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ORCIDNucleic Acids Research, Volume 50
Volume 50, Number D1, January 2022
- Daniel J. Rigden
, Xosé M. Fernández:
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. 1-10 - Gaia Cantelli, Alex Bateman, Cath Brooksbank, Anton I. Petrov, Rahuman S. Malik-Sheriff, Michele Ide-Smith, Henning Hermjakob, Paul Flicek, Rolf Apweiler, Ewan Birney, Johanna R. McEntyre:
The European Bioinformatics Institute (EMBL-EBI) in 2021. 11-19 - Eric W. Sayers, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Ryan Connor, Kathryn Funk, Chris Kelly, Sunghwan Kim, Tom Madej, Aron Marchler-Bauer, Christopher J. Lanczycki, Stacy Lathrop, Zhiyong Lu, Françoise Thibaud-Nissen, Terence D. Murphy, Lon Phan, Yuri Skripchenko, Tony Tse, Jiyao Wang, Rebecca Williams, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the national center for biotechnology information. 20-26 - Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Jingyao Zeng, Yadong Zhang, Yunfei Shang, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zhenglin Du, Yinying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Peilin Jia, Shuai Jiang, Qiheng Qian, Tongtong Zhu, Wenting Zong, Tong Jin, Yuansheng Zhang, Dong Zou, Qiang Du, Changrui Feng, Lina Ma, Sisi Zhang, Anke Wang, Lili Dong, Yanqing Wang, Wan Liu, Xing Yan, Yunchao Ling, Zhihua Zhou, Wang Kang, Tao Zhang, Shuai Ma, Haoteng Yan, Zunpeng Liu, Zejun Ji, Yusheng Cai, Si Wang, Moshi Song, Jie Ren, Qi Zhou, Jing Qu, Weiqi Zhang, Guanghui Liu, Xu Chen, Tingting Chen, Yanling Sun, Caixia Yu, Bixia Tang, Junwei Zhu, Shuang Zhai, Yubin Sun, Qiancheng Chen, Xiaoyu Yang, Xin Zhang, Zhengqi Sang, Yonggang Wang, Yilin Zhao, Huanxin Chen, Li Lan, Yingke Ma, Yaokai Jia, Xinchang Zheng, Meili Chen, Ming Chen, Guangyi Niu, Rong Pan, Wei Jing, Jian Sang, Chang Liu, Yujia Xiong, Mochen Zhang, Guoliang Wang, Lizhi Yi, Wei Zhao, Song Wu, Zhuang Xiong, Rujiao Li, Zheng Gong, Lin Liu, Zhao Li, Qianpeng Li, Sicheng Luo, Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Yanyan Li, Fei Yang, Mengwei Li, Zhaohua Li, Dongmei Tian, Xiaonan Liu, Cuiping Li, Xufei Teng, Shuhui Song, Yang Zhang, Ruru Chen, Rongqin Zhang, Feng Xu, Yifan Wang, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yungang He, Zhen Yang, Lun Li, Na Li, Ying Cui, Guangya Duan, Gangao Wu, Tianhao Huang, Enhui Jin, Hailong Kang, Zhonghuang Wang, Hua Chen, Mingkun Li, Wanshan Ning, Yu Xue, Yanhu Liu, Qijun Zhou, Xingyan Liu, Longlong Zhang, Bingyu Mao, Shihua Zhang, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Haichun Jing, Yitong Pan, Leisheng Shi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Dan Liu, Chi Zhang, Zheng Zhao, Tao Jiang, Wanying Wu, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Shaofeng Lin, Chuijie Liu, Anyuan Guo, Hao Yuan, Tianhan Su, Yong E. Zhang, Yincong Zhou, Guoji Guo, Shanshan Fu, Xiaodan Tan, Weizhi Zhang, Mei Luo, Yubin Xie, Chenwei Wang, Xingyu Liao, Xin Gao, Jianxin Wang, Guiyan Xie, Chunhui Yuan, Feng Tian, Dechang Yang, Ge Gao, Dachao Tang, Wenyi Wu, Yujie Gou, Cheng Han, Qinghua Cui, Xiangshang Li, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. 27-38 - Ya Cui, Fanglue Peng, Dan Wang, Yumei Li, Jason Sheng Li, Lei Li, Wei Li:
3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues. 39-45 - Weiwei Jin, Guanghui Jiang, Yanbo Yang, Jianye Yang, Wenqian Yang, Dongyang Wang, Xiaohui Niu, Rong Zhong, Zhao Zhang, Jing Gong:
Animal-eRNAdb: a comprehensive animal enhancer RNA database. 46-53 - José Manuel Rodriguez, Fernando Pozo, Daniel Cerdán-Vélez, Tomás Di Domenico, Jesús Vázquez, Michael L. Tress:
APPRIS: selecting functionally important isoforms. 54-59 - Qiangwei Zhou, Pengpeng Guan, Zhixian Zhu, Sheng Cheng, Cong Zhou, Huanhuan Wang, Qian Xu, Wing-Kin Sung, Guoliang Li:
ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms. 60-71 - Xiaolu Zhao, Leisheng Shi, Shasha Ruan, Wenjian Bi, Yifan Chen, Lin Chen, Yifan Liu, MingKun Li, Jie Qiao, Fengbiao Mao:
CircleBase: an integrated resource and analysis platform for human eccDNAs. 72-82 - Wenliang Zhang, Yang Liu, Zhuochao Min, Guodong Liang, Jing Mo, Zhen Ju, Binghui Zeng, Wen Guan, Yan Zhang, Jianliang Chen, Qianshen Zhang, Hanguang Li, Chunxia Zeng, Yanjie Wei, Godfrey Chi-Fung Chan:
circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome. 83-92 - Yigang Chen, Lantian Yao, Yun Tang, Jhih-Hua Jhong, Jingting Wan, Jingyue Chang, Shi-Dong Cui, Yijun Luo, Xiao-Xuan Cai, Wenshuo Li, Qi Chen, Hsi-Yuan Huang, Zhuo Wang, Weiming Chen, Tzu-Hao Chang, Feng-Xiang Wei, Tzong-Yi Lee, Hsien-Da Huang:
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers. 93-101 - Toshihisa Okido, Yuichi Kodama, Jun Mashima, Takehide Kosuge, Takatomo Fujisawa, Osamu Ogasawara:
DNA Data Bank of Japan (DDBJ) update report 2021. 102-105 - Carla A. Cummins, Alisha Ahamed, Raheela Aslam, Josephine Burgin, Rajkumar Devraj, Ossama Edbali, Dipayan Gupta, Peter W. Harrison, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Simon Kay, Manish Kumar, Ankur Lathi, Rasko Leinonen, Fábio Madeira, Nandana Madhusoodanan, Milena Mansurova, Colman O'Cathail, Matt Pearce, Stephane Pesant, Nadim Rahman, Jeena Rajan, Gabriele Rinck, Sandeep Selvakumar, Alexey Sokolov, Swati Suman, Ross Thorne, Prabhat Totoo, Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Rodrigo Lopez, Tony Burdett, Guy Cochrane:
The European Nucleotide Archive in 2021. 106-110 - Chun-Jie Liu, Gui-Yan Xie, Ya-Ru Miao, Meng-Xuan Xia, Yi Wang, Qian Lei, Qiong Zhang, An-Yuan Guo:
EVAtlas: a comprehensive database for ncRNA expression in human extracellular vesicles. 111-117 - Hongyan Lai, Yuchen Li, Hena Zhang, Jia Hu, Jiatao Liao, Ying Su, Qin Li, Bing Chen, Caiping Li, Zhen Wang, Yan Li, Jialei Wang, Zhiqiang Meng, Zhaohui Huang, Shenglin Huang:
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids. 118-128 - Pablo A. Moreno, Silvie Fexova, Nancy George, Jonathan R. Manning, Zhichao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer Fuentes, Anja Füllgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti Jaiswal Kundu, Shengbo Wang, Mathias Walzer, Laura Clarke, David Osumi-Sutherland, Marcela Karey Tello-Ruiz, Sunita Kumari, Doreen Ware, Jana Eliasova, Mark J. Arends, Martijn C. Nawijn, Kerstin B. Meyer, Tony Burdett, John C. Marioni, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma, Irene Papatheodorou:
Expression Atlas update: gene and protein expression in multiple species. 129-140 - Henry E. Pratt, Gregory R. Andrews, Nishigandha Phalke, Jack D. Huey, Michael J. Purcaro, Arjan van der Velde, Jill Moore, Zhiping Weng:
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. 141-149 - Yu-Huan Wang, Qian-Fan Yang, Xiao Lin, Die Chen, Zhi-Yin Wang, Bin Chen, Hua-Yi Han, Hao-Di Chen, Kai-Cong Cai, Qian Li, Shu Yang, Ya-Lin Tang, Feng Li:
G4LDB 2.2: a database for discovering and studying G-quadruplex and i-Motif ligands. 150-160 - Eric W. Sayers, Mark Cavanaugh, Karen Clark, Kim D. Pruitt, Conrad L. Schoch, Stephen T. Sherry, Ilene Karsch-Mizrachi:
GenBank. 161-164 - Jaime Abraham Castro-Mondragón, Rafael Riudavets Puig, Ieva Rauluseviciute, Roza Berhanu lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol Fornes, Tiffany Y. Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel Schmelter, Damir Baranasic, Benoît Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth W. Wasserman, François Parcy, Anthony Mathelier:
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. 165-173 - Lihua Jia, Yang Li, Fangfang Huang, Yingru Jiang, Haoran Li, Zhizhan Wang, Tiantian Chen, Jiaming Li, Zhang Zhang, Wen Yao:
LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes. 174-182 - Peng Wang, Qiuyan Guo, Yue Qi, Yangyang Hao, Yue Gao, Hui Zhi, Yuanfu Zhang, Yue Sun, Yakun Zhang, Mengyu Xin, Yunpeng Zhang, Shangwei Ning, Xia Li:
LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine. 183-189 - Lin Liu, Zhao Li, Chang Liu, Dong Zou, Qianpeng Li, Changrui Feng, Wei Jing, Sicheng Luo, Zhang Zhang, Lina Ma:
LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. 190-195 - Jiongming Ma, Bowen Song, Zhen Wei, Daiyun Huang, Yuxin Zhang, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng, Kunqi Chen:
m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. 196-203 - Bastian Fromm, Eirik Høye, Diana Domanska, Xiangfu Zhong, Ernesto Aparicio-Puerta, Vladimir Ovchinnikov, Sinan U. Umu, Peter J. Chabot, Wenjing Kang, Morteza Aslanzadeh, Marcel Tarbier, Emilio Mármol-Sánchez, Gianvito Urgese, Morten Johansen, Eivind Hovig, Michael Hackenberg, Marc R. Friedländer, Kevin J. Peterson:
MirGeneDB 2.1: toward a complete sampling of all major animal phyla. 204-210 - Andreas Keller, Laura Gröger, Thomas Tschernig, Jeffrey Solomon, Omar Laham, Nicholas Schaum, Viktoria Wagner, Fabian Kern, Georges Pierre Schmartz, Yongping Li, Adam Borcherding, Carola Meier, Tony Wyss-Coray, Eckart Meese, Tobias Fehlmann, Nicole Ludwig:
miRNATissueAtlas2: an update to the human miRNA tissue atlas. 211-221 - Hsi-Yuan Huang, Yang-Chi-Dung Lin, Shi-Dong Cui, Yixian Huang, Yun Tang, Jia-Tong Xu, Jiayang Bao, Yulin Li, Jia Wen, Hua-Li Zuo, Weijuan Wang, Jing Li, Jie Ni, Yini Ruan, Liping Li, Yidan Chen, Yue-Yang Xie, Zihao Zhu, Xiao-Xuan Cai, Xin-Yi Chen, Lantian Yao, Yigang Chen, Yijun Luo, Shupeng Luxu, Mengqi Luo, Chih-Min Chiu, Kun Ma, Lizhe Zhu, Gui-Juan Cheng, Chen Bai, Ying-Chih Chiang, Liping Wang, Feng-Xiang Wei, Tzong-Yi Lee, Hsien-Da Huang:
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. 222-230 - Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elzbieta Purta, Malgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, Gülben Avsar, Antonia Romitelli, Pinar Pir, Erik Dassi, Silvestro G. Conticello, Francesc Aguiló, Janusz M. Bujnicki:
MODOMICS: a database of RNA modification pathways. 2021 update. 2231-235 - Xingyu Liao, Kang Hu, Adil Salhi, You Zou, Jianxin Wang, Xin Gao:
msRepDB: a comprehensive repetitive sequence database of over 80 000 species. 236-245 - Erik Poppleton, Aatmik Mallya, Swarup Dey, Joel Joseph, Petr Sulc:
Nanobase.org: a repository for DNA and RNA nanostructures. 246-252 - Tomasz Zok, Natalia Kraszewska, Joanna Miskiewicz, Paulina Pielacinska, Michal Zurkowski, Marta Szachniuk:
ONQUADRO: a database of experimentally determined quadruplex structures. 253-258 - David Rosenkranz, Hans Zischler, Daniel Gebert:
piRNAclusterDB 2.0: update and expansion of the piRNA cluster database. 259-264 - Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Zhiye Ying, Haopeng Yu, Yanyan Li, Yi Zhao, Xiaoxi Zeng, Shunmin He, Runsheng Chen:
piRBase: integrating piRNA annotation in all aspects. 265-272 - Georges Pierre Schmartz, Anna Hartung, Pascal Hirsch, Fabian Kern, Tobias Fehlmann, Rolf Müller, Andreas Keller:
PLSDB: advancing a comprehensive database of bacterial plasmids. 273-278 - Li Cai, Jia-Jia Xuan, Qiao Lin, Junhao Wang, Shurong Liu, Fangzhou Xie, Ling-Ling Zheng, Bin Li, Liang-Hu Qu, Jianhua Yang:
Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. 279-286 - Weihao Zhao, Shang Zhang, Yumin Zhu, Xiaochen Xi, Pengfei Bao, Ziyuan Ma, Thomas H. Kapral, Shuyuan Chen, Bojan Zagrovic, Yu-Cheng T. Yang, Zhi John Lu:
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. 287-294 - Christian-Alexander Dudek, Dieter Jahn:
PRODORIC: state-of-the-art database of prokaryotic gene regulation. 295-302 - Ruoyao Lin, Xiaoming Zhong, Yongli Zhou, Huichao Geng, Qingxi Hu, Zhihao Huang, Jun Hu, Xiang-Dong Fu, Liang Chen, Jia-Yu Chen:
R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation. 303-315 - Fayrouz Hammal, Pierre de langen, Aurélie Bergon, Fabrice Lopez, Benoît Ballester:
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. 316-325 - Juanjuan Kang, Qiang Tang, Jun He, Le Li, Nianling Yang, Shuiyan Yu, Mengyao Wang, Yuchen Zhang, Jiahao Lin, Tianyu Cui, Yongfei Hu, Puwen Tan, Jun Cheng, Hailong Zheng, Dong Wang, Xi Su, Wei Chen, Yan Huang:
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. 326-332 - Tianyu Cui, Yiying Dou, Puwen Tan, Zhen Ni, Tianyuan Liu, Duolin Wang, Yan Huang, Kaican Cai, Xiaoyang Zhao, Dong Xu, Hao Lin, Dong Wang:
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. 333-339 - Haibo Zhu, Hao Fu, Tianyu Cui, Lin Ning, Huaguo Shao, Yehan Guo, Yanting Ke, Jiayi Zheng, Hongyan Lin, Xin Wu, Guanghao Liu, Jun He, Xin Han, Wenlin Li, Xiaoyang Zhao, Huasong Lu, Dong Wang, Kongfa Hu, Xiaopei Shen:
RNAPhaSep: a resource of RNAs undergoing phase separation. 340-346 - Mengni Liu, Huiqin Li, Xiaotong Luo, Jieyi Cai, Tianjian Chen, Yubin Xie, Jian Ren, Zhixiang Zuo:
RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation. 347-355 - Xiaoxiao Yang, Yang Tong, Gerui Liu, Jiapei Yuan, Yang Yang:
scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse. 356-364 - Sheng Zhu, Qiwei Lian, Wenbin Ye, Wei Qin, Zhe Wu, Guoli Ji, Xiaohui Wu:
scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution. 365-370 - Tianshun Gao, Zilong Zheng, Yihang Pan, Chengming Zhu, Fuxin Wei, Jinqiu Yuan, Rui Sun, Shuo Fang, Nan Wang, Yang Zhou, Jiang Qian:
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species. 371-379 - Wenting Zong, Hongen Kang, Zhuang Xiong, Yingke Ma, Tong Jin, Zheng Gong, Lizhi Yi, Mochen Zhang, Song Wu, Guoliang Wang, Yiming Bao, Rujiao Li:
scMethBank: a database for single-cell whole genome DNA methylation maps. 380-386 - Kenneth S. Katz, Oleg Shutov, Richard Lapoint, Michael Kimelman, J. Rodney Brister, Christopher O'Sullivan:
The Sequence Read Archive: a decade more of explosive growth. 387-390 - Yuexin Zhang, Chao Song, Yimeng Zhang, Yuezhu Wang, Chenchen Feng, Jiaxin Chen, Ling Wei, Qi Pan, Desi Shang, Yanbing Zhu, Jiang Zhu, Shuangsang Fang, Jun Zhao, Yongsan Yang, Xilong Zhao, Xiaozheng Xu, Qiuyu Wang, Jincheng Guo, Chunquan Li:
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. 391-412 - Dezhong Lv, Zhenghong Chang, Yangyang Cai, Junyi Li, Liping Wang, Qiushuang Jiang, Kang Xu, Na Ding, Xia Li, Juan Xu, Yongsheng Li:
TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome. 413-420 - Jun-Hao Wang, Wen-Xin Chen, Shi-Qiang Mei, Yue-Dong Yang, Jian-Hua Yang, Liang-Hu Qu, Ling-Ling Zheng:
tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data. 421-431 - Benjamin D. Lee, Uri Neri, Caleb J. Oh, Peter Simmonds, Eugene V. Koonin:
ViroidDB: a database of viroids and viroid-like circular RNAs. 432-438 - Mihaly Varadi, Stephen Anyango, Mandar S. Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Zídek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard J. Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar:
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. 439-444 - Mingjie Gao, Aurélien F. A. Moumbock, Ammar Qaseem, Qianqing Xu, Stefan Günther:
CovPDB: a high-resolution coverage of the covalent protein-ligand interactome. 445-450 - Weizhi Zhang, Xiaodan Tan, Shaofeng Lin, Yujie Gou, Cheng Han, Chi Zhang, Wanshan Ning, Chenwei Wang, Yu Xue:
CPLM 4.0: an updated database with rich annotations for protein lysine modifications. 451-459 - Jhih-Hua Jhong, Lantian Yao, Yuxuan Pang, Zhongyan Li, Chia-Ru Chung, Rulan Wang, Shangfu Li, Wenshuo Li, Mengqi Luo, Renfei Ma, Yuqi Huang, Xiaoning Zhu, Jiahong Zhang, Hexiang Feng, Qifan Cheng, Chunxuan Wang, Kun Xi, Li-Ching Wu, Tzu-Hao Chang, Jorng-Tzong Horng, Lizhe Zhu, Ying-Chih Chiang, Zhuo Wang, Tzong-Yi Lee:
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. 460-470 - Zhongyan Li, Shangfu Li, Mengqi Luo, Jhih-Hua Jhong, Wenshuo Li, Lantian Yao, Yuxuan Pang, Zhuo Wang, Rulan Wang, Renfei Ma, Jinhan Yu, Yuqi Huang, Xiaoning Zhu, Qifan Cheng, Hexiang Feng, Jiahong Zhang, Chunxuan Wang, Justin Bo-Kai Hsu, Wen-Chi Chang, Feng-Xiang Wei, Hsien-Da Huang, Tzong-Yi Lee:
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. 471-479 - Federica Quaglia, Bálint Mészáros, Edoardo Salladini, András Hatos, Rita Pancsa, Lucía B. Chemes, Mátyás Pajkos, Tamas Lazar, Samuel Peña-Díaz, Jaime Santos, Veronika Ács, Nazanin Farahi, Erzsébet Fichó, Maria Cristina Aspromonte, Claudio Bassot, Anastasia Chasapi, Norman E. Davey, Radoslav Davidovic, Laszlo Dobson, Arne Elofsson, Gábor Erdös, Pascale Gaudet, Michelle G. Giglio, Juliana Glavina, Javier Iserte, Valentín Iglesias, Zsófia L. Kálmán, Matteo Lambrughi, Emanuela Leonardi, Sonia Longhi, Sandra Macedo-Ribeiro, Emiliano Maiani, Julia Marchetti, Cristina Marino Buslje, Attila Meszaros, Alexander Miguel Monzon, Giovanni Minervini, Suvarna Nadendla, Juliet F. Nilsson, Marián Novotný, Christos A. Ouzounis, Nicolas Palopoli, Elena Papaleo, Pedro J. Barbosa Pereira, Gabriele Pozzati, Vasilis J. Promponas, Jordi Pujols, Alma Carolina Sanchez Rocha, Martin Salas, Luciana Rodriguez Sawicki, Éva Schád, Aditi Shenoy, Tamás Szaniszló, Konstantinos D. Tsirigos, Nevena Veljkovic, Gustavo D. Parisi, Salvador Ventura, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan:
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. 480-487 - Guobang Shi, Xinyue Kang, Fanyi Dong, Yanchao Liu, Ning Zhu, Yuxuan Hu, Hanmei Xu, Xingzhen Lao, Heng Zheng:
DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides. 488-496 - Manjeet Kumar, Sushama Michael, Jesús Alvarado Valverde, Bálint Mészáros, Hugo Sámano-Sánchez, András Zeke, Laszlo Dobson, Tamas Lazar, Mihkel Örd, Anurag Nagpal, Nazanin Farahi, Melanie Käser, Ramya Kraleti, Norman E. Davey, Rita Pancsa, Lucía B. Chemes, Toby J. Gibson:
The Eukaryotic Linear Motif resource: 2022 release. 497-508 - András Hatos, Alexander Miguel Monzon, Silvio C. E. Tosatto, Damiano Piovesan, Mónika Fuxreiter:
FuzDB: a new phase in understanding fuzzy interactions. 509-517 - Gáspár Pándy-Szekeres, Mauricio Esguerra, Alexander S. Hauser, Jimmy Caroli, Christian Munk, Steven Pilger, György M. Keserü, Albert J. Kooistra, David E. Gloriam:
The G protein database, GproteinDb. 518-525 - Michael A. R. Hollas, Matthew T. Robey, Ryan T. Fellers, Richard D. LeDuc, Paul M. Thomas, Neil L. Kelleher:
The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms. 526-533 - Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar:
PDBe-KB: collaboratively defining the biological context of structural data. 534-542 - Yasset Pérez-Riverol, Jingwen Bai, Chakradhar Bandla, David García-Seisdedos, Suresh Hewapathirana, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Ananth Prakash, Anika Frericks-Zipper, Martin Eisenacher, Mathias Walzer, Shengbo Wang, Alvis Brazma, Juan Antonio Vizcaíno:
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. 543-552 - John-Marc Chandonia, Lindsey Guan, Shiangyi Lin, Changhua Yu, Naomi K. Fox, Steven E. Brenner:
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. 553-559 - Xiaona Wang, Fengcheng Li, Wenqi Qiu, Binbin Xu, Yanlin Li, Xichen Lian, Hongyan Yu, Zhao Zhang, Jianxin Wang, Zhaorong Li, Weiwei Xue, Feng Zhu:
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. 560-570 - Elodie Drula, Marie-Line Garron, Suzan Dogan, Vincent Lombard, Bernard Henrissat, Nicolas Terrapon:
The carbohydrate-active enzyme database: functions and literature. 571-577 - Birgit H. M. Meldal, Livia Perfetto, Colin W. Combe, Tiago Lubiana, João Vitor Ferreira Cavalcante, Hema Bye-A-Jee, Andra Waagmeester, Noemi del-Toro, Anjali Shrivastava, Elisabet Barrera, Edith D. Wong, Bernhard Mlecnik, Gabriela Bindea, Kalpana Panneerselvam, Egon L. Willighagen, Juri Rappsilber, Pablo Porras, Henning Hermjakob, Sandra E. Orchard:
Complex Portal 2022: new curation frontiers. 578-586 - Atanas Kamburov, Ralf Herwig:
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. 587-595 - Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen:
DISCO: a database of Deeply Integrated human Single-Cell Omics data. 596-602 - Moritz E. Beber, Mattia G. Gollub, Dana Mozaffari, Kevin M. Shebek, Avi I. Flamholz, Ron Milo, Elad Noor:
eQuilibrator 3.0: a database solution for thermodynamic constant estimation. 603-609 - Marouen Ben Guebila, Camila Miranda Lopes-Ramos, Deborah A. Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L. Kuijjer, John Quackenbush:
GRAND: a database of gene regulatory network models across human conditions. 610-621 - David S. Wishart, Anchi Guo, Eponine Oler, Fei Wang, Afia Anjum, Harrison Peters, Raynard Dizon, Zinat Sayeeda, Siyang Tian, Brian L. Lee, Mark V. Berjanskii, Robert Mah, Mai Yamamoto, Juan Jovel, Claudia Torres-Calzada, Mickel Hiebert-Giesbrecht, Vicki W. Lui, Dorna Varshavi, Dorsa Varshavi, Dana Allen, David Arndt, Nitya Khetarpal, Aadhavya Sivakumaran, Karxena Harford, Selena Sanford, Kristen Yee, Xuan Cao, Zachary Budinski, Jaanus Liigand, Lun Zhang, Jiamin Zheng, Rupasri Mandal, Naama Karu, Maija Dambrova, Helgi B. Schiöth, Russell Greiner, Vasuk Gautam:
HMDB 5.0: the Human Metabolome Database for 2022. 622-631 - Chan Yeong Kim, Seungbyn Baek, Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, G. Traver Hart, Insuk Lee:
HumanNet v3: an improved database of human gene networks for disease research. 632-639 - Max Kotlyar, Chiara Pastrello, Zuhaib Ahmed, Justin Chee, Zofia Varyova, Igor Jurisica:
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. 640-647 - Noemi del-Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin W. Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Bálint Mészáros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret J. Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwínski, Sandra E. Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob:
The IntAct database: efficient access to fine-grained molecular interaction data. 648-653 - Vivek Modi, Roland L. Dunbrack Jr.:
Kincore: a web resource for structural classification of protein kinases and their inhibitors. 654-664 - David S. Wishart, Zinat Sayeeda, Zachary Budinski, Anchi Guo, Brian L. Lee, Mark V. Berjanskii, Manoj Rout, Harrison Peters, Raynard Dizon, Robert Mah, Claudia Torres-Calzada, Mickel Hiebert-Giesbrecht, Dorna Varshavi, Dorsa Varshavi, Eponine Oler, Dana Allen, Xuan Cao, Vasuk Gautam, Andrew Maras, Ella F. Poynton, Pegah Tavangar, Vera Yang, Jeffrey A. van Santen, Rajarshi Ghosh, Saurav Sarma, Eleanor Knutson, Victoria Sullivan, Amy M. Jystad, Ryan S. Renslow, Lloyd W. Sumner, Roger G. Linington, John R. Cort:
NP-MRD: the Natural Products Magnetic Resonance Database. 665-677 - Anju Sharma, Bishal Kumar Saha, Rajnish Kumar, Pritish Kumar Varadwaj:
OlfactionBase: a repository to explore odors, odorants, olfactory receptors and odorant-receptor interactions. 678-686 - Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek M. Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary D. Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The reactome pathway knowledgebase 2022. 687-692 - Parit Bansal, Anne Morgat, Kristian B. Axelsen, Venkatesh Muthukrishnan, Elisabeth Coudert, Lucila Aimo, Nevila Hyka-Nouspikel, Elisabeth Gasteiger, Arnaud Kerhornou, Teresa Batista Neto, Monica Pozzato, Marie-Claude Blatter, Alexandr Ignatchenko, Nicole Redaschi, Alan J. Bridge:
Rhea, the reaction knowledgebase in 2022. 693-700 - Luca Csabai, Dávid Fazekas, Tamás Kadlecsik, Máté Szalay-Beko, Balázs Bohár, Matthew Madgwick, Dezsö Módos, Marton Olbei, Lejla Gul, Padhmanand Sudhakar, János Kubisch, Oyebode J. Oyeyemi, Orsolya Liska, Eszter Ari, Bernadette Hotzi, Viktor A. Billes, Eszter Molnár, László Földvári-Nagy, Kitti Csályi, Amanda Demeter, Nóra Pápai, Mihály Koltai, Máté Varga, Katalin Lenti, Illés J. Farkas, Dénes Türei, Péter Csermely, Tibor Vellai, Tamás Korcsmáros:
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. 701-709 - Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Yuanfang Guan, Jianxin Wang:
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. 710-718 - Xun Wang, Yang Li, Mengqi He, Xiangren Kong, Peng Jiang, Xi Liu, Lihong Diao, Xinlei Zhang, Honglei Li, Xinping Ling, Simin Xia, Zhongyang Liu, Yuan Liu, Chun-Ping Cui, Yan Wang, Liujun Tang, Lingqiang Zhang, Fuchu He, Dong Li:
UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. 719-728 - Junwon Yang, Jonghyun Park, Yeonjae Jung, Jongsik Chun:
AMDB: a database of animal gut microbial communities with manually curated metadata. 729-735 - Mehmet Direnç Mungan, Kai Blin, Nadine Ziemert:
ARTS-DB: a database for antibiotic resistant targets. 736-740 - Lorenz Christian Reimer, Joaquim Sardà Carbasse, Julia Koblitz, Christian Ebeling, Adam Podstawka, Jörg Overmann:
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data. 741-746 - Wenliang Zhang, Yan Zhang, Zhuochao Min, Jing Mo, Zhen Ju, Wen Guan, Binghui Zeng, Yang Liu, Jianliang Chen, Qianshen Zhang, Hanguang Li, Chunxia Zeng, Yanjie Wei, Godfrey Chi-Fung Chan:
COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale. 747-757 - Peng Zhou, Li Wang, Hai Liu, Chunyan Li, Zhimin Li, Jinxiang Wang, Xiaoming Tan:
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. 758-764 - Nishadi De Silva, Jyothish Bhai, Marc Chakiachvili, Bruno Contreras-Moreira, Carla A. Cummins, Adam Frankish, Astrid Gall, Thiago Augusto Lopes Genez, Kevin L. Howe, Sarah E. Hunt, Fergal J. Martin, Benjamin Moore, Denye N. Oheh, Anne Parker, Andrew Parton, Magali Ruffier, Manoj Pandian Sakthivel, Dan Sheppard, John G. Tate, Anja Thormann, David Thybert, Stephen J. Trevanion, Andrea Winterbottom, Daniel R. Zerbino, Robert D. Finn, Paul Flicek, Andrew D. Yates:
The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. 765-770 - Mercy Rophina, Kavita Pandhare, Afra Shamnath, Mohamed Imran, Bani Jolly, Vinod Scaria:
ESC: a comprehensive resource for SARS-CoV-2 immune escape variants. 771-776 - Die Dai, Jiaying Zhu, Chuqing Sun, Min Li, Jinxin Liu, Sicheng Wu, Ning Kang, Lijie He, Xing-Ming Zhao, Wei-Hua Chen:
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison. 777-784 - Donovan H. Parks, Maria Chuvochina, Christian Rinke, Aaron J. Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz:
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. 785-794 - Liang Cheng, Changlu Qi, Haixiu Yang, Minke Lu, Yiting Cai, Tongze Fu, Jialiang Ren, Qu Jin, Xue Zhang:
gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites. 795-800 - Jan P. Meier-Kolthoff, Joaquim Sardà Carbasse, Rosa L. Peinado-Olarte, Markus Göker:
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. 801-807 - Hanbo Jin, Guoru Hu, Chuqing Sun, Yiqian Duan, Zhenmo Zhang, Zhi Liu, Xing-Ming Zhao, Wei-Hua Chen:
mBodyMap: a curated database for microbes across human body and their associations with health and diseases. 808-816 - Zhidong Tang, Weiliang Fan, Qiming Li, Dehe Wang, Miaomiao Wen, Junhao Wang, Xingqiao Li, Yu Zhou:
MVIP: multi-omics portal of viral infection. 817-836 - Martin Urban, Alayne Cuzick, James Seager, Valerie Wood, Kim Rutherford, Shilpa Yagwakote Venkatesh, Jashobanta Sahu, S. Vijaylakshmi Iyer, Lokanath Khamari, Nishadi De Silva, Manuel Carbajo Martinez, Helder Pedro, Andrew D. Yates, Kim E. Hammond-Kosack:
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. 837-847 - Wei Dai, Jiahui Li, Qi Li, Jiasheng Cai, Jianzhong Su, Christopher Stubenrauch, Jiawei Wang:
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. 848-857 - Mariona Torrens-Fontanals, Alejandro Peralta-García, Carmine Talarico, Ramon Guixà-González, Toni Giorgino, Jana Selent:
SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. 858-866 - Changlu Qi, Chao Wang, Lingling Zhao, Zijun Zhu, Ping Wang, Sainan Zhang, Liang Cheng, Xue Zhang:
SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues. 867-874 - Tiago Pedreira, Christoph Elfmann, Jörg Stülke:
The current state of SubtiWiki, the database for the model organism Bacillus subtilis. 875-882 - Stepan A. Nersisyan, Anton Zhiyanov, Maxim U. Shkurnikov, Alexander G. Tonevitsky:
T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations. 883-887 - Qinglan Sun, Chang Shu, Wenyu Shi, Yingfeng Luo, Guomei Fan, Jingyi Nie, Yuhai Bi, Qihui Wang, Jianxun Qi, Jian Lu, Yuanchun Zhou, Zhihong Shen, Zhen Meng, Xinjiao Zhang, Zhengfei Yu, Shenghan Gao, Linhuan Wu, Juncai Ma, Songnian Hu:
VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes. 888-897 - Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba, Ana Barreto, Evelina Y. Basenko, Wojciech Bazant, Robert Belnap, Ann S. Blevins, Ulrike Böhme, John Brestelli, Brian P. Brunk, Mark J. Caddick, Danielle Callan, Lahcen I. Campbell, Mikkel B. Christensen, George K. Christophides, Kathryn Crouch, Kristina Davis, Jeremy D. DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria I. Giraldo-Calderón, Omar S. Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J. Hickman, Connor Howington, Sufen Hu, Jay C. Humphrey, John Iodice, Andrew R. Jones, John Judkins, Sarah A. Kelly, Jessica C. Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M. MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S. Roos, Samuel S. C. Rund, Stephanie wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J. Stoeckert Jr., Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A. Wilkinson, Lin Xu, Jie Zheng:
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. 898-911 - Bo Liu, Dandan Zheng, Siyu Zhou, Lihong Chen, Jian Yang:
VFDB 2022: a general classification scheme for bacterial virulence factors. 912-917 - Ying Wang, Yuantao Tong, Zeyu Zhang, Rongbin Zheng, Danqi Huang, Jinxuan Yang, Hui Zong, Fanglin Tan, Yujia Xie, Honglian Huang, Xiaoyan Zhang:
ViMIC: a database of human disease-related virus mutations, integration sites and cis-effects. 918-927 - Jun Cheng, Yunqing Lin, Linfu Xu, Kechen Chen, Qi Li, Kaixin Xu, Lin Ning, Juanjuan Kang, Tianyu Cui, Yan Huang, Xiaoyang Zhao, Dong Wang, Yanhui Li, Xi Su, Bin Yang:
ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation. 928-933 - Dongsheng Chen, Cong Tan, Peiwen Ding, Lihua Luo, Jiacheng Zhu, Xiaosen Jiang, Zhihua Ou, Xiangning Ding, Tianming Lan, Yixin Zhu, Yi Jia, Yanan Wei, Runchu Li, Qiuyu Qin, Chengcheng Sun, Wandong Zhao, Zhiyuan Lv, Haoyu Wang, Wendi Wu, Yuting Yuan, Mingyi Pu, Yuejiao Li, Yanan Zhang, Ashley Chang, Guoji Guo, Yong Bai, Xin Jin, Huan Liu:
VThunter: a database for single-cell screening of virus target cells in the animal kingdom. 934-942 - Siyu Zhou, Bo Liu, Yelin Han, Yuyang Wang, Lihong Chen, Zhiqiang Wu, Jian Yang:
ZOVER: the database of zoonotic and vector-borne viruses. 943-949 - Cheng Quan, Jie Ping, Hao Lu, Gangqiao Zhou, Yiming Lu:
3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database. 950-955 - Zhi-Liang Hu, Carissa A. Park, James M. Reecy:
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. 956-961 - Shuai Jiang, Qiang Du, Changrui Feng, Lina Ma, Zhang Zhang:
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. 962-969 - Bradley I. Arshinoff, Gregory A. Cary, Kamran Karimi, Saoirse Foley, Sergei Agalakov, Francisco Delgado, Vaneet S. Lotay, Carolyn Ku, Troy J. Pells, Thomas R. Beatman, Eugene Kim, R. Andrew Cameron, Peter D. Vize, Cheryl A. Telmer, Jenifer C. Croce, Charles A. Ettensohn, Veronica F. Hinman:
Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms. 970-979 - Mallory Ann Freeberg, Lauren A. Fromont, Teresa D'altri, Anna Foix Romero, Jorge Izquierdo Ciges, Aina Jene, Giselle Kerry, Mauricio Moldes, Roberto Ariosa, Silvia Bahena, Daniel Barrowdale, Marcos Casado Barbero, Dietmar Fernández-Orth, Carles Garcia-Linares, Emilio Garcia-Rios, Frédéric Haziza, Bela Juhasz, Oscar Martinez Llobet, Gemma Milla, Anand Mohan, Manuel Rueda, Aravind Sankar, Dona Shaju, Ashutosh Shimpi, Babita Singh, Coline Thomas, Sabela de la Torre, Umuthan Uyan, Claudia Vasallo, Paul Flicek, Roderic Guigó, Arcadi Navarro, Helen E. Parkinson, Thomas M. Keane, Jordi Rambla:
The European Genome-phenome Archive in 2021. 980-987 - Fiona Cunningham, James E. Allen, Jamie Allen, Jorge Álvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Ruth Bennett, Andrew E. Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla A. Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Sarah M. Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos García-Girón, Thiago A. L. Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Thomas Juettemann, Vinay Kaikala, Mike P. Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N. Oheh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, José G. Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Natalie L. Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish, Stefano Giorgetti, Leanne Haggerty, Sarah E. Hunt, Garth IIsley, Jane E. Loveland, Fergal J. Martin, Benjamin Moore, Jonathan M. Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, John G. Tate, David Thybert, Stephen J. Trevanion, Sarah Dyer, Peter W. Harrison, Kevin L. Howe, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
Ensembl 2022. 988-995 - Andrew D. Yates, James E. Allen, M. Ridwan Amode, Andrey G. Azov, Matthieu Barba, Andrés Becerra, Jyothish Bhai, Lahcen I. Campbell, Manuel Carbajo Martinez, Marc Chakiachvili, Kapeel Chougule, Mikkel B. Christensen, Bruno Contreras-Moreira, Alayne Cuzick, Luca Da Rin Fioretto, Paul Davis, Nishadi De Silva, Stavros Diamantakis, Sarah Dyer, Justin Elser, Carla V. Filippi, Astrid Gall, Dionysios Grigoriadis, Cristina Guijarro-Clarke, Parul Gupta, Kim E. Hammond-Kosack, Kevin L. Howe, Pankaj Jaiswal, Vinay Kaikala, Vivek Kumar, Sunita Kumari, Nick Langridge, Tuan Le, Manuel Luypaert, Gareth Maslen, Thomas Maurel, Benjamin Moore, Matthieu Muffato, Aleena Mushtaq, Guy Naamati, Sushma Naithani, Andrew Olson, Anne Parker, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Mark Quinton-Tulloch, Faye Rodgers, Marc Rosello, Magali Ruffier, James Seager, Vasily Sitnik, Michal Szpak, John G. Tate, Marcela K. Tello-Ruiz, Stephen J. Trevanion, Martin Urban, Doreen Ware, Sharon Wei, Gary Williams, Andrea Winterbottom, Magdalena Zarowiecki, Robert D. Finn, Paul Flicek:
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. 996-1003 - Zhuang Xiong, Fei Yang, Mengwei Li, Yingke Ma, Wei Zhao, Guoliang Wang, Zhaohua Li, Xinchang Zheng, Dong Zou, Wenting Zong, Hongen Kang, Yaokai Jia, Rujiao Li, Zhang Zhang, Yiming Bao:
EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. 1004-1009 - Sue A. Krause, Gayle Overend, Julian A. T. Dow, David P. Leader:
FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas. 1010-1015 - Yuansheng Zhang, Dong Zou, Tongtong Zhu, Tianyi Xu, Ming Chen, Guangyi Niu, Wenting Zong, Rong Pan, Wei Jing, Jian Sang, Chang Liu, Yujia Xiong, Yubin Sun, Shuang Zhai, Huanxin Chen, Wenming Zhao, Jing-Fa Xiao, Yiming Bao, Lili Hao, Zhang Zhang:
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. 1016-1024 - Nga Thi Thuy Nguyen, Pierre Vincens, Jean-François Dufayard, Hugues Roest Crollius, Alexandra Louis:
Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors. 1025-1031 - Amy T. Walsh, Deborah A. Triant, Justin J. Le Tourneau, Md. Shamimuzzaman, Christine G. Elsik:
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. 1032-1039 - Yang Mei, Dong Jing, Shenyang Tang, Xi Chen, Hao Chen, Haonan Duanmu, Yuyang Cong, Mengyao Chen, Xinhai Ye, Hang Zhou, Kang He, Fei Li:
InsectBase 2.0: a comprehensive gene resource for insects. 1040-1045 - Jinding Liu, Fei Yin, Kun Lang, Wencai Jie, Suxu Tan, Rongjing Duan, Shuiqing Huang, Wen Huang:
MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species. 1046-1054 - Ioannis Kavakiotis, Athanasios Alexiou, Spyros Tastsoglou, Ioannis S. Vlachos, Artemis G. Hatzigeorgiou:
DIANA-miTED: a microRNA tissue expression database. 1055-1061 - Diego Fuentes, Manuel Molina, Uciel Chorostecki, Salvador Capella-Gutiérrez, Marina Marcet-Houben, Toni Gabaldón:
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. 1062-1068 - Aina Colomer-Vilaplana, Jesús Murga-Moreno, Aleix Canalda-Baltrons, Clara Inserte, Daniel Soto, Marta Coronado-Zamora, Antonio Barbadilla, Sònia Casillas:
PopHumanVar: an interactive application for the functional characterization and prioritization of adaptive genomic variants in humans. 1069-1076 - Katherine Decker, Ye Gao, Kevin Rychel, Tahani Al Bulushi, Siddharth M. Chauhan, Donghyuk Kim, Byung-Kwan Cho, Bernhard O. Palsson:
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. 1077-1090 - Weiwei Fu, Rui Wang, Hojjat Asadollahpour Nanaei, Jinxin Wang, Dexiang Hu, Yu Jiang:
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. 1091-1099 - Shixiang Sun, Yujue Wang, Alexander Y. Maslov, Xiao Dong, Jan Vijg:
SomaMutDB: a database of somatic mutations in normal human tissues. 1100-1108 - Massimo Andreatta, Fabrice P. A. David, Christian Iseli, Nicolas Guex, Santiago J. Carmona:
SPICA: Swiss portal for immune cell analysis. 1109-1114 - Brian T. Lee, Galt P. Barber, Anna Benet-Pagès, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clayton M. Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Christopher M. Lee, Pranav Muthuraman, Luis R. Nassar, Beagan Nguy, Tiana Pereira, Gerardo Perez, Brian J. Raney, Kate R. Rosenbloom, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent:
The UCSC Genome Browser database: 2022 update. 1115-1122 - Chen Cao, Jianhua Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, Quan Zou:
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. 1123-1130 - Lin Liu, Yang Zhang, Guangyi Niu, Qianpeng Li, Zhao Li, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Tianyi Xu, Ruru Chen, Xufei Teng, Rongqin Zhang, Dong Zou, Lina Ma, Zhang Zhang:
BrainBase: a curated knowledgebase for brain diseases. 1131-1138 - Ruidong Li, Han Qu, Shibo Wang, John M. Chater, Xuesong Wang, Yanru Cui, Lei Yu, Rui Zhou, Qiong Jia, Ryan Traband, Meiyue Wang, Weibo Xie, Dongbo Yuan, Jianguo Zhu, Wei-De Zhong, Zhenyu Jia:
CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer. 1139-1146 - Jingyao Zeng, Yadong Zhang, Yunfei Shang, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zaichao Zhang, Yang Li, Zhenglin Du, Jing-Fa Xiao:
CancerSCEM: a database of single-cell expression map across various human cancers. 1147-1155 - Cari Martini, Ying Frances Liu, Hui Gong, Nicole Sayers, German Segura, Jennifer Fostel:
CEBS update: curated toxicology database with enhanced tools for data integration. 1156-1163 - Yin-Ying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Yiming Bao, Peilin Jia:
CeDR Atlas: a knowledgebase of cellular drug response. 1164-1171 - Mustafa S. Pir, Halil Ibrahim Bilgin, Ahmet Sayici, Fatih Coskun, Furkan M. Torun, Pei Zhao, Yahong Kang, Sebiha Cevik, Oktay I. Kaplan:
ConVarT: a search engine for matching human genetic variants with variants from non-human species. 1172-1178 - Jing Feng, Wenbo Chen, Xin Dong, Jun Wang, Xiangfei Mei, Jin Deng, Siqi Yang, Chenjian Zhuo, Xiaoyu Huang, Lin Shao, Rongyu Zhang, Jing Guo, Ronghui Ma, Juan Liu, Feng Li, Ying Wu, Leng Han, Chunjiang He:
CSCD2: an integrated interactional database of cancer-specific circular RNAs. 1179-1183 - Zhongyang Liu, Jiale Liu, Xinyue Liu, Xun Wang, Qiaosheng Xie, Xinlei Zhang, Xiangya Kong, Mengqi He, Yuting Yang, Xinru Deng, Lele Yang, Yaning Qi, Jiajun Li, Yuan Liu, Liying Yuan, Lihong Diao, Fuchu He, Dong Li:
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. 1184-1199 - Guo-Li Xiong, Zhi-Jiang Yang, Jiacai Yi, Ningning Wang, Lei Wang, Huimin Zhu, Chengkun Wu, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dongsheng Cao:
DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety. 1200-1207 - Jie Xing, Ruiyang Zhai, Cong Wang, Honghao Liu, Jiaqi Zeng, Dianshuang Zhou, Mengyan Zhang, Liru Wang, Qiong Wu, Yue Gu, Yan Zhang:
DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database. 1208-1215 - Timothee Cezard, Fiona Cunningham, Sarah E. Hunt, Baron Koylass, Nitin Kumar, Gary Saunders, April Shen, Andres f Silva, Kirill Tsukanov, Sundararaman Venkataraman, Paul Flicek, Helen E. Parkinson, Thomas M. Keane:
The European Variation Archive: a FAIR resource of genomic variation for all species. 1216-1220 - Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou:
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. 1221-1230 - Hang Ruan, Qiang Li, Yuan Liu, Yaoming Liu, Charles Lussier, Lixia Diao, Leng Han:
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers. 1231-1237 - Deyu Yan, Genhui Zheng, Caicui Wang, Zikun Chen, Tiantian Mao, Jian Gao, Yu Yan, Xiangyi Chen, Xuejie Ji, Jinyu Yu, Saifeng Mo, Haonan Wen, Wenhao Han, Mengdi Zhou, Yuan Wang, Jun Wang, Kailin Tang, Zhiwei Cao:
HIT 2.0: an enhanced platform for Herbal Ingredients' Targets. 1238-1243 - Lize Wu, Ziwei Xue, Siqian Jin, Jinchun Zhang, Yixin Guo, Yadan Bai, Xuexiao Jin, Chaochen Wang, Lie Wang, Zuozhu Liu, James Q. Wang, Linrong Lu, Wanlu Liu:
huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level. 1244-1254 - Lynn M. Schriml, James B. Munro, Mike Schor, Dustin Olley, Carrie McCracken, Victor Felix, J. Allen Baron, Rebecca C. Jackson, Susan M. Bello, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion, Michelle G. Giglio, Carol Greene:
The Human Disease Ontology 2022 update. 1255-1261 - Taciana Manso, Géraldine Folch, Véronique Giudicelli, Joumana Jabado-Michaloud, Anjana Kushwaha, Viviane Nguefack Ngoune, Maria Georga, Ariadni Papadaki, Chahrazed Debbagh, Perrine Pégorier, Morgane Bertignac, Saida Hadi-Saljoqi, Imène Chentli, Karima Cherouali, Safa Aouinti, Amar El Hamwi, Alexandre Albani, Merouane Elazami Elhassani, Benjamin Viart, Agathe Goret, Anna Tran, Gaoussou Sanou, Maël Rollin, Patrice Duroux, Sofia Kossida:
IMGT® databases, related tools and web resources through three main axes of research and development. 1262-1272 - Piotr Deszynski, Jakub Mlokosiewicz, Adam Volanakis, Igor Jaszczyszyn, Natalie Castellana, Stefano Bonissone, Rajkumar Ganesan, Konrad Krawczyk:
INDI - integrated nanobody database for immunoinformatics. 1273-1281 - Simon D. Harding, Jane F. Armstrong, Elena Faccenda, Christopher Southan, Stephen P. H. Alexander, Anthony P. Davenport, Adam J. Pawson, Michael Spedding, Jamie A. Davies:
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials. 1282-1294 - Mengyuan Yang, Huifen Lu, Jiajia Liu, Sijia Wu, Pora Kim, Xiaobo Zhou:
lncRNAfunc: a knowledgebase of lncRNA function in human cancer. 1295-1306 - Vishal B. Siramshetty, Ivan Grishagin, Ðac-Trung Nguyen, Tyler Peryea, Yulia Skovpen, Oleg Stroganov, Daniel Katzel, Timothy Sheils, Ajit Jadhav, Ewy A. Mathé, Noel Southall:
NCATS Inxight Drugs: a comprehensive and curated portal for translational research. 1307-1316 - Jeffrey A. van Santen, Ella F. Poynton, Dasha Iskakova, Emily McMann, Tyler A. Alsup, Trevor N. Clark, Claire H. Fergusson, David P. Fewer, Alison H. Hughes, Caitlin A McCadden, Jonathan Parra, Sylvia Soldatou, Jeffrey D. Rudolf, Elisabeth M.-L. Janssen, Katherine R. Duncan, Roger G. Linington:
The Natural Products Atlas 2.0: a database of microbially-derived natural products. 1317-1323 - Xueni Sun, Yintao Zhang, Ying Zhou, Xichen Lian, Lili Yan, Ting Pan, Ting Jin, Han Xie, Zimao Liang, Wenqi Qiu, Jianxin Wang, Zhaorong Li, Feng Zhu, Xinbing Sui:
NPCDR: natural product-based drug combination and its disease-specific molecular regulation. 1324-1333 - Gongyu Tang, Minsu Cho, Xiaowei Wang:
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer. 1334-1339 - Yangjun Zhang, Xiangyang Yao, Hui Zhou, Xiaoliang Wu, Jianbo Tian, Jin Zeng, Libin Yan, Chen Duan, Haoran Liu, Heng Li, Ke Chen, Zhiquan Hu, Zhangqun Ye, Hua Xu:
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. 1340-1347 - Nikta Feizi, Sisira Kadambat Nair, Petr Smirnov, Gangesh Beri, Christopher Eeles, Parinaz Nasr Esfahani, Minoru Nakano, Denis Tkachuk, Anthony Mammoliti, Evgeniya Gorobets, Arvind Singh Mer, Eva Lin, Yihong Yu, Scott Martin, Marc Hafner, Benjamin Haibe-Kains:
PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. 1348-1357 - Hai Fang, Julian C. Knight:
Priority index: database of genetic targets in immune-mediated disease. 1358-1367 - Constantin Schneider, Matthew I. J. Raybould, Charlotte M. Deane:
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker. 1368-1372 - Xiaotong Luo, Yuantai Huang, Huiqin Li, Yihai Luo, Zhixiang Zuo, Jian Ren, Yubin Xie:
SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients. 1373-1381 - Alessandro Cuozzo, Antoine Daina, Marta A. S. Perez, Olivier Michielin, Vincent Zoete:
SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface. 1382-1390 - Zexian Zeng, Cheryl J. Wong, Lin Yang, Nofal Ouardaoui, Dian Li, Wubing Zhang, Shengqing Gu, Yi Zhang, Yang Liu, Xiaoqing Wang, Jingxin Fu, Liye Zhou, Boning Zhang, Sarah Kim, Kathleen B. Yates, Myles Brown, Gordon J. Freeman, Ravindra Uppaluri, Robert Manguso, X. Shirley Liu:
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. 1391-1397 - Ying Zhou, Yintao Zhang, Xichen Lian, Fengcheng Li, Chaoxin Wang, Feng Zhu, Yunqing Qiu, Yuzong Chen:
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents. 1398-1407 - Dandan Huang, Yao Zhou, Xianfu Yi, Xutong Fan, Jianhua Wang, Hongcheng Yao, Pak Chung Sham, Jihui Hao, Kexin Chen, Mulin Jun Li:
VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. 1408-1416 - Tingting Fu, Fengcheng Li, Yang Zhang, Jiayi Yin, Wenqi Qiu, Xuedong Li, Xingang Liu, Wenwen Xin, Chengzhao Wang, Lushan Yu, Jianqing Gao, Qingchuan Zheng, Su Zeng, Feng Zhu:
VARIDT 2.0: structural variability of drug transporter. 1417-1431 - Haixu Chen, Tianpeng Wang, Xiaoning He, Xu Cai, Runmao Lin, Jianli Liang, Jian Wu, Graham King, Xiaowu Wang:
BRAD V3.0: an upgraded Brassicaceae database. 1432-1441 - Marco Di Marsico, Andreu Paytuví Gallart, Walter Sanseverino, Riccardo Aiese Cigliano:
GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. 1442-1447 - Jingjing Jin, Peng Lu, Yalong Xu, Jiemeng Tao, Zefeng Li, Shuaibin Wang, Shizhou Yu, Chen Wang, Xiaodong Xie, Junping Gao, Qiansi Chen, Lin Wang, Wenxuan Pu, Peijian Cao:
PCMDB: a curated and comprehensive resource of plant cell markers. 1448-1455 - Xuelian Ma, Hengyu Yan, Jiaotong Yang, Yue Liu, Zhongqiu Li, Minghao Sheng, Yaxin Cao, Xinyue Yu, Xin Yi, Wenying Xu, Zhen Su:
PlantGSAD: a comprehensive gene set annotation database for plant species. 1456-1467 - Michiel Van Bel, Francesca Silvestri, Eric M. Weitz, Lukasz Kreft, Alexander Botzki, Frederik Coppens, Klaas Vandepoele:
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants. 1468-1474 - Zhonglong Guo, Zheng Kuang, Yongxin Zhao, Yang Deng, Hao He, Miaomiao Wan, Yihan Tao, Dong Wang, Jianhua Wei, Lei Li, Xiaozeng Yang:
PmiREN2.0: from data annotation to functional exploration of plant microRNAs. 1475-1482 - Joan Calle García, Anna Guadagno, Andreu Paytuví Gallart, Alfonso Saera-Vila, Ciro Gianmaria Amoroso, Daniela D'Esposito, Giuseppe Andolfo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria Raffaella Ercolano:
PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process. 1483-1490 - Han Xue, Qingfeng Zhang, Panqin Wang, Bijin Cao, Chongchong Jia, Ben Cheng, Yuhua Shi, Weifeng Guo, Zhenlong Wang, Zexian Liu, Han Cheng:
qPTMplants: an integrative database of quantitative post-translational modifications in plants. 1491-1499 - Mélanie Courtot, Dipayan Gupta, Isuru Udara Liyanage, Fuqi Xu, Tony Burdett:
BioSamples database: FAIRer samples metadata to accelerate research data management. 1500-1507 - Rita Pancsa, Erzsébet Fichó, Daniel Molnar, Éva Viola Surányi, Tamás Trombitás, Dóra Füzesi, Hanna Lóczi, Péter Szijjártó, Rita Hírmondó, Judit E. Szabó, Judit Tóth:
dNTPpoolDB: a manually curated database of experimentally determined dNTP pools and pool changes in biological samples. 1508-1514 - Suvarna Nadendla, Rebecca C. Jackson, James B. Munro, Federica Quaglia, Bálint Mészáros, Dustin Olley, Elizabeth T. Hobbs, Stephen M. Goralski, Marcus C. Chibucos, Christopher J. Mungall, Silvio C. E. Tosatto, Ivan Erill, Michelle G. Giglio:
ECO: the Evidence and Conclusion Ontology, an update for 2022. 1515-1521 - Tao Chen, Jie Ma, Yi Liu, Zhiguang Chen, Nong Xiao, Yutong Lu, Yinjin Fu, Chunyuan Yang, Mansheng Li, Songfeng Wu, Xue Wang, Dongsheng Li, Fuchu He, Henning Hermjakob, Yunping Zhu:
iProX in 2021: connecting proteomics data sharing with big data. 1522-1527 - Kannan Harini, Ambuj Srivastava, Arulsamy Kulandaisamy, M. Michael Gromiha:
ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants. 1528-1534 - Lukasz Pawel Kozlowski:
Proteome-pI 2.0: proteome isoelectric point database update. 1535-1540 - Ludwig Lautenbacher, Patroklos Samaras, Julian Müller, Andreas Grafberger, Marwin Shraideh, Johannes Rank, Simon T. Fuchs, Tobias K. Schmidt, Matthew The, Christian Dallago, Holger Wittges, Burkhard Rost, Helmut Krcmar, Bernhard Küster, Mathias Wilhelm:
ProteomicsDB: toward a FAIR open-source resource for life-science research. 1541-
Volume 50, Number W1, July 2022
- Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022. 1-3
- Polina Belokopytova, Emil Viesná, Mateusz Chilinski, Yifeng Qi, Hossein Salari, Marco Di Stefano, Andrea Esposito, Mattia Conte, Andrea Maria Chiariello, Vladimir B. Teif, Dariusz Plewczynski, Bin Zhang, Daniel Jost, Veniamin Fishman:
3DGenBench: a web-server to benchmark computational models for 3D Genomics. 4-12 - Jake E. McGreig, Hannah Uri, Magdalena Antczak, Michael J. E. Sternberg, Martin Michaelis, Mark N. Wass:
3DLigandSite: structure-based prediction of protein-ligand binding sites. 13-20 - Chih-Chieh Chen, Yen-Yi Liu, Ya-Chu Yang, Chu-Yi Hsu:
5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey. 21-28 - René Staritzbichler, Emily Yaklich, Edoardo Sarti, Nikola Ristic, Peter W. Hildebrand, Lucy R. Forrest:
AlignMe: an update of the web server for alignment of membrane protein sequences. 29-35 - Minh N. Nguyen, Nora L. Krutz, Vachiranee Limviphuvadh, Andreas L. Lopata, G. Frank Gerberick, Sebastian Maurer-Stroh:
AllerCatPro 2.0: a web server for predicting protein allergenicity potential. 36-43 - Wanda Niemyska, Pawel Rubach, Bartosz Ambrozy Gren, Mai Lan Nguyen, Wojciech Garstka, Fernando Bruno da Silva, Eric J. Rawdon, Joanna I. Sulkowska:
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods. 44-50 - Alexandr Boytsov, Sergey Abramov, Ariuna Z. Aiusheeva, Alexandra M. Kasianova, Eugene Baulin, Ivan A. Kuznetsov, Yurii S. Aulchenko, Semyon Kolmykov, Ivan S. Yevshin, Fedor A. Kolpakov, Ilya E. Vorontsov, Vsevolod J. Makeev, Ivan V. Kulakovskiy:
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. 51-56 - Zhu Liu, Tremayne Mushayahama, Bryan Queme, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Paul D. Thomas, Huaiyu Mi:
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. 57-65 - Qifan Zeng, Baojun Zhao, Hao Wang, Mengqiu Wang, Mingxuan Teng, Jingjie Hu, Zhenmin Bao, Yangfan Wang:
Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture. 66-74 - Yi Yang, Yufeng Mao, Ruoyu Wang, Haoran Li, Ye Liu, Haijiao Cheng, Zhenkun Shi, Yu Wang, Meng Wang, Ping Zheng, Xiaoping Liao, Hongwu Ma:
AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms. 75-82 - Robin Steinhaus, Felix Boschann, Melanie Vogel, Björn Fischer-Zirnsak, Dominik Seelow:
AutozygosityMapper: Identification of disease-mutations in consanguineous families. 83-89 - András Micsonai, Éva Moussong, Frank Wien, Eszter Boros, Henrietta Vadászi, Nikoletta Murvai, Young-Ho Lee, Tamás Molnár, Matthieu Réfrégiers, Yuji Goto, Ágnes Tantos, József Kardos:
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy. 90-98 - Genís Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpí:
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. 99-107 - Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. 108-114 - David S. Wishart, Siyang Tian, Dana Allen, Eponine Oler, Harrison Peters, Vicki W. Lui, Vasuk Gautam, Yannick Djoumbou Feunang, Russell Greiner, Thomas O. Metz:
BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products. 115-123 - Fedor A. Kolpakov, Ilya R. Akberdin, Ilya Kiselev, Semyon Kolmykov, Yury V. Kondrakhin, Mikhail Kulyashov, Elena Kutumova, Sergey Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Sergey Zhatchenko, Alexander E. Kel:
BioUML - towards a universal research platform. 124-131 - Georges Pierre Schmartz, Pascal Hirsch, Jérémy Amand, Jan Dastbaz, Tobias Fehlmann, Fabian Kern, Rolf Müller, Andreas Keller:
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning. 132-137 - Michael Hartung, Elisa Anastasi, Zeinab M. Mamdouh, Cristian Nogales, Harald H. H. W. Schmidt, Jan Baumbach, Olga I. Zolotareva, Markus List:
Cancer driver drug interaction explorer. 138-144 - Antonin Kunka, David Lacko, Jan Stourac, Jirí Damborský, Zbynek Prokop, Stanislav Mazurenko:
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. 145-151 - David Kuták, Lucas Melo, Fabian Schroeder, Zoe Jelic-Matosevic, Natalie Mutter, Branimir Bertosa, Ivan Barisic:
CATANA: an online modelling environment for proteins and nucleic acid nanostructures. 152-158 - Yang Liu, Xiaocong Yang, Jianhong Gan, Shuang Chen, Zhixiong Xiao, Yang Cao:
CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting. 159-164 - Fei Wang, Dana Allen, Siyang Tian, Eponine Oler, Vasuk Gautam, Russell Greiner, Thomas O. Metz, David S. Wishart:
CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. 165-174 - Zhaonan Zou, Tazro Ohta, Fumihito Miura, Shinya Oki:
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. 175-182 - Muntaha Samad, Forest Agostinelli, Tomoki Sato, Kohei Shimaji, Pierre Baldi:
CircadiOmics: circadian omic web portal. 183-190 - Vasileios Konstantakos, Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras:
CRISPRedict: a CRISPR-Cas9 web tool for interpretable efficiency predictions. 191-198 - Thach Nguyen, Haribaskar Ramachandran, Soraia Martins, Jean Krutmann, Andrea Rossi:
Identification of genome edited cells using CRISPRnano. 199-203 - Carlos H. M. Rodrigues, David B. Ascher:
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. 204-209 - Liisa Holm:
Dali server: structural unification of protein families. 210-215 - Brad T. Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W. Baseler, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang:
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). 216-221 - Ludovica Montanucci, Emidio Capriotti, Giovanni Birolo, Silvia Benevenuta, Corrado Pancotti, Dennis Lal, Piero Fariselli:
DDGun: an untrained predictor of protein stability changes upon amino acid variants. 222-227 - Vineet Thumuluri, José Juan Almagro Armenteros, Alexander Rosenberg Johansen, Henrik Nielsen, Ole Winther:
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. 228-234 - Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang:
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. 235-245 - Fei Ji, Gracia Bonilla, Rustem Krykbaev, Gary Ruvkun, Yuval Tabach, Ruslan I. Sadreyev:
DEPCOD: a tool to detect and visualize co-evolution of protein domains. 246-253 - Suyeon Wy, Daehong Kwon, Kisang Kwon, Jaebum Kim:
DLEB: a web application for building deep learning models in biological research. 254-260 - Razieh Mohammadi-Arani, Fatemeh Javadi-Zarnaghi, Pietro Boccaletto, Janusz M. Bujnicki, Almudena Ponce-Salvatierra:
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes. 261-265 - Christopher P. Jurich, Amir Brivanlou, Silvi Rouskin, Joseph D. Yesselman:
Web-based platform for analysis of RNA folding from high throughput chemical probing data. 266-271 - Aleksandr Ianevski, Ronja M. Simonsen, Vegard Myhre, Tanel Tenson, Valentyn Oksenych, Magnar Bjørås, Denis E. Kainov:
DrugVirus.info 2.0: an integrative data portal for broad-spectrum antivirals (BSA) and BSA-containing drug combinations (BCCs). 272-275 - Fábio Madeira, Matt Pearce, Adrian R. N. Tivey, Prasad Basutkar, Joon Lee, Ossama Edbali, Nandana Madhusoodanan, Anton Kolesnikov, Rodrigo Lopez:
Search and sequence analysis tools services from EMBL-EBI in 2022. 276-279 - Michael Soutschek, Tomás Germade, Pierre-Luc Germain, Gerhard Schratt:
enrichMiR predicts functionally relevant microRNAs based on target collections. 280-289 - Li Tang, Zhizhou Zhong, Yisheng Lin, Yifei Yang, Jun Wang, James F. Martin, Min Li:
EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions. 290-297 - Zhitao Mao, Ruoyu Wang, Haoran Li, Yixin Huang, Qiang Zhang, Xiaoping Liao, Hongwu Ma:
ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database. 298-304 - Marc-André Legault, Louis-Philippe Lemieux Perreault, Jean-Claude Tardif, Marie-Pierre Dubé:
ExPheWas: a platform for cis-Mendelian randomization and gene-based association scans. 305-311 - Xian Liu, Kaikun Xu, Xin Tao, Ronghua Yin, Guangming Ren, Miao Yu, Changyan Li, Hui Chen, Ke Zhao, Shensi Xiang, Huiying Gao, Xiaochen Bo, Cheng Chang, Xiaoming Yang:
ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data. 312-321 - Robin Steinhaus, Peter N. Robinson, Dominik Seelow:
FABIAN-variant: predicting the effects of DNA variants on transcription factor binding. 322-329 - Anne de Jong, Oscar P. Kuipers, Jan Kok:
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. 330-336 - András Hatos, Silvio C. E. Tosatto, Michele Vendruscolo, Mónika Fuxreiter:
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins. 337-344 - Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. 345-351 - Jorge Botas, Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Jaime Huerta-Cepas:
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. 352-357 - Christopher A. Mancuso, Patrick S. Bills, Douglas Krum, Jacob Newsted, Renming Liu, Arjun Krishnan:
GenePlexus: a web-server for gene discovery using network-based machine learning. 358-366 - Guy P. Hunt, Luigi Grassi, Rafael Henkin, Fabrizio Smeraldi, Thomas P. Spargo, Renata Kabiljo, Sulev Koks, Zina M. Ibrahim, Richard J. B. Dobson, Ammar Al-Chalabi, Michael R. Barnes, Alfredo Iacoangeli:
GEOexplorer: a webserver for gene expression analysis and visualisation. 367-374 - Nur Syatila Abdul Ghani, Reeki Emrizal, Sabrina Mohamed Moffit, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus Raih:
GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA. 375-383 - Erich R. Kuechler, Matthew Jacobson, Thibault Mayor, Jörg Gsponer:
GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents. 384-391 - Charles Abreu Santana, Sandro C. Izidoro, Raquel Cardoso de Melo Minardi, Jonathan D. Tyzack, António J. M. Ribeiro, Douglas E. V. Pires, Janet M. Thornton, Sabrina de Azevedo Silveira:
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. 392-397 - Deniz Seçilmis, Thomas Hillerton, Erik L. L. Sonnhammer:
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods. 398-404 - Wanshan Ning, Yuxiang Wei, Letian Gao, Cheng Han, Yujie Gou, Shanshan Fu, Dan Liu, Chi Zhang, Xinhe Huang, Sicheng Wu, Di Peng, Chenwei Wang, Yu Xue:
HemI 2.0: an online service for heatmap illustration. 405-411 - Francesco Oteri, Edoardo Sarti, Francesca Nadalin, Alessandra Carbone:
iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families. 412-419 - Yubin Xie, Huiqin Li, Xiaotong Luo, Hongyu Li, Qiuyuan Gao, Luowanyue Zhang, Yuyan Teng, Qi Zhao, Zhixiang Zuo, Jian Ren:
IBS 2.0: an upgraded illustrator for the visualization of biological sequences. 420-426 - Andrew Jiang, Klaus Lehnert, Linya You, Russell G. Snell:
ICARUS, an interactive web server for single cell RNA-seq analysis. 427-433 - Zhen Chen, Xuhan Liu, Pei Zhao, Chen Li, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Chris Bain, Robin B. Gasser, Junzhou Li, Zuoren Yang, Xin Gao, Lukasz A. Kurgan, Jiangning Song:
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. 434-447 - Dmitri S. Pavlichin, Hojoon Lee, Stephanie U. Greer, Susan M. Grimes, Tsachy Weissman, Hanlee P. Ji:
KmerKeys: a web resource for searching indexed genome assemblies and variants. 448-453 - Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Peter L. Freddolino, Yang Zhang:
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. 454-464 - Joan Planas-Iglesias, Filip Opálený, Pavol Ulbrich, Jan Stourac, Zainab K. Sanusi, Gaspar R. P. Pinto, Andrea Schenkmayerova, Jan Byska, Jirí Damborský, Barbora Kozlíková, David Bednar:
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. 465-473 - Aleksandra E. Badaczewska-Dawid, Chandran Nithin, Karol Wroblewski, Mateusz Kurcinski, Sebastian Kmiecik:
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes. 474-482 - Michelle Kampfrath, René Staritzbichler, Guillermo Pérez Hernández, Alexander S. Rose, Johanna K. S. Tiemann, Gerik Scheuermann, Daniel Wiegreffe, Peter W. Hildebrand:
MDsrv: visual sharing and analysis of molecular dynamics simulations. 483-489 - Fabio Marchiano, Margaux Haering, Bianca Hermine Habermann:
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context. 490-499 - Shu-Cheng Liu, Yan-Ru Ju, Chin Lung Lu:
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes. 500-509 - Magnus Haraldson Høie, Erik Nicolas Kiehl, Bent Petersen, Morten Nielsen, Ole Winther, Henrik Nielsen, Jeppe Hallgren, Paolo Marcatili:
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning. 510-515 - Caroline Vernette, Julien Lecubin, Pablo Sánchez, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stephane Pesant, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker, Tom O. Delmont, Eric Pelletier, Magali Lescot:
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. 516-526 - Guangyan Zhou, Zhiqiang Pang, Yao Lu, Jessica Ewald, Jianguo Xia:
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics. 527-533 - Ivan S. Ilnitskiy, Anastasia Zharikova, Andrey Mironov:
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins. 534-540 - Leighton J. Payne, Sean Meaden, Mario R. Mestre, Chris Palmer, Nicolás Toro, Peter C. Fineran, Simon A. Jackson:
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. 541-550 - Tianyuan Liu, Pedro Salguero, Marko Petek, Carlos Martínez-Mira, Leandro Balzano-Nogueira, Ziva Ramsak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa:
PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. 551-559 - Mirko Schmitz, Anne Schultze, Raimonds Vanags, Karsten Voigt, Barbara Di Ventura, Mehmet Ali Öztürk:
patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures. 560-567 - Chao Xue, Lin Jiang, Miao Zhou, Qihan Long, Ying Chen, Xiangyi Li, Wenjie Peng, Qi Yang, Miao-Xin Li:
PCGA: a comprehensive web server for phenotype-cell-gene association analysis. 568-576 - Ziqi Deng, Jorge Botas, Carlos P. Cantalapiedra, Ana Hernández-Plaza, Jordi Burguet-Castell, Jaime Huerta-Cepas:
PhyloCloud: an online platform for making sense of phylogenomic data. 577-582 - Hai Fang:
PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions. 583-592 - David Jakubec, Petr Skoda, Radoslav Krivák, Marian Novotny, David Hoksza:
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. 593-597 - Marin Matic, Gurdeep Singh, Francesco Carli, Natalia De Oliveira Rosa, Pasquale Miglionico, Lorenzo Magni, J. Silvio Gutkind, Robert B. Russell, Asuka Inoue, Francesco Raimondi:
PRECOGx: exploring GPCR signaling mechanisms with deep protein representations. 598-610 - Katrin Schöning-Stierand, Konrad Diedrich, Christiane Ehrt, Florian Flachsenberg, Joel Graef, Jochen Sieg, Patrick Penner, Martin Poppinga, Annett Ungethüm, Matthias Rarey:
ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. 611-615 - Peng-Hsuan Li, Ting-Fu Chen, Jheng-Ying Yu, Shang-Hung Shih, Chan-Hung Su, Yin-Hung Lin, Huai-Kuang Tsai, Hsueh-Fen Juan, Chien-Yu Chen, Jia-Hsin Huang:
pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature. 616-622 - Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codó, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Pilizota, Cristina Guijarro-Clarke, Adrian M. Altenhoff, Elspeth A. Bruford, Christophe Dessimoz, Ingo Ebersberger, David M. Emms, Toni Gabaldón, Natasha M. Glover, Yanhui Hu, Wataru Iwasaki, Odile Lecompte, Benjamin Linard, María J. Martín, David S. Roos, Erik Sonhammer, Paul D. Thomas, David Thybert, Klaas Vandepoele, Salvador Capella-Gutiérrez, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas, Dmitry Repchevsky, Vicky Sundesha, Erik L. L. Sonnhammer:
The Quest for Orthologs orthology benchmark service in 2022. 623-632 - Lei Zheng, Dongyang Liu, Yuan Alex Li, Siqi Yang, Yuchao Liang, Yongqiang Xing, Yongchun Zuo:
RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets. 633-638 - Zoe Weiss, Saurja Dasgupta:
REVERSE: a user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments. 639-650 - Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Giorgia F. Camagni, Giovanni Minervini, Damiano Piovesan, Silvio C. E. Tosatto:
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles. 651-656 - Marcin Magnus:
rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow. 657-662 - Kamil Luwanski, Vladyslav Hlushchenko, Mariusz Popenda, Tomasz Zok, Joanna Sarzynska, Daniil Martsich, Marta Szachniuk, Maciej Antczak:
RNAspider: a webserver to analyze entanglements in RNA 3D structures. 663-669 - Walter Santana-Garcia, Jaime Abraham Castro-Mondragón, Mónica Padilla-Gálvez, Nga Thi Thuy Nguyen, Ana Elizondo-Salas, Najla Ksouri, François Gerbes, Denis Thieffry, Pierre Vincens, Bruno Contreras-Moreira, Jacques van Helden, Morgane Thomas-Chollier, Alejandra Medina-Rivera:
RSAT 2022: regulatory sequence analysis tools. 670-676 - Robin Steinhaus, Sebastian Proft, Evelyn Seelow, Tobias Schalau, Peter N. Robinson, Dominik Seelow:
Deep phenotyping: symptom annotation made simple with SAMS. 677-681 - Mehmet Direnç Mungan, Theresa Anisja Harbig, Naybel Hernandez Perez, Simone Edenhart, Evi Stegmann, Kay Nieselt, Nadine Ziemert:
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. 682-689 - Mariia Emelianova, Anastasiia N. Gainullina, Nikolay Poperechnyi, Alexander A. Loboda, Maxim N. Artyomov, Alexey A. Sergushichev:
Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks. 690-696 - John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Alexander Lachmann, Minji Jeon, Kerwin Chen, Kathleen M. Jagodnik, Sherry L. Jenkins, Maxim V. Kuleshov, Megan L. Wojciechowicz, Stephan C. Schürer, Mario Medvedovic, Avi Ma'ayan:
SigCom LINCS: data and metadata search engine for a million gene expression signatures. 697-709 - Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Chantal Scheepbouwer, Adrián García-Moreno, Pedro Carmona-Saez, Bastian Fromm, Michiel Pegtel, Andreas Keller, Juan Antonio Marchal, Michael Hackenberg:
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. 710-717 - Joanne Watson, Michael Smith, Chiara Francavilla, Jean-Marc Schwartz:
SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment. 718-725 - Kathleen Gallo, Andrean Goede, Robert Preissner, Björn-Oliver Gohlke:
SuperPred 3.0: drug classification and target prediction - a machine learning approach. 726-731 - Gabriel Cretin, Tatiana Galochkina, Yann Vander Meersche, Alexandre G. de Brevern, Guillaume Postic, Jean-Christophe Gelly:
SWORD2: hierarchical analysis of protein 3D structures. 732-738 - Aleksandr Ianevski, Anil K. Giri, Tero Aittokallio:
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. 739-743 - Barbara Poszewiecka, Victor Murcia Pienkowski, Karol Nowosad, Jérôme D. Robin, Krzysztof Gogolewski, Anna Gambin:
TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure. 744-752 - Dominique Sydow, Jaime Rodríguez-Guerra, Talia B. Kimber, David Schaller, Corey J. Taylor, Yonghui Chen, Mareike Leja, Sakshi Misra, Michele Wichmann, Armin Ariamajd, Andrea Volkamer:
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. 753-760 - Li Chen, Tianjian Chen, Ya Zhang, Haichen Lin, Ruihan Wang, Yihang Wang, Hongyu Li, Zhixiang Zuo, Jian Ren, Yubin Xie:
TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response. 761-767 - Meng Wang, Ying-Xian Goh, Cui Tai, Hui Wang, Zixin Deng, Hong-Yu Ou:
VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens. 768-773 - Daofeng Li, Deepak Purushotham, Jessica K. Harrison, Silas Hsu, Xiaoyu Zhuo, Changxu Fan, Shane Liu, Vincent Xu, Samuel Chen, Jason Xu, Shinyi Ouyang, Angela S. Wu, Ting Wang:
WashU Epigenome Browser update 2022. 774-781 - Yulin Dai, Ruifeng Hu, Andi Liu, Kyung Serk Cho, Astrid Marilyn Manuel, Xiaoyang Li, Xianjun Dong, Peilin Jia, Zhongming Zhao:
WebCSEA: web-based cell-type-specific enrichment analysis of genes. 782-
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