Nucleic Acids Research, Volume 36

Volume 36, Number Database-Issue, January 2008

• Alex Bateman:
  Editorial. 1
  Electronic Edition (link) BibTeX

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2008 update. 2-4
  Electronic Edition (link) BibTeX
• Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James K. Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim J. P. Hubbard, Ewan Birney:
  Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. 5-12
  Electronic Edition (link) BibTeX
• David L. Wheeler, 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, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Martin Shumway, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko:
  Database resources of the National Center for Biotechnology Information. 13-21
  Electronic Edition (link) BibTeX
• Hideaki Sugawara, Osamu Ogasawara, Kousaku Okubo, Takashi Gojobori, Yoshio Tateno:
  DDBJ with new system and face. 22-24
  Electronic Edition (link) BibTeX
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 25-30
  Electronic Edition (link) BibTeX
• Yu Zhou, Chen Lu, Qi-Jia Wu, Yu Wang, Zhi-Tao Sun, Jia-Cong Deng, Yi Zhang:
  GISSD: Group I Intron Sequence and Structure Database. 31-37
  Electronic Edition (link) BibTeX
• C. Lloréns, R. Futami, D. Bezemer, A. Moya:
  The Gypsy Database (GyDB) of mobile genetic elements. 38-46
  Electronic Edition (link) BibTeX
• Asaf Levy, Noa Sela, Gil Ast:
  TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. 47-52
  Electronic Edition (link) BibTeX
• Veenu Aishwarya, P. C. Sharma:
  UgMicroSatdb: database for mining microsatellites from unigenes. 53-56
  Electronic Edition (link) BibTeX
• Marco Mangone, Philip MacMenamin, Charles Zegar, Fabio Piano, Kristin C. Gunsalus:
  UTRome.org: a platform for 3'UTR biology in C. elegans. 57-62
  Electronic Edition (link) BibTeX
• Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, Ralf Zimmer:
  ProSAS: a database for analyzing alternative splicing in the context of protein structures. 63-68
  Electronic Edition (link) BibTeX
• Amrita Pati, Ying Jin, Karsten Klage, Richard F. Helm, Lenwood S. Heath, Naren Ramakrishnan:
  CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining. 69-76
  Electronic Edition (link) BibTeX
• Takeshi Obayashi, Shinpei Hayashi, Masayuki Shibaoka, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita:
  COXPRESdb: a database of coexpressed gene networks in mammals. 77-82
  Electronic Edition (link) BibTeX
• Lei Bao, Mi Zhou, Yan Cui:
  CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators. 83-87
  Electronic Edition (link) BibTeX
• Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, Sarah A. Teichmann:
  DBD--taxonomically broad transcription factor predictions: new content and functionality. 88-92
  Electronic Edition (link) BibTeX
• Nicolas Sierro, Yuko Makita, Michiel J. L. de Hoon, Kenta Nakai:
  DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. 93-96
  Electronic Edition (link) BibTeX
• Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai:
  DBTSS: database of transcription start sites, progress report 2008. 97-101
  Electronic Edition (link) BibTeX
• Jan Christian Bryne, Eivind Valen, Man-Hung Eric Tang, Troels Torben Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin:
  JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. 102-106
  Electronic Edition (link) BibTeX
• Obi L. Griffith, Stephen Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter J. De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth W. Wasserman, Ross C. Hardison, Casey M. Bergman, Steven J. M. Jones:
  ORegAnno: an open-access community-driven resource for regulatory annotation. 107-113
  Electronic Edition (link) BibTeX
• Gang-Qing Hu, Xiaobin Zheng, Yi-Fan Yang, Philippe Ortet, Zhen-Su She, Huaiqiu Zhu:
  ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. 114-119
  Electronic Edition (link) BibTeX
• Socorro Gama-Castro, Verónica Jiménez-Jacinto, Martín Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spínola, Bruno Contreras-Moreira, Juan Segura-Salazar, Luis Muñiz-Rascado, Irma Martínez-Flores, Heladia Salgado, César Bonavides-Martínez, Cei Abreu-Goodger, Carlos Rodríguez Penagos, Juan Miranda-Ríos, Enrique Morett, Enrique Merino, Araceli M. Huerta, Luis Treviño-Quintanilla, Julio Collado-Vides:
  RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. 120-124
  Electronic Edition (link) BibTeX
• Barrett C. Foat, Ronald G. Tepper, Harmen J. Bussemaker:
  TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. 125-131
  Electronic Edition (link) BibTeX
• Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d'Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas:
  YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. 132-136
  Electronic Edition (link) BibTeX
• Anason S. Halees, Rashad El-Badrawi, Khalid S. A. Khabar:
  ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse. 137-140
  Electronic Edition (link) BibTeX
• Oleg Kikin, Zachary Zappala, Lawrence D'Antonio, Paramjeet Bagga:
  GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs. 141-148
  Electronic Edition (link) BibTeX
• Doron Betel, Manda Wilson, Aaron Gabow, Debora S. Marks, Chris Sander:
  The microRNA.org resource: targets and expression. 149-153
  Electronic Edition (link) BibTeX
• Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, Anton J. Enright:
  miRBase: tools for microRNA genomics. 154-158
  Electronic Edition (link) BibTeX
• Seungyoon Nam, Bumjin Kim, Seokmin Shin, Sanghyuk Lee:
  miRGator: an integrated system for functional annotation of microRNAs. 159-164
  Electronic Edition (link) BibTeX
• Sheng-Da Hsu, Chia-Huei Chu, Ann-Ping Tsou, Shu-Jen Chen, Hua-Chien Chen, Paul Wei-Che Hsu, Yung-Hao Wong, Yi-Hsuan Chen, Gian-Hung Chen, Hsien-Da Huang:
  miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. 165-169
  Electronic Edition (link) BibTeX
• Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, Runsheng Chen:
  NONCODE v2.0: decoding the non-coding. 170-172
  Electronic Edition (link) BibTeX
• S. Sai Lakshmi, Shipra Agrawal:
  piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. 173-177
  Electronic Edition (link) BibTeX
• Dorota Piekna-Przybylska, Wayne A. Decatur, Maurille J. Fournier:
  The 3D rRNA modification maps database: with interactive tools for ribosome analysis. 178-183
  Electronic Edition (link) BibTeX
• Sung-Chou Li, Cheng-Kai Shiau, Wen-chang Lin:
  Vir-Mir db: prediction of viral microRNA candidate hairpins. 184-189
  Electronic Edition (link) BibTeX
• The UniProt Consortium:
  The Universal Protein Resource (UniProt). 190-195
  Electronic Edition (link) BibTeX
• Hans-Werner Mewes, Sabine Dietmann, Dmitrij Frishman, Richard Gregory, Gertrud Mannhaupt, Klaus F. X. Mayer, Martin Münsterkötter, Andreas Ruepp, Manuel Spannagl, Volker Stümpflen, Thomas Rattei:
  MIPS: analysis and annotation of genome information in 2007. 196-201
  Electronic Edition (link) BibTeX
• Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, Minoru Kanehisa:
  AAindex: amino acid index database, progress report 2008. 202-205
  Electronic Edition (link) BibTeX
• Conan K. L. Wang, Quentin Kaas, Laurent Chiche, David J. Craik:
  CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. 206-210
  Electronic Edition (link) BibTeX
• Hua Cheng, Bong-Hyun Kim, Nick V. Grishin:
  MALISAM: a database of structurally analogous motifs in proteins. 211-217
  Electronic Edition (link) BibTeX
• Ganesan Pugalenthi, Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Saikat Chakrabarti:
  MegaMotifBase: a database of structural motifs in protein families and superfamilies. 218-221
  Electronic Edition (link) BibTeX
• David S. Wishart, David Arndt, Mark V. Berjanskii, Anchi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou, Guohui Lin:
  PPT-DB: the protein property prediction and testing database. 222-229
  Electronic Edition (link) BibTeX
• Josefine Sprenger, J. Lynn Fink, Seetha Karunaratne, Kelly Hanson, Nicholas A. Hamilton, Rohan D. Teasdale:
  LOCATE: a mammalian protein subcellular localization database. 230-233
  Electronic Edition (link) BibTeX
• Gábor E. Tusnády, Lajos Kalmár, István Simon:
  TOPDB: topology data bank of transmembrane proteins. 234-239
  Electronic Edition (link) BibTeX
• Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson:
  Phospho.ELM: a database of phosphorylation sites - update 2008. 240-244
  Electronic Edition (link) BibTeX
• Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Béatrice A. Cuche, Edouard De Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, Christian J. A. Sigrist:
  The 20 years of PROSITE. 245-249
  Electronic Edition (link) BibTeX
• Lars Juhl Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, Peer Bork:
  eggNOG: automated construction and annotation of orthologous groups of genes. 250-254
  Electronic Edition (link) BibTeX
• Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang, Yixue Li:
  EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. 255-262
  Electronic Edition (link) BibTeX
• Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer:
  InParanoid 6: eukaryotic ortholog clusters with inparalogs. 263-266
  Electronic Edition (link) BibTeX
• Andreas Heger, Chris P. Ponting:
  OPTIC: orthologous and paralogous transcripts in clades. 267-270
  Electronic Edition (link) BibTeX
• Evgenia V. Kriventseva, Nazim Rahman, Octavio Espinosa, Evgeni M. Zdobnov:
  OrthoDB: the hierarchical catalog of eukaryotic orthologs. 271-275
  Electronic Edition (link) BibTeX
• Andreas Heger, Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, Liisa Holm:
  PairsDB atlas of protein sequence space. 276-280
  Electronic Edition (link) BibTeX
• Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
  The Pfam protein families database. 281-288
  Electronic Edition (link) BibTeX
• Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, Hans-Werner Mewes:
  SIMAP - structuring the network of protein similarities. 289-292
  Electronic Edition (link) BibTeX
• Quan-Yuan He, Quan-Ze He, Xing-Can Deng, Lei Yao, Er Meng, Zhong-Hua Liu, Song-Ping Liang:
  ATDB: a uni-database platform for animal toxins. 293-297
  Electronic Edition (link) BibTeX
• Karla Gendler, Tara Paulsen, Carolyn Napoli:
  ChromDB: The Chromatin Database. 298-302
  Electronic Edition (link) BibTeX
• Jianwen Fang, Yinghua Dong, Nazila Salamat-Miller, C. Russell Middaugh:
  DB-PABP: a database of polyanion-binding proteins. 303-306
  Electronic Edition (link) BibTeX
• Charles J. Reedy, Margaret M. Elvekrog, Brian R. Gibney:
  Development of a heme protein structure-electrochemical function database. 307-313
  Electronic Edition (link) BibTeX
• Jérôme Gracy, Dung Le-Nguyen, Jean-Christophe Gelly, Quentin Kaas, Annie Heitz, Laurent Chiche:
  KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007. 314-319
  Electronic Edition (link) BibTeX
• Neil D. Rawlings, Fraser R. Morton, Chai Yin Kok, Jun Kong, Alan J. Barrett:
  MEROPS: the peptidase database. 320-325
  Electronic Edition (link) BibTeX
• Ségolène Caboche, Maude Pupin, Valérie Leclère, Arnaud Fontaine, Philippe Jacques, Gregory Kucherov:
  NORINE: a database of nonribosomal peptides. 326-331
  Electronic Edition (link) BibTeX
• Sergi Castellano, Vadim N. Gladyshev, Roderic Guigó, Marla J. Berry:
  SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements. 332-338
  Electronic Edition (link) BibTeX
• Joshua D. Podlevsky, Christopher J. Bley, Rebecca V. Omana, Xiaodong Qi, Julian J.-L. Chen:
  The Telomerase Database. 339-343
  Electronic Edition (link) BibTeX
• Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, Michael Ashburner:
  ChEBI: a database and ontology for chemical entities of biological interest. 344-350
  Electronic Edition (link) BibTeX
• Kathleen Petri Seiler, Gregory A. George, Mary Pat Happ, Nicole E. Bodycombe, Hyman A. Carrinski, Stephanie Norton, Steve Brudz, John P. Sullivan, Jeremy Muhlich, Martin Serrano, Paul Ferraiolo, Nicola J. Tolliday, Stuart L. Schreiber, Paul A. Clemons:
  ChemBank: a small-molecule screening and cheminformatics resource database. 351-359
  Electronic Edition (link) BibTeX
• François-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, Piotr Cieplak:
  R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries. 360-367
  Electronic Edition (link) BibTeX
• Taku Nakahara, Ryo Hashimoto, Hiroaki Nakagawa, Kenji Monde, Nobuaki Miura, Shin-Ichiro Nishimura:
  Glycoconjugate Data Bank: Structures - an annotated glycan structure database and N-glycan primary structure verification service. 368-371
  Electronic Edition (link) BibTeX
• Ren Zhang, Yan Lin, Chun-Ting Zhang:
  Greglist: a database listing potential G-quadruplex regulated genes. 372-376
  Electronic Edition (link) BibTeX
• Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, Jörg Schultz:
  The ITS2 Database II: homology modelling RNA structure for molecular systematics. 377-380
  Electronic Edition (link) BibTeX
• Vinod Kumar Yadav, James Kappukalayil Abraham, Prithvi Mani, Rashi Kulshrestha, Shantanu Chowdhury:
  QuadBase: genome-wide database of G4 DNA - occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes. 381-385
  Electronic Edition (link) BibTeX
• Mariusz Popenda, Marek Blazewicz, Marta Szachniuk, Ryszard W. Adamiak:
  RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. 386-391
  Electronic Edition (link) BibTeX
• Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, Bruce A. Shapiro:
  RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. 392-397
  Electronic Edition (link) BibTeX
• Fabian Birzele, Jan E. Gewehr, Ralf Zimmer:
  AutoPSI: a database for automatic structural classification of protein sequences and structures. 398-401
  Electronic Edition (link) BibTeX
• Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, John L. Markley:
  BioMagResBank. 402-408
  Electronic Edition (link) BibTeX
• Hidetoshi Kono, Tomo Yuasa, Shinya Nishiue, Kei Yura:
  coliSNP database server mapping nsSNPs on protein structures. 409-413
  Electronic Edition (link) BibTeX
• Corin Yeats, Jonathan Lees, Adam Reid, Paul Kellam, Nigel J. Martin, Xinhui Liu, Christine A. Orengo:
  Gene3D: comprehensive structural and functional annotation of genomes. 414-418
  Electronic Edition (link) BibTeX
• Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin:
  Data growth and its impact on the SCOP database: new developments. 419-425
  Electronic Edition (link) BibTeX
• Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John M. C. Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim Vranken, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman:
  Remediation of the protein data bank archive. 426-433
  Electronic Edition (link) BibTeX
• Andreas Schlicker, Mario Albrecht:
  FunSimMat: a comprehensive functional similarity database. 434-439
  Electronic Edition (link) BibTeX
• The Gene Ontology project in 2008. 440-444
  Electronic Edition (link) BibTeX
• Elspeth A. Bruford, Michael J. Lush, Mathew W. Wright, Tam P. Sneddon, Sue Povey, Ewan Birney:
  The HGNC Database in 2008: a resource for the human genome. 445-448
  Electronic Edition (link) BibTeX
• Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Yon Rhee, Martin M. Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, Doreen Ware:
  The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. 449-454
  Electronic Edition (link) BibTeX
• In Seok Yang, Chunsun Ryu, Ki Joon Cho, Jin Kwang Kim, Swee Hoe Ong, Wayne P. Mitchell, Bong Su Kim, Hee-Bok Oh, Kyung Hyun Kim:
  IDBD: Infectious Disease Biomarker Database. 455-460
  Electronic Edition (link) BibTeX
• Nicolas J. Tourasse, Anne-Brit Kolstø:
  SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis). 461-468
  Electronic Edition (link) BibTeX
• Pierre Lechat, Laurence Hummel, Sandrine Rousseau, Ivan Moszer:
  GenoList: an integrated environment for comparative analysis of microbial genomes. 469-474
  Electronic Edition (link) BibTeX
• Konstantinos Liolios, Konstantinos Mavrommatis, Nektarios Tavernarakis, Nikos Kyrpides:
  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. 475-479
  Electronic Edition (link) BibTeX
• Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi:
  KEGG for linking genomes to life and the environment. 480-484
  Electronic Edition (link) BibTeX
• Emmanuel Courcelle, Yoann Beausse, Sébastien Letort, Olivier Stahl, Romain Fremez, Catherine Ngom-Bru, Jérôme Gouzy, Thomas Faraut:
  Narcisse: a mirror view of conserved syntenies. 485-490
  Electronic Edition (link) BibTeX
• Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, Toni Gabaldón:
  PhylomeDB: a database for genome-wide collections of gene phylogenies. 491-496
  Electronic Edition (link) BibTeX
• Burke Squires, Catherine Macken, Adolfo Garcia-Sastre, Shubhada Godbole, Jyothi Noronha, Victoria Hunt, Roger Chang, Christopher N. Larsen, Ed Klem, Kevin Biersack, Richard H. Scheuermann:
  BioHealthBase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence. 497-503
  Electronic Edition (link) BibTeX
• Yi Huang, Susanna K. P. Lau, Patrick C. Y. Woo, Kwok-yung Yuen:
  CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes. 504-511
  Electronic Edition (link) BibTeX
• Carla Kuiken, Peter Hraber, James Thurmond, Karina Yusim:
  The hepatitis C sequence database in Los Alamos. 512-516
  Electronic Edition (link) BibTeX
• Inti Pedroso, Gustavo Rivera, Felipe Lazo, Max Chacón, Francisco Ossandón, Felipe A. Veloso, David S. Holmes:
  AlterORF: a database of alternate open reading frames. 517-518
  Electronic Edition (link) BibTeX
• Jeremy D. Glasner, Guy Plunkett III, Bradley D. Anderson, David J. Baumler, Bryan S. Biehl, Valerie Burland, Eric L. Cabot, Aaron E. Darling, Bob Mau, Eric C. Neeno-Eckwall, David Pot, Yu Qiu, Anna I. Rissman, Sara Worzella, Sam Zaremba, Joel Fedorko, Tom Hampton, Paul Liss, Michael Rusch, Matthew Shaker, Lorie Shaull, Panna Shetty, Silpa Thotakura, Jon Whitmore, Frederick R. Blattner, John M. Greene, Nicole T. Perna:
  Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. 519-523
  Electronic Edition (link) BibTeX
• Pere Puigbò, Antoni Romeu, Santiago Garcia-Vallvé:
  HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. 524-527
  Electronic Edition (link) BibTeX
• Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
  The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. 528-533
  Electronic Edition (link) BibTeX
• Victor M. Markowitz, Natalia Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Yuri Grechkin, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Philip Hugenholtz, Nikos Kyrpides:
  IMG/M: a data management and analysis system for metagenomes. 534-538
  Electronic Edition (link) BibTeX
• Jian Yang, Lihong Chen, Lilian Sun, Jun Yu, Qi Jin:
  VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. 539-542
  Electronic Edition (link) BibTeX
• Roy R. Chaudhuri, Nicholas J. Loman, Lori A. S. Snyder, Christopher M. Bailey, Dov J. Stekel, Mark J. Pallen:
  xBASE2: a comprehensive resource for comparative bacterial genomics. 543-546
  Electronic Edition (link) BibTeX
• Alberto M. R. Dávila, Pablo N. Mendes, Glauber Wagner, Diogo A. Tschoeke, Rafael R. C. Cuadrat, Felipe Liberman, Luciana Matos, Thiago S. Satake, Kary A. C. S. Ocaña, Omar Triana, Sérgio M. S. Cruz, Henrique C. L. Jucá, Juliano C. Cury, Fabricio N. Silva, Guilherme A. Geronimo, Margarita Ruiz, Eduardo Ruback, Floriano P. Silva Jr., Christian M. Probst, Edmundo C. Grisard, Marco A. Krieger, Samuel Goldenberg, Maria Cláudia Reis Cavalcanti, Milton O. Moraes, Maria Luiza Machado Campos, Marta Mattoso:
  ProtozoaDB: dynamic visualization and exploration of protozoan genomes. 547-552
  Electronic Edition (link) BibTeX
• Bindu Gajria, Amit Bahl, John Brestelli, Jennifer Dommer, Steve Fischer, Xin Gao, Mark Heiges, John Iodice, Jessica C. Kissinger, Aaron J. Mackey, Deborah F. Pinney, David S. Roos, Christian J. Stoeckert Jr., Haiming Wang, Brian P. Brunk:
  ToxoDB: an integrated Toxoplasma gondii database resource. 553-556
  Electronic Edition (link) BibTeX
• Tristan Rossignol, Pierre Lechat, Christina Cuomo, Qiandong Zeng, Ivan Moszer, Christophe d'Enfert:
  CandidaDB: a multi-genome database for Candida species and related Saccharomycotina. 557-561
  Electronic Edition (link) BibTeX
• Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Kwangyul Yu, Jaeyoung Choi, Sunghyung Kong, Jaejin Park, Seryun Kim, Hyojeong Kim, Soonok Kim, Jihyun F. Kim, Jaime E. Blair, Kwangwon Lee, Seogchan Kang, Yong-Hwan Lee:
  CFGP: a web-based, comparative fungal genomics platform. 562-571
  Electronic Edition (link) BibTeX
• Rainer Winnenburg, Martin Urban, Andrew Beacham, Thomas K. Baldwin, Sabrina Holland, Magdalen Lindeberg, Hilde Hansen, Christopher J. Rawlings, Kim E. Hammond-Kosack, Jacob Köhler:
  PHI-base update: additions to the pathogen-host interaction database. 572-576
  Electronic Edition (link) BibTeX
• Eurie L. Hong, Rama Balakrishnan, Qing Dong, Karen R. Christie, Julie Park, Gail Binkley, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kathy K. Zhu, Kara Dolinski, David Botstein, J. Michael Cherry:
  Gene Ontology annotations at SGD: new data sources and annotation methods. 577-581
  Electronic Edition (link) BibTeX
• Alexie Papanicolaou, Steffi Gebauer-Jung, Mark L. Blaxter, W. Owen McMillan, Chris D. Jiggins:
  ButterflyBase: a platform for lepidopteran genomics. 582-587
  Electronic Edition (link) BibTeX
• Robert J. Wilson, Joshua L. Goodman, Victor B. Strelets, The FlyBase Consortium:
  FlyBase: integration and improvements to query tools. 588-593
  Electronic Edition (link) BibTeX
• Marc S. Halfon, Steven M. Gallo, Casey M. Bergman:
  REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. 594-598
  Electronic Edition (link) BibTeX
• Sofia M. C. Robb, Eric Ross, Alejandro Sánchez Alvarado:
  SmedGD: the Schmidtea mediterranea genome database. 599-606
  Electronic Edition (link) BibTeX
• James C. Sullivan, Adam M. Reitzel, John R. Finnerty:
  Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis. 607-611
  Electronic Edition (link) BibTeX
• Anthony Rogers, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Carol Bastiani, Payan Canaran, Juancarlos Chan, Wen J. Chen, Paul Davis, Jolene Fernandes, Tristan J. Fiedler, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon McKay, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, Paul W. Sternberg:
  WormBase 2007. 612-617
  Electronic Edition (link) BibTeX
• Matthew Bashton, Irene Nobeli, Janet M. Thornton:
  PROCOGNATE: a cognate ligand domain mapping for enzymes. 618-622
  Electronic Edition (link) BibTeX
• Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne M. Paley, Seung Yon Rhee, Alexander G. Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang, Peter D. Karp:
  The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. 623-631
  Electronic Edition (link) BibTeX
• Chong Su, José M. Peregrin-Alvarez, Gareth Butland, Sadhna Phanse, Vincent Fong, Andrew Emili, John Parkinson:
  Bacteriome.org - an integrated protein interaction database for E. coli. 632-636
  Electronic Edition (link) BibTeX
• Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Michael S. Livstone, Rose Oughtred, Daniel H. Lackner, Jürg Bähler, Valerie Wood, Kara Dolinski, Mike Tyers:
  The BioGRID Interaction Database: 2008 update. 637-640
  Electronic Edition (link) BibTeX
• Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi:
  The cell cycle DB: a systems biology approach to cell cycle analysis. 641-645
  Electronic Edition (link) BibTeX
• Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou Doudieu, Volker Stümpflen, Hans-Werner Mewes:
  CORUM: the comprehensive resource of mammalian protein complexes. 646-650
  Electronic Edition (link) BibTeX
• Philipp Pagel, Matthias Oesterheld, Oksana Tovstukhina, Normann Strack, Volker Stümpflen, Dmitrij Frishman:
  DIMA 2.0 - predicted and known domain interactions. 651-655
  Electronic Edition (link) BibTeX
• Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, Raja Jothi:
  DOMINE: a database of protein domain interactions. 656-661
  Electronic Edition (link) BibTeX
• Emre Guney, Nurcan Tuncbag, Ozlem Keskin, Attila Gürsoy:
  HotSprint: database of computational hot spots in protein interfaces. 662-666
  Electronic Edition (link) BibTeX
• Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, Shoshana J. Wodak:
  LigASite - a database of biologically relevant binding sites in proteins with known apo-structures. 667-673
  Electronic Edition (link) BibTeX
• Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John Beaver, Peter Dresslar, Jason Nerothin, Heather A. Carlson:
  Binding MOAD, a high-quality protein-ligand database. 674-678
  Electronic Edition (link) BibTeX
• Wuming Gong, Dihan Zhou, Yongliang Ren, Yejun Wang, Zhixiang Zuo, Yanping Shen, Feifei Xiao, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao, Tongbin Li:
  PepCyber: P~PEP: a database of human protein-protein interactions mediated by phosphoprotein-binding domains. 679-683
  Electronic Edition (link) BibTeX
• Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, Peer Bork:
  STITCH: interaction networks of chemicals and proteins. 684-688
  Electronic Edition (link) BibTeX
• Jürgen Dönitz, Björn Goemann, Muriel Lizé, Holger Michael, Nicole Sasse, Edgar Wingender, Anatolij Potapov:
  EndoNet: an information resource about regulatory networks of cell-to-cell communication. 689-694
  Electronic Edition (link) BibTeX
• Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, Tony Pawson:
  NetworKIN: a resource for exploring cellular phosphorylation networks. 695-699
  Electronic Edition (link) BibTeX
• Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, Shankar Subramaniam:
  The Molecule Pages database. 700-706
  Electronic Edition (link) BibTeX
• Paul Flicek, B. L. Aken, K. Beal, B. Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, G. Coates, Fiona Cunningham, Tim Cutts, Thomas A. Down, S. C. Dyer, T. Eyre, S. Fitzgerald, J. Fernandez-Banet, Stefan Gräf, S. Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, K. Howe, N. Johnson, A. Jenkinson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, I. Longden, Karine Megy, Patrick Meidl, B. Overduin, A. Parker, B. Pritchard, Andreas Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, Guy Slater, Damian Smedley, G. Spudich, S. Trevanion, Albert J. Vilella, J. Vogel, S. White, M. Wood, Ewan Birney, Tony Cox, Val Curwen, Richard Durbin, X. M. Fernandez-Suarez, J. Herrero, Tim J. P. Hubbard, Arek Kasprzyk, Glenn Proctor, James Smith, Abel Ureta-Vidal, Stephen M. J. Searle:
  Ensembl 2008. 707-714
  Electronic Edition (link) BibTeX
• Ann-Marie Mallon, Andrew Blake, John M. Hancock:
  EuroPhenome and EMPReSS: online mouse phenotyping resource. 715-718
  Electronic Edition (link) BibTeX
• Carl J. Schmidt, Michael Romanov, Oliver Ryder, Vincent Magrini, Matthew T. Hickenbotham, Jarret Glasscock, Sean McGrath, Elaine R. Mardis, Lincoln D. Stein:
  Gallus GBrowse: a unified genomic database for the chicken. 719-723
  Electronic Edition (link) BibTeX
• Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Judith A. Blake:
  The Mouse Genome Database (MGD): mouse biology and model systems. 724-728
  Electronic Edition (link) BibTeX
• Ling V. Sun, Ke Jin, Yiming Liu, Wenwei Yang, Xing Xie, Lin Ye, Li Wang, Lin Zhu, Sheng Ding, Yi Su, Jie Zhou, Min Han, Yuan Zhuang, Tian Xu, Xiaohui Wu, Ning Gu, Yang Zhong:
  PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice. 729-734
  Electronic Edition (link) BibTeX
• Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin:
  TreeFam: 2008 Update. 735-740
  Electronic Edition (link) BibTeX
• Guglielmo Roma, Marco Sardiello, Gilda Cobellis, Pedro Cruz, Giampiero Lago, Remo Sanges, Elia Stupka:
  The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones. 741-746
  Electronic Edition (link) BibTeX
• Budrul Ahsan, Daisuke Kobayashi, Tomoyuki Yamada, Masahiro Kasahara, Shin Sasaki, Taro L. Saito, Yukinobu Nagayasu, Koichiro Doi, Yoichiro Nakatani, Wei Qu, Tomoko Jindo, Atsuko Shimada, Kiyoshi Naruse, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda, Yuji Kohara, Shinichi Morishita:
  UTGB/medaka: genomic resource database for medaka biology. 747-752
  Electronic Edition (link) BibTeX
• L. G. Wilming, J. G. R. Gilbert, K. Howe, S. Trevanion, Tim J. P. Hubbard, J. L. Harrow:
  The vertebrate genome annotation (Vega) database. 753-760
  Electronic Edition (link) BibTeX
• Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen, Nicolas Pollet, Peter D. Vize:
  Xenbase: a Xenopus biology and genomics resource. 761-767
  Electronic Edition (link) BibTeX
• Judy Sprague, Leyla Bayraktaroglu, Yvonne Bradford, Tom Conlin, Nathan Dunn, David Fashena, Ken Frazer, Melissa Haendel, Douglas G. Howe, Jonathan Knight, Prita Mani, Sierra A. T. Moxon, Christian Pich, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Xiang Shao, Amy Singer, Peiran Song, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield:
  The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. 768-772
  Electronic Edition (link) BibTeX
• Donna Karolchik, Robert M. Kuhn, Robert Baertsch, Galt P. Barber, Hiram Clawson, Mark Diekhans, Belinda Giardine, Rachel A. Harte, Angela S. Hinrichs, Fan Hsu, K. M. Kober, Webb Miller, J. S. Pedersen, Andy Pohl, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Kayla E. Smith, Mario Stanke, Archana Thakkapallayil, Heather Trumbower, T. Wang, Ann S. Zweig, David Haussler, W. James Kent:
  The UCSC Genome Browser Database: 2008 update. 773-779
  Electronic Edition (link) BibTeX
• Tim Yates, Michal J. Okoniewski, Crispin J. Miller:
  X: Map: annotation and visualization of genome structure for Affymetrix exon array analysis. 780-786
  Electronic Edition (link) BibTeX
• Akihiro Matsuya, Ryuichi Sakate, Yoshihiro Kawahara, Kanako O. Koyanagi, Yoshiharu Sato, Yasuyuki Fujii, Chisato Yamasaki, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Kaori Yamaguchi, Toshinori Endo, Satoshi Ota, Wojciech Makalowski, Kazuho Ikeo, Yoshiyuki Suzuki, Kousuke Hanada, Katsuyuki Hashimoto, Momoki Hirai, Hisakazu Iwama, Naruya Saitou, Aiko T. Hiraki, Lihua Jin, Yayoi Kaneko, Masako Kanno, Katsuhiko Murakami, Akiko Ogura Noda, Naomi Saichi, Ryoko Sanbonmatsu, Mami Suzuki, Jun-ichi Takeda, Masayuki Tanaka, Takashi Gojobori, Tadashi Imanishi, Takeshi Itoh:
  Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. 787-792
  Electronic Edition (link) BibTeX
• The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. 793-799
  Electronic Edition (link) BibTeX
• Gabrielle C. Nickel, David Tefft, Mark D. Adams:
  Human PAML browser: a database of positive selection on human genes using phylogenetic methods. 800-808
  Electronic Edition (link) BibTeX
• Julian Lange, Helen Skaletsky, George W. Bell, David C. Page:
  MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome. 809-814
  Electronic Edition (link) BibTeX
• Arti Singh, Adebayo Olowoyeye, Peter H. Baenziger, Jessica Dantzer, Maricel G. Kann, Predrag Radivojac, Randy Heiland, Sean D. Mooney:
  MutDB: update on development of tools for the biochemical analysis of genetic variation. 815-819
  Electronic Edition (link) BibTeX
• Phil Hyoun Lee, Hagit Shatkay:
  F-SNP: computationally predicted functional SNPs for disease association studies. 820-824
  Electronic Edition (link) BibTeX
• Joke Reumers, Lucía Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost J. J. van Durme, Joaquín Dopazo, Frederic Rousseau, Joost Schymkowitz:
  Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. 825-829
  Electronic Edition (link) BibTeX
• Ilari Scheinin, Samuel Myllykangas, Ioana Borze, Tom Böhling, Sakari Knuutila, Juha Saharinen:
  CanGEM: mining gene copy number changes in cancer. 830-835
  Electronic Edition (link) BibTeX
• Ximiao He, Suhua Chang, Jiajie Zhang, Qian Zhao, Haizhen Xiang, Kanthida Kusonmano, Liu Yang, Zhong Sheng Sun, Huanming Yang, Jing Wang:
  MethyCancer: the database of human DNA methylation and cancer. 836-841
  Electronic Edition (link) BibTeX
• Maté Ongenaert, Leander Van Neste, Tim De Meyer, Gerben Menschaert, Sofie Bekaert, Wim Van Criekinge:
  PubMeth: a cancer methylation database combining text-mining and expert annotation. 842-846
  Electronic Edition (link) BibTeX
• Yannick Haudry, Hugo Berube, Ivica Letunic, Paul-Daniel Weeber, Julien Gagneur, Charles Girardot, Misha Kapushesky, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich:
  4DXpress: a database for cross-species expression pattern comparisons. 847-853
  Electronic Edition (link) BibTeX
• Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, Thomas Skøt Jensen:
  Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. 854-859
  Electronic Edition (link) BibTeX
• Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Lorna Richardson, Nicholas Burton, Thomas P. Perry, Paul Smith, Richard A. Baldock, Duncan Davidson, Jeffrey H. Christiansen:
  EMAGE - Edinburgh Mouse Atlas of Gene Expression: 2008 update. 860-865
  Electronic Edition (link) BibTeX
• Jeremiah J. Faith, Michael E. Driscoll, Vincent A. Fusaro, Elissa J. Cosgrove, Boris Hayete, Frank S. Juhn, Stephen J. Schneider, Timothy S. Gardner:
  Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. 866-870
  Electronic Edition (link) BibTeX
• Robert J. Marinelli, Kelli Montgomery, Chih Long Liu, Nigam H. Shah, Wijan Prapong, Michael Nitzberg, Zachariah K. Zachariah, Gavin Sherlock, Yasodha Natkunam, Robert B. West, Matt van de Rijn, Patrick O. Brown, Catherine A. Ball:
  The Stanford Tissue Microarray Database. 871-877
  Electronic Edition (link) BibTeX
• Philip Jones, Richard G. Côté, Sang Yun Cho, Sebastian Klie, Lennart Martens, Antony F. Quinn, David Thorneycroft, Henning Hermjakob:
  PRIDE: new developments and new datasets. 878-883
  Electronic Edition (link) BibTeX
• C. Zhang, Oswald Crasta, S. Cammer, Rebecca Will, Ron Kenyon, D. Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, Tian Xue, Y. Zhang, M. Moore, Peter B. McGarvey, Hongzhan Huang, Yongxing Chen, J. Zhang, Raja Mazumder, Cathy H. Wu, Bruno W. S. Sobral:
  An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. 884-891
  Electronic Edition (link) BibTeX
• Michael D. Waters, Stanley Stasiewicz, B. Alex Merrick, Kenneth B. Tomer, Pierre R. Bushel, Richard S. Paules, Nancy Stegman, Gerald Nehls, Kenneth J. Yost III, C. Harris Johnson, Scott F. Gustafson, Sandhya Xirasagar, Nianqing Xiao, Cheng-Cheng Huang, Paul Boyer, Denny D. Chan, Qinyan Pan, Hui Gong, John Taylor, Danielle Choi, Asif Rashid, Ayazaddin Ahmed, Reese Howle, James Selkirk, Raymond Tennant, Jennifer Fostel:
  CEBS - Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. 892-900
  Electronic Edition (link) BibTeX
• David S. Wishart, Craig Knox, Anchi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, Murtaza Hassanali:
  DrugBank: a knowledgebase for drugs, drug actions and drug targets. 901-906
  Electronic Edition (link) BibTeX
• Yasushi Okuno, Akiko Tamon, Hiroaki Yabuuchi, Satoshi Niijima, Yohsuke Minowa, Koichiro Tonomura, Ryo Kunimoto, Chunlai Feng:
  GLIDA: GPCR - ligand database for chemical genomics drug discovery - database and tools update. 907-912
  Electronic Edition (link) BibTeX
• Tina Hernandez-Boussard, Michelle Whirl Carrillo, Joan M. Hebert, Li Gong, Ryan Owen, Mei Gong, Winston Gor, Feng Liu, Chuong Truong, Ryan Whaley, Mark Woon, Tina Zhou, Russ B. Altman, Teri E. Klein:
  The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. 913-918
  Electronic Edition (link) BibTeX
• Stefan Günther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo Garcia Urdiales, Andreas Gewiess, Lars Juhl Jensen, Reinhard Schneider, Roman Skoblo, Robert B. Russell, Philip E. Bourne, Peer Bork, Robert Preissner:
  SuperTarget and Matador: resources for exploring drug-target relationships. 919-922
  Electronic Edition (link) BibTeX
• Zuoshuang Xiang, Thomas Todd, Kim P. Ku, Bethany L. Kovacic, Charles B. Larson, Fang Chen, Andrew P. Hodges, Yuying Tian, Elizabeth A. Olenzek, Boyang Zhao, Lesley A. Colby, Howard G. Rush, Janet R. Gilsdorf, George W. Jourdian, Yongqun He:
  VIOLIN: vaccine investigation and online information network. 923-928
  Electronic Edition (link) BibTeX
• Shoji Mano, Tomoki Miwa, Shuh-ichi Nishikawa, Tetsuro Mimura, Mikio Nishimura:
  The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research. 929-937
  Electronic Edition (link) BibTeX
• Yong Seok Lee, Jeongsu Oh, Young Uk Kim, Namchul Kim, Sungjin Yang, Ui Wook Hwang:
  Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals. 938-942
  Electronic Edition (link) BibTeX
• Samart Wanchana, Supat Thongjuea, Victor Jun M. Ulat, Mylah Anacleto, Ramil Mauleon, Matthieu Conte, Mathieu Rouard, Manuel Ruiz, Nandini Krishnamurthy, Kimmen Sjölander, Theo van Hintum, Richard M. Bruskiewich:
  The Generation Challenge Programme comparative plant stress-responsive gene catalogue. 943-946
  Electronic Edition (link) BibTeX
• Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry M. Casstevens, Bonnie Hurwitz, Susan McCouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Tecle, Jim Thomason, Chih-Wei Tung, Xuehong Wei, Immanuel Yap, Ken Youens-Clark, Doreen Ware, Lincoln Stein:
  Gramene: a growing plant comparative genomics resource. 947-953
  Electronic Edition (link) BibTeX
• Eva Grafahrend-Belau, Stephan Weise, Dirk Koschützki, Uwe Scholz, Björn H. Junker, Falk Schreiber:
  MetaCrop: a detailed database of crop plant metabolism. 954-958
  Electronic Edition (link) BibTeX
• Jon Duvick, Ann Fu, Usha Muppirala, Mukul Sabharwal, Matthew D. Wilkerson, Carolyn J. Lawrence, Carol Lushbough, Volker Brendel:
  PlantGDB: a resource for comparative plant genomics. 959-965
  Electronic Edition (link) BibTeX
• Anyuan Guo, Xin Chen, Ge Gao, He Zhang, Qi-Hui Zhu, Xiao-Chuan Liu, Yingfu Zhong, Xiaocheng Gu, Kun He, Jingchu Luo:
  PlantTFDB: a comprehensive plant transcription factor database. 966-969
  Electronic Edition (link) BibTeX
• P. Kerr Wall, James Leebens-Mack, Kai F. Müller, Dawn Field, Naomi S. Altman, Claude W. dePamphilis:
  PlantTribes: a gene and gene family resource for comparative genomics in plants. 970-976
  Electronic Edition (link) BibTeX
• Yoshiharu Y. Yamamoto, Junichi Obokata:
  ppdb: a plant promoter database. 977-981
  Electronic Edition (link) BibTeX
• Tyler W. H. Backman, Christopher M. Sullivan, Jason S. Cumbie, Zachary A. Miller, Elisabeth J. Chapman, Noah Fahlgren, Scott A. Givan, James C. Carrington, Kristin D. Kasschau:
  Update of ASRP: the Arabidopsis Small RNA Project database. 982-985
  Electronic Edition (link) BibTeX
• Séverine Gagnot, Jean-Philippe Tamby, Marie-Laure Martin-Magniette, Frédérique Bitton, Ludivine Taconnat, Sandrine Balzergue, Sébastien Aubourg, Jean-Pierre Renou, Alain Lecharny, Véronique Brunaud:
  CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. 986-990
  Electronic Edition (link) BibTeX
• M. G. Conte, S. Gaillard, N. Lanau, M. Rouard, C. Périn:
  GreenPhylDB: a database for plant comparative genomics. 991-998
  Electronic Edition (link) BibTeX
• Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yi-Xue Li, Tieliu Shi:
  AtPID: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology. 999-1008
  Electronic Edition (link) BibTeX
• David Swarbreck, Christopher Wilks, Philippe Lamesch, Tanya Z. Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang, Eva Huala:
  The Arabidopsis Information Resource (TAIR): gene structure and function annotation. 1009-1014
  Electronic Edition (link) BibTeX
• Joshua L. Heazlewood, Pawel Durek, Jan Hummel, Joachim Selbig, Wolfram Weckwerth, Dirk Walther, Waltraud X. Schulze:
  PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. 1015-1021
  Electronic Edition (link) BibTeX
• Pierre Larmande, Céline Gay, Mathias Lorieux, Christophe Périn, Matthieu Bouniol, Gaëtan Droc, Christophe Sallaud, Pascual Perez, Isabelle Barnola, Corinne Biderre-Petit, Jérôme Martin, Jean Benoît Morel, Alexander A. T. Johnson, Fabienne Bourgis, Alain Ghesquière, Manuel Ruiz, Brigitte Courtois, Emmanuel Guiderdoni:
  Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library. 1022-1027
  Electronic Edition (link) BibTeX
• The Rice Annotation Project Database (RAP-DB): 2008 update. 1028-1033
  Electronic Edition (link) BibTeX
• Sook Jung, Margaret Staton, Taein Lee, Anna Blenda, Randall Svancara, Albert Abbott, Dorrie Main:
  GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. 1034-1040
  Electronic Edition (link) BibTeX
• Payan Canaran, Edward S. Buckler, Jeffrey Glaubitz, Lincoln Stein, Qi Sun, Wei Zhao, Doreen Ware:
  Panzea: an update on new content and features. 1041-1043
  Electronic Edition (link) BibTeX
• Guo-Zhang Wu, Qiu-Ming Shi, Ya Niu, Mei-Qing Xing, Hong-Wei Xue:
  Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica. 1044-1047
  Electronic Edition (link) BibTeX
• V. Aidinis, C. Chandras, M. Manoloukos, A. Thanassopoulou, K. Kranidioti, M. Armaka, E. Douni, D. L. Kontoyiannis, M. Zouberakis, G. Kollias:
  MUGEN mouse database; Animal models of human immunological diseases. 1048-1054
  Electronic Edition (link) BibTeX