Nucleic Acids Research, Volume 37

Volume 37, Number Database-Issue, January 2009

• Michael Y. Galperin, Guy Cochrane:
  Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009. 1-4
  
• 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 Karsch-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, Jian Ye:
  Database resources of the National Center for Biotechnology Information. 5-15
  
• Hideaki Sugawara, Kazuho Ikeo, Satoshi Fukuchi, Takashi Gojobori, Yoshio Tateno:
  DDBJ dealing with mass data produced by the second generation sequencer. 16-18
  
• Guy Cochrane, Ruth Akhtar, James K. Bonfield, Lawrence Bower, Fehmi Demiralp, Nadeem Faruque, Richard Gibson, Gemma Hoad, Tim J. P. 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, Ewan Birney:
  Petabyte-scale innovations at the European Nucleotide Archive. 19-25
  
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
  GenBank. 26-31
  
• Kim D. Pruitt, Tatiana A. Tatusova, William Klimke, Donna R. Maglott:
  NCBI Reference Sequences: current status, policy and new initiatives. 32-36
  
• Maik Friedel, Swetlana Nikolajewa, Jürgen Sühnel, Thomas Wilhelm:
  DiProDB: a database for dinucleotide properties. 37-40
  
• 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, Carlo Maria Croce:
  UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. 41-48
  
• Budrul Ahsan, Taro L. Saito, Shin-ichi Hashimoto, Keigo Muramatsu, Manabu Tsuda, Atsushi Sasaki, Kouji Matsushima, Toshiro Aigaki, Shinichi Morishita:
  MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. 49-53
  
• Elodie Portales-Casamar, David J. Arenillas, Jonathan S. Lim, Magdalena I. Swanson, Steven Jiang, Anthony McCallum, Stefan Kirov, Wyeth W. Wasserman:
  The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. 54-60
  
• Andreas Grote, Johannes Klein, Ida Retter, Isam Haddad, Susanne Behling, Boyke Bunk, Ilona Biegler, Svitlana Yarmolinetz, Dieter Jahn, Richard Münch:
  PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. 61-65
  
• Logan Everett, Antony Vo, Sridhar Hannenhalli:
  PTM-Switchboard - a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. 66-71
  
• Grant H. Jacobs, Augustine Chen, Stewart G. Stevens, Peter A. Stockwell, Michael A. Black, Warren Tate, Chris M. Brown:
  Transterm: a database to aid the analysis of regulatory sequences in mRNAs. 72-76
  
• Daniel E. Newburger, Martha L. Bulyk:
  UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. 77-82
  
• Yurong Xin, Wilma K. Olson:
  BPS: a database of RNA base-pair structures. 83-88
  
• Toutai Mituyama, Kouichirou Yamada, Emi Hattori, Hiroaki Okida, Yukiteru Ono, Goro Terai, Aya Yoshizawa, Takashi Komori, Kiyoshi Asai:
  The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. 89-92
  
• Patricia P. Chan, Todd M. Lowe:
  GtRNAdb: a database of transfer RNA genes detected in genomic sequence. 93-97
  
• Qinghua Jiang, Yadong Wang, Yangyang Hao, Liran Juan, Mingxiang Teng, Xinjun Zhang, Meimei Li, Guohua Wang, Yunlong Liu:
  miR2Disease: a manually curated database for microRNA deregulation in human disease. 98-104
  
• Feifei Xiao, Zhixiang Zuo, Guoshuai Cai, Shuli Kang, Xiaolian Gao, Tongbin Li:
  miRecords: an integrated resource for microRNA-target interactions. 105-110
  
• Daniel Gerlach, Evgenia V. Kriventseva, Nazim Rahman, Charles E. Vejnar, Evgeni M. Zdobnov:
  miROrtho: computational survey of microRNA genes. 111-117
  
• Anna Czerwoniec, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Katarzyna H. Kaminska, Joanna M. Kasprzak, Janusz M. Bujnicki, Henri Grosjean, Kristian Rother: MODOMICS: a database of RNA modification pathways. 2008 update. 118-121 http: //dx.doi.org/10.1093/nar/gkn710
• Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, Mark L. Crowe, Sean M. Grimmond, John S. Mattick:
  NRED: a database of long noncoding RNA expression. 122-126
  
• Michela Taufer, Abel Licon, Roberto Araiza, David Mireles, F. H. D. van Batenburg, Alexander P. Gultyaev, Ming-Ying Leung:
  PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. 127-135
  
• 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, Alex Bateman:
  Rfam: updates to the RNA families database. 136-140
  
• James R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, Ryan J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, Terry L. Marsh, George M. Garrity, James M. Tiedje:
  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. 141-145
  
• Yongliang Ren, Wuming Gong, Haiyan Zhou, Yejun Wang, Feifei Xiao, Tongbin Li:
  siRecords: a database of mammalian RNAi experiments and efficacies. 146-149
  
• Hsi-Yuan Huang, Heng-Yi Chang, Chih-Hung Chou, Ching-Ping Tseng, Shinn-Ying Ho, Chi-Dung Yang, Yih-Wei Ju, Hsien-Da Huang:
  sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. 150-154
  
• Giorgos L. Papadopoulos, Martin Reczko, Victor A. Simossis, Praveen Sethupathy, Artemis G. Hatzigeorgiou:
  The database of experimentally supported targets: a functional update of TarBase. 155-158
  
• Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, Joern Pütz:
  tRNAdb 2009: compilation of tRNA sequences and tRNA genes. 159-162
  
• Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi:
  tRNADB-CE: tRNA gene database curated manually by experts. 163-168
  
• The UniProt Consortium:
  The Universal Protein Resource (UniProt) 2009. 169-174
  
• Rubén Nogales-Cadenas, Federico Abascal, Javier Díez-Pérez, José María Carazo, Alberto D. Pascual-Montano:
  CentrosomeDB: a human centrosomal proteins database. 175-180
  
• Yasmeen Ahmad, François-Michel Boisvert, Peter Gregor, Andy Cobley, Angus I. Lamond:
  NOPdb: Nucleolar Proteome Database - 2008 update. 181-184
  
• Sanguthevar Rajasekaran, Sudha Balla, Patrick Gradie, Michael R. Gryk, Krishna Kadaveru, Vamsi Kundeti, Mark W. Maciejewski, Tian Mi, Nicholas Rubino, Jay Vyas, Martin R. Schiller:
  Minimotif miner 2nd release: a database and web system for motif search. 185-190
  
• Jason E. Donald, Eugene I. Shakhnovich:
  SDR: a database of predicted specificity-determining residues in proteins. 191-194
  
• Raphael André Bauer, Stefan Günther, Dominic Jansen, Carolin Heeger, Paul Florian Thaben, Robert Preissner:
  SuperSite: dictionary of metabolite and drug binding sites in proteins. 195-200
  
• M. Michael Gromiha, Yukimitsu Yabuki, M. Xavier Suresh, A. Mary Thangakani, Makiko Suwa, Kazuhiko Fukui:
  TMFunction: database for functional residues in membrane proteins. 201-204
  
• 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, Stephen H. Bryant:
  CDD: specific functional annotation with the Conserved Domain Database. 205-210
  
• 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 H. 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 J. Mulder, Darren A. Natale, Christine A. Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. A. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats:
  InterPro: the integrative protein signature database. 211-215
  
• 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, Tatiana A. Tatusova:
  The National Center for Biotechnology Information's Protein Clusters Database. 216-223
  
• Abraham O. Samson, Michael Levitt:
  Protein segment finder: an online search engine for segment motifs in the PDB. 224-228
  
• Ivica Letunic, Tobias Doerks, Peer Bork:
  SMART 6: recent updates and new developments. 229-232
  
• Brandi L. Cantarel, Pedro M. Coutinho, Corinne Rancurel, Thomas Bernard, Vincent Lombard, Bernard Henrissat:
  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. 233-238
  
• Víctor Quesada, Gonzalo R. Ordóñez, Luis M. Sánchez, Xose S. Puente, Carlos López-Otín:
  The Degradome database: mammalian proteases and diseases of proteolysis. 239-243
  
• David M. A. Martin, Diego Miranda-Saavedra, Geoffrey J. Barton:
  Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. 244-250
  
• Chuan-Yun Li, Qing-Rong Liu, Ping-Wu Zhang, Xiao-Mo Li, Liping Wei, George R. Uhl:
  OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. 251-260
  
• Dominique Koua, Lorenzo Cerutti, Laurent Falquet, Christian J. A. Sigrist, Grégory Theiler, Nicolas Hulo, Christophe Dunand:
  PeroxiBase: a database with new tools for peroxidase family classification. 261-266
  
• Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li, Hans-Jürgen Thiesen:
  SysZNF: the C2H2 zinc finger gene database. 267-273
  
• Milton H. Saier Jr., Ming Ren Yen, Keith Noto, Dorjee G. Tamang, Charles Elkan:
  The Transporter Classification Database: recent advances. 274-278
  
• Fengli Fu, Jeffry D. Sander, Morgan Maeder, Stacey Thibodeau-Beganny, J. Keith Joung, Drena Dobbs, Leslie L. Miller, Daniel F. Voytas:
  Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. 279-283
  
• Joel Masciocchi, Gianfranco Frau, Marco Fanton, Mattia Sturlese, Matteo Floris, Luca Pireddu, Piergiorgio Palla, Fabian Cedrati, Patricia Rodriguez-Tomé, Stefano Moro:
  MMsINC: a large-scale chemoinformatics database. 284-290
  
• Mathias Dunkel, Ulrike Schmidt, Swantje Struck, Lena Berger, Bjoern Gruening, Julia Hossbach, Ines S. Jaeger, Uta Effmert, Birgit Piechulla, Roger Eriksson, Jette Knudsen, Robert Preissner:
  SuperScent - a database of flavors and scents. 291-294
  
• Ulrike Schmidt, Swantje Struck, Bjoern Gruening, Julia Hossbach, Ines S. Jaeger, Roza Parol, Ulrike Lindequist, Eberhard Teuscher, Robert Preissner:
  SuperToxic: a comprehensive database of toxic compounds. 295-299
  
• Amelie Stein, Alejandro Panjkovich, Patrick Aloy:
  3did Update: domain-domain and peptide-mediated interactions of known 3D structure. 300-304
  
• Masafumi Shionyu, Akihiro Yamaguchi, Kazuki Shinoda, Ken-ichi Takahashi, Mitiko Go:
  AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. 305-309
  
• Alison L. Cuff, Ian Sillitoe, Tony Lewis, Oliver Redfern, Richard Garratt, Janet M. Thornton, Christine A. Orengo:
  The CATH classification revisited - architectures reviewed and new ways to characterize structural divergence in superfamilies. 310-314
  
• Oliver D. Testa, Efrosini Moutevelis, Derek N. Woolfson:
  CC+: a relational database of coiled-coil structures. 315-322
  
• Ofir Goldenberg, Elana Erez, Guy Nimrod, Nir Ben-Tal:
  The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. 323-327
  
• Wei-Cheng Lo, Chi-Ching Lee, Che-Yu Lee, Ping-Chiang Lyu:
  CPDB: a database of circular permutation in proteins. 328-332
  
• Satoshi Fukuchi, Keiichi Homma, Shigetaka Sakamoto, Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori, Ken Nishikawa:
  The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. 333-337
  
• Stefan Günther, Joachim von Eichborn, Patrick May, Robert Preissner:
  JAIL: a structure-based interface library for macromolecules. 338-341
  
• Natalya S. Bogatyreva, Alexander A. Osypov, Dmitry N. Ivankov:
  KineticDB: a database of protein folding kinetics. 342-346
  
• Ursula Pieper, Narayanan Eswar, Ben M. Webb, David Eramian, Libusha Kelly, David T. Barkan, Hannah Carter, Parminder Mankoo, Rachel Karchin, Marc A. Martí-Renom, Fred P. Davis, Andrej Sali:
  MODBASE, a database of annotated comparative protein structure models and associated resources. 347-354
  
• Roman A. Laskowski:
  PDBsum new things. 355-359
  
• Miho Higurashi, Takashi Ishida, Kengo Kinoshita:
  PiSite: a database of protein interaction sites using multiple binding states in the PDB. 360-364
  
• 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, Joshua La Baer:
  The protein structure initiative structural genomics knowledgebase. 365-368
  
• Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson:
  RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases. 369-373
  
• Mathieu Lonquety, Zoé Lacroix, Nikolaos Papandreou, Jacques Chomilier:
  SPROUTS: a database for the evaluation of protein stability upon point mutation. 374-379
  
• Derek Wilson, Ralph Pethica, Yiduo Zhou, Charles Talbot, Christine Vogel, Martin Madera, Cyrus Chothia, Julian Gough:
  SUPERFAMILY - sophisticated comparative genomics, data mining, visualization and phylogeny. 380-386
  
• Florian Kiefer, Konstantin Arnold, Michael Künzli, Lorenza Bordoli, Torsten Schwede:
  The SWISS-MODEL Repository and associated resources. 387-392
  
• Kristian Rother, Peter Werner Hildebrand, Andrean Goede, Bjoern Gruening, Robert Preissner:
  Voronoia: analyzing packing in protein structures. 393-395
  
• Daniel Barrell, Emily Dimmer, Rachael P. Huntley, David Binns, Claire O'Donovan, Rolf Apweiler:
  The GOA database in 2009 - an integrated Gene Ontology Annotation resource. 396-403
  
• Estelle Proux, Romain A. Studer, Sébastien Moretti, Marc Robinson-Rechavi:
  Selectome: a database of positive selection. 404-407
  
• 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, Dmitrij Frishman:
  PEDANT covers all complete RefSeq genomes. 408-411
  
• Lars Juhl Jensen, Michael Kuhn, Manuel Stark, Samuel Chaffron, Chris Creevey, Jean Muller, Tobias Doerks, Philippe Julien, Alexander Roth, Milan Simonovic, Peer Bork, Christian von Mering:
  STRING 8 - a global view on proteins and their functional interactions in 630 organisms. 412-416
  
• William Fu, Brigitte E. Sanders-Beer, Kenneth S. Katz, Donna R. Maglott, Kim D. Pruitt, Roger G. Ptak:
  Human immunodeficiency virus type 1, human protein interaction database at NCBI. 417-422
  
• In Seok Yang, Joo-Yeon Lee, Joon Seung Lee, Wayne P. Mitchell, Hee-Bok Oh, Chun Kang, Kyung Hyun Kim:
  Influenza sequence and epitope database. 423-430
  
• Robert Belshaw, Tulio de Oliveira, Sidney Markowitz, Andrew Rambaut:
  The RNA Virus Database. 431-435
  
• Mauricio Carrillo-Tripp, Craig M. Shepherd, Ian A. Borelli, Sangita Venkataraman, Gabriel Lander, Padmaja Natarajan, John E. Johnson, Charles L. Brooks III, Vijay S. Reddy:
  VIPERdb²: an enhanced and web API enabled relational database for structural virology. 436-442
  
• Bo Liu, Mihai Pop:
  ARDB - Antibiotic Resistance Genes Database. 443-447
  
• Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf, Eugene V. Koonin, Inna Dubchak:
  ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. 448-454
  
• Ren Zhang, Yan Lin:
  DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. 455-458
  
• Fenglou Mao, PhuongAn Dam, Jacky Chou, Victor Olman, Ying Xu:
  DOOR: a database for prokaryotic operons. 459-463
  
• Ingrid M. Keseler, César Bonavides-Martínez, Julio Collado-Vides, Socorro Gama-Castro, Robert P. Gunsalus, D. Aaron Johnson, Markus Krummenacker, Laura M. Nolan, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Alberto D. Santos-Zavaleta, Alexander Glennon Shearer, Peter D. Karp:
  EcoCyc: A comprehensive view of Escherichia coli biology. 464-470
  
• 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, Amos Bairoch:
  HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. 471-478
  
• Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff, Steven L. Salzberg:
  OperonDB: a comprehensive database of predicted operons in microbial genomes. 479-482
  
• Geoffrey L. Winsor, Thea Van Rossum, Raymond Lo, Bhavjinder Khaira, Matthew D. Whiteside, Robert E. W. Hancock, Fiona S. L. Brinkman:
  Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. 483-488
  
• Zarraz May-Ping Lee, Carl Bussema III, Thomas M. Schmidt:
  rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. 489-493
  
• Johannes Klein, Richard Münch, Ilona Biegler, Isam Haddad, Ida Retter, 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). 494-498
  
• T. B. K. Reddy, Robert Riley, Farrell Wymore, Phillip Montgomery, David 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, Gary K. Schoolnik:
  TB database: an integrated platform for tuberculosis research. 499-508
  
• Jane E. Mabey Gilsenan, Graham Atherton, Jennifer Bartholomew, Peter F. Giles, Teresa K. Attwood, David W. Denning, Paul Bowyer:
  Aspergillus Genomes and the Aspergillus Cloud. 509-514
  
• Petra Fey, Pascale Gaudet, Tomaz Curk, Blaz Zupan, Eric M. Just, Siddhartha Basu, Sohel N. Merchant, Yulia A. Bushmanova, Gad Shaulsky, Warren A. Kibbe, Rex L. Chisholm:
  dictyBase - a Dictyostelium bioinformatics resource update. 515-519
  
• Hiroyuki Wakaguri, Yutaka Suzuki, Toshiaki Katayama, Shuichi Kawashima, Eri Kibukawa, Kazushi Hiranuka, Masahide Sasaki, Sumio Sugano, Junichi Watanabe:
  Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009. 520-525
  
• Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jane M. Carlton, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Gregory R. 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, Haiming Wang:
  GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. 526-530
  
• John W. Whitaker, Ivica Letunic, Glenn A. McConkey, David R. Westhead:
  metaTIGER: a metabolic evolution resource. 531-538
  
• Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Gregory R. 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, Haiming Wang:
  PlasmoDB: a functional genomic database for malaria parasites. 539-543
  
• Alejandro A. Ackermann, Santiago J. Carmona, Fernán Agüero:
  TcSNP: a database of genetic variation in Trypanosoma cruzi. 544-549
  
• David James Sherman, Tiphaine Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, Pascal Durrens:
  Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. 550-554
  
• Susan Tweedie, Michael Ashburner, Kathleen Falls, Paul Leyland, Peter McQuilton, Steven Marygold, Gillian H. Millburn, David Osumi-Sutherland, Andrew Schroeder, Ruth Seal, Haiyan Zhang:
  FlyBase: enhancing Drosophila Gene Ontology annotations. 555-559
  
• Andrei Pisarev, Ekaterina Poustelnikova, Maria Samsonova, John Reinitz:
  FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. 560-566
  
• Doris Chen, Jürg Berger, Michaela Fellner, Takashi Suzuki:
  FLYSNPdb: a high-density SNP database of Drosophila melanogaster. 567-570
  
• John C. Martin, Sahar Abubucker, Todd Wylie, Yong Yin, Zhengyuan Wang, Makedonka Dautova Mitreva:
  Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. 571-578
  
• Adhemar Zerlotini, Mark Heiges, Haiming Wang, Romulo L. V. Moraes, Anderson J. Dominitini, Jerônimo C. Ruiz, Jessica C. Kissinger, Guilherme Oliveira:
  SchistoDB: a Schistosoma mansoni genome resource. 579-582
  
• 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, Gregory R. 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, Frank H. Collins:
  VectorBase: a data resource for invertebrate vector genomics. 583-587
  
• Antje Chang, Maurice Scheer, Andreas Grote, Ida Schomburg, Dietmar Schomburg:
  BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. 588-592
  
• Andrew G. McDonald, Sinéad Boyce, Keith F. Tipton:
  ExplorEnz: the primary source of the IUBMB enzyme list. 593-597
  
• Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia, Ildefonso Cases:
  Bionemo: molecular information on biodegradation metabolism. 598-602
  
• David S. Wishart, Craig Knox, Anchi 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, Russell Greiner, Alsu Nazyrova, Rustem Shaykhutdinov, Liang Li, Hans J. Vogel, Ian J. Forsythe:
  HMDB: a knowledgebase for the human metabolome. 603-610
  
• Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael L. Blinov, Salmaz S. Ibragimova, Sarah Boyd, Boris Ratnikov, Piotr Cieplak, Adam Godzik, Jeffrey W. Smith, Andrei Osterman, Alexey M. Eroshkin:
  PMAP: databases for analyzing proteolytic events and pathways. 611-618
  
• Lisa Matthews, Gopal Gopinath, Marc Gillespie, Michael Caudy, David Croft, Bernard de Bono, Phani Garapati, Jill Hemish, Henning Hermjakob, Bijay Jassal, Alexander Kanapin, Suzanna Lewis, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik, Guanming Wu, Ewan Birney, Lincoln Stein, Peter D'Eustachio:
  Reactome knowledgebase of human biological pathways and processes. 619-622
  
• Atanas Kamburov, Christoph K. Wierling, Hans Lehrach, Ralf Herwig:
  ConsensusPathDB - a database for integrating human functional interaction networks. 623-628
  
• Eduardo Andrés León, Iakes Ezkurdia, Beatriz García, Alfonso Valencia, David de Juan:
  EcID. A database for the inference of functional interactions in E. coli. 629-635
  
• Pankaj Kumar, Bu-Cong Han, Z. Shi, J. Jia, Y. P. Wang, Y. T. Zhang, L. Liang, Q. F. Liu, Zhi Liang Ji, Y. Z. Chen:
  Update of KDBI: Kinetic Data of Bio-molecular Interaction database. 636-641
  
• V. Glenn Tarcea, Terry E. Weymouth, Alexander S. Ade, Aaron V. Bookvich, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Özgür, Yuanyuan Tian, Jim Cavalcoli, Barbara Mirel, Jignesh M. Patel, Dragomir R. Radev, Brian D. Athey, David J. States, H. V. Jagadish:
  Michigan molecular interactions r2: from interacting proteins to pathways. 642-646
  
• Tim Driscoll, Matthew D. Dyer, T. M. Murali, Bruno W. S. Sobral:
  PIG - the pathogen interaction gateway. 647-650
  
• Mark D. McDowall, Michelle S. Scott, Geoffrey J. Barton:
  PIPs: human protein-protein interaction prediction database. 651-656
  
• Gautam Chaurasia, Soniya Malhotra, Jenny Russ, Sigrid Schnoegl, Christian Hänig, Erich E. Wanker, Matthias E. Futschik:
  UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. 657-660
  
• Vincent Navratil, Benoît de Chassey, Laurène Meyniel, Stéphane Delmotte, Christian Gautier, Patrice André, Vincent Lotteau, Chantal Rabourdin-Combe:
  VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. 661-668
  
• Andrew Chatr-aryamontri, Arnaud Ceol, Daniele Peluso, Aurelio Nardozza, Simona Panni, Francesca Sacco, Michele Tinti, Alex Smolyar, Luisa Castagnoli, Marc Vidal, Michael E. Cusick, Gianni Cesareni:
  VirusMINT: a viral protein interaction database. 669-673
  
• Carl F. Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay, Kenneth H. Buetow:
  PID: the Pathway Interaction Database. 674-679
  
• 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, Michael Spedding:
  IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. 680-685
  
• Byungwook Lee, Gwangsik Shin:
  CleanEST: a database of cleansed EST libraries. 686-689
  
• Tim J. P. Hubbard, B. L. Aken, Sarah C. Ayling, Benoit Ballester, Kathryn Beal, E. Bragin, S. Brent, Yuan Chen, P. Clapham, Laura Clarke, G. Coates, S. Fairley, S. Fitzgerald, J. Fernandez-Banet, L. Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Andrew M. Jenkinson, N. Johnson, Andreas Kähäri, Damian Keefe, S. Keenan, R. Kinsella, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, I. Longden, Karine Megy, Patrick Meidl, B. Overduin, A. Parker, B. Pritchard, D. Rios, M. Schuster, Guy Slater, Damian Smedley, William Spooner, G. Spudich, S. Trevanion, Albert J. Vilella, J. Vogel, S. White, S. Wilder, Arek Zadissa, Ewan Birney, Fiona Cunningham, Val Curwen, Richard Durbin, X. M. Fernandez-Suarez, Javier Herrero, Arek Kasprzyk, Glenn Proctor, James Smith, Stephen M. J. Searle, Paul Flicek:
  Ensembl 2009. 690-697
  
• Dae-Soo Kim, Chi-Young Cho, Jae-Won Huh, Heui-Soo Kim, Hwan-Gue Cho:
  EVOG: a database for evolutionary analysis of overlapping genes. 698-702
  
• Ashwini Bhasi, Philge Philip, Vinu Manikandan, Periannan Senapathy:
  ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. 703-711
  
• Judith A. Blake, Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson:
  The Mouse Genome Database genotypes: : phenotypes. 712-719
  
• Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult, Molly A. Bogue:
  Mouse Phenome Database. 720-730
  
• Tim Hulsen, Peter M. A. Groenen, Jacob de Vlieg, Wynand Alkema:
  PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. 731-737
  
• Hugo Y. K. Lam, Ekta Khurana, Gang Fang, Philip Cayting, Nicholas Carriero, Kei-Hoi Cheung, Mark B. Gerstein:
  Pseudofam: the pseudogene families database. 738-743
  
• Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-Gungor, Jeffrey DePons, Stanley Laulederkind, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer Smith, Alexander Stoddard, Simon N. Twigger, Howard J. Jacob:
  The Rat Genome Database 2009: variation, ontologies and pathways. 744-749
  
• R. Andrew Cameron, Manoj Samanta, Autumn Yuan, Dong He, Eric H. Davidson:
  SpBase: the sea urchin genome database and web site. 750-754
  
• Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, T. Wang, Kayla E. Smith, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, M. Pheasant, L. Meyer, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Belinda Giardine, P. Fujita, Mark Diekhans, T. Dreszer, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
  The UCSC Genome Browser Database: update 2009. 755-761
  
• Yukio Maruyama, Ai Wakamatsu, Yoshifumi Kawamura, Kouichi Kimura, Jun-ichi Yamamoto, Tetsuo Nishikawa, Yasutomo Kisu, Sumio Sugano, Naoki Goshima, Takao Isogai, Nobuo Nomura:
  Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. 762-766
  
• 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, S. Sujatha Mohan, Prathibha Ranganathan, Subhashri Ramabadran, Raghothama Chaerkady, Akhilesh Pandey:
  Human Protein Reference Database - 2009 update. 767-772
  
• 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, Akhilesh Pandey:
  Human Proteinpedia: a unified discovery resource for proteomics research. 773-781
  
• Nobutaka Mitsuhashi, Kaori Fujieda, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi, Kousaku Okubo:
  BodyParts3D: 3D structure database for anatomical concepts. 782-785
  
• Allan Peter Davis, Cynthia G. Murphy, Cynthia A. Saraceni-Richards, Michael C. Rosenstein, Thomas C. Wiegers, Carolyn J. Mattingly:
  Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. 786-792
  
• Joanna S. Amberger, Carol A. Bocchini, Alan F. Scott, Ada Hamosh:
  McKusick's Online Mendelian Inheritance in Man (OMIM®). 793-796
  
• Gudmundur A. Thorisson, Owen Lancaster, Robert C. Free, Robert K. Hastings, Pallavi Sarmah, Debasis Dash, Samir K. Brahmachari, Anthony J. Brookes:
  HGVbaseG2P: a central genetic association database. 797-802
  
• Alexander R. Pico, Ivan V. Smirnov, Jeffrey S. Chang, Ru-Fang Yeh, Joseph Wiemels, John Wiencke, Tarik Tihan, Bruce R. Conklin, Margaret R. Wrensch:
  SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. 803-809
  
• Makoto K. Shimada, Ryuzou Matsumoto, Yosuke Hayakawa, Ryoko Sanbonmatsu, Craig Gough, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Tadashi Imanishi, Takashi Gojobori:
  VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. 810-815
  
• 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, Otavia L. Caballero, Amos Bairoch, Eva Kiesler, Sarah L. White, Andrew J. G. Simpson, Lloyd J. Old, Anamaria A. Camargo, Ana Tereza R. Vasconcelos:
  CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. 816-819
  
• Mandeep Kaur, Aleksandar Radovanovic, Magbubah Essack, Ulf Schaefer, Monique Maqungo, Tracey Kibler, Sebastian Schmeier, Alan Christoffels, Kothandaraman Narasimhan, Mahesh Choolani, Vladimir B. Bajic:
  Database for exploration of functional context of genes implicated in ovarian cancer. 820-823
  
• Christopher J. Richardson, Qiong Gao, Costas Mitsopoulous, Marketa Zvelebil, Laurence H. Pearl, Frances M. G. Pearl:
  MoKCa database - mutations of kinases in cancer. 824-831
  
• Saumyendra N. Basu, Ravi Kollu, Sharmila Banerjee-Basu:
  AutDB: a gene reference resource for autism research. 832-836
  
• Sue Cotterill, Stephen E. Kearsey:
  DNAReplication: a database of information and resources for the eukaryotic DNA replication community. 837-839
  
• An-Yuan Guo, Bradley T. Webb, Michael F. Miles, Mark P. Zimmerman, Kenneth S. Kendler, Zhongming Zhao:
  ERGR: An ethanol-related gene resource. 840-845
  
• Michael D. R. Croning, Michael C. Marshall, Peter McLaren, J. Douglas Armstrong, Seth G. N. Grant:
  G2Cdb: the Genes to Cognition database. 846-851
  
• Shamith A. Samarajiwa, Sam Forster, Katie Auchettl, Paul J. Hertzog:
  INTERFEROME: the database of interferon regulated genes. 852-857
  
• Suisheng Tang, Zhuo Zhang, Gopalakrishnan Kavitha, Eng-King Tan, See-Kiong Ng:
  MDPD: an integrated genetic information resource for Parkinson's disease. 858-862
  
• 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, S. Sujatha Mohan:
  RAPID: Resource of Asian Primary Immunodeficiency Diseases. 863-867
  
• Helen E. Parkinson, Misha Kapushesky, Nikolay Kolesnikov, Gabriella Rustici, Mohammadreza 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 Ibne 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, Alvis Brazma:
  ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. 868-872
  
• Diego Miranda-Saavedra, Subhajyoti De, Matthew W. Trotter, Sarah A. Teichmann, Berthold Göttgens:
  BloodExpress: a database of gene expression in mouse haematopoiesis. 873-879
  
• Viviane Praz, Philipp Bucher:
  CleanEx: new data extraction and merging tools based on MeSH term annotation. 880-884
  
• 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, Ron Edgar:
  NCBI GEO: archive for high-throughput functional genomic data. 885-890
  
• Tin-Lap Lee, Hoi-Hung Cheung, Janek Claus, Chandan Sastry, Sumeeta Singh, Loc Vu, Owen Rennert, Wai-Yee Chan:
  GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development. 891-897
  
• Jeremy Hubble, Janos Demeter, Heng Jin, Maria Mao, Michael Nitzberg, T. B. K. Reddy, Farrell Wymore, Zachariah K. Zachariah, Gavin Sherlock, Catherine A. Ball:
  Implementation of GenePattern within the Stanford Microarray Database. 898-901
  
• Florian Gnad, Mario Oroshi, Ewan Birney, Matthias Mann:
  MAPU 2.0: high-accuracy proteomes mapped to genomes. 902-906
  
• Su-Jun Li, Mao Peng, Hong Li, Boshu Liu, Chuan Wang, Jia-Rui Wu, Yi-Xue Li, Rong Zeng:
  Sys-BodyFluid: a systematical database for human body fluid proteome research. 907-912
  
• Hong Xi, Jongsun Park, Guohui Ding, Yong-Hwan Lee, Yixue Li:
  SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. 913-920
  
• Mounir Errami, Zhaohui Sun, Tara C. Long, Angela C. George, Harold R. Garner:
  Déjà vu: a database of highly similar citations in the scientific literature. 921-924
  
• Paolo Romano, Maria Assunta Manniello, Ottavia Aresu, Massimiliano Armento, Michela Cesaro, Barbara Parodi:
  Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines. 925-932
  
• Guangshun Wang, Xia Li, Zhe Wang:
  APD2: the updated antimicrobial peptide database and its application in peptide design. 933-937
  
• Jean-Marie Rouillard, Erdogan Gulari:
  OligoArrayDb: pangenomic oligonucleotide microarray probe sets database. 938-941
  
• Steve Lefever, Jo Vandesompele, Frank Speleman, Filip Pattyn:
  RTPrimerDB: the portal for real-time PCR primers and probes. 942-945
  
• Emmet A. O'Brien, Yue Zhang, Eric Wang, Veronique Marie, Wole Badejoko, B. Franz Lang, Gertraud Burger:
  GOBASE: an organelle genome database. 946-950
  
• Chris Duran, Nikki Appleby, Terry Clark, David Wood, Michael Imelfort, Jacqueline Batley, David Edwards:
  AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. 951-953
  
• Diego Mauricio Riaño-Pachón, Axel Nagel, Jost Neigenfind, Robert Wagner, Rico Basekow, Elke Weber, Bernd Mueller-Roeber, Svenja Diehl, Birgit Kersten:
  GabiPD: the GABI primary database - a plant integrative 'omics' database. 954-959
  
• Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, Dong Xu:
  P³DB: a plant protein phosphorylation database. 960-962
  
• Riadh Hammami, Jeannette Ben Hamida, Gérard Vergoten, Ismail Fliss:
  PhytAMP: a database dedicated to antimicrobial plant peptides. 963-968
  
• Qi Sun, Boris Zybailov, Wojciech Majeran, Giulia Friso, Paul Dominic B. Olinares, Klaas J. van Wijk:
  PPDB, the Plant Proteomics Database at Cornell. 969-974
  
• 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, Hongwei Guo:
  Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis. 975-982
  
• Lorenz Bülow, Stefan Engelmann, Martin Schindler, Reinhard Hehl:
  AthaMap, integrating transcriptional and post-transcriptional data. 983-986
  
• Takeshi Obayashi, Shinpei Hayashi, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita:
  ATTED-II provides coexpressed gene networks for Arabidopsis. 987-991
  
• Gaëtan Droc, Christophe Périn, Sébastien Fromentin, Pierre Larmande:
  OryGenesDB 2008 update: database interoperability for functional genomics of rice. 992-995
  
• Supat Thongjuea, Vinitchan Ruanjaichon, Richard M. Bruskiewich, Apichart Vanavichit:
  RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. 996-1000
  
• Uma Maheswari, Thomas Mock, E. Virginia Armbrust, Chris Bowler:
  Update of the Diatom EST Database: a new tool for digital transcriptomics. 1001-1005
  
• 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, Patrice Duroux:
  IMGT®, the international ImMunoGeneTics information system®. 1006-1012
  
• James Robinson, Matthew J. Waller, Sylvie C. Fail, Hamish McWilliam, Rodrigo Lopez, Peter Parham, Steven G. E. Marsh:
  The IMGT/HLA database. 1013-1017
  
• Nelson Axelrod, Yuan Lin, Pauline C. Ng, Timothy B. Stockwell, Jonathan Crabtree, Jiaqi Huang, Ewen Kirkness, Robert Strausberg, Marvin Frazier, J. Craig Venter, Saul Kravitz, Samuel Levy:
  The HuRef Browser: a web resource for individual human genomics. 1018-1024
  
• Guoqing Li, Lijia Ma, Chao Song, Zhentao Yang, Xiulan Wang, Hui Huang, Yingrui Li, Ruiqiang Li, Xiuqing Zhang, Huanming Yang, Jian Wang, Jun Wang:
  The YH database: the first Asian diploid genome database. 1025-1028
  

Volume 37, Number Web-Server-Issue, July 2009

• Gary Benson:
  Nucleic Acids Research annual Web Server Issue in 2009. 1-2
  

• Michelle D. Brazas, Joseph Tadashi Yamada, B. F. Francis Ouellette:
  Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory. 3-5
  
• Hamish McWilliam, Franck Valentin, Mickael Goujon, Weizhong Li, Menaka Narayanasamy, Jenny Martin, Teresa Miyar, Rodrigo Lopez:
  Web services at the European Bioinformatics Institute-2009. 6-10
  
• Yeondae Kwon, Yasumasa Shigemoto, Yoshikazu Kuwana, Hideaki Sugawara:
  Web API for biology with a workflow navigation system. 11-16
  
• Tadashi Imanishi, Hajime Nakaoka:
  Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. 17-22
  
• Syed Haider, Benoit Ballester, Damian Smedley, Junjun Zhang, Peter M. Rice, Arek Kasprzyk:
  BioMart Central Portal - unified access to biological data. 23-27
  
• Jeff Elhai, Arnaud Taton, J. P. Massar, John K. Myers, Michael Travers, Johnny Casey, Mark Slupesky, Jeff Shrager:
  BioBIKE: A Web-based, programmable, integrated biological knowledge base. 28-32
  
• Xiao-Qiao Liu, Jianmin Wu, Jun Wang, Xiao-Chuan Liu, Shuqi Zhao, Zhe Li, Lei Kong, Xiaocheng Gu, Jingchu Luo, Ge Gao:
  WebLab: a data-centric, knowledge-sharing bioinformatic platform. 33-39
  
• Michael J. Czar, Yizhi Cai, Jean Peccoud:
  Writing DNA with GenoCAD^TM. 40-47
  
• Bernd W. Brandt, Jaap Heringa:
  webPRC: the Profile Comparer for alignment-based searching of public domain databases. 48-52
  
• Marianne M. Lee, Michael K. Chan, Ralf Bundschuh:
  SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches. 53-56
  
• Akihiro Matsushima, Norio Kobayashi, Yoshiki Mochizuki, Manabu Ishii, Shuji Kawaguchi, Takaho A. Endo, Ryo Umetsu, Yuko Makita, Tetsuro Toyoda:
  OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. 57-62
  
• Fiona Achcar, Jean-Michel Camadro, Denis Mestivier:
  AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology. 63-67
  
• Michael Hackenberg, Martin Sturm, David Langenberger, Juan Manuel Falcón-Pérez, Ana M. Aransay:
  miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. 68-76
  
• Chun Liang, Lin Liu, Guoli Ji:
  WebGMAP: a web service for mapping and aligning cDNA sequences to genomes. 77-83
  
• Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander:
  Berkeley PHOG: PhyloFacts orthology group prediction web server. 84-89
  
• Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin:
  COMPASS server for homology detection: improved statistical accuracy, speed and functionality. 90-94
  
• Bruno Contreras-Moreira, Bernardo Sachman-Ruiz, Iraís Figueroa-Palacios, Pablo Vinuesa:
  primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. 95-100
  
• Katharina J. Hoff, Thomas Lingner, Peter Meinicke, Maike Tech:
  Orphelia: predicting genes in metagenomic sequencing reads. 101-105
  
• Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan:
  Torque: topology-free querying of protein interaction networks. 106-108
  
• Pablo Minguez, Stefan Götz, David Montaner, Fátima Al-Shahrour, Joaquín Dopazo:
  SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. 109-114
  
• Zhenjun Hu, Jui-Hung Hung, Yan Wang, Yi-Chien Chang, Chia-Ling Huang, Matt Huyck, Charles DeLisi:
  VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. 115-121
  
• Hagen Blankenburg, Fidel Ramírez, Joachim Büch, Mario Albrecht:
  DASMIweb: online integration, analysis and assessment of distributed protein interaction data. 122-128
  
• Chih-Hung Chou,