Volume 31,
Number 1,
January 2003
- Andreas D. Baxevanis:
The Molecular Biology Database Collection: 2003 update.
1-12 BibTeX
- Satoru Miyazaki, Hideaki Sugawara, Takashi Gojobori, Yoshio Tateno:
DNA Data Bank of Japan (DDBJ) in XML.
13-16 BibTeX
- Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Francesco Nardone, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan:
The EMBL Nucleotide Sequence Database: major new developments.
17-22 BibTeX
- Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
GenBank.
23-27 BibTeX
- David L. Wheeler, Deanna M. Church, Scott Federhen, Alex E. Lash, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tatiana A. Tatusova, Lukas Wagner:
Database resources of the National Center for Biotechnology.
28-33 BibTeX
- Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
NCBI Reference Sequence Project: update and current status.
34-37 BibTeX
- Michele E. Clamp, T. Daniel Andrews, Daniel Barker, Paul Bevan, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas Down, Richard Durbin, Eduardo Eyras, James Gilbert, Martin Hammond, Tim J. P. Hubbard, Arek Kasprzyk, Damian Keefe, Heikki Lehväslaiho, V. Iyer, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Alastair Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Ewan Birney:
Ensembl 2002: accommodating comparative genomics.
38-42 BibTeX
- Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola J. Mulder, Claire O'Donovan, Helen E. Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron:
The European Bioinformatics Institute's data resources.
43-50 BibTeX
- Donna Karolchik, Robert Baertsch, Mark Diekhans, Terrence S. Furey, Angela S. Hinrichs, Y. T. Lu, Krishna M. Roskin, M. Schwartz, Charles W. Sugnet, Daryl J. Thomas, R. J. Weber, David Haussler, W. James Kent:
The UCSC Genome Browser Database.
51-54 BibTeX
- Christoph Dieterich, Haiyan Wang, Katja Rateitschak, Hannes Luz, Martin Vingron:
CORG: a database for COmparative Regulatory Genomics.
55-57 BibTeX
- Ikuo Uchiyama:
MBGD: microbial genome database for comparative analysis.
58-62 BibTeX
- Magalie Leveugle, Karine Prat, Nadine Perrier, Daniel Birnbaum, François Coulier:
ParaDB: a tool for paralogy mapping in vertebrate genomes.
63-67 BibTeX
- Alvis Brazma, Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, Susanna-Assunta Sansone:
ArrayExpress - a public repository for microarray gene expression data at the EBI.
68-71 BibTeX
- Thorsten Henrich, Mirana Ramialison, Rebecca Quiring, Beate Wittbrodt, Makoto Furutani-Seiki, Joachim Wittbrodt, Hisato Kondoh:
MEPD: a Medaka gene expression pattern database.
72-74 BibTeX
- Céline Amoreira, Winfried Hindermann, Christoph Grunau:
An improved version of the DNA methylation database (MethDB).
75-77 BibTeX
- Kevin Roberg-Perez, Corey M. Carlson, David A. Largaespada:
MTID: a database of Sleeping Beauty transposon insertions in mice.
78-81 BibTeX
- Guoying Liu, Ann E. Loraine, Ron Shigeta, Melissa S. Cline, Jill Cheng, Venu Valmeekam, Shaw Sun, David Kulp, Michael A. Siani-Rose:
NetAffx: Affymetrix probesets and annotations.
82-86 BibTeX
- Pavel V. Baranov, Olga L. Gurvich, Andrew W. Hammer, Raymond F. Gesteland, John F. Atkins:
RECODE 2003.
87-89 BibTeX
- Iris Tzafrir, Allan Dickerman, Olga Brazhnik, Quoc Nguyen, John McElver, Catherine Frye, David Patton, David Meinke:
The Arabidopsis SeedGenes Project.
90-93 BibTeX
- Jeremy Gollub, Catherine A. Ball, Gail Binkley, Janos Demeter, David B. Finkelstein, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, Miroslava Kaloper, John C. Matese, Mark Schroeder, Patrick O. Brown, David Botstein, Gavin Sherlock:
The Stanford Microarray Database: data access and quality assessment tools.
94-96 BibTeX
- Mathias Krull, Nico Voss, Claudia Choi, Susanne Pistor, Anatolij Potapov, Edgar Wingender:
TRANSPATH: An integrated database on signal transduction and a tool for array analysis.
97-100 BibTeX
- Christopher Lee, Levan Atanelov, Barmak Modrek, Yi Xing:
ASAP: the Alternative Splicing Annotation Project.
101-105 BibTeX
- Vattipally B. Sreenu, Vishwanath Alevoor, Javaregowda Nagaraju, Hampapathalu A. Nagarajaram:
MICdb: database of prokaryotic microsatellites.
106-108 BibTeX
- William C. Ray, Charles J. Daniels:
PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features.
109-113 BibTeX
- Ilham A. Shahmuradov, Alex J. Gammerman, John M. Hancock, Peter M. Bramley, Victor V. Solovyev:
PlantProm: a database of plant promoter sequences.
114-117 BibTeX
- Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Anatoly S. Frolov, Vadim P. Valuev, Mikhail P. Ponomarenko:
rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation.
118-121 BibTeX
- Filip Pattyn, Frank Speleman, Anne De Paepe, Jo Vandesompele:
RTPrimerDB: the Real-Time PCR primer and probe database.
122-123 BibTeX
- Gudmundur A. Thorisson, Lincoln Stein:
The SNP Consortium website: past, present and future.
124-127 BibTeX
- Stephen Rudd, Hans-Werner Mewes, Klaus F. X. Mayer:
Sputnik: a database platform for comparative plant genomics.
128-132 BibTeX
- Todd W. Harris, Raymond Lee, Erich M. Schwarz, Keith Bradnam, Daniel Lawson, Wen J. Chen, Darin Blasiar, Eimear Kenny, Fiona Cunningham, Ranjana Kishore, Juancarlos Chan, Hans-Michael Müller, Andrei Petcherski, Gudmundur Thorisson, Allen Day, Tamberlyn Bieri, Anthony Rogers, Chao-Kung Chen, John Spieth, Paul W. Sternberg, Richard Durbin, Lincoln D. Stein:
WormBase: a cross-species database for comparative genomics.
133-137 BibTeX
- Emmanuelle Karsenty, Emmanuel Barillot, Gwenola Tosser-Klopp, Yvette Lahbib-Mansais, Denis Milan, Francois Hatey, Susanna Cirera, Milena Sawera, Claus B. Jørgensen, Bhanu Chowdhary, Merete Fredholm, Klaus Wimmers, Siriluck Ponsuksili, Roberta Davoli, Luca Fontanesi, Silvia Braglia, Paolo Zambonelli, Daniele Bigi, Stefan Neuenschwander, Joël Gellin:
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa).
138-141 BibTeX
- Marilyn Safran, Vered Chalifa-Caspi, Orit Shmueli, Tsviya Olender, Michal Lapidot, Naomi Rosen, Michael Shmoish, Yakov Peter, Gustavo Glusman, Ester Feldmesser, Avital Adato, Inga Peter, Miriam Khen, Tal Atarot, Yoram Groner, Doron Lancet:
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE.
142-146 BibTeX
- Jeremy D. Glasner, Paul Liss, Guy Plunkett III, Aaron E. Darling, Tejasvini Prasad, Michael Rusch, Alexis Byrnes, Michael K. Gilson, Bryan S. Biehl, Frederick R. Blattner, Nicole T. Perna:
ASAP, a systematic annotation package for community analysis of genomes.
147-151 BibTeX
- John W. Urbance, James R. Cole, Paul Saxman, James M. Tiedje:
BSD: the Biodegradative Strain Database.
152-155 BibTeX
- Mark L. Crowe, Carine Serizet, Vincent Thareau, Sébastien Aubourg, Pierre Rouzé, Pierre Hilson, Jim Beynon, Peter Weisbeek, Paul van Hummelen, Philippe Reymond, Javier Paz-Ares, Wilfried Nietfeld, Martin Trick:
CATMA: a complete Arabidopsis GST database.
156-158 BibTeX
- Joseph F. Ryan, John R. Finnerty:
CnidBase: The Cnidarian Evolutionary Genomics Database.
159-163 BibTeX
- Ross A. Overbeek, Niels Larsen, Theresa Walunas, Mark D'Souza, Gordon D. Pusch, Evgeni Selkov Jr., Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vassieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, Nikos Kyrpides:
The ERGOTM genome analysis and discovery system.
164-171 BibTeX
- Emmet A. O'Brien, Elarbi Badidi, Ania Barbasiewicz, Cristina deSousa, B. Franz Lang, Gertraud Burger:
GOBASE - a database of mitochondrial and chloroplast information.
176-178 BibTeX
- Delphine Samson, Fabrice Legeai, Emmanuelle Karsenty, Sébastien Reboux, Jean-Baptiste Veyrieras, Jeremy Just, Emmanuel Barillot:
GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics.
179-182 BibTeX
- David E. Matthews, Victoria L. Carollo, Gerard R. Lazo, Olin D. Anderson:
GrainGenes, the genome database for small-grain crops.
183-186 BibTeX
- Santiago Garcia-Vallvé, Eduard Guzmán, M. A. Montero, Antoni Romeu:
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes.
187-189 BibTeX
- Wojciech M. Karlowski, Heiko Schoof, Vijayalakshmi Janakiraman, Volker Stümpflen, Klaus F. X. Mayer:
MOsDB: an integrated information resource for rice genomics.
190-192 BibTeX
- Judith A. Blake, Joel E. Richardson, Carol J. Bult, James A. Kadin, Janan T. Eppig:
MGD: the Mouse Genome Database.
193-195 BibTeX
- Anne-Françoise J. Lamblin, John A. Crow, James E. Johnson, Kevin A. T. Silverstein, Timothy M. Kunau, Alan Kilian, Diane Benz, Martina V. Stromvik, Gabriella Endré, Kathryn A. VandenBosch, Douglas R. Cook, Nevin D. Young, Ernest F. Retzel:
MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome.
196-201 BibTeX
- Daniel Jameson, Andrew P. Gibson, Cendrine Hudelot, Paul G. Higgs:
OGRe: a relational database for comparative analysis of mitochondrial genomes.
202-206 BibTeX
- Dmitrij Frishman, Martin Mokrejs, Denis Kosykh, Gabi Kastenmüller, Grigory Kolesov, Igor Zubrzycki, Christian Gruber, Birgitta Geier, Andreas Kaps, Kaj Albermann, Andreas Volz, Christian Wagner, Matthias Fellenberg, Klaus Heumann, Hans-Werner Mewes:
The PEDANT genome database.
207-211 BibTeX
- Amit Bahl, Brian P. Brunk, Jonathan Crabtree, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, Hagai Ginsburg, Dinesh Gupta, Jessica C. Kissinger, Philip Labo, Li Li, Matthew D. Mailman, Arthur J. Milgram, David S. Pearson, David S. Roos, Jonathan Schug, Christian J. Stoeckert Jr., Patricia L. Whetzel:
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.
212-215 BibTeX
- Shuai Weng, Qing Dong, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Laurie Issel-Tarver, Anand Sethuraman, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Christopher Lane, Mark Schroeder, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.
216-218 BibTeX
- Maximilian Diehn, Gavin Sherlock, Gail Binkley, Heng Jin, John C. Matese, Tina Hernandez-Boussard, Christian A. Rees, J. Michael Cherry, David Botstein, Patrick O. Brown, Ash A. Alizadeh:
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.
219-223 BibTeX
- Seung Yon Rhee, William D. Beavis, Tanya Z. Berardini, Guanghong Chen, David A. Dixon, Aisling Doyle, Margarita Garcia-Hernandez, Eva Huala, Gabriel Lander, Mary Montoya, Neil Miller, Lukas A. Mueller, Suparna Mundodi, Leonore Reiser, Julie Tacklind, Dan C. Weems, Yihe Wu, Iris Xu, Daniel Yoo, Jungwon Yoon, Peifen Zhang:
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
224-228 BibTeX
- Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard Suh, Foo Cheung, Razvan Sultana, Daniel Lee, John Quackenbush, C. Robin Buell:
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.
229-233 BibTeX
- Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, David S. Roos:
ToxoDB: accessing the Toxoplasma gondii genome.
234-236 BibTeX
- Philippe Vaglio, Philippe Lamesch, Jérôme Reboul, Jean-François Rual, Monica Martinez, David Hill, Marc Vidal:
WorfDB: the Caenorhabditis elegans ORFeome Database.
237-240 BibTeX
- Judy Sprague, Dave Clements, Tom Conlin, Pat Edwards, Ken Frazer, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, Monte Westerfield:
The Zebrafish Information Network (ZFIN): the zebrafish model organism database.
241-243 BibTeX
- Qunfeng Dong, Laura Roy, Michael Freeling, Virginia Walbot, Volker Brendel:
ZmDB, an integrated database for maize genome research.
244-247 BibTeX
- Gary D. Bader, Doron Betel, Christopher W. V. Hogue:
BIND: the Biomolecular Interaction Network Database.
248-250 BibTeX
- See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan, Kui Lin:
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes.
251-254 BibTeX
- Zhi Liang Ji, X. Chen, C. J. Zheng, L. X. Yao, L. Y. Han, W. K. Yeo, P. C. Chung, H. S. Puy, Y. T. Tay, A. Muhammad, Yu Zong Chen:
KDBI: Kinetic Data of Bio-molecular Interactions database.
255-257 BibTeX
- Christian von Mering, Martijn A. Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, Berend Snel:
STRING: a database of predicted functional associations between proteins.
258-261 BibTeX
- Lynda B. M. Ellis, Bo Kyeng Hou, Wenjun Kang, Lawrence P. Wackett:
The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining.
262-265 BibTeX
- Richard Münch, Karsten Hiller, Heiko Barg, Dana Heldt, Simone Linz, Edgar Wingender, Dieter Jahn:
PRODORIC: prokaryotic database of gene regulation.
266-269 BibTeX
- H. Rajeevan, Michael V. Osier, Kei-Hoi Cheung, H. Deng, L. Druskin, R. Heinzen, Judith R. Kidd, S. Stein, Andrew J. Pakstis, Nick P. Tosches, C.-C. Yeh, Perry L. Miller, Kenneth K. Kidd:
ALFRED: the ALelle FREquency Database. Update.
270-271 BibTeX
- Jean-Loup Huret, Philippe Dessen, Alain Bernheim:
Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003.
272-274 BibTeX
- Frank W. Nicholas:
Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals.
275-277 BibTeX
- Doug Stryke, Michiko Kawamoto, Conrad C. Huang, Susan J. Johns, Leslie A. King, Courtney A. Harper, Elaine C. Meng, Roy E. Lee, Alice Yee, Larry L'Italien, Pao-Tien Chuang, Stephen G. Young, William C. Skarnes, Patricia C. Babbitt, Thomas E. Ferrin:
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.
278-281 BibTeX
- Cyril Sarrauste de Menthière, Stéphane Terrière, Denis Pugnère, Manuel Ruiz, Jacques Demaille, Isabelle Touitou:
INFEVERS: the Registry for FMF and hereditary inflammatory disorders mutations.
282-285 BibTeX
- Denis Pugnère, Manuel Ruiz, Cyril Sarrauste de Menthière, Benjamin Masdoua, Jacques Demaille, Isabelle Touitou:
The MetaFMF website: a high quality tool for meta-analysis of FMF.
286-290 BibTeX
- Long-Cheng Li, Hong Zhao, Hiroaki Shiina, Christopher J. Kane, Rajvir Dahiya:
PGDB: a curated and integrated database of genes related to the prostate.
291-293 BibTeX
- Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, Gerrit Vriend:
GPCRDB information system for G protein-coupled receptors.
294-297 BibTeX
- Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, Robert W. Shafer:
Human immunodeficiency virus reverse transcriptase and protease sequence database.
298-303 BibTeX
- Sharmila Banerjee-Basu, Travis Moreland, Benjamin J. Hsu, Kenneth L. Trout, Andreas D. Baxevanis:
The Homeodomain Resource: 2003 update.
304-306 BibTeX
- Marie-Paule Lefranc:
IMGT, the international ImMunoGeneTics database®.
307-310 BibTeX
- James Robinson, Matthew J. Waller, Peter Parham, Natasja de Groot, Ronald Bontrop, Lorna J. Kennedy, Peter Stoehr, Steven G. E. Marsh:
IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.
311-314 BibTeX
- Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, Evgeni M. Zdobnov:
The InterPro Database, 2003 brings increased coverage and new features.
315-318 BibTeX
- Markus Fischer, Jürgen Pleiss:
The Lipase Engineering Database: a navigation and analysis tool for protein families.
319-321 BibTeX
- Marco Sardiello, Flavio Licciulli, Domenico Catalano, Marcella Attimonelli, Corrado Caggese:
MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion.
322-324 BibTeX
- Ryan Lister, Monika W. Murcha, James Whelan:
The Mitochondrial Protein Import Machinery of Plants (MPIMP) database.
325-327 BibTeX
- G. Dellaire, R. Farrall, W. A. Bickmore:
The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome.
328-330 BibTeX
- Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, Gert Vriend:
NRMD: Nuclear Receptor Mutation Database.
331-333 BibTeX
- Paul D. Thomas, Anish Kejariwal, Michael J. Campbell, Huaiyu Mi, Karen Diemer, Nan Guo, Istvan Ladunga, Betty Lazareva-Ulitsky, Anushya Muruganujan, Steven Rabkin, Jody A. Vandergriff, Olivier Doremieux:
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.
334-341 BibTeX
- Jason H. Tchieu, Fariba Fana, J. Lynn Fink, Jeffrey Harper, T. Murlidharan Nair, R. Hannes Niedner, Douglas W. Smith, Kenneth Steube, Tobey M. Tam, Stella Veretnik, Degeng Wang, Michael Gribskov:
The PlantsP and PlantsT Functional Genomics Databases.
342-344 BibTeX
- Cathy H. Wu, Lai-Su L. Yeh, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhang-Zhi Hu, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, C. R. Vinayaka, Jian Zhang, Winona C. Barker:
The Protein Information Resource.
345-347 BibTeX
- Ori Sasson, Avishay Vaaknin, Hillel Fleischer, Elon Portugaly, Yonatan Bilu, Nathan Linial, Michal Linial:
ProtoNet: hierarchical classification of the protein space.
348-352 BibTeX
- Julien Grassot, Guy Mouchiroud, Guy Perrière:
RTKdb: database of receptor tyrosine kinase.
353-358 BibTeX
- Ovidiu Ivanciuc, Catherine H. Schein, Werner Braun:
SDAP: database and computational tools for allergenic proteins.
359-362 BibTeX
- Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson:
SRPDB: Signal Recognition Particle Database.
363-364 BibTeX
- Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-Claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria Jesus Martin, Karine Michoud, Claire O'Donovan, Isabelle Phan, Sandrine Pilbout, Michel Schneider:
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
365-370 BibTeX
- Daniel H. Haft, Jeremy D. Selengut, Owen White:
The TIGRFAMs database of protein families.
371-373 BibTeX
- V. Matys, Ellen Fricke, R. Geffers, Ellen Gößling, Martin Haubrock, R. Hehl, Klaus Hornischer, Dagmar Karas, Alexander E. Kel, Olga V. Kel-Margoulis, Dorothee-U. Kloos, Sigrid Land, Birgit Lewicki-Potapov, Holger Michael, Richard Münch, Ingmar Reuter, Stella Rotert, H. Saxel, Maurice Scheer, S. Thiele, Edgar Wingender:
TRANSFAC®: transcriptional regulation, from patterns to profiles.
374-378 BibTeX
- Angelo M. Facchiano, Antonio Facchiano, Francesco Facchiano:
Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences.
379-382 BibTeX
- Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant:
CDD: a curated Entrez database of conserved domain alignments.
383-387 BibTeX
- Evgenia V. Kriventseva, Florence Servant, Rolf Apweiler:
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters.
388-389 BibTeX
- Hongzhan Huang, Winona C. Barker, Yongxing Chen, Cathy H. Wu:
iProClass: an integrated database of protein family, function and structure information.
390-392 BibTeX
- Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, Søren Brunak:
NESbase version 1.0: a database of nuclear export signals.
393-396 BibTeX
- Rajesh Nair, Phil Carter, Burkhard Rost:
NLSdb: database of nuclear localization signals.
397-399 BibTeX
- Terri K. Attwood, Paul Bradley, Darren R. Flower, Anna Gaulton, Neil Maudling, Alex Mitchell, G. Moulton, A. Nordle, K. Paine, P. Taylor, A. Uddin, Christianna Zygouri:
PRINTS and its automatic supplement, prePRINTS.
400-402 BibTeX
- Kristian Vlahovicek, László Kaján, János Murvai, Zoltán Hegeds, Sándor Pongor:
The SBASE domain sequence library, release 10: domain architecture prediction.
403-405 BibTeX
- Masami Ikeda, Masafumi Arai, Toshikatsu Okuno, Toshio Shimizu:
TMPDB: a database of experimentally-characterized transmembrane topologies.
406-409 BibTeX
- Phil Carter, Jinfeng Liu, Burkhard Rost:
PEP: Predictions for Entire Proteomes.
410-413 BibTeX
- Manuela Pruess, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler:
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.
414-417 BibTeX
- Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
REBASE: restriction enzymes and methyltransferases.
418-420 BibTeX
- Tala Bakheet, Bryan R. G. Williams, Khalid S. A. Khabar:
ARED 2.0: an update of AU-rich element mRNA database.
421-423 BibTeX
- Lixin Dai, Navtej Toor, Robert Olson, Andrew Keeping, Steven Zimmerly:
Database for mobile group II introns.
424-426 BibTeX
- Sophie Bonnal, Christel Boutonnet, Leonel Prado-Lourenço, Stéphan Vagner:
IRESdb: the Internal Ribosome Entry Site database.
427-428 BibTeX
- Maciej Szymanski, Volker A. Erdmann, Jan Barciszewski:
Noncoding regulatory RNAs database.
429-431 BibTeX
- John W. S. Brown, Manuel Echeverria, Liang-Hu Qu, Todd M. Lowe, Jean-Pierre Bachellerie, Alexander Hüttenhofer, James P. Kastenmayer, Pamela J. Green, Paul Shaw, David F. Marshall:
Plant snoRNA database.
432-435 BibTeX
- Guglielmo Rainaldi, Mariateresa Volpicella, Flavio Licciulli, Sabino Liuni, Raffaele Gallerani, Luigi R. Ceci:
PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes.
436-438 BibTeX
- Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R. Eddy:
Rfam: an RNA family database.
439-441 BibTeX
- James R. Cole, B. Chai, Terry L. Marsh, Ryan J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, Thomas M. Schmidt, George M. Garrity, James M. Tiedje:
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.
442-443 BibTeX
- Martin Pelchat, Lynda Rocheleau, Jonathan Perreault, Jean-Pierre Perreault:
SubViral RNA: a database of the smallest known auto-replicable RNA species.
444-445 BibTeX
- Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, Jacek Wower:
tmRDB (tmRNA database).
446-447 BibTeX
- S. S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi, Krishna Sekar:
CADB: Conformation Angles DataBase of proteins.
448-451 BibTeX
- Frances M. G. Pearl, C. F. Bennett, James E. Bray, Andrew P. Harrison, Nigel J. Martin, Adrian J. Shepherd, Ian Sillitoe, Janet M. Thornton, Christine A. Orengo:
The CATH database: an extended protein family resource for structural and functional genomics.
452-455 BibTeX
- Giacomo Finocchiaro, Ting Wang, René Hoffmann, Aitor Gonzalez, Rebecca C. Wade:
DSMM: a Database of Simulated Molecular Motions.
456-457 BibTeX
- Harry Boutselakis, Dimitris Dimitropoulos, Joël Fillon, Adel Golovin, Kim Henrick, A. Hussain, John M. C. Ionides, Melford John, Peter A. Keller, Evgeny B. Krissinel, P. McNeil, Avi Naim, Richard Newman, Thomas Oldfield, Jorge Pineda, Abdel-Krim Rachedi, J. Copeland, Andrey Sitnov, Siamak Sobhany, A. Suarez-Uruena, Jawahar Swaminathan, Mohammed Tagari, John G. Tate, Swen Tromm, Samir S. Velankar, Wim Vranken:
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.
458-462 BibTeX
- Akihiro Yamaguchi, Mitsuo Iwadate, Ei-ichiro Suzuki, Kei Yura, Shigetsugu Kawakita, Hideaki Umeyama, Mitiko Go:
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species.
463-468 BibTeX
- Daniel W. A. Buchan, Stuart C. G. Rison, James E. Bray, David Lee, Frances M. G. Pearl, Janet M. Thornton, Christine A. Orengo:
Gene3D: structural assignments for the biologist and bioinformaticist alike.
469-473 BibTeX
- Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant:
MMDB: Entrez's 3D-structure database.
474-477 BibTeX
- Nathaniel Echols, Duncan Milburn, Mark Gerstein:
MolMovDB: analysis and visualization of conformational change and structural flexibility.
478-482 BibTeX
- Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Nap Tak Ma, Lai Fan Chiu, Chung Wai Leung, Steve Chik Fun Au-Yeung:
NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0.
483-485 BibTeX
- V. S. Gowri, Shashi B. Pandit, P. S. Karthik, Narayanaswamy Srinivasan, S. Balaji:
Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database.
486-488 BibTeX
- John D. Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M. Berman:
The Protein Data Bank and structural genomics.
489-491 BibTeX
- Tamotsu Noguchi, Yutaka Akiyama:
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003.
492-493 BibTeX
- Andrea Schafferhans, Joachim E. W. Meyer, Seán I. O'Donoghue:
The PSSH database of alignments between protein sequences and tertiary structures.
494-498 BibTeX
- John S. Garavelli:
The RESID Database of Protein Modifications: 2003 developments.
499-501 BibTeX
- Venkatesh L. Murthy, George D. Rose:
RNABase: an annotated database of RNA structures.
502-504 BibTeX
- Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt:
The Structure Superposition Database.
505-510 BibTeX
- Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins, Nicolle H. Packer:
GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003, update.
511-513 BibTeX
- Alexander Loy, Matthias Horn, Michael Wagner:
probeBase: an online resource for rRNA-targeted oligonucleotide probes.
514-516 BibTeX
Volume 31,
Number 13,
July 2003
- Krzysztof Ginalski, Leszek Rychlewski:
Detection of reliable and unexpected protein fold predictions using 3D-Jury.
3291-3292 BibTeX
- Phil Carter, Claus A. F. Andersen, Burkhard Rost:
DSSPcont: continuous secondary structure assignments for proteins.
3293-3295 BibTeX
- Ling-Hong Hung, Ram Samudrala:
PROTINFO: secondary and tertiary protein structure prediction.
3296-3299 BibTeX
- Burkhard Rost, Jinfeng Liu:
The PredictProtein server.
3300-3304 BibTeX
- Michal A. Kurowski, Janusz M. Bujnicki:
GeneSilico protein structure prediction meta-server.
3305-3307 BibTeX
- Volker A. Eyrich, Burkhard Rost:
META-PP: single interface to crucial prediction servers.
3308-3310 BibTeX
- Ingrid Y. Y. Koh, Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, Narayanan Eswar, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost:
EVA: evaluation of protein structure prediction servers.
3311-3315 BibTeX
- Leigh Willard, Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, David S. Wishart:
VADAR: a web server for quantitative evaluation of protein structure quality.
3316-3319 BibTeX
- Patrice Gouet, Xavier Robert, Emmanuel Courcelle:
ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins.
3320-3323 BibTeX
- Mike P. Liang, D. Rey Banatao, Teri E. Klein, Douglas L. Brutlag, Russ B. Altman:
WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures.
3324-3327 BibTeX
- Steven P. Bennett, Lin Lu, Douglas L. Brutlag:
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs.
3328-3332 BibTeX
- Anna Gaulton, Terri K. Attwood:
Motif3D: relating protein sequence motifs to 3D structure.
3333-3336 BibTeX
- Rajesh Nair, Burkhard Rost:
LOC3D: annotate sub-cellular localization for protein structures.
3337-3340 BibTeX
- Alexander Stark, Robert B. Russell:
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.
3341-3344 BibTeX
- M. Madan Babu:
NCI: a server to identify non-canonical interactions in protein structures.
3345-3348 BibTeX
- Razif R. Gabdoulline, Rebecca C. Wade, Dirk Walther:
MolSurfer: a macromolecular interface navigator.
3349-3351 BibTeX
- T. Andrew Binkowski, Shapor Naghibzadeh, Jie Liang:
CASTp: Computed Atlas of Surface Topography of proteins.
3352-3355 BibTeX
- A. S. Z. Hussain, Ch. Kiran Kumar, C. K. Rajesh, S. S. Sheik, Krishna Sekar:
SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules.
3356-3358 BibTeX
- Zsuzsanna Dosztányi, Csaba Magyar, Gábor E. Tusnády, Miklós Cserzo, András Fiser, István Simon:
Servers for sequence-structure relationship analysis and prediction.
3359-3363 BibTeX
- Luigi Cavallo, Jens Kleinjung, Franca Fraternali:
POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level.
3364-3366 BibTeX
- Takeshi Kawabata:
MATRAS: a program for protein 3D structure comparison.
3367-3369 BibTeX
- Adam Zemla:
LGA: a method for finding 3D similarities in protein structures.
3370-3374 BibTeX
- Narayanan Eswar, Bino John, Nebojsa Mirkovic, András Fiser, Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Mallur S. Madhusudhan, Bozidar Yerkovich, Andrej Sali:
Tools for comparative protein structure modeling and analysis.
3375-3380 BibTeX
- Torsten Schwede, Jürgen Kopp, Nicolas Guex, Manuel C. Peitsch:
SWISS-MODEL: an automated protein homology-modeling server.
3381-3385 BibTeX
- Goran Neshich, Roberto C. Togawa, Adauto L. Mancini, Paula R. Kuser, Michel E. B. Yamagishi, Georgios Joannis Pappas Jr., Wellington V. Torres, Tharsis Fonseca e Campos, Leonardo L. Ferreira, Fabio M. Luna, Adilton G. Oliveira, Ronald T. Miura, Marcus K. Inoue, Luiz G. Horita, Dimas F. de Souza, Fabiana Dominiquini, Alexandre Alvaro, Cleber S. Lima, Fabio O. Ogawa, Gabriel B. Gomes, Juliana F. Palandrani, Gabriela F. dos Santos, Esther M. de Freitas, Amanda R. Mattiuz, Ivan C. Costa, Celso L. de Almeida, Savio Souza, Christian Baudet, Roberto H. Higa:
STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.
3386-3392 BibTeX
- Guy Perrière, Christophe Combet, Simon Penel, Christophe Blanchet, Jean Thioulouse, Christophe Geourjon, Julien Grassot, Céline Charavay, Manolo Gouy, Laurent Duret, Gilbert Deléage:
Integrated databanks access and sequence/structure analysis services at the PBIL.
3393-3399 BibTeX
- Emmanuel Bettler, Roland Krause, Florence Horn, Gert Vriend:
NRSAS: Nuclear Receptor Structure Analysis Servers.
3400-3403 BibTeX
- V. Shanthi, P. Selvarani, Ch. Kiran Kumar, C. S. Mohire, Krishna Sekar:
SSEP: secondary structural elements of proteins.
3404-3405 BibTeX
- Michael Zuker:
Mfold web server for nucleic acid folding and hybridization prediction.
3406-3415 BibTeX
- Mirela Andronescu, Rosalía Aguirre-Hernández, Anne Condon, Holger H. Hoos:
RNAsoft: a suite of RNA secondary structure prediction and design software tools.
3416-3422 BibTeX
- Bjarne Knudsen, Jotun Hein:
Pfold: RNA secondary structure prediction using stochastic context-free grammars.
3423-3428 BibTeX
- Ivo L. Hofacker:
Vienna RNA secondary structure server.
3429-3431 BibTeX
- Kyungsook Han, Yanga Byun:
PSEUDOVIEWER2: visualization of RNA pseudoknots of any type.
3432-3440 BibTeX
- Peter Bengert, Thomas Dandekar:
A software tool-box for analysis of regulatory RNA elements.
3441-3445 BibTeX
- Yuh-Jyh Hu:
GPRM: a genetic programming approach to finding common RNA secondary structure elements.
3446-3449 BibTeX
- Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John D. Westbrook, Helen M. Berman, Eric Westhof:
Tools for the automatic identification and classification of RNA base pairs.
3450-3460 BibTeX
- Javier Herrero, Fátima Al-Shahrour, Ramón Díaz-Uriarte, Álvaro Mateos, Juan M. Vaquerizas, Javier Santoyo, Joaquín Dopazo:
GEPAS: a web-based resource for microarray gene expression data analysis.
3461-3467 BibTeX
- Bert Coessens, Gert Thijs, Stein Aerts, Kathleen Marchal, Frank De Smet, Kristof Engelen, Patrick Glenisson, Yves Moreau, Janick Mathys, Bart De Moor:
INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis.
3468-3470 BibTeX
- Steen Knudsen, Christopher T. Workman, Thomas Sicheritz-Ponten, Carsten Friis:
GenePublisher: automated analysis of DNA microarray data.
3471-3476 BibTeX
- Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, Mark Gerstein:
ExpressYourself: a modular platform for processing and visualizing microarray data.
3477-3482 BibTeX
- Sheng Zhong, Cheng Li, Wing Hung Wong:
ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis.
3483-3486 BibTeX
- Crispin Roven, Harmen J. Bussemaker:
REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data.
3487-3490 BibTeX
- Henrik Bjørn Nielsen, Rasmus Wernersson, Steen Knudsen:
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.
3491-3496 BibTeX
- Chenna Ramu, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie Dawn Thompson:
Multiple sequence alignment with the Clustal series of programs.
3497-3500 BibTeX
- Davinder K. Kohli, Anand K. Bachhawat:
CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics.
3501-3502 BibTeX
- Olivier Poirot, Eamonn O'Toole, Cédric Notredame:
Tcoffee add igs: a web server for computing, evaluating and combining multiple sequence alignments.
3503-3506 BibTeX
- Simon Cawley, Lior Pachter, Marina Alexandersson:
SLAM web server for comparative gene finding and alignment.
3507-3509 BibTeX
- Yvonne J. K. Edwards, Tim J. Carver, Tanya Vavouri, Martin C. Frith, Martin J. Bishop, Greg Elgar:
Theatre: a software tool for d
