> https://biorxiv.org/content/10.1101/591479v1?rss=1 Warrier, V. Cluzeau, C. Chen, B.-C. Green-Saxena, A. Bergey, D. E. Betzig, E. Saxena, A. 2019-03-28 doi:10.1101/591479 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Structural basis for the differential regulatory roles of the PDZ domain in C-terminal processing proteases ]]> https://biorxiv.org/content/10.1101/621037v1?rss=1 Chueh, C.-K. Som, N. Ke, L.-C. Ho, M.-R. Reddy, M. Chang, C.-I. 2019-04-27 doi:10.1101/621037 Cold Spring Harbor Laboratory Press 2019-04-27 <![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[ Sonogenetic modulation of cellular activities using an engineered auditory-sensing protein ]]> https://biorxiv.org/content/10.1101/625533v1?rss=1 Huang, Y.-S. Fan, C.-H. Hsu, N. Wu, C.-Y. Chang, C.-Y. Hong, S.-R. Chang, Y.-C. Wu, A. Y.-T. Guo, V. Chiang, Y.-C. Hsu, W.-C. Chiu, N.-H. Chen, L. Lai, C. P.-K. Yeh, C.-K. LIN, Y. C. 2019-05-03 doi:10.1101/625533 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection ]]> https://biorxiv.org/content/10.1101/627794v1?rss=1 Morella, N. M. Weng, F. C.-H. Joubert, P. M. Metcalf, C. J. E. Lindow, S. Koskella, B. 2019-05-05 doi:10.1101/627794 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Characterization of Single Protein Dynamics in Cell Plasma Membrane Derived Polymer Cushioned Lipid Bilayers ]]> https://biorxiv.org/content/10.1101/641258v1?rss=1 Wong, W. C. Juo, J.-Y. Liao, Y.-H. Cheng, C.-Y. Lin, C.-H. Hsieh, C.-L. 2019-05-17 doi:10.1101/641258 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Two different pathways for initiation of Trichoderma reesei Rad51-only meiotic recombination ]]> https://biorxiv.org/content/10.1101/644443v1?rss=1 Li, W.-C. Chuang, Y.-C. Chen, C.-L. Wang, C.-L. Chen, Y.-J. Timofejeva, L. Pong, W.-L. Wang, T.-F. 2019-05-21 doi:10.1101/644443 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Predicting the prognosis of non-small cell lung cancer by integrating microarray and clinical data with deep learning ]]> https://biorxiv.org/content/10.1101/656140v1?rss=1 Lai, Y.-H. Chen, W.-N. Hsu, T.-C. Lin, C. Tsao, Y. Wu, S. 2019-06-11 doi:10.1101/656140 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ Fungal Feature Tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi ]]> https://biorxiv.org/content/10.1101/659672v1?rss=1 Vidal-Diez de Ulzurrun, G. Huang, T.-Y. Chang, C.-W. Lin, H.-C. Hsueh, Y.-P. 2019-06-04 doi:10.1101/659672 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Working out Classic Examples of Metabolic Networks Structural Analysis with Wolfram Language ]]> https://biorxiv.org/content/10.1101/672881v1?rss=1 Liang, K. K. 2019-06-18 doi:10.1101/672881 Cold Spring Harbor Laboratory Press 2019-06-18 <![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[ Genome analysis of the steroid-degrading denitrifying Denitratisoma oestradiolicum DSM 16959 and Denitratisoma sp. strain DHT3 ]]> https://biorxiv.org/content/10.1101/710707v1?rss=1 Chen, Y.-L. Wei, S. Chiang, Y.-R. 2019-07-22 doi:10.1101/710707 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Genome-wide, integrative analysis implicates circular RNA dysregulation in autism and the corresponding circular RNA-microRNA-mRNA regulatory axes ]]> https://biorxiv.org/content/10.1101/712331v1?rss=1 Chen, Y.-J. Chen, C.-Y. Mai, T.-L. Chuang, C.-F. Gupta, S. K. Yen, L. Wang, Y.-D. Chuang, T.-J. 2019-07-24 doi:10.1101/712331 Cold Spring Harbor Laboratory Press 2019-07-24 <![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[ Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering ]]> https://biorxiv.org/content/10.1101/714949v1?rss=1 You, S.-T. Jhou, Y.-T. Kao, C.-F. Leu, J.-Y. 2019-07-25 doi:10.1101/714949 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ It takes two vanilloid ligand bindings per channel to transduce painful capsaicin stimuli ]]> https://biorxiv.org/content/10.1101/725598v1?rss=1 Liu, T.-Y. Chu, Y. Mei, H.-R. Chang, D. S. Chuang, H.-h. 2019-08-12 doi:10.1101/725598 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ A single TRPV1 amino acid controls species sensitivity to capsaicin ]]> https://biorxiv.org/content/10.1101/732701v1?rss=1 Chu, Y. Cohen, B. Chuang, H.-h. A. 2019-08-12 doi:10.1101/732701 Cold Spring Harbor Laboratory Press 2019-08-12 <![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[ Redundancy and specificity of type VI secretion vgrG loci in antibacterial activity of Agrobacterium tumefaciens 1D1609 strain ]]> https://biorxiv.org/content/10.1101/740209v1?rss=1 Santos, M. N. M. Cho, S.-T. Wu, C.-F. Chang, C.-J. Kuo, C.-H. Lai, E.-M. 2019-08-19 doi:10.1101/740209 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance ]]> https://biorxiv.org/content/10.1101/751792v1?rss=1 Mullis, A. Lu, Z. Zhan, Y. Wang, T.-Y. Rodriguez, J. Rajeh, A. Chatrath, A. Lin, Z. 2019-08-31 doi:10.1101/751792 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Input dose differentiation by NF-κB ]]> https://biorxiv.org/content/10.1101/752394v1?rss=1 Son, M. Wang, A. Tu, H.-L. Metzig, M. O. Patel, P. Husain, K. Lin, J. Murugan, A. Hoffmann, A. Tay, S. 2019-09-04 doi:10.1101/752394 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Engineering recombination between diverged yeast species reveals genetic incompatibilities ]]> https://biorxiv.org/content/10.1101/755165v1?rss=1 Bozdag, G. O. Ono, J. Denton, J. A. Karakoc, E. Hunter, N. Leu, J.-Y. Greig, D. 2019-09-05 doi:10.1101/755165 Cold Spring Harbor Laboratory Press 2019-09-05 <![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[ Nest microbiota and pathogen abundance impact hatching success in sea turtle conservation ]]> https://biorxiv.org/content/10.1101/776773v1?rss=1 Hoh, D. Z. Lin, Y.-f. Liu, W.-A. Sidique, S. N. M. Tsai, I. J. 2019-09-20 doi:10.1101/776773 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ GSAlign - an efficient sequence alignment tool for intra-species genomes ]]> https://biorxiv.org/content/10.1101/782193v1?rss=1 Lin, H.-N. Hsu, W.-L. 2019-09-25 doi:10.1101/782193 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Perinatal exposure to lead results in altered DNA methylation in adult mouse liver and blood: Implications for target versus surrogate tissue use in environmental epigenetics ]]> https://biorxiv.org/content/10.1101/783209v1?rss=1 Svoboda, L. K. Neier, K. E. Cavalcante, R. G. Tsai, Z. T.-Y. Jones, T. R. Liu, S. Goodrich, J. M. Lalancette, C. Colacino, J. Sartor, M. Dolinoy, D. C. 2019-10-02 doi:10.1101/783209 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ MapCaller - An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data ]]> https://biorxiv.org/content/10.1101/783605v1?rss=1 Lin, H.-N. Hsu, W.-L. 2019-09-26 doi:10.1101/783605 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Differential Effects of SUMO1/2 on Circadian Protein PER2 Stability and Function ]]> https://biorxiv.org/content/10.1101/789222v1?rss=1 Chen, L.-C. Hsieh, Y.-L. Kuo, T.-Y. Chou, Y.-C. Hsu, P.-H. Hwang-Verslues, W. W. 2019-10-01 doi:10.1101/789222 Cold Spring Harbor Laboratory Press 2019-10-01 <![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[ StrainPro: a highly accurate Metagenomic strain-level profiling tool ]]> https://biorxiv.org/content/10.1101/807149v1?rss=1 Lin, H.-N. Lin, Y.-L. Hsu, W.-L. 2019-10-16 doi:10.1101/807149 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Dynamic-ultrastructural cell volume (3D) correlative microscopy facilitated by intracellular fluorescent nanodiamonds as multi-modal probes ]]> https://biorxiv.org/content/10.1101/823278v1?rss=1 Prabhakar, N. Belevich, I. Peurla, M. Heiligenstein, X. Chang, H.-C. Sahlgren, C. Jokitalo, E. Rosenholm, J. 2019-10-29 doi:10.1101/823278 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ The assembly of the Drosophila mushroom body circuit and its regulation by Semaphorin 1a ]]> https://biorxiv.org/content/10.1101/835595v1?rss=1 Lin, C.-H. Lin, S. 2019-11-08 doi:10.1101/835595 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Natural diversity in the predatory behavior facilitates the establishment of a new robust model strain for nematode-trapping fungi ]]> https://biorxiv.org/content/10.1101/843698v1?rss=1 Yang, C.-T. Vidal-Diez de Ulzurrun, G. Goncalves, A. P. Lin, H.-C. Chang, C.-W. Huang, T.-Y. Chen, S.-A. Lai, C.-K. Tsai, I. J. Schroeder, F. C. Stajich, J. E. Hsueh, Y.-P. 2019-11-15 doi:10.1101/843698 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Enhancer regulation for induced WNT3A expression during neuronal regeneration ]]> https://biorxiv.org/content/10.1101/861153v1?rss=1 Chang, C.-Y. Hung, J.-H. Wu, C.-C. Liang, M.-Z. Huang, P.-Y. Li, J. Chen, H.-I. Yet, S.-F. Fung, K. S. Kao, C.-F. Chen, L. 2019-12-02 doi:10.1101/861153 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Astrocytic mechanism of glutamate modulation underlying synchronous bursting in cortical cultures ]]> https://biorxiv.org/content/10.1101/870915v1?rss=1 Kumar, R. Huang, Y.-T. Chen, C.-C. Tzeng, S.-F. Chan, C.-K. 2019-12-11 doi:10.1101/870915 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Anemonefish are better taxonomists than humans. ]]> https://biorxiv.org/content/10.1101/2023.09.11.557259v1?rss=1 Kashimoto, R. Mercader, M. Zwahlen, J. Miura, S. Tanimoto, M. Yanagi, K. Reimer, J. D. Khalturin, K. Laudet, V. 2023-09-11 doi:10.1101/2023.09.11.557259 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Structure and dynamics of the contractile vacuole complex in Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/2023.09.13.557576v1?rss=1 Cheng, C.-Y. Romero, D. P. Zoltner, M. Yao, M.-C. Turkewitz, A. 2023-09-14 doi:10.1101/2023.09.13.557576 Cold Spring Harbor Laboratory Press 2023-09-14 <![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[ Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches ]]> https://biorxiv.org/content/10.1101/2023.09.13.557568v1?rss=1 Hsieh, Y. E. Tandon, K. Verbruggen, H. Nikoloski, Z. 2023-09-17 doi:10.1101/2023.09.13.557568 Cold Spring Harbor Laboratory Press 2023-09-17 <![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[ The interactome of histone deacetylase HDA19 in dark-grown Arabidopsis seedlings ]]> https://biorxiv.org/content/10.1101/2023.09.19.558523v1?rss=1 Schmidt, W. Velez Bermudez, I. C. 2023-09-21 doi:10.1101/2023.09.19.558523 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics ]]> https://biorxiv.org/content/10.1101/2023.09.25.559365v1?rss=1 Mc Cartney, A. M. Formenti, G. Mouton, A. Ciofi, C. Waterhouse, R. M. Mazzoni, C. J. De Panis, D. Schlude Marins, L. S. Leitao, H. G. Diedericks, G. Kirangwa, J. Morselli, M. Salces, J. Escudero, N. Iannucci, A. Natali, C. Svardal, H. Fernandez, R. De Pooter, T. Joris, G. Strazisar, M. Wood, J. Herron, K. E. Seehausen, O. Watts, P. C. Shaw, F. Davey, R. P. Minotto, A. Fernandez Gonzalez, J. M. Bohne, A. Alegria, C. Alioto, T. Alves, P. C. Amorim, I. R. Aury, J.-M. Backstrom, N. Baldrian, P. Ballarin, L. Baltrunaite, L. Barta, E. BedHom, B. Belser, C. B 2023-09-28 doi:10.1101/2023.09.25.559365 Cold Spring Harbor Laboratory Press 2023-09-28 <![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[ Brassinosteroid recruits FERONIA to safeguard cell expansion in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2023.10.01.560400v1?rss=1 Chaudhary, A. Hsiao, Y.-C. Yeh, F.-L. J. Wu, H.-M. Cheung, A. Y. Xu, S.-L. Wang, Z.-Y. 2023-10-02 doi:10.1101/2023.10.01.560400 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ The impact of light and thioredoxins on the plant thiol-disulfide proteome ]]> https://biorxiv.org/content/10.1101/2023.10.17.562744v1?rss=1 Hou, L.-Y. Sommer, F. K. Poeker, L. Dziubek, D. Schroda, M. Geigenberger, P. 2023-10-20 doi:10.1101/2023.10.17.562744 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes ]]> https://biorxiv.org/content/10.1101/2023.10.20.563379v1?rss=1 Wu, T.-Y. Li, Y.-R. Chang, K.-J. Urano, D. Liu, M.-J. 2023-10-21 doi:10.1101/2023.10.20.563379 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ The NRC0 gene cluster of sensor and helper NLR immune receptors is functionally conserved across asterid plants ]]> https://biorxiv.org/content/10.1101/2023.10.23.563533v1?rss=1 Sakai, T. Martinez-Anaya, C. Contreras, M. P. Kamoun, S. Wu, C.-H. Adachi, H. 2023-10-23 doi:10.1101/2023.10.23.563533 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ NRC immune receptor networks show diversified hierarchical genetic architecture across plant lineages ]]> https://biorxiv.org/content/10.1101/2023.10.25.563953v1?rss=1 Goh, F.-J. Huang, C.-Y. Derevnina, L. Wu, C.-H. 2023-10-27 doi:10.1101/2023.10.25.563953 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Chromosome-level genome assemblies of two hemichordates provide new insights into deuterostome origin and chromosome evolution ]]> https://biorxiv.org/content/10.1101/2023.11.01.564642v1?rss=1 Lin, C.-Y. Marletaz, F. Perez-Posada, A. Martinez Garcia, P. M. Schloissnig, S. Peluso, P. Conception, G. T. Bump, P. Chen, Y.-C. Chou, C. Lin, C.-Y. Fan, T.-P. Tsai, C.-T. Gomez Skarmeta, J. L. Tena, J. J. Lowe, C. J. Rank, D. R. Rokhsar, D. S. Yu, J.-K. Su, Y.-H. 2023-11-02 doi:10.1101/2023.11.01.564642 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ On the independent irritability of goldfish eggs and embryos -- a living communication on the rhythmic yolk contractions in goldfish ]]> https://biorxiv.org/content/10.1101/2023.11.02.564871v1?rss=1 Sanchez, P. G. L. Wang, C.-Y. Li, I.-J. Ota, K. G. 2023-11-03 doi:10.1101/2023.11.02.564871 Cold Spring Harbor Laboratory Press 2023-11-03 <![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[ The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogen Parastagonospora nodorum ]]> https://biorxiv.org/content/10.1101/2023.11.13.566949v1?rss=1 Morikawa, S. Verdonk, C. John, E. Lenzo, L. Sbaraini, N. Turo, C. J. Li, H. Jiang, D. Chooi, Y.-H. Tan, K.-C. 2023-11-14 doi:10.1101/2023.11.13.566949 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ A Whole-Cell Screening Platform to Discover Cell Adhesion Molecules that Enable Programmable Bacterial Cell-Cell Adhesion ]]> https://biorxiv.org/content/10.1101/2023.12.03.569830v1?rss=1 Ting, S.-Y. Chen, P.-Y. Chen, Y.-C. Chen, P.-P. Lin, K.-T. Wang, W.-L. Hsia, K.-C. 2023-12-04 doi:10.1101/2023.12.03.569830 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Hybrid Neural Networks of the Olfactory Learning Center in the Drosophila Brain ]]> https://biorxiv.org/content/10.1101/2023.12.06.570338v1?rss=1 Cheng, L.-S. Charng, C.-C. Chen, R.-H. Feng, K.-L. Chiang, A.-S. Lo, C.-C. Lee, T.-K. 2023-12-06 doi:10.1101/2023.12.06.570338 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ A chloroplast sulfate transporter modulates glutathione-mediated redox cycling to regulate cell division ]]> https://biorxiv.org/content/10.1101/2023.12.07.570675v1?rss=1 Huang, P.-j. Chen, C.-H. Lin, Y.-L. Lin, H.-Y. Fang, S.-C. 2023-12-08 doi:10.1101/2023.12.07.570675 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Temporal Transcriptome Analysis Uncovers Regulatory Modules Programming Embryo Development from Embryonic Morphogenesis to Post-Germination ]]> https://biorxiv.org/content/10.1101/2023.12.26.573376v1?rss=1 Wang, Y.-C. Hsieh, W.-H. Huang, C.-J. Jhan, Y.-T. Zhan, J. Chang, C.-C. Hsieh, T.-F. Lin, J.-Y. 2023-12-27 doi:10.1101/2023.12.26.573376 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Microscopy-guided subcellular proteomic discovery by high-speed ultra-content photo-biotinylation ]]> https://biorxiv.org/content/10.1101/2023.12.27.573388v1?rss=1 Liao, J.-C. Chen, Y.-D. Chang, C.-W. Cheung, C. H. Y. Chang, H.-J. Sie, Y.-D. Chung, C.-W. Huang, C.-K. Huang, C.-C. Chong, W. M. Liu, Y.-P. Lin, Y.-C. Kai, H.-J. J. Wang, P.-J. 2023-12-27 doi:10.1101/2023.12.27.573388 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Glycolysis-Wnt signaling axis tunes developmental timing of embryo segmentation ]]> https://biorxiv.org/content/10.1101/2024.01.22.576629v1?rss=1 Miyazawa, H. Rada, J. Sanchez, P. G. L. Esposito, E. Bunina, D. Girardot, C. Zaugg, J. Aulehla, A. 2024-01-22 doi:10.1101/2024.01.22.576629 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[ Human iPSC-derived Committed Cardiac Progenitors Generate Cardiac Tissue Grafts in a Swine Ischemic Cardiomyopathy Model without Triggering Ventricular Arrhythmias ]]> https://biorxiv.org/content/10.1101/2024.02.14.580375v1?rss=1 Raval, A. N. Schmuck, E. G. Roy, S. Saito, Y. Zhou, T. Conklin, J. Hacker, T. A. Koonce, C. Boyer, M. Stack, K. Hebron, E. Nagle, S. K. Hsieh, P. C. H. Kamp, T. J. 2024-02-17 doi:10.1101/2024.02.14.580375 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ Generic rules of lumen nucleation and fusion in epithelial organoids ]]> https://biorxiv.org/content/10.1101/2024.02.20.581158v1?rss=1 Lu, L. Fuji, K. Guyomar, T. Lieb, M. Tanida, S. Nonomura, M. Hiraiwa, T. Alcheikh, Y. Yennek, S. Petzold, H. Martin-Lemaitre, C. Grapin-Botton, A. Honigmann, A. Sano, M. Riveline, D. 2024-02-23 doi:10.1101/2024.02.20.581158 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Cryo-EM inspired NMR analysis reveals a pH-induced conformational switching mechanism for imparting dynamics to Betanodavirus protrusions ]]> https://biorxiv.org/content/10.1101/2024.03.08.584019v1?rss=1 Sterbova, P. Wang, C.-H. Carillo, K. J. D. Lou, Y.-C. Kato, T. Namba, K. Tzou, D.-L. M. Chang, W.-H. 2024-03-08 doi:10.1101/2024.03.08.584019 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Border-zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration ]]> https://biorxiv.org/content/10.1101/2024.03.12.584570v1?rss=1 Constanty, F. Wu, B. Wei, K.-H. Lin, I.-T. Dallmann, J. Guenther, S. Lautenschlaeger, T. Priya, R. Lai, S.-L. Stainier, D. Y. R. Beisaw, A. 2024-03-13 doi:10.1101/2024.03.12.584570 Cold Spring Harbor Laboratory Press 2024-03-13 <![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[ Neurosphere culture derived from aged hippocampal dentate gyrus ]]> https://biorxiv.org/content/10.1101/2024.03.16.585365v1?rss=1 12 months old) mouse brain and how to differentiate cultured neurospheres into neurons and astrocytes. Culturing adult and aged NPCs provides an important in vitro model to (1) investigate cellular and molecular properties of this unique cell population and (2) expand the understanding of plasticity in the adult and aging brain. This protocol requires [~]2 hours to complete dissection, dissociation and culture plating, while differentiation to neuronal and astrocytic lineages takes 9 days. By focusing on neurospheres obtained from animals at later ages this model facilitates investigation of important biological questions related to development and differentiation of hippocampal neurons generated throughout adult life. ]]> Vafaeva, O. Namchaiw, P. Murray, K. D. Diaz, E. Cheng, H.-J. 2024-03-17 doi:10.1101/2024.03.16.585365 Cold Spring Harbor Laboratory Press 2024-03-17 <![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[ PREDICT: Advancing Accurate Gene Expression Prediction and Motif Identification in Plant Stress Responses ]]> https://biorxiv.org/content/10.1101/2024.03.28.587275v1?rss=1 Wu, T.-Y. Liu, M.-J. Thalimaraw, L. Eo, W. X. H. 2024-03-31 doi:10.1101/2024.03.28.587275 Cold Spring Harbor Laboratory Press 2024-03-31 <![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[ RGF1 controls PLT2 protein stability through ROS-dependent regulation of a cysteine residue in root meristem development ]]> https://biorxiv.org/content/10.1101/2024.04.08.588570v1?rss=1 Hsiao, Y.-C. Shiue, S.-Y. Yen, M.-R. Lai, J.-K. YAMADA, M. 2024-04-11 doi:10.1101/2024.04.08.588570 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Coupling of cell growth modulation to asymmetric division and cell cycle regulation in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/2024.04.10.587378v1?rss=1 Glenn, S. Lin, W.-H. Papagiannakis, A. Kato, S. Jacobs-Wagner, C. 2024-04-10 doi:10.1101/2024.04.10.587378 Cold Spring Harbor Laboratory Press 2024-04-10 <![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[ Worldwide soundscape ecology patterns across realms ]]> https://biorxiv.org/content/10.1101/2024.04.10.588860v1?rss=1 Darras, K. F. Rountree, R. Van Wilgenburg, S. Dong, L. Gasc, A. Chen, Y. Lin, T.-H. Diaz, P. M. Wu, S.-H. Salton, M. Marley, S. Cord, A. F. Aparecido Do Nascimento, L. Astaras, C. Barbaro, L. Bellisario, K. Ben David, A. Berger-Tal, O. Bhalla, I. Bolgan, M. Bradfer-Lawrence, T. Briers, R. A. Budka, M. Cerezo-Araujo, M. Cerwen, G. Desjonqueres, C. Diniz, P. Duarte, A. Enari, H. Enari, H. S. Freitas, B. Friedman, N. Froidevaux, J. Gogoleva, S. Goodale, E. Greenhalgh, J. Hagge, J. Jacot, A. Jahn, O. Kepfer Rojas, S. Lloyd, K. J. Mammides, C. Marcacci, G. 2024-04-14 doi:10.1101/2024.04.10.588860 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[ Evolution engineering of methylotrophic E. coli enables faster growth than native methylotrophs ]]> https://biorxiv.org/content/10.1101/2024.04.18.589993v1?rss=1 Nieh, L.-Y. Chen, F. Y.- H. Jung, H.-W. Su, K.-Y. Tsuei, C.-Y. Lin, C. T. Lee, Y.-Q. Liao, J. C. 2024-04-18 doi:10.1101/2024.04.18.589993 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Genetic purging of strongly deleterious mutations underlies black-necked crane's unusual escape from an extinction vortex ]]> https://biorxiv.org/content/10.1101/2024.04.18.590004v1?rss=1 Cui, N. Ma, X. Wu, H. Chen, X. Hung, C.-M. Zhang, L. Lei, F. Yang, L. Yan, D. Yang, X. Dong, F. 2024-04-21 doi:10.1101/2024.04.18.590004 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ StomaVision: stomatal trait analysis through deep learning ]]> https://biorxiv.org/content/10.1101/2024.04.24.590919v1?rss=1 and available for local use in a containerized environment at , this tool ensures long-term usability by minimizing the impact of software updates and maintaining functionality with minimal setup requirements. The application of StomaVision has provided significant physiological insights, such as variations in stomatal density, opening rates, and total pore area under heat stress. These traits correlate with critical physiological processes, including gas exchange, carbon assimilation, and water use efficiency, demonstrating the tools utility in advancing our understanding of plant physiology. The ability of StomaVision to identify differences in responses to varying durations of heat treatment highlights its value in plant science research. Plain language summaryStomaVision is a tool that automatically counts and measures tiny openings on plant leaves, helping us learn how plants deal with their surroundings. It is easy to use and works well with various plant species. This tool helps scientists see how plants change under stress, making plant research easier and more accurate. ]]> Wu, T.-L. Chen, P.-Y. Du, X. Wu, H. Ou, J.-Y. Zheng, P.-X. Wu, Y.-L. Wang, R.-S. Hsu, T.-C. Lin, C.-Y. Lin, W.-Y. Chang, P.-L. Ho, C.-M. K. Lin, Y.-C. 2024-04-28 doi:10.1101/2024.04.24.590919 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Proteomic Dynamics and Heat Stress Response in Arabidopsis Seedlings ]]> https://biorxiv.org/content/10.1101/2024.04.30.591943v1?rss=1 Fan, K.-T. Xu, Y. 2024-04-30 doi:10.1101/2024.04.30.591943 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Syngeneic natural killer cell therapy activates dendritic and T cells in metastatic lungs and effectively treat low-burden metastases ]]> https://biorxiv.org/content/10.1101/2024.05.03.592329v1?rss=1 Huang, S.-W. Lai, Y.-G. Liao, H.-T. Chang, C.-L. Ma, R.-Y. Chen, Y.-H. Liou, Y.-H. Wu, Z.-Q. Wu, Y.-C. Liu, K.-J. Huang, Y.-T. Yang, J.-L. Dai, M.-S. Liao, N.-S. 2024-05-05 doi:10.1101/2024.05.03.592329 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Naa10 regulates hippocampal neurite outgrowth via Btbd3 N-α-acetylation-mediated actin dynamics ]]> https://biorxiv.org/content/10.1101/2024.05.09.583166v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@180da41org.highwire.dtl.DTLVardef@7921c6org.highwire.dtl.DTLVardef@9859b0org.highwire.dtl.DTLVardef@28687c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chou, C.-T. Kang, M.-L. Lee, C.-C. Hsu, P.-H. Juan, L.-J. 2024-05-10 doi:10.1101/2024.05.09.583166 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Predation by nematode-trapping fungus triggers mechanosensory-dependent quiescence in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.05.14.594062v1?rss=1 Lin, T.-H. Chang, H.-W. Tay, R. J. Hsueh, Y.-P. 2024-05-14 doi:10.1101/2024.05.14.594062 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Cathepsin X is a conserved cell death protein involved in algal response to environmental stress ]]> https://biorxiv.org/content/10.1101/2024.05.15.594278v1?rss=1 Mizrachi, A. Sadeh, M. Ben-Dor, S. Dym, O. Ku, C. Feldmesser, E. Zarfin, A. Brunson, J. K. Allen, A. E. Jinkerson, R. E. Schatz, D. Vardi, A. 2024-05-15 doi:10.1101/2024.05.15.594278 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians ]]> https://biorxiv.org/content/10.1101/2024.05.15.594353v1?rss=1 Lewin, T. D. Liao, I. J.-Y. Luo, Y.-J. 2024-05-18 doi:10.1101/2024.05.15.594353 Cold Spring Harbor Laboratory Press 2024-05-18 <![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[ Control of lumen geometry and topology by cell proliferation rate and pressure ]]> https://biorxiv.org/content/10.1101/2024.05.29.596462v1?rss=1 Lee, B. H. Fuji, K. Petzold, H. Seymour, P. A. Yennek, S. Schewin, C. Lewis, A. Riveline, D. Hiraiwa, T. Sano, M. Grapin-Botton, A. 2024-05-30 doi:10.1101/2024.05.29.596462 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Brachiopod genome unveils the evolution of the BMP-Chordin network in bilaterian body patterning ]]> https://biorxiv.org/content/10.1101/2024.05.28.596352v1?rss=1 Lewin, T. D. Shimizu, K. Liao, I. J.-Y. Chen, M.-E. Endo, K. Satoh, N. Holland, P. W. H. Wong, Y. H. Luo, Y.-J. 2024-06-02 doi:10.1101/2024.05.28.596352 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ The tumor-maintaining function of UTX/KDM6A in DNA replication and the PARP1-dependent repair pathway ]]> https://biorxiv.org/content/10.1101/2024.05.31.596824v1?rss=1 Wang, S.-P. Yeh, L.-W. Chen, J.-W. Yeh, J.-Y. Kao, M.-H. Hong, H.-C. Wu, S. Cheung, W.-M. Liu, T.-Y. Aberin, M. A. E. Paas-Oliveros, E. Escajeda, A. Shih, E. Tarn, W.-Y. Chang, Y.-M. Wang, L.-H. 2024-06-03 doi:10.1101/2024.05.31.596824 Cold Spring Harbor Laboratory Press 2024-06-03 <![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[ Thymic self-recognition-mediated TCR signal strength modulates antigen-specific CD8+ T cell pathogenicity in non-obese diabetic mice ]]> https://biorxiv.org/content/10.1101/2024.06.10.596762v1?rss=1 Ho, C.-L. Yeh, L.-T. Liu, Y.-W. Dong, J.-L. Sytwu, H.-K. 2024-06-12 doi:10.1101/2024.06.10.596762 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Cytokinin-inducible DIRIGENT13 involved in lignan synthesis and ROS accumulation promotes root growth and abiotic stress tolerance in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2024.06.25.600713v1?rss=1 Melnikava, A. Perreau, F. Paniagua, C. Cheng, S.-C. Huang, L.-M. Ubogoeva, E. Zemlyanskaya, E. Yang, Y.-L. Mouille, G. Arnaud, D. Hejatko, J. 2024-06-29 doi:10.1101/2024.06.25.600713 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ CoPR: Collective Pattern Recognition-a Framework for Microbial Community Activity Analysis ]]> https://biorxiv.org/content/10.1101/2024.06.30.601456v1?rss=1 Vidanaarachchi, R. Tang, S.-L. Halgamuge, S. K. 2024-07-02 doi:10.1101/2024.06.30.601456 Cold Spring Harbor Laboratory Press 2024-07-02 <![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[ Endophytic pyrroloquinoline quinone enhances banana growth and immunity against Fusarium wilt for plant-microbe mutualisms ]]> https://biorxiv.org/content/10.1101/2024.08.20.608638v1?rss=1 Hung, S.-H. W. Yu, M.-Y. Liu, C.-H. Huang, T.-C. Peng, J.-H. Jang, N.-Y. Kuo, C.-H. Ho, Y.-N. Chiang, E.-P. I. Hwang, H.-H. Huang, C.-C. 2024-08-21 doi:10.1101/2024.08.20.608638 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Asymmetry of acto-myosin cortices as active fluids shape cells in organoids ]]> https://biorxiv.org/content/10.1101/2024.08.22.609097v1?rss=1 Guyomar, T. Lu, L. Hiraiwa, T. Riveline, D. 2024-08-22 doi:10.1101/2024.08.22.609097 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes ]]> https://biorxiv.org/content/10.1101/2024.08.22.609105v1?rss=1 Chang, H.-Y. Yen, H.-C. Chu, H.-A. Kuo, C.-H. 2024-08-22 doi:10.1101/2024.08.22.609105 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Cell wall arabinogalactan is responsible for Fungitell(R) cross reactivity in nocardiosis ]]> https://biorxiv.org/content/10.1101/2024.08.22.608962v1?rss=1 Mariller, C. Letowski, P. Chang, W.-T. Lowary, T. Ulrich, M. Faure, K. Loridant, S. Sendid, B. Wallet, F. Poulain, D. Hazzan, M. Frimat, M. Guerardel, Y. Titecat, M. 2024-08-26 doi:10.1101/2024.08.22.608962 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Lamellar Schwann cells in the Pacinian corpuscle potentiate vibration perception ]]> https://biorxiv.org/content/10.1101/2024.08.23.609459v1?rss=1 Chen, Y.-T. de Thomas Wagner, D. Loutit, A. J. Nourizonoz, A. Croisier-Coeytaux, M.-C. Blanc, J. Knott, G. Lee, K.-S. Huber, D. 2024-08-26 doi:10.1101/2024.08.23.609459 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Dynamic positioning of a TFIIE-related winged-helix domain in RNA polymerase elongation complex III underpins its multi-functionality ]]> https://biorxiv.org/content/10.1101/2024.08.27.609947v1?rss=1 Wu, J.-S. Lin, Y.-C. Wei, Y.-Y. Lin, H.-H. Liu, Y.-C. Chang, J.-W. Tu, I.-P. Chen, H.-T. Chang, W.-H. 2024-08-28 doi:10.1101/2024.08.27.609947 Cold Spring Harbor Laboratory Press 2024-08-28 <![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[ Influenza A virus exploits the motility of membrane cytoskeletal actomyosin filaments for its genome packaging in the host cell ]]> https://biorxiv.org/content/10.1101/2024.09.11.612468v1?rss=1 Wang, I.-H. Usukura, J. Miyake, Y. Usukura, E. Narita, A. Yamauchi, Y. Kawaoka, Y. 2024-09-12 doi:10.1101/2024.09.11.612468 Cold Spring Harbor Laboratory Press 2024-09-12 <![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[ Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN ]]> https://biorxiv.org/content/10.1101/2024.09.16.613176v1?rss=1 Herreros, D. Mata, C. P. Noddings, C. Irene, D. Krieger, J. M. Agard, D. Tsai, M.-D. Sorzano, C. O. S. Carazo, J. M. 2024-09-19 doi:10.1101/2024.09.16.613176 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ A helper NLR targets organellar membranes to trigger immunity ]]> https://biorxiv.org/content/10.1101/2024.09.19.613839v1?rss=1 Ibrahim, T. Yuen, E. L. H. Wang, H.-Y. King, F. J. Toghani, A. Kourelis, J. Vuolo, C. Adamkova, V. Castel, B. Jones, J. D. Wu, C.-H. Kamoun, S. Bozkurt, T. O. 2024-09-22 doi:10.1101/2024.09.19.613839 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Spatiotemporal dynamics and assembly process differ in fungal communities across contiguous habitats in tropical forests ]]> https://biorxiv.org/content/10.1101/2024.09.20.614103v1?rss=1 Lin, C.-P. Lin, Y.-F. Liu, Y.-C. Lu, M.-Y. J. Ke, H.-M. Tsai, I. J. 2024-09-24 doi:10.1101/2024.09.20.614103 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ From Genes to Pathways: A Curated Gene Approach to Accurate Pathway Reconstruction in Teleost Fish Transcriptomics ]]> https://biorxiv.org/content/10.1101/2024.09.23.614382v1?rss=1 Herrera, M. Vianello, S. D. Mitchell, L. Chamot, Z. Lorin-Nebel, C. Roux, N. Besseau, L. Gibert, Y. Laudet, V. 2024-09-24 doi:10.1101/2024.09.23.614382 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Longhorn Beetles form Structural Colour Using Calcium Phosphate Biominerals ]]> https://biorxiv.org/content/10.1101/2024.10.01.616160v1?rss=1 Chang, Y. Tseng, H.-H. Masahiko, T. Pohl, D. Rellinghaus, B. Bertinetti, L. Politi, Y. 2024-10-01 doi:10.1101/2024.10.01.616160 Cold Spring Harbor Laboratory Press 2024-10-01 <![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[ 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[ Impact of mutations in the HEADING DATE 1 gene on transcription and cell wall composition of rice ]]> https://biorxiv.org/content/10.1101/2024.10.16.618758v1?rss=1 Biancucci, M. Chirivi, D. Baldini, A. Badenhorst, E. Dobetti, F. Khahani, B. Formentin, E. Eguen, T. Turck, F. K. Moore, J. P. Tavakol, E. Wenkel, S. Lo Schiavo, F. L. Ezquer, I. Brambilla, V. Horner, D. S. Chiara, M. Perrella, G. Betti, C. Fornara, F. 2024-10-18 doi:10.1101/2024.10.16.618758 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Personalized cancer treatment strategies incorporating irreversible and reversible drug resistance mechanisms ]]> https://biorxiv.org/content/10.1101/2024.11.03.621749v1?rss=1 He, W. McCoy, M. D. Riggins, R. B. Beckman, R. A. Yeang, C.-H. 2024-11-04 doi:10.1101/2024.11.03.621749 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Elucidating the Mechanism Underlying UBA7-UBE2L6 Disulfide Complex Formation ]]> https://biorxiv.org/content/10.1101/2024.11.07.622398v1?rss=1 Chen, P.-T. Yeh, J.-Y. Weng, J.-H. Wu, K.-P. 2024-11-08 doi:10.1101/2024.11.07.622398 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Conformational plasticity of mitochondrial VDAC2 controls the kinetics of its interaction with cytosolic proteins ]]> https://biorxiv.org/content/10.1101/2024.11.08.622687v1?rss=1 Rosencrans, W. M. Khuntia, H. Larimi, M. G. Mahalakshmi, R. Yu, T.-Y. D. Bezrukov, S. M. Rostovtseva, T. K. 2024-11-11 doi:10.1101/2024.11.08.622687 Cold Spring Harbor Laboratory Press 2024-11-11 <![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[ The Bacteria of a Fig Microcommunity ]]> https://biorxiv.org/content/10.1101/2024.11.22.624729v1?rss=1 Woodruff, G. C. Moser, K. A. Wang, J. 2024-11-22 doi:10.1101/2024.11.22.624729 Cold Spring Harbor Laboratory Press 2024-11-22 <![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[ The effects of early-life ambient temperature on the gut microbiome of a wild bird? an experimental approach ]]> https://biorxiv.org/content/10.1101/2024.11.26.625491v1?rss=1 Ruuskanen, S. Hollmen, L. Stier, A. Hsu, B.-Y. Cossin-Sevrin, N. Marciau, C. Hukkanen, M. Vesterinen, E. 2024-11-28 doi:10.1101/2024.11.26.625491 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Circadian Activity Predicts Breeding Phenology in the Asian Burying Beetle Nicrophorus nepalensis ]]> https://biorxiv.org/content/10.1101/2024.11.30.626159v1?rss=1 Chen, H. Rubenstein, D. R. Mai, G.-S. Chang, C.-F. Shen, S.-F. 2024-12-01 doi:10.1101/2024.11.30.626159 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Repeated evolution of supergenes on an ancient social chromosome ]]> https://biorxiv.org/content/10.1101/2024.12.01.626239v1?rss=1 Lajmi, A. Cohen, P. Lee, C.-C. Frenkel, Z. Pellen, Y. Privman, E. 2024-12-02 doi:10.1101/2024.12.01.626239 Cold Spring Harbor Laboratory Press 2024-12-02 <![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[ Deep homology of a brachyury regulatory syntax and origin of the notochord ]]> https://biorxiv.org/content/10.1101/2024.12.12.628285v1?rss=1 Fan, T.-P. Lee, J.-R. Lin, C.-Y. Chen, Y.-C. Cutting, A. E. Cameron, R. A. Yu, J.-K. Su, Y.-H. 2024-12-13 doi:10.1101/2024.12.12.628285 Cold Spring Harbor Laboratory Press 2024-12-13 <![CDATA[ An Interbacterial Cysteine Protease Toxin Inhibits Cell Growth by Targeting Type II DNA Topoisomerases GyrB and ParE ]]> https://biorxiv.org/content/10.1101/2024.12.30.630690v1?rss=1 Song, P.-Y. Tsai, C.-E. Chen, Y.-C. Chen, P.-P. Wang, T.-H. Hu, C.-Y. Chen, P.-Y. Ku, C. Hsia, K.-C. Ting, S.-Y. 2024-12-31 doi:10.1101/2024.12.30.630690 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ A cytoskeletal scaffold promotes motile cilia assembly by regulating transition-zone integrity ]]> https://biorxiv.org/content/10.1101/2025.01.10.632296v1?rss=1 Park, H. Choi, M. Cheung, H. O.-L. Zhang, Y. Makino, S. Yoshikawa, Y. Qi, H. Liu, Z. Lan, G. Fu, G. Wang, Q. Guo, S. S. Liu, P. Liu, Z. Ti, S.-C. Wang, W.-J. Li, X. D. Ni, T. Hui, C. C. He, M. 2025-01-10 doi:10.1101/2025.01.10.632296 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ 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[ Structural basis of K11/K48-branched ubiquitin chain recognition by the human 26S proteasome ]]> https://biorxiv.org/content/10.1101/2025.01.13.632666v1?rss=1 Draczkowski, P. Chen, S.-N. Chen, T. Wang, Y.-S. Huang, J. Y. C. Tsai, M.-C. Lin, S.-Y. Viner, R. Chang, Y.-C. Wu, K.-P. Hsu, S.-T. D. 2025-01-13 doi:10.1101/2025.01.13.632666 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Comparative genomic analysis of a novel heat-tolerant and euryhaline strain of unicellular marine cyanobacterium Cyanobacterium sp. DS4 from a high-temperature lagoon ]]> https://biorxiv.org/content/10.1101/2025.01.17.633688v1?rss=1 Chen, C.-N. N. Lin, K.-M. Lin, Y.-C. Chang, H.-Y. Yong, T. C. Chiu, Y.-F. Kuo, C.-H. Chu, H.-A. 2025-01-22 doi:10.1101/2025.01.17.633688 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ A hydrophobic core in the coiled-coil domain essential for NRC resistosome function ]]> https://biorxiv.org/content/10.1101/2025.01.21.634219v1?rss=1 Wang, H.-Y. Lee, K.-T. Goh, F.-J. Bozkurt, T. O. Wu, C.-H. 2025-01-24 doi:10.1101/2025.01.21.634219 Cold Spring Harbor Laboratory Press 2025-01-24 <![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[ Orthologous transcription factor replacement reveals that stable TFIIIC complexes are required for proper mitotic chromosome segregation ]]> https://biorxiv.org/content/10.1101/2025.01.30.635671v1?rss=1 Gupta, A. Hsu, P.-C. Litan, R. R. R. Leu, J.-Y. 2025-01-31 doi:10.1101/2025.01.30.635671 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Shared Alteration of Whole-Brain Connectivity and Olfactory Deficits in Multiple Autism Mouse Models ]]> https://biorxiv.org/content/10.1101/2025.02.02.636175v1?rss=1 Hsu, T.-T. Chen, C.-P. Lin, M.-H. Huang, T.-N. Wang, C.-Y. Lee, C.-M. Chen, B.-C. Wang, C.-Y. Hsueh, Y.-P. 2025-02-03 doi:10.1101/2025.02.02.636175 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ Mismatch repair and homologous recombination are yin-yang partners in hybrid zygote meiosis ]]> https://biorxiv.org/content/10.1101/2025.02.08.636946v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@db6794org.highwire.dtl.DTLVardef@6d5947org.highwire.dtl.DTLVardef@1004489org.highwire.dtl.DTLVardef@938403_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMMR and HR antagonize each other in intraspecies hybrid zygotes. C_LIO_LIThe HR proteins Rad51, Rad54, and ZMM exhibit anti-MMR activities. C_LIO_LIMMR overrides HR in hybrid zygotes with anti-MMR mutations, causing hybrid sterility. C_LI ]]> Chuang, C.-N. Hung, Y.-L. Kim, H.-X. Yao, J.-S. Liu, H.-C. Chen, S.-Y. Jovanska, L. Hsueh, Y.-P. Chen, R.-S. Wang, T.-F. 2025-02-10 doi:10.1101/2025.02.08.636946 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Natural Killer Cell Receptor Signaling and Activation Depend on Cell Cycle Stages ]]> https://biorxiv.org/content/10.1101/2025.02.24.639882v1?rss=1 Wethington, D. Nayak, I. Jensen, H. Stewart, W. C. Aguilar, O. A. Chen, S.-Y. Nolan, G. P. Behbehani, G. K. Lanier, L. L. Das, J. 2025-02-28 doi:10.1101/2025.02.24.639882 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Assigning Targetable Molecular Pathways to Transdiagnostic Subgroups Across Autism and Related Neurodevelopmental Disorders ]]> https://biorxiv.org/content/10.1101/2025.03.04.641443v1?rss=1 Ellegood, J. Beauchamp, A. Yee, Y. Devenyi, G. Ziolkowski, J. Qiu, L. Askalan, R. Ayub, M. Suetterlin, P. Donovan, A. Basson, M. A. Quesnel, K. M. Berube, N. G. Woo, T. Beversdorf, D. Bjornsson, H. Blakely, R. Crawley, J. Crosbie, J. Orr, B. O. Davis, G. W. Genestine, M. DiCicco-Bloom, E. Egan, S. Fink, K. D. Asbury, S. Lai, J. Rilett, K. Foster, J. A. Vincent, J. B. Frankland, P. Georgiades, S. Penagarikano, O. Geschwind, D. Giger, R. J. Markx, S. Gogos, J. Golzio, C. Pagani, M. Gozzi, A. Pacey, L. K. Hampson, D. Huang, T.-N. Yen, T.-L. Hsueh, Y.-P. 2025-03-10 doi:10.1101/2025.03.04.641443 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Unusual Ecofunctional Traits of Endozoicomonas: A Pan-Genomic Perspective ]]> https://biorxiv.org/content/10.1101/2025.03.06.641946v1?rss=1 Lim, S. L. Chin, C.-H. Chiou, Y.-J. Hsu, M.-T. Chiang, P.-W. Chen, H.-J. Tu, Y.-C. Tang, S.-L. 2025-03-11 doi:10.1101/2025.03.06.641946 Cold Spring Harbor Laboratory Press 2025-03-11 <![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[ Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation ]]> https://biorxiv.org/content/10.1101/2025.03.20.644374v1?rss=1 Jin, C. Lundstrom, J. Cori, C. R. Guu, S.-Y. Bennett, A. R. Dannborg, M. Bengtsson-Palme, J. Hevey, R. Khoo, K.-H. Bojar, D. 2025-03-20 doi:10.1101/2025.03.20.644374 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ The cellular and behavioral blueprints of chordate rheotaxis. ]]> https://biorxiv.org/content/10.1101/2025.03.22.644710v1?rss=1 Tolstenkov, O. Ozawa, A. Allombert-Blaise, C. Hiraiwa, T. Chatzigeorgiou, M. 2025-03-24 doi:10.1101/2025.03.22.644710 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Misregulation of the jasmonate signaling pathway leads to altered plant microbiota interaction and plant stress responses ]]> https://biorxiv.org/content/10.1101/2025.03.29.646076v1?rss=1 Lu, T.-T. Isip, M. Shih, H.-J. S. Perin, S. Ma, K.-W. 2025-03-31 doi:10.1101/2025.03.29.646076 Cold Spring Harbor Laboratory Press 2025-03-31 <![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[ Natural spider silk enhances mechanical performance of collagen scaffold under stretching conditions ]]> https://biorxiv.org/content/10.1101/2025.03.27.645864v1?rss=1 Tso, I.-M. Tsiareshyna, M. Huang, S. Y. T. Liao, C.-P. Tang, M.-J. Wong, T.-Y. 2025-04-01 doi:10.1101/2025.03.27.645864 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ N-glycosylation Enables Smut Fungal Nge1 Orthologs to Prevent the Escape of Maize Evolved-PMEIs ]]> https://biorxiv.org/content/10.1101/2025.04.01.646729v1?rss=1 Bhaskar, C. Chau, M.-Q. Tsai, W.-L. Teh, O.-K. Ma, L.-S. 2025-04-02 doi:10.1101/2025.04.01.646729 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ A high-quality chromosome-level genome of an undescribed Meretrix species using Nanopore and Hi-C technologies ]]> https://biorxiv.org/content/10.1101/2025.04.01.646383v1?rss=1 Chen, C.-C. Hsu, T.-H. Lu, H.-Y. Tang, S.-L. Ho, Y.-N. 2025-04-06 doi:10.1101/2025.04.01.646383 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ Spatiotemporal differences of GABAergic polarization and shunting during dendritic integration ]]> https://biorxiv.org/content/10.1101/2025.04.05.647352v1?rss=1 Dembitskaya, Y. Kirsanov, A. Wu, Y.-W. Brazhe, A. Semyanov, A. 2025-04-07 doi:10.1101/2025.04.05.647352 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Evolutionary dynamics of FoxQ2 transcription factors across metazoans: A tale of three ancient paralogs ]]> https://biorxiv.org/content/10.1101/2025.04.23.650082v1?rss=1 Gattoni, G. Lin, C.-Y. York, J. R. Keitley, D. LaBonne, C. Yu, J.-K. Gillis, A. Benito-Gutierrez, E. 2025-04-24 doi:10.1101/2025.04.23.650082 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Age-related declines in niche self-renewal factors controls testis aging and spermatogonial stem cell competition through Hairless, Imp, and Chinmo ]]> https://biorxiv.org/content/10.1101/2025.05.01.651651v1?rss=1 Zheng, Y. Lee, Y.-C. Wang, Y.-T. Chiang, P.-K. Chang, S.-L. Hsu, H.-J. Hsu, L.-S. Bach, E. Tseng, C.-Y. 2025-05-02 doi:10.1101/2025.05.01.651651 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Floral Stage Optimization and Immune Evasion Enhance Agrobacterium-Mediated Genome Editing in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.05.07.652770v1?rss=1 Liu, M.-S. Huang, T.-K. Wang, Y.-C. Wang, S.-C. WU, C.-H. Kuo, C.-H. Lai, E.-M. 2025-05-08 doi:10.1101/2025.05.07.652770 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Spatial proteomics reveals lipid droplet reorganization in symbiotic Paramecium bursaria cells ]]> https://biorxiv.org/content/10.1101/2025.05.12.652804v1?rss=1 Chen, Y.-J. Kamal, M. M. Hsu, C.-C. Leu, J.-Y. 2025-05-12 doi:10.1101/2025.05.12.652804 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ An early evolutionary stage of mutualistic endosymbiosis reveals a parasitic aspect of endosymbionts ]]> https://biorxiv.org/content/10.1101/2025.05.12.653378v1?rss=1 Kamal, M. M. Cheng, Y.-H. Chu, L.-W. Nguyen, P. T. Jeff Liu, C.-F. Liao, C.-W. Posch, T. Leu, J.-Y. 2025-05-15 doi:10.1101/2025.05.12.653378 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Five new Caenorhabditis species from Indonesia provide exceptions to Haldane's rule and partial fertility of interspecific hybrids ]]> https://biorxiv.org/content/10.1101/2025.05.14.653126v1?rss=1 Devi, M. P. Haryoso, E. Rais, E. I. Karuniawan, A. Yahya, M. Q. Richaud, A. Wang, J. Rockman, M. V. Tarno, H. Felix, M.-A. 2025-05-17 doi:10.1101/2025.05.14.653126 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ A Ventromedial Hypothalamic Neuron Subset Encodes a Conspecific-Tuned Behavior State Driving Social Investigation ]]> https://biorxiv.org/content/10.1101/2025.05.30.650902v1?rss=1 Lin, S.-C. A. Hsu, J.-Y. Su, T.-A. Lee, H.-Z. Yang, S.-B. 2025-05-30 doi:10.1101/2025.05.30.650902 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Abnormal synaptic proteomes, impaired neural ensembles, and defective behaviors in autism mouse models are ameliorated by dietary intervention with nutrient mixtures ]]> https://biorxiv.org/content/10.1101/2025.05.29.656761v1?rss=1 Huang, T.-N. Lin, M.-H. Hsu, T.-T. Yu, C.-H. Hsueh, Y.-P. 2025-06-01 doi:10.1101/2025.05.29.656761 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Developmental system drift in dorsoventral patterning is linked to transitions to autonomous development in Annelida ]]> https://biorxiv.org/content/10.1101/2025.05.29.656861v1?rss=1 Carrillo-Baltodano, A. M. Haillot, E. Meha, S. M. Luqman, I. Pashaj, A. Lee, Y.-J. Lu, T.-M. Ferrier, D. E. K. Schneider, S. Q. Martin-Duran, J. M. 2025-06-01 doi:10.1101/2025.05.29.656861 Cold Spring Harbor Laboratory Press 2025-06-01 <![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[ Evaluation of Multiplexed Liquid Glycan Array (LiGA) for Serological Detection of Glycan-binding Antibodies ]]> https://biorxiv.org/content/10.1101/2025.06.23.660925v1?rss=1 Reddy, R. Carpenter, E. J. Halpin, A. Sojitra, M. Peng, C. Lima, G. M. Xue, X. Yan, K. Pearcy, J. Ellis, M. Motyka, B. Lowary, T. L. West, L. J. Derda, R. 2025-06-27 doi:10.1101/2025.06.23.660925 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Single-cell-resolved calcium and organelle dynamics in resistosome-mediated cell death ]]> https://biorxiv.org/content/10.1101/2025.06.27.662017v1?rss=1 Chen, Y.-F. Lin, K.-Y. Huang, C.-Y. Hou, L.-Y. Yuen, E. L. H. Sun, W.-C. J. Chiang, B.-J. Chang, C.-W. Wang, H.-Y. Bozkurt, T. O. Wu, C.-H. 2025-07-01 doi:10.1101/2025.06.27.662017 Cold Spring Harbor Laboratory Press 2025-07-01 <![CDATA[ Deconstructing the common anteroposterior organisation of adult bilaterian guts ]]> https://biorxiv.org/content/10.1101/2025.07.02.662275v1?rss=1 Vianello, S. D. Lin, C.-Y. Pinem, W. C. Li, H.-R. Li, K.-L. Sonia, G. Lee, S.-H. Wu, S.-K. Laudet, V. Su, Y.-H. Yu, J.-K. Schneider, S. Q. 2025-07-03 doi:10.1101/2025.07.02.662275 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Virus-induced upregulation of mitochondrial metabolism modulates cytosolic redox balance and defense responses ]]> https://biorxiv.org/content/10.1101/2025.07.05.663277v1?rss=1 Hou, L.-Y. Wu, C.-H. Lin, N.-S. 2025-07-06 doi:10.1101/2025.07.05.663277 Cold Spring Harbor Laboratory Press 2025-07-06 <![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[ A Hierarchical Robust Linear Model for Cryo-EM Map Analysis ]]> https://biorxiv.org/content/10.1101/2025.07.10.664269v1?rss=1 Tu, I.-P. Zheng, S.-C. Lien, Y.-H. Lin, S. H. Lin, P.-C. Chang, W.-H. 2025-07-14 doi:10.1101/2025.07.10.664269 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ A plant pathogen effector blocks stepwise assembly of a helper NLR resistosome ]]> https://biorxiv.org/content/10.1101/2025.07.14.664264v1?rss=1 Seager, B. A. Harant, A. Contreras, M. P. Hou, L.-Y. Wu, C.-H. Kamoun, S. Madhuprakash, J. 2025-07-14 doi:10.1101/2025.07.14.664264 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Fine-tuning RIPENING INHIBITOR (RIN) expression by introducing allelic mutations in its promoter using CRISPR/Cas9 multiplex editing ]]> https://biorxiv.org/content/10.1101/2025.07.14.664838v1?rss=1 Zhou, J. Yang, C.-L. Beckles, D. M. 2025-07-18 doi:10.1101/2025.07.14.664838 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ The genome of the early diverged amphioxus, Asymmetron lucayanum, illuminates the evolution of genome architecture and gene repertoires in cephalochordates ]]> https://biorxiv.org/content/10.1101/2025.07.21.665930v1?rss=1 Ren, Y. Miao, Z. Lin, C.-Y. Yang, L. Li, H. Holland, L. Z. Cho, S.-J. Yu, J.-K. Yue, J.-X. 2025-07-22 doi:10.1101/2025.07.21.665930 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Temporal coordination of tissue transformation, olfactory sensory neural development and central axon projections through morphogens ]]> https://biorxiv.org/content/10.1101/2025.07.21.666031v1?rss=1 Chen, S.-C. Lu, T.-M. Lin, C.-T. Low, I. Z. Q. Chou, Y.-H. 2025-07-22 doi:10.1101/2025.07.21.666031 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Regulation of mRNA polyadenylation governs mammalian body plan formation in gastruloids ]]> https://biorxiv.org/content/10.1101/2025.07.22.666114v1?rss=1 Taborsky, D. Valdivia-Francia, F. Ranjbar, N. Llop-Grau, L. Dure, C. Ghoshdastider, U. Renz, P. F. Weber, R. Yigit, M. Mironov, A. Hyams, K. Vianello, S. Zavolan, M. Lutolf, M. P. Sendoel, A. 2025-07-22 doi:10.1101/2025.07.22.666114 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ The Multifaceted Role of EXOC6A in Ciliogenesis ]]> https://biorxiv.org/content/10.1101/2025.07.25.666797v1?rss=1 Tang, T. K. Wu, C.-T. Lin, T.-L. 2025-07-26 doi:10.1101/2025.07.25.666797 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ A sensitive orange fluorescent calcium ion indicator for imaging neural activity ]]> https://biorxiv.org/content/10.1101/2025.07.28.667269v1?rss=1 Aggarwal, A. Baker, H. A. Durst, C. D. Chen, I.-W. de Chambrier, P. Gonzales, J. M. Marvin, J. S. Vandal, M. Lundberg, T. Sakoi, K. Patel, R. H. Wang, C.-Y. Visser, F. Fouad, Y. Sunil, S. Wiens, M. Terai, T. Takahashi-Yamashiro, K. Thompson, R. J. Brown, T. A. Nasu, Y. Nguyen, M. D. Gordon, G. R. J. McFarlane, S. Podgorski, K. Holtmaat, A. Campbell, R. E. Lohman, A. W. 2025-07-31 doi:10.1101/2025.07.28.667269 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Two pore domain THIK2 channel is involved in acute and chronic pain signal regulation ]]> https://biorxiv.org/content/10.1101/2025.08.08.669258v1?rss=1 Gilbert, N. Chatelain, F. C. Gibaud, S. Lorivel, T. Shen, Y.-L. kerros, M.-E. Feliciangeli, S. Fiore, F. Chen, C.-C. Lesage, F. Delphine, B. 2025-08-12 doi:10.1101/2025.08.08.669258 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Distinct Flower signaling domains orchestrate cellular fitness via secreted vesicles in Aβ-induced neurodegeneration ]]> https://biorxiv.org/content/10.1101/2025.08.08.669265v1?rss=1 Chang, H.-F. Tu, S.-M. Lin, C.-H. Liu, Y. Hohneck, J. Jung, M. Clemenz, A. Rother, S. Schirra, C. Schwarz, Y. Krause, E. Schulz-Schaeffer, W. J. Flockerzi, V. Yao, C.-K. 2025-08-12 doi:10.1101/2025.08.08.669265 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Multigram-scale stereoselective synthesis of neurosteroid isomers by gut microbial isolates using plant biomass-derived medium ]]> https://biorxiv.org/content/10.1101/2025.08.20.671209v1?rss=1 95% progesterone conversion into target neurosteroid isomers. The inherent stereoselectivity of these whole-cell biotransformations bypasses downstream chiral chromatographic separation, enabling pharmaceutical-grade product recovery through a simple open-column purification. Compared to using peptone-yeast-glucose media for whole-cell biotransformation, MOM reduced production costs by 90% and carbon footprint by 95% that embodies sustainable bioeconomy principles in pharmaceutical biotechnology. Technology Readiness BoxWe argue that this gut microbiota-derived neurosteroid bioproduction technology has reached a Technology Readiness Level (TRL) of 4, having been validated in laboratory environments with the demonstrated multigram-scale synthesis of high-purity neurosteroids. The platform integrates stereoselective bacterial isolates (Holdemania filiformis, Clostridium innocuum, and Hungatella effluvii) with a sustainable plant-based fermentation medium (molasses-okara medium), achieving >90% progesterone conversion efficiency, >99.9% stereochemical purity, and the successful production of 0.7-0.9 g of neurosteroids per gram of progesterone across multiple 1 L fed-batch fermentations. Compared with conventional chemical synthesis approaches that require expensive chiral catalysts and multi-step purification, this microbial platform offers inherent stereoselectivity while eliminating animal-derived media components. Despite these advantages, several challenges remain for industrial implementation, including scale-up validation beyond laboratory conditions, optimization of anaerobic bioprocess control at pilot scale, and ensuring consistent performance under variable industrial feedstock conditions. Addressing these issues will require pilot-scale demonstration (10-50 L bioreactors), process robustness validation, and supply chain development for plant-based feedstocks. Regulatory pathway development will also be essential for pharmaceutical applications, particularly establishing precedents for gut microbiota-derived therapeutic compounds under existing cGMP frameworks HighlightsO_LIIdentification of gut bacteria for stereoselective synthesis of neurosteroid isomers (isopregnanolone, epipregnanolone, pregnanolone) with >99% chiral purity C_LIO_LISustainable plant biomass-based medium replacing animal-derived components for whole-cell progesterone biotransformation C_LIO_LIMulti-gram scale production of progestogenic neurosteroids and one-step-open-column purification bypassing chiral chromatographic separation C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/671209v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@11147b0org.highwire.dtl.DTLVardef@1799d64org.highwire.dtl.DTLVardef@14c33deorg.highwire.dtl.DTLVardef@1e14e21_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gicana, R. G. Wang, P.-H. Huang, Y.-H. Huang, M.-H. Wu, T.-Y. Lai, Y.-L. Brandon-Mong, G.-J. Wei, Y. Yeo, W. W. Z. Ng, I.-S. Chiang, Y.-R. 2025-08-24 doi:10.1101/2025.08.20.671209 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ Cell-cell communication as underlying principle governing color pattern formation in fishes ]]> https://biorxiv.org/content/10.1101/2025.08.21.671633v1?rss=1 Klann, M. Miura, S. Lee, S.-H. Vianello, S. D. Ross, R. Watanabe, M. Gairin, E. Liang, Y. Hutto, H. W. McCluskey, B. M. Herrera, M. Solnica-Krezel, L. Besseau, L. Pigolotti, S. Parichy, D. M. Kinoshita, M. Laudet, V. 2025-08-25 doi:10.1101/2025.08.21.671633 Cold Spring Harbor Laboratory Press 2025-08-25 <![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[ Pleistocene demographic histories dominate contemporary genomic diversity in a continental radiation of Himalayan-Hengduan songbirds ]]> https://biorxiv.org/content/10.1101/2025.08.28.672032v1?rss=1 Liu, Y. Hung, C.-M. He, Y. Wu, F. Yan, D. Song, G. Dong, F. 2025-08-30 doi:10.1101/2025.08.28.672032 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ What Large Language Models Know About Plant Molecular Biology ]]> https://biorxiv.org/content/10.1101/2025.08.31.672925v1?rss=1 Fernandez Burda, M. Ferrero, L. Gaggion, N. Fonouni-Farde, C. Iglesias, M. J. Fragkostefanakis, S. Tonelli, M. L. Zanetti, M. E. Krapp, A. Mencia, R. Romani, F. Muschietti, J. P. Mansilla, N. Casal, J. Pagnussat, L. A. Ballare, C. L. Mammarella, M. F. Blanco, F. A. Roy, S. Maroniche, G. A. Rivarola, M. Fiol, D. F. Cubas, P. Dezar, C. Casati, P. Ibanez, F. Fernanda, d. C.-N. Staiger, D. Fusari, C. M. Auge, G. Arana, M. V. Parmar, R. Zhang, W. Mathur, S. Verslues, P. E. V. Manavella, P. A. Mateos, J. L. Bouche, N. Lucero, L. E. Drincovich, M. F. Traubenik, 2025-09-04 doi:10.1101/2025.08.31.672925 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Critical phenomenon underlies de novo luminogenesis during mammalian follicle development ]]> https://biorxiv.org/content/10.1101/2025.09.09.674793v1?rss=1 Leong, K. W. Lou, Y. Biswas, A. Tan, J. Y. Ng, B. H. Lu, X. Teo, X. P. Lu, T. B. Bevilacqua, C. Bonne, I. Prevedel, R. Hiraiwa, T. Chan, C. J. 2025-09-11 doi:10.1101/2025.09.09.674793 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ H3N2 influenza virus tropism shifts to glycan receptors on tracheal ciliated cells ]]> https://biorxiv.org/content/10.1101/2025.09.12.675939v1?rss=1 Kikuchi, C. Antonopoulos, A. Wang, S. Biyasheva, A. Chien, Y.-C. Bharat, A. McBride, R. Nycholat, C. M. Thompson, A. J. Dell, A. Khoo, K.-H. Schleimer, R. Haslam, S. M. Paulson, J. C. 2025-09-13 doi:10.1101/2025.09.12.675939 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Eco-genomic analysis uncovers precision-conservation targets for the western Pacific's southernmost salmonid ]]> https://biorxiv.org/content/10.1101/2025.09.09.675276v1?rss=1 Lee, Y.-C. Shen, Z.-Y. Lin, W.-R. Wang, T.-Y. Liu, M. Yeh, Y.-C. Chan, S.-F. Lu, M.-Y. J. Wang, H.-Y. Liao, L.-Y. Li, W.-H. Huang, J.-P. Tsai, I. J. Shen, S.-F. 2025-09-15 doi:10.1101/2025.09.09.675276 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Genome dynamics across the radiation of a mega-diverse genus ]]> https://biorxiv.org/content/10.1101/2025.09.17.676772v1?rss=1 Campos-Dominguez, L. Kongsted, T. E. Cure, L. Downie, M. Martinez-Martinez, A. Fan, C. Dong, L. N. Tseng, Y. H. Hu, A. Q. Chung, K. F. Pellicer, J. Leitch, I. J. Bombarely, A. Twyford, A. D. Kidner, C. A. 2025-09-20 doi:10.1101/2025.09.17.676772 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Novel Tissue Mechanics-Guided Cellular Flows Enable the Evolution of Feather Follicles ]]> https://biorxiv.org/content/10.1101/2025.10.01.679696v1?rss=1 Harn, H. I.-C. Jiang, T.-X. Huang, C.-H. Juan, W.-T. Liu, T.-Y. Chuang, T.-C. Liao, W.-C. Wang, Y. Weijer, C. J. Wu, P. Guo, C.-L. Chuong, C.-M. 2025-10-01 doi:10.1101/2025.10.01.679696 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Ca2+ Plateau Potentials Reflect Cross-Theta Cortico-Hippocampal Input Dynamics and Acetylcholine for Rapid Formation of Efficient Place-Cell Code ]]> https://biorxiv.org/content/10.1101/2025.10.01.676159v1?rss=1 Wang, H.-Y. Hsu, Y.-C. Huang, H.-P. Chen, C.-T. Huang, X.-B. Wang, C.-T. Naud, R. Hsu, C.-L. 2025-10-02 doi:10.1101/2025.10.01.676159 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Histological divergence underlying globular body shapes in ornamental goldfish ]]> https://biorxiv.org/content/10.1101/2025.10.01.679695v1?rss=1 Ota, K. G. Abe, G. Wang, C.-Y. Li, I.-J. Sanchez, P. G. L. 2025-10-02 doi:10.1101/2025.10.01.679695 Cold Spring Harbor Laboratory Press 2025-10-02 <![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[ Pervasive suppressors halt the spread of selfish Segregation Distorter in a natural population ]]> https://biorxiv.org/content/10.1101/2025.10.13.681989v1?rss=1 Chang, C.-H. Handler, T. Fuda, N. Pascua, D. Mouton, T. Larracuente, A. M. 2025-10-14 doi:10.1101/2025.10.13.681989 Cold Spring Harbor Laboratory Press 2025-10-14 <![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[ Bacteriophages of the predominant coral symbiont Endozoicomonas: novel models for coral holobiont interactions ]]> https://biorxiv.org/content/10.1101/2025.10.29.685362v1?rss=1 Chuang, P.-S. Chen, M. Chiang, P.-W. Chen, H.-J. Wang, F.-Q. Chen, Y.-H. Yu, S.-P. Chen, F.-C. Shih, K.-N. Chang, Y.-P. Lim, S. L. Chang, H.-F. Jane, W.-N. Tang, S.-L. 2025-10-30 doi:10.1101/2025.10.29.685362 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ MEX3A control of mitochondrial fitness is essential for ovarian clear cell carcinoma tumorigenesis and liver metastasis ]]> https://biorxiv.org/content/10.1101/2025.11.05.686880v1?rss=1 Vinothkumar, P. Lin, P.-Y. Cheng, L.-T. Yu, C.-H. Hsu, P.-H. Chou, Y.-C. Hwang-Verslues, W. W. 2025-11-07 doi:10.1101/2025.11.05.686880 Cold Spring Harbor Laboratory Press 2025-11-07 <![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[ Targeting STING-ATM axis overcomes radiotherapy-induced immune suppression and restores anti-tumor immunity in nasopharyngeal carcinoma ]]> https://biorxiv.org/content/10.1101/2025.11.12.687945v1?rss=1 Liu, T.-T. Chang, K.-P. Wang, Y.-N. OuYang, C.-N. Li, M.-H. Tsang, N.-M. Jiang, S. S. Sui, Y.-H. Hu, C.-M. Chou, Y.-C. Chen, H.-C. Liu, S.-C. 2025-11-13 doi:10.1101/2025.11.12.687945 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Structure and functional analyses of Vaccinia virus entry- fusion complex component J5 protein ]]> https://biorxiv.org/content/10.1101/2025.11.13.688282v1?rss=1 Chang, W. Chiu, H.-J. Tzou, D.-L. Carillo, K. J. Hsieh, L. T.-H. 2025-11-14 doi:10.1101/2025.11.13.688282 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Establishment of a Congenic Strain for the Oyster mushroom reveals the Structure and Evolution of Mating-Type Loci ]]> https://biorxiv.org/content/10.1101/2025.11.21.689727v1?rss=1 Lee, Y.-Y. Vidal-Diez de Ulzurrun, G. Tay, R. J. Hsueh, Y.-P. 2025-11-21 doi:10.1101/2025.11.21.689727 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening ]]> https://biorxiv.org/content/10.1101/2025.11.24.690302v1?rss=1 Hsieh, W.-H. Hung, Y.-H. Zhang, J.-H. Chen, H.-Y. Lin, L.-P. He, M.-H. Wang, Y.-C. Ho, Y.-Y. Fernandez, G. Perkins-Veazie, P. Le, B. Li, X. Hsieh, T.-F. Lin, J.-Y. 2025-11-27 doi:10.1101/2025.11.24.690302 Cold Spring Harbor Laboratory Press 2025-11-27 <![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[ Root meristem growth factor (RGF) peptide signaling as a molecular bridge between root development and non-lethal thermal stress adaptation ]]> https://biorxiv.org/content/10.1101/2025.11.27.690926v1?rss=1 Hsiao, Y.-C. Lai, J.-K. Shiue, S.-Y. YAMADA, M. 2025-11-28 doi:10.1101/2025.11.27.690926 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ A 3D Amphioxus Brain Atlas Illuminates the Blueprint of the Ancestral Chordate Brain ]]> https://biorxiv.org/content/10.1101/2025.11.27.690639v1?rss=1 Lin, C.-Y. Hsu, W.-H. Lu, M.-Y. J. Chen, Y.-H. Chen, Y.-C. Su, Y.-H. Chou, S.-J. Yu, J.-K. 2025-11-29 doi:10.1101/2025.11.27.690639 Cold Spring Harbor Laboratory Press 2025-11-29 <![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[ Deep Mediation Analysis for Multimodal Genotype-Imaging Associations with Disease Phenotypes ]]> https://biorxiv.org/content/10.64898/2025.11.20.689376v1?rss=1 Golderzahi, V. Wang, G.-J. Hu, J. Yeang, C.-H. 2025-12-05 doi:10.64898/2025.11.20.689376 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ OsIDS3L, a Non-Canonical Dioxygenase Enhancing Iron Homeostasis and Micronutrient Biofortification in Rice ]]> https://biorxiv.org/content/10.64898/2025.12.07.692860v1?rss=1 Aggarwal, J. Yeh, K.-C. 2025-12-09 doi:10.64898/2025.12.07.692860 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes ]]> https://biorxiv.org/content/10.64898/2025.12.08.693002v1?rss=1 Moya, N. D. Wang, B. Tanny, R. E. Sauria, M. E. G. O'Connor, L. M. Khorshidian, A. McKeown, R. Gosse, C. Dilks, C. M. Crombie, T. A. Zhang, G. Rais, E. Frezal, L. Dang, V. D. Haryoso, E. Devi, M. P. Gimond, C. Cook, D. E. Hsu, J.-C. Shaver, A. O. Zdraljevic, S. Richaud, A. Wen, T. Mehraj, A. H, S. Arulprakasam, K. R. Koury, E. J. Roberto, N. M. Schaye, E. S. Singh, V. Tarno, H. Ailion, M. Paaby, A. B. Zhao, Z. Cutter, A. D. Wang, J. Rockman, M. V. Braendle, C. Andersen, E. C. 2025-12-11 doi:10.64898/2025.12.08.693002 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Retention of a single Cenp-C gene in different syntenic locations in the montium group of Drosophila species ]]> https://biorxiv.org/content/10.64898/2025.12.11.693522v1?rss=1 Soares, R. F. Chang, C.-H. Koerich, L. B. Malik, H. S. KUHN, G. C. S. 2025-12-15 doi:10.64898/2025.12.11.693522 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ A novel, fig-associated microbe promotes reproductive success via variable life history mechanisms in C. elegans and C. inopinata ]]> https://biorxiv.org/content/10.64898/2025.12.16.694684v1?rss=1 Link, A. C. Moser, K. A. Wang, J. Woodruff, G. C. 2025-12-19 doi:10.64898/2025.12.16.694684 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Dynamic evolution of AT-rich isochores shapes the genome of an intertidal fungus Annulohypoxylon annulatoides ]]> https://biorxiv.org/content/10.64898/2025.12.16.694779v1?rss=1 Kuo, C.-Y. T.-U. Liu, Y.-C. Yang, C.-J. Lin, C.-P. Chen, H.-W. Hsieh, H.-M. Ju, Y.-M. Liu, T.-H. Lee, Y.-C. Tsai, I. J. 2025-12-19 doi:10.64898/2025.12.16.694779 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Scube2 Modulates Coronary Vessel Formation during Cardiac Growth and Regeneration in Zebrafish ]]> https://biorxiv.org/content/10.64898/2025.12.17.695032v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@7c5b5org.highwire.dtl.DTLVardef@451c40org.highwire.dtl.DTLVardef@141c88forg.highwire.dtl.DTLVardef@1d63765_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lai, S.-L. B. Lee, A. N. Wei, K.-H. Chowdhury, K. Rouf, M. A. Chu, A.-J. Hung, Y.-J. Tsao, K.-C. Chen, Y.-T. Lin, Y.-C. Chang, Y.-M. Marin-Juez, R. Yang, R.-B. 2025-12-19 doi:10.64898/2025.12.17.695032 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Molecular bases for USP48 cis-activity regulation and hyperactivation by Cushing's disease-associated mutations ]]> https://biorxiv.org/content/10.64898/2025.12.27.696724v1?rss=1 Ando, G. Tsujimoto, Y. Moritsugu, K. Kakihara, K. Kidera, A. Yamada, S. Komada, M. Fukuoka, H. Fukushima, T. 2025-12-28 doi:10.64898/2025.12.27.696724 Cold Spring Harbor Laboratory Press 2025-12-28 <![CDATA[ Rescuing Neurodevelopmental Deficits in AMPA Receptor Gain-of-Function Mutant ]]> https://biorxiv.org/content/10.64898/2025.12.30.697121v1?rss=1 Chen, C.-M. Huang, Y.-M. Chung, C.-C. Johnson, R. C. Tsai, C.-Y. Chen, Y.-H. Tan, H. L. Hsiao, F.-Y. Huganir, R. L. Chiu, S.-L. 2025-12-31 doi:10.64898/2025.12.30.697121 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Resilience and reassembly of redox-structured microbial functional networks after rare holomixis in a meromictic lake ]]> https://biorxiv.org/content/10.64898/2026.01.18.698864v1?rss=1 Chan, Y.-F. Chiang, P.-W. Lim, S. L. Rogozin, D. Zykov, V. Ye, C.-H. Tang, S.-L. 2026-01-19 doi:10.64898/2026.01.18.698864 Cold Spring Harbor Laboratory Press 2026-01-19 <![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[ A haploid wild yeast resource for exploring the natural ecology of Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.64898/2026.02.13.705822v1?rss=1 Yang, C.-J. Yeh, Y.-C. Hsiao, C. Liu, Y.-H. Lu, M. R. Liu, Y.-C. Liti, G. Tsai, I. J. Ke, H.-M. 2026-02-16 doi:10.64898/2026.02.13.705822 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Structure and functional analyses of vaccinia virus J5 protein reveal distinct determinants for entry-fusion complex assembly and activation ]]> https://biorxiv.org/content/10.64898/2026.03.08.710424v1?rss=1 Chiu, H.-J. Carillo, K. J. D. Hsieh, L. T.-H. Lou, Y.-C. Lin, C. S.-H. Tzou, D.-L. M. Chang, W. 2026-03-09 doi:10.64898/2026.03.08.710424 Cold Spring Harbor Laboratory Press 2026-03-09 <![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[ Oxidative Stress-Induced Microglial CD22 Upregulation Impairs Phagocytosis and Exacerbates Huntingtons Disease ]]> https://biorxiv.org/content/10.64898/2026.03.11.710967v1?rss=1 Lee, Y. H. Siew, J. J. Lee, C.-W. Chen, H.-M. Lu, Y.-T. Sridharan, D. Huang, P.-C. J. Chang, H.-C. Guu, S.-Y. Wang, P.-Y. Wang, Y.-F. Liang, S.-Y. Khoo, K.-H. Angata, T. Chern, Y. 2026-03-13 doi:10.64898/2026.03.11.710967 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Calcium modulates intramolecular long-range contacts to form a polymorphic α-synuclein A53T fibril ]]> https://biorxiv.org/content/10.64898/2026.03.14.711779v1?rss=1 Huang, J. Y. C. Wu, K.-P. 2026-03-17 doi:10.64898/2026.03.14.711779 Cold Spring Harbor Laboratory Press 2026-03-17 <![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[ IFN-γ-Dependent Macrophage Reprogramming Coordinates Inflammatory Resolution and Matrix Remodeling in Heart Regeneration ]]> https://biorxiv.org/content/10.64898/2026.03.18.712551v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@8cb384org.highwire.dtl.DTLVardef@15dd8d6org.highwire.dtl.DTLVardef@46dcc4org.highwire.dtl.DTLVardef@47e2ac_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lim, K. L. Chowdhury, K. Hung, Y.-J. Lai, S.-L. 2026-03-20 doi:10.64898/2026.03.18.712551 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Effect of spatial heterogeneities on minimal stochastic models of cell polarity ]]> https://biorxiv.org/content/10.64898/2026.03.27.714696v1?rss=1 Anfray, V. Shih, H.-Y. 2026-03-28 doi:10.64898/2026.03.27.714696 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ Root Hydraulic and Metabolic Regulation Drives Drought Tolerance in Napier Grass ]]> https://biorxiv.org/content/10.64898/2026.03.28.714958v1?rss=1 Ko, S.-S. Wu, Y.-C. Cheng, S.-C. Li, M.-J. Li, T.-R. Lin, J.- B. Sun, C.-H. Chou, C. C.- K. Yeh, K.-C. 2026-03-31 doi:10.64898/2026.03.28.714958 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Endosymbiotic algal photosynthesis shapes diel transcriptome architecture in its ciliate host Paramecium bursaria ]]> https://biorxiv.org/content/10.64898/2026.03.31.715701v1?rss=1 Kamal, M. M. Cheng, Y.-H. Yang, C.-L. Jeff Liu, C.-F. Ku, C. Leu, J.-Y. 2026-04-01 doi:10.64898/2026.03.31.715701 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 <![CDATA[ Evolutionary landscapes of zygotic genome activation across animals ]]> https://biorxiv.org/content/10.64898/2026.04.16.718233v1?rss=1 Campo-Bes, I. Mantica, F. Permanyer, J. Rodriguez-Marin, C. Guynes, K. Senar-Serra, T. Quiroga-Artigas, G. Liang, Y. Carrillo-Baltodano, A. M. Cruz, J. Annunziata, R. Chevalier, S. Iglesias, M. Sugahara, F. Luo, Y.-J. Schoenauer, A. Corbacho, J. Paganos, P. Caccavale, F. Sepe, R. M. Iniguez, L. P. Handberg-Thorsager, M. Zakas, C. Sommer, R. J. Arnone, M. I. McGregor, A. P. Martinez-Morales, J. R. Satoh, N. Escriva, H. Bertrand, S. Sebe-Pedros, A. D'Aniello, E. Pascual-Anaya, J. Houliston, E. Franch-Marro, X. Martin, D. Somorjai, I. M. L. Almudi, I. Martin- 2026-04-17 doi:10.64898/2026.04.16.718233 Cold Spring Harbor Laboratory Press 2026-04-17 <![CDATA[ An N-degron proteolytic pathway modulates recipient susceptibility to T6SS DNase effectors ]]> https://biorxiv.org/content/10.64898/2026.04.17.719174v1?rss=1 Wen, Y.-H. V. Lin, H.-H. Zheng, X.-T. Hwang, H.-H. Lai, E.-M. 2026-04-19 doi:10.64898/2026.04.17.719174 Cold Spring Harbor Laboratory Press 2026-04-19 <![CDATA[ A broad-host-range Rhizobium rhizogenes strain enables transient expression across diverse crops and establishes functional assays in faba bean ]]> https://biorxiv.org/content/10.64898/2026.04.20.719558v1?rss=1 King, F. Lopez-Agudelo, J. C. Stephens, C. Aung, M. H. Ibrahim, T. Yuen, E. L. H. Chen, A. Eilmann, N. M. Jenkins, S. Vuolo, C. Swee, Y.-N. Liu, W.-J. Bruty, S. Toghani, A. Kuo, C.-H. Lai, E.-M. Kourelis, J. Derevnina, L. Wu, C.-H. Bozkurt, T. O. 2026-04-22 doi:10.64898/2026.04.20.719558 Cold Spring Harbor Laboratory Press 2026-04-22