Subject: Nucleic Acids Research Table of Contents for 08 January 2019 ------=_Part_2104309194.1547225703265 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_2104309194.1547225703265 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 47 Issue D1
 
08 January 2019
 
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The PRIDE database and related tools and resources in 2019: improving support for quantification data border= 
 
Yasset Perez-Riverol; Attila Csordas; Jingwen Bai; Manuel Bernal-Llinares; Suresh Hewapathirana ...
 
 
 
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InterPro in 2019: improving coverage, classification and access to protein sequence annotations border= 
 
Alex L Mitchell; Teresa K Attwood; Patricia C Babbitt; Matthias Blum; Peer Bork ...
 
 
 
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Ensembl 2019 border= 
 
Fiona Cunningham; Premanand Achuthan; Wasiu Akanni ; James Allen; M Ridwan Amode ...
 
 
 
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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources border=  
 
Sebastian Köhler; Leigh Carmody; Nicole Vasilevsky ; Julius O B Jacobsen; Daniel Danis ...
 
 
 
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ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins border= 
 
Ricky Wai Tak Leung; Xiaosen Jiang; Ka Hou Chu; Jing Qin
 
 
 
Editorial
 
 
 
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection border= 
 
Daniel J Rigden; Xosé M Fernández
 
 
 
Front Matter
 
 
 
Database Resources of the BIG Data Center in 2019 border=  
 
Zhang Zhang; Wenming Zhao; Jingfa Xiao ; Yiming Bao; Fan Wang ...
 
 
The European Bioinformatics Institute in 2018: tools, infrastructure and training border=  
 
Charles E Cook; Rodrigo Lopez; Oana Stroe ; Guy Cochrane; Cath Brooksbank ...
 
 
Database resources of the National Center for Biotechnology Information 
 
Eric W Sayers; Richa Agarwala; Evan E Bolton; J Rodney Brister ; Kathi Canese ...
 
 
 
Nucleic acid sequence, structure, and regulation
 
 
 
AmtDB: a database of ancient human mitochondrial genomes border=  
 
Edvard Ehler; Ji┼Öí Novotný; Anna Juras ; Maciej Chyle┼"ski; Ond┼Öej Morav─Źík ...
 
 
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors border= 
 
Hui Hu; Ya-Ru Miao ; Long-Hao Jia; Qing-Yang Yu; Qiong Zhang ...
 
 
CAGm: a repository of germline microsatellite variations in the 1000 genomes project border=  
 
Nicholas Kinney; Kyle Titus-Glover; Jonathan D Wren ; Robin T Varghese; Pawel Michalak ...
 
 
ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP) border=  
 
Stefan Kurtenbach; Rohit Reddy; J William Harbour
 
 
CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates border=  
 
Xavier Meyer; Linda Dib; Nicolas Salamin
 
 
COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference border= 
 
Takeshi Obayashi ; Yuki Kagaya; Yuichi Aoki; Shu Tadaka; Kengo Kinoshita
 
 
CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs border=  
 
Wen Chen; Guoqiang Zhang; Jing Li ; Xuan Zhang; Shulan Huang ...
 
 
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data border=  
 
Yuichi Kodama; Jun Mashima; Takehide Kosuge ; Osamu Ogasawara
 
 
DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids border=  
 
Hao Luo; Feng Gao
 
 
Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human border=  
 
Guangyi Niu; Dong Zou; Mengwei Li ; Yuansheng Zhang; Jian Sang ...
 
 
The European Nucleotide Archive in 2018 border= 
 
Peter W Harrison; Blaise Alako; Clara Amid ; Ana Cerdeño-Tárraga; Iain Cleland ...
 
 
EVmiRNA: a database of miRNA profiling in extracellular vesicles border= 
 
Teng Liu; Qiong Zhang; Jiankun Zhang ; Chao Li; Ya-Ru Miao ...
 
 
GenBank 
 
Eric W Sayers; Mark Cavanaugh; Karen Clark; James Ostell ; Kim D Pruitt ...
 
 
GTRD: a database on gene transcription regulation'2019 update border= 
 
Ivan Yevshin; Ruslan Sharipov; Semyon Kolmykov ; Yury Kondrakhin; Fedor Kolpakov
 
 
HACER: an atlas of human active enhancers to interpret regulatory variants border=  
 
Jing Wang; Xizhen Dai; Lynne D Berry ; Joy D Cogan; Qi Liu ...
 
 
liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies border=  
 
Ernesto Aparicio-Puerta; David Jáspez; Ricardo Lebrón ; Danijela Koppers-Lalic; Juan A Marchal ...
 
 
LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments border= 
 
Peng Wang ; Xin Li; Yue Gao; Qiuyan Guo; Yanxia Wang ...
 
 
LncBook: a curated knowledgebase of human long non-coding RNAs border= 
 
Lina Ma; Jiabao Cao; Lin Liu ; Qiang Du; Zhao Li ...
 
 
LNCipedia 5: towards a reference set of human long non-coding RNAs border=  
 
Pieter-Jan Volders; Jasper Anckaert; Kenneth Verheggen ; Justine Nuytens; Lennart Martens ...
 
 
LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse border=  
 
Liang Cheng; Pingping Wang; Rui Tian ; Song Wang; Qinghua Guo ...
 
 
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles border= 
 
Quy Xiao Xuan Lin ; Stephanie Sian; Omer An; Denis Thieffry; Sudhakar Jha ...
 
 
miRBase: from microRNA sequences to function border= 
 
Ana Kozomara; Maria Birgaoanu; Sam Griffiths-Jones
 
 
NucMap: a database of genome-wide nucleosome positioning map across species border=  
 
Yongbing Zhao; Jinyue Wang; Fang Liang ; Yanxia Liu; Qi Wang ...
 
 
Plant editosome database: a curated database of RNA editosome in plants border=  
 
Man Li; Lin Xia; Yuansheng Zhang ; Guangyi Niu; Mengwei Li ...
 
 
piRBase: a comprehensive database of piRNA sequences border= 
 
Jiajia Wang; Peng Zhang; Yiping Lu ; Yanyan Li; Yu Zheng ...
 
 
piRTarBase: a database of piRNA targeting sites and their roles in gene regulation border=  
 
Wei-Sheng Wu; Jordan S Brown; Tsung-Te Chen ; Yu-Han Chu; Wei-Che Huang ...
 
 
Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data border=  
 
Tiago F Jesus; Bruno Ribeiro-Gonçalves; Diogo N Silva ; Valeria Bortolaia; Mário Ramirez ...
 
 
PLSDB: a resource of complete bacterial plasmids border= 
 
Valentina Galata; Tobias Fehlmann; Christina Backes ; Andreas Keller
 
 
POSTAR2: deciphering the post-transcriptional regulatory logics border= 
 
Yumin Zhu; Gang Xu; Yucheng T Yang ; Zhiyu Xu; Xinduo Chen ...
 
 
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12 border= 
 
Alberto Santos-Zavaleta; Heladia Salgado ; Socorro Gama-Castro; Mishael Sánchez-Pérez; Laura Gómez-Romero ...
 
 
RNAcentral: a hub of information for non-coding RNA sequences border= 
 
Blake A Sweeney; Anton I Petrov; Boris Burkov ; Robert D Finn; Alex Bateman ...
 
 
RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling border=  
 
Hongwei Wang; Ludong Yang; Yan Wang ; Leshi Chen; Huihui Li ...
 
 
SEdb: a comprehensive human super-enhancer database border= 
 
Yong Jiang; Fengcui Qian; Xuefeng Bai ; Yuejuan Liu; Qiuyu Wang ...
 
 
SSRome: an integrated database and pipelines for exploring microsatellites in all organisms border=  
 
Morad M Mokhtar; Mohamed A M Atia
 
 
TransmiR v2.0: an updated transcription factor-microRNA regulation database border=  
 
Zhan Tong; Qinghua Cui; Juan Wang ; Yuan Zhou
 
 
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications border=  
 
Rolf Henrik Nilsson; Karl-Henrik Larsson; Andy F S Taylor ; Johan Bengtsson-Palme; Thomas S Jeppesen ...
 
 
 
Protein sequence and structure, motifs, and domains
 
 
 
AlloMAPS: allosteric mutation analysis and polymorphism of signaling database border=  
 
Zhen Wah Tan; Wei-Ven Tee; Enrico Guarnera ; Lauren Booth; Igor N Berezovsky
 
 
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life border=  
 
Xiaosong Huang; Laurent-Philippe Albou; Tremayne Mushayahama ; Anushya Muruganujan; Haiming Tang ...
 
 
CATH: expanding the horizons of structure-based functional annotations for genome sequences border=  
 
Ian Sillitoe; Natalie Dawson; Tony E Lewis ; Sayoni Das; Jonathan G Lees ...
 
 
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data border= 
 
Jhih-Hua Jhong ; Yu-Hsiang Chi; Wen-Chi Li; Tsai-Hsuan Lin; Kai-Yao Huang ...
 
 
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications border=  
 
Kai-Yao Huang; Tzong-Yi Lee; Hui-Ju Kao ; Chen-Tse Ma; Chao-Chun Lee ...
 
 
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses border= 
 
Jaime Huerta-Cepas ; Damian Szklarczyk; Davide Heller; Ana Hernández-Plaza; Sofia K Forslund ...
 
 
EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins 
 
Edoardo Sarti; Antoniya A Aleksandrova; Srujan K Ganta; Amarendra S Yavatkar ; Lucy R Forrest
 
 
The Gene Ontology Resource: 20 years and still GOing strong border= 
 
 
 
The Immune Epitope Database (IEDB): 2018 update border= 
 
Randi Vita; Swapnil Mahajan; James A Overton ; Sandeep Kumar Dhanda; Sheridan Martini ...
 
 
iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains border= 
 
Yaping Guo ; Di Peng; Jiaqi Zhou; Shaofeng Lin; Chenwei Wang ...
 
 
KinaMetrix: a web resource to investigate kinase conformations and inhibitor space border=  
 
Rayees Rahman; Peter Man-Un Ung; Avner Schlessinger
 
 
KnotProt 2.0: a database of proteins with knots and other entangled structures border=  
 
Pawel Dabrowski-Tumanski; Pawel Rubach; Dimos Goundaroulis ; Julien Dorier; Piotr Sułkowski ...
 
 
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions border=  
 
Olivier Clerc; Madeline Deniaud; Sylvain D Vallet ; Alexandra Naba; Alain Rivet ...
 
 
MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons border= 
 
Ikuo Uchiyama ; Motohiro Mihara; Hiroyo Nishide; Hirokazu Chiba; Masaki Kato
 
 
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions border=  
 
Thomas D Newport; Mark S P Sansom; Phillip J Stansfeld
 
 
MoonDB 2.0: an updated database of extreme multifunctional and moonlighting proteins border=  
 
Diogo M Ribeiro; Galadriel Briere; Benoit Bely ; Lionel Spinelli; Christine Brun
 
 
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes border=  
 
Marie A Brunet; Mylène Brunelle; Jean-François Lucier ; Vivian Delcourt; Maxime Levesque ...
 
 
OrthoInspector 3.0: open portal for comparative genomics border= 
 
Yannis Nevers; Arnaud Kress; Audrey Defosset ; Raymond Ripp; Benjamin Linard ...
 
 
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools border=  
 
Huaiyu Mi; Anushya Muruganujan; Dustin Ebert ; Xiaosong Huang; Paul D Thomas
 
 
The Pfam protein families database in 2019 border= 
 
Sara El-Gebali; Jaina Mistry; Alex Bateman ; Sean R Eddy; Aurélien Luciani ...
 
 
15 years of PhosphoSitePlus® : integrating post-translationally modified sites, disease variants and isoforms border= 
 
Peter V Hornbeck; Jon M Kornhauser ; Vaughan Latham; Beth Murray; Vidhisha Nandhikonda ...
 
 
qPhos: a database of protein phosphorylation dynamics in humans border= 
 
Kai Yu; Qingfeng Zhang; Zekun Liu ; Qi Zhao; Xiaolong Zhang ...
 
 
RaftProt V2: understanding membrane microdomain function through lipid raft proteomes border=  
 
Ahmed Mohamed; Anup D Shah; David Chen ; Michelle M Hill
 
 
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy border= 
 
Stephen K Burley ; Helen M Berman; Charmi Bhikadiya; Chunxiao Bi; Li Chen ...
 
 
SCOPe: classification of large macromolecular structures in the structural classification of proteins'extended database border= 
 
John-Marc Chandonia ; Naomi K Fox; Steven E Brenner
 
 
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins border= 
 
Jose M Dana ; Aleksandras Gutmanas; Nidhi Tyagi; Guoying Qi; Claire O'Donovan ...
 
 
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver border=  
 
Arun Prasad Pandurangan; Jonathan Stahlhacke; Matt E Oates ; Ben Smithers; Julian Gough
 
 
Translocatome: a novel resource for the analysis of protein translocation between cellular organelles border=  
 
Péter Mendik; Levente Dobronyi; Ferenc Hári ; Csaba Kerepesi; Leonardo Maia-Moço ...
 
 
UniProt: a worldwide hub of protein knowledge border= 
 
 
 
Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles border=  
 
Mohashin Pathan; Pamali Fonseka; Sai V Chitti ; Taeyoung Kang; Rahul Sanwlani ...
 
 
Protein Data Bank: the single global archive for 3D macromolecular structure data border=  
 
Stephen K Burley; Helen M Berman; Charmi Bhikadiya ; Chunxiao Bi; Li Chen ...
 
 
 
Metabolic and signalling pathways, enzymes
 
 
 
The BioGRID interaction database: 2019 update border=  
 
Rose Oughtred; Chris Stark; Bobby-Joe Breitkreutz ; Jennifer Rust; Lorrie Boucher ...
 
 
BRENDA in 2019: a European ELIXIR core data resource border= 
 
Lisa Jeske; Sandra Placzek; Ida Schomburg ; Antje Chang; Dietmar Schomburg
 
 
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes border=  
 
Birgit H M Meldal; Hema Bye-A-Jee; Luká┼í Gajdo┼í ; Zuzana Hammerová; Aneta Horá─Źková ...
 
 
CORUM: the comprehensive resource of mammalian protein complexes'2019 border=  
 
Madalina Giurgiu; Julian Reinhard; Barbara Brauner ; Irmtraud Dunger-Kaltenbach; Gisela Fobo ...
 
 
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes border=  
 
Lorna J Richardson; Neil D Rawlings; Gustavo A Salazar ; Alexandre Almeida; David R Haft ...
 
 
HumanNet v2: human gene networks for disease research border= 
 
Sohyun Hwang; Chan Yeong Kim; Sunmo Yang ; Eiru Kim; Traver Hart ...
 
 
IID 2018 update: context-specific physical protein'protein interactions in human, model organisms and domesticated species border= 
 
Max Kotlyar ; Chiara Pastrello; Zara Malik; Igor Jurisica
 
 
New approach for understanding genome variations in KEGG border= 
 
Minoru Kanehisa; Yoko Sato; Miho Furumichi ; Kanae Morishima; Mao Tanabe
 
 
Updates in Rhea: SPARQLing biochemical reaction data border= 
 
Thierry Lombardot; Anne Morgat; Kristian B Axelsen ; Lucila Aimo; Nevila Hyka-Nouspikel ...
 
 
RNAct: Protein'RNA interaction predictions for model organisms with supporting experimental data border=  
 
Benjamin Lang; Alexandros Armaos; Gian G Tartaglia
 
 
STRING v11: protein'protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets border= 
 
Damian Szklarczyk ; Annika L Gable; David Lyon; Alexander Junge; Stefan Wyder ...
 
 
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease border=  
 
Alberto Noronha; Jennifer Modamio; Yohan Jarosz ; Elisabeth Guerard; Nicolas Sompairac ...
 
 
 
Viruses, bacteria, protozoa and fungi
 
 
 
The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters border= 
 
Kai Blin; Victòria Pascal Andreu; Emmanuel L C de los Santos; Francesco Del Carratore; Sang Yup Lee ...
 
 
BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis border=  
 
Lorenz Christian Reimer; Anna Vetcininova; Joaquim Sardà Carbasse ; Carola Söhngen; Dorothea Gleim ...
 
 
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data border= 
 
Wenyu Shi ; Heyuan Qi; Qinglan Sun; Guomei Fan; Shuangjiang Liu ...
 
 
Genomes OnLine database (GOLD) v.7: updates and new features 
 
Supratim Mukherjee; Dimitri Stamatis; Jon Bertsch; Galina Ovchinnikova ; Hema Y Katta ...
 
 
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements border=  
 
Meng Liu; Xiaobin Li; Yingzhou Xie ; Dexi Bi; Jingyong Sun ...
 
 
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes 
 
I-Min A Chen; Ken Chu; Krishna Palaniappan; Manoj Pillay ; Anna Ratner ...
 
 
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes border=  
 
David Paez-Espino; Simon Roux; I-Min A Chen ; Krishna Palaniappan; Anna Ratner ...
 
 
VFDB 2019: a comparative pathogenomic platform with an interactive web interface border=  
 
Bo Liu; Dandan Zheng; Qi Jin ; Lihong Chen; Jian Yang
 
 
Victors: a web-based knowledge base of virulence factors in human and animal pathogens border=  
 
Samantha Sayers; Li Li; Edison Ong ; Shunzhou Deng; Guanghua Fu ...
 
 
 
Human genome, model organisms, comparative genomics
 
 
 
Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB border= 
 
Zhi-Liang Hu ; Carissa A Park; James M Reecy
 
 
ArrayExpress update ' from bulk to single-cell expression data border= 
 
Awais Athar; Anja Füllgrabe; Nancy George ; Haider Iqbal; Laura Huerta ...
 
 
BACTOME'a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates border= 
 
Klaus Hornischer; Ariane Khaledi ; Sarah Pohl; Monika Schniederjans; Lorena Pezoldt ...
 
 
CellMarker: a manually curated resource of cell markers in human and mouse border=  
 
Xinxin Zhang; Yujia Lan; Jinyuan Xu ; Fei Quan; Erjie Zhao ...
 
 
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis border=  
 
Rongbin Zheng; Changxin Wan; Shenglin Mei ; Qian Qin; Qiu Wu ...
 
 
EndoDB: a database of endothelial cell transcriptomics data border= 
 
Shawez Khan; Federico Taverna; Katerina Rohlenova ; Lucas Treps; Vincent Geldhof ...
 
 
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases border=  
 
Marina Lizio; Imad Abugessaisa; Shuhei Noguchi ; Atsushi Kondo; Akira Hasegawa ...
 
 
FlyBase 2.0: the next generation border= 
 
Jim Thurmond; Joshua L Goodman; Victor B Strelets ; Helen Attrill; L Sian Gramates ...
 
 
GENCODE reference annotation for the human and mouse genomes border= 
 
Adam Frankish; Mark Diekhans; Anne-Maud Ferreira ; Rory Johnson; Irwin Jungreis ...
 
 
The mouse Gene Expression Database (GXD): 2019 update border= 
 
Constance M Smith; Terry F Hayamizu; Jacqueline H Finger ; Susan M Bello; Ingeborg J McCright ...
 
 
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans border=  
 
Jarny Choi; Tracey M Baldwin; Mae Wong ; Jessica E Bolden; Kirsten A Fairfax ...
 
 
Genenames.org: the HGNC and VGNC resources in 2019 border= 
 
Bryony Braschi; Paul Denny; Kristian Gray ; Tamsin Jones; Ruth Seal ...
 
 
iDog: an integrated resource for domestic dogs and wild canids border= 
 
Bixia Tang; Qing Zhou; Lili Dong ; Wulue Li; Xiangquan Zhang ...
 
 
Mouse Genome Database (MGD) 2019 border= 
 
Carol J Bult; Judith A Blake; Cynthia L Smith ; James A Kadin; Joel E Richardson ...
 
 
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs border= 
 
Evgenia V Kriventseva ; Dmitry Kuznetsov; Fredrik Tegenfeldt; Mosè Manni; Renata Dias ...
 
 
PlanMine 3.0'improvements to a mineable resource of flatworm biology and biodiversity border=  
 
Andrei Rozanski; HongKee Moon; Holger Brandl ; José M Martín-Durán; Markus A Grohme ...
 
 
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information border= 
 
Antonia Lock ; Kim Rutherford; Midori A Harris; Jacqueline Hayles; Stephen G Oliver ...
 
 
REDfly: the transcriptional regulatory element database for Drosophila border=  
 
John Rivera; Soile V E Keränen; Steven M Gallo ; Marc S Halfon
 
 
SAGD: a comprehensive sex-associated gene database from transcriptomes border=  
 
Meng-Wei Shi; Na-An Zhang; Chuan-Ping Shi ; Chun-Jie Liu; Zhi-Hui Luo ...
 
 
Stemformatics: visualize and download curated stem cell data border= 
 
Jarny Choi; Chris M Pacheco; Rowland Mosbergen ; Othmar Korn; Tyrone Chen ...
 
 
Trips-Viz: a transcriptome browser for exploring Ribo-Seq data border= 
 
Stephen J Kiniry; Patrick B F O'Connor; Audrey M Michel ; Pavel V Baranov
 
 
The UCSC Genome Browser database: 2019 update border= 
 
Maximilian Haeussler; Ann S Zweig; Cath Tyner ; Matthew L Speir; Kate R Rosenbloom ...
 
 
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks border= 
 
Masahiko Morita ; Kazuro Shimokawa; Masaomi Nishimura; Sakiko Nakamura; Yuki Tsujimura ...
 
 
The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources border= 
 
Leyla Ruzicka ; Douglas G Howe; Sridhar Ramachandran; Sabrina Toro; Ceri E Van Slyke ...
 
 
 
Genomic variation, diseases, and drugs
 
 
 
AWESOME: a database of SNPs that affect protein post-translational modifications border= 
 
Yang Yang; Xiating Peng ; Pingting Ying; Jianbo Tian; Jiaoyuan Li ...
 
 
BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles border= 
 
Frederik Otzen Bagger ; Savvas Kinalis; Nicolas Rapin
 
 
CADD: predicting the deleteriousness of variants throughout the human genome border=  
 
Philipp Rentzsch; Daniela Witten; Gregory M Cooper ; Jay Shendure; Martin Kircher
 
 
Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets border=  
 
Mayya Sedova; Mallika Iyer; Zhanwen Li ; Lukasz Jaroszewski; Kai W Post ...
 
 
CancerSEA: a cancer single-cell state atlas border= 
 
Huating Yuan; Min Yan; Guanxiong Zhang ; Wei Liu; Chunyu Deng ...
 
 
CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer border=  
 
Jianbo Tian; Zhihua Wang; Shufang Mei ; Nan Yang; Yang Yang ...
 
 
canSAR: update to the cancer translational research and drug discovery knowledgebase border=  
 
Elizabeth A Coker; Costas Mitsopoulos; Joesph E Tym ; Angeliki Komianou; Christos Kannas ...
 
 
Cell Model Passports'a hub for clinical, genetic and functional datasets of preclinical cancer models border=  
 
Dieudonne van der Meer; Syd Barthorpe; Wanjuan Yang ; Howard Lightfoot; Caitlin Hall ...
 
 
ChEMBL: towards direct deposition of bioassay data border= 
 
David Mendez; Anna Gaulton; A Patrícia Bento ; Jon Chambers; Marleen De Veij ...
 
 
COSMIC: the Catalogue Of Somatic Mutations In Cancer border= 
 
John G Tate; Sally Bamford; Harry C Jubb ; Zbyslaw Sondka; David M Beare ...
 
 
The Comparative Toxicogenomics Database: update 2019 border= 
 
Allan Peter Davis; Cynthia J Grondin; Robin J Johnson ; Daniela Sciaky; Roy McMorran ...
 
 
Human Disease Ontology 2018 update: classification, content and workflow expansion border=  
 
Lynn M Schriml; Elvira Mitraka; James Munro ; Becky Tauber; Mike Schor ...
 
 
DrugCentral 2018: an update 
 
Oleg Ursu; Jayme Holmes; Cristian G Bologa; Jeremy J Yang ; Stephen L Mathias ...
 
 
DSMNC: a database of somatic mutations in normal cells border= 
 
Xuexia Miao; Xi Li; Lifei Wang ; Caihong Zheng; Jun Cai
 
 
ETCM: an encyclopaedia of traditional Chinese medicine border= 
 
Hai-Yu Xu; Yan-Qiong Zhang; Zhen-Ming Liu ; Tong Chen; Chuan-Yu Lv ...
 
 
EWAS Atlas: a curated knowledgebase of epigenome-wide association studies border=  
 
Mengwei Li; Dong Zou; Zhaohua Li ; Ran Gao; Jian Sang ...
 
 
EWASdb: epigenome-wide association study database border= 
 
Di liu; Linna Zhao; Zhaoyang Wang ; Xu Zhou; Xiuzhao Fan ...
 
 
FusionGDB: fusion gene annotation DataBase border= 
 
Pora Kim; Xiaobo Zhou
 
 
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 border=  
 
Annalisa Buniello; Jacqueline A L MacArthur; Maria Cerezo ; Laura W Harris; James Hayhurst ...
 
 
HMDD v3.0: a database for experimentally supported human microRNA'disease associations border=  
 
Zhou Huang; Jiangcheng Shi; Yuanxu Gao ; Chunmei Cui; Shan Zhang ...
 
 
Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers border=  
 
Yue Gao; Peng Wang; Yanxia Wang ; Xueyan Ma; Hui Zhi ...
 
 
LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases border=  
 
Zhenyu Bao; Zhen Yang; Zhou Huang ; Yiran Zhou; Qinghua Cui ...
 
 
OMIM.org: leveraging knowledge across phenotype'gene relationships border=  
 
Joanna S Amberger; Carol A Bocchini; Alan F Scott ; Ada Hamosh
 
 
OncoBase: a platform for decoding regulatory somatic mutations in human cancers border=  
 
Xianfeng Li; Leisheng Shi; Yan Wang ; Jianing Zhong; Xiaolu Zhao ...
 
 
Open Targets Platform: new developments and updates two years on border= 
 
Denise Carvalho-Silva; Andrea Pierleoni; Miguel Pignatelli ; ChuangKee Ong; Luca Fumis ...
 
 
Pancan-meQTL: a database to systematically evaluate the effects of genetic variants on methylation in human cancer border=  
 
Jing Gong; Hao Wan; Shufang Mei ; Hang Ruan; Zhao Zhang ...
 
 
PDX Finder: A portal for patient-derived tumor xenograft model discovery border=  
 
Nathalie Conte; Jeremy C Mason; Csaba Halmagyi ; Steven Neuhauser; Abayomi Mosaku ...
 
 
PopHumanScan: the online catalog of human genome adaptation border= 
 
Jesús Murga-Moreno; Marta Coronado-Zamora; Alejandra Bodelón ; Antonio Barbadilla; Sònia Casillas
 
 
PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs border= 
 
Ying Yu ; Yunjin Wang; Zhaojie Xia; Xiangyu Zhang; Kailiang Jin ...
 
 
PubChem 2019 update: improved access to chemical data 
 
Sunghwan Kim; Jie Chen; Tiejun Cheng; Asta Gindulyte ; Jia He ...
 
 
SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping border=  
 
Yang Wu; Feilong Zhang; Kuo Yang ; Shuangsang Fang; Dechao Bu ...
 
 
 
Plant databases
 
 
 
CMAUP: a database of collective molecular activities of useful plants border=  
 
Xian Zeng; Peng Zhang; Yali Wang ; Chu Qin; Shangying Chen ...
 
 
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops border=  
 
Yi Zheng; Shan Wu; Yang Bai ; Honghe Sun; Chen Jiao ...
 
 
15 years of GDR: New data and functionality in the Genome Database for Rosaceae 
 
Sook Jung; Taein Lee; Chun-Huai Cheng; Katheryn Buble ; Ping Zheng ...
 
 
MaizeGDB 2018: the maize multi-genome genetics and genomics database 
 
John L Portwood, II; Margaret R Woodhouse; Ethalinda K Cannon; Jack M Gardiner ; Lisa C Harper ...
 
 
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants border= 
 
Chi-Nga Chow ; Tzong-Yi Lee; Yu-Cheng Hung; Guan-Zhen Li; Kuan-Chieh Tseng ...
 
 
 
Other databases
 
 
 
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation border= 
 
Patrick V Phaneuf; Dennis Gosting ; Bernhard O Palsson; Adam M Feist
 
 
BioSamples database: an updated sample metadata hub border= 
 
Mélanie Courtot; Luca Cherubin; Adam Faulconbridge ; Daniel Vaughan; Matthew Green ...
 
 
BitterDB: taste ligands and receptors database in 2019 border= 
 
Ayana Dagan-Wiener; Antonella Di Pizio; Ido Nissim ; Malkeet S Bahia; Nitzan Dubovski ...
 
 
ECO, the Evidence & Conclusion Ontology: community standard for evidence information border=  
 
Michelle Giglio; Rebecca Tauber; Suvarna Nadendla ; James Munro; Dustin Olley ...
 
 
Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update) border=  
 
Michael Böhm; Andreas Bohne-Lang; Martin Frank ; Alexander Loss; Miguel A Rojas-Macias ...
 
 
HmtVar: a new resource for human mitochondrial variations and pathogenicity data border=  
 
Roberto Preste; Ornella Vitale; Rosanna Clima ; Giuseppe Gasparre; Marcella Attimonelli
 
 
iProX: an integrated proteome resource border= 
 
Jie Ma; Tao Chen; Songfeng Wu; Chunyuan Yang; Mingze Bai ...
 
 
The jPOST environment: an integrated proteomics data repository and database border=  
 
Yuki Moriya; Shin Kawano; Shujiro Okuda ; Yu Watanabe; Masaki Matsumoto ...
 
 
MitoMiner v4.0: an updated database of mitochondrial localization evidence, phenotypes and diseases border=  
 
Anthony C Smith; Alan J Robinson
 
 
RetroRules: a database of reaction rules for engineering biology border= 
 
Thomas Duigou; Melchior du Lac; Pablo Carbonell ; Jean-Loup Faulon
 
 
UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands border= 
 
François Bonnardel ; Julien Mariethoz; Sebastian Salentin; Xavier Robin; Michael Schroeder ...
 
 
YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries border=  
 
Benjamin Dubreuil; Ehud Sass; Yotam Nadav ; Meta Heidenreich; Joseph M Georgeson ...
 
 
 
Corrigendum
 
 
 
RNAcentral: a hub of information for non-coding RNA sequences border=  
 
Blake A Sweeney; Anton I Petrov; Boris Burkov ; Robert D Finn; Alex Bateman ...
 
 
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