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ORCIDNucleic Acids Research, Volume 47
Volume 47, Number Database-Issue, January 2019
- Daniel J. Rigden, Xosé M. Fernández-Suárez:
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. D1-D7
- BIG Data Center:
Database Resources of the BIG Data Center in 2019. D8-D14 - 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 - 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
- Edvard Ehler, Jiri Novotný, Anna Juras, Maciej Chylenski, Ondrej Moravcík, Jan Paces:
AmtDB: a database of ancient human mitochondrial genomes. D29-D32 - 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 - 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 - Stefan Kurtenbach, Rohit Reddy, J. William Harbour:
ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP). D46-D49 - Xavier Meyer, Linda Dib, Nicolas Salamin:
CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates. D50-D54 - 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 - 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 - 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 - 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 - 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 - 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 - Eric W. Sayers, Mark Cavanaugh, Karen Clark, James Ostell, Kim D. Pruitt, Ilene Karsch-Mizrachi:
GenBank. D94-D99 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones:
miRBase: from microRNA sequences to function. D155-D162 - 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 - 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 - 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 - 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 - 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 - Valentina Galata, Tobias Fehlmann, Christina Backes, Andreas Keller:
PLSDB: a resource of complete bacterial plasmids. D195-D202 - 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 - 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 - The RNAcentral Consortium:
RNAcentral: a hub of information for non-coding RNA sequences. D221-D229 - 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 - 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 - Morad M. Mokhtar, Mohamed A. M. Atia:
SSRome: an integrated database and pipelines for exploring microsatellites in all organisms. D244-D252 - Zhan Tong, Qinghua Cui, Juan Wang, Yuan Zhou:
TransmiR v2.0: an updated transcription factor-microRNA regulation database. D253-D258 - 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
- Zhen Wah Tan, Wei-Ven Tee, Enrico Guarnera, Lauren Booth, Igor N. Berezovsky:
AlloMAPS: allosteric mutation analysis and polymorphism of signaling database. D265-D270 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - The Gene Ontology Consortium:
The Gene Ontology Resource: 20 years and still GOing strong. D330-D338 - 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 - 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 - Alex L. Mitchell, Teresa K. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, Alan 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 - Rayees Rahman, Peter Man-Un Ung, Avner Schlessinger:
KinaMetrix: a web resource to investigate kinase conformations and inhibitor space. D361-D366 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - Ahmed Mohamed, Anup Shah, David Chen, Michelle M. Hill:
RaftProt V2: understanding membrane microdomain function through lipid raft proteomes. D459-D463 - 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 - 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 - 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 - 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 - 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 - The UniProt Consortium:
UniProt: a worldwide hub of protein knowledge. D506-D515 - 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
- 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 - Lisa Jeske, Sandra Placzek, Ida Schomburg, Antje Chang, Dietmar Schomburg:
BRENDA in 2019: a European ELIXIR core data resource. D542-D549 - 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 - Thierry Lombardot, Anne Morgat, Kristian B. Axelsen, Lucila Aimo, Nevila Hyka-Nouspikel, Anne Niknejad, Alexandr Ignatchenko, Ioannis Xenarios, Elisabeth Coudert, Nicole Redaschi, Alan 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 - 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 - 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
- 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 - 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 - 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
- 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