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Nucleic Acids Research
2005, volume: 33, number: Database-Issue

  1. Alex Bateman
    Editorial. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:1- [Journal]
  2. Dov Greenbaum, Andrew Smith, Mark Gerstein
    Editorial. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:3-4 [Journal]
  3. Michael Y. Galperin
    The Molecular Biology Database Collection: 2005 update. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:5-24 [Journal]
  4. Yoshio Tateno, Naruya Saitou, Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori
    DDBJ in collaboration with mass-sequencing teams on annotation. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:25-28 [Journal]
  5. Carola Kanz, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Federico Garcia Diez, Nicola Harte, Tamara Kulikova, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Siamak Sobhany, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
    The EMBL Nucleotide Sequence Database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:29-33 [Journal]
  6. Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler
    GenBank. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:34-38 [Journal]
  7. David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Joan U. Pontius, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O. Suzek, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko
    Database resources of the National Center for Biotechnology Information. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:39-45 [Journal]
  8. Catherine Brooksbank, Graham Cameron, Janet M. Thornton
    The European Bioinformatics Institute's data resources: towards systems biology. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:46-53 [Journal]
  9. Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova
    Entrez Gene: gene-centered information at NCBI. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:54-58 [Journal]
  10. Adel Khelifi, Laurent Duret, Dominique Mouchiroud
    HOPPSIGEN: a database of human and mouse processed pseudogenes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:59-66 [Journal]
  11. Victor G. Levitsky, Aleksey V. Katokhin, Olga A. Podkolodnaya, Dagmara P. Furman, Nikolay A. Kolchanov
    NPRD: Nucleosome Positioning Region Database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:67-70 [Journal]
  12. Yuandan Lee, Jennifer Tsai, S. Sunkara, Svetlana Karamycheva, Geo Pertea, Razvan Sultana, Valentin Antonescu, A. Chan, Foo Cheung, John Quackenbush
    The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:71-74 [Journal]
  13. Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, Sanghyuk Lee
    ECgene: genome annotation for alternative splicing. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:75-79 [Journal]
  14. Hsien-Da Huang, Jorng-Tzong Horng, Feng-Mao Lin, Yu-Chung Chang, Chen-Chia Huang
    SpliceInfo: an information repository for mRNA alternative splicing in human genome. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:80-85 [Journal]
  15. Endre Barta, Endre Sebestyén, Tamás B. Pálfy, Gábor Tóth, Csaba P. Ortutay, László Patthy
    DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:86-90 [Journal]
  16. Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva
    The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:91-97 [Journal]
  17. Abel D. González, Vladimir Espinosa, Ana Tereza R. Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides
    TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:98-102 [Journal]
  18. Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang
    TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:103-107 [Journal]
  19. Matthias Truss, Maciej Swat, Szymon M. Kielbasa, Reinhold Schäfer, Hanspeter Herzel, Christian Hagemeier
    HuSiDa - the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:108-111 [Journal]
  20. Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen
    NONCODE: an integrated knowledge database of non-coding RNAs. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:112-115 [Journal]
  21. Haibo Zhang, Jun Hu, Michael Recce, Bin Tian
    PolyA_DB: a database for mammalian mRNA polyadenylation. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:116-120 [Journal]
  22. Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Alex Bateman
    Rfam: annotating non-coding RNAs in complete genomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:121-124 [Journal]
  23. Ken C. Pang, Stuart Stephen, Pär G. Engström, Khairina Tajul-Arifin, Weisan Chen, Claes Wahlestedt, Boris Lenhard, Yoshihide Hayashizaki, John S. Mattick
    RNAdb - a comprehensive mammalian noncoding RNA database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:125-130 [Journal]
  24. Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer
    siRNAdb: a database of siRNA sequences. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:131-134 [Journal]
  25. James A. McCloskey, Jef Rozenski
    The Small Subunit rRNA Modification Database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:135-138 [Journal]
  26. Mathias Sprinzl, Konstantin S. Vassilenko
    Compilation of tRNA sequences and sequences of tRNA genes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:139-140 [Journal]
  27. Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul Kersey, Jorge Duarte, Cecilia Saccone, Graziano Pesole
    UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:141-146 [Journal]
  28. Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, Nicholas Lamb
    PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:147-153 [Journal]
  29. Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, María J. Martín, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh
    The Universal Protein Resource (UniProt). [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:154-159 [Journal]
  30. Sven Mika, Burkhard Rost
    NMPdb: Database of Nuclear Matrix Proteins. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:160-163 [Journal]
  31. Sébastien Rey, Michael Acab, Jennifer L. Gardy, Matthew R. Laird, Katalin de Fays, Christophe G. Lambert, Fiona S. L. Brinkman
    PSORTdb: a protein subcellular localization database for bacteria. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:164-168 [Journal]
  32. Yunjia Chen, Yong Zhang, Yanbin Yin, Ge Gao, Songgang Li, Ying Jiang, Xiaocheng Gu, Jingchu Luo
    SPD - a web-based secreted protein database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:169-173 [Journal]
  33. Ya-Hui Chang, Wen-Hui Su, Tso-Ching Lee, Hsiao-Fang Sunny Sun, Chia-Hsiang Chen, Wen-Harn Pan, Shih-Feng Tsai, Yuh-Shan Jou
    TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:174-177 [Journal]
  34. Qiaojuan Jane Su, Lin Lu, Serge Saxonov, Douglas L. Brutlag
    eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:178-182 [Journal]
  35. Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, Nikolay A. Kolchanov
    PDBSite: a database of the 3D structure of protein functional sites. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:183-187 [Journal]
  36. Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, Liisa Holm
    ADDA: a domain database with global coverage of the protein universe. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:188-191 [Journal]
  37. Aron Marchler-Bauer, John B. Anderson, Praveen F. Cherukuri, Carol DeWeese-Scott, Lewis Y. Geer, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant
    CDD: a Conserved Domain Database for protein classification. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:192-196 [Journal]
  38. Saraswathi Abhiman, Erik L. L. Sonnhammer
    FunShift: a database of function shift analysis on protein subfamilies. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:197-200 [Journal]
  39. Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu
    InterPro, progress and status in 2005. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:201-205 [Journal]
  40. Shu-Hsien Sheu, David R. Lancia Jr., Karl H. Clodfelter, Melissa R. Landon, Sandor Vajda
    PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:206-211 [Journal]
  41. Catherine Bru, Emmanuel Courcelle, Sébastien Carrère, Yoann Beausse, Sandrine Dalmar, Daniel Kahn
    The ProDom database of protein domain families: more emphasis on 3D. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:212-215 [Journal]
  42. Noam Kaplan, Ori Sasson, Uri Inbar, Moriah Friedlich, Menachem Fromer, Hillel Fleischer, Elon Portugaly, Nathan Linial, Michal Linial
    ProtoNet 4.0: A hierarchical classification of one million protein sequences. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:216-218 [Journal]
  43. James A. Casbon, Mansoor A. S. Saqi
    S4: structure-based sequence alignments of SCOP superfamilies. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:219-222 [Journal]
  44. Kristian Vlahovicek, László Kaján, Vilmos Ágoston, Sándor Pongor
    The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:223-225 [Journal]
  45. Thomas Meinel, Antje Krause, Hannes Luz, Martin Vingron, Eike Staub
    The SYSTERS Protein Family Database in 2005. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:226-229 [Journal]
  46. Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis
    REBASE - restriction enzymes and DNA methyltransferases. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:230-232 [Journal]
  47. Nita Deshpande, Kenneth J. Addess, Wolfgang Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John D. Westbrook, Helen M. Berman, Philip E. Bourne
    The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:233-237 [Journal]
  48. Jae-Min Shin, Doo-Ho Cho
    PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:238-241 [Journal]
  49. Thomas Lütteke, Martin Frank, Claus-Wilhelm von der Lieth
    Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:242-246 [Journal]
  50. Frances M. G. Pearl, Annabel E. Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony E. Lewis, Christopher Bennett, Russell L. Marsden, Alastair Grant, David Lee, Adrian Akpor, Michael Maibaum, Andrew P. Harrison, Timothy Dallman, Gabrielle A. Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline Johnston, Antonio Sillero, Janet M. Thornton, Christine A. Orengo
    The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:247-251 [Journal]
  51. Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini
    GenDiS: Genomic Distribution of protein structural domain Superfamilies. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:252-255 [Journal]
  52. Véronique Giudicelli, Denys Chaume, Marie-Paule Lefranc
    IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:256-261 [Journal]
  53. Samir S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, Daniel Barrell, Rolf Apweiler, Kim Henrick
    E-MSD: an integrated data resource for bioinformatics. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:262-265 [Journal]
  54. Roman A. Laskowski, Victor V. Chistyakov, Janet M. Thornton
    PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:266-268 [Journal]
  55. Goran Neshich, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Ivan P. Pinto, Juliana F. Palandrani, João N. Krauchenco, Christian Baudet, Arnaldo J. Montagner, Roberto H. Higa
    STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:269-274 [Journal]
  56. Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon
    PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:275-278 [Journal]
  57. Kate F. Fulton, Glyn L. Devlin, Rachel A. Jodun, Linda Silvestri, Stephen P. Bottomley, Alan R. Fersht, Ashley M. Buckle
    PFD: a database for the investigation of protein folding kinetics and stability. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:279-283 [Journal]
  58. Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody A. Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano, Paul D. Thomas
    The PANTHER database of protein families, subfamilies, functions and pathways. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:284-288 [Journal]
  59. Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman
    Biomedical term mapping databases. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:289-293 [Journal]
  60. James R. Cole, B. Chai, Ryan J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, George M. Garrity, James M. Tiedje
    The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:294-296 [Journal]
  61. Paul Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter Mclaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, Rolf Apweiler
    Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:297-302 [Journal]
  62. José M. Peregrin-Alvarez, Andrew Yam, Gaya Sivakumar, John Parkinson
    PartiGeneDB - collating partial genomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:303-307 [Journal]
  63. M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, Dmitrij Frishman
    The PEDANT genome database in 2005. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:308-310 [Journal]
  64. Elliot J. Lefkowitz, Chris Upton, Shankar S. Changayil, Charles Buck, Paula Traktman, R. Mark L. Buller
    Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:311-316 [Journal]
  65. Paul Stothard, Gary H. Van Domselaar, Savita Shrivastava, Anchi Guo, Brian O'Neill, Joseph A. Cruz, Michael Ellison, David S. Wishart
    BacMap: an interactive picture atlas of annotated bacterial genomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:317-320 [Journal]
  66. Hiroyuki Ogata, Jean-Michel Claverie
    Metagrowth: a new resource for the building of metabolic hypotheses in microbiology. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:321-324 [Journal]
  67. Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, Qi Jin
    VFDB: a reference database for bacterial virulence factors. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:325-328 [Journal]
  68. Raju V. Misra, Richard S. P. Horler, Wolfgang Reindl, Igor Goryanin, Gavin H. Thomas
    EchoBASE: an integrated post-genomic database for Escherichia coli. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:329-333 [Journal]
  69. Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp
    EcoCyc: a comprehensive database resource for Escherichia coli. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:334-337 [Journal]
  70. Geoffrey L. Winsor, Raymond Lo, Shannan J. Ho Sui, Korine S. E. Ung, Shao-Shan Huang, Dean Cheng, Wai-Kay Ho Ching, Robert E. W. Hancock, Fiona S. L. Brinkman
    Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:338-343 [Journal]
  71. Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy, K. R. Rajyashri, Villoo Morawala Patell, Chris Bowler
    The Diatom EST Database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:344-347 [Journal]
  72. Leandro Hermida, Sophie Brachat, Sylvia Voegeli, Peter Philippsen, Michael Primig
    The Ashbya Genome Database (AGD) - a tool for the yeast community and genome biologists. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:348-352 [Journal]
  73. C. d'Enfert, S. Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, L. Jones, Fredj Tekaia, O. Bader, Antje Albrecht, L. Castillo, A. Dominguez, J. F. Ernst, C. Fradin, C. Gaillardin, S. Garcia-Sanchez, P. de Groot, B. Hube, F. M. Klis, S. Krishnamurthy, D. Kunze, M.-C. Lopez, A. Mavor, N. Martin, I. Moszer, D. Onésime, J. Perez Martin, R. Sentandreu, E. Valentin, A. J. P. Brown
    CandidaDB: a genome database for Candida albicans pathogenomics. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:353-357 [Journal]
  74. Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Gail Binkley, Christopher Lane, Stuart R. Miyasato, Gavin Sherlock
    The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. [Citation Graph (0, 0)][DBLP]
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  81. Andre R. O. Cavalcanti, Thomas H. Clarke, Laura F. Landweber
    MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates. [Citation Graph (0, 0)][DBLP]
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  82. Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Chen Ye, Cheng Lu, Jun Wang, Songgang Li, Gane Ka-Shu Wong, Huanming Yang, Jian Wang, Zhonghuai Xiang, Zeyang Zhou, Jun Yu
    SilkDB: a knowledgebase for silkworm biology and genomics. [Citation Graph (0, 0)][DBLP]
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    SilkSatDb: a microsatellite database of the silkworm, Bombyx mori. [Citation Graph (0, 0)][DBLP]
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    EzCatDB: the Enzyme Catalytic-mechanism Database. [Citation Graph (0, 0)][DBLP]
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    3did: interacting protein domains of known three-dimensional structure. [Citation Graph (0, 0)][DBLP]
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  86. C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, Doron Betel, B. Bobechko, K. Boutilier, E. Burgess, K. Buzadzija, R. Cavero, C. D'Abreo, Ian Donaldson, D. Dorairajoo, M. J. Dumontier, M. R. Dumontier, V. Earles, R. Farrall, H. Feldman, E. Garderman, Y. Gong, R. Gonzaga, V. Grytsan, E. Gryz, V. Gu, E. Haldorsen, A. Halupa, R. Haw, A. Hrvojic, L. Hurrell, Ruth Isserlin, F. Jack, F. Juma, A. Khan, T. Kon, S. Konopinsky, V. Le, E. Lee, S. Ling, M. Magidin, J. Moniakis, J. Montojo, S. Moore, B. Muskat, I. Ng, J. P. Paraiso, B. Parker, Greg Pintilie, R. Pirone, John J. Salama, S. Sgro, T. Shan, Y. Shu, J. Siew, D. Skinner, Kevin A. Snyder, R. Stasiuk, D. Strumpf, Brigitte Tuekam, S. Tao, Z. Wang, M. White, R. Willis, Cheryl Wolting, S. Wong, A. Wrong, C. Xin, R. Yao, B. Yates, S. Zhang, K. Zheng, Tony Pawson, B. F. Francis Ouellette, Christopher W. V. Hogue
    The Biomolecular Interaction Network Database and related tools 2005 update. [Citation Graph (0, 0)][DBLP]
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    GeneNet in 2005. [Citation Graph (0, 0)][DBLP]
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  88. G. Joshi-Tope, Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal, G. R. Gopinath, G. R. Wu, Lisa Matthews, Suzanna Lewis, Ewan Birney, Lincoln Stein
    Reactome: a knowledgebase of biological pathways. [Citation Graph (0, 0)][DBLP]
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  89. Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork
    STRING: known and predicted protein-protein associations, integrated and transferred across organisms. [Citation Graph (0, 0)][DBLP]
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  90. Jing Wang, Ximiao He, Jue Ruan, Mingtao Dai, Jie Chen, Yong Zhang, Yafeng Hu, Chen Ye, Shengting Li, Lijuan Cong, Lin Fang, Bin Liu, Songgang Li, Jian Wang, David W. Burt, Gane Ka-Shu Wong, Jun Yu, Huanming Yang, Jun Wang
    ChickVD: a sequence variation database for the chicken genome. [Citation Graph (0, 0)][DBLP]
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  91. Vamsi Veeramachaneni, Wojciech Makalowski
    DED: Database of Evolutionary Distances. [Citation Graph (0, 0)][DBLP]
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    Ensembl 2005. [Citation Graph (0, 0)][DBLP]
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  93. Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, W. James Kent
    The UCSC Proteome Browser. [Citation Graph (0, 0)][DBLP]
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    The Vertebrate Genome Annotation (Vega) database. [Citation Graph (0, 0)][DBLP]
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  95. Laura Elnitski, Belinda Giardine, Prachi Shah, Yi Zhang, Cathy Riemer, Matthew Weirauch, Richard Burhans, Webb Miller, Ross C. Hardison
    Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. [Citation Graph (0, 0)][DBLP]
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  96. Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake
    The Mouse Genome Database (MGD): from genes to mice - a community resource for mouse biology. [Citation Graph (0, 0)][DBLP]
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    Inparanoid: a comprehensive database of eukaryotic orthologs. [Citation Graph (0, 0)][DBLP]
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    Polymorphix: a sequence polymorphism database. [Citation Graph (0, 0)][DBLP]
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    The Rat Genome Database (RGD): developments towards a phenome database. [Citation Graph (0, 0)][DBLP]
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    RatMap - rat genome tools and data. [Citation Graph (0, 0)][DBLP]
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  101. Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sælensminde, David A. Liberles
    The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. [Citation Graph (0, 0)][DBLP]
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    L1Base: from functional annotation to prediction of active LINE-1 elements. [Citation Graph (0, 0)][DBLP]
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  103. Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott
    NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:501-504 [Journal]
  104. Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, Sandro Banfi
    DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:505-510 [Journal]
  105. Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia
    HCAD, closing the gap between breakpoints and genes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:511-513 [Journal]
  106. Ada Hamosh, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, Victor A. McKusick
    Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. [Citation Graph (0, 0)][DBLP]
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    FESD: a Functional Element SNPs Database in human. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:518-522 [Journal]
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    IPD - the Immuno Polymorphism Database. [Citation Graph (0, 0)][DBLP]
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    SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. [Citation Graph (0, 0)][DBLP]
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  110. Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai
    Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. [Citation Graph (0, 0)][DBLP]
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    HAGR: the Human Ageing Genomic Resources. [Citation Graph (0, 0)][DBLP]
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    T1DBase, a community web-based resource for type 1 diabetes research. [Citation Graph (0, 0)][DBLP]
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  113. Yasuhiro Kasai, Shin-ichi Hashimoto, Tomoyuki Yamada, Jun Sese, Sumio Sugano, Kouji Matsushima, Shinichi Morishita
    5'SAGE: 5'-end Serial Analysis of Gene Expression database. [Citation Graph (0, 0)][DBLP]
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    ArrayExpress - a public repository for microarray gene expression data at the EBI. [Citation Graph (0, 0)][DBLP]
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  115. Maxim Shklar, Liora Strichman-Almashanu, Orit Shmueli, Michael Shmoish, Marilyn Safran, Doron Lancet
    GeneTide - Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:556-561 [Journal]
  116. Tanya Barrett, Tugba O. Suzek, Dennis B. Troup, Stephen E. Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex E. Lash, Wataru Fujibuchi, Ron Edgar
    NCBI GEO: mining millions of expression profiles - database and tools. [Citation Graph (0, 0)][DBLP]
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    The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. [Citation Graph (0, 0)][DBLP]
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    The Stanford Microarray Database accommodates additional microarray platforms and data formats. [Citation Graph (0, 0)][DBLP]
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    MetaRouter: bioinformatics for bioremediation. [Citation Graph (0, 0)][DBLP]
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    IMGT, the international ImMunoGeneTics information system®. [Citation Graph (0, 0)][DBLP]
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  123. Nuwee Wiwatwattana, Anuj Kumar
    Organelle DB: a cross-species database of protein localization and function. [Citation Graph (0, 0)][DBLP]
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  124. Joshua L. Heazlewood, A. Harvey Millar
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  125. Marty C. Brandon, Marie T. Lott, Kevin Cuong Nguyen, Syawal Spolim, Shamkant B. Navathe, Pierre Baldi, Douglas C. Wallace
    MITOMAP: a human mitochondrial genome database - 2004 update. [Citation Graph (0, 0)][DBLP]
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  126. Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, Julie A. Dickerson
    BarleyBase - an expression profiling database for plant genomics. [Citation Graph (0, 0)][DBLP]
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  127. C. Künne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse, U. Scholz
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    openSputnik - a database to ESTablish comparative plant genomics using unsaturated sequence collections. [Citation Graph (0, 0)][DBLP]
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  129. Stephen Rudd, Heiko Schoof, Klaus F. X. Mayer
    PlantMarkers - a database of predicted molecular markers from plants. [Citation Graph (0, 0)][DBLP]
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    ASRP: the Arabidopsis Small RNA Project Database. [Citation Graph (0, 0)][DBLP]
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    GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. [Citation Graph (0, 0)][DBLP]
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  133. Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Motoaki Seki, Takashi Kuromori, Takuya Ito, Akihiko Konagaya, Tetsuro Toyoda, Kazuo Shinozaki
    RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. [Citation Graph (0, 0)][DBLP]
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  134. Yuichi Ito, Kohji Arikawa, Baltazar A. Antonio, Isamu Ohta, Shinji Naito, Yoshiyuki Mukai, Atsuko Shimano, Masatoshi Masukawa, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Junri Yokoyama, Yasumichi Sakai, Katsumi Sakata, Yoshiaki Nagamura, Nobukazu Namiki, Takashi Matsumoto, Kenichi Higo, Takuji Sasaki
    Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics. [Citation Graph (0, 0)][DBLP]
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  135. Christopher G. Love, Andrew J. Robinson, Geraldine A. C. Lim, Clare J. Hopkins, Jacqueline Batley, Gary Barker, German C. Spangenberg, David Edwards
    Brassica ASTRA: an integrated database for Brassica genomic research. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:656-659 [Journal]
  136. Michael D. Gonzales, Eric Archuleta, Andrew D. Farmer, Kamal Gajendran, David Grant, Randy C. Shoemaker, William D. Beavis, Mark E. Waugh
    The Legume Information System (LIS): an integrated information resource for comparative legume biology. [Citation Graph (0, 0)][DBLP]
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    PoMaMo - a comprehensive database for potato genome data. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:666-670 [Journal]
  138. Ida Retter, Hans Helmar Althaus, Richard Münch, Werner Müller
    VBASE2, an integrative V gene database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:671-674 [Journal]
  139. Susie Stephens, Jake Yue Chen, Marcel G. Davidson, Shiby Thomas, Barry M. Trute
    Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:675-679 [Journal]
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