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Nucleic Acids Research, Volume 49

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Volume 49, Number Database-Issue, January 2021

Editorial

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Daniel J. Rigden, Xosé M. Fernández:
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. D1-D9

Major Multi-Database Resources

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Eric W. Sayers, Jeffrey Beck, Evan Bolton, Devon Bourexis, James R. Brister, Kathi Canese, Donald C. Comeau, Kathryn Funk, Sunghwan Kim, William Klimke, Aron Marchler-Bauer, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Nuala A. O'Leary, Lon Phan, Sanjida H. Rangwala, Valerie A. Schneider, Yuri Skripchenko, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the National Center for Biotechnology Information. D10-D17
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Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Shuhui Song, Lina Ma, Dong Zou, Dongmei Tian, Cuiping Li, Junwei Zhu, Zheng Gong, Meili Chen, Anke Wang, Yingke Ma, Mengwei Li, Xufei Teng, Ying Cui, Guangya Duan, Mochen Zhang, Tong Jin, Chengmin Shi, Zhenglin Du, Yadong Zhang, Chuandong Liu, Rujiao Li, Jingyao Zeng, Lili Hao, Shuai Jiang, Hua Chen, Dali Han, Tao Zhang, Wang Kang, Fei Yang, Jing Qu, Weiqi Zhang, Guanghui Liu, Lin Liu, Yang Zhang, Guangyi Niu, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Zhao Li, Ruru Chen, Qianpeng Li, Zhongyi Hua, Chao Jiang, Ziyuan Chen, Fangshu He, Yuyang Zhao, Yan Jin, Luqi Huang, Yuan Yuan, Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Qiang Du, Wenting Zong, Hongen Kang, Zhuang Xiong, Wendi Huan, Sirui Zhang, Qiguang Xia, Xiaojuan Fan, Zefeng Wang, Xu Chen, Tingting Chen, Sisi Zhang, Bixia Tang, Lili Dong, Zhewen Zhang, Zhonghuang Wang, Hailong Kang, Yanqing Wang, Song Wu, Ming Chen, Chang Liu, Yujia Xiong, Xueying Shao, Yanyan Li, Honghong Zhou, Xiaomin Chen, Yu Zheng, Quan Kang, Di Hao, Lili Zhang, Huaxia Luo, Yajing Hao, Peng Zhang, Zhi Nie, Shuhuan Yu, Jian Sang, Zhaohua Li, Xiangquan Zhang, Qing Zhou, Shuang Zhai, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Jun Yan, Chen Li, Zhennan Wang, Xiangfeng Wang, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Hai-Chun Jing, Lianhe Zhao, Jiajia Wang, Tinrui Song, Yi Zhao, Furrukh Mehmood, Shahid Ali, Amjad Ali, Shoaib Saleem, Irfan Hussain, Amir Ali Abbasi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Yiran Tu, Yu Xue, Wanying Wu, Peifeng Ji, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Wanshan Ning, Shaofeng Lin, Teng Liu, An-Yuan Guo, Hao Yuan, Yong E. Zhang, Xiaodan Tan, Weizhi Zhang, Yubin Xie, Chenwei Wang, Chun-Jie Liu, De-Chang Yang, Feng Tian, Ge Gao, Dachao Tang, Lan Yao, Qinghua Cui, Ni A. An, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. D18-D28
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Gaia Cantelli, Guy Cochrane, Cath Brooksbank, Ellen M. McDonagh, Paul Flicek, Johanna R. McEntyre, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. D29-D37

Nucleic Acid Sequence, Structure and Regulation

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Kyukwang Kim, Insu Jang, Mooyoung Kim, Jinhyuk Choi, Minseo Kim, Byungwook Lee, Inkyung Jung:
3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome. D38-D46
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Weiwei Jin, Qizhao Zhu, Yanbo Yang, Wenqian Yang, Dongyang Wang, Jiajun Yang, Xiaohui Niu, Debing Yu, Jing Gong:
Animal-APAdb: a comprehensive animal alternative polyadenylation database. D47-D54
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Fan Wang, Xuefeng Bai, Yuezhu Wang, Yong Jiang, Bo Ai, Yong Zhang, Yuejuan Liu, Mingcong Xu, Qiuyu Wang, Xiaole Han, Qi Pan, Yanyu Li, Xuecang Li, Jian Zhang, Jun Zhao, Guorui Zhang, Chenchen Feng, Jiang Zhu, Chunquan Li:
ATACdb: a comprehensive human chromatin accessibility database. D55-D64
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Yan Huang, Jing Wang, Yue Zhao, Huafeng Wang, Tianyuan Liu, Yuhe Li, Tianyu Cui, Weiyi Li, Yige Feng, Jiaxin Luo, Jiaqi Gong, Lin Ning, Yong Zhang, Dong Wang, Yang Zhang:
cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function. D65-D70
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Asami Fukuda, Yuichi Kodama, Jun Mashima, Takatomo Fujisawa, Osamu Ogasawara:
DDBJ update: streamlining submission and access of human data. D71-D75
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Almudena Ponce-Salvatierra, Pietro Boccaletto, Janusz M. Bujnicki:
DNAmoreDB, a database of DNAzymes. D76-D81
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Peter W. Harrison, Alisha Ahamed, Raheela Aslam, Blaise T. F. Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O'Cathail, Amir Pakseresht, Young Mi Park, Stephane Pesant, Nadim Rahman, Jeena Rajan, Alexey Sokolov, Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Tony Burdett, Guy Cochrane:
The European Nucleotide Archive in 2020. D82-D85
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Bailing Zhou, Baohua Ji, Kui Liu, Guodong Hu, Fei Wang, Qingshuai Chen, Ru Yu, Pingping Huang, Jing Ren, Chengang Guo, Huiying Zhao, Hongmei Zhang, Dongbo Zhao, Zhiwei Li, Qiangcheng Zeng, Jiafeng Yu, Yunqiang Bian, Zanxia Cao, Shicai Xu, Yuedong Yang, Yaoqi Zhou, Jihua Wang:
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. D86-D91
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Eric W. Sayers, Mark Cavanaugh, Karen Clark, Kim D. Pruitt, Conrad L. Schoch, Stephen T. Sherry, Ilene Karsch-Mizrachi:
GenBank. D92-D96
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Li Fang, Yunjin Li, Lu Ma, Qiyue Xu, Fei Tan, Geng Chen:
GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions. D97-D103
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Semyon Kolmykov, Ivan S. Yevshin, Mikhail Kulyashov, Ruslan N. Sharipov, Yury V. Kondrakhin, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Alexander E. Kel, Fedor A. Kolpakov:
GTRD: an integrated view of transcription regulation. D104-D111
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Kevin Rychel, Katherine Decker, Anand V. Sastry, Patrick V. Phaneuf, Saugat Poudel, Bernhard O. Palsson:
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. D112-D120
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Masanori Arita, Ilene Karsch-Mizrachi, Guy Cochrane:
The international nucleotide sequence database collaboration. D121-D124
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Peng Wang, Qiuyan Guo, Yangyang Hao, Qian Liu, Yue Gao, Hui Zhi, Xin Li, Shipeng Shang, Shuang Guo, Yunpeng Zhang, Shangwei Ning, Xia Li:
LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution. D125-D133
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Yujiao Tang, Kunqi Chen, Bowen Song, Jiongming Ma, Xiangyu Wu, Qingru Xu, Zhen Wei, Jionglong Su, Gang Liu, Rong Rong, Zhiliang Lu, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng:
m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. D134-D143
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Zhidan Li, Yiming Zhang, Stephen J. Bush, Chao Tang, Li Chen, Dan Zhang, Araxi O. Urrutia, Jing-Wen Lin, Lu Chen:
MeDAS: a Metazoan Developmental Alternative Splicing database. D144-D150
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Nikos Perdikopanis, Georgios K. Georgakilas, Dimitris Grigoriadis, Vasileios Pierros, Ioannis Kavakiotis, Panagiotis Alexiou, Artemis G. Hatzigeorgiou:
DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs. D151-D159
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Lin Ning, Tianyu Cui, Boyang Zheng, Nuo Wang, Jiaxin Luo, Beilei Yang, Mengze Du, Jun Cheng, Yiying Dou, Dong Wang:
MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation. D160-D164
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Lianhe Zhao, Jiajia Wang, Yanyan Li, Tingrui Song, Yang Wu, Shuangsang Fang, Dechao Bu, Hui Li, Liang Sun, Dong Pei, Yu Zheng, Jianqin Huang, Mingqing Xu, Runsheng Chen, Yi Zhao, Shunmin He:
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. D165-D171
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Vinícius G. Contessoto, Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F. Mello, Erez Lieberman Aiden, Peter G. Wolynes, Michele Di Pierro, José N. Onuchic:
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. D172-D182
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Pan Li, Xiaolin Zhou, Kui Xu, Qiangfeng Cliff Zhang:
RASP: an atlas of transcriptome-wide RNA secondary structure probing data. D183-D191
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Ioanna Kalvari, Eric P. Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, Manja Marz, Sam Griffiths-Jones, Claire Toffano-Nioche, Daniel Gautheret, Zasha Weinberg, Elena Rivas, Sean R. Eddy, Robert D. Finn, Alex Bateman, Anton I. Petrov:
Rfam 14: expanded coverage of metagenomic, viral and microRNA families. D192-D200
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Qin Li, Hongyan Lai, Yuchen Li, Bing Chen, Siyuan Chen, Yan Li, Zhaohui Huang, Zhiqiang Meng, Peng Wang, Zhixiang Hu, Shenglin Huang:
RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. D201-D211
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Blake A. Sweeney, Anton I. Petrov, Carlos Eduardo Ribas, Robert D. Finn, Alex Bateman, Maciej Szymanski, Wojciech M. Karlowski, Stefan E. Seemann, Jan Gorodkin, Jamie J. Cannone, Robin Ray Gutell, Simon Kay, Steven J. Marygold, Gilberto dos Santos, Adam Frankish, Jonathan M. Mudge, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth L. Seal, Elspeth A. Bruford, Simona Panni, Pablo Porras, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle S. Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg:
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. D212-D220
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Wanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang:
SilencerDB: a comprehensive database of silencers. D221-D228
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Jorge A. Marchand, Merrick D. Pierson smela, Thomas H. H. Jordan, Kamesh Narasimhan, George M. Church:
TBDB: a database of structurally annotated T-box riboswitch: tRNA pairs. D229-D235
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Wendi Huang, Yunchao Ling, Sirui Zhang, Qiguang Xia, Ruifang Cao, Xiaojuan Fan, Zhaoyuan Fang, Zefeng Wang, Guoqing Zhang:
TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence. D236-D242
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Federico Marini, Denise Scherzinger, Sven Danckwardt:
TREND-DB - a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. D243-D253
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Ningshan Li, Nayang Shan, Lingeng Lu, Zuoheng Wang:
tRFtarget: a database for transfer RNA-derived fragment targets. D254-D260

Protein Sequence and Structure, Motifs and Domains

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Vinay Ayyappan, Ricky Wat, Calvin Barber, Christina A. Vivelo, Kathryn Gauch, Pat Visanpattanasin, Garth Cook, Christos Sazeides, Anthony Kar Lun Leung:
ADPriboDB 2.0: an updated database of ADP-ribosylated proteins. D261-D265
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Ian Sillitoe, Nicola Bordin, Natalie L. Dawson, Vaishali P. Waman, Paul Ashford, Harry M. Scholes, Camilla S. M. Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen, Mahnaz Abbasian, Sean Le Cornu, Su Datt Lam, Karel Berka, Ivana Hutarová Vareková, Radka Svobodová Vareková, Jonathan G. Lees, Christine A. Orengo:
CATH: increased structural coverage of functional space. D266-D273
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Michael Y. Galperin, Yuri I. Wolf, Kira S. Makarova, Roberto Vera Alvarez, David Landsman, Eugene V. Koonin:
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. D274-D281
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Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Jared Adolf-Bryfogle, William R. Schief, Brian G. Pierce:
CoV3D: a database of high resolution coronavirus protein structures. D282-D287
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  - journals/nar/PirtskhalavaAGC21
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Malak Pirtskhalava, Anthony A. Amstrong, Maia Grigolava, Mindia Chubinidze, Evgenia Alimbarashvili, Boris Vishnepolsky, Andrei E. Gabrielian, Alex Rosenthal, Darrell E. Hurt, Michael Tartakovsky:
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics. D288-D297
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Bi Zhao, Akila Katuwawala, Christopher J. Oldfield, A. Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz A. Kurgan:
DescribePROT: database of amino acid-level protein structure and function predictions. D298-D308
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Zakaria Louadi, Kevin Yuan, Alexander Greß, Olga Tsoy, Olga V. Kalinina, Jan Baumbach, Tim Kacprowski, Markus List:
DIGGER: exploring the functional role of alternative splicing in protein interactions. D309-D318
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Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jirí Damborský, Stanislav Mazurenko, David Bednar:
FireProtDB: database of manually curated protein stability data. D319-D324
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Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani V. Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James B. Munro, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan J. Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser:
The Gene Ontology resource: enriching a GOld mine. D325-D334
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Albert J. Kooistra, Stefan Mordalski, Gáspár Pándy-Szekeres, Mauricio Esguerra, Alibek Mamyrbekov, Christian Munk, György M. Keserü, David E. Gloriam:
GPCRdb in 2021: integrating GPCR sequence, structure and function. D335-D343
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Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasamy, Alex L. Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna J. Richardson, Gustavo A. Salazar, Lowri Williams, Peer Bork, Alan J. Bridge, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman, Robert D. Finn:
The InterPro protein families and domains database: 20 years on. D344-D354
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Georgina Csizmadia, Gábor Erdös, Hedvig Tordai, Rita Padányi, Silvio C. E. Tosatto, Zsuzsanna Dosztányi, Tamás Hegedüs:
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. D355-D360
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Damiano Piovesan, Marco Necci, Nahuel Escobedo, Alexander Miguel Monzon, András Hatos, Ivan Micetic, Federica Quaglia, Lisanna Paladin, Pathmanaban Ramasamy, Zsuzsanna Dosztányi, Wim F. Vranken, Norman E. Davey, Gustavo D. Parisi, Mónika Fuxreiter, Silvio C. E. Tosatto:
MobiDB: intrinsically disordered proteins in 2021. D361-D367
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Chang Chen, Haipeng Liu, Shadi Zabad, Nina Rivera, Emily Rowin, Maheen Hassan, Stephanie M. Gomez de Jesus, Paola S. Llinás santos, Karyna Kravchenko, Mariia Mikhova, Sophia Ketterer, Annabel Shen, Sophia Shen, Erin Navas, Bryan Horan, Jaak Raudsepp, Constance J. Jeffery:
MoonProt 3.0: an update of the moonlighting proteins database. D368-D372
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Adrian M. Altenhoff, Clément-Marie Train, Kimberly J. Gilbert, Ishita Mediratta, Tarcisio Mendes de Farias, David Moi, Yannis Nevers, Hale-Seda Radoykova, Victor Rossier, Alex Warwick Vesztrocy, Natasha M. Glover, Christophe Dessimoz:
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. D373-D379
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Marie A. Brunet, Jean-François Lucier, Maxime Levesque, Sébastien Leblanc, Jean-Francois Jacques, Hassan R. H. Al-Saedi, Noé Guilloy, Frédéric Grenier, Mariano Avino, Isabelle Fournier, Michel Salzet, Aïda Ouangraoua, Michelle S. Scott, François-Michel Boisvert, Xavier Roucou:
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. D380-D388
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Evgeny M. Zdobnov, Dmitry Kuznetsov, Fredrik Tegenfeldt, Mosè Manni, Matthew Berkeley, Evgenia V. Kriventseva:
OrthoDB in 2020: evolutionary and functional annotations of orthologs. D389-D393
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Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayahama, Paul D. Thomas:
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. D394-D411
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Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A. Salazar, Erik L. L. Sonnhammer, Silvio C. E. Tosatto, Lisanna Paladin, Shriya Raj, Lorna J. Richardson, Robert D. Finn, Alex Bateman:
Pfam: The protein families database in 2021. D412-D419
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Rahul Nikam, A. Kulandaisamy, K. Harini, Divya Sharma, M. Michael Gromiha:
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years. D420-D424
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Maiwen Caudron-Herger, Ralf E. Jansen, Elsa Wassmer, Sven Diederichs:
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. D425-D436
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Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V. Crichlow, Cole H. Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sai Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Persikova, Christopher Randle, Alexander S. Rose, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Maria Voigt, John D. Westbrook, Jasmine Young, Christine Zardecki, Marina Zhuravleva:
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. D437-D451
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Lisanna Paladin, Martina Bevilacqua, Sara Errigo, Damiano Piovesan, Ivan Micetic, Marco Necci, Alexander Miguel Monzon, Maria Laura Fabre, José Luis López, Juliet F. Nilsson, Javier Ríos, Pablo Lorenzano Menna, Maia Cabrera, Martin Gonzalez Buitron, Mariane Gonçalves Kulik, Sebastian Fernandez Alberti, María Silvina Fornasari, Gustavo D. Parisi, Antonio Lagares, Layla Hirsh, Miguel A. Andrade-Navarro, Andrey V. Kajava, Silvio C. E. Tosatto:
RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. D452-D457
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Ivica Letunic, Supriya Khedkar, Peer Bork:
SMART: recent updates, new developments and status in 2020. D458-D460
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Milton H. Saier Jr., Vamsee S. Reddy, Gabriel Moreno-Hagelsieb, Kevin J. Hendargo, Yichi Zhang, Vasu Iddamsetty, Katie Jing Kay Lam, Nuo Tian, Steven Russum, Jianing Wang, Arturo Medrano-Soto:
The Transporter Classification Database (TCDB): 2021 update. D461-D467
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Si-Yi Chen, Tao Yue, Qian Lei, An-Yuan Guo:
TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function. D468-D474
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Joicymara S. Xavier, Thanh-Binh Nguyen, Malancha Karmarkar, Stephanie Portelli, Pâmela M. Rezende, João P. L. Velloso, David B. Ascher, Douglas E. V. Pires:
ThermoMutDB: a thermodynamic database for missense mutations. D475-D479
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Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan W. Sousa da Silva, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Leyla Jael García Castro, Penelope Garmiri, George E. Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodríguez-López, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan J. Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard De Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Béatrice A. Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, Jian Zhang, Patrick Ruch, Douglas Teodoro:
UniProt: the universal protein knowledgebase in 2021. D480-D489

Metabolic and Signalling Pathways, Enzymes

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Satria A. Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H. Medema:
BiG-FAM: the biosynthetic gene cluster families database. D490-D497
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Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg:
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. D498-D508
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  - journals/nar/LyuCQLWZL21
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Chuanyu Lyu, Tong Chen, Bo Qiang, Ningfeng Liu, Heyu Wang, Liangren Zhang, Zhenming Liu:
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. D509-D515
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Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh, Jonathan R. Karr:
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. D516-D522
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Catherine Ausland, Jinfang Zheng, Haidong Yi, Bowen Yang, Tang Li, Xuehuan Feng, Bo Zheng, Yanbin Yin:
dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates. D523-D528
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  - journals/nar/BerginskiMLGSG21
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Matthew E. Berginski, Nienke Moret, Changchang Liu, Dennis Goldfarb, Peter K. Sorger, Shawn M. Gomez:
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. D529-D535
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Shu Tadaka, Eiji Hishinuma, Shohei Komaki, Ikuko N. Motoike, Junko Kawashima, Daisuke Saigusa, Jin Inoue, Jun Takayama, Yasunobu Okamura, Yuichi Aoki, Matsuyuki Shirota, Akihito Otsuki, Fumiki Katsuoka, Atsushi Shimizu, Gen Tamiya, Seizo Koshiba, Makoto Sasaki, Masayuki Yamamoto, Kengo Kinoshita:
jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population. D536-D544
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Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe:
KEGG: integrating viruses and cellular organisms. D545-D551
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Ruifeng Hu, Hao-Dong Xu, Peilin Jia, Zhongming Zhao:
KinaseMD: kinase mutations and drug response database. D552-D561
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  - journals/nar/KanevGWEK21
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Georgi K. Kanev, Chris de Graaf, Bart A. Westerman, Iwan J. P. de Esch, Albert J. Kooistra:
KLIFS: an overhaul after the first 5 years of supporting kinase research. D562-D569
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  - journals/nar/MorettiTMIP21
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  - https://dblp.org/rec/journals/nar/MorettiTMIP21
Sébastien Moretti, T. Van Du Tran, Florence Mehl, Mark Ibberson, Marco Pagni:
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. D570-D574
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Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, James G. Jeffryes, José P. Faria, Janaka N. Edirisinghe, Michael B. Mundy, Nicholas Chia, Elad Noor, Moritz Emanuel Beber, Aaron A. Best, Matthew DeJongh, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry:
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. D575-D588
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Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Dang, James J. Cimino, Jake Y. Chen:
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. D589-D599
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Aurélien F. A. Moumbock, Mingjie Gao, Ammar Qaseem, Jianyu Li, Pascal A. Kirchner, Bakoh Ndingkokhar, Boris D. Bekono, Conrad Veranso Simoben, Smith B. Babiaka, Yvette I. Malange, Florian Sauter, Paul F. Zierep, Fidele Ntie-Kang, Stefan Günther:
StreptomeDB 3.0: an updated compendium of streptomycetes natural products. D600-D604
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  - journals/nar/SzklarczykGNLKP21
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Damian Szklarczyk, Annika L. Gable, Katerina C. Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T. Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars Juhl Jensen, Christian von Mering:
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. D605-D612
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Marvin Martens, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N. Slenter, Kristina Hanspers, Ryan A. Miller, Daniela Digles, Elisson N. Lopes, Friederike Ehrhart, Lauren J. Dupuis, Laurent A. Winckers, Susan L. Coort, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico, Martina Kutmon:
WikiPathways: connecting communities. D613-D621

Viruses, Bacteria and Fungi

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Le Huang, Bowen Yang, Haidong Yi, Amina Asif, Jiawei Wang, Trevor Lithgow, Han Zhang, Fayyaz ul Amir Afsar Minhas, Yanbin Yin:
AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses. D622-D629
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Jiawei Wang, Wei Dai, Jiahui Li, Qi Li, Ruopeng Xie, Yanju Zhang, Christopher Stubenrauch, Trevor Lithgow:
AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins. D630-D638
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Kai Blin, Simon Shaw, Satria A. Kautsar, Marnix H. Medema, Tilmann Weber:
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes. D639-D643
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Ye Feng, Shengmei Zou, Hangfei Chen, Yunsong Yu, Zhi Ruan:
BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking. D644-D650
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Jiawei Wang, Jiahui Li, Yi Hou, Wei Dai, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Tieli Zhou, Von Torres, Iain Hay, Christopher Stubenrauch, Yanju Zhang, Jiangning Song, Trevor Lithgow:
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. D651-D659
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Rafael Mamede, Pedro Vila-Cerqueira, Mickael Silva, João A. Carriço, Mário Ramirez:
Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas. D660-D666
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Laurence Garczarek, Ulysse Guyet, Hugo Doré, Gregory K. Farrant, Mark Hoebeke, Loraine Brillet-Guéguen, Antoine Bisch, Mathilde Ferrieux, Jukka Siltanen, Erwan Le Corre, Gildas Le Corguillé, Morgane Ratin, Frances D. Pitt, Martin Ostrowski, Maël Conan, Anne Siegel, Karine Labadie, Jean-Marc Aury, Patrick Wincker, David J. Scanlan, Frédéric Partensky:
Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. D667-D676
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Hao Luo, Yan Lin, Tao Liu, Fei-Liao Lai, Chun-Ting Zhang, Feng Gao, Ren Zhang:
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. D677-D686
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Javier Macho Rendón, Benjamin Lang, Marc Ramos llorens, Gian Gaetano Tartaglia, Marc Torrent Burgas:
DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes. D687-D693
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Wenyu Shi, Qinglan Sun, Guomei Fan, Hideaki Sugawara, Moriya Ohkuma, Takashi Itoh, Yuguang Zhou, Man Cai, Song-Gun Kim, Jung-Sook Lee, Ivo Sedlacek, David R. Arahal, Teresa Lucena, Hiroko Kawasaki, Lyudmila Evtushenko, Bevan S. Weir, Sarah Alexander, Dlauchy Dénes, Somboon Tanasupawat, Lily Eurwilaichitr, Supawadee Ingsriswang, Bruno Gomez-Gil, Manzour H. Hazbón, Marco A. Riojas, Chatrudee Suwannachart, Su Yao, Peter Vandamme, Fang Peng, Zenghui Chen, Dongmei Liu, Xiuqiang Sun, Xinjiao Zhang, Yuanchun Zhou, Zhen Meng, Linhuan Wu, Juncai Ma:
gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. D694-D705
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Shuyi Fang, Kailing Li, Jikui Shen, Sheng Liu, Juli Liu, Lei Yang, Chang-Deng Hu, Jun Wan:
GESS: a database of global evaluation of SARS-CoV-2/hCoV-19 sequences. D706-D714
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Jing Tang, Xianglu Wu, Minjie Mou, Chuan Wang, Lidan Wang, Fengcheng Li, Maiyuan Guo, Jiayi Yin, Wenqin Xie, Xiaona Wang, Yingxiong Wang, Yubin Ding, Weiwei Xue, Feng Zhu:
GIMICA: host genetic and immune factors shaping human microbiota. D715-D722
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  - journals/nar/MukherjeeSBOSLK21
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Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Jagadish Chandrabose Sundaramurthi, Janey Lee, Mahathi Kandimalla, I-Min A. Chen, Nikos Kyrpides, T. B. K. Reddy:
Genomes OnLine Database (GOLD) v.8: overview and updates. D723-D733
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Heather Huot Creasy, Victor Felix, Jain Aluvathingal, Jonathan Crabtree, Olukemi O. Ifeonu, James Matsumura, Carrie McCracken, Lance Nickel, Joshua Orvis, Mike Schor, Michelle G. Giglio, Anup Mahurkar, Owen White:
HMPDACC: a Human Microbiome Project Multi-omic data resource. D734-D742
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  - journals/nar/KasmanasBCTJHBS21
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Jonas Coelho Kasmanas, Alexander Bartholomäus, Felipe Borim Corrêa, Tamara L. Tal, Nico Jehmlich, Gunda Herberth, Martin von Bergen, Peter F. Stadler, André Carlos Ponce de Leon Ferreira de Carvalho, Ulisses Nunes da Rocha:
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. D743-D750
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I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan Ritter, Neha Varghese, Rekha Seshadri, Simon Roux, Tanja Woyke, Emiley A. Eloe-Fadrosh, Natalia N. Ivanova, Nikos Kyrpides:
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. D751-D763
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Simon Roux, David Páez-Espino, I-Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, T. B. K. Reddy, Stephen Nayfach, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos Kyrpides:
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. D764-D775
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Xian Zeng, Xue Yang, Jiajun Fan, Ying Tan, Lingyi Ju, Wanxiang Shen, Yali Wang, Xinghao Wang, Weiping Chen, Dianwen Ju, Yuzong Chen:
MASI: microbiota - active substance interactions database. D776-D782
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Senying Lai, Long-Hao Jia, Balakrishnan Subramanian, Shaojun Pan, Jinglong Zhang, Yanqi Dong, Wei-Hua Chen, Xing-Ming Zhao:
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. D783-D791
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  - journals/nar/PonseroBBYHWDH21
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Alise J. Ponsero, Matthew Bomhoff, Kai Blumberg, Ken Youens-Clark, Nina M. Herz, Elisha M. Wood-Charlson, Edward F. Delong, Bonnie L. Hurwitz:
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. D792-D802
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  - journals/nar/LauHJWMGLLB21
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Wing Yin Venus Lau, Gemma Hoad, Vivian Jin, Geoffrey L. Winsor, Ashmeet Madyan, Kristen L. Gray, Matthew R. Laird, Raymond Lo, Fiona S. L. Brinkman:
PSORTdb 4.0: expanded and redesigned bacterial and archaeal protein subcellular localization database incorporating new secondary localizations. D803-D808
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  - journals/nar/Montiel-GarciaS21
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Daniel Montiel-Garcia, Nelly Beatriz Santoyo-Rivera, Phuong Ho, Mauricio Carrillo-Tripp, Charles L. Brooks III, John E. Johnson, Vijay S. Reddy:
VIPERdb v3.0: a structure-based data analytics platform for viral capsids. D809-D816
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  - journals/nar/CanakogluP0AMC21
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Arif Canakoglu, Pietro Pinoli, Anna Bernasconi, Tommaso Alfonsi, Damianos P. Melidis, Stefano Ceri:
ViruSurf: an integrated database to investigate viral sequences. D817-D824

Human Genome, Model Organisms, Comparative Genomics

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Guang-Hui Liu, Yiming Bao, Jing Qu, Weiqi Zhang, Tao Zhang, Wang Kang, Fei Yang, Qianzhao Ji, Xiaoyu Jiang, Yingke Ma, Shuai Ma, Zunpeng Liu, Siyu Chen, Si Wang, Shuhui Sun, Lingling Geng, Kaowen Yan, Pengze Yan, Yanling Fan, Moshi Song, Jie Ren, Qiaoran Wang, Shanshan Yang, Yuanhan Yang, Muzhao Xiong, Chuqiang Liang, Lan-Zhu Li, Tianling Cao, Jianli Hu, Ping Yang, Jiale Ping, Huifang Hu, Yandong Zheng, Guoqiang Sun, Jiaming Li, Lixiao Liu, Zhiran Zou, Yingjie Ding, Mingheng Li, Di Liu, Min Wang, Xiaoyan Sun, Cui Wang, Shijia Bi, Hezhen Shan, Xiao Zhuo:
Aging Atlas: a multi-omics database for aging biology. D825-D830
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  - journals/nar/BastianRNCCFMPL21
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Frederic B. Bastian, Julien Roux, Anne Niknejad, Aurélie Comte, Sara S. Fonseca Costa, Tarcisio Mendes de Farias, Sébastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angélique Escoriza, Walid H. Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi:
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. D831-D847
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  - journals/nar/CuiCCSCGDCZLZYL21
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Yingbo Cui, Xiaolong Cheng, Qing Chen, Bicna Song, Anthony Chiu, Yuan Gao, Tyson Dawson, Lumen Chao, Wubing Zhang, Dian Li, Zexiang Zeng, Jijun Yu, Zexu Li, Teng Fei, Shaoliang Peng, Wei Li:
CRISP-view: a database of functional genetic screens spanning multiple phenotypes. D848-D854
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Florian Störtz, Peter Minary:
crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays. D855-D861
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  - journals/nar/Dai0MLJZ21
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Yulin Dai, Ruifeng Hu, Astrid Marilyn Manuel, Andi Liu, Peilin Jia, Zhongming Zhao:
CSEA-DB: an omnibus for human complex trait and cell type associations. D862-D870
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  - journals/nar/GoodenESCC21
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Alexander A. Gooden, Christine N. Evans, Timothy P. Sheets, Michelle E. Clapp, Raj Chari:
dbGuide: a database of functionally validated guide RNAs for genome editing in human and mouse cells. D871-D876
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Fangzhou Xie, Shurong Liu, Junhao Wang, Jia-Jia Xuan, Xiaoqin Zhang, Liang-Hu Qu, Ling-Ling Zheng, Jianhua Yang:
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data. D877-D883
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Kevin L. Howe, Premanand Achuthan, James E. Allen, Jamie Allen, Jorge Álvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Andrey G. Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla A. Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos García-Girón, Tiago Grego, Cristina Guijarro-Clarke, Leanne Haggerty, Anmol Hemrom, Thibaut Hourlier, Osagie G. Izuogu, Thomas Juettemann, Vinay Kaikala, Mike P. Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, José Carlos Marugán, Thomas Maurel, Aoife C. McMahon, Shamika Mohanan, Benjamin Moore, Matthieu Muffato, Denye N. Oheh, Dimitrios Paraschas, Anne Parker, Andrew Parton, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, Emily Steed, Michal Szpak, Marek Szuba, Kieron R. Taylor, Anja Thormann, Glen Threadgold, Brandon Walts, Andrea Winterbottom, Marc Chakiachvili, Ameya Chaubal, Nishadi De Silva, Bethany Flint, Adam Frankish, Sarah E. Hunt, Garth IIsley, Nick Langridge, Jane E. Loveland, Fergal J. Martin, Jonathan M. Mudge, Joannella Morales, Emily Perry, Magali Ruffier, John G. Tate, David Thybert, Stephen J. Trevanion, Fiona Cunningham, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
Ensembl 2021. D884-D891
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Imad Abugessaisa, Jordan A. Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Shuhei Noguchi, Chi Wai Yip, Jasmine Li Ching Ooi, Michihira Tagami, Fumi Hori, Saumya Agrawal, Chung-Chau Hon, Mélissa Cardon, Shuya Ikeda, Hiromasa Ono, Hidemasa Bono, Masaki Kato, Kosuke Hashimoto, Alessandro Bonetti, Norio Kobayashi, Jay W. Shin, Michiel J. L. de Hoon, Yoshihide Hayashizaki, Piero Carninci, Hideya Kawaji, Takeya Kasukawa:
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. D892-D898
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Aoife Larkin, Steven J. Marygold, Giulia Antonazzo, Helen Attrill, Gilberto dos Santos, Phani V. Garapati, Joshua L. Goodman, L. Sian Gramates, Gillian H. Millburn, Victor B. Strelets, Christopher J. Tabone, Jim Thurmond, Norbert Perrimon, Susan Russo Gelbart, Julie Agapite, Kris Broll, Madeline A. Crosby, Kathleen Falls, Victoria Jenkins, Ian Longden, Beverley Matthews, Carol Sutherland, Pinglei Zhou, Mark Zytkovicz, Nick Brown, Phani Garapati, Steven Marygold, Alexander McLachlan, Clare Pilgrim, Arzu Ozturk-Colak, Vitor Trovisco, Thomas C. Kaufman, Brian R. Calvi, Richard Cripps, Tyanna Lovato:
FlyBase: updates to the Drosophila melanogaster knowledge base. D899-D907
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Yanhui Hu, Aram Comjean, Jonathan Rodiger, Yifang Liu, Yue Gao, Verena Chung, Jonathan Zirin, Norbert Perrimon, Stephanie E. Mohr:
FlyRNAi.org - the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update. D908-D915
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Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinrui Xu, Yucheng T. Yang, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek:
GENCODE 2021. D916-D923
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Richard M. Baldarelli, Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Jingxia Xu, David R. Shaw, Jonathan S. Beal, Olin Blodgett, Jeff Campbell, Lori E. Corbani, Pete J. Frost, Sharon C. Giannatto, Dave Miers, James A. Kadin, Joel E. Richardson, Martin Ringwald:
The mouse Gene Expression Database (GXD): 2021 update. D924-D931
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Zhao Zhang, Wei Hong, Hang Ruan, Ying Jing, Shengli Li, Yaoming Liu, Jun Wang, Wenbo Li, Lixia Diao, Leng Han:
HeRA: an atlas of enhancer RNAs across human tissues. D932-D938
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Susan Tweedie, Bryony Braschi, Kristian A. Gray, Tamsin E. M. Jones, Ruth L. Seal, Bethan Yates, Elspeth A. Bruford:
Genenames.org: the HGNC and VGNC resources in 2021. D939-D955
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Ahyoung Choi, Insu Jang, Heewon Han, Minseo Kim, Jinhyuk Choi, Jieun Lee, Sung-Yup Cho, Yukyung Jun, Charles Lee, Jaesang Kim, Byungwook Lee, Sanghyuk Lee:
iCSDB: an integrated database of CRISPR screens. D956-D961
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Zhao Li, Lin Liu, Shuai Jiang, Qianpeng Li, Changrui Feng, Qiang Du, Dong Zou, Jing-Fa Xiao, Zhang Zhang, Lina Ma:
LncExpDB: an expression database of human long non-coding RNAs. D962-D968
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Jiaxin Chen, Jian Zhang, Yu Gao, Yanyu Li, Chenchen Feng, Chao Song, Ziyu Ning, Xinyuan Zhou, Jianmei Zhao, Minghong Feng, Yuexin Zhang, Ling Wei, Qi Pan, Yong Jiang, Fengcui Qian, Junwei Han, Yongsan Yang, Qiuyu Wang, Chunquan Li:
LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. D969-D980
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Judith A. Blake, Richard M. Baldarelli, James A. Kadin, Joel E. Richardson, Cynthia L. Smith, Carol J. Bult, Anna V. Anagnostopoulos, Jon S. Beal, Susan M. Bello, Olin Blodgett, Nancy E. Butler, Jeff Campbell, Karen R. Christie, Lori E. Corbani, Mary E. Dolan, Harold J. Drabkin, María Flores, Susan L. Giannatto, Angelina Guerra, Paul Hale, David P. Hill, Jonathan Judd, Meiyee Law, Monica McAndrews, Dave Miers, Cailey Mitchell, Howie Motenko, Li Ni, Hiroaki Onda, Janice Ormsby, Michelle Perry, Jill M. Recla, David R. Shaw, Dmitry Sitnikov, Monika Tomczuk, Laurens G. Wilming, Yunxia Sophia Zhu:
Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology. D981-D987
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Fuyun Liu, Yuli Li, Hongwei Yu, Lingling Zhang, Jingjie Hu, Zhenmin Bao, Shi Wang:
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. D988-D997
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Sanathoi Gurumayum, Puzi Jiang, Xiaowen Hao, Tulio de Lima Campos, Neil D. Young, Pasi K. Korhonen, Robin B. Gasser, Peer Bork, Xing-Ming Zhao, Lijie He, Wei-Hua Chen:
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. D998-D1003
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Igor V. Grigoriev, Richard D. Hayes, Sara Calhoun, Bishoy Kamel, Alice Wang, Steven Ahrendt, Serge Dusheyko, Roman Nikitin, Stephen M. J. Searle, Asaf A. Salamov, Igor Shabalov, Alan Kuo:
PhycoCosm, a comparative algal genomics resource. D1004-D1011
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Luigi Mansi, Marco Antonio Tangaro, Claudio Lo Giudice, Tiziano Flati, Eli Kopel, Amos Avraham Schaffer, Tiziana Castrignanò, Giovanni Chillemi, Graziano Pesole, Ernesto Picardi:
REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments. D1012-D1019
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Wenjun Li, Kathleen O'Neill, Daniel H. Haft, Michael DiCuccio, Vyacheslav Chetvernin, Azat Badretdin, George Coulouris, Farideh Chitsaz, Myra K. Derbyshire, A. Scott Durkin, Noreen R. Gonzales, Marc Gwadz, Christopher J. Lanczycki, James S. Song, Narmada Thanki, Jiyao Wang, Roxanne A. Yamashita, Mingzhang Yang, Chanjuan Zheng, Aron Marchler-Bauer, Françoise Thibaud-Nissen:
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. D1020-D1028
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Liting Song, Shaojun Pan, Zichao Zhang, Long-Hao Jia, Wei-Hua Chen, Xing-Ming Zhao:
STAB: a spatio-temporal cell atlas of the human brain. D1029-D1037
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Yuanli Zuo, Lei Zhu, Zhixin Guo, Wenrong Liu, Jiting Zhang, Zhen Zeng, Qingbin Wu, Jian Cheng, Xin Fu, Yang Jin, Yun Zhao, Yong Peng:
tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species. D1038-D1045
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Jairo Navarro Gonzalez, Ann S. Zweig, Matthew L. Speir, Daniel Schmelter, Kate R. Rosenbloom, Brian J. Raney, Conner C. Powell, Luis R. Nassar, Nathan D. Maulding, Christopher M. Lee, Brian T. Lee, Angie S. Hinrichs, Alastair C. Fyfe, Jason D. Fernandes, Mark Diekhans, Hiram Clawson, Jonathan Casper, Anna Benet-Pagès, Galt P. Barber, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent:
The UCSC Genome Browser database: 2021 update. D1046-D1057
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Douglas G. Howe, Sridhar Ramachandran, Yvonne M. Bradford, David Fashena, Sabrina Toro, Anne E. Eagle, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock, Christian Pich, Leyla Ruzicka, Kevin Schaper, Xiang Shao, Amy Singer, Ceri E. Van Slyke, Monte Westerfield:
The Zebrafish Information Network: major gene page and home page updates. D1058-D1064

Genomic Variation, Diseases and Drugs

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Jianbo Tian, Yimin Cai, Yue Li, Zequn Lu, Jinyu Huang, Yao Deng, Nan Yang, Xiaoyang Wang, Pingting Ying, Shanshan Zhang, Ying Zhu, Huilan Zhang, Rong Zhong, Jiang Chang, Xiaoping Miao:
CancerImmunityQTL: a database to systematically evaluate the impact of genetic variants on immune infiltration in human cancer. D1065-D1073
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Costas Mitsopoulos, Patrizio Di Micco, Eloy D. Villasclaras-Fernández, Daniela Dolciami, Esty Holt, Ioan L. Mica, Elizabeth A. Coker, Joseph E. Tym, James Campbell, Ka Hing Che, Bugra Ozer, Christos C. Kannas, Albert A. Antolin, Paul Workman, Bissan Al-Lazikani:
canSAR: update to the cancer translational research and drug discovery knowledgebase. D1074-D1082
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Augustin Luna, Fathi Elloumi, Sudhir Varma, Yanghsin Wang, Vinodh N. Rajapakse, Mirit I. Aladjem, Jacques Robert, Chris Sander, Yves Pommier, William C. Reinhold:
CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics. D1083-D1093
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Eric Minwei Liu, Alexander Martínez-Fundichely, Rajesh Bollapragada, Maurice Spiewack, Ekta Khurana:
CNCDatabase: a database of non-coding cancer drivers. D1094-D1101
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Balázs Balogh, Márton Ivánczi, Bilal Nizami, Tamás Beke-Somfai, István Mándity:
ConjuPepDB: a database of peptide-drug conjugates. D1102-D1112
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Dmitry Tworowski, Alessandro Gorohovski, Sumit Mukherjee, Gon Carmi, Eliad Levy, Rajesh Detroja, Sunanda Biswas Mukherjee, Milana Frenkel-Morgenstern:
COVID19 Drug Repository: text-mining the literature in search of putative COVID19 therapeutics. D1113-D1121
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Hongyan Du, Junbo Gao, Gaoqi Weng, Jun-Jie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dong-Sheng Cao, Tingjun Hou:
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. D1122-D1129
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María Peña-Chilet, Gema Roldán, Javier Perez-Florido, Francisco M. Ortuño, Rosario Carmona, Virginia Aquino, Daniel López-López, Carlos Loucera, Jose Luis Fernandez-Rueda, Asunción Gallego, Francisco García-García, Anna González-Neira, Guillermo Pita, Rocío Núñez-Torres, Javier Santoyo-Lopez, Carmen Ayuso, Pablo Minguez, Almudena Avila-Fernandez, Marta Corton, Miguel Ángel Moreno-Pelayo, Matías Morin, Alvaro Gallego-Martinez, Jose A. Lopez-Escamez, Salud Borrego, Guillermo Antiñolo, Jorge Amigo, Josefa Salgado-Garrido, Sara Pasalodos-Sanchez, Beatriz Morte, Fátima Al-Shahrour, Rafael Artuch, Javier Benitez, Luis Antonio Castaño, Ignacio Del Castillo, Aitor Delmiro, Carmina Espinos, Roser González, Daniel Grinberg, Encarnación Guillén, Pablo Lapunzina, Esther López, Ramon Martí, Montserrat Milá, Jose M. Millán, Virginia Nunes, Francesc Palau, Belen Perez, Luis A. Pérez-Jurado, Rosario Perona, Aurora Pujol, Feliciano Ramos, Antonia Ribes, Jordi Rosell, Eulalia Rovira, Jordi Surrallés, Isabel Tejada, Magdalena Ugarte, Ángel Carracedo, Ángel Alonso, Joaquín Dopazo:
CSVS, a crowdsourcing database of the Spanish population genetic variability. D1130-D1137
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Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly:
Comparative Toxicogenomics Database (CTD): update 2021. D1138-D1143
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Sharon L. Freshour, Susanna Kiwala, Kelsy C. Cotto, Adam C. Coffman, Joshua F. McMichael, Jonathan J. Song, Malachi Griffith, Obi L. Griffith, Alex H. Wagner:
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. D1144-D1151
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Ting-Fu Chen, Yu-Chuan Chang, Yi Hsiao, Ko-Han Lee, Yu-Chun Hsiao, Yu-Hsiang Lin, Yi-Chin Ethan Tu, Hsuan-Cheng Huang, Chien-Yu Chen, Hsueh-Fen Juan:
DockCoV2: a drug database against SARS-CoV-2. D1152-D1159
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Sorin I. Avram, Cristian Bologa, Jayme Holmes, Giovanni Bocci, Thomas B. Wilson, Dac-Trung Nguyen, Ramona Curpan, Liliana Halip, Alina Bora, Jeremy J. Yang, Jeffrey Knockel, Suman Sirimulla, Oleg Ursu, Tudor I. Oprea:
DrugCentral 2021 supports drug discovery and repositioning. D1160-D1169
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Tianbiao Yang, Zhaojun Li, Yingjia Chen, Dan Feng, Guangchao Wang, Zunyun Fu, Xiaoyu Ding, Xiaoqin Tan, Jihui Zhao, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng:
DrugSpaceX: a large screenable and synthetically tractable database extending drug space. D1170-D1178
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Tyler Peryea, Noel Southall, Mitch Miller, Daniel Katzel, Niko Anderson, Jorge Neyra, Sarah Stemann, Dac-Trung Nguyen, Dammika Amugoda, Archana Newatia, Ramez Ghazzaoui, Elaine Johanson, Herman Diederik, Larry Callahan, Frank Switzer:
Global Substance Registration System: consistent scientific descriptions for substances related to health. D1179-D1185
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Cuiping Li, Dongmei Tian, Bixia Tang, Xiaonan Liu, Xufei Teng, Wenming Zhao, Zhang Zhang, Shuhui Song:
Genome Variation Map: a worldwide collection of genome variations across multiple species. D1186-D1191
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Belinda Giardine, Philippe Joly, Serge Pissard, Henri Wajcman, David H. K. Chui, Ross C. Hardison, George P. Patrinos:
Clinically relevant updates of the HbVar database of human hemoglobin variants and thalassemia mutations. D1192-D1196
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Shuangsang Fang, Lei Dong, Liu Liu, Jincheng Guo, Lianhe Zhao, Jiayuan Zhang, Dechao Bu, Xinkui Liu, Peipei Huo, Wanchen Cao, Qiongye Dong, Jiarui Wu, Xiaoxi Zeng, Yang Wu, Yi Zhao:
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. D1197-D1206
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Sebastian Köhler, Michael A. Gargano, Nicolas Matentzoglu, Leigh Carmody, David Lewis-Smith, Nicole A. Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M. Brower, Tiffany J. Callahan, Christopher G. Chute, Johanna L. Est, Peter D. Galer, Shiva Ganesan, Matthias Griese, Matthias Haimel, Julia Pazmandi, Marc Hanauer, Nomi L. Harris, Michael Hartnett, Maximilian Hastreiter, Fabian Hauck, Yongqun He, Tim Jeske, Hugh Kearney, Gerhard Kindle, Christoph Klein, Katrin Knoflach, Roland Krause, David Lagorce, Julie A. McMurry, Jillian A. Miller, Monica C. Munoz-Torres, Rebecca L. Peters, Christina K. Rapp, Ana Rath, Shahmir A. Rind, Avi Z. Rosenberg, Michael M. Segal, Markus G. Seidel, Damian Smedley, Tomer Talmy, Yarlalu Thomas, Samuel A. Wiafe, Julie Xian, Zafer Yüksel, Ingo Helbig, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson:
The Human Phenotype Ontology in 2021. D1207-D1217
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Jing Wu, Danjun Li, Xinyi Liu, Qian Li, Xinheng He, Jiale Wei, Xinyi Li, Mingyu Li, Ashfaq Ur Rehman, Yujia Xia, Chengwei Wu, Jian Zhang, Xuefeng Lu:
IDDB: a comprehensive resource featuring genes, variants and characteristics associated with infertility. D1218-D1232
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Jiayi Yin, Fengcheng Li, Ying Zhou, Minjie Mou, Yinjing Lu, Kangli Chen, Jia Xue, Yongchao Luo, Jianbo Fu, Xu He, Jianqing Gao, Su Zeng, Lushan Yu, Feng Zhu:
INTEDE: interactome of drug-metabolizing enzymes. D1233-D1243
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Yue Gao, Xin Li, Shipeng Shang, Shuang Guo, Peng Wang, Dailin Sun, Jing Gan, Jie Sun, Yakun Zhang, Junwei Wang, Xinyue Wang, Xia Li, Yunpeng Zhang, Shangwei Ning:
LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements. D1244-D1250
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Yue Gao, Shipeng Shang, Shuang Guo, Xin Li, Hanxiao Zhou, Hongjia Liu, Yue Sun, Junwei Wang, Peng Wang, Hui Zhi, Xia Li, Shangwei Ning, Yunpeng Zhang:
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data. D1251-D1258
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David S. Wishart, Brendan Bartok, Eponine Oler, Kevin Y. H. Liang, Zachary Budinski, Mark V. Berjanskii, Anchi Guo, Xuan Cao, Michael Wilson:
MarkerDB: an online database of molecular biomarkers. D1259-D1267
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Hsi-Yuan Huang, Jing Li, Yun Tang, Yi-Xian Huang, Yi-Gang Chen, Yue-Yang Xie, Zhe-Yuan Zhou, Xin-Yi Chen, Si-Yuan Ding, Meng-Fan Luo, Chen-Nan Jin, Le-Shan Zhao, Jia-Tong Xu, Ying Zhou, Yang-Chi-Dung Lin, Hsiao-Chin Hong, Hua-Li Zuo, Si-Yao Hu, Pei-Yi Xu, Xin Li, Hsien-Da Huang:
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. D1268-D1275
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Chun-Jie Liu, Xin Fu, Meng-Xuan Xia, Qiong Zhang, Zhifeng Gu, An-Yuan Guo:
miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets. D1276-D1281
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Stefano Castellana, Tommaso Biagini, Francesco Petrizzelli, Luca Parca, Noemi Panzironi, Viviana Caputo, Angelo L. Vescovi, Massimo Carella, Tommaso Mazza:
MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits. D1282-D1288
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Tao Wang, Shasha Ruan, Xiaolu Zhao, Xiaohui Shi, Huajing Teng, Jianing Zhong, Mingcong You, Kun Xia, Zhongsheng Sun, Fengbiao Mao:
OncoVar: an integrated database and analysis platform for oncogenic driver variants in cancers. D1289-D1301
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David Ochoa, Andrew Hercules, Miguel Carmona, Daniel Suveges, Asier Gonzalez-Uriarte, Cinzia Malangone, Alfredo Miranda, Luca Fumis, Denise Carvalho-Silva, Michaela Spitzer, Jarrod Baker, Javier Ferrer, Arwa Bin Raies, Olesya Razuvayevskaya, Adam Faulconbridge, Eirini Petsalaki, Prudence Mutowo-Meullenet, Sandra Machlitt-Northen, Gareth Peat, Elaine McAuley, Chuang Kee Ong, Edward Mountjoy, Maya Ghoussaini, Andrea Pierleoni, Eliseo Papa, Miguel Pignatelli, Gautier Koscielny, Mohd Anisul Karim, Jeremy Schwartzentruber, David G. Hulcoop, Ian Dunham, Ellen M. McDonagh:
Open Targets Platform: supporting systematic drug-target identification and prioritisation. D1302-D1310
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Maya Ghoussaini, Edward Mountjoy, Miguel Carmona, Gareth Peat, Ellen M. Schmidt, Andrew Hercules, Luca Fumis, Alfredo Miranda, Denise Carvalho-Silva, Annalisa Buniello, Tony Burdett, James D. Hayhurst, Jarrod Baker, Javier Ferrer, Asier Gonzalez-Uriarte, Simon Jupp, Mohd Anisul Karim, Gautier Koscielny, Sandra Machlitt-Northen, Cinzia Malangone, Zoë May Pendlington, Paola Roncaglia, Daniel Suveges, Daniel Wright, Olga Vrousgou, Eliseo Papa, Helen E. Parkinson, Jacqueline A. L. MacArthur, John A. Todd, Jeffrey C. Barrett, Jeremy Schwartzentruber, David G. Hulcoop, David Ochoa, Ellen M. McDonagh, Ian Dunham:
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. D1311-D1320
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Juechen Yang, Qilin Li, Nighat Noureen, Yanbing Fang, Raushan Kurmasheva, Peter J. Houghton, Xiaojing Wang, Siyuan Zheng:
PCAT: an integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models. D1321-D1327
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Giorgos Skoufos, Filippos S. Kardaras, Athanasios Alexiou, Ioannis Kavakiotis, Anastasia Lambropoulou, Vasiliki Kotsira, Spyros Tastsoglou, Artemis G. Hatzigeorgiou:
Peryton: a manual collection of experimentally supported microbe-disease associations. D1328-D1333
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Timothy Sheils, Stephen L. Mathias, Keith J. Kelleher, Vishal B. Siramshetty, Dac-Trung Nguyen, Cristian Bologa, Lars Juhl Jensen, Dusica Vidovic, Amar Koleti, Stephan C. Schürer, Anna Waller, Jeremy J. Yang, Jayme Holmes, Giovanni Bocci, Noel Southall, Poorva Dharkar, Ewy A. Mathé, Anton Simeonov, Tudor I. Oprea:
TCRD and Pharos 2021: mining the human proteome for disease biology. D1334-D1346
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Tatiana Shashkova, Eugene D. Pakhomov, Denis D. Gorev, Lennart C. Karssen, Peter K. Joshi, Yurii S. Aulchenko:
PheLiGe: an interactive database of billions of human genotype-phenotype associations. D1347-D1350
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Yang Du, Meng Cai, Xiaofang Xing, Jiafu Ji, Ence Yang, Jianmin Wu:
PINA 3.0: mining cancer interactome. D1351-D1357
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Jan Grzegorzewski, Janosch Brandhorst, Kathleen Green, Dimitra Eleftheriadou, Yannick Duport, Florian Barthorscht, Adrian Köller, Danny Yu Jia Ke, Sara De Angelis, Matthias König:
PK-DB: pharmacokinetics database for individualized and stratified computational modeling. D1358-D1364
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Lisa Dwane, Fiona M. Behan, Emanuel J. V. Gonçalves, Howard Lightfoot, Wanjuan Yang, Dieudonne van der Meer, Rebecca Shepherd, Miguel Pignatelli, Francesco Iorio, Mathew Garnett:
Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets. D1365-D1372
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  - journals/nar/GalloGEMPG21
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Kathleen Gallo, Andrean Goede, Andreas Eckert, Barbara Moahamed, Robert Preissner, Björn-Oliver Gohlke:
PROMISCUOUS 2.0: a resource for drug-repositioning. D1373-D1380
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Gaoqi Weng, Chao Shen, Dong-Sheng Cao, Junbo Gao, Xiaowu Dong, Qiaojun He, Bo Yang, Dan Li, Jian Wu, Tingjun Hou:
PROTAC-DB: an online database of PROTACs. D1381-D1387
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  - journals/nar/00020CGHHLSTYZ021
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Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A. Shoemaker, Paul A. Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan Bolton:
PubChem in 2021: new data content and improved web interfaces. D1388-D1395
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Kunqi Chen, Bowen Song, Yujiao Tang, Zhen Wei, Qingru Xu, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng:
RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. D1396-D1404
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Xiaotong Luo, Huiqin Li, Jiaqi Liang, Qi Zhao, Yubin Xie, Jian Ren, Zhixiang Zuo:
RMVar: an updated database of functional variants involved in RNA modifications. D1405-D1412
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Tianyi Zhao, Shuxuan Lyu, Guilin Lu, Liran Juan, Xi Zeng, Zhongyu Wei, Jianye Hao, Jiajie Peng:
SC2disease: a manually curated database of single-cell transcriptome for human diseases. D1413-D1419
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Dongqing Sun, Jin Wang, Ya Han, Xin Dong, Jun Ge, Rongbin Zheng, Xiaoying Shi, Binbin Wang, Ziyi Li, Pengfei Ren, Liangdong Sun, Yilv Yan, Peng Zhang, Fan Zhang, Taiwen Li, Chenfei Wang:
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. D1420-D1430
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Qi Pan, Yuejuan Liu, Xuefeng Bai, Xiaole Han, Yong Jiang, Bo Ai, Shanshan Shi, Fan Wang, Mingcong Xu, Yuezhu Wang, Jun Zhao, Jiaxin Chen, Jian Zhang, Xuecang Li, Jiang Zhu, Guorui Zhang, Qiuyu Wang, Chunquan Li:
VARAdb: a comprehensive variation annotation database for human. D1431-D1444

Plants

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Yiheng Lan, Ruikun Sun, Jian Ouyang, Wubin Ding, Min-Jun Kim, Jun Wu, Yuhua Li, Tieliu Shi:
AtMAD: Arabidopsis thaliana multi-omics association database. D1445-D1451
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Marcela K. Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari, Vivek Kumar, Bruno Contreras-Moreira, Guy Naamati, Nancy George, Justin Cook, Dan M. Bolser, Peter D'Eustachio, Lincoln D. Stein, Amit Gupta, Weijia Xu, Jennifer Regala, Irene Papatheodorou, Paul J. Kersey, Paul Flicek, Crispin Taylor, Pankaj Jaiswal, Doreen Ware:
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. D1452-D1463
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  - journals/nar/GuignonTDDCR21
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Valentin Guignon, Abdel Toure, Gaëtan Droc, Jean-François Dufayard, Matthieu G. Conte, Mathieu Rouard:
GreenPhylDB v5: a comparative pangenomic database for plant genomes. D1464-D1471
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Xinbin Dai, Zhaohong Zhuang, Clarissa Boschiero, Yibo Dong, Patrick X. Zhao:
LegumeIP V3: from models to crops - an integrative gene discovery platform for translational genomics in legumes. D1472-D1479
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Yingjie Gao, Zhiquan Yang, Wenqian Yang, Yanbo Yang, Jing Gong, Qing-Yong Yang, Xiaohui Niu:
Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation. D1480-D1488
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Jingjing Jin, Peng Lu, Yalong Xu, Zefeng Li, Shizhou Yu, Jun Liu, Huan Wang, Nam-Hai Chua, Peijian Cao:
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs. D1489-D1495
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  - journals/nar/BrownCHWGWCGN21
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Anne V. Brown, Shawn I. Conners, Wei Huang, Andrew P. Wilkey, David M. Grant, Nathan T. Weeks, Steven B. Cannon, Michelle A. Graham, Rex T. Nelson:
A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database. D1496-D1501

Other Databases

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Ugis Sarkans, Anja Füllgrabe, Ahmed Ali, Awais Athar, Ehsan Behrangi, Nestor Diaz, Silvie Fexova, Nancy George, Haider Iqbal, Sandeep Kurri, Jhoan Munoz, Juan Camillo Rada, Irene Papatheodorou, Alvis Brazma:
From ArrayExpress to BioStudies. D1502-D1506
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  - journals/nar/FergusonAFGHHIL21
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Christine Ferguson, Dayane Araújo, Lynne Faulk, Yuci Gou, Audrey Hamelers, Zhan Huang, Michele Ide-Smith, Maria Levchenko, Nikos Marinos, Rakesh Nambiar, Maaly Nassar, Michael Parkin, Xingjun Pi, Faisal Rahman, Frances Rogers, Yogmatee Roochun, Shyamasree Saha, Mohamed Selim, Zunaira Shafique, Shrey Sharma, David Stephenson, Francesco Talo', Arthur Thouvenin, Santosh Tirunagari, Vid Vartak, Aravind Venkatesan, Xiao Yang, Johanna R. McEntyre:
Europe PMC in 2020. D1507-D1514
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  - journals/nar/BerriosGGGC21
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Daniel C. Berrios, Jonathan M. Galazka, Kirill Grigorev, Samrawit Gebre, Sylvain V. Costes:
NASA GeneLab: interfaces for the exploration of space omics data. D1515-D1522
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  - journals/nar/WatanabeAIO21
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Yu Watanabe, Kiyoko F. Aoki-Kinoshita, Yasushi Ishihama, Shujiro Okuda:
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. D1523-D1528
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  - journals/nar/FujitaASMTSOYA21
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Akihiro Fujita, Nobuyuki P. Aoki, Daisuke Shinmachi, Masaaki Matsubara, Shinichiro Tsuchiya, Masaaki Shiota, Tamiko Ono, Issaku Yamada, Kiyoko F. Aoki-Kinoshita:
The international glycan repository GlyTouCan version 3.0. D1529-D1533
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  - journals/nar/0001AL21
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Qingyu Chen, Alexis Allot, Zhiyong Lu:
LitCovid: an open database of COVID-19 literature. D1534-D1540
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  - journals/nar/RathSGACDGGHHJJ21
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Sneha Rath, Rohit Sharma, Rahul Gupta, Tslil Ast, Connie Chan, Timothy J. Durham, Russell P. Goodman, Zenon Grabarek, Mary E. Haas, Wendy H. W. Hung, Pallavi R. Joshi, Alexis A. Jourdain, Sharon H. Kim, Anna V. Kotrys, Stephanie S. Lam, Jason G. McCoy, Joshua D. Meisel, Maria Miranda, Apekshya Panda, Anupam Patgiri, Robert Rogers, Shayan Sadre, Hardik Shah, Owen S. Skinner, Tsz Leung To, Melissa A. Walker, Hong Wang, Patrick S. Ward, Jordan Wengrod, Chen-Ching Yuan, Sarah E. Calvo, Vamsi K. Mootha:
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. D1541-D1547
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François Bonnardel, Julien Mariethoz, Serge Pérez, Anne Imberty, Frédérique Lisacek:
LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification. D1548-D1554

Corrigendum

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Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, James G. Jeffryes, José P. Faria, Janaka N. Edirisinghe, Michael B. Mundy, Nicholas Chia, Elad Noor, Moritz Emanuel Beber, Aaron A. Best, Matthew DeJongh, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry:
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes (Corrigendum). D1555
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Fuyun Liu, Yuli Li, Hongwei Yu, Lingling Zhang, Jingjie Hu, Zhenmin Bao, Shi Wang:
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca (Corrigendum). D1556

Volume 49, Number Webserver-Issue, July 2021

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Editorial: the 19th annual Nucleic Acids Research web server issue 2021. 1-4
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Guo-Li Xiong, Zhenxing Wu, Jia-Cai Yi, Li Fu, Zhi-Jiang Yang, Chang-Yu Hsieh, Mingzhu Yin, Xiangxiang Zeng, Chengkun Wu, Ai-Ping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao:
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. 5-14
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Jirí Vymetal, David Jakubec, Jakub Galgonek, Jirí Vondrásek:
Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures. 15-20
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Véronique Geoffroy, Thomas Guignard, Arnaud Kress, Jean-Baptiste Gaillard, Tor Solli-Nowlan, Audrey Schalk, Vincent Gatinois, Hélène Dollfus, Sophie Scheidecker, Jean Muller:
AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis. 21-28
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Kai Blin, Simon Shaw, Alexander M. Kloosterman, Zachary Charlop-Powers, Gilles P. van Wezel, Marnix H. Medema, Tilmann Weber:
antiSMASH 6.0: improving cluster detection and comparison capabilities. 29-35
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Evangelos Karatzas, Fotis A. Baltoumas, Nikolaos A. Panayiotou, Reinhard Schneider, Georgios A. Pavlopoulos:
Arena3Dweb: interactive 3D visualization of multilayered networks. 36-45
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Tobias Fehlmann, Fabian Kern, Pascal Hirsch, Robin Steinhaus, Dominik Seelow, Andreas Keller:
Aviator: a web service for monitoring the availability of web services. 46-51
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Luciano Porto Kagami, Gabriele Orlando, Daniele Raimondi, François Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez, Konstantina Tzavella, Wim F. Vranken:
b2bTools: online predictions for protein biophysical features and their conservation. 52-59
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Davide Baldazzi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio:
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. 60-66
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Andrea Guarracino, Gerardo Pepe, Francesco Ballesio, Marta Adinolfi, Marco Pietrosanto, Elisa Sangiovanni, Ilio Vitale, Gabriele Ausiello, Manuela Helmer-Citterich:
BRIO: a web server for RNA sequence and structure motif scan. 67-71
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Alexandros Armaos, Alessio Colantoni, Gabriele Proietti, Jakob Rupert, Gian Gaetano Tartaglia:
catRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions. 72-79
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Irepan Salvador-Martínez, Marco Grillo, Michalis Averof, Maximilian J. Telford:
CeLaVi: an interactive cell lineage visualization tool. 80-85
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Dariusz Brzezinski, Przemyslaw J. Porebski, Marcin Kowiel, Joanna M. Macnar, Wladek Minor:
Recognizing and validating ligands with CheckMyBlob. 86-92
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Francisco Requena, Hamza Hadj Abdallah, Alejandro García, Patrick Nitschké, Sergi Romana, Valérie Malan, Antonio Rausell:
CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients. 93-103
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Jeffrey Molendijk, Marcus M. Seldin, Benjamin L. Parker:
CoffeeProt: an online tool for correlation and functional enrichment of systems genetics data. 104-113
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Hung Nguyen, Duc Tran, Jonathan M. Galazka, Sylvain V. Costes, Afshin Beheshti, Juli Petereit, Sorin Draghici, Tin Nguyen:
CPA: a web-based platform for consensus pathway analysis and interactive visualization. 114-124
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Omer S. Alkhnbashi, Alexander Mitrofanov, Robson Bonidia, Martin Raden, Van Dinh Tran, Florian Eggenhofer, Shiraz A. Shah, Ekrem Öztürk, Victor Alexandre Padilha, Danilo Sipoli Sanches, André C. P. L. F. de Carvalho, Rolf Backofen:
CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. 125-130
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Guangsheng Pei, Ruifeng Hu, Peilin Jia, Zhongming Zhao:
DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner. 131-139
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Maxat Kulmanov, Fernando Zhapa-Camacho, Robert Hoehndorf:
DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. 140-146
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Md Hossain Shuvo, Muhammad Gulfam, Debswapna Bhattacharya:
DeepRefiner: high-accuracy protein structure refinement by deep network calibration. 147-152
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Jiajing Hu, Rosalba Lepore, Richard J. B. Dobson, Ammar Al-Chalabi, Daniel Bean, Alfredo Iacoangeli:
DGLinker: flexible knowledge-graph prediction of disease-gene associations. 153-161
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Shani T. Gal-Oz, Nimrod Haiat, Dana Eliyahu, Guy Shani, Tal Shay:
DoChaP: the domain change presenter. 162-168
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Pascal Schläpfer, Devang Mehta, Cameron Ridderikhoff, R. Glen Uhrig:
DomainViz: intuitive visualization of consensus domain distributions across groups of proteins. 169-173
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Shuyu Zheng, Jehad Aldahdooh, Tolou Shadbahr, Yinyin Wang, Dalal Aldahdooh, Jie Bao, Wenyu Wang, Jing Tang:
DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. 174-184
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Marius A. Dieckmann, Sebastian Beyvers, Rudel Christian Nkouamedjo-Fankep, Patrick Harald Georg Hanel, Lukas Jelonek, Jochen Blom, Alexander Goesmann:
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. 185-192
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Shuntaro Chiba, Kenji Rowel Q. Lim, Narin Sheri, Saeed Anwar, Esra Erkut, Md Nur Ahad Shah, Tejal Aslesh, Stanley Woo, Omar Sheikh, Rika Maruyama, Hiroaki Takano, Katsuhiko Kunitake, William Duddy, Yasushi Okuno, Yoshitsugu Aoki, Toshifumi Yokota:
eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping. 193-198
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Pietro Di Lena, Claudia Sala, Christine Nardini:
Estimage: a webserver hub for the computation of methylation age. 199-206
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Xuanjin Cheng, Junran Yan, Yongxing Liu, Jiahe Wang, Stefan Taubert:
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis. 207-215
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Severine Duvaud, Chiara Gabella, Frédérique Lisacek, Heinz Stockinger, Vassilios Ioannidis, Christine Durinx:
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users. 216-227
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Shuai Zeng, Ziting Mao, Yijie Ren, Duolin Wang, Dong Xu, Trupti Joshi:
G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. 228-236
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Taeyong Park, Jonghun Won, Minkyung Baek, Chaok Seok:
GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking. 237-241
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Chenwei Li, Zefang Tang, Wenjie Zhang, Zhaochen Ye, Fenglin Liu:
GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA. 242-246
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Przemyslaw Miszta, Pawel Pasznik, Szymon Niewieczerzal, Jakub Jakowiecki, Slawomir Filipek:
GPCRsignal: webserver for analysis of the interface between G-protein-coupled receptors and their effector proteins by dynamics and mutations. 247-256
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Heyuan Zeng, Jinbiao Zhang, Gabriel A. Preising, Tobias Rubel, Pramesh Singh, Anna M. Ritz:
Graphery: interactive tutorials for biological network algorithms. 257-262
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Victòria Pascal Andreu, Jorge Roel-Touris, Dylan Dodd, Michael A. Fischbach, Marnix H. Medema:
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota. 263-270
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Muhammad Arif, Cheng Zhang, Xiangyu Li, Cem Güngör, Bugra Çakmak, Metin Arslantürk, Abdellah Tebani, Berkay Özcan, Oguzhan Subas, Wenyu Zhou, Brian Piening, Hasan Turkez, Linn Fagerberg, Nathan Price, Leroy Hood, Michael Snyder, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu:
iNetModels 2.0: an interactive visualization and database of multi-omics data. 271-276
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Chloé Quignot, Guillaume Postic, Hélène Bret, Julien Rey, Pierre Granger, Samuel Murail, Pablo Chacón, Jessica Andreani, Pierre Tufféry, Raphaël Guérois:
InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps. 277-284
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Lukasz Pawel Kozlowski:
IPC 2.0: prediction of isoelectric point and pKa dissociation constants. 285-292
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Ivica Letunic, Peer Bork:
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. 293-296
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Gábor Erdös, Mátyás Pajkos, Zsuzsanna Dosztányi:
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation. 297-303
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Maxim V. Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan:
KEA3: improved kinase enrichment analysis via data integration. 304-316
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Dechao Bu, Haitao Luo, Peipei Huo, Zhihao Wang, Shan Zhang, Zihao He, Yang Wu, Lianhe Zhao, Jingjia Liu, Jincheng Guo, Shuangsang Fang, Wanchen Cao, Lan Yi, Yi Zhao, Lei Kong:
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. 317-325
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Luca Pinzi, Annachiara Tinivella, Luca Gagliardelli, Domenico Beneventano, Giulio Rastelli:
LigAdvisor: a versatile and user-friendly web-platform for drug design. 326-335
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Wen-Jen Lin, Pei-Chun Shen, Hsiu-Cheng Liu, Yi-Chun Cho, Min-Kung Hsu, I-Chen Lin, Fang-Hsin Chen, Juan-Cheng Yang, Wen-Lung Ma, Wei-Chung Cheng:
LipidSig: a web-based tool for lipidomic data analysis. 336-345
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Ahmed Mohamed, Michelle M. Hill:
LipidSuite: interactive web server for lipidomics differential and enrichment analysis. 346-351
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Alexis Allot, Kyubum Lee, Qingyu Chen, Ling Luo, Zhiyong Lu:
LitSuggest: a web-based system for literature recommendation and curation using machine learning. 352-358
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Charles Christoffer, Siyang Chen, Vijay Bharadwaj, Tunde Aderinwale, Vidhur Kumar, Matin Hormati, Daisuke Kihara:
LZerD webserver for pairwise and multiple protein-protein docking. 359-365
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Juan Carlos González-Sánchez, Mustafa F. R. Ibrahim, Ivo C. Leist, Kyle R. Weise, Robert B. Russell:
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants. 366-374
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Jessica Ding, Montgomery Blencowe, Thien Nghiem, Sung-min Ha, Yen-Wei Chen, Gaoyan Li, Xia Yang:
Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics. 375-387
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Zhiqiang Pang, Jasmine Chong, Guangyan Zhou, David A. de Lima Morais, Le Chang, Michel Barrette, Carol Gauthier, Pierre-Étienne Jacques, Shuzhao Li, Jianguo Xia:
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights. 388-396
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Tobias Fehlmann, Fabian Kern, Omar Laham, Christina Backes, Jeffrey Solomon, Pascal Hirsch, Carsten Volz, Rolf Müller, Andreas Keller:
miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale. 397-408
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Fabian Kern, Ernesto Aparicio-Puerta, Yongping Li, Tobias Fehlmann, Tim Kehl, Viktoria Wagner, Kamalika Ray, Nicole Ludwig, Hans-Peter Lenhof, Eckart Meese, Andreas Keller:
miRTargetLink 2.0 - interactive miRNA target gene and target pathway networks. 409-416
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Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher:
mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. 417-424
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Liam J. McGuffin, Fahd M. F. Aldowsari, Shuaa M. A Alharbi, Recep Adiyaman:
ModFOLD8: accurate global and local quality estimates for 3D protein models. 425-430
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David Sehnal, Sebastian Bittrich, Mandar S. Deshpande, Radka Svobodová Vareková, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K. Burley, Jaroslav Koca, Alexander S. Rose:
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. 431-437
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Michael Silk, Douglas E. V. Pires, Carlos H. M. Rodrigues, Elston N. D'souza, Moshe Olshansky, Natalie Thorne, David B. Ascher:
MTR3D: identifying regions within protein tertiary structures under purifying selection. 438-445
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Robin Steinhaus, Sebastian Proft, Markus Schuelke, David N. Cooper, Jana Marie Schwarz, Dominik Seelow:
MutationTaster2021. 446-451
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Riccardo Vicedomini, Clémence Blachon, Francesco Oteri, Alessandra Carbone:
MyCLADE: a multi-source domain annotation server for sequence functional exploration. 452-458
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Yuwei Zhang, Dechao Bu, Peipei Huo, Zhihao Wang, Hao Rong, Yanguo Li, Jingjia Liu, Meng Ye, Yang Wu, Zheng Jiang, Qi Liao, Yi Zhao:
ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs. 459-468
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Shuwei Yao, Ronghui You, Shaojun Wang, Yi Xiong, Xiaodi Huang, Shanfeng Zhu:
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. 469-475
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Guangyan Zhou, Jessica Ewald, Jianguo Xia:
OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data. 476-482
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Shengquan Chen, Qiao Liu, Xuejian Cui, Zhan-Ying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang:
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. 483-490
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Erik Poppleton, Roger Romero, Aatmik Mallya, Lorenzo Rovigatti, Petr Sulc:
OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures. 491-498
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Gue-Ho Hwang, You Kyeong Jeong, Omer Habib, Sung-Ah Hong, Kayeong Lim, Jin-Soo Kim, Sangsu Bae:
PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing. 499-504
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Mads Valdemar Anderson, Jakob Haldrup, Emil Aagaard Thomsen, Jonas holst Wolff, Jacob giehm Mikkelsen:
pegIT - a web-based design tool for prime editing. 505-509
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Muhammad Farhan Khalid, Kanzal Iman, Amna Ghafoor, Mujtaba Saboor, Ahsan Ali, Urwa Muaz, Abdul Rehman Basharat, Taha Tahir, Muhammad Abubakar, Momina Amer Akhter, Syed Waqar Nabi, Wim Vanderbauwhede, Fayyaz Ahmad, Bilal Wajid, Safee Ullah Chaudhary:
PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics. 510-515
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Matthew J. McGuffie, Jeffrey E. Barrick:
pLannotate: engineered plasmid annotation. 516-522
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Hu Zhao, Zhuo Tu, Yinmeng Liu, Zhanxiang Zong, Jiacheng Li, Hao Liu, Feng Xiong, Jinling Zhan, Xuehai Hu, Weibo Xie:
PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants. 523-529
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Melissa F. Adasme, Katja L. Linnemann, Sarah Naomi Bolz, Florian Kaiser, Sebastian Salentin, V. Joachim Haupt, Michael Schroeder:
PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. 530-534
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Michael Bernhofer, Christian Dallago, Timothy Karl, Venkata P. Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, László Kaján, Seán I. O'Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost:
PredictProtein - Predicting Protein Structure and Function for 29 Years. 535-540
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Martin Gühmann, Stefanie Reuter, Jan Hartung, Ralf Mrowka:
Preselector.uni-jena.de: optimize your cloning - a resource for identifying restriction enzymes for preselection reactions. 541-543
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Besmir Sejdiu, D. Peter Tieleman:
ProLint: a web-based framework for the automated data analysis and visualization of lipid-protein interactions. 544-550
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Sophia Mersmann, Léonie Strömich, Florian J. Song, Nan Wu, Francesca V. Vianello, Mauricio Barahona, Sophia N. Yaliraki:
ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules. 551-558
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Noelia Ferruz, Steffen Schmidt, Birte Höcker:
ProteinTools: a toolkit to analyze protein structures. 559-566
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Guillaume Postic, Jessica Andreani, Julien Marcoux, Victor Reys, Raphaël Guérois, Julien Rey, Emmanuelle Mouton-Barbosa, Yves Vandenbrouck, Sarah Cianférani, Odile Burlet-Schiltz, Gilles Labesse, Pierre Tufféry:
Proteo3Dnet: a web server for the integration of structural information with interactomics data. 567-572
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Evangelos Theodorakis, Andreas N. Antonakis, Ismini Baltsavia, Georgios A. Pavlopoulos, Martina Samiotaki, Grigoris D. Amoutzias, Theodosios Theodosiou, Oreste Acuto, Georgios Efstathiou, Ioannis Iliopoulos:
ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics. 573-577
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Petar I. Penev, Holly M. McCann, Caeden D. Meade, Claudia Alvarez-Carreño, Aparna Maddala, Chad R. Bernier, Vasanta l Chivukula, Maria Ahmad, Burak Gulen, Aakash Sharma, Loren Dean Williams, Anton S. Petrov:
ProteoVision: web server for advanced visualization of ribosomal proteins. 578-588
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Recep Adiyaman, Liam J. McGuffin:
ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts. 589-596
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Bilal Shaikh, Gnaneswara Marupilla, Mike Wilson, Michael L. Blinov, Ion I. Moraru, Jonathan R. Karr:
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. 597-602
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Niccolo Tesi, Sven van der Lee, Marc Hulsman, Henne Holstege, Marcel J. T. Reinders:
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets. 603-612
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Mark Wappett, Adam Harris, Alexander L. R. Lubbock, Ian Lobb, Simon S. McDade, Ian M. Overton:
SynLeGG: analysis and visualization of multiomics data for discovery of cancer 'Achilles Heels' and gene function relationships. 613-618
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Peter W. Harrison, Rodrigo Lopez, Nadim Rahman, Stefan Gutnick Allen, Raheela Aslam, Nicola Buso, Carla A. Cummins, Yasmin Fathy, Eloy Felix, Mihai Glont, Suran Jayathilaka, Sandeep Kadam, Manish Kumar, Katharina B. Lauer, Geetika Malhotra, Abayomi Mosaku, Ossama Edbali, Young Mi Park, Andrew Parton, Matt Pearce, Jose Francisco Estrada pena, Joseph Rossetto, Craig Russell, Sandeep Selvakumar, Xènia Pérez Sitjà, Alexey Sokolov, Ross Thorne, Marianna Ventouratou, Peter Walter, Galabina Yordanova, Amonida Zadissa, Guy Cochrane, Niklas Blomberg, Rolf Apweiler:
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. 619-623
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Denis Yuen, Louise Cabansay, Andrew G. Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen, Elizabeth Sheets, Ash O'farrell, Kim Cullion, Brian D. O'Connor, Benedict Paten, Lincoln Stein:
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols. 624-632
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Alexander L. R. Lubbock, Leonard A. Harris, Vito Quaranta, Darren R. Tyson, Carlos F. Lopez:
Thunor: visualization and analysis of high-throughput dose-response datasets. 633-640
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Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, Erica Larschan:
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. 641-653
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Bikash K. Bhandari, Chun Shen Lim, Paul P. Gardner:
TISIGNER.com: web services for improving recombinant protein production. 654-661
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  - journals/nar/KiniryJMB21
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Stephen J. Kiniry, Ciara E. Judge, Audrey M. Michel, Pavel V. Baranov:
Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data. 662-670
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Edison Ong, Michael F. Cooke, Anthony Huffman, Zuoshuang Xiang, Mei U. Wong, Haihe Wang, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He:
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. 671-678
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  - journals/nar/FritzPB21
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Franziska Fritz, Robert Preissner, Priyanka Banerjee:
VirtualTaste: a web server for the prediction of organoleptic properties of chemical compounds. 679-684
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René Staritzbichler, Nikola Ristic, Andrean Goede, Robert Preissner, Peter Werner Hildebrand:
Voronoia 4-ever. 685-

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