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    Databases in Molecular Biology (2004):

    An overview about molecular biological databases is given each year in a special issue (January) of Nucleic Acids Research. The published articles are very useful to get fast and qualified answers to related questions. Please enjoy the list of articles published in January 2004:

  • Michael Y. Galperin
    The Molecular Biology Database Collection: 2004 update
    Nucleic Acids Res. 32: D3-D22. Database Listing

  • Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
    GenBank: update
    Nucleic Acids Res. 32: D23-D26.

  • Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Maria Garcia-Pastor, Nicola Harte, Carola Kanz, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Peter Stoehr, Guenter Stoesser, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler
    The EMBL Nucleotide Sequence Database
    Nucleic Acids Res. 32: D27-D30.

  • S. Miyazaki, H. Sugawara, K. Ikeo, T. Gojobori, and Y. Tateno
    DDBJ in the stream of various biological data
    Nucleic Acids Res. 32: D31-D34.

  • David L. Wheeler, Deanna M. Church, Ron Edgar, Scott Federhen, Wolfgang Helmberg, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tugba O. Suzek, Tatiana A. Tatusova, and Lukas Wagner
    Database resources of the National Center for Biotechnology Information: update
    Nucleic Acids Res. 32: D35-D40.

  • H. W. Mewes, C. Amid, R. Arnold, D. Frishman, U. Güldener, G. Mannhaupt, M. Münsterkötter, P. Pagel, N. Strack, V. Stümpflen, J. Warfsmann, and A. Ruepp
    MIPS: analysis and annotation of proteins from whole genomes
    Nucleic Acids Res. 32: D41-D44.

  • Raphaël Leplae, Aline Hebrant, Shoshana J. Wodak, and Ariane Toussaint
    ACLAME: A CLAssification of Mobile genetic Elements
    Nucleic Acids Res. 32: D45-D49.

  • Jan Paces, Adam Pavlícek, Radek Zika, Vladimir V. Kapitonov, Jerzy Jurka, and Václav Paces
    HERVd: the Human Endogenous RetroViruses Database: update
    Nucleic Acids Res. 32: D50.

  • Thierry-Pascal Baum, Nicolas Pasqual, Florence Thuderoz, Vivien Hierle, Denys Chaume, Marie-Paule Lefranc, Evelyne Jouvin-Marche, Patrice-Noël Marche, and Jacques Demongeot
    IMGT/GeneInfo: enhancing V(D)J recombination database accessibility
    Nucleic Acids Res. 32: D51-D54.

  • Yogita Mantri and Kelly P. Williams
    Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
    Nucleic Acids Res. 32: D55-D58.

  • Vivek Gopalan, Tin Wee Tan, Bernett T. K. Lee, and Shoba Ranganathan
    Xpro: database of eukaryotic protein-encoding genes
    Nucleic Acids Res. 32: D59-D63.

  • T. A. Thanaraj, Stefan Stamm, Francis Clark, Jean-Jack Riethoven, Vincent Le Texier, and Juha Muilu
    ASD: the Alternative Splicing Database
    Nucleic Acids Res. 32: D64-D69.

  • Heike Pospisil, Alexander Herrmann, Ralf H. Bortfeldt, and Jens G. Reich
    EASED: Extended Alternatively Spliced EST Database
    Nucleic Acids Res. 32: D70-D74.

  • Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, and Kenta Nakai
    DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
    Nucleic Acids Res. 32: D75-D77.

  • Yutaka Suzuki, Riu Yamashita, Sumio Sugano, and Kenta Nakai
    DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
    Nucleic Acids Res. 32: D78-D81.

  • Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaïda Périer, and Philipp Bucher
    The Eukaryotic Promoter Database EPD: the impact of in silico primer extension
    Nucleic Acids Res. 32: D82-D85.

  • Twyla T. Pohar, Hao Sun, and Ramana V. Davuluri
    HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development
    Nucleic Acids Res. 32: D86-D90.

  • Albin Sandelin, Wynand Alkema, Pär Engström, Wyeth W. Wasserman, and Boris Lenhard
    JASPAR: an open-access database for eukaryotic transcription factor binding profiles
    Nucleic Acids Res. 32: D91-D94.

  • Jennifer F. Lee, Jay R. Hesselberth, Lauren Ancel Meyers, and Andrew D. Ellington
    Aptamer Database
    Nucleic Acids Res. 32: D95-D100.

  • Jan Wuyts, Guy Perrière, and Yves Van de Peer
    The European ribosomal RNA database
    Nucleic Acids Res. 32: D101-D103.

  • Pulcherie Gueneau de Novoa and Kelly P. Williams
    The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts
    Nucleic Acids Res. 32: D104-D108.

  • Sam Griffiths-Jones
    The microRNA Registry
    Nucleic Acids Res. 32: D109-D111.

  • Cathy H. Wu, Anastasia Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, C. R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, and Winona C. Barker
    PIRSF: family classification system at the Protein Information Resource
    Nucleic Acids Res. 32: D112-D114.

  • Rolf Apweiler, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J. Martin, Darren A. Natale, Claire O’Donovan, Nicole Redaschi, and Lai-Su L. Yeh
    UniProt: the Universal Protein knowledgebase
    Nucleic Acids Res. 32: D115-D119.

  • K. Abdulla Bava, M. Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, and Akinori Sarai
    ProTherm, version 4.0: thermodynamic database for proteins and mutants
    Nucleic Acids Res. 32: D120-D121.

  • Tao Guo, Sujun Hua, Xinglai Ji, and Zhirong Sun
    DBSubLoc: database of protein subcellular localization
    Nucleic Acids Res. 32: D122-D124.

  • S. A. Fernando, P. Selvarani, Soma Das, Ch. Kiran Kumar, Sukanta Mondal, S. Ramakumar, and K. Sekar
    THGS: a web-based database of Transmembrane Helices in Genome Sequences
    Nucleic Acids Res. 32: D125-D128.

  • Craig T. Porter, Gail J. Bartlett, and Janet M. Thornton
    The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    Nucleic Acids Res. 32: D129-D133.

  • Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, and Amos Bairoch
    Recent improvements to the PROSITE database
    Nucleic Acids Res. 32: D134-D137.

  • Alex Bateman, Lachlan Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, and Sean R. Eddy
    The Pfam protein families database
    Nucleic Acids Res. 32: D138-D141.

  • Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, and Peer Bork
    SMART 4.0: towards genomic data integration
    Nucleic Acids Res. 32: D142-D144.

  • Thierry Hotelier, Ludovic Renault, Xavier Cousin, Vincent Negre, Pascale Marchot, and Arnaud Chatonnet
    ESTHER, the database of the α/β-hydrolase fold superfamily of proteins
    Nucleic Acids Res. 32: D145-D147.

  • David A. Lee, Sandrine Fefeu, Adrian A. Edo-Ukeh, Christine A. Orengo, and Christine Slingsby
    EyeSite: a semi-automated database of protein families in the eye
    Nucleic Acids Res. 32: D148-D152.

  • A. Krupa, K. R. Abhinandan, and N. Srinivasan
    KinG: a database of protein kinases in genomes
    Nucleic Acids Res. 32: D153-D155.

  • Jean-Christophe Gelly, Jérôme Gracy, Quentin Kaas, Dung Le-Nguyen, Annie Heitz, and Laurent Chiche
    The KNOTTIN website and database: a new information system dedicated to the knottin scaffold
    Nucleic Acids Res. 32: D156-D159.

  • Neil D. Rawlings, Dominic P. Tolle, and Alan J. Barrett
    MEROPS: the peptidase database
    Nucleic Acids Res. 32: D160-D164.

  • David Ruau, Jorge Duarte, Tarik Ourjdal, Guy Perrière, Vincent Laudet, and Marc Robinson-Rechavi
    Update of NUREBASE: nuclear hormone receptor functional genomics
    Nucleic Acids Res. 32: D165-D167.

  • Akihiro Nakao, Maki Yoshihama, and Naoya Kenmochi
    RPG: the Ribosomal Protein Gene database
    Nucleic Acids Res. 32: D168-D170.

  • Antoni Hermoso, Daniel Aguilar, Francesc X. Aviles, and Enrique Querol
    TrSDB: a proteome database of transcription factors
    Nucleic Acids Res. 32: D171-D173.

  • Michael M. Hoffman, Maksim A. Khrapov, J. Colin Cox, Jianchao Yao, Lingnan Tong, and Andrew D. Ellington
    AANT: the Amino Acid–Nucleotide Interaction Database
    Nucleic Acids Res. 32: D174-D181.

  • Makio Tamura, Donna K. Hendrix, Peter S. Klosterman, Nancy R. B. Schimmelman, Steven E. Brenner, and Stephen R. Holbrook
    SCOR: Structural Classification of RNA, version 2.0
    Nucleic Acids Res. 32: D182-D184.

  • Jordi Espadaler, Narcis Fernandez-Fuentes, Antonio Hermoso, Enrique Querol, Francesc X. Aviles, Michael J. E. Sternberg, and Baldomero Oliva
    ArchDB: automated protein loop classification as a tool for structural genomics
    Nucleic Acids Res. 32: D185-D188.

  • John-Marc Chandonia, Gary Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, and Steven E. Brenner
    The ASTRAL Compendium in 2004
    Nucleic Acids Res. 32: D189-D192.

  • R. Aroul Selvam and Rajkumar Sasidharan
    DomIns: a web resource for domain insertions in known protein structures
    Nucleic Acids Res. 32: D193-D195.

  • Liam J. McGuffin, Stefano A. Street, Kevin Bryson, SŅren-Aksel SŅrensen, and David T. Jones
    The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
    Nucleic Acids Res. 32: D196-D199.

  • A. Vinayagam, G. Pugalenthi, R. Rajesh, and R. Sowdhamini
    DSDBASE: a consortium of native and modelled disulphide bonds in proteins
    Nucleic Acids Res. 32: D200-D202.

  • Lucy A. Stebbings and Kenji Mizuguchi
    HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
    Nucleic Acids Res. 32: D203-D207.

  • Quentin Kaas, Manuel Ruiz, and Marie-Paule Lefranc
    IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data
    Nucleic Acids Res. 32: D208-D210.

  • A. Golovin, T. J. Oldfield, J. G. Tate, S. Velankar, G. J. Barton, H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Hussain, J. M. C. Ionides, M. John, P. A. Keller, E. Krissinel, P. McNeil, A. Naim, R. Newman, A. Pajon, J. Pineda, A. Rachedi, J. Copeland, A. Sitnov, S. Sobhany, A. Suarez-Uruena, G. J. Swaminathan, M. Tagari, S. Tromm, W. Vranken, and K. Henrick
    E-MSD: an integrated data resource for bioinformatics
    Nucleic Acids Res. 32: D211-D216.

  • Ursula Pieper, Narayanan Eswar, Hannes Braberg, M. S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Marti-Renom, Andras Fiser, Ben Webb, Daniel Greenblatt, Conrad C. Huang, Thomas E. Ferrin, and Andrej Sali
    MODBASE, a database of annotated comparative protein structure models, and associated resources
    Nucleic Acids Res. 32: D217-D222.

  • Philip E. Bourne, Kenneth J. Addess, Wolfgang F. Bluhm, Li Chen, Nita Deshpande, Zukang Feng, Ward Fleri, Rachel Green, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Helge Weissig, John Westbrook, and Helen M. Berman
    The distribution and query systems of the RCSB Protein Data Bank
    Nucleic Acids Res. 32: D223-D225.

  • Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin
    SCOP database in 2004: refinements integrate structure and sequence family data
    Nucleic Acids Res. 32: D226-D229.

  • Jürgen Kopp and Torsten Schwede
    The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
    Nucleic Acids Res. 32: D230-D234.

  • Martin Madera, Christine Vogel, Sarah K. Kummerfeld, Cyrus Chothia, and Julian Gough
    The SUPERFAMILY database in 2004: additions and improvements
    Nucleic Acids Res. 32: D235-D239.

  • Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, and Manuela Helmer-Citterich
    SURFACE: a database of protein surface regions for functional annotation
    Nucleic Acids Res. 32: D240-D244.

  • Keiran Fleming, Arne Müller, Robert M. MacCallum, and Michael J. E. Sternberg
    3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
    Nucleic Acids Res. 32: D245-D250.

  • Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, and David R. Westhead
    TOPS: an enhanced database of protein structural topology
    Nucleic Acids Res. 32: D251-D254.

  • Hester M. Wain, Michael J. Lush, Fabrice Ducluzeau, Varsha K. Khodiyar, and Sue Povey
    Genew: the Human Gene Nomenclature Database, 2004 updates
    Nucleic Acids Res. 32: D255-D257.

  • Gene Ontology Consortium
    The Gene Ontology (GO) database and informatics resource
    Nucleic Acids Res. 32: D258-D261.

  • Evelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, and Rolf Apweiler
    The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
    Nucleic Acids Res. 32: D262-D266.

  • Olivier Bodenreider
    The Unified Medical Language System (UMLS): integrating biomedical terminology
    Nucleic Acids Res. 32: D267-D270.

  • Ren Zhang, Hong-Yu Ou, and Chun-Ting Zhang
    DEG: a database of essential genes
    Nucleic Acids Res. 32: D271-D272.

  • Karsten Suhre and Jean-Michel Claverie
    FusionDB: a database for in-depth analysis of prokaryotic gene fusion events
    Nucleic Acids Res. 32: D273-D276.

  • Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, and Masahiro Hattori
    The KEGG resource for deciphering the genome
    Nucleic Acids Res. 32: D277-D280.

  • Naomi Siew, Yaniv Azaria, and Daniel Fischer
    The ORFanage: an ORFan database
    Nucleic Acids Res. 32: D281-D283.

  • Qinghu Ren, Katherine H. Kang, and Ian T. Paulsen
    TransportDB: a relational database of cellular membrane transport systems
    Nucleic Acids Res. 32: D284-D288.

  • Urmila Kulkarni-Kale, Shriram Bhosle, G. Sunitha Manjari, and A. S. Kolaskar
    VirGen: a comprehensive viral genome resource
    Nucleic Acids Res. 32: D289-D292.

  • Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani, Paul Stothard, Michael Ellison, and David S. Wishart
    The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
    Nucleic Acids Res. 32: D293-D295.

  • Roy R. Chaudhuri, Arshad M. Khan, and Mark J. Pallen
    coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics
    Nucleic Acids Res. 32: D296-D299.

  • Margrethe H. Serres, Sulip Goswami, and Monica Riley
    GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins
    Nucleic Acids Res. 32: D300-D302.

  • Heladia Salgado, Socorro Gama-Castro, Agustino Martínez-Antonio, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Martín Peralta-Gil, Delfino Garcia-Alonso, Verónica Jiménez-Jacinto, Alberto Santos-Zavaleta, César Bonavides-Martínez, and Julio Collado-Vides
    RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
    Nucleic Acids Res. 32: D303-D306.

  • Aurélien Barré, Antoine de Daruvar, and Alain Blanchard
    MolliGen, a database dedicated to the comparative genomics of Mollicutes
    Nucleic Acids Res. 32: D307-D310.

  • Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, and J. Michael Cherry
    Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
    Nucleic Acids Res. 32: D311-D314.

  • David Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, and Jean-Luc Souciet for the Génolevures Consortium
    Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
    Nucleic Acids Res. 32: D315-D318.

  • Taro L. Saito, Miwaka Ohtani, Hiroshi Sawai, Fumi Sano, Ayaka Saka, Daisuke Watanabe, Masashi Yukawa, Yoshikazu Ohya, and Shinichi Morishita
    SCMD: Saccharomyces cerevisiae Morphological Database
    Nucleic Acids Res. 32: D319-D322.

  • Gaëlle Lelandais, Stéphane Le Crom, Frédéric Devaux, Stéphane Vialette, George M. Church, Claude Jacq, and Philippe Marc
    yMGV: a cross-species expression data mining tool
    Nucleic Acids Res. 32: D323-D325.

  • Li Li, Jonathan Crabtree, Steve Fischer, Deborah Pinney, Christian J. Stoeckert, Jr, L. David Sibley, and David S. Roos
    ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
    Nucleic Acids Res. 32: D326-D328.

  • Daniela Puiu, Shinichiro Enomoto, Gregory A. Buck, Mitchell S. Abrahamsen, and Jessica C. Kissinger
    CryptoDB: the Cryptosporidium genome resource
    Nucleic Acids Res. 32: D329-D331.

  • Lisa Kreppel, Petra Fey, Pascale Gaudet, Eric Just, Warren A. Kibbe, Rex L. Chisholm, and Alan R. Kimmel
    dictyBase: a new Dictyostelium discoideum genome database
    Nucleic Acids Res. 32: D332-D333.

  • Junichi Watanabe, Yutaka Suzuki, Masahide Sasaki, and Sumio Sugano
    Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species
    Nucleic Acids Res. 32: D334-D338.

  • Christiane Hertz-Fowler, Chris S. Peacock, Valerie Wood, Martin Aslett, Arnaud Kerhornou, Paul Mooney, Adrian Tivey, Matthew Berriman, Neil Hall, Kim Rutherford, Julian Parkhill, Alasdair C. Ivens, Marie-Adele Rajandream, and Bart Barrell
    GeneDB: a resource for prokaryotic and eukaryotic organisms
    Nucleic Acids Res. 32: D339-D343.

  • Michael Luchtan, Chetna Warade, D. Brent Weatherly, Wim M. Degrave, Rick L. Tarleton, and Jessica C. Kissinger
    TcruziDB: an integrated Trypanosoma cruzi genome resource
    Nucleic Acids Res. 32: D344-D346.

  • Franck Samson, Véronique Brunaud, Sylvain Duchêne, Yannick De Oliveira, Michel Caboche, Alain Lecharny, and Sébastien Aubourg
    FLAGdb++: a database for the functional analysis of the Arabidopsis genome
    Nucleic Acids Res. 32: D347-D350.

  • S. Mohseni-Zadeh, A. Louis, P. Brézellec, and J.-L. Risler
    PHYTOPROT: a database of clusters of plant proteins
    Nucleic Acids Res. 32: D351-D353.

  • Qunfeng Dong, Shannon D. Schlueter, and Volker Brendel
    PlantGDB, plant genome database and analysis tools
    Nucleic Acids Res. 32: D354-D359.

  • Shu Ouyang and C. Robin Buell
    The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
    Nucleic Acids Res. 32: D360-D363.

  • Manuel Ruiz, Mathieu Rouard, Louis Marie Raboin, Marc Lartaud, Pierre Lagoda, and Brigitte Courtois
    TropGENE-DB, a multi-tropical crop information system
    Nucleic Acids Res. 32: D364-D367.

  • Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow, and Reinhard Hehl
    AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
    Nucleic Acids Res. 32: D368-D372.

  • Heiko Schoof, Rebecca Ernst, Vladimir Nazarov, Lukas Pfeifer, Hans-Werner Mewes, and Klaus F. X. Mayer
    MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics
    Nucleic Acids Res. 32: D373-D376.

  • Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, and Jun Wang
    BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
    Nucleic Acids Res. 32: D377-D382.

  • Junshi Yazaki, Keiichi Kojima, Kouji Suzuki, Naoki Kishimoto, and Shoshi Kikuchi
    The Rice PIPELINE: a unification tool for plant functional genomics
    Nucleic Acids Res. 32: D383-D387.

  • Setsuko Komatsu, Keiichi Kojima, Kouji Suzuki, Kazuo Ozaki, and Kenichi Higo
    Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003
    Nucleic Acids Res. 32: D388-D392.

  • Carolyn J. Lawrence, Qunfeng Dong, Mary L. Polacco, Trent E. Seigfried, and Volker Brendel
    MaizeGDB, the community database for maize genetics and genomics
    Nucleic Acids Res. 32: D393-D397.

  • Nadim W. Alkharouf and Benjamin F. Matthews
    SGMD: the Soybean Genomics and Microarray Database
    Nucleic Acids Res. 32: D398-D400.

  • J. E. Mabey, M. J. Anderson, P. F. Giles, C. J. Miller, T. K. Attwood, N. W. Paton, E. Bornberg-Bauer, G. D. Robson, S. G. Oliver, and D. W. Denning
    CADRE: the Central Aspergillus Data REpository
    Nucleic Acids Res. 32: D401-D405.

  • Kristin C. Gunsalus, Wan-Chen Yueh, Philip MacMenamin, and Fabio Piano
    RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects
    Nucleic Acids Res. 32: D406-D410.

  • Todd W. Harris, Nansheng Chen, Fiona Cunningham, Marcela Tello-Ruiz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Muller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W. Sternberg, and Lincoln D. Stein
    WormBase: a multi-species resource for nematode biology and genomics
    Nucleic Acids Res. 32: D411-D417.

  • Reed J. Kelso, Michael Buszczak, Ana T. Quiñones, Claudia Castiblanco, Stacy Mazzalupo, and Lynn Cooley
    Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster
    Nucleic Acids Res. 32: D418-D420.

  • Jagan Srinivasan, Georg W. Otto, Ulrich Kahlow, Robert Geisler, and Ralf J. Sommer
    AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus
    Nucleic Acids Res. 32: D421-D422.

  • Todd Wylie, John C. Martin, Michael Dante, Makedonka Dautova Mitreva, Sandra W. Clifton, Asif Chinwalla, Robert H. Waterston, Richard K. Wilson, and James P. McCarter
    Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
    Nucleic Acids Res. 32: D423-D426.

  • John Parkinson, Claire Whitton, Ralf Schmid, Marian Thomson, and Mark Blaxter
    NEMBASE: a resource for parasitic nematode ESTs
    Nucleic Acids Res. 32: D427-D430.

  • Ida Schomburg, Antje Chang, Christian Ebeling, Marion Gremse, Christian Heldt, Gregor Huhn, and Dietmar Schomburg
    BRENDA, the enzyme database: updates and major new developments
    Nucleic Acids Res. 32: D431-D433.

  • Astrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Wolfgang Fleischmann, Sinéad Boyce, Kristian B. Axelsen, Amos Bairoch, Dietmar Schomburg, Keith F. Tipton, and Rolf Apweiler
    IntEnz, the integrated relational enzyme database
    Nucleic Acids Res. 32: D434-D437.

  • Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne Paley, Martha Arnaud, John Pick, Seung Y. Rhee, and Peter D. Karp
    MetaCyc: a multiorganism database of metabolic pathways and enzymes
    Nucleic Acids Res. 32: D438-D442.

  • Christian Lemer, Erick Antezana, Fabian Couche, Frédéric Fays, Xavier Santolaria, Rekin's Janky, Yves Deville, Jean Richelle, and Shoshana J. Wodak
    The aMAZE LightBench: a web interface to a relational database of cellular processes
    Nucleic Acids Res. 32: D443-D448.

  • Lukasz Salwinski, Christopher S. Miller, Adam J. Smith, Frank K. Pettit, James U. Bowie, and David Eisenberg
    The Database of Interacting Proteins: 2004 update
    Nucleic Acids Res. 32: D449-D451.

  • Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David Sherman, and Rolf Apweiler
    IntAct: an open source molecular interaction database
    Nucleic Acids Res. 32: D452-D455.

  • Ming Chen, Susana Lin, and Ralf Hofestaedt
    STCDB: Signal Transduction Classification Database
    Nucleic Acids Res. 32: D456-D458.

  • C. Andreoli, H. Prokisch, K. Hörtnagel, J. C. Mueller, M. Münsterkötter, C. Scharfe, and T. Meitinger
    MitoP2, an integrated database on mitochondrial proteins in yeast and man
    Nucleic Acids Res. 32: D459-D462.

  • Dawn Cotter, Purnima Guda, Eoin Fahy, and Shankar Subramaniam
    MitoProteome: mitochondrial protein sequence database and annotation system
    Nucleic Acids Res. 32: D463-D467.

  • E. Birney, D. Andrews, P. Bevan, M. Caccamo, G. Cameron, Y. Chen, L. Clarke, G. Coates, T. Cox, J. Cuff, V. Curwen, T. Cutts, T. Down, R. Durbin, E. Eyras, X. M. Fernandez-Suarez, P. Gane, B. Gibbins, J. Gilbert, M. Hammond, H. Hotz, V. Iyer, A. Kahari, K. Jekosch, A. Kasprzyk, D. Keefe, S. Keenan, H. Lehvaslaiho, G. McVicker, C. Melsopp, P. Meidl, E. Mongin, R. Pettett, S. Potter, G. Proctor, M. Rae, S. Searle, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, A. Ureta-Vidal, C. Woodwark, M. Clamp, and T. Hubbard
    Ensembl 2004
    Nucleic Acids Res. 32: D468-D470.

  • Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, RIKEN GER Group, GSL Members, Akihiko Konagaya, and Christian Schönbach
    FREP: a database of functional repeats in mouse cDNAs
    Nucleic Acids Res. 32: D471-D475.

  • Carol J. Bult, Judith A. Blake, Joel E. Richardson, James A. Kadin, Janan T. Eppig, and the Mouse Genome Database Group
    The Mouse Genome Database (MGD): integrating biology with the genome
    Nucleic Acids Res. 32: D476-D481.

  • Petr Divina and Jirí Forejt
    The Mouse SAGE Site: database of public mouse SAGE libraries
    Nucleic Acids Res. 32: D482-D483.

  • Hirohide Uenishi, Tomoko Eguchi, Kohei Suzuki, Tetsuya Sawazaki, Daisuke Toki, Hiroki Shinkai, Naohiko Okumura, Noriyuki Hamasima, and Takashi Awata
    PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries
    Nucleic Acids Res. 32: D484-D488.

  • Tal Dagan, Rotem Sorek, Eilon Sharon, Gil Ast, and Dan Graur
    AluGene: a database of Alu elements incorporated within protein-coding genes
    Nucleic Acids Res. 32: D489-D492.

  • Donna Karolchik, Angela S. Hinrichs, Terrence S. Furey, Krishna M. Roskin, Charles W. Sugnet, David Haussler, and W. James Kent
    The UCSC Table Browser data retrieval tool
    Nucleic Acids Res. 32: D493-D496.

  • Suraj Peri, J. Daniel Navarro, Troels Z. Kristiansen, Ramars Amanchy, Vineeth Surendranath, Babylakshmi Muthusamy, T. K. B. Gandhi, K. N. Chandrika, Nandan Deshpande, Shubha Suresh, B. P. Rashmi, K. Shanker, N. Padma, Vidya Niranjan, H. C. Harsha, Naveen Talreja, B. M. Vrushabendra, M. A. Ramya, A. J. Yatish, Mary Joy, H. N. Shivashankar, M. P. Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Neelanjana Ghosh, R. Saravana, Sreenath Chandran, Sujatha Mohan, Chandra Kiran Jonnalagadda, C. K. Prasad, Chandan Kumar-Sinha, Krishna S. Deshpande, and Akhilesh Pandey
    Human protein reference database as a discovery resource for proteomics
    Nucleic Acids Res. 32: D497-D501.

  • Reiko Kikuno, Takahiro Nagase, Manabu Nakayama, Hisashi Koga, Noriko Okazaki, Daisuke Nakajima, and Osamu Ohara
    HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE
    Nucleic Acids Res. 32: D502-D504.

  • Detlev Bannasch, Alexander Mehrle, Karl-Heinz Glatting, Rainer Pepperkok, Annemarie Poustka, and Stefan Wiemann
    LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system
    Nucleic Acids Res. 32: D505-D508.

  • Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, and C. Victor Jongeneel
    trome, trEST and trGEN: databases of predicted protein sequences
    Nucleic Acids Res. 32: D509-D511.

  • Paul N. Schofield, Jonathan B. L. Bard, Catherine Booth, Jacques Boniver, Vincenzo Covelli, Philippe Delvenne, Michele Ellender, Wilhelm Engstrom, Wolfgang Goessner, Michael Gruenberger, Heinz Hoefler, John Hopewell, Mariatheresa Mancuso, Carmel Mothersill, Christopher S. Potten, Leticia Quintanilla-Fend, Bjorn Rozell, Hannu Sariola, John P. Sundberg, and Andrew Ward
    Pathbase: a database of mutant mouse pathology
    Nucleic Acids Res. 32: D512-D515.

  • D. Fredman, G. Munns, D. Rios, F. Sjöholm, M. Siegfried, B. Lenhard, H. Lehväslaiho, and A. J. Brookes
    HGVbase: a curated resource describing human DNA variation and phenotype relationships
    Nucleic Acids Res. 32: D516-D519.

  • Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif, and Jie Liang
    topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
    Nucleic Acids Res. 32: D520-D522.

  • Keiko Akagi, Takeshi Suzuki, Robert M. Stephens, Nancy A. Jenkins, and Neal G. Copeland
    RTCGD: retroviral tagged cancer gene database
    Nucleic Acids Res. 32: D523-D527.

  • Bernice R. Packer, Meredith Yeager, Brian Staats, Robert Welch, Andrew Crenshaw, Maureen Kiley, Andrew Eckert, Michael Beerman, Edward Miller, Andrew Bergen, Nathaniel Rothman, Robert Strausberg, and Stephen J. Chanock
    SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes
    Nucleic Acids Res. 32: D528-D532.

  • Suisheng Tang, Hao Han, and Vladimir B. Bajic
    ERGDB: Estrogen Responsive Genes Database
    Nucleic Acids Res. 32: D533-D536.

  • George P. Patrinos, Belinda Giardine, Cathy Riemer, Webb Miller, David H. K. Chui, Nicholas P. Anagnou, Henri Wajcman, and Ross C. Hardison
    Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies
    Nucleic Acids Res. 32: D537-D541.

  • Viviane Praz, Vidhya Jagannathan, and Philipp Bucher
    CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature
    Nucleic Acids Res. 32: D542-D547.

  • Itoshi Nikaido, Chika Saito, Akiko Wakamoto, Yasuhiro Tomaru, Takahiro Arakawa, Yoshihide Hayashizaki, and Yasushi Okazaki
    EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes
    Nucleic Acids Res. 32: D548-D551.

  • Axel Visel, Christina Thaller, and Gregor Eichele
    GenePaint.org: an atlas of gene expression patterns in the mouse embryo
    Nucleic Acids Res. 32: D552-D556.

  • Christine To, Trevor Epp, Tammy Reid, Qing Lan, Mei Yu, Carol Y. J. Li, Minako Ohishi, Paula Hant, Nora Tsao, Guillermo Casallo, Janet Rossant, Lucy R. Osborne, and William L. Stanford
    The Centre for Modeling Human Disease Gene Trap resource
    Nucleic Acids Res. 32: D557-D559.

  • C. Wiederkehr, R. Basavaraj, C. Sarrauste de Menthière, L. Hermida, R. Koch, U. Schlecht, A. Amon, S. Brachat, M. Breitenbach, P. Briza, S. Caburet, M. Cherry, R. Davis, A. Deutschbauer, H. G. Dickinson, T. Dumitrescu, M. Fellous, A. Goldman, J. A. Grootegoed, R. Hawley, R. Ishii, B. Jégou, R. J. Kaufman, F. Klein, N. Lamb, B. Maro, K. Nasmyth, A. Nicolas, T. Orr-Weaver, P. Philippsen, C. Pineau, K. P. Rabitsch, V. Reinke, H. Roest, W. Saunders, M. Schröder, T. Schedl, M. Siep, A. Villeneuve, D. J. Wolgemuth, M. Yamamoto, D. Zickler, R. E. Esposito, and M. Primig
    GermOnline, a cross-species community knowledgebase on germ cell differentiation
    Nucleic Acids Res. 32: D560-D567.

  • David P. Hill, Dale A. Begley, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Constance M. Smith, Jon S. Beal, Lori E. Corbani, Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and Martin Ringwald
    The mouse Gene Expression Database (GXD): updates and enhancements
    Nucleic Acids Res. 32: D568-D571.

  • Sung-Ho Goh, Y. Terry Lee, Gerard G. Bouffard, and Jeffery L. Miller
    Hembase: browser and genome portal for hematology and erythroid biology
    Nucleic Acids Res. 32: D572-D574.

  • David J. Craigon, Nick James, John Okyere, Janet Higgins, Joan Jotham, and Sean May
    NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service
    Nucleic Acids Res. 32: D575-D577.

  • Josephine Chen, Po Zhao, Donald Massaro, Linda B. Clerch, Richard R. Almon, Debra C. DuBois, William J. Jusko, and Eric P. Hoffman
    The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface
    Nucleic Acids Res. 32: D578-D581.

  • György Babnigg and Carol S. Giometti
    GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes
    Nucleic Acids Res. 32: D582-D585.

  • M. Brahmachary, S. P. T. Krishnan, J. L. Y. Koh, A. M. Khan, S. H. Seah, T. W. Tan, V. Brusic, and V. B. Bajic
    ANTIMIC: a database of antimicrobial sequences
    Nucleic Acids Res. 32: D586-D589.

  • Zhe Wang and Guangshun Wang
    APD: the Antimicrobial Peptide Database
    Nucleic Acids Res. 32: D590-D592.

  • Lee Whitmore and B. A. Wallace
    The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols
    Nucleic Acids Res. 32: D593-D594.

  • Feng Liang, Udayakumar Matrubutham, Babak Parvizi, Jessica Yen, Daniel Duan, Jyotika Mirchandani, Sandra Hashima, Uyen Nguyen, Eric Ubil, Jake Loewenheim, Xin Yu, Sara Sipes, Wendy Williams, Ling Wang, Robert Bennett, and John Carrino
    ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection
    Nucleic Acids Res. 32: D595-D599.

 

Latest update: January 14, 2004


Ralf Koebnik
Institut de recherche pour le dèveloppement
UMR 5096, CNRS-UP-IRD
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