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Nucleic 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
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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
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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