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Articles
Guy R. Cochrane and Michael Y. Galperin
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources
Nucleic Acids Research Advance Access published on December 3, 2009
Nucl. Acids Res. 2010 38: D1-D4; doi:10.1093/nar/gkp1077 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Database Summaries]
Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna Panchenko, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, and Jian Ye
Database resources of the National Center for Biotechnology Information
Nucleic Acids Research Advance Access published on November 12, 2009
Nucl. Acids Res. 2010 38: D5-D16; doi:10.1093/nar/gkp967 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Catherine Brooksbank, Graham Cameron, and Janet Thornton
The European Bioinformatics Institute’s data resources
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: D17-D25; doi:10.1093/nar/gkp986 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Yukiko Yamazaki, Ryo Akashi, Yutaka Banno, Takashi Endo, Hiroshi Ezura, Kaoru Fukami-Kobayashi, Kazuo Inaba, Tadashi Isa, Katsuhiko Kamei, Fumie Kasai, Masatomo Kobayashi, Nori Kurata, Makoto Kusaba, Tetsuro Matuzawa, Shohei Mitani, Taro Nakamura, Yukio Nakamura, Norio Nakatsuji, Kiyoshi Naruse, Hironori Niki, Eiji Nitasaka, Yuichi Obata, Hitoshi Okamoto, Moriya Okuma, Kazuhiro Sato, Tadao Serikawa, Toshihiko Shiroishi, Hideaki Sugawara, Hideko Urushibara, Masatoshi Yamamoto, Yoshio Yaoita, Atsushi Yoshiki, and Yuji Kohara
NBRP databases: databases of biological resources in Japan
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: D26-D32; doi:10.1093/nar/gkp996 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, and Yasukazu Nakamura
DDBJ launches a new archive database with analytical tools for next-generation sequence data
Nucleic Acids Research Advance Access published on October 22, 2009
Nucl. Acids Res. 2010 38: D33-D38; doi:10.1093/nar/gkp847 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Rasko Leinonen, Ruth Akhtar, Ewan Birney, James Bonfield, Lawrence Bower, Matt Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra Ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel Zerbino, and Guy Cochrane
Improvements to services at the European Nucleotide Archive
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D39-D45; doi:10.1093/nar/gkp998 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and Eric W. Sayers
GenBank
Nucleic Acids Research Advance Access published on November 12, 2009
Nucl. Acids Res. 2010 38: D46-D51; doi:10.1093/nar/gkp1024 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Weizhong Li, Hamish McWilliam, Ana Richart de la Torre, Adam Grodowski, Irina Benediktovich, Mickael Goujon, Stephane Nauche, and Rodrigo Lopez
Non-redundant patent sequence databases with value-added annotations at two levels
Nucleic Acids Research Advance Access published on November 1, 2009
Nucl. Acids Res. 2010 38: D52-D56; doi:10.1093/nar/gkp960 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Raphaël Leplae, Gipsi Lima-Mendez, and Ariane Toussaint
ACLAME: A CLAssification of Mobile genetic Elements, update 2010
Nucleic Acids Research Advance Access published on November 23, 2009
Nucl. Acids Res. 2010 38: D57-D61; doi:10.1093/nar/gkp938 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Pryavahiny Kichenaradja, Patricia Siguier, Jocelyne Pérochon, and Michael Chandler
ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D62-D68; doi:10.1093/nar/gkp947 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Michaël Bekaert, Andrew E. Firth, Yan Zhang, Vadim N. Gladyshev, John F. Atkins, and Pavel V. Baranov
Recode-2: new design, new search tools, and many more genes
Nucleic Acids Research Advance Access published on September 25, 2009
Nucl. Acids Res. 2010 38: D69-D74; doi:10.1093/nar/gkp788 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Giorgio Grillo, Antonio Turi, Flavio Licciulli, Flavio Mignone, Sabino Liuni, Sandro Banfi, Vincenzo Alessandro Gennarino, David S. Horner, Giulio Pavesi, Ernesto Picardi, and Graziano Pesole
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
Nucleic Acids Research Advance Access published on October 30, 2009
Nucl. Acids Res. 2010 38: D75-D80; doi:10.1093/nar/gkp902 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Pora Kim, Suhyeon Yoon, Namshin Kim, Sanghyun Lee, Minjeong Ko, Haeseung Lee, Hyunjung Kang, Jaesang Kim, and Sanghyuk Lee
ChimerDB 2.0—a knowledgebase for fusion genes updated
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D81-D85; doi:10.1093/nar/gkp982 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Takashi Gojobori, Tadashi Imanishi, and Sumio Sugano
H-DBAS: human-transcriptome database for alternative splicing: update 2010
Nucleic Acids Research Advance Access published on December 7, 2009
Nucl. Acids Res. 2010 38: D86-D90; doi:10.1093/nar/gkp984 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Bruno Contreras-Moreira
3D-footprint: a database for the structural analysis of protein–DNA complexes
Nucleic Acids Research Advance Access published on September 18, 2009
Nucl. Acids Res. 2010 38: D91-D97; doi:10.1093/nar/gkp781 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai
DBTSS provides a tissue specific dynamic view of Transcription Start Sites
Nucleic Acids Research Advance Access published on November 12, 2009
Nucl. Acids Res. 2010 38: D98-D104; doi:10.1093/nar/gkp1017 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, and Albin Sandelin
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D105-D110; doi:10.1093/nar/gkp950 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, and Dmitry A. Rodionov
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
Nucleic Acids Research Advance Access published on November 1, 2009
Nucl. Acids Res. 2010 38: D111-D118; doi:10.1093/nar/gkp894 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Juan Wang, Ming Lu, Chengxiang Qiu, and Qinghua Cui
TransmiR: a transcription factor–microRNA regulation database
Nucleic Acids Research Advance Access published on September 28, 2009
Nucl. Acids Res. 2010 38: D119-D122; doi:10.1093/nar/gkp803 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Jian-Hua Yang, Peng Shao, Hui Zhou, Yue-Qin Chen, and Liang-Hu Qu
deepBase: a database for deeply annotating and mining deep sequencing data
Nucleic Acids Research Advance Access published on December 4, 2009
Nucl. Acids Res. 2010 38: D123-D130; doi:10.1093/nar/gkp943 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Martin Mokrejs, Tomás Masek, Václav Vopálensky, Petr Hlubucek, Philippe Delbos, and Martin Pospísek
IRESite—a tool for the examination of viral and cellular internal ribosome entry sites
Nucleic Acids Research Advance Access published on November 16, 2009
Nucl. Acids Res. 2010 38: D131-D136; doi:10.1093/nar/gkp981 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Panagiotis Alexiou, Thanasis Vergoulis, Martin Gleditzsch, George Prekas, Theodore Dalamagas, Molly Megraw, Ivo Grosse, Timos Sellis, and Artemis G. Hatzigeorgiou
miRGen 2.0: a database of microRNA genomic information and regulation
Nucleic Acids Research Advance Access published on October 22, 2009
Nucl. Acids Res. 2010 38: D137-D141; doi:10.1093/nar/gkp888 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
The UniProt Consortium
The Universal Protein Resource (UniProt) in 2010
Nucleic Acids Research Advance Access published on October 20, 2009
Nucl. Acids Res. 2010 38: D142-D148; doi:10.1093/nar/gkp846 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Yan Zhang, Jie Lv, Hongbo Liu, Jiang Zhu, Jianzhong Su, Qiong Wu, Yunfeng Qi, Fang Wang, and Xia Li
HHMD: the human histone modification database
Nucleic Acids Research Advance Access published on November 5, 2009
Nucl. Acids Res. 2010 38: D149-D154; doi:10.1093/nar/gkp968 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Jian Ren, Zexian Liu, Xinjiao Gao, Changjiang Jin, Mingliang Ye, Hanfa Zou, Longping Wen, Zhaolei Zhang, Yu Xue, and Xuebiao Yao
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore
Nucleic Acids Research Advance Access published on September 25, 2009
Nucl. Acids Res. 2010 38: D155-D160; doi:10.1093/nar/gkp784 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Christian J. A. Sigrist, Lorenzo Cerutti, Edouard de Castro, Petra S. Langendijk-Genevaux, Virginie Bulliard, Amos Bairoch, and Nicolas Hulo
PROSITE, a protein domain database for functional characterization and annotation
Nucleic Acids Research Advance Access published on October 25, 2009
Nucl. Acids Res. 2010 38: D161-D166; doi:10.1093/nar/gkp885 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Cathryn M. Gould, Francesca Diella, Allegra Via, Pål Puntervoll, Christine Gemünd, Sophie Chabanis-Davidson, Sushama Michael, Ahmed Sayadi, Jan Christian Bryne, Claudia Chica, Markus Seiler, Norman E. Davey, Niall Haslam, Robert J. Weatheritt, Aidan Budd, Tim Hughes, Jakub Pas, Leszek Rychlewski, Gilles Travé, Rein Aasland, Manuela Helmer-Citterich, Rune Linding, and Toby J. Gibson
ELM: the status of the 2010 eukaryotic linear motif resource
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: D167-D180; doi:10.1093/nar/gkp1016 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Annalisa Marsico, Kerstin Scheubert, Anne Tuukkanen, Andreas Henschel, Christof Winter, Rainer Winnenburg, and Michael Schroeder
MeMotif: a database of linear motifs in -helical transmembrane proteins Nucleic Acids Research Advance Access published on November 12, 2009
Nucl. Acids Res. 2010 38: D181-D189; doi:10.1093/nar/gkp1042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
J. Muller, D. Szklarczyk, P. Julien, I. Letunic, A. Roth, M. Kuhn, S. Powell, C. von Mering, T. Doerks, L. J. Jensen, and P. Bork
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
Nucleic Acids Research Advance Access published on November 9, 2009
Nucl. Acids Res. 2010 38: D190-D195; doi:10.1093/nar/gkp951 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, and Erik L. L. Sonnhammer
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
Nucleic Acids Research Advance Access published on November 5, 2009
Nucl. Acids Res. 2010 38: D196-D203; doi:10.1093/nar/gkp931 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Huaiyu Mi, Qing Dong, Anushya Muruganujan, Pascale Gaudet, Suzanna Lewis, and Paul D. Thomas
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
Nucleic Acids Research Advance Access published on December 16, 2009
Nucl. Acids Res. 2010 38: D204-D210; doi:10.1093/nar/gkp1019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Robert D. Finn, Jaina Mistry, John Tate, Penny Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, and Alex Bateman
The Pfam protein families database
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: D211-D222; doi:10.1093/nar/gkp985 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Thomas Rattei, Patrick Tischler, Stefan Götz, Marc-André Jehl, Jonathan Hoser, Roland Arnold, Ana Conesa, and Hans-Werner Mewes
SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D223-D226; doi:10.1093/nar/gkp949 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Neil D. Rawlings, Alan J. Barrett, and Alex Bateman
MEROPS: the peptidase database
Nucleic Acids Research Advance Access published on November 5, 2009
Nucl. Acids Res. 2010 38: D227-D233; doi:10.1093/nar/gkp971 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
Nucleic Acids Research Advance Access published on October 21, 2009
Nucl. Acids Res. 2010 38: D234-D236; doi:10.1093/nar/gkp874 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Saskia Preissner, Katharina Kroll, Mathias Dunkel, Christian Senger, Gady Goldsobel, Daniel Kuzman, Stefan Guenther, Rainer Winnenburg, Michael Schroeder, and Robert Preissner
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: D237-D243; doi:10.1093/nar/gkp970 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Andreas Schlicker and Mario Albrecht
FunSimMat update: new features for exploring functional similarity
Nucleic Acids Research Advance Access published on November 18, 2009
Nucl. Acids Res. 2010 38: D244-D248; doi:10.1093/nar/gkp979 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Paula de Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, and Christoph Steinbeck
Chemical Entities of Biological Interest: an update
Nucleic Acids Research Advance Access published on October 23, 2009
Nucl. Acids Res. 2010 38: D249-D254; doi:10.1093/nar/gkp886 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Yanli Wang, Evan Bolton, Svetlana Dracheva, Karen Karapetyan, Benjamin A. Shoemaker, Tugba O. Suzek, Jiyao Wang, Jewen Xiao, Jian Zhang, and Stephen H. Bryant
An overview of the PubChem BioAssay resource
Nucleic Acids Research Advance Access published on November 19, 2009
Nucl. Acids Res. 2010 38: D255-D266; doi:10.1093/nar/gkp965 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Guohui Zheng, Andrew V. Colasanti, Xiang-Jun Lu, and Wilma K. Olson
3DNALandscapes: a database for exploring the conformational features of DNA
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D267-D274; doi:10.1093/nar/gkp959 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Christian Koetschan, Frank Förster, Alexander Keller, Tina Schleicher, Benjamin Ruderisch, Roland Schwarz, Tobias Müller, Matthias Wolf, and Jörg Schultz
The ITS2 Database III—sequences and structures for phylogeny
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: D275-D279; doi:10.1093/nar/gkp966 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Douglas H. Turner and David H. Mathews
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
Nucleic Acids Research Advance Access published on October 30, 2009
Nucl. Acids Res. 2010 38: D280-D282; doi:10.1093/nar/gkp892 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, and Oxana V. Galzitskaya
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D283-D287; doi:10.1093/nar/gkp963 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Yan Yuan Tseng, Z. Jeffrey Chen, and Wen-Hsiung Li
fPOP: footprinting functional pockets of proteins by comparative spatial patterns
Nucleic Acids Research Advance Access published on October 30, 2009
Nucl. Acids Res. 2010 38: D288-D295; doi:10.1093/nar/gkp900 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Jonathan Lees, Corin Yeats, Oliver Redfern, Andrew Clegg, and Christine Orengo
Gene3D: merging structure and function for a Thousand genomes
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D296-D300; doi:10.1093/nar/gkp987 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
François Ehrenmann, Quentin Kaas, and Marie-Paule Lefranc
IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF
Nucleic Acids Research Advance Access published on November 9, 2009
Nucl. Acids Res. 2010 38: D301-D307; doi:10.1093/nar/gkp946 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman, T. Oldfield, A. Pajon, C. J. Penkett, J. Pineda-Castillo, G. Sahni, S. Sen, R. Slowley, A. Suarez-Uruena, J. Swaminathan, G. van Ginkel, W. F. Vranken, K. Henrick, and G. J. Kleywegt
PDBe: Protein Data Bank in Europe
Nucleic Acids Research Advance Access published on October 25, 2009
Nucl. Acids Res. 2010 38: D308-D317; doi:10.1093/nar/gkp916 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Sven Griep and Uwe Hobohm
PDBselect 1992–2009 and PDBfilter-select
Nucleic Acids Research Advance Access published on September 25, 2009
Nucl. Acids Res. 2010 38: D318-D319; doi:10.1093/nar/gkp786 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Donald S. Berkholz, Peter B. Krenesky, John R. Davidson, and P. Andrew Karplus
Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D320-D325; doi:10.1093/nar/gkp1013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Patrick May, Annika Kreuchwig, Thomas Steinke, and Ina Koch
PTGL: a database for secondary structure-based protein topologies
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D326-D330; doi:10.1093/nar/gkp980 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
The Gene Ontology Consortium
The Gene Ontology in 2010: extensions and refinements
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: D331-D335; doi:10.1093/nar/gkp1018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Johannes Goll, Robert Montgomery, Lauren M. Brinkac, Seth Schobel, Derek M. Harkins, Yinong Sebastian, Susmita Shrivastava, Scott Durkin, and Granger Sutton
The Protein Naming Utility: a rules database for protein nomenclature
Nucleic Acids Research Advance Access published on December 8, 2009
Nucl. Acids Res. 2010 38: D336-D339; doi:10.1093/nar/gkp958 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Tanja Davidsen, Erin Beck, Anuradha Ganapathy, Robert Montgomery, Nikhat Zafar, Qi Yang, Ramana Madupu, Phil Goetz, Kevin Galinsky, Owen White, and Granger Sutton
The comprehensive microbial resource
Nucleic Acids Research Advance Access published on November 5, 2009
Nucl. Acids Res. 2010 38: D340-D345; doi:10.1093/nar/gkp912 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Konstantinos Liolios, I-Min A. Chen, Konstantinos Mavromatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, and Nikos C. Kyrpides
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
Nucleic Acids Research Advance Access published on November 13, 2009
Nucl. Acids Res. 2010 38: D346-D354; doi:10.1093/nar/gkp848 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Minoru Kanehisa, Susumu Goto, Miho Furumichi, Mao Tanabe, and Mika Hirakawa
KEGG for representation and analysis of molecular networks involving diseases and drugs
Nucleic Acids Research Advance Access published on October 30, 2009
Nucl. Acids Res. 2010 38: D355-D360; doi:10.1093/nar/gkp896 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Ikuo Uchiyama, Toshio Higuchi, and Mikihiko Kawai
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D361-D365; doi:10.1093/nar/gkp948 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Lubos Klucar, Matej Stano, and Matus Hajduk
phiSITE: database of gene regulation in bacteriophages
Nucleic Acids Research Advance Access published on November 9, 2009
Nucl. Acids Res. 2010 38: D366-D370; doi:10.1093/nar/gkp911 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
J. Pellet, L. Tafforeau, M. Lucas-Hourani, V. Navratil, L. Meyniel, G. Achaz, A. Guironnet-Paquet, A. Aublin-Gex, G. Caignard, P. Cassonnet, A. Chaboud, T. Chantier, A. Deloire, C. Demeret, M. Le Breton, G. Neveu, L. Jacotot, P. Vaglio, S. Delmotte, C. Gautier, C. Combet, G. Deleage, M. Favre, F. Tangy, Y. Jacob, P. Andre, V. Lotteau, C. Rabourdin-Combe, and P. O. Vidalain
ViralORFeome: an integrated database to generate a versatile collection of viral ORFs
Nucleic Acids Research Advance Access published on December 8, 2009
Nucl. Acids Res. 2010 38: D371-D378; doi:10.1093/nar/gkp1000 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Mitsuteru Nakao, Shinobu Okamoto, Mitsuyo Kohara, Tsunakazu Fujishiro, Takatomo Fujisawa, Shusei Sato, Satoshi Tabata, Takakazu Kaneko, and Yasukazu Nakamura
CyanoBase: the cyanobacteria genome database update 2010
Nucleic Acids Research Advance Access published on October 30, 2009
Nucl. Acids Res. 2010 38: D379-D381; doi:10.1093/nar/gkp915 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova, and Nikos C. Kyrpides
The integrated microbial genomes system: an expanding comparative analysis resource
Nucleic Acids Research Advance Access published on October 28, 2009
Nucl. Acids Res. 2010 38: D382-D390; doi:10.1093/nar/gkp887 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Renzo Kottmann, Ivalyo Kostadinov, Melissa Beth Duhaime, Pier Luigi Buttigieg, Pelin Yilmaz, Wolfgang Hankeln, Jost Waldmann, and Frank Oliver Glöckner
Megx.net: integrated database resource for marine ecological genomics
Nucleic Acids Research Advance Access published on October 25, 2009
Nucl. Acids Res. 2010 38: D391-D395; doi:10.1093/nar/gkp918 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Paramvir S. Dehal, Marcin P. Joachimiak, Morgan N. Price, John T. Bates, Jason K. Baumohl, Dylan Chivian, Greg D. Friedland, Katherine H. Huang, Keith Keller, Pavel S. Novichkov, Inna L. Dubchak, Eric J. Alm, and Adam P. Arkin
MicrobesOnline: an integrated portal for comparative and functional genomics
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D396-D400; doi:10.1093/nar/gkp919 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Luke E. Ulrich and Igor B. Zhulin
The MiST2 database: a comprehensive genomics resource on microbial signal transduction
Nucleic Acids Research Advance Access published on November 9, 2009
Nucl. Acids Res. 2010 38: D401-D407; doi:10.1093/nar/gkp940 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Lauren M. Brinkac, Tanja Davidsen, Erin Beck, Anuradha Ganapathy, Elisabet Caler, Robert J. Dodson, A. Scott Durkin, Derek M. Harkins, Hernan Lorenzi, Ramana Madupu, Yinong Sebastian, Susmita Shrivastava, Mathangi Thiagarajan, Joshua Orvis, Jaideep P. Sundaram, Jonathon Crabtree, Kevin Galens, Yongmei Zhao, Jason M. Inman, Robert Montgomery, Seth Schobel, Kevin Galinsky, David M. Tanenbaum, Adam Resnick, Nikhat Zafar, Owen White, and Granger Sutton
Pathema: a clade-specific bioinformatics resource center for pathogen research
Nucleic Acids Research Advance Access published on October 20, 2009
Nucl. Acids Res. 2010 38: D408-D414; doi:10.1093/nar/gkp850 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen T. Kraemer, Wei Li, John A. Miller, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Ganesh Srinivasamoorthy, Christian J. Stoeckert, Jr, Ryan Thibodeau, Charles Treatman, and Haiming Wang
EuPathDB: a portal to eukaryotic pathogen databases
Nucleic Acids Research Advance Access published on November 13, 2009
Nucl. Acids Res. 2010 38: D415-D419; doi:10.1093/nar/gkp941 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Martha B. Arnaud, Marcus C. Chibucos, Maria C. Costanzo, Jonathan Crabtree, Diane O. Inglis, Adil Lotia, Joshua Orvis, Prachi Shah, Marek S. Skrzypek, Gail Binkley, Stuart R. Miyasato, Jennifer R. Wortman, and Gavin Sherlock
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community
Nucleic Acids Research Advance Access published on September 22, 2009
Nucl. Acids Res. 2010 38: D420-D427; doi:10.1093/nar/gkp751 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Marek S. Skrzypek, Martha B. Arnaud, Maria C. Costanzo, Diane O. Inglis, Prachi Shah, Gail Binkley, Stuart R. Miyasato, and Gavin Sherlock
New tools at the Candida Genome Database: biochemical pathways and full-text literature search
Nucleic Acids Research Advance Access published on October 6, 2009
Nucl. Acids Res. 2010 38: D428-D432; doi:10.1093/nar/gkp836 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Stacia R. Engel, Rama Balakrishnan, Gail Binkley, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Eurie L. Hong, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert Nash, Rose Oughtred, Julie Park, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kara Dolinski, David Botstein, and J. Michael Cherry
Saccharomyces Genome Database provides mutant phenotype data
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D433-D436; doi:10.1093/nar/gkp917 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Hee Shin Kim, Terence Murphy, Jing Xia, Doina Caragea, Yoonseong Park, Richard W. Beeman, Marcé D. Lorenzen, Stephen Butcher, J. Robert Manak, and Susan J. Brown
BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum
Nucleic Acids Research Advance Access published on October 9, 2009
Nucl. Acids Res. 2010 38: D437-D442; doi:10.1093/nar/gkp807 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Ulrike Pfreundt, Daniel P. James, Susan Tweedie, Derek Wilson, Sarah A. Teichmann, and Boris Adryan
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database
Nucleic Acids Research Advance Access published on November 1, 2009
Nucl. Acids Res. 2010 38: D443-D447; doi:10.1093/nar/gkp910 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Moritz Gilsdorf, Thomas Horn, Zeynep Arziman, Oliver Pelz, Evgeny Kiner, and Michael Boutros
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update
Nucleic Acids Research Advance Access published on November 12, 2009
Nucl. Acids Res. 2010 38: D448-D452; doi:10.1093/nar/gkp1038 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Jun Duan, Ruiqiang Li, Daojun Cheng, Wei Fan, Xingfu Zha, Tingcai Cheng, Yuqian Wu, Jun Wang, Kazuei Mita, Zhonghuai Xiang, and Qingyou Xia
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology
Nucleic Acids Research Advance Access published on September 30, 2009
Nucl. Acids Res. 2010 38: D453-D456; doi:10.1093/nar/gkp801 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Martin Aslett, Cristina Aurrecoechea, Matthew Berriman, John Brestelli, Brian P. Brunk, Mark Carrington, Daniel P. Depledge, Steve Fischer, Bindu Gajria, Xin Gao, Malcolm J. Gardner, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Robin Houston, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, Flora J. Logan, John A. Miller, Siddhartha Mitra, Peter J. Myler, Vishal Nayak, Cary Pennington, Isabelle Phan, Deborah F. Pinney, Gowthaman Ramasamy, Matthew B. Rogers, David S. Roos, Chris Ross, Dhileep Sivam, Deborah F. Smith, Ganesh Srinivasamoorthy, Christian J. Stoeckert, Jr, Sandhya Subramanian, Ryan Thibodeau, Adrian Tivey, Charles Treatman, Giles Velarde, and Haiming Wang
TriTrypDB: a functional genomic resource for the Trypanosomatidae
Nucleic Acids Research Advance Access published on October 20, 2009
Nucl. Acids Res. 2010 38: D457-D462; doi:10.1093/nar/gkp851 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Todd W. Harris, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Juancarlos Chan, Wen J. Chen, Norie De La Cruz, Paul Davis, Margaret Duesbury, Ruihua Fang, Jolene Fernandes, Michael Han, Ranjana Kishore, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, and Paul W. Sternberg
WormBase: a comprehensive resource for nematode research
Nucleic Acids Research Advance Access published on November 12, 2009
Nucl. Acids Res. 2010 38: D463-D467; doi:10.1093/nar/gkp952 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Vineet K. Sharma, Naveen Kumar, Tulika Prakash, and Todd D. Taylor
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D468-D472; doi:10.1093/nar/gkp1001 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Suzanne Paley, Liviu Popescu, Anuradha Pujar, Alexander G. Shearer, Peifen Zhang, and Peter D. Karp
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Nucleic Acids Research Advance Access published on October 22, 2009
Nucl. Acids Res. 2010 38: D473-D479; doi:10.1093/nar/gkp875 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Alex Frolkis, Craig Knox, Emilia Lim, Timothy Jewison, Vivian Law, David D. Hau, Phillip Liu, Bijaya Gautam, Son Ly, An Chi Guo, Jianguo Xia, Yongjie Liang, Savita Shrivastava, and David S. Wishart
SMPDB: The Small Molecule Pathway Database
Nucleic Acids Research Advance Access published on November 30, 2009
Nucl. Acids Res. 2010 38: D480-D487; doi:10.1093/nar/gkp1002 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Junfeng Gao, Lynda B. M. Ellis, and Lawrence P. Wackett
The University of Minnesota Biocatalysis/Biodegradation Database: improving public access
Nucleic Acids Research Advance Access published on September 18, 2009
Nucl. Acids Res. 2010 38: D488-D491; doi:10.1093/nar/gkp771 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Lewis Y. Geer, Aron Marchler-Bauer, Renata C. Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, and Stephen H. Bryant
The NCBI BioSystems database
Nucleic Acids Research Advance Access published on October 23, 2009
Nucl. Acids Res. 2010 38: D492-D496; doi:10.1093/nar/gkp858 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Andreas Ruepp, Brigitte Waegele, Martin Lechner, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, and H.-Werner Mewes
CORUM: the comprehensive resource of mammalian protein complexes—2009
Nucleic Acids Research Advance Access published on November 1, 2009
Nucl. Acids Res. 2010 38: D497-D501; doi:10.1093/nar/gkp914 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Judice L. Y. Koh, Huiming Ding, Michael Costanzo, Anastasia Baryshnikova, Kiana Toufighi, Gary D. Bader, Chad L. Myers, Brenda J. Andrews, and Charles Boone
DRYGIN: a database of quantitative genetic interaction networks in yeast
Nucleic Acids Research Advance Access published on October 30, 2009
Nucl. Acids Res. 2010 38: D502-D507; doi:10.1093/nar/gkp820 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Milana Frenkel-Morgenstern, Ariel A. Cohen, Naama Geva-Zatorsky, Eran Eden, Jaime Prilusky, Irina Issaeva, Alex Sigal, Cellina Cohen-Saidon, Yuvalal Liron, Lydia Cohen, Tamar Danon, Natalie Perzov, and Uri Alon
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells
Nucleic Acids Research Advance Access published on October 9, 2009
Nucl. Acids Res. 2010 38: D508-D512; doi:10.1093/nar/gkp808 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Petras J. Kundrotas, Zhengwei Zhu, and Ilya A. Vakser
GWIDD: Genome-wide protein docking database
Nucleic Acids Research Advance Access published on November 9, 2009
Nucl. Acids Res. 2010 38: D513-D517; doi:10.1093/nar/gkp944 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, and Anna R. Panchenko
Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites
Nucleic Acids Research Advance Access published on October 20, 2009
Nucl. Acids Res. 2010 38: D518-D524; doi:10.1093/nar/gkp842 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
B. Aranda, P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann, A. T. Ghanbarian, S. Kerrien, J. Khadake, J. Kerssemakers, C. Leroy, M. Menden, M. Michaut, L. Montecchi-Palazzi, S. N. Neuhauser, S. Orchard, V. Perreau, B. Roechert, K. van Eijk, and H. Hermjakob
The IntAct molecular interaction database in 2010
Nucleic Acids Research Advance Access published on October 22, 2009
Nucl. Acids Res. 2010 38: D525-D531; doi:10.1093/nar/gkp878 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Arnaud Ceol, Andrew Chatr Aryamontri, Luana Licata, Daniele Peluso, Leonardo Briganti, Livia Perfetto, Luisa Castagnoli, and Gianni Cesareni
MINT, the molecular interaction database: 2009 update
Nucleic Acids Research Advance Access published on November 6, 2009
Nucl. Acids Res. 2010 38: D532-D539; doi:10.1093/nar/gkp983 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman, and Andreas Ruepp
The Negatome database: a reference set of non-interacting protein pairs
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: D540-D544; doi:10.1093/nar/gkp1026 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Peter Vanhee, Joke Reumers, Francois Stricher, Lies Baeten, Luis Serrano, Joost Schymkowitz, and Frederic Rousseau
PepX: a structural database of non-redundant protein–peptide complexes
Nucleic Acids Research Advance Access published on October 30, 2009
Nucl. Acids Res. 2010 38: D545-D551; doi:10.1093/nar/gkp893 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Monica Campillos, Christian von Mering, Lars Juhl Jensen, Andreas Beyer, and Peer Bork
STITCH 2: an interaction network database for small molecules and proteins
Nucleic Acids Research Advance Access published on November 6, 2009
Nucl. Acids Res. 2010 38: D552-D556; doi:10.1093/nar/gkp937 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Paul Flicek, Bronwen L. Aken, Benoit Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William McLaren, Karine Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y. Amy Tang, Stephen Trevanion, Albert Vilella, Jan Vogel, Simon White, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suarez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, James Smith, and Stephen M. J. Searle
Ensembl’s 10th year
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D557-D562; doi:10.1093/nar/gkp972 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
P. J. Kersey, D. Lawson, E. Birney, P. S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Kähäri, R. J. Kinsella, E. Kulesha, U. Maheswari, K. Megy, M. Nuhn, G. Proctor, D. Staines, F. Valentin, A. J. Vilella, and A. Yates
Ensembl Genomes: Extending Ensembl across the taxonomic space
Nucleic Acids Research Advance Access published on November 1, 2009
Nucl. Acids Res. 2010 38: D563-D569; doi:10.1093/nar/gkp871 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Phil Wilkinson, Jitka Sengerova, Raffaele Matteoni, Chao-Kung Chen, Gaetan Soulat, Abel Ureta-Vidal, Sabine Fessele, Michael Hagn, Marzia Massimi, Karen Pickford, Richard H. Butler, Susan Marschall, Ann-Marie Mallon, Amanda Pickard, Marcello Raspa, Ferdinando Scavizzi, Martin Fray, Vanessa Larrigaldie, Johan Leyritz, Ewan Birney, Glauco P. Tocchini-Valentini, Steve Brown, Yann Herault, Lluis Montoliu, Martin Hrabé de Angelis, and Damian Smedley
EMMA—mouse mutant resources for the international scientific community
Nucleic Acids Research Advance Access published on September 26, 2009
Nucl. Acids Res. 2010 38: D570-D576; doi:10.1093/nar/gkp799 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Hugh Morgan, Tim Beck, Andrew Blake, Hilary Gates, Niels Adams, Guillaume Debouzy, Sophie Leblanc, Christoph Lengger, Holger Maier, David Melvin, Hamid Meziane, Dave Richardson, Sara Wells, Jacqui White, Joe Wood, The EUMODIC Consortium, Martin Hrabé de Angelis, Steve D. M. Brown, John M. Hancock, and Ann-Marie Mallon
EuroPhenome: a repository for high-throughput mouse phenotyping data
Nucleic Acids Research Advance Access published on November 23, 2009
Nucl. Acids Res. 2010 38: D577-D585; doi:10.1093/nar/gkp1007 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, Janan T Eppig, and the Mouse Genome Database Group
The Mouse Genome Database: enhancements and updates
Nucleic Acids Research Advance Access published on October 27, 2009
Nucl. Acids Res. 2010 38: D586-D592; doi:10.1093/nar/gkp880 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Andrew Blake, Karen Pickford, Simon Greenaway, Steve Thomas, Amanda Pickard, Christine M. Williamson, Niels C. Adams, Alison Walling, Tim Beck, Martin Fray, Jo Peters, Tom Weaver, Steve D. M. Brown, John M. Hancock, and Ann-Marie Mallon
MouseBook: an integrated portal of mouse resources
Nucleic Acids Research Advance Access published on October 23, 2009
Nucl. Acids Res. 2010 38: D593-D599; doi:10.1093/nar/gkp867 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Keiko Akagi, Robert M. Stephens, Jingfeng Li, Evgenji Evdokimov, Michael R. Kuehn, Natalia Volfovsky, and David E. Symer
MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains
Nucleic Acids Research Advance Access published on November 20, 2009
Nucl. Acids Res. 2010 38: D600-D606; doi:10.1093/nar/gkp1046 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Chris J. Jarabek, Kenan Azam, Aaron M. Zorn, and Peter D. Vize
Xenbase: gene expression and improved integration
Nucleic Acids Research Advance Access published on November 1, 2009
Nucl. Acids Res. 2010 38: D607-D612; doi:10.1093/nar/gkp953 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Brooke Rhead, Donna Karolchik, Robert M. Kuhn, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Mark Diekhans, Kayla E. Smith, Kate R. Rosenbloom, Brian J. Raney, Andy Pohl, Michael Pheasant, Laurence R. Meyer, Katrina Learned, Fan Hsu, Jennifer Hillman-Jackson, Rachel A. Harte, Belinda Giardine, Timothy R. Dreszer, Hiram Clawson, Galt P. Barber, David Haussler, and W. James Kent
The UCSC Genome Browser database: update 2010
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D613-D619; doi:10.1093/nar/gkp939 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Kate R. Rosenbloom, Timothy R. Dreszer, Michael Pheasant, Galt P. Barber, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Ting Wang, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Katrina Learned, Brooke Rhead, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, David Haussler, and W. James Kent
ENCODE whole-genome data in the UCSC Genome Browser
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: D620-D625; doi:10.1093/nar/gkp961 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Chisato Yamasaki, Katsuhiko Murakami, Jun-ichi Takeda, Yoshiharu Sato, Akiko Noda, Ryuichi Sakate, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Akihiro Matsuya, Tadashi Imanishi, and Takashi Gojobori
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts
Nucleic Acids Research Advance Access published on November 23, 2009
Nucl. Acids Res. 2010 38: D626-D632; doi:10.1093/nar/gkp1020 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Jon W. Huss, III, Pierre Lindenbaum, Michael Martone, Donabel Roberts, Angel Pizarro, Faramarz Valafar, John B. Hogenesch, and Andrew I. Su
The Gene Wiki: community intelligence applied to human gene annotation
Nucleic Acids Research Advance Access published on September 15, 2009
Nucl. Acids Res. 2010 38: D633-D639; doi:10.1093/nar/gkp760 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Samuel Hiard, Carole Charlier, Wouter Coppieters, Michel Georges, and Denis Baurain
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D640-D651; doi:10.1093/nar/gkp926 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Simon A. Forbes, Gurpreet Tang, Nidhi Bindal, Sally Bamford, Elisabeth Dawson, Charlotte Cole, Chai Yin Kok, Mingming Jia, Rebecca Ewing, Andrew Menzies, Jon W. Teague, Michael R. Stratton, and P. Andrew Futreal
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D652-D657; doi:10.1093/nar/gkp995 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie, and Yixue Li
dbDEPC: a database of Differentially Expressed Proteins in human Cancers
Nucleic Acids Research Advance Access published on November 9, 2009
Nucl. Acids Res. 2010 38: D658-D664; doi:10.1093/nar/gkp933 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Lishan Wang, Yuanyuan Xiong, Yihua Sun, Zhaoyuan Fang, Li Li, Hongbin Ji, and Tieliu Shi
HLungDB: an integrated database of human lung cancer research
Nucleic Acids Research Advance Access published on November 9, 2009
Nucl. Acids Res. 2010 38: D665-D669; doi:10.1093/nar/gkp945 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Adnan S. Syed, Matteo D’Antonio, and Francesca D. Ciccarelli
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D670-D675; doi:10.1093/nar/gkp957 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Brian A. Kennedy, Wenqing Gao, Tim H.-M. Huang, and Victor X. Jin
HRTBLDb: an informative data resource for hormone receptors target binding loci
Nucleic Acids Research Advance Access published on September 22, 2009
Nucl. Acids Res. 2010 38: D676-D681; doi:10.1093/nar/gkp734 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Stefan M. Woerner, Yan P. Yuan, Axel Benner, Sebastian Korff, Magnus von Knebel Doeberitz, and Peer Bork
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology
Nucleic Acids Research Advance Access published on October 9, 2009
Nucl. Acids Res. 2010 38: D682-D689; doi:10.1093/nar/gkp839 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen Parkinson, and Alvis Brazma
Gene Expression Atlas at the European Bioinformatics Institute
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D690-D698; doi:10.1093/nar/gkp936 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Nicholas Paul Gauthier, Lars Juhl Jensen, Rasmus Wernersson, Søren Brunak, and Thomas S. Jensen
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: D699-D702; doi:10.1093/nar/gkp1044 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Lorna Richardson, Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Nicholas Burton, Jianguo Rao, Malcolm Fisher, Richard A. Baldock, Duncan R. Davidson, and Jeffrey H. Christiansen
EMAGE mouse embryo spatial gene expression database: 2010 update
Nucleic Acids Research Advance Access published on September 18, 2009
Nucl. Acids Res. 2010 38: D703-D709; doi:10.1093/nar/gkp763 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Jun Zhao, Graham Klyne, Elizabeth Benson, Elin Gudmannsdottir, Helen White-Cooper, and David Shotton
FlyTED: the Drosophila Testis Gene Expression Database
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: D710-D715; doi:10.1093/nar/gkp1006 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Aedín C. Culhane, Thomas Schwarzl, Razvan Sultana, Kermshlise C. Picard, Shaita C. Picard, Tim H. Lu, Katherine R. Franklin, Simon J. French, Gerald Papenhausen, Mick Correll, and John Quackenbush
GeneSigDB—a curated database of gene expression signatures
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: D716-D725; doi:10.1093/nar/gkp1015 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Ramil N. Nurtdinov, Mikhail O. Vasiliev, Anna S. Ershova, Ilia S. Lossev, and Anna S. Karyagina
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D726-D730; doi:10.1093/nar/gkp969 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Li Ji, Tanya Barrett, Oluwabukunmi Ayanbule, Dennis B. Troup, Dmitry Rudnev, Rolf N. Muertter, Maxim Tomashevsky, Alexandra Soboleva, and Douglas J. Slotta
NCBI Peptidome: a new repository for mass spectrometry proteomics data
Nucleic Acids Research Advance Access published on November 26, 2009
Nucl. Acids Res. 2010 38: D731-D735; doi:10.1093/nar/gkp1047 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Juan Antonio Vizcaíno, Richard Côté, Florian Reisinger, Harald Barsnes, Joseph M. Foster, Jonathan Rameseder, Henning Hermjakob, and Lennart Martens
The Proteomics Identifications database: 2010 update
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D736-D742; doi:10.1093/nar/gkp964 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Catherine Y. Cormier, Stephanie E. Mohr, Dongmei Zuo, Yanhui Hu, Andreas Rolfs, Jason Kramer, Elena Taycher, Fontina Kelley, Michael Fiacco, Greggory Turnbull, and Joshua LaBaer
Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D743-D749; doi:10.1093/nar/gkp999 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Ron Milo, Paul Jorgensen, Uri Moran, Griffin Weber, and Michael Springer
BioNumbers—the database of key numbers in molecular and cell biology
Nucleic Acids Research Advance Access published on October 23, 2009
Nucl. Acids Res. 2010 38: D750-D753; doi:10.1093/nar/gkp889 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Lynn M. Schriml, Cesar Arze, Suvarna Nadendla, Anu Ganapathy, Victor Felix, Anup Mahurkar, Katherine Phillippy, Aaron Gussman, Sam Angiuoli, Elodie Ghedin, Owen White, and Neil Hall
GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
Nucleic Acids Research Advance Access published on October 22, 2009
Nucl. Acids Res. 2010 38: D754-D764; doi:10.1093/nar/gkp832 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Liwei Li, Khuchtumur Bum-Erdene, Peter H. Baenziger, Joshua J. Rosen, Jamison R. Hemmert, Joy A. Nellis, Marlon E. Pierce, and Samy O. Meroueh
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome
Nucleic Acids Research Advance Access published on November 18, 2009
Nucl. Acids Res. 2010 38: D765-D773; doi:10.1093/nar/gkp852 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Shaini Thomas, Shreyas Karnik, Ram Shankar Barai, V. K. Jayaraman, and Susan Idicula-Thomas
CAMP: a useful resource for research on antimicrobial peptides
Nucleic Acids Research Advance Access published on November 18, 2009
Nucl. Acids Res. 2010 38: D774-D780; doi:10.1093/nar/gkp1021 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Emilia Lim, Allison Pon, Yannick Djoumbou, Craig Knox, Savita Shrivastava, An Chi Guo, Vanessa Neveu, and David S. Wishart
T3DB: a comprehensively annotated database of common toxins and their targets
Nucleic Acids Research Advance Access published on November 6, 2009
Nucl. Acids Res. 2010 38: D781-D786; doi:10.1093/nar/gkp934 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Feng Zhu, BuCong Han, Pankaj Kumar, XiangHui Liu, XiaoHua Ma, XiaoNa Wei, Lu Huang, YangFan Guo, LianYi Han, ChanJuan Zheng, and YuZong Chen
Update of TTD: Therapeutic Target Database
Nucleic Acids Research Advance Access published on November 20, 2009
Nucl. Acids Res. 2010 38: D787-D791; doi:10.1093/nar/gkp1014 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Athanasia Spandidos, Xiaowei Wang, Huajun Wang, and Brian Seed
PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D792-D799; doi:10.1093/nar/gkp1005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Agatha Schlüter, Alejandro Real-Chicharro, Toni Gabaldón, Francisca Sánchez-Jiménez, and Aurora Pujol
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome
Nucleic Acids Research Advance Access published on November 5, 2009
Nucl. Acids Res. 2010 38: D800-D805; doi:10.1093/nar/gkp935 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Zhenhai Zhang, Jingyin Yu, Daofeng Li, Zuyong Zhang, Fengxia Liu, Xin Zhou, Tao Wang, Yi Ling, and Zhen Su
PMRD: plant microRNA database
Nucleic Acids Research Advance Access published on October 6, 2009
Nucl. Acids Res. 2010 38: D806-D813; doi:10.1093/nar/gkp818 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Walter Sanseverino, Guglielmo Roma, Marco De Simone, Luigi Faino, Sara Melito, Elia Stupka, Luigi Frusciante, and Maria Raffaella Ercolano
PRGdb: a bioinformatics platform for plant resistance gene analysis
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D814-D821; doi:10.1093/nar/gkp978 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Paulino Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Corrêa, Stefan A. Rensing, Birgit Kersten, and Bernd Mueller-Roeber
PlnTFDB: updated content and new features of the plant transcription factor database
Nucleic Acids Research Advance Access published on October 25, 2009
Nucl. Acids Res. 2010 38: D822-D827; doi:10.1093/nar/gkp805 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Pawel Durek, Robert Schmidt, Joshua L. Heazlewood, Alexandra Jones, Daniel MacLean, Axel Nagel, Birgit Kersten, and Waltraud X. Schulze
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update
Nucleic Acids Research Advance Access published on October 30, 2009
Nucl. Acids Res. 2010 38: D828-D834; doi:10.1093/nar/gkp810 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Motohiro Mihara, Takeshi Itoh, and Takeshi Izawa
SALAD database: a motif-based database of protein annotations for plant comparative genomics
Nucleic Acids Research Advance Access published on October 23, 2009
Nucl. Acids Res. 2010 38: D835-D842; doi:10.1093/nar/gkp831 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
David Grant, Rex T. Nelson, Steven B. Cannon, and Randy C. Shoemaker
SoyBase, the USDA-ARS soybean genetics and genomics database
Nucleic Acids Research Advance Access published on December 14, 2009
Nucl. Acids Res. 2010 38: D843-D846; doi:10.1093/nar/gkp798 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Hifzur Rahman Ansari, Darren R. Flower, and G. P. S. Raghava
AntigenDB: an immunoinformatics database of pathogen antigens
Nucleic Acids Research Advance Access published on October 9, 2009
Nucl. Acids Res. 2010 38: D847-D853; doi:10.1093/nar/gkp830 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
Randi Vita, Laura Zarebski, Jason A. Greenbaum, Hussein Emami, Ilka Hoof, Nima Salimi, Rohini Damle, Alessandro Sette, and Bjoern Peters
The Immune Epitope Database 2.0
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: D854-D862; doi:10.1093/nar/gkp1004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]
James Robinson, Kavita Mistry, Hamish McWilliam, Rodrigo Lopez, and Steven G. E. Marsh
IPD—the Immuno Polymorphism Database
Nucleic Acids Research Advance Access published on October 29, 2009
Nucl. Acids Res. 2010 38: D863-D869; doi:10.1093/nar/gkp879 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Martin Shumway, Guy Cochrane, and Hideaki Sugawara
Archiving next generation sequencing data
Nucleic Acids Research Advance Access published on December 3, 2009
Nucl. Acids Res. 2010 38: D870-D871; doi:10.1093/nar/gkp1078 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 38 DATABASE ISSUE JANUARY 1, 2010
Nucl. Acids Res. 2010 38: i; doi:10.1093/nar/gkp1212 [Extract] [FREE Full Text] [Print PDF][Screen PDF]
Nucleic Acids Research
Nucl. Acids Res. 2010 38: ii; doi:10.1093/nar/gkp1211 [Extract] [FREE Full Text] [Print PDF][Screen PDF]
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Nucl. Acids Res. 2010 38: iii; doi:10.1093/nar/gkp1213 [Extract] [FREE Full Text] [Print PDF][Screen PDF]
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