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  		Contents: Volume 37, Database issue, January 2009   [Index by Author] 

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Michael Y. Galperin and Guy R. Cochrane
Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: D1-D4; doi:10.1093/nar/gkn942 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Database Summaries]  

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, Ilene Mizrachi, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko, and Jian Ye
Database resources of the National Center for Biotechnology Information
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2009 37: D5-D15; doi:10.1093/nar/gkn741 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hideaki Sugawara, Kazuho Ikeo, Satoshi Fukuchi, Takashi Gojobori, and Yoshio Tateno
DDBJ dealing with mass data produced by the second generation sequencer
Nucleic Acids Research Advance Access published on October 16, 2008
Nucl. Acids Res. 2009 37: D16-D18; doi:10.1093/nar/gkn724 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guy Cochrane, Ruth Akhtar, James Bonfield, Lawrence Bower, Fehmi Demiralp, Nadeem Faruque, Richard Gibson, Gemma Hoad, Tim Hubbard, Christopher Hunter, Mikyung Jang, Szilveszter Juhos, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Sheila Plaister, Rajesh Radhakrishnan, Stephen Robinson, Siamak Sobhany, Petra Ten Hoopen, Robert Vaughan, Vadim Zalunin, and Ewan Birney
Petabyte-scale innovations at the European Nucleotide Archive
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2009 37: D19-D25; doi:10.1093/nar/gkn765 [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 October 21, 2008
Nucl. Acids Res. 2009 37: D26-D31; doi:10.1093/nar/gkn723 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kim D. Pruitt, Tatiana Tatusova, William Klimke, and Donna R. Maglott
NCBI Reference Sequences: current status, policy and new initiatives
Nucleic Acids Research Advance Access published on October 16, 2008
Nucl. Acids Res. 2009 37: D32-D36; doi:10.1093/nar/gkn721 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Maik Friedel, Swetlana Nikolajewa, Jürgen Sühnel, and Thomas Wilhelm
DiProDB: a database for dinucleotide properties
Nucleic Acids Research Advance Access published on September 19, 2008
Nucl. Acids Res. 2009 37: D37-D40; doi:10.1093/nar/gkn597 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Cristian Taccioli, Enrica Fabbri, Rosa Visone, Stefano Volinia, George A. Calin, Louise Y. Fong, Roberto Gambari, Arianna Bottoni, Mario Acunzo, John Hagan, Marilena V. Iorio, Claudia Piovan, Giulia Romano, and Carlo Maria Croce
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function
Nucleic Acids Research Advance Access published on October 22, 2008
Nucl. Acids Res. 2009 37: D41-D48; doi:10.1093/nar/gkn702 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Budrul Ahsan, Taro L. Saito, Shin-ichi Hashimoto, Keigo Muramatsu, Manabu Tsuda, Atsushi Sasaki, Kouji Matsushima, Toshiro Aigaki, and Shinichi Morishita
MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D49-D53; doi:10.1093/nar/gkn694 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Elodie Portales-Casamar, David Arenillas, Jonathan Lim, Magdalena I. Swanson, Steven Jiang, Anthony McCallum, Stefan Kirov, and Wyeth W. Wasserman
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences
Nucleic Acids Research Advance Access published on October 29, 2008
Nucl. Acids Res. 2009 37: D54-D60; doi:10.1093/nar/gkn783 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Andreas Grote, Johannes Klein, Ida Retter, Isam Haddad, Susanne Behling, Boyke Bunk, Ilona Biegler, Svitlana Yarmolinetz, Dieter Jahn, and Richard Münch
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D61-D65; doi:10.1093/nar/gkn837 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Logan Everett, Antony Vo, and Sridhar Hannenhalli
PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2009 37: D66-D71; doi:10.1093/nar/gkn731 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Grant H. Jacobs, Augustine Chen, Stewart G. Stevens, Peter A. Stockwell, Michael A. Black, Warren P. Tate, and Chris M. Brown
Transterm: a database to aid the analysis of regulatory sequences in mRNAs
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D72-D76; doi:10.1093/nar/gkn763 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daniel E. Newburger and Martha L. Bulyk
UniPROBE: an online database of protein binding microarray data on protein–DNA interactions
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D77-D82; doi:10.1093/nar/gkn660 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yurong Xin and Wilma K. Olson
BPS: a database of RNA base-pair structures
Nucleic Acids Research Advance Access published on October 9, 2008
Nucl. Acids Res. 2009 37: D83-D88; doi:10.1093/nar/gkn676 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Toutai Mituyama, Kouichirou Yamada, Emi Hattori, Hiroaki Okida, Yukiteru Ono, Goro Terai, Aya Yoshizawa, Takashi Komori, and Kiyoshi Asai
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D89-D92; doi:10.1093/nar/gkn805 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Patricia P. Chan and Todd M. Lowe
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D93-D97; doi:10.1093/nar/gkn787 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Qinghua Jiang, Yadong Wang, Yangyang Hao, Liran Juan, Mingxiang Teng, Xinjun Zhang, Meimei Li, Guohua Wang, and Yunlong Liu
miR2Disease: a manually curated database for microRNA deregulation in human disease
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2009 37: D98-D104; doi:10.1093/nar/gkn714 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Feifei Xiao, Zhixiang Zuo, Guoshuai Cai, Shuli Kang, Xiaolian Gao, and Tongbin Li
miRecords: an integrated resource for microRNA–target interactions
Nucleic Acids Research Advance Access published on November 7, 2008
Nucl. Acids Res. 2009 37: D105-D110; doi:10.1093/nar/gkn851 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daniel Gerlach, Evgenia V. Kriventseva, Nazim Rahman, Charles E. Vejnar, and Evgeny M. Zdobnov
miROrtho: computational survey of microRNA genes
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2009 37: D111-D117; doi:10.1093/nar/gkn707 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Anna Czerwoniec, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Katarzyna H. Kaminska, Joanna M. Kasprzak, Janusz M. Bujnicki, Henri Grosjean, and Kristian Rother
MODOMICS: a database of RNA modification pathways. 2008 update
Nucleic Acids Research Advance Access published on October 14, 2008
Nucl. Acids Res. 2009 37: D118-D121; doi:10.1093/nar/gkn710 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, Mark L. Crowe, Sean M. Grimmond, and John S. Mattick
NRED: a database of long noncoding RNA expression
Nucleic Acids Research Advance Access published on October 1, 2008
Nucl. Acids Res. 2009 37: D122-D126; doi:10.1093/nar/gkn617 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Michela Taufer, Abel Licon, Roberto Araiza, David Mireles, F. H. D. van Batenburg, Alexander P. Gultyaev, and Ming-Ying Leung
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
Nucleic Acids Research Advance Access published on November 6, 2008
Nucl. Acids Res. 2009 37: D127-D135; doi:10.1093/nar/gkn806 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Paul P. Gardner, Jennifer Daub, John G. Tate, Eric P. Nawrocki, Diana L. Kolbe, Stinus Lindgreen, Adam C. Wilkinson, Robert D. Finn, Sam Griffiths-Jones, Sean R. Eddy, and Alex Bateman
Rfam: updates to the RNA families database
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D136-D140; doi:10.1093/nar/gkn766 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity, and J. M. Tiedje
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Nucleic Acids Research Advance Access published on November 12, 2008
Nucl. Acids Res. 2009 37: D141-D145; doi:10.1093/nar/gkn879 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yongliang Ren, Wuming Gong, Haiyan Zhou, Yejun Wang, Feifei Xiao, and Tongbin Li
siRecords: a database of mammalian RNAi experiments and efficacies
Nucleic Acids Research Advance Access published on November 7, 2008
Nucl. Acids Res. 2009 37: D146-D149; doi:10.1093/nar/gkn817 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hsi-Yuan Huang, Heng-Yi Chang, Chih-Hung Chou, Ching-Ping Tseng, Shinn-Ying Ho, Chi-Dung Yang, Yih-Wei Ju, and Hsien-Da Huang
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes
Nucleic Acids Research Advance Access published on November 16, 2008
Nucl. Acids Res. 2009 37: D150-D154; doi:10.1093/nar/gkn852 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Giorgos L. Papadopoulos, Martin Reczko, Victor A. Simossis, Praveen Sethupathy, and Artemis G. Hatzigeorgiou
The database of experimentally supported targets: a functional update of TarBase
Nucleic Acids Research Advance Access published on October 27, 2008
Nucl. Acids Res. 2009 37: D155-D158; doi:10.1093/nar/gkn809 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, and Joern Pütz
tRNAdb 2009: compilation of tRNA sequences and tRNA genes
Nucleic Acids Research Advance Access published on October 28, 2008
Nucl. Acids Res. 2009 37: D159-D162; doi:10.1093/nar/gkn772 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, and Hachiro Inokuchi
tRNADB-CE: tRNA gene database curated manually by experts
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D163-D168; doi:10.1093/nar/gkn692 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

The UniProt Consortium
The Universal Protein Resource (UniProt) 2009
Nucleic Acids Research Advance Access published on October 4, 2008
Nucl. Acids Res. 2009 37: D169-D174; doi:10.1093/nar/gkn664 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rubén Nogales-Cadenas, Federico Abascal, Javier Díez-Pérez, José María Carazo, and Alberto Pascual-Montano
CentrosomeDB: a human centrosomal proteins database
Nucleic Acids Research Advance Access published on October 29, 2008
Nucl. Acids Res. 2009 37: D175-D180; doi:10.1093/nar/gkn815 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yasmeen Ahmad, François-Michel Boisvert, Peter Gregor, Andy Cobley, and Angus I. Lamond
NOPdb: Nucleolar Proteome Database—2008 update
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D181-D184; doi:10.1093/nar/gkn804 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sanguthevar Rajasekaran, Sudha Balla, Patrick Gradie, Michael R. Gryk, Krishna Kadaveru, Vamsi Kundeti, Mark W. Maciejewski, Tian Mi, Nicholas Rubino, Jay Vyas, and Martin R. Schiller
Minimotif miner 2nd release: a database and web system for motif search
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2009 37: D185-D190; doi:10.1093/nar/gkn865 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jason E. Donald and Eugene I. Shakhnovich
SDR: a database of predicted specificity-determining residues in proteins
Nucleic Acids Research Advance Access published on October 16, 2008
Nucl. Acids Res. 2009 37: D191-D194; doi:10.1093/nar/gkn716 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Raphael André Bauer, Stefan Günther, Dominic Jansen, Carolin Heeger, Paul Florian Thaben, and Robert Preissner
SuperSite: dictionary of metabolite and drug binding sites in proteins
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D195-D200; doi:10.1093/nar/gkn618 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

M. Michael Gromiha, Yukimitsu Yabuki, M. Xavier Suresh, A. Mary Thangakani, Makiko Suwa, and Kazuhiko Fukui
TMFunction: database for functional residues in membrane proteins
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D201-D204; doi:10.1093/nar/gkn672 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Aron Marchler-Bauer, John B. Anderson, Farideh Chitsaz, Myra K. Derbyshire, Carol DeWeese-Scott, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Asba Tasneem, Narmada Thanki, Roxanne A. Yamashita, Dachuan Zhang, Naigong Zhang, and Stephen H. Bryant
CDD: specific functional annotation with the Conserved Domain Database
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D205-D210; doi:10.1093/nar/gkn845 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, Robert D. Finn, Julian Gough, Daniel Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Nicola Mulder, Darren Natale, Christine Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. A. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, and Corin Yeats
InterPro: the integrative protein signature database
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2009 37: D211-D215; doi:10.1093/nar/gkn785 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

William Klimke, Richa Agarwala, Azat Badretdin, Slava Chetvernin, Stacy Ciufo, Boris Fedorov, Boris Kiryutin, Kathleen O’Neill, Wolfgang Resch, Sergei Resenchuk, Susan Schafer, Igor Tolstoy, and Tatiana Tatusova
The National Center for Biotechnology Information's Protein Clusters Database
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2009 37: D216-D223; doi:10.1093/nar/gkn734 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Abraham O. Samson and Michael Levitt
Protein segment finder: an online search engine for segment motifs in the PDB
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D224-D228; doi:10.1093/nar/gkn833 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ivica Letunic, Tobias Doerks, and Peer Bork
SMART 6: recent updates and new developments
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2009 37: D229-D232; doi:10.1093/nar/gkn808 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Brandi L. Cantarel, Pedro M. Coutinho, Corinne Rancurel, Thomas Bernard, Vincent Lombard, and Bernard Henrissat
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
Nucleic Acids Research Advance Access published on October 5, 2008
Nucl. Acids Res. 2009 37: D233-D238; doi:10.1093/nar/gkn663 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Víctor Quesada, Gonzalo R. Ordóñez, Luis M. Sánchez, Xose S. Puente, and Carlos López-Otín
The Degradome database: mammalian proteases and diseases of proteolysis
Nucleic Acids Research Advance Access published on September 6, 2008
Nucl. Acids Res. 2009 37: D239-D243; doi:10.1093/nar/gkn570 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David M. A. Martin, Diego Miranda-Saavedra, and Geoffrey J. Barton
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D244-D250; doi:10.1093/nar/gkn834 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chuan-Yun Li, Qing-Rong Liu, Ping-Wu Zhang, Xiao-Mo Li, Liping Wei, and George R. Uhl
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules
Nucleic Acids Research Advance Access published on September 12, 2008
Nucl. Acids Res. 2009 37: D251-D260; doi:10.1093/nar/gkn568 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Dominique Koua, Lorenzo Cerutti, Laurent Falquet, Christian J. A. Sigrist, Grégory Theiler, Nicolas Hulo, and Christophe Dunand
PeroxiBase: a database with new tools for peroxidase family classification
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D261-D266; doi:10.1093/nar/gkn680 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li, and Hans-Juergen Thiesen
SysZNF: the C2H2 zinc finger gene database
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D267-D273; doi:10.1093/nar/gkn782 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Milton H. Saier, Jr, Ming Ren Yen, Keith Noto, Dorjee G. Tamang, and Charles Elkan
The Transporter Classification Database: recent advances
Nucleic Acids Research Advance Access published on November 20, 2008
Nucl. Acids Res. 2009 37: D274-D278; doi:10.1093/nar/gkn862 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fengli Fu, Jeffry D. Sander, Morgan Maeder, Stacey Thibodeau-Beganny, J. Keith Joung, Drena Dobbs, Leslie Miller, and Daniel F. Voytas
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays
Nucleic Acids Research Advance Access published on September 23, 2008
Nucl. Acids Res. 2009 37: D279-D283; doi:10.1093/nar/gkn606 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Joel Masciocchi, Gianfranco Frau, Marco Fanton, Mattia Sturlese, Matteo Floris, Luca Pireddu, Piergiorgio Palla, Fabian Cedrati, Patricia Rodriguez-Tomé, and Stefano Moro
MMsINC: a large-scale chemoinformatics database
Nucleic Acids Research Advance Access published on October 17, 2008
Nucl. Acids Res. 2009 37: D284-D290; doi:10.1093/nar/gkn727 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Mathias Dunkel, Ulrike Schmidt, Swantje Struck, Lena Berger, Bjoern Gruening, Julia Hossbach, Ines S. Jaeger, Uta Effmert, Birgit Piechulla, Roger Eriksson, Jette Knudsen, and Robert Preissner
SuperScent—a database of flavors and scents
Nucleic Acids Research Advance Access published on October 17, 2008
Nucl. Acids Res. 2009 37: D291-D294; doi:10.1093/nar/gkn695 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ulrike Schmidt, Swantje Struck, Bjoern Gruening, Julia Hossbach, Ines S. Jaeger, Roza Parol, Ulrike Lindequist, Eberhard Teuscher, and Robert Preissner
SuperToxic: a comprehensive database of toxic compounds
Nucleic Acids Research Advance Access published on November 12, 2008
Nucl. Acids Res. 2009 37: D295-D299; doi:10.1093/nar/gkn850 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Amelie Stein, Alejandro Panjkovich, and Patrick Aloy
3did Update: domain–domain and peptide-mediated interactions of known 3D structure
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D300-D304; doi:10.1093/nar/gkn690 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Masafumi Shionyu, Akihiro Yamaguchi, Kazuki Shinoda, Ken-ichi Takahashi, and Mitiko Go
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
Nucleic Acids Research Advance Access published on November 10, 2008
Nucl. Acids Res. 2009 37: D305-D309; doi:10.1093/nar/gkn869 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alison L. Cuff, Ian Sillitoe, Tony Lewis, Oliver C. Redfern, Richard Garratt, Janet Thornton, and Christine A. Orengo
The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies
Nucleic Acids Research Advance Access published on November 7, 2008
Nucl. Acids Res. 2009 37: D310-D314; doi:10.1093/nar/gkn877 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Oliver D. Testa, Efrosini Moutevelis, and Derek N. Woolfson
CC+: a relational database of coiled-coil structures
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D315-D322; doi:10.1093/nar/gkn675 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ofir Goldenberg, Elana Erez, Guy Nimrod, and Nir Ben-Tal
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
Nucleic Acids Research Advance Access published on October 29, 2008
Nucl. Acids Res. 2009 37: D323-D327; doi:10.1093/nar/gkn822 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Wei-Cheng Lo, Chi-Ching Lee, Che-Yu Lee, and Ping-Chiang Lyu
CPDB: a database of circular permutation in proteins
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D328-D332; doi:10.1093/nar/gkn679 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Satoshi Fukuchi, Keiichi Homma, Shigetaka Sakamoto, Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori, and Ken Nishikawa
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D333-D337; doi:10.1093/nar/gkn855 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stefan Günther, Joachim von Eichborn, Patrick May, and Robert Preissner
JAIL: a structure-based interface library for macromolecules
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2009 37: D338-D341; doi:10.1093/nar/gkn599 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Natalya S. Bogatyreva, Alexander A. Osypov, and Dmitry N. Ivankov
KineticDB: a database of protein folding kinetics
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D342-D346; doi:10.1093/nar/gkn696 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ursula Pieper, Narayanan Eswar, Ben M. Webb, David Eramian, Libusha Kelly, David T. Barkan, Hannah Carter, Parminder Mankoo, Rachel Karchin, Marc A. Marti-Renom, Fred P. Davis, and Andrej Sali
MODBASE, a database of annotated comparative protein structure models and associated resources
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D347-D354; doi:10.1093/nar/gkn791 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Roman A. Laskowski
PDBsum new things
Nucleic Acids Research Advance Access published on November 7, 2008
Nucl. Acids Res. 2009 37: D355-D359; doi:10.1093/nar/gkn860 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Miho Higurashi, Takashi Ishida, and Kengo Kinoshita
PiSite: a database of protein interaction sites using multiple binding states in the PDB
Nucleic Acids Research Advance Access published on October 4, 2008
Nucl. Acids Res. 2009 37: D360-D364; doi:10.1093/nar/gkn659 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Helen M. Berman, John D. Westbrook, Margaret J. Gabanyi, Wendy Tao, Raship Shah, Andrei Kouranov, Torsten Schwede, Konstantin Arnold, Florian Kiefer, Lorenza Bordoli, Jürgen Kopp, Michael Podvinec, Paul D. Adams, Lester G. Carter, Wladek Minor, Rajesh Nair, and Joshua La Baer
The protein structure initiative structural genomics knowledgebase
Nucleic Acids Research Advance Access published on November 14, 2008
Nucl. Acids Res. 2009 37: D365-D368; doi:10.1093/nar/gkn790 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexandra Shulman-Peleg, Ruth Nussinov, and Haim J. Wolfson
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D369-D373; doi:10.1093/nar/gkn759 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mathieu Lonquety, Zoé Lacroix, Nikolaos Papandreou, and Jacques Chomilier
SPROUTS: a database for the evaluation of protein stability upon point mutation
Nucleic Acids Research Advance Access published on October 22, 2008
Nucl. Acids Res. 2009 37: D374-D379; doi:10.1093/nar/gkn704 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Derek Wilson, Ralph Pethica, Yiduo Zhou, Charles Talbot, Christine Vogel, Martin Madera, Cyrus Chothia, and Julian Gough
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: D380-D386; doi:10.1093/nar/gkn762 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Florian Kiefer, Konstantin Arnold, Michael Künzli, Lorenza Bordoli, and Torsten Schwede
The SWISS-MODEL Repository and associated resources
Nucleic Acids Research Advance Access published on October 18, 2008
Nucl. Acids Res. 2009 37: D387-D392; doi:10.1093/nar/gkn750 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kristian Rother, Peter Werner Hildebrand, Andrean Goede, Bjoern Gruening, and Robert Preissner
Voronoia: analyzing packing in protein structures
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D393-D395; doi:10.1093/nar/gkn769 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daniel Barrell, Emily Dimmer, Rachael P. Huntley, David Binns, Claire O’Donovan, and Rolf Apweiler
The GOA database in 2009—an integrated Gene Ontology Annotation resource
Nucleic Acids Research Advance Access published on October 27, 2008
Nucl. Acids Res. 2009 37: D396-D403; doi:10.1093/nar/gkn803 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Estelle Proux, Romain A. Studer, Sébastien Moretti, and Marc Robinson-Rechavi
Selectome: a database of positive selection
Nucleic Acids Research Advance Access published on October 28, 2008
Nucl. Acids Res. 2009 37: D404-D407; doi:10.1093/nar/gkn768 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mathias C. Walter, Thomas Rattei, Roland Arnold, Ulrich Güldener, Martin Münsterkötter, Karamfilka Nenova, Gabi Kastenmüller, Patrick Tischler, Andreas Wölling, Andreas Volz, Norbert Pongratz, Ralf Jost, Hans-Werner Mewes, and Dmitrij Frishman
PEDANT covers all complete RefSeq genomes
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2009 37: D408-D411; doi:10.1093/nar/gkn749 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lars J. Jensen, Michael Kuhn, Manuel Stark, Samuel Chaffron, Chris Creevey, Jean Muller, Tobias Doerks, Philippe Julien, Alexander Roth, Milan Simonovic, Peer Bork, and Christian von Mering
STRING 8—a global view on proteins and their functional interactions in 630 organisms
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2009 37: D412-D416; doi:10.1093/nar/gkn760 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

William Fu, Brigitte E. Sanders-Beer, Kenneth S. Katz, Donna R. Maglott, Kim D. Pruitt, and Roger G. Ptak
Human immunodeficiency virus type 1, human protein interaction database at NCBI
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2009 37: D417-D422; doi:10.1093/nar/gkn708 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Seok Yang, Joo-Yeon Lee, Joon Seung Lee, Wayne P. Mitchell, Hee-Bok Oh, Chun Kang, and Kyung Hyun Kim
Influenza sequence and epitope database
Nucleic Acids Research Advance Access published on November 9, 2008
Nucl. Acids Res. 2009 37: D423-D430; doi:10.1093/nar/gkn881 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Robert Belshaw, Tulio de Oliveira, Sidney Markowitz, and Andrew Rambaut
The RNA Virus Database
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D431-D435; doi:10.1093/nar/gkn729 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Mauricio Carrillo-Tripp, Craig M. Shepherd, Ian A. Borelli, Sangita Venkataraman, Gabriel Lander, Padmaja Natarajan, John E. Johnson, Charles L. Brooks, III, and Vijay S. Reddy
VIPERdb2: an enhanced and web API enabled relational database for structural virology
Nucleic Acids Research Advance Access published on November 3, 2008
Nucl. Acids Res. 2009 37: D436-D442; doi:10.1093/nar/gkn840 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bo Liu and Mihai Pop
ARDB—Antibiotic Resistance Genes Database
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2009 37: D443-D447; doi:10.1093/nar/gkn656 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf, Eugene V. Koonin, and Inna Dubchak
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes
Nucleic Acids Research Advance Access published on October 9, 2008
Nucl. Acids Res. 2009 37: D448-D454; doi:10.1093/nar/gkn684 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ren Zhang and Yan Lin
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D455-D458; doi:10.1093/nar/gkn858 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fenglou Mao, Phuongan Dam, Jacky Chou, Victor Olman, and Ying Xu
DOOR: a database for prokaryotic operons
Nucleic Acids Research Advance Access published on November 6, 2008
Nucl. Acids Res. 2009 37: D459-D463; doi:10.1093/nar/gkn757 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ingrid M. Keseler, César Bonavides-Martínez, Julio Collado-Vides, Socorro Gama-Castro, Robert P. Gunsalus, D. Aaron Johnson, Markus Krummenacker, Laura M. Nolan, Suzanne Paley, Ian T. Paulsen, Martin Peralta-Gil, Alberto Santos-Zavaleta, Alexander Glennon Shearer, and Peter D. Karp
EcoCyc: A comprehensive view of Escherichia coli biology
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D464-D470; doi:10.1093/nar/gkn751 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tania Lima, Andrea H. Auchincloss, Elisabeth Coudert, Guillaume Keller, Karine Michoud, Catherine Rivoire, Virginie Bulliard, Edouard de Castro, Corinne Lachaize, Delphine Baratin, Isabelle Phan, Lydie Bougueleret, and Amos Bairoch
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
Nucleic Acids Research Advance Access published on October 11, 2008
Nucl. Acids Res. 2009 37: D471-D478; doi:10.1093/nar/gkn661 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff, and Steven L. Salzberg
OperonDB: a comprehensive database of predicted operons in microbial genomes
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D479-D482; doi:10.1093/nar/gkn784 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Geoffrey L. Winsor, Thea Van Rossum, Raymond Lo, Bhavjinder Khaira, Matthew D. Whiteside, Robert E. W. Hancock, and Fiona S. L. Brinkman
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2009 37: D483-D488; doi:10.1093/nar/gkn861 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zarraz May-Ping Lee, Carl Bussema, III, and Thomas M. Schmidt
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D489-D493; doi:10.1093/nar/gkn689 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Johannes Klein, Richard Münch, Ilona Biegler, Isam Haddad, Ida Retter, and Dieter Jahn
Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform ‘Open Genome Resource’ (OGeR)
Nucleic Acids Research Advance Access published on October 14, 2008
Nucl. Acids Res. 2009 37: D494-D498; doi:10.1093/nar/gkn674 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

T. B. K. Reddy, Robert Riley, Farrell Wymore, Phillip Montgomery, Dave DeCaprio, Reinhard Engels, Marcel Gellesch, Jeremy Hubble, Dennis Jen, Heng Jin, Michael Koehrsen, Lisa Larson, Maria Mao, Michael Nitzberg, Peter Sisk, Christian Stolte, Brian Weiner, Jared White, Zachariah K. Zachariah, Gavin Sherlock, James E. Galagan, Catherine A. Ball, and Gary K. Schoolnik
TB database: an integrated platform for tuberculosis research
Nucleic Acids Research Advance Access published on October 3, 2008
Nucl. Acids Res. 2009 37: D499-D508; doi:10.1093/nar/gkn652 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jane E. Mabey Gilsenan, Graham Atherton, Jennifer Bartholomew, Peter F. Giles, Teresa K. Attwood, David W. Denning, and Paul Bowyer
Aspergillus Genomes and the Aspergillus Cloud
Nucleic Acids Research Advance Access published on November 27, 2008
Nucl. Acids Res. 2009 37: D509-D514; doi:10.1093/nar/gkn876 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Petra Fey, Pascale Gaudet, Tomaz Curk, Blaz Zupan, Eric M. Just, Siddhartha Basu, Sohel N. Merchant, Yulia A. Bushmanova, Gad Shaulsky, Warren A. Kibbe, and Rex L. Chisholm
dictyBase—a Dictyostelium bioinformatics resource update
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D515-D519; doi:10.1093/nar/gkn844 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Hiroyuki Wakaguri, Yutaka Suzuki, Toshiaki Katayama, Shuichi Kawashima, Eri Kibukawa, Kazushi Hiranuka, Masahide Sasaki, Sumio Sugano, and Junichi Watanabe
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D520-D525; doi:10.1093/nar/gkn856 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jane M. Carlton, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, John A. Miller, Hilary G. Morrison, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Christian J. Stoeckert, Jr, Steven Sullivan, Charles Treatman, and Haiming Wang
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
Nucleic Acids Research Advance Access published on September 29, 2008
Nucl. Acids Res. 2009 37: D526-D530; doi:10.1093/nar/gkn631 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

John W. Whitaker, Ivica Letunic, Glenn A. McConkey, and David R. Westhead
metaTIGER: a metabolic evolution resource
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D531-D538; doi:10.1093/nar/gkn826 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, John A. Miller, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Christian J. Stoeckert, Jr., Charles Treatman, and Haiming Wang
PlasmoDB: a functional genomic database for malaria parasites
Nucleic Acids Research Advance Access published on October 28, 2008
Nucl. Acids Res. 2009 37: D539-D543; doi:10.1093/nar/gkn814 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alejandro A. Ackermann, Santiago J. Carmona, and Fernán Agüero
TcSNP: a database of genetic variation in Trypanosoma cruzi
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D544-D549; doi:10.1093/nar/gkn874 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David J. Sherman, Tiphaine Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, and Pascal Durrens for the Génolevures Consortium
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes
Nucleic Acids Research Advance Access published on November 16, 2008
Nucl. Acids Res. 2009 37: D550-D554; doi:10.1093/nar/gkn859 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Susan Tweedie, Michael Ashburner, Kathleen Falls, Paul Leyland, Peter McQuilton, Steven Marygold, Gillian Millburn, David Osumi-Sutherland, Andrew Schroeder, Ruth Seal, Haiyan Zhang, and The FlyBase Consortium
FlyBase: enhancing Drosophila Gene Ontology annotations
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D555-D559; doi:10.1093/nar/gkn788 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andrei Pisarev, Ekaterina Poustelnikova, Maria Samsonova, and John Reinitz
FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D560-D566; doi:10.1093/nar/gkn717 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Doris Chen, Jürg Berger, Michaela Fellner, and Takashi Suzuki
FLYSNPdb: a high-density SNP database of Drosophila melanogaster
Nucleic Acids Research Advance Access published on September 10, 2008
Nucl. Acids Res. 2009 37: D567-D570; doi:10.1093/nar/gkn583 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

John Martin, Sahar Abubucker, Todd Wylie, Yong Yin, Zhengyuan Wang, and Makedonka Mitreva
Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2009 37: D571-D578; doi:10.1093/nar/gkn744 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Adhemar Zerlotini, Mark Heiges, Haiming Wang, Romulo L. V. Moraes, Anderson J. Dominitini, Jerônimo C. Ruiz, Jessica C. Kissinger, and Guilherme Oliveira
SchistoDB: a Schistosoma mansoni genome resource
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D579-D582; doi:10.1093/nar/gkn681 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, Martin Hammond, Catherine A. Hill, Nathan Konopinski, Neil F. Lobo, Robert M. MacCallum, Greg Madey, Karine Megy, Jason Meyer, Seth Redmond, David W. Severson, Eric O. Stinson, Pantelis Topalis, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, and Frank H. Collins
VectorBase: a data resource for invertebrate vector genomics
Nucleic Acids Research Advance Access published on November 21, 2008
Nucl. Acids Res. 2009 37: D583-D587; doi:10.1093/nar/gkn857 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Antje Chang, Maurice Scheer, Andreas Grote, Ida Schomburg, and Dietmar Schomburg
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D588-D592; doi:10.1093/nar/gkn820 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andrew G. McDonald, Sinéad Boyce, and Keith F. Tipton
ExplorEnz: the primary source of the IUBMB enzyme list
Nucleic Acids Research Advance Access published on September 6, 2008
Nucl. Acids Res. 2009 37: D593-D597; doi:10.1093/nar/gkn582 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia, and Ildefonso Cases
Bionemo: molecular information on biodegradation metabolism
Nucleic Acids Research Advance Access published on November 5, 2008
Nucl. Acids Res. 2009 37: D598-D602; doi:10.1093/nar/gkn864 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David S. Wishart, Craig Knox, An Chi Guo, Roman Eisner, Nelson Young, Bijaya Gautam, David D. Hau, Nick Psychogios, Edison Dong, Souhaila Bouatra, Rupasri Mandal, Igor Sinelnikov, Jianguo Xia, Leslie Jia, Joseph A. Cruz, Emilia Lim, Constance A. Sobsey, Savita Shrivastava, Paul Huang, Philip Liu, Lydia Fang, Jun Peng, Ryan Fradette, Dean Cheng, Dan Tzur, Melisa Clements, Avalyn Lewis, Andrea De Souza, Azaret Zuniga, Margot Dawe, Yeping Xiong, Derrick Clive, Russ Greiner, Alsu Nazyrova, Rustem Shaykhutdinov, Liang Li, Hans J. Vogel, and Ian Forsythe
HMDB: a knowledgebase for the human metabolome
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D603-D610; doi:10.1093/nar/gkn810 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael Blinov, Salmaz S. Ibragimova, Sarah Boyd, Boris Ratnikov, Piotr Cieplak, Adam Godzik, Jeffrey W. Smith, Andrei L. Osterman, and Alexey M. Eroshkin
PMAP: databases for analyzing proteolytic events and pathways
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D611-D618; doi:10.1093/nar/gkn683 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Lisa Matthews, Gopal Gopinath, Marc Gillespie, Michael Caudy, David Croft, Bernard de Bono, Phani Garapati, Jill Hemish, Henning Hermjakob, Bijay Jassal, Alex Kanapin, Suzanna Lewis, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik, Guanming Wu, Ewan Birney, Lincoln Stein, and Peter D’Eustachio
Reactome knowledgebase of human biological pathways and processes
Nucleic Acids Research Advance Access published on November 3, 2008
Nucl. Acids Res. 2009 37: D619-D622; doi:10.1093/nar/gkn863 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Atanas Kamburov, Christoph Wierling, Hans Lehrach, and Ralf Herwig
ConsensusPathDB—a database for integrating human functional interaction networks
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2009 37: D623-D628; doi:10.1093/nar/gkn698 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Eduardo Andres Leon, Iakes Ezkurdia, Beatriz García, Alfonso Valencia, and David Juan
EcID. A database for the inference of functional interactions in E. coli
Nucleic Acids Research Advance Access published on November 12, 2008
Nucl. Acids Res. 2009 37: D629-D635; doi:10.1093/nar/gkn853 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Pankaj Kumar, B. C. Han, Z. Shi, J. Jia, Y. P. Wang, Y. T. Zhang, L. Liang, Q. F. Liu, Z. L. Ji, and Y. Z. Chen
Update of KDBI: Kinetic Data of Bio-molecular Interaction database
Nucleic Acids Research Advance Access published on October 29, 2008
Nucl. Acids Res. 2009 37: D636-D641; doi:10.1093/nar/gkn839 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

V. Glenn Tarcea, Terry Weymouth, Alex Ade, Aaron Bookvich, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Özgür, Yuanyuan Tian, Jim Cavalcoli, Barbara Mirel, Jignesh Patel, Dragomir Radev, Brian Athey, David States, and H. V. Jagadish
Michigan molecular interactions r2: from interacting proteins to pathways
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2009 37: D642-D646; doi:10.1093/nar/gkn722 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tim Driscoll, Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral
PIG—the pathogen interaction gateway
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D647-D650; doi:10.1093/nar/gkn799 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mark D. McDowall, Michelle S. Scott, and Geoffrey J. Barton
PIPs: human protein–protein interaction prediction database
Nucleic Acids Research Advance Access published on November 6, 2008
Nucl. Acids Res. 2009 37: D651-D656; doi:10.1093/nar/gkn870 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gautam Chaurasia, Soniya Malhotra, Jenny Russ, Sigrid Schnoegl, Christian Hänig, Erich E. Wanker, and Matthias E. Futschik
UniHI 4: new tools for query, analysis and visualization of the human protein–protein interactome
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D657-D660; doi:10.1093/nar/gkn841 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Vincent Navratil, Benoît de Chassey, Laurène Meyniel, Stéphane Delmotte, Christian Gautier, Patrice André, Vincent Lotteau, and Chantal Rabourdin-Combe
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus–host interaction networks
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D661-D668; doi:10.1093/nar/gkn794 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Andrew Chatr-aryamontri, Arnaud Ceol, Daniele Peluso, Aurelio Nardozza, Simona Panni, Francesca Sacco, Michele Tinti, Alex Smolyar, Luisa Castagnoli, Marc Vidal, Michael E. Cusick, and Gianni Cesareni
VirusMINT: a viral protein interaction database
Nucleic Acids Research Advance Access published on October 30, 2008
Nucl. Acids Res. 2009 37: D669-D673; doi:10.1093/nar/gkn739 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Carl F. Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay, and Kenneth H. Buetow
PID: the Pathway Interaction Database
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2009 37: D674-D679; doi:10.1093/nar/gkn653 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Anthony J. Harmar, Rebecca A. Hills, Edward M. Rosser, Martin Jones, O. Peter Buneman, Donald R. Dunbar, Stuart D. Greenhill, Valerie A. Hale, Joanna L. Sharman, Tom I. Bonner, William A. Catterall, Anthony P. Davenport, Philippe Delagrange, Colin T. Dollery, Steven M. Foord, George A. Gutman, Vincent Laudet, Richard R. Neubig, Eliot H. Ohlstein, Richard W. Olsen, John Peters, Jean-Philippe Pin, Robert R. Ruffolo, David B. Searls, Mathew W. Wright, and Michael Spedding
IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D680-D685; doi:10.1093/nar/gkn728 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Byungwook Lee and Gwangsik Shin
CleanEST: a database of cleansed EST libraries
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2009 37: D686-D689; doi:10.1093/nar/gkn648 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

T. J. P. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, G. Coates, S. Fairley, S. Fitzgerald, J. Fernandez-Banet, L. Gordon, S. Graf, S. Haider, M. Hammond, R. Holland, K. Howe, A. Jenkinson, N. Johnson, A. Kahari, D. Keefe, S. Keenan, R. Kinsella, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, D. Rios, M. Schuster, G. Slater, D. Smedley, W. Spooner, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, S. Wilder, A. Zadissa, E. Birney, F. Cunningham, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, A. Kasprzyk, G. Proctor, J. Smith, S. Searle, and P. Flicek
Ensembl 2009
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: D690-D697; doi:10.1093/nar/gkn828 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Dae-Soo Kim, Chi-Young Cho, Jae-Won Huh, Heui-Soo Kim, and Hwan-Gue Cho
EVOG: a database for evolutionary analysis of overlapping genes
Nucleic Acids Research Advance Access published on November 5, 2008
Nucl. Acids Res. 2009 37: D698-D702; doi:10.1093/nar/gkn813 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ashwini Bhasi, Philge Philip, Vinu Manikandan, and Periannan Senapathy
ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D703-D711; doi:10.1093/nar/gkn746 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Judith A. Blake, Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and the Mouse Genome Database Group
The Mouse Genome Database genotypes::phenotypes
Nucleic Acids Research Advance Access published on November 3, 2008
Nucl. Acids Res. 2009 37: D712-D719; doi:10.1093/nar/gkn886 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult, and Molly A. Bogue
Mouse Phenome Database
Nucleic Acids Research Advance Access published on November 5, 2008
Nucl. Acids Res. 2009 37: D720-D730; doi:10.1093/nar/gkn778 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tim Hulsen, Peter M. A. Groenen, Jacob de Vlieg, and Wynand Alkema
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2009 37: D731-D737; doi:10.1093/nar/gkn645 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hugo Y. K. Lam, Ekta Khurana, Gang Fang, Philip Cayting, Nicholas Carriero, Kei-Hoi Cheung, and Mark B. Gerstein
Pseudofam: the pseudogene families database
Nucleic Acids Research Advance Access published on October 28, 2008
Nucl. Acids Res. 2009 37: D738-D743; doi:10.1093/nar/gkn758 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-Gungor, Jeffrey DePons, Stanley Laulederkind, Timothy Lowry, Rajni Nigram, Victoria Petri, Jennifer Smith, Alexander Stoddard, Simon N. Twigger, and Howard J. Jacob and the RGD Team
The Rat Genome Database 2009: variation, ontologies and pathways
Nucleic Acids Research Advance Access published on November 7, 2008
Nucl. Acids Res. 2009 37: D744-D749; doi:10.1093/nar/gkn842 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

R. Andrew Cameron, Manoj Samanta, Autumn Yuan, Dong He, and Eric Davidson
SpBase: the sea urchin genome database and web site
Nucleic Acids Research Advance Access published on November 14, 2008
Nucl. Acids Res. 2009 37: D750-D754; doi:10.1093/nar/gkn887 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, L. Meyer, F. Hsu, A. S. Hinrichs, R. A. Harte, B. Giardine, P. Fujita, M. Diekhans, T. Dreszer, H. Clawson, G. P. Barber, D. Haussler, and W. J. Kent
The UCSC Genome Browser Database: update 2009
Nucleic Acids Research Advance Access published on November 7, 2008
Nucl. Acids Res. 2009 37: D755-D761; doi:10.1093/nar/gkn875 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yukio Maruyama, Ai Wakamatsu, Yoshifumi Kawamura, Kouichi Kimura, Jun-ichi Yamamoto, Tetsuo Nishikawa, Yasutomo Kisu, Sumio Sugano, Naoki Goshima, Takao Isogai, and Nobuo Nomura
Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics
Nucl. Acids Res. 2009 37: D762-D766; doi:10.1093/nar/gkn872 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

T. S. Keshava Prasad, Renu Goel, Kumaran Kandasamy, Shivakumar Keerthikumar, Sameer Kumar, Suresh Mathivanan, Deepthi Telikicherla, Rajesh Raju, Beema Shafreen, Abhilash Venugopal, Lavanya Balakrishnan, Arivusudar Marimuthu, Sutopa Banerjee, Devi S. Somanathan, Aimy Sebastian, Sandhya Rani, Somak Ray, C. J. Harrys Kishore, Sashi Kanth, Mukhtar Ahmed, Manoj K. Kashyap, Riaz Mohmood, Y. L. Ramachandra, V. Krishna, B. Abdul Rahiman, Sujatha Mohan, Prathibha Ranganathan, Subhashri Ramabadran, Raghothama Chaerkady, and Akhilesh Pandey
Human Protein Reference Database—2009 update
Nucleic Acids Research Advance Access published on November 6, 2008
Nucl. Acids Res. 2009 37: D767-D772; doi:10.1093/nar/gkn892 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kumaran Kandasamy, Shivakumar Keerthikumar, Renu Goel, Suresh Mathivanan, Nandini Patankar, Beema Shafreen, Santosh Renuse, Harsh Pawar, Y. L. Ramachandra, Pradip Kumar Acharya, Prathibha Ranganathan, Raghothama Chaerkady, T. S. Keshava Prasad, and Akhilesh Pandey
Human Proteinpedia: a unified discovery resource for proteomics research
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D773-D781; doi:10.1093/nar/gkn701 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nobutaka Mitsuhashi, Kaori Fujieda, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi, and Kousaku Okubo
BodyParts3D: 3D structure database for anatomical concepts
Nucleic Acids Research Advance Access published on October 3, 2008
Nucl. Acids Res. 2009 37: D782-D785; doi:10.1093/nar/gkn613 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Allan Peter Davis, Cynthia G. Murphy, Cynthia A. Saraceni-Richards, Michael C. Rosenstein, Thomas C. Wiegers, and Carolyn J. Mattingly
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks
Nucleic Acids Research Advance Access published on September 9, 2008
Nucl. Acids Res. 2009 37: D786-D792; doi:10.1093/nar/gkn580 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Joanna Amberger, Carol A. Bocchini, Alan F. Scott, and Ada Hamosh
McKusick's Online Mendelian Inheritance in Man (OMIM®)
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D793-D796; doi:10.1093/nar/gkn665 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gudmundur A. Thorisson, Owen Lancaster, Robert C. Free, Robert K. Hastings, Pallavi Sarmah, Debasis Dash, Samir K. Brahmachari, and Anthony J. Brookes
HGVbaseG2P: a central genetic association database
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D797-D802; doi:10.1093/nar/gkn748 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexander R. Pico, Ivan V. Smirnov, Jeffrey S. Chang, Ru-Fang Yeh, Joseph L. Wiemels, John K. Wiencke, Tarik Tihan, Bruce R. Conklin, and Margaret Wrensch
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D803-D809; doi:10.1093/nar/gkn756 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Makoto K. Shimada, Ryuzou Matsumoto, Yosuke Hayakawa, Ryoko Sanbonmatsu, Craig Gough, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Tadashi Imanishi, and Takashi Gojobori
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D810-D815; doi:10.1093/nar/gkn798 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Luiz Gonzaga Almeida, Noboru J. Sakabe, Alice R. deOliveira, Maria Cristina C. Silva, Alex S. Mundstein, Tzeela Cohen, Yao-Tseng Chen, Ramon Chua, Sita Gurung, Sacha Gnjatic, Achim A. Jungbluth, Otávia L. Caballero, Amos Bairoch, Eva Kiesler, Sarah L. White, Andrew J. G. Simpson, Lloyd J. Old, Anamaria A. Camargo, and Ana Tereza R. Vasconcelos
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens
Nucleic Acids Research Advance Access published on October 5, 2008
Nucl. Acids Res. 2009 37: D816-D819; doi:10.1093/nar/gkn673 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mandeep Kaur, Aleksandar Radovanovic, Magbubah Essack, Ulf Schaefer, Monique Maqungo, Tracey Kibler, Sebastian Schmeier, Alan Christoffels, Kothandaraman Narasimhan, Mahesh Choolani, and Vladimir B. Bajic
Database for exploration of functional context of genes implicated in ovarian cancer
Nucleic Acids Research Advance Access published on September 12, 2008
Nucl. Acids Res. 2009 37: D820-D823; doi:10.1093/nar/gkn593 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Christopher J. Richardson, Qiong Gao, Costas Mitsopoulous, Marketa Zvelebil, Laurence H. Pearl, and Frances M. G. Pearl
MoKCa database—mutations of kinases in cancer
Nucleic Acids Research Advance Access published on November 5, 2008
Nucl. Acids Res. 2009 37: D824-D831; doi:10.1093/nar/gkn832 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Saumyendra N. Basu, Ravi Kollu, and Sharmila Banerjee-Basu
AutDB: a gene reference resource for autism research
Nucleic Acids Research Advance Access published on November 10, 2008
Nucl. Acids Res. 2009 37: D832-D836; doi:10.1093/nar/gkn835 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sue Cotterill and Stephen E. Kearsey
DNAReplication: a database of information and resources for the eukaryotic DNA replication community
Nucleic Acids Research Advance Access published on October 17, 2008
Nucl. Acids Res. 2009 37: D837-D839; doi:10.1093/nar/gkn726 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

An-Yuan Guo, Bradley T. Webb, Michael F. Miles, Mark P. Zimmerman, Kenneth S. Kendler, and Zhongming Zhao
ERGR: An ethanol-related gene resource
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2009 37: D840-D845; doi:10.1093/nar/gkn816 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mike D. R. Croning, Michael C. Marshall, Peter McLaren, J. Douglas Armstrong, and Seth G. N. Grant
G2Cdb: the Genes to Cognition database
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D846-D851; doi:10.1093/nar/gkn700 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shamith A. Samarajiwa, Sam Forster, Katie Auchettl, and Paul J. Hertzog
INTERFEROME: the database of interferon regulated genes
Nucleic Acids Research Advance Access published on November 7, 2008
Nucl. Acids Res. 2009 37: D852-D857; doi:10.1093/nar/gkn732 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Suisheng Tang, Zhuo Zhang, Gopalakrishnan Kavitha, Eng-King Tan, and See Kiong Ng
MDPD: an integrated genetic information resource for Parkinson's disease
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D858-D862; doi:10.1093/nar/gkn770 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shivakumar Keerthikumar, Rajesh Raju, Kumaran Kandasamy, Atsushi Hijikata, Subhashri Ramabadran, Lavanya Balakrishnan, Mukhtar Ahmed, Sandhya Rani, Lakshmi Dhevi N. Selvan, Devi S. Somanathan, Somak Ray, Mitali Bhattacharjee, Sashikanth Gollapudi, Y. L. Ramachandra, Sahely Bhadra, Chiranjib Bhattacharyya, Kohsuke Imai, Shigeaki Nonoyama, Hirokazu Kanegane, Toshio Miyawaki, Akhilesh Pandey, Osamu Ohara, and Sujatha Mohan
RAPID: Resource of Asian Primary Immunodeficiency Diseases
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D863-D867; doi:10.1093/nar/gkn682 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Helen Parkinson, Misha Kapushesky, Nikolay Kolesnikov, Gabriella Rustici, Mohammad Shojatalab, Niran Abeygunawardena, Hugo Berube, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Ele Holloway, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Tim F. Rayner, Faisal Rezwan, Anjan Sharma, Eleanor Williams, Xiangqun Zheng Bradley, Tomasz Adamusiak, Marco Brandizi, Tony Burdett, Richard Coulson, Maria Krestyaninova, Pavel Kurnosov, Eamonn Maguire, Sudeshna Guha Neogi, Philippe Rocca-Serra, Susanna-Assunta Sansone, Nataliya Sklyar, Mengyao Zhao, Ugis Sarkans, and Alvis Brazma
ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression
Nucleic Acids Research Advance Access published on November 10, 2008
Nucl. Acids Res. 2009 37: D868-D872; doi:10.1093/nar/gkn889 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Diego Miranda-Saavedra, Subhajyoti De, Matthew W. Trotter, Sarah A. Teichmann, and Berthold Göttgens
BloodExpress: a database of gene expression in mouse haematopoiesis
Nucleic Acids Research Advance Access published on November 4, 2008
Nucl. Acids Res. 2009 37: D873-D879; doi:10.1093/nar/gkn854 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Viviane Praz and Philipp Bucher
CleanEx: new data extraction and merging tools based on MeSH term annotation
Nucl. Acids Res. 2009 37: D880-D884; doi:10.1093/nar/gkn878 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Rolf N. Muertter, and Ron Edgar
NCBI GEO: archive for high-throughput functional genomic data
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2009 37: D885-D890; doi:10.1093/nar/gkn764 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tin-Lap Lee, Hoi-Hung Cheung, Janek Claus, Chandan Sastry, Sumeeta Singh, Loc Vu, Owen Rennert, and Wai-Yee Chan
GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2009 37: D891-D897; doi:10.1093/nar/gkn644 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jeremy Hubble, Janos Demeter, Heng Jin, Maria Mao, Michael Nitzberg, T. B. K. Reddy, Farrell Wymore, Zachariah K. Zachariah, Gavin Sherlock, and Catherine A. Ball
Implementation of GenePattern within the Stanford Microarray Database
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D898-D901; doi:10.1093/nar/gkn786 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Florian Gnad, Mario Oroshi, Ewan Birney, and Matthias Mann
MAPU 2.0: high-accuracy proteomes mapped to genomes
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D902-D906; doi:10.1093/nar/gkn773 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Su-Jun Li, Mao Peng, Hong Li, Bo-Shu Liu, Chuan Wang, Jia-Rui Wu, Yi-Xue Li, and Rong Zeng
Sys-BodyFluid: a systematical database for human body fluid proteome research
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2009 37: D907-D912; doi:10.1093/nar/gkn849 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hong Xi, Jongsun Park, Guohui Ding, Yong-Hwan Lee, and Yixue Li
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: D913-D920; doi:10.1093/nar/gkn848 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mounir Errami, Zhaohui Sun, Tara C. Long, Angela C. George, and Harold R. Garner
Déjà vu: a database of highly similar citations in the scientific literature
Nucleic Acids Research Advance Access published on August 30, 2008
Nucl. Acids Res. 2009 37: D921-D924; doi:10.1093/nar/gkn546 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Paolo Romano, Assunta Manniello, Ottavia Aresu, Massimiliano Armento, Michela Cesaro, and Barbara Parodi
Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2009 37: D925-D932; doi:10.1093/nar/gkn730 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guangshun Wang, Xia Li, and Zhe Wang
APD2: the updated antimicrobial peptide database and its application in peptide design
Nucleic Acids Research Advance Access published on October 28, 2008
Nucl. Acids Res. 2009 37: D933-D937; doi:10.1093/nar/gkn823 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jean-Marie Rouillard and Erdogan Gulari
OligoArrayDb: pangenomic oligonucleotide microarray probe sets database
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D938-D941; doi:10.1093/nar/gkn761 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Steve Lefever, Jo Vandesompele, Frank Speleman, and Filip Pattyn
RTPrimerDB: the portal for real-time PCR primers and probes
Nucleic Acids Research Advance Access published on October 23, 2008
Nucl. Acids Res. 2009 37: D942-D945; doi:10.1093/nar/gkn777 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Emmet A. O’Brien, Yue Zhang, Eric Wang, Veronique Marie, Wole Badejoko, B. Franz Lang, and Gertraud Burger
GOBASE: an organelle genome database
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D946-D950; doi:10.1093/nar/gkn819 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chris Duran, Nikki Appleby, Terry Clark, David Wood, Michael Imelfort, Jacqueline Batley, and David Edwards
AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants
Nucleic Acids Research Advance Access published on October 14, 2008
Nucl. Acids Res. 2009 37: D951-D953; doi:10.1093/nar/gkn650 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Diego Mauricio Riaño-Pachón, Axel Nagel, Jost Neigenfind, Robert Wagner, Rico Basekow, Elke Weber, Bernd Mueller-Roeber, Svenja Diehl, and Birgit Kersten
GabiPD: the GABI primary database—a plant integrative ‘omics’ database
Nucleic Acids Research Advance Access published on September 23, 2008
Nucl. Acids Res. 2009 37: D954-D959; doi:10.1093/nar/gkn611 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, and Dong Xu
P3DB: a plant protein phosphorylation database
Nucleic Acids Research Advance Access published on October 17, 2008
Nucl. Acids Res. 2009 37: D960-D962; doi:10.1093/nar/gkn733 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Riadh Hammami, Jeannette Ben Hamida, Gérard Vergoten, and Ismail Fliss
PhytAMP: a database dedicated to antimicrobial plant peptides
Nucleic Acids Research Advance Access published on October 4, 2008
Nucl. Acids Res. 2009 37: D963-D968; doi:10.1093/nar/gkn655 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Qi Sun, Boris Zybailov, Wojciech Majeran, Giulia Friso, Paul Dominic B. Olinares, and Klaas J. van Wijk
PPDB, the Plant Proteomics Database at Cornell
Nucleic Acids Research Advance Access published on October 2, 2008
Nucl. Acids Res. 2009 37: D969-D974; doi:10.1093/nar/gkn654 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zhi-yu Peng, Xin Zhou, Linchuan Li, Xiangchun Yu, Hongjiang Li, Zhiqiang Jiang, Guangyu Cao, Mingyi Bai, Xingchun Wang, Caifu Jiang, Haibin Lu, Xianhui Hou, Lijia Qu, Zhiyong Wang, Jianru Zuo, Xiangdong Fu, Zhen Su, Songgang Li, and Hongwei Guo
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis
Nucleic Acids Research Advance Access published on November 10, 2008
Nucl. Acids Res. 2009 37: D975-D982; doi:10.1093/nar/gkn873 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Lorenz Bülow, Stefan Engelmann, Martin Schindler, and Reinhard Hehl
AthaMap, integrating transcriptional and post-transcriptional data
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2009 37: D983-D986; doi:10.1093/nar/gkn709 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Takeshi Obayashi, Shinpei Hayashi, Motoshi Saeki, Hiroyuki Ohta, and Kengo Kinoshita
ATTED-II provides coexpressed gene networks for Arabidopsis
Nucleic Acids Research Advance Access published on October 25, 2008
Nucl. Acids Res. 2009 37: D987-D991; doi:10.1093/nar/gkn807 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gaëtan Droc, Christophe Périn, Sébastien Fromentin, and Pierre Larmande
OryGenesDB 2008 update: database interoperability for functional genomics of rice
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: D992-D995; doi:10.1093/nar/gkn821 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Supat Thongjuea, Vinitchan Ruanjaichon, Richard Bruskiewich, and Apichart Vanavichit
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome
Nucleic Acids Research Advance Access published on September 27, 2008
Nucl. Acids Res. 2009 37: D996-D1000; doi:10.1093/nar/gkn638 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Uma Maheswari, Thomas Mock, E. Virginia Armbrust, and Chris Bowler
Update of the Diatom EST Database: a new tool for digital transcriptomics
Nucleic Acids Research Advance Access published on November 23, 2008
Nucl. Acids Res. 2009 37: D1001-D1005; doi:10.1093/nar/gkn905 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marie-Paule Lefranc, Véronique Giudicelli, Chantal Ginestoux, Joumana Jabado-Michaloud, Géraldine Folch, Fatena Bellahcene, Yan Wu, Elodie Gemrot, Xavier Brochet, Jérôme Lane, Laetitia Regnier, François Ehrenmann, Gérard Lefranc, and Patrice Duroux
IMGT®, the international ImMunoGeneTics information system®
Nucleic Acids Research Advance Access published on October 31, 2008
Nucl. Acids Res. 2009 37: D1006-D1012; doi:10.1093/nar/gkn838 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

James Robinson, Matthew J. Waller, Sylvie C. Fail, Hamish McWilliam, Rodrigo Lopez, Peter Parham, and Steven G. E. Marsh
The IMGT/HLA database
Nucleic Acids Research Advance Access published on October 5, 2008
Nucl. Acids Res. 2009 37: D1013-D1017; doi:10.1093/nar/gkn662 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nelson Axelrod, Yuan Lin, Pauline C. Ng, Timothy B. Stockwell, Jonathan Crabtree, Jiaqi Huang, Ewen Kirkness, Robert L. Strausberg, Marvin E. Frazier, J. Craig Venter, Saul Kravitz, and Samuel Levy
The HuRef Browser: a web resource for individual human genomics
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: D1018-D1024; doi:10.1093/nar/gkn939 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Guoqing Li, Lijia Ma, Chao Song, Zhentao Yang, Xiulan Wang, Hui Huang, Yingrui Li, Ruiqiang Li, Xiuqing Zhang, Huanming Yang, Jian Wang, and Jun Wang
The YH database: the first Asian diploid genome database
Nucl. Acids Res. 2009 37: D1025-D1028; doi:10.1093/nar/gkn966 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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Nucleic Acids Research: VOLUME 37 DATABASE ISSUE JANUARY 1, 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkn1017 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkn1016 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkn1021 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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