Nucleic Acids Research, Volume 47

Volume 47, Number Database-Issue, January 2019

Editorial

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  Daniel J. Rigden, Xosé M. Fernández-Suárez:
  The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. D1-D7

Front Matter

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  BIG Data Center:
  Database Resources of the BIG Data Center in 2019. D8-D14
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  Charles E. Cook, Rodrigo Lopez, Oana Stroe, Guy Cochrane, Cath Brooksbank, Ewan Birney, Rolf Apweiler:
  The European Bioinformatics Institute in 2018: tools, infrastructure and training. D15-D22
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  Eric W. Sayers, Richa Agarwala, Evan Bolton, J. Rodney Brister, Kathi Canese, Karen Clark, Ryan Connor, Nicolas Fiorini, Kathryn Funk, Timothy Hefferon, J. Bradley Holmes, Sunghwan Kim, Avi Kimchi, Paul A. Kitts, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Aron Marchler-Bauer, Lon Phan, Valerie A. Schneider, Conrad L. Schoch, Kim D. Pruitt, James Ostell:
  Database resources of the National Center for Biotechnology Information. D23-D28

Nucleic acid sequence, structure, and regulation

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  Edvard Ehler, Jiri Novotný, Anna Juras, Maciej Chylenski, Ondrej Moravcík, Jan Paces:
  AmtDB: a database of ancient human mitochondrial genomes. D29-D32
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  Hui Hu, Ya-Ru Miao, Long-Hao Jia, Qing-Yang Yu, Qiong Zhang, An-Yuan Guo:
  AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. D33-D38
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  Nicholas Kinney, Kyle Titus-Glover, Jonathan D. Wren, Robin T. Varghese, Pawel Michalak, Han Liao, Ramu Anandakrishnan, Arichanah Pulenthiran, Lin Kang, Harold R. Garner:
  CAGm: a repository of germline microsatellite variations in the 1000 genomes project. D39-D45
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  Stefan Kurtenbach, Rohit Reddy, J. William Harbour:
  ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP). D46-D49
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  Xavier Meyer, Linda Dib, Nicolas Salamin:
  CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates. D50-D54
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  Takeshi Obayashi, Yuki Kagaya, Yuichi Aoki, Shu Tadaka, Kengo Kinoshita:
  COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference. D55-D62
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  Wen Chen, Guoqiang Zhang, Jing Li, Xuan Zhang, Shulan Huang, Shuanglin Xiang, Xiang Hu, Changning Liu:
  CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs. D63-D68
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  Yuichi Kodama, Jun Mashima, Takehide Kosuge, Osamu Ogasawara:
  DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data. D69-D73
• 
  Hao Luo, Feng Gao:
  DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. D74-D77
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  Guangyi Niu, Dong Zou, Mengwei Li, Yuansheng Zhang, Jian Sang, Lin Xia, Man Li, Lin Liu, Jiabao Cao, Yang Zhang, Pei Wang, Songnian Hu, Lili Hao, Zhang Zhang:
  Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human. D78-D83
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  Peter W. Harrison, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Sam Holt, Abdulrahman Hussein, Suran Jayathilaka, Simon Kay, Thomas M. Keane, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Annalisa Milano, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Edward Richards, Marc Rossello, Nicole Silvester, Dmitriy Smirnov, Ana Luisa Toribio, Senthilnathan Vijayaraja, Guy Cochrane:
  The European Nucleotide Archive in 2018. D84-D88
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  Teng Liu, Qiong Zhang, Jiankun Zhang, Chao Li, Ya-Ru Miao, Qian Lei, Qiubai Li, An-Yuan Guo:
  EVmiRNA: a database of miRNA profiling in extracellular vesicles. D89-D93
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  Eric W. Sayers, Mark Cavanaugh, Karen Clark, James Ostell, Kim D. Pruitt, Ilene Karsch-Mizrachi:
  GenBank. D94-D99
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  Ivan S. Yevshin, Ruslan N. Sharipov, Semyon Kolmykov, Yury V. Kondrakhin, Fedor A. Kolpakov:
  GTRD: a database on gene transcription regulation - 2019 update. D100-D105
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  Jing Wang, Xizhen Dai, Lynne D. Berry, Joy D. Cogan, Qi Liu, Yu Shyr:
  HACER: an atlas of human active enhancers to interpret regulatory variants. D106-D112
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  Ernesto Aparicio-Puerta, David Jáspez, Ricardo Lebrón, Danijela Koppers-Lalic, Juan Antonio Marchal, Michael Hackenberg:
  liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies. D113-D120
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  Peng Wang, Xin Li, Yue Gao, Qiuyan Guo, Yanxia Wang, Ying Fang, Xueyan Ma, Hui Zhi, Dianshuang Zhou, Weitao Shen, Weisha Liu, Lihua Wang, Yunpeng Zhang, Shangwei Ning, Xia Li:
  LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments. D121-D127
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  Lina Ma, Jiabao Cao, Lin Liu, Qiang Du, Zhao Li, Dong Zou, Vladimir B. Bajic, Zhang Zhang:
  LncBook: a curated knowledgebase of human long non-coding RNAs. D128-D134
• 
  Pieter-Jan Volders, Jasper Anckaert, Kenneth Verheggen, Justine Nuytens, Lennart Martens, Pieter Mestdagh, Jo Vandesompele:
  LNCipedia 5: towards a reference set of human long non-coding RNAs. D135-D139
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  Liang Cheng, Pingping Wang, Rui Tian, Song Wang, Qinghua Guo, Meng Luo, Wenyang Zhou, Guiyou Liu, Huijie Jiang, Qinghua Jiang:
  LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse. D140-D144
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  Quy Xiao Xuan Lin, Stephanie Sian, Omer An, Denis Thieffry, Sudhakar Jha, Touati Benoukraf:
  MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. D145-D154
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  Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones:
  miRBase: from microRNA sequences to function. D155-D162
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  Yongbing Zhao, Jinyue Wang, Fang Liang, Yanxia Liu, Qi Wang, Hao Zhang, Meiye Jiang, Zhewen Zhang, Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan W. Asmann, Rujiao Li, Jing-Fa Xiao:
  NucMap: a database of genome-wide nucleosome positioning map across species. D163-D169
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  Man Li, Lin Xia, Yuansheng Zhang, Guangyi Niu, Mengwei Li, Pei Wang, Yang Zhang, Jian Sang, Dong Zou, Songnian Hu, Lili Hao, Zhang Zhang:
  Plant editosome database: a curated database of RNA editosome in plants. D170-D174
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  Jiajia Wang, Peng Zhang, Yiping Lu, Yanyan Li, Yu Zheng, Yunchao Kan, Runsheng Chen, Shunmin He:
  piRBase: a comprehensive database of piRNA sequences. D175-D180
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  Wei-Sheng Wu, Jordan S. Brown, Tsung-Te Chen, Yu-Han Chu, Wei-Che Huang, Shikui Tu, Heng-Chi Lee:
  piRTarBase: a database of piRNA targeting sites and their roles in gene regulation. D181-D187
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  Tiago F. Jesus, Bruno Ribeiro-Gonçalves, Diogo N. Silva, Valeria Bortolaia, Mário Ramirez, João A. Carriço:
  Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data. D188-D194
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  Valentina Galata, Tobias Fehlmann, Christina Backes, Andreas Keller:
  PLSDB: a resource of complete bacterial plasmids. D195-D202
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  Yumin Zhu, Gang Xu, Yu-Cheng T. Yang, Zhiyu Xu, Xinduo Chen, Binbin Shi, Daoxin Xie, Zhi John Lu, Pengyuan Wang:
  POSTAR2: deciphering the post-transcriptional regulatory logics. D203-D211
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  Alberto Santos-Zavaleta, Heladia Salgado, Socorro Gama-Castro, Mishael Sánchez-Pérez, Laura Gómez-Romero, Daniela Ledezma-Tejeida, Jair Santiago García-Sotelo, Kevin Alquicira-Hernández, Luis Muñiz-Rascado, Pablo Peña-Loredo, Cecilia Ishida-Gutiérrez, David A. Velázquez-Ramírez, Victor del Moral-Chávez, César Bonavides-Martínez, Carlos-Francisco Méndez-Cruz, James E. Galagan, Julio Collado-Vides:
  RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. D212-D220
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  The RNAcentral Consortium:
  RNAcentral: a hub of information for non-coding RNA sequences. D221-D229
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  Hongwei Wang, Ludong Yang, Yan Wang, Leshi Chen, Huihui Li, Zhi Xie:
  RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling. D230-D234
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  Yong Jiang, Fengcui Qian, Xuefeng Bai, Yuejuan Liu, Qiuyu Wang, Bo Ai, Xiaole Han, Shanshan Shi, Jian Zhang, Xuecang Li, Zhidong Tang, Qi Pan, Yuezhu Wang, Fan Wang, Chunquan Li:
  SEdb: a comprehensive human super-enhancer database. D235-D243
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  Morad M. Mokhtar, Mohamed A. M. Atia:
  SSRome: an integrated database and pipelines for exploring microsatellites in all organisms. D244-D252
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  Zhan Tong, Qinghua Cui, Juan Wang, Yuan Zhou:
  TransmiR v2.0: an updated transcription factor-microRNA regulation database. D253-D258
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  R. Henrik Nilsson, Karl-Henrik Larsson, Andy F. S. Taylor, Johan Bengtsson-Palme, Thomas S. Jeppesen, Dmitry Schigel, Peter Kennedy, Kathryn Picard, Frank Oliver Glöckner, Leho Tedersoo, Irja Saar, Urmas Kõljalg, Kessy Abarenkov:
  The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. D259-D264

Protein sequence and structure, motifs, and domains

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  Zhen Wah Tan, Wei-Ven Tee, Enrico Guarnera, Lauren Booth, Igor N. Berezovsky:
  AlloMAPS: allosteric mutation analysis and polymorphism of signaling database. D265-D270
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  Xiaosong Huang, Laurent-Philippe Albou, Tremayne Mushayahama, Anushya Muruganujan, Haiming Tang, Paul D. Thomas:
  Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life. D271-D279
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  Ian Sillitoe, Natalie L. Dawson, Tony E. Lewis, Sayoni Das, Jonathan G. Lees, Paul Ashford, Adeyelu Tolulope, Harry M. Scholes, Ilya Senatorov, Andra Bujan, Fatima Ceballos Rodriguez-Conde, Benjamin Dowling, Janet M. Thornton, Christine A. Orengo:
  CATH: expanding the horizons of structure-based functional annotations for genome sequences. D280-D284
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  Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Tsai-Hsuan Lin, Kai-Yao Huang, Tzong-Yi Lee:
  dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. D285-D297
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  Kai-Yao Huang, Tzong-Yi Lee, Hui-Ju Kao, Chen-Tse Ma, Chao-Chun Lee, Tsai-Hsuan Lin, Wen-Chi Chang, Hsien-Da Huang:
  dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications. D298-D308
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  Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K. Forslund, Helen Cook, Daniel R. Mende, Ivica Letunic, Thomas Rattei, Lars Juhl Jensen, Christian von Mering, Peer Bork:
  eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. D309-D314
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  Edoardo Sarti, Antoniya A. Aleksandrova, Srujan K. Ganta, Amarendra S. Yavatkar, Lucy R. Forrest:
  EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins. D315-D321
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  Ricky Wai Tak Leung, Xiaosen Jiang, Ka Hou Chu, Jing Qin:
  ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins. D322-D329
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  The Gene Ontology Consortium:
  The Gene Ontology Resource: 20 years and still GOing strong. D330-D338
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  Randi Vita, Swapnil Mahajan, James A. Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R. Cantrell, Daniel K. Wheeler, Alessandro Sette, Bjoern Peters:
  The Immune Epitope Database (IEDB): 2018 update. D339-D343
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  Yaping Guo, Di Peng, Jiaqi Zhou, Shaofeng Lin, Chenwei Wang, Wanshan Ning, Hao-Dong Xu, Wankun Deng, Yu Xue:
  iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains. D344-D350
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  Alex L. Mitchell, Teresa K. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, Alan J. Bridge, Shoshana D. Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez, Aurelien Luciani, Fábio Madeira, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Arun Prasad Pandurangan, Typhaine Paysan-Lafosse, Sebastien Pesseat, Simon C. Potter, Matloob Qureshi, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Gustavo A. Salazar, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Siew-Yit Yong, Robert D. Finn:
  InterPro in 2019: improving coverage, classification and access to protein sequence annotations. D351-D360
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  Rayees Rahman, Peter Man-Un Ung, Avner Schlessinger:
  KinaMetrix: a web resource to investigate kinase conformations and inhibitor space. D361-D366
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  Pawel Dabrowski-Tumanski, Pawel Rubach, Dimos Goundaroulis, Julien Dorier, Piotr Sulkowski, Kenneth C. Millett, Eric J. Rawdon, Andrzej Stasiak, Joanna I. Sulkowska:
  KnotProt 2.0: a database of proteins with knots and other entangled structures. D367-D375
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  Olivier Clerc, Madeline Deniaud, Sylvain D. Vallet, Alexandra Naba, Alain Rivet, Serge Pérez, Nicolas Thierry-Mieg, Sylvie Ricard-Blum:
  MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. D376-D381
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  Ikuo Uchiyama, Motohiro Mihara, Hiroyo Nishide, Hirokazu Chiba, Masaki Kato:
  MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons. D382-D389
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  Thomas D. Newport, Mark S. P. Sansom, Phillip J. Stansfeld:
  The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. D390-D397
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  Diogo M. Ribeiro, Galadriel Brière, Benoit Bely, Lionel Spinelli, Christine Brun:
  MoonDB 2.0: an updated database of extreme multifunctional and moonlighting proteins. D398-D402
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  Marie A. Brunet, Mylène Brunelle, Jean-François Lucier, Vivian Delcourt, Maxime Levesque, Frédéric Grenier, Sondos Samandi, Sébastien Leblanc, Jean-David Aguilar, Pascal Dufour, Jean-Francois Jacques, Isabelle Fournier, Aïda Ouangraoua, Michelle S. Scott, François-Michel Boisvert, Xavier Roucou:
  OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. D403-D410
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  Yannis Nevers, Arnaud Kress, Audrey Defosset, Raymond Ripp, Benjamin Linard, Julie Dawn Thompson, Olivier Poch, Odile Lecompte:
  OrthoInspector 3.0: open portal for comparative genomics. D411-D418
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  Huaiyu Mi, Anushya Muruganujan, Dustin Ebert, Xiaosong Huang, Paul D. Thomas:
  PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. D419-D426
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  Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R. Eddy, Aurelien Luciani, Simon C. Potter, Matloob Qureshi, Lorna J. Richardson, Gustavo A. Salazar, Alfredo Smart, Erik L. L. Sonnhammer, Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto, Robert D. Finn:
  The Pfam protein families database in 2019. D427-D432
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  Peter V. Hornbeck, Jon M. Kornhauser, Vaughan Latham, Beth Murray, Vidhisha Nandhikonda, Alex S. Nord, Elzbieta Skrzypek, Travis J. Wheeler, Bin Zhang, Florian Gnad:
  15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. D433-D441
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  Yasset Pérez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal Llinares, Suresh Hewapathirana, Deepti Jaiswal Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher, Enrique Pérez, Julian Uszkoreit, Julianus Pfeuffer, Timo Sachsenberg, Sule Yilmaz, Shivani Tiwary, Jürgen Cox, Enrique Audain, Mathias Walzer, Andrew F. Jarnuczak, Tobias Ternent, Alvis Brazma, Juan Antonio Vizcaíno:
  The PRIDE database and related tools and resources in 2019: improving support for quantification data. D442-D450
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  Kai Yu, Qingfeng Zhang, Zekun Liu, Qi Zhao, Xiaolong Zhang, Yan Wang, Zi-Xian Wang, Ying Jin, Xiaoxing Li, Zexian Liu, Rui-Hua Xu:
  qPhos: a database of protein phosphorylation dynamics in humans. D451-D458
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  Ahmed Mohamed, Anup Shah, David Chen, Michelle M. Hill:
  RaftProt V2: understanding membrane microdomain function through lipid raft proteomes. D459-D463
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  Stephen K. Burley, Helen M. Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole H. Christie, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Tara Kalro, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Periskova, Andreas Prlic, Christopher Randle, Alexander S. Rose, Peter W. Rose, Raul Sala, Monica Sekharan, Chenghua Shao, Lihua Tan, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D. Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Marina Zhuravleva, Christine Zardecki:
  RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. D464-D474
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  John-Marc Chandonia, Naomi K. Fox, Steven E. Brenner:
  SCOPe: classification of large macromolecular structures in the structural classification of proteins - extended database. D475-D481
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  Jose M. Dana, Aleksandras Gutmanas, Nidhi Tyagi, Guoying Qi, Claire O'Donovan, Maria Jesus Martin, Sameer Velankar:
  SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. D482-D489
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  Arun Prasad Pandurangan, Jonathan Stahlhacke, Matt E. Oates, Ben Smithers, Julian Gough:
  The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. D490-D494
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  Péter Mendik, Levente Dobronyi, Ferenc Hári, Csaba Kerepesi, Leonardo Maia-Moço, Donát Buszlai, Peter Csermely, Dániel V. Veres:
  Translocatome: a novel resource for the analysis of protein translocation between cellular organelles. D495-D505
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  The UniProt Consortium:
  UniProt: a worldwide hub of protein knowledge. D506-D515
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  Mohashin Pathan, Pamali Fonseka, Sai V. Chitti, Taeyoung Kang, Rahul Sanwlani, Jan Van Deun, An Hendrix, Suresh Mathivanan:
  Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles. D516-D519
• 
  wwPDB consortium:
  Protein Data Bank: the single global archive for 3D macromolecular structure data. D520-D528

Metabolic and signalling pathways, enzymes

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  Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, Jennifer M. Rust, Lorrie Boucher, Christie S. Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam, Frederick Zhang, Sonam Dolma, Andrew Willems, Jasmin Coulombe-Huntington, Andrew Chatr-aryamontri, Kara Dolinski, Mike Tyers:
  The BioGRID interaction database: 2019 update. D529-D541
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  Lisa Jeske, Sandra Placzek, Ida Schomburg, Antje Chang, Dietmar Schomburg:
  BRENDA in 2019: a European ELIXIR core data resource. D542-D549
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  Birgit H. M. Meldal, Hema Bye-A-Jee, Lukás Gajdos, Zuzana Hammerová, Aneta Horácková, Filip Melicher, Livia Perfetto, Daniel Pokorný, Milagros Rodríguez-López, Alzbeta Türková, Edith D. Wong, Zengyan Xie, Elisabeth Barrera Casanova, Noemi del-Toro, Maximilian Koch, Pablo Porras, Henning Hermjakob, Sandra E. Orchard:
  Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. D550-D558
• 
  Madalina Giurgiu, Julian Reinhard, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Andreas Ruepp:
  CORUM: the comprehensive resource of mammalian protein complexes - 2019. D559-D563
• 
  Lorna J. Richardson, Neil D. Rawlings, Gustavo A. Salazar, Alexandre Almeida, David Haft, Gregory Ducq, Granger G. Sutton, Robert D. Finn:
  Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. D564-D572
• 
  Sohyun Hwang, Chan Yeong Kim, Sunmo Yang, Eiru Kim, G. Traver Hart, Edward M. Marcotte, Insuk Lee:
  HumanNet v2: human gene networks for disease research. D573-D580
• 
  Max Kotlyar, Chiara Pastrello, Zara Malik, Igor Jurisica:
  IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. D581-D589
• 
  Minoru Kanehisa, Yoko Sato, Miho Furumichi, Kanae Morishima, Mao Tanabe:
  New approach for understanding genome variations in KEGG. D590-D595
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  Thierry Lombardot, Anne Morgat, Kristian B. Axelsen, Lucila Aimo, Nevila Hyka-Nouspikel, Anne Niknejad, Alexandr Ignatchenko, Ioannis Xenarios, Elisabeth Coudert, Nicole Redaschi, Alan J. Bridge:
  Updates in Rhea: SPARQLing biochemical reaction data. D596-D600
• 
  Benjamin Lang, Alexandros Armaos, Gian Gaetano Tartaglia:
  RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data. D601-D606
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  Damian Szklarczyk, Annika L. Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T. Doncheva, John H. Morris, Peer Bork, Lars Juhl Jensen, Christian von Mering:
  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. D607-D613
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  Alberto Noronha, Jennifer Modamio, Yohan Jarosz, Elisabeth Guerard, Nicolas Sompairac, German A. Preciat Gonzalez, Anna Dröfn Daníelsdóttir, Max Krecke, Diane Merten, Hulda S. Haraldsdóttir, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Dmitry A. Ravcheev, Swagatika Sahoo, Piotr Gawron, Lucia Friscioni, Beatriz Garcia Santa Cruz, Mabel Prendergast, Alberto Puente, Mariana Rodrigues, Akansha Roy, Mouss Rouquaya, Luca Wiltgen, Alise Zagare, Elisabeth John, Maren Krueger, Inna Kuperstein, Andrei Yu. Zinovyev, Reinhard Schneider, Ronan M. T. Fleming, Ines Thiele:
  The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. D614-D624

Viruses, bacteria, protozoa and fungi

• 
  Kai Blin, Victòria Pascal Andreu, Emmanuel L. C. de los Santos, Francesco Del Carratore, Sang Yup Lee, Marnix H. Medema, Tilmann Weber:
  The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters. D625-D630
• 
  Lorenz Christian Reimer, Anna Vetcininova, Joaquim Sardà Carbasse, Carola Söhngen, Dorothea Gleim, Christian Ebeling, Jörg Overmann:
  BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis. D631-D636
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  Wenyu Shi, Heyuan Qi, Qinglan Sun, Guomei Fan, Shuangjiang Liu, Jun Wang, Baoli Zhu, Hongwei Liu, Fangqing Zhao, Xiaochen Wang, Xiaoxuan Hu, Wei Li, Jia Liu, Ye Tian, Linhuan Wu, Juncai Ma:
  gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. D637-D648
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  Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Hema Y. Katta, Alejandro Mojica, I-Min A. Chen, Nikos Kyrpides, T. B. K. Reddy:
  Genomes OnLine database (GOLD) v.7: updates and new features. D649-D659
• 
  Meng Liu, Xiaobin Li, Yingzhou Xie, Dexi Bi, Jingyong Sun, Jun Li, Cui Tai, Zixin Deng, Hong-Yu Ou:
  ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. D660-D665
• 
  I-Min A. Chen, Ken Chu, Krishna Palaniappan, Manoj Pillay, Anna Ratner, Jinghua Huang, Marcel Huntemann, Neha Varghese, James R. White, Rekha Seshadri, Tatyana Smirnova, Edward Kirton, Sean P. Jungbluth, Tanja Woyke, Emiley A. Eloe-Fadrosh, Natalia N. Ivanova, Nikos Kyrpides:
  IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. D666-D677
• 
  David Páez-Espino, Simon Roux, I-Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, Marcel Huntemann, T. B. K. Reddy, Joan Carles Pons, Mercè Llabrés, Emiley A. Eloe-Fadrosh, Natalia N. Ivanova, Nikos Kyrpides:
  IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. D678-D686
• 
  Bo Liu, Dandan Zheng, Qi Jin, Lihong Chen, Jian Yang:
  VFDB 2019: a comparative pathogenomic platform with an interactive web interface. D687-D692
• 
  Samantha Sayers, Li Li, Edison Ong, Shunzhou Deng, Guanghua Fu, Yu Lin, Brian Yang, Shelley Zhang, Zhenzong Fa, Bin Zhao, Zuoshuang Xiang, Yongqing Li, Xing-Ming Zhao, Michal Olszewski, Luonan Chen, Yongqun He:
  Victors: a web-based knowledge base of virulence factors in human and animal pathogens. D693-D700

Human genome, model organisms, comparative genomics

• 
  Zhi-Liang Hu, Carissa A. Park, James M. Reecy:
  Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. D701-D710
• 
  Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A. Fonseca, Robert Petryszak, Irene Papatheodorou, Ugis Sarkans, Alvis Brazma:
  ArrayExpress update - from bulk to single-cell expression data. D711-D715
• 
  Klaus Hornischer, Ariane Khaledi, Sarah Pohl, Monika Schniederjans, Lorena Pezoldt, Fiordiligie Casilag, Uthayakumar Muthukumarasamy, Sebastian Bruchmann, Janne Thöming, Adrian Kordes, Susanne Häussler:
  BACTOME - a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates. D716-D720
• 
  Xinxin Zhang, Yujia Lan, Jinyuan Xu, Fei Quan, Erjie Zhao, Chunyu Deng, Tao Luo, Liwen Xu, Gaoming Liao, Min Yan, Yanyan Ping, Feng Li, Aiai Shi, Jing Bai, Tingting Zhao, Xia Li, Yun Xiao:
  CellMarker: a manually curated resource of cell markers in human and mouse. D721-D728
• 
  Rongbin Zheng, Changxin Wan, Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Chen-Hao Chen, Myles Brown, Xiaoyan Zhang, Clifford A. Meyer, Xiaole Shirley Liu:
  Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. D729-D735
• 
  Shawez Khan, Federico Taverna, Katerina Rohlenova, Lucas Treps, Vincent Geldhof, Laura de Rooij, Liliana Sokol, Andreas Pircher, Lena-Christin Conradi, Joanna Kalucka, Luc Schoonjans, Guy Eelen, Mieke Dewerchin, Tobias K. Karakach, Xuri Li, Jermaine Goveia, Peter Carmeliet:
  EndoDB: a database of endothelial cell transcriptomics data. D736-D744
• 
  Fiona Cunningham, Premanand Achuthan, Wasiu A. Akanni, James E. Allen, M. Ridwan Amode, Irina M. Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla A. Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Astrid Gall, Carlos García-Girón, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Mike P. Kay, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, José Carlos Marugán, Thomas Maurel, Aoife C. McMahon, Benjamin Moore, Joannella Morales, Jonathan M. Mudge, Michael Nuhn, Denye N. Ogeh, Anne Parker, Andrew Parton, Mateus Patricio, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Daniel Sheppard, Helen Sparrow, Eloise Stapleton, Marek Szuba, Kieron R. Taylor, Glen Threadgold, Anja Thormann, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nick Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
  Ensembl 2019. D745-D751
• 
  Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung-Chau Hon, Michiel J. L. de Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki, Piero Carninci, Takeya Kasukawa, Hideya Kawaji:
  Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. D752-D758
• 
  Jim Thurmond, Joshua L. Goodman, Victor B. Strelets, Helen Attrill, L. Sian Gramates, Steven J. Marygold, Beverley Matthews, Gillian H. Millburn, Giulia Antonazzo, Vitor Trovisco, Thomas C. Kaufman, Brian R. Calvi, The FlyBase Consortium:
  FlyBase 2.0: the next generation. D759-D765
• 
  Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Silvia Carbonell Sala, Jacqueline Chrast, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Toby Hunt, Osagie G. Izuogu, Julien Lagarde, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Jinrui Xu, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Bronwen L. Aken, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Alexandre Reymond, Michael L. Tress, Paul Flicek:
  GENCODE reference annotation for the human and mouse genomes. D766-D773
• 
  Constance M. Smith, Terry F. Hayamizu, Jacqueline H. Finger, Susan M. Bello, Ingeborg J. McCright, Jingxia Xu, Richard M. Baldarelli, Jon S. Beal, Jeff Campbell, Lori E. Corbani, Pete J. Frost, Jill R. Lewis, Sharon C. Giannatto, Dave Miers, David R. Shaw, James A. Kadin, Joel E. Richardson, Cynthia L. Smith, Martin Ringwald:
  The mouse Gene Expression Database (GXD): 2019 update. D774-D779
• 
  Jarny Choi, Tracey M. Baldwin, Mae Wong, Jessica E. Bolden, Kirsten A. Fairfax, Erin C. Lucas, Rebecca Cole, Christine Biben, Clare Morgan, Kerry A. Ramsay, Ashley P. Ng, Maria Kauppi, Lynn M. Corcoran, Wei Shi, Nick Wilson, Michael J. Wilson, Warren S. Alexander, Douglas J. Hilton, Carolyn A. de Graaf:
  Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans. D780-D785
• 
  Bryony Braschi, Paul Denny, Kristian A. Gray, Tamsin E. M. Jones, Ruth L. Seal, Susan Tweedie, Bethan Yates, Elspeth A. Bruford:
  Genenames.org: the HGNC and VGNC resources in 2019. D786-D792
• 
  Bixia Tang, Qing Zhou, Lili Dong, Wulue Li, Xiangquan Zhang, Li Lan, Shuang Zhai, Jing-Fa Xiao, Zhang Zhang, Yiming Bao, Ya-Ping Zhang, Guo-Dong Wang, Wenming Zhao:
  iDog: an integrated resource for domestic dogs and wild canids. D793-D800
• 
  Carol J. Bult, Judith A. Blake, Cynthia L. Smith, James A. Kadin, Joel E. Richardson, The Mouse Genome Database Group:
  Mouse Genome Database (MGD) 2019. D801-D806
• 
  Evgenia V. Kriventseva, Dmitry Kuznetsov, Fredrik Tegenfeldt, Mosè Manni, Renata Dias, Felipe A. Simão, Evgeny M. Zdobnov:
  OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. D807-D811
• 
  Andrei Rozanski, HongKee Moon, Holger Brandl, José M. Martín-Durán, Markus A. Grohme, Katja Hüttner, Kerstin Bartscherer, Ian Henry, Jochen C. Rink:
  PlanMine 3.0 - improvements to a mineable resource of flatworm biology and biodiversity. D812-D820
• 
  Antonia Lock, Kim Rutherford, Midori A. Harris, Jacqueline Hayles, Stephen G. Oliver, Jürg Bähler, Valerie Wood:
  PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. D821-D827
• 
  John Rivera, Soile V. E. Keränen, Steven M. Gallo, Marc S. Halfon:
  REDfly: the transcriptional regulatory element database for Drosophila. D828-D834
• 
  Meng-Wei Shi, Na-An Zhang, Chuan-Ping Shi, Chun-Jie Liu, Zhi-Hui Luo, Dan-Yang Wang, An-Yuan Guo, Zhen-Xia Chen:
  SAGD: a comprehensive sex-associated gene database from transcriptomes. D835-D840
• 
  Jarny Choi, Chris M. Pacheco, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Isha Nagpal, Steve Englart, Paul W. Angel, Christine A. Wells:
  Stemformatics: visualize and download curated stem cell data. D841-D846
• 
  Stephen J. Kiniry, Patrick B. F. O'Connor, Audrey M. Michel, Pavel V. Baranov:
  Trips-Viz: a transcriptome browser for exploring Ribo-Seq data. D847-D852
• 
  Maximilian Haeussler, Ann S. Zweig, Cath Tyner, Matthew L. Speir, Kate R. Rosenbloom, Brian J. Raney, Christopher M. Lee, Brian T. Lee, Angie S. Hinrichs, Jairo Navarro Gonzalez, David Gibson, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent:
  The UCSC Genome Browser database: 2019 update. D853-D858
• 
  Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Sakiko Nakamura, Yuki Tsujimura, Satoko Takemoto, Takehiro Tawara, Hideo Yokota, Shuhei Wemler, Daisuke Miyamoto, Hidetoshi Ikeno, Akira Sato, Teiichi Furuichi, Norio Kobayashi, Yoshihiro Okumura, Yoko Shiraishi-Yamaguchi, Yuko Okamura-Oho:
  ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks. D859-D866
• 
  Leyla Ruzicka, Douglas G. Howe, Sridhar Ramachandran, Sabrina Toro, Ceri E. Van Slyke, Yvonne M. Bradford, Anne E. Eagle, David Fashena, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock, Christian Pich, Kevin Schaper, Xiang Shao, Amy Singer, Monte Westerfield:
  The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources. D867-D873

Genomic variation, diseases, and drugs

• 
  Yang Yang, Xiating Peng, Pingting Ying, Jianbo Tian, Jiaoyuan Li, Juntao Ke, Ying Zhu, Yajie Gong, Danyi Zou, Nan Yang, Xiaoyang Wang, Shufang Mei, Rong Zhong, Jing Gong, Jiang Chang, Xiaoping Miao:
  AWESOME: a database of SNPs that affect protein post-translational modifications. D874-D880
• 
  Frederik Otzen Bagger, Savvas Kinalis, Nicolas Rapin:
  BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles. D881-D885
• 
  Philipp Rentzsch, Daniela M. Witten, Gregory M. Cooper, Jay Shendure, Martin Kircher:
  CADD: predicting the deleteriousness of variants throughout the human genome. D886-D894
• 
  Mayya Sedova, Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Kai W. Post, Thomas Hrabe, Eduard Porta-Pardo, Adam Godzik:
  Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets. D895-D899
• 
  Huating Yuan, Min Yan, Guanxiong Zhang, Wei Liu, Chunyu Deng, Gaoming Liao, Liwen Xu, Tao Luo, Haoteng Yan, Zhilin Long, Aiai Shi, Tingting Zhao, Yun Xiao, Xia Li:
  CancerSEA: a cancer single-cell state atlas. D900-D908
• 
  Jianbo Tian, Zhihua Wang, Shufang Mei, Nan Yang, Yang Yang, Juntao Ke, Ying Zhu, Yajie Gong, Danyi Zou, Xiating Peng, Xiaoyang Wang, Hao Wan, Rong Zhong, Jiang Chang, Jing Gong, Leng Han, Xiaoping Miao:
  CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer. D909-D916
• 
  Elizabeth A. Coker, Costas Mitsopoulos, Joseph E. Tym, Angeliki Komianou, Christos C. Kannas, Patrizio Di Micco, Eloy D. Villasclaras-Fernández, Bugra Ozer, Albert A. Antolin, Paul Workman, Bissan Al-Lazikani:
  canSAR: update to the cancer translational research and drug discovery knowledgebase. D917-D922
• 
  Dieudonne van der Meer, Syd Barthorpe, Wanjuan Yang, Howard Lightfoot, Caitlin Hall, James P. Gilbert, Hayley E. Francies, Mathew Garnett:
  Cell Model Passports - a hub for clinical, genetic and functional datasets of preclinical cancer models. D923-D929
• 
  David Mendez, Anna Gaulton, A. Patrícia Bento, Jon Chambers, Marleen De Veij, Eloy Felix, María P. Magariños, Juan F. Mosquera, Prudence Mutowo-Meullenet, Michal Nowotka, María Gordillo-Marañón, Fiona M. I. Hunter, Laura Junco, Grace Mugumbate, Milagros Rodríguez-López, Francis Atkinson, Nicolas Bosc, Chris J. Radoux, Aldo Segura-Cabrera, Anne Hersey, Andrew R. Leach:
  ChEMBL: towards direct deposition of bioassay data. D930-D940
• 
  John G. Tate, Sally Bamford, Harry Jubb, Zbyslaw Sondka, David Beare, Nidhi Bindal, Harry Boutselakis, Charlotte Cole, Celestino Creatore, Elisabeth Dawson, Peter Fish, Bhavana Harsha, Charlie Hathaway, Steve C. Jupe, Chai Yin Kok, Kate Noble, Laura Ponting, Christopher C. Ramshaw, Claire E. Rye, Helen E. Speedy, Raymund Stefancsik, Sam L. Thompson, Shicai Wang, Sari Ward, Peter J. Campbell, Simon A. Forbes:
  COSMIC: the Catalogue Of Somatic Mutations In Cancer. D941-D947
• 
  Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Roy McMorran, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly:
  The Comparative Toxicogenomics Database: update 2019. D948-D954
• 
  Lynn M. Schriml, Elvira Mitraka, James B. Munro, Becky Tauber, Mike Schor, Lance Nickle, Victor Felix, Linda Jeng, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion, Brooke Hyman, David Kurland, Connor Patrick Oates, Siobhan Kibbey, Poorna Sreekumar, Chris Le, Michelle G. Giglio, Carol Greene:
  Human Disease Ontology 2018 update: classification, content and workflow expansion. D955-D962
• 
  Oleg Ursu, Jayme Holmes, Cristian Bologa, Jeremy J. Yang, Stephen L. Mathias, Vasileios Stathias, Dac-Trung Nguyen, Stephan C. Schürer, Tudor I. Oprea:
  DrugCentral 2018: an update. D963-D970
• 
  Xuexia Miao, Xi Li, Lifei Wang, Caihong Zheng, Jun Cai:
  DSMNC: a database of somatic mutations in normal cells. D971-D975
• 
  Hai-Yu Xu, Yan-Qiong Zhang, Zhen-Ming Liu, Tong Chen, Chuan-Yu Lv, Shi-Huan Tang, Xiao-Bo Zhang, Wei Zhang, Zhi-Yong Li, Rong-Rong Zhou, Hong-Jun Yang, Xiu-Jie Wang, Lu-Qi Huang:
  ETCM: an encyclopaedia of traditional Chinese medicine. D976-D982
• 
  Mengwei Li, Dong Zou, Zhaohua Li, Ran Gao, Jian Sang, Yuansheng Zhang, Rujiao Li, Lin Xia, Tao Zhang, Guangyi Niu, Yiming Bao, Zhang Zhang:
  EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. D983-D988
• 
  Di Liu, Linna Zhao, Zhaoyang Wang, Xu Zhou, Xiuzhao Fan, Yong Li, Jing Xu, Simeng Hu, Miaomiao Niu, Xiuling Song, Ying Li, Lijiao Zuo, Changgui Lei, Meng Zhang, Guoping Tang, Min Huang, Nan (Andy) Zhang, Lian Duan, Hongchao Lv, Mingming Zhang, Jin Li, Liangde Xu, Fanwu Kong, Rennan Feng, Yongshuai Jiang:
  EWASdb: epigenome-wide association study database. D989-D993
• 
  Pora Kim, Xiaobo Zhou:
  FusionGDB: fusion gene annotation DataBase. D994-D1004
• 
  Annalisa Buniello, Jacqueline A. L. MacArthur, Maria Cerezo, Laura W. Harris, James D. Hayhurst, Cinzia Malangone, Aoife McMahon, Joannella Morales, Edward Mountjoy, Elliot Sollis, Daniel Suveges, Olga Vrousgou, Patricia L. Whetzel, M. Ridwan Amode, Jose A. Guillen, Harpreet Singh Riat, Stephen J. Trevanion, Peggy Hall, Heather Junkins, Paul Flicek, Tony Burdett, Lucia A. Hindorff, Fiona Cunningham, Helen E. Parkinson:
  The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. D1005-D1012
• 
  Zhou Huang, Jiangcheng Shi, Yuanxu Gao, Chunmei Cui, Shan Zhang, Jianwei Li, Yuan Zhou, Qinghua Cui:
  HMDD v3.0: a database for experimentally supported human microRNA-disease associations. D1013-D1017
• 
  Sebastian Köhler, Leigh Carmody, Nicole A. Vasilevsky, Julius O. B. Jacobsen, Daniel Danis, Jean-Philippe F. Gourdine, Michael A. Gargano, Nomi L. Harris, Nicolas Matentzoglu, Julie A. McMurry, David Osumi-Sutherland, Valentina Cipriani, James P. Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh J. S. Dawkins, Michael Segal, Anna C. Jansen, Ahmed Muaz, Willie H. Chang, Jenna Bergerson, Stanley J. F. Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F. Freeman, Panagiotis I. Sergouniotis, Daniel Durkin, Andrea L. Storm, Marc Hanauer, Michael Brudno, Susan M. Bello, Murat Sincan, Kayli Rageth, Matthew T. Wheeler, Renske Oegema, Halima Lourghi, Maria G. Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C. Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin Aaron Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia L. Smith, Joshua D. Milner, Dorothée Leroux, Cornelius F. Boerkoel, Amy Klion, Melody C. Carter, Tudor Groza, Damian Smedley, Melissa A. Haendel, Chris Mungall, Peter N. Robinson:
  Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. D1018-D1027
• 
  Yue Gao, Peng Wang, Yanxia Wang, Xueyan Ma, Hui Zhi, Dianshuang Zhou, Xin Li, Ying Fang, Weitao Shen, Yingqi Xu, Shipeng Shang, Lihua Wang, Li Wang, Shangwei Ning, Xia Li:
  Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers. D1028-D1033
• 
  Zhenyu Bao, Zhen Yang, Zhou Huang, Yiran Zhou, Qinghua Cui, Dong Dong:
  LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. D1034-D1037
• 
  Joanna S. Amberger, Carol A. Bocchini, Alan F. Scott, Ada Hamosh:
  OMIM.org: leveraging knowledge across phenotype-gene relationships. D1038-D1043
• 
  Xianfeng Li, Leisheng Shi, Yan Wang, Jianing Zhong, Xiaolu Zhao, Huajing Teng, Xiaohui Shi, Haonan Yang, Shasha Ruan, MingKun Li, Zhongsheng Sun, Qimin Zhan, Fengbiao Mao:
  OncoBase: a platform for decoding regulatory somatic mutations in human cancers. D1044-D1055
• 
  Denise Carvalho-Silva, Andrea Pierleoni, Miguel Pignatelli, Chuang Kee Ong, Luca Fumis, Nikiforos Karamanis, Miguel Carmona, Adam Faulconbridge, Andrew Hercules, Elaine McAuley, Alfredo Miranda, Gareth Peat, Michaela Spitzer, Jeffrey Barrett, David G. Hulcoop, Eliseo Papa, Gautier Koscielny, Ian Dunham:
  Open Targets Platform: new developments and updates two years on. D1056-D1065
• 
  Jing Gong, Hao Wan, Shufang Mei, Hang Ruan, Zhao Zhang, Chun-Jie Liu, An-Yuan Guo, Lixia Diao, Xiaoping Miao, Leng Han:
  Pancan-meQTL: a database to systematically evaluate the effects of genetic variants on methylation in human cancer. D1066-D1072
• 
  Nathalie Conte, Jeremy C. Mason, Csaba Halmagyi, Steven B. Neuhauser, Abayomi Mosaku, Galabina Yordanova, Aikaterini Chatzipli, Dale A. Begley, Debra M. Krupke, Helen E. Parkinson, Terrence F. Meehan, Carol C. Bult:
  PDX Finder: A portal for patient-derived tumor xenograft model discovery. D1073-D1079
• 
  Jesús Murga-Moreno, Marta Coronado-Zamora, Alejandra Bodelón, Antonio Barbadilla, Sònia Casillas:
  PopHumanScan: the online catalog of human genome adaptation. D1080-D1089
• 
  Ying Yu, Yunjin Wang, Zhaojie Xia, Xiangyu Zhang, Kailiang Jin, Jingcheng Yang, Luyao Ren, Zheng Zhou, Dong Yu, Tao Qing, Chengdong Zhang, Li Jin, Yuanting Zheng, Li Guo, Leming Shi:
  PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. D1090-D1101
• 
  Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A. Shoemaker, Paul A. Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan Bolton:
  PubChem 2019 update: improved access to chemical data. D1102-D1109
• 
  Yang Wu, Feilong Zhang, Kuo Yang, Shuangsang Fang, Dechao Bu, Hui Li, Liang Sun, Hairuo Hu, Kuo Gao, Wei Wang, Xuezhong Zhou, Yi Zhao, Jianxin Chen:
  SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping. D1110-D1117

Plant databases

• 
  Xian Zeng, Peng Zhang, Yali Wang, Chu Qin, Shangying Chen, Weidong He, Lin Tao, Ying Tan, Dan Gao, Bo-hua Wang, Zhe Chen, Weiping Chen, Yu Yang Jiang, Yuzong Chen:
  CMAUP: a database of collective molecular activities of useful plants. D1118-D1127
• 
  Yi Zheng, Shan Wu, Yang Bai, Honghe Sun, Chen Jiao, Shaogui Guo, Kun Zhao, Jose M. Blanca, Zhonghua Zhang, Sanwen Huang, Yong Xu, Yiqun Weng, Michael Mazourek, Umesh K. Reddy, Kaori Ando, James D. McCreight, Arthur A. Schaffer, Joseph Burger, Yaakov Tadmor, Nurit Katzir, Xuemei Tang, Yang Liu, James J. Giovannoni, Kai-Shu Ling, W. Patrick Wechter, Amnon Levi, Jordi Garcia-Mas, Rebecca Grumet, Zhangjun Fei:
  Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. D1128-D1136
• 
  Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi L. Humann, Stephen P. Ficklin, Ksenija Gasic, Kristin Scott, Morgan Frank, Sushan Ru, Heidi Hough, Kate Evans, Cameron Peace, Mercy A. Olmstead, Lisa W. DeVetter, James McFerson, Michael Coe, Jill L. Wegrzyn, Margaret E. Staton, Albert G. Abbott, Dorrie Main:
  15 years of GDR: New data and functionality in the Genome Database for Rosaceae. D1137-D1145
• 
  John L. Portwood II, Margaret Woodhouse, Ethalinda K. S. Cannon, Jack M. Gardiner, Lisa C. Harper, Mary L. Schaeffer, Jesse R. Walsh, Taner Z. Sen, Kyoung Tak Cho, David A. Schott, Bremen L. Braun, Miranda Dietze, Brittney Dunfee, Christine G. Elsik, Nancy Manchanda, Ed Coe, Marty Sachs, Philip Stinard, Josh Tolbert, Shane Zimmerman, Carson M. Andorf:
  MaizeGDB 2018: the maize multi-genome genetics and genomics database. D1146-D1154
• 
  Chi-Nga Chow, Tzong-Yi Lee, Yu-Cheng Hung, Guan-Zhen Li, Kuan-Chieh Tseng, Ya-Hsin Liu, Po-Li Kuo, Han-Qin Zheng, Wen-Chi Chang:
  PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. D1155-D1163

Other databases

• 
  Patrick V. Phaneuf, Dennis Gosting, Bernhard O. Palsson, Adam M. Feist:
  ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. D1164-D1171
• 
  Mélanie Courtot, Luca Cherubin, Adam Faulconbridge, Daniel Vaughan, Matthew Green, David Richardson, Peter W. Harrison, Patricia L. Whetzel, Helen E. Parkinson, Tony Burdett:
  BioSamples database: an updated sample metadata hub. D1172-D1178
• 
  Ayana Dagan-Wiener, Antonella Di Pizio, Ido Nissim, Malkeet Singh Bahia, Nitzan Dubovski, Eitan Margulis, Masha Y. Niv:
  BitterDB: taste ligands and receptors database in 2019. D1179-D1185
• 
  Michelle G. Giglio, Rebecca Tauber, Suvarna Nadendla, James B. Munro, Dustin Olley, Shoshannah Ball, Elvira Mitraka, Lynn M. Schriml, Pascale Gaudet, Elizabeth T. Hobbs, Ivan Erill, Deborah A. Siegele, James C. Hu, Chris Mungall, Marcus C. Chibucos:
  ECO, the Evidence & Conclusion Ontology: community standard for evidence information. D1186-D1194
• 
  Michael Böhm, Andreas Bohne-Lang, Martin Frank, Alexander Loß, Miguel A. Rojas-Macias, Thomas Lütteke:
  Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update). D1195-D1201
• 
  Roberto Preste, Ornella Vitale, Rosanna Clima, Giuseppe Gasparre, Marcella Attimonelli:
  HmtVar: a new resource for human mitochondrial variations and pathogenicity data. D1202-D1210
• 
  Jie Ma, Tao Chen, Songfeng Wu, Chunyuan Yang, Mingze Bai, Kunxian Shu, Kenli Li, Guoqing Zhang, Zhong Jin, Fuchu He, Henning Hermjakob, Yunping Zhu:
  iProX: an integrated proteome resource. D1211-D1217
• 
  Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Yoshinori Yamanouchi, Norie Araki, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Mio Iwasaki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, Yasushi Ishihama:
  The jPOST environment: an integrated proteomics data repository and database. D1218-D1224
• 
  Anthony C. Smith, Alan J. Robinson:
  MitoMiner v4.0: an updated database of mitochondrial localization evidence, phenotypes and diseases. D1225-D1228
• 
  Thomas Duigou, Melchior du Lac, Pablo Carbonell, Jean-Loup Faulon:
  RetroRules: a database of reaction rules for engineering biology. D1229-D1235
• 
  François Bonnardel, Julien Mariethoz, Sebastian Salentin, Xavier Robin, Michael Schroeder, Serge Pérez, Frédérique Lisacek, Anne Imberty:
  UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. D1236-D1244
• 
  Benjamin Dubreuil, Ehud Sass, Yotam Nadav, Meta Heidenreich, James Georgeson, Uri Weill, Yuanqiang Duan, Matthias Meurer, Maya Schuldiner, Michael Knop, Emmanuel D. Levy:
  YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries. D1245-D1249

Corrigendum

• 
  The RNAcentral Consortium:
  RNAcentral: a hub of information for non-coding RNA sequences. D1250-D1251

Volume 47, Number Webserver-Issue, July 2019

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  Editorial: The 17th Annual Nucleic Acids Research Web Server Issue 2019. W1-W4
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  John Rozewicki, Songling Li, Karlou Mar Amada, Daron M. Standley, Kazutaka Katoh:
  MAFFT-DASH: integrated protein sequence and structural alignment. W5-W10
• 
  Jia Lu, Xiaoyi Cao, Sheng Zhong:
  EpiAlignment: alignment with both DNA sequence and epigenomic data. W11-W19
• 
  Benjamin D. Lee, Michael A. Timony, Pablo Ruiz:
  DNAvisualization.org: a serverless web tool for DNA sequence visualization. W20-W25
• 
  Shuxiang Li, Wilma K. Olson, Xiang-Jun Lu:
  Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures. W26-W34
• 
  Jiahua He, Jun Wang, Huanyu Tao, Yi Xiao, Sheng-You Huang:
  HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures. W35-W42
• 
  Bulat Zagidullin, Jehad Aldahdooh, Shuyu Zheng, Wenyu Wang, Yinyin Wang, Joseph Saad, Alina Malyutina, Mohieddin Jafari, ZiaurRehman Tanoli, Alberto Pessia, Jing Tang:
  DrugComb: an integrative cancer drug combination data portal. W43-W51
• 
  Ling Xu, Zhaobin Dong, Lu Fang, Yongjiang Luo, Zhaoyuan Wei, Hailong Guo, Guoqing Zhang, Yong Q. Gu, Devin Coleman-Derr, Qingyou Xia, Yi Wang:
  OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. W52-W58
• 
  Stephan Greiner, Pascal Lehwark, Ralph Bock:
  OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. W59-W64
• 
  Linchun Shi, Haimei Chen, Mei Jiang, Liqiang Wang, Xi Wu, Linfang Huang, Chang Liu:
  CPGAVAS2, an integrated plastome sequence annotator and analyzer. W65-W73
• 
  Wenchen Song, Hai-Xi Sun, Carolyn Zhang, Li Cheng, Ye Peng, Ziqing Deng, Dan Wang, Yun Wang, Ming Hu, Wenen Liu, Huanming Yang, Yue Shen, Junhua Li, Lingchong You, Minfeng Xiao:
  Prophage Hunter: an integrative hunting tool for active prophages. W74-W80
• 
  Kai Blin, Simon Shaw, Katharina Steinke, Rasmus Villebro, Nadine Ziemert, Sang Yup Lee, Marnix H. Medema, Tilmann Weber:
  antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. W81-W87
• 
  Oren Avram, Dana Rapoport, Shir Portugez, Tal Pupko:
  M1CR0B1AL1Z3R - a user-friendly web server for the analysis of large-scale microbial genomics data. W88-W92
• 
  Alexandre Renaux, Sofia Papadimitriou, Nassim Versbraegen, Charlotte Nachtegael, Simon Boutry, Ann Nowé, Guillaume Smits, Tom Lenaerts:
  ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations. W93-W98
• 
  Eduardo Pérez-Palma, Marie Gramm, Peter Nürnberg, Patrick May, Dennis Lal:
  Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database. W99-W105
• 
  Jana Marie Schwarz, Daniela Hombach, Sebastian Köhler, David N. Cooper, Markus Schuelke, Dominik Seelow:
  RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants. W106-W113
• 
  Daniela Hombach, Markus Schuelke, Ellen Knierim, Nadja Ehmke, Jana Marie Schwarz, Björn Fischer-Zirnsak, Dominik Seelow:
  MutationDistiller: user-driven identification of pathogenic DNA variants. W114-W120
• 
  Michael Silk, Slavé Petrovski, David B. Ascher:
  MTR-Viewer: identifying regions within genes under purifying selection. W121-W126
• 
  Vincentius Martin, Jingkang Zhao, Ariel Afek, Zachery Mielko, Raluca Gordân:
  QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. W127-W135
• 
  Emidio Capriotti, Ludovica Montanucci, Giuseppe Profiti, Ivan Rossi, Diana Giannuzzi, Luca Aresu, Piero Fariselli:
  Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome. W136-W141
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  Selim Kalayci, Myvizhi Esai Selvan, Irene Ramos, Chris Cotsapas, Eva Harris, Eun-Young Kim, Ruth R. Montgomery, Gregory A. Poland, Bali Pulendran, John S. Tsang, Robert J. Klein, Zeynep H. Gümüs:
  ImmuneRegulation: a web-based tool for identifying human immune regulatory elements. W142-W150
• 
  Camilo Andres Perez-Romero, Bram Weytjens, Dries Decap, Toon Swings, Jan Michiels, Dries De Maeyer, Kathleen Marchal:
  IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations. W151-W157
• 
  Daofeng Li, Silas Hsu, Deepak Purushotham, Renee L. Sears, Ting Wang:
  WashU Epigenome Browser update 2019. W158-W165
• 
  Julie Krainer, Andreas Weinhäusel, Karel Hanak, Walter Pulverer, Seza Özen, Klemens Vierlinger, Stephan Pabinger:
  EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies. W166-W170
• 
  Kornel Labun, Tessa G. Montague, Maximilian Krause, Yamila N. Torres cleuren, Håkon Tjeldnes, Eivind Valen:
  CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. W171-W174
• 
  Carla M. Mann, Gabriel Martínez-Gálvez, Jordan M. Welker, Wesley A. Wierson, Hirotaka Ata, Maira P. Almeida, Karl J. Clark, Jeffrey J. Essner, Maura McGrail, Stephen C. Ekker, Drena Dobbs:
  The Gene Sculpt Suite: a set of tools for genome editing. W175-W182
• 
  Maxim V. Kuleshov, Jennifer E. L. Diaz, Zachary N. Flamholz, Alexandra B. Keenan, Alexander Lachmann, Megan L. Wojciechowicz, Ross L. Cagan, Avi Ma'ayan:
  modEnrichr: a suite of gene set enrichment analysis tools for model organisms. W183-W190
• 
  Uku Raudvere, Liis Kolberg, Ivan Kuzmin, Tambet Arak, Priit Adler, Hedi Peterson, Jaak Vilo:
  g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). W191-W198
• 
  Yuxing Liao, Jing Wang, Eric J. Jaehnig, Zhiao Shi, Bing Zhang:
  WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. W199-W205
• 
  Shaojuan Li, Changxin Wan, Rongbin Zheng, Jingyu Fan, Xin Dong, Clifford A. Meyer, Xiaole Shirley Liu:
  Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. W206-W211
• 
  Alexandra B. Keenan, Denis Torre, Alexander Lachmann, Ariel K. Leong, Megan L. Wojciechowicz, Vivian Utti, Kathleen M. Jagodnik, Eryk Kropiwnicki, Zichen Wang, Avi Ma'ayan:
  ChEA3: transcription factor enrichment analysis by orthogonal omics integration. W212-W224
• 
  Fedor A. Kolpakov, Ilya R. Akberdin, Timur A. Kashapov, llya Kiselev, Semyon Kolmykov, Yury V. Kondrakhin, Elena Kutumova, Nikita Mandrik, Sergey S. Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Alexander E. Kel:
  BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. W225-W133
• 
  Guangyan Zhou, Othman Soufan, Jessica Ewald, Robert E. W. Hancock, Niladri Basu, Jianguo Xia:
  NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis. W234-W241
• 
  Omer Basha, Omry Mauer, Eyal Simonovsky, Rotem Shpringer, Esti Yeger Lotem:
  ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues. W242-W247
• 
  Fengcui Qian, Xuecang Li, Jincheng Guo, Jianmei Zhao, Yanyu Li, Zhidong Tang, Liwei Zhou, Jian Zhang, Xuefeng Bai, Yong Jiang, Qi Pan, Qiuyu Wang, Enmin Li, Chunquan Li, Liyan Xu, Dechen Lin:
  SEanalysis: a web tool for super-enhancer associated regulatory analysis. W248-W255
• 
  Ivica Letunic, Peer Bork:
  Interactive Tree Of Life (iTOL) v4: recent updates and new developments. W256-W259
• 
  Frédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia, Olivier Gascuel:
  NGPhylogeny.fr: new generation phylogenetic services for non-specialists. W260-W265
• 
  Nikola Jovanovic, Alexander S. Mikheyev:
  Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO. W266-W269
• 
  Balakrishnan Subramanian, Shenghan Gao, Martin J. Lercher, Songnian Hu, Wei-Hua Chen:
  Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees. W270-W275
• 
  Mohammad Alanjary, Katharina Steinke, Nadine Ziemert:
  AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. W276-W282
• 
  Jesús Murga-Moreno, Marta Coronado-Zamora, Sergi Hervas, Sònia Casillas, Antonio Barbadilla:
  iMKT: the integrative McDonald and Kreitman test. W283-W288
• 
  Fatemeh Sharifi, Yuzhen Ye:
  MyDGR: a server for identification and characterization of diversity-generating retroelements. W289-W294
• 
  Ralf Gabriels, Lennart Martens, Sven Degroeve:
  Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques. W295-W299
• 
  Aleksander Kuriata, Valentin Iglesias, Jordi Pujols, Mateusz Kurcinski, Sebastian Kmiecik, Salvador Ventura:
  Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility. W300-W307
• 
  Dmitry A. Suplatov, Daria Timonina, Yana A. Sharapova, Vytas K. Svedas:
  Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families. W308-W314
• 
  Kun Song, Qian Li, Wei Gao, Shaoyong Lu, Qiancheng Shen, Xinyi Liu, Yongyan Wu, Binquan Wang, Houwen Lin, Guoqiang Chen, Jian Zhang:
  AlloDriver: a method for the identification and analysis of cancer driver targets. W315-W321
• 
  Gaoqi Weng, Ercheng Wang, Zhe Wang, Hui Liu, Feng Zhu, Dan Li, Tingjun Hou:
  HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. W322-W330
• 
  Ankit A. Roy, Abhilesh S. Dhawanjewar, Parichit Sharma, Gulzar Singh, M. S. Madhusudhan:
  Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions. W331-W337
• 
  Carlos H. M. Rodrigues, Yoochan Myung, Douglas E. V. Pires, David B. Ascher:
  mCSM-PPI2: predicting the effects of mutations on protein-protein interactions. W338-W344
• 
  Lukás Jendele, Radoslav Krivák, Petr Skoda, Marian Novotny, David Hoksza:
  PrankWeb: a web server for ligand binding site prediction and visualization. W345-W349
• 
  Nur Syatila Abdul Ghani, Effirul Ikhwan Ramlan, Mohd Firdaus Raih:
  Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning. W350-W356
• 
  Antoine Daina, Olivier Michielin, Vincent Zoete:
  SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. W357-W364
• 
  Julien Rey, Inès Rasolohery, Pierre Tufféry, Frédéric Guyon, Gautier Moroy:
  PatchSearch: a web server for off-target protein identification. W365-W372
• 
  Damiano Piovesan, Silvio C. E. Tosatto:
  INGA 2.0: improving protein function prediction for the dark proteome. W373-W378
• 
  Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu:
  NetGO: improving large-scale protein function prediction with massive network information. W379-W387
• 
  Chen Zhou, Zikun Chen, Lu Zhang, Deyu Yan, Tiantian Mao, Kailin Tang, Tianyi Qiu, Zhiwei Cao:
  SEPPA 3.0 - enhanced spatial epitope prediction enabling glycoprotein antigens. W388-W394
• 
  Gurdeep Singh, Asuka Inoue, J. Silvio Gutkind, Robert B. Russell, Francesco Raimondi:
  PRECOG: PREdicting COupling probabilities of G-protein coupled receptors. W395-W401
• 
  Daniel W. A. Buchan, David T. Jones:
  The PSIPRED Protein Analysis Workbench: 20 years on. W402-W407
• 
  Liam J. McGuffin, Recep Adiyaman, Ali H. A. Maghrabi, Ahmad N. Shuid, Danielle A. Brackenridge, John O. Nealon, Limcy S. Philomina:
  IntFOLD: an integrated web resource for high performance protein structure and function prediction. W408-W413
• 
  Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar R. P. Pinto, Jan Brezovsky, Jirí Damborský, David Bednar:
  Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. W414-W422
• 
  Yasaman Karami, Julien Rey, Guillaume Postic, Samuel Murail, Pierre Tufféry, Sjoerd Jacob de Vries:
  DaReUS-Loop: a web server to model multiple loops in homology models. W423-W428
• 
  Wei Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang:
  LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. W429-W436
• 
  Kliment Olechnovic, Ceslovas Venclovas:
  VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes. W437-W442
• 
  Wenbo Wang, Zhaoyu Li, Junlin Wang, Dong Xu, Yi Shang:
  PSICA: a fast and accurate web service for protein model quality analysis. W443-W450
• 
  Gyu Rie Lee, Jonghun Won, Lim Heo, Chaok Seok:
  GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure. W451-W455
• 
  Mangesh Damre, Alessandro Marchetto, Alejandro Giorgetti:
  MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics. W456-W461
• 
  Broto Chakrabarty, Varun Naganathan, Kanak Garg, Yash Agarwal, Nita Parekh:
  NAPS update: network analysis of molecular dynamics data and protein-nucleic acid complexes. W462-W470
• 
  Rasim Murat Aydinkal, Onur Serçinoglu, Pemra Ozbek:
  ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism. W471-W476
• 
  Elliot D. Drew, Robert W. Janes:
  2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content. W477-W481
• 
  Minh N. Nguyen, Chandra S. Verma, Pingyu Zhong:
  AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models. W482-W489
• 
  Milene B. Carvalho, Franck Molina, Liza Figueredo Felicori:
  Yvis: antibody high-density alignment visualization and analysis platform with an integrated database. W490-W495
• 
  Fabio Dall'antonia, Walter Keller:
  SPADE web service for prediction of allergen IgE epitopes. W496-W501
• 
  Sandeep Kumar Dhanda, Swapnil Mahajan, Sinu Paul, Zhen Yan, Haeuk Kim, Martin Closter Jespersen, Vanessa Isabell Jurtz, Massimo Andreatta, Jason A. Greenbaum, Paolo Marcatili, Alessandro Sette, Morten Nielsen, Bjoern Peters:
  IEDB-AR: immune epitope database - analysis resource in 2019. W502-W506
• 
  Carsten Kemena, Elias Dohmen, Erich Bornberg-Bauer:
  DOGMA: a web server for proteome and transcriptome quality assessment. W507-W510
• 
  Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingström, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen, Björn A. Grüning:
  The RNA workbench 2.0: next generation RNA data analysis. W511-W515
• 
  Jincheng Guo, Shuangsang Fang, Yang Wu, Jianhua Zhang, Yang Chen, Jing Liu, Bo Wu, Jiarui Wu, Enmin Li, Liyan Xu, Liang Sun, Yi Zhao:
  CNIT: a fast and accurate web tool for identifying protein-coding and long non-coding transcripts based on intrinsic sequence composition. W516-W522
• 
  Joana Carlevaro-Fita, Leibo Liu, Yuan Zhou, Shan Zhang, Panagiotis Chouvardas, Rory Johnson, Jianwei Li:
  LnCompare: gene set feature analysis for human long non-coding RNAs. W523-W529
• 
  Ernesto Aparicio-Puerta, Ricardo Lebrón, Antonio Rueda, Cristina Gómez-Martín, Stavros Giannoukakos, David Jáspez, José María Medina, Andreja Zubkovic, Igor Jurak, Bastian Fromm, Juan Antonio Marchal, José L. Oliver, Michael Hackenberg:
  sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression. W530-W535
• 
  Jianwei Li, Shan Zhang, Yanping Wan, Yingshu Zhao, Jiangcheng Shi, Yuan Zhou, Qinghua Cui:
  MISIM v2.0: a web server for inferring microRNA functional similarity based on microRNA-disease associations. W536-W541
• 
  Brian Y. Lin, Patricia P. Chan, Todd M. Lowe:
  tRNAviz: explore and visualize tRNA sequence features. W542-W547
• 
  Qi Liu, Richard I. Gregory:
  RNAmod: an integrated system for the annotation of mRNA modifications. W548-W555
• 
  Zefang Tang, Boxi Kang, Chenwei Li, Tianxiang Chen, Zemin Zhang:
  GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. W556-W560
• 
  Alexander Koch, Jana Jeschke, Wim Van Criekinge, Manon van Engeland, Tim De Meyer:
  MEXPRESS update 2019. W561-W565
• 
  Cong Liu, Fabricio Sampaio Peres Kury, Ziran Li, Casey N. Ta, Kai Wang, Chunhua Weng:
  Doc2Hpo: a web application for efficient and accurate HPO concept curation. W566-W570
• 
  Alexander Lachmann, Brian M. Schilder, Megan L. Wojciechowicz, Denis Torre, Maxim V. Kuleshov, Alexandra B. Keenan, Avi Ma'ayan:
  Geneshot: search engine for ranking genes from arbitrary text queries. W571-W577
• 
  Zongliang Yue, Christopher D. Willey, Anita B. Hjelmeland, Jake Y. Chen:
  BEERE: a web server for biomedical entity expansion, ranking and explorations. W578-W586
• 
  Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu:
  PubTator central: automated concept annotation for biomedical full text articles. W587-W593
• 
  Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
  LitSense: making sense of biomedical literature at sentence level. W594-W599
• 
  Jose Espinosa-Carrasco, Antonio Hermoso Pulido, Ionas Erb, Mara Dierssen, Julia V. Ponomarenko, Cédric Notredame:
  Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. W600-W604
• 
  Benedict Röder, Nicolas Kersten, Marius Herr, Nora K. Speicher, Nico Pfeifer:
  web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning. W605-W609
• 
  Kun Wang, Haiwei Li, Yue Xu, Qianzhi Shao, Jianming Yi, Ruichao Wang, Wanshi Cai, Xingyi Hang, Chenggang Zhang, Haoyang Cai, Wubin Qu:
  MFEprimer-3.0: quality control for PCR primers. W610-W613
• 
  Hajin Jeon, Jeongmin Bae, Sang-Hyun Hwang, Kyu-Young Whang, Hyun-Seob Lee, Hyerin Kim, Min-Soo Kim:
  MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments. W614-W622
• 
  Peng Zhang, Bertrand Boisson, Peter D. Stenson, David N. Cooper, Jean-Laurent Casanova, Laurent Abel, Yuval Itan:
  SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data. W623-W631
• 
  Lukas Bartonek, Bojan Zagrovic:
  VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences. W632-W635
• 
  Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R. N. Tivey, Simon C. Potter, Robert D. Finn, Rodrigo Lopez:
  The EMBL-EBI search and sequence analysis tools APIs in 2019. W636-W641