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ORCIDNucleic Acids Research, Volume 33
Volume 33, Database-Issue, January 1 2005
- Alex Bateman
:
Editorial. 1 - Dov Greenbaum, Andrew K. Smith, Mark Gerstein:
Editorial. 3-4
- Michael Y. Galperin:
The Molecular Biology Database Collection: 2005 update. 5-24 - Yoshio Tateno, Naruya Saitou, Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori:
DDBJ in collaboration with mass-sequencing teams on annotation. 25-28 - 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 Y. 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. 29-33 - Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
GenBank. 34-38 - 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. 39-45 - Catherine Brooksbank, Graham Cameron, Janet M. Thornton:
The European Bioinformatics Institute's data resources: towards systems biology. 46-53 - Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
Entrez Gene: gene-centered information at NCBI. 54-58 - Adel Khelifi, Laurent Duret, Dominique Mouchiroud:
HOPPSIGEN: a database of human and mouse processed pseudogenes. 59-66 - Victor G. Levitsky, Aleksey V. Katokhin, Olga A. Podkolodnaya, Dagmara P. Furman, Nikolay A. Kolchanov:
NPRD: Nucleosome Positioning Region Database. 67-70 - Yuandan Lee, Jennifer Tsai, S. Sunkara, Svetlana Karamycheva, Geo Pertea, Razvan Sultana, Valentin Antonescu, Agnes P. Chan, Foo Cheung, John Quackenbush:
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. 71-74 - Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, Sanghyuk Lee:
ECgene: genome annotation for alternative splicing. 75-79 - 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. 80-85 - 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. 86-90 - Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva:
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. 91-97 - Abel D. González, Vladimir Espinosa Angarica, Ana Tereza Ribeiro de Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides:
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. 98-102 - Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang:
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. 103-107 - 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. 108-111 - 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. 112-115 - Haibo Zhang, Jun Hu, Michael Recce, Bin Tian:
PolyA_DB: a database for mammalian mRNA polyadenylation. 116-120 - Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Alex Bateman:
Rfam: annotating non-coding RNAs in complete genomes. 121-124 - 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. 125-130 - Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer:
siRNAdb: a database of siRNA sequences. 131-134 - James A. McCloskey, Jef Rozenski:
The Small Subunit rRNA Modification Database. 135-138 - Mathias Sprinzl, Konstantin S. Vassilenko:
Compilation of tRNA sequences and sequences of tRNA genes. 139-140 - Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul J. Kersey, Jorge Duarte, Cecilia Saccone, Graziano Pesole:
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. 141-146 - 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. 147-153 - Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh:
The Universal Protein Resource (UniProt). 154-159 - Sven Mika, Burkhard Rost:
NMPdb: Database of Nuclear Matrix Proteins. 160-163 - 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. 164-168 - Yunjia Chen, Yong Zhang, Yanbin Yin, Ge Gao, Songgang Li, Ying Jiang, Xiaocheng Gu, Jingchu Luo:
SPD - a web-based secreted protein database. 169-173 - 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. 174-177 - Qiaojuan Jane Su, Lin Lu, Serge Saxonov, Douglas L. Brutlag:
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. 178-182 - Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, Nikolay A. Kolchanov:
PDBSite: a database of the 3D structure of protein functional sites. 183-187 - Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, Liisa Holm:
ADDA: a domain database with global coverage of the protein universe. 188-191 - 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. 192-196 - Saraswathi Abhiman, Erik L. L. Sonnhammer:
FunShift: a database of function shift analysis on protein subfamilies. 197-200 - 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 L. 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. 201-205 - 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. 206-211 - Catherine Bru, Emmanuel Courcelle, Sébastien Carrère, Yoann Beausse, Sandrine Dalmar, Daniel Kahn:
The ProDom database of protein domain families: more emphasis on 3D. 212-215 - 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. 216-218 - James A. Casbon, Mansoor A. S. Saqi:
S4: structure-based sequence alignments of SCOP superfamilies. 219-222 - Kristian Vlahovicek, László Kaján, Vilmos Ágoston, Sándor Pongor:
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. 223-225 - Thomas Meinel, Antje Krause, Hannes Luz, Martin Vingron, Eike Staub:
The SYSTERS Protein Family Database in 2005. 226-229 - Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
REBASE - restriction enzymes and DNA methyltransferases. 230-232 - 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. 233-237 - Jae-Min Shin, Doo-Ho Cho:
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. 238-241 - Thomas Lütteke, Martin Frank, Claus-Wilhelm von der Lieth:
Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. 242-246 - Frances M. G. Pearl, Annabel E. Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony E. Lewis, Christopher Bennett, Russell L. Marsden, Alastair Grant, David A. Lee, Adrian Akpor, Michael Maibaum, Andrew P. Harrison, Timothy Dallman, Gabrielle A. Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline E. 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. 247-251 - Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
GenDiS: Genomic Distribution of protein structural domain Superfamilies. 252-255 - Véronique Giudicelli, Denys Chaume, Marie-Paule Lefranc:
IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. 256-261 - Samir S. Velankar, P. McNeil, Virginie Mittard-Runte, A. Suarez, Daniel Barrell, Rolf Apweiler, Kim Henrick:
E-MSD: an integrated data resource for bioinformatics. 262-265 - 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. 266-268 - 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. 269-274 - Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon:
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. 275-278 - 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. 279-283 - 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. 284-288 - Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman:
Biomedical term mapping databases. 289-293 - James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, S. A. Kulam, Donna M. McGarrell, George M. Garrity, James M. Tiedje:
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. 294-296 - Paul J. 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. 297-302 - José M. Peregrín-Alvarez, Andrew Yam, Gaya Sivakumar, John Parkinson:
PartiGeneDB - collating partial genomes. 303-307 - M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, Dmitrij Frishman:
The PEDANT genome database in 2005. 308-310 - 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. 311-316 - 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. 317-320 - Hiroyuki Ogata, Jean-Michel Claverie:
Metagrowth: a new resource for the building of metabolic hypotheses in microbiology. 321-324 - Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, Qi Jin:
VFDB: a reference database for bacterial virulence factors. 325-328 - Raju V. Misra, Richard S. P. Horler, Wolfgang Reindl, Igor Goryanin, Gavin H. Thomas:
EchoBASE: an integrated post-genomic database for Escherichia coli. 329-333 - 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. 334-337 - 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. 338-343 - Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy, K. R. Rajyashri, Villoo Morawala Patell, Chris Bowler:
The Diatom EST Database. 344-347 - Leandro Hermida, Sophie Brachat, Sylvia Voegeli, Peter Philippsen, Michael Primig:
The Ashbya Genome Database (AGD) - a tool for the yeast community and genome biologists. 348-352 - Christophe d'Enfert, Sophie Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, Louis M. Jones, Fredj Tekaia, Oliver Bader, Antje Albrecht, L. Castillo, A. Dominguez, J. F. Ernst, Chantal Fradin, C. Gaillardin, S. Garcia-Sanchez, P. de Groot, Bernhard Hube, F. M. Klis, S. Krishnamurthy, D. Kunze, M.-C. Lopez, A. Mavor, N. Martin, Ivan Moszer, D. Onésime, Jose Perez-Martin, R. Sentandreu, Eulogio Valentin, A. J. P. Brown:
CandidaDB: a genome database for Candida albicans pathogenomics. 353-357 - 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. 358-363 - Ulrich Güldener, Martin Münsterkötter, Gabi Kastenmüller, Normann Strack, Jacques van Helden, Christian Lemer, J. Richelles, Shoshana J. Wodak, J. García-Martínez, José E. Pérez-Ortín, Holger Michael, Andreas Kaps, E. Talla, Bernard Dujon, Bruno André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, Hans-Werner Mewes:
CYGD: the Comprehensive Yeast Genome Database. 364-368 - Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Ilona Pylvänäinen, Graham J. L. Kemp, Olle Nerman, Anders Blomberg:
PROPHECY - a database for high-resolution phenomics. 369-373 - Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Anand Sethuraman, Shuai Weng, David Botstein, J. Michael Cherry:
Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). 374-377 - Michael Riffle, Lars Malmström, Trisha N. Davis:
The Yeast Resource Center Public Data Repository. 378-382 - Nansheng Chen, Todd W. Harris, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Payan Canaran, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Fiona Cunningham, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Shraddha Pai, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W. Sternberg, Lincoln D. Stein:
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. 383-389 - Rachel A. Drysdale, Madeline A. Crosby:
FlyBase: genes and gene models. 390-395 - Andre R. O. Cavalcanti, Thomas H. Clarke, Laura F. Landweber:
MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates. 396-398 - 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. 399-402 - M. D. Prasad, M. Muthulakshmi, K. P. Arunkumar, M. Madhu, Vattipally B. Sreenu, V. Pavithra, Buddhaditta Bose, Hampapathalu A. Nagarajaram, K. Mita, Toru Shimada, Javaregowda Nagaraju:
SilkSatDb: a microsatellite database of the silkworm, Bombyx mori. 403-406 - Nozomi Nagano:
EzCatDB: the Enzyme Catalytic-mechanism Database. 407-412 - Amelie Stein, Robert B. Russell, Patrick Aloy:
3did: interacting protein domains of known three-dimensional structure. 413-417 - C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, Martha Bajec, K. Bantoft, Doron Betel, B. Bobechko, K. Boutilier, E. Burgess, K. Buzadzija, R. Cavero, C. D'Abreo, Ian M. Donaldson, D. Dorairajoo, Michel Justin Dumontier, M. R. Dumontier, V. Earles, R. Farrall, Howard J. Feldman, E. Garderman, Y. Gong, R. Gonzaga, V. Grytsan, E. Gryz, V. Gu, E. Haldorsen, A. Halupa, Robin 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, Benjamin D. 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, Shudong Zhang, K. Zheng, Tony Pawson, B. F. Francis Ouellette, Christopher W. V. Hogue:
The Biomolecular Interaction Network Database and related tools 2005 update. 418-424 - Elena A. Ananko, Nikolay L. Podkolodny, Irina L. Stepanenko, Olga A. Podkolodnaya, D. A. Rasskazov, Denis S. Miginsky, Vitali A. Likhoshvai, Alexander V. Ratushny, N. N. Podkolodnaya, Nikolay A. Kolchanov:
GeneNet in 2005. 425-427 - G. Joshi-Tope, Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal, Gopal R. Gopinath, G. R. Wu, Lisa Matthews, Suzanna Lewis, Ewan Birney, Lincoln Stein:
Reactome: a knowledgebase of biological pathways. 428-432 - 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. 433-437 - 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. 438-441 - Vamsi Veeramachaneni, Wojciech Makalowski:
DED: Database of Evolutionary Distances. 442-446 - Tim J. P. Hubbard, D. Andrews, Mario Cáccamo, Graham Cameron, Yuan Chen, Michele E. Clamp, Laura Clarke, Guy Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Xosé M. Fernández-Suárez, James G. R. Gilbert, Martin Hammond, Javier Herrero, H. Hotz, Kevin L. Howe, Vivek Iyer, Kerstin Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Felix Kokocinski, D. London, Ian Longden, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Simon C. Potter, Glenn Proctor, Mark Rae, Daniel Rios, Michael Schuster, Stephen M. J. Searle, Jessica Severin, Guy Slater, Damian Smedley, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, Stephen J. Trevanion, Abel Ureta-Vidal, Jan Vogel, Simon White, Cara Woodwark, Ewan Birney:
Ensembl 2005. 447-453 - Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, W. James Kent:
The UCSC Proteome Browser. 454-458 - J. L. Ashurst, C.-K. Chen, James G. R. Gilbert, Kerstin Jekosch, Stephen Keenan, Patrick Meidl, Stephen M. J. Searle, Jim Stalker, R. Storey, Stephen J. Trevanion, Laurens G. Wilming, Tim J. P. Hubbard:
The Vertebrate Genome Annotation (Vega) database. 459-465 - Laura Elnitski, Belinda Giardine, Prachi Shah, Yi Zhang, Cathy Riemer, Matthew T. Weirauch, Richard Burhans, Webb Miller, Ross C. Hardison:
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. 466-470 - 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. 471-475 - Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer:
Inparanoid: a comprehensive database of eukaryotic orthologs. 476-480 - Eric Bazin, Laurent Duret, Simon Penel, Nicolas Galtier:
Polymorphix: a sequence polymorphism database. 481-484 - Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon N. Twigger, Jiali Chen, Chin-Fu Chen, Chunyu Fan, Cindy Foote, Gopal R. Gopinath, Glenn Harris, Aubrey Hughes, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Natalya Nenasheva, Jeff Nie, Rajni Nigam, Victoria Petri, Dorothy Reilly, Weiye Wang, Wenhua Wu, Angela Zuniga-Meyer, Lan Zhao, Anne E. Kwitek, Peter J. Tonellato, Howard J. Jacob:
The Rat Genome Database (RGD): developments towards a phenome database. 485-491 - Greta Petersen, Per Johnson, Lars Andersson, Karin Klinga-Levan, Pedro M. Gómez-Fabre, Fredrik Ståhl:
RatMap - rat genome tools and data. 492-494 - Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sælensminde, David A. Liberles:
The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. 495-497 - Tobias Penzkofer, Thomas Dandekar, Tomasz Zemojtel:
L1Base: from functional annotation to prediction of active LINE-1 elements. 498-500 - Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. 501-504 - 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. 505-510 - Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia:
HCAD, closing the gap between breakpoints and genes. 511-513 - 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. 514-517