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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 - Jose 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 - Yi-Gang 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, Yi-Gang 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,