Volume 35,
Number Database-Issue,
January 2007
All articles in this issue are published under an open access model:
Articles:
- Michael Y. Galperin:
The Molecular Biology Database Collection: 2007 update.
3-4
Electronic Edition (link) BibTeX
- David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Vadim Miller, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko:
Database resources of the National Center for Biotechnology Information.
5-12
Electronic Edition (link) BibTeX
- Hideaki Sugawara, Takashi Abe, Takashi Gojobori, Yoshio Tateno:
DDBJ working on evaluation and classification of bacterial genes in INSDC.
13-15
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- Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Carola Kanz, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Sheila Plaister, Siamak Sobhany, Peter Stoehr, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler:
EMBL Nucleotide Sequence Database in 2006.
16-20
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- Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
GenBank.
21-25
Electronic Edition (link) BibTeX
- Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
Entrez Gene: gene-centered information at NCBI.
26-31
Electronic Edition (link) BibTeX
- Christoph Dieterich, M. W. Franz, Martin Vingron:
Developments in CORG: a gene-centric comparative genomics resource.
32-35
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- Sunil Archak, Eshwar Meduri, P. Sravana Kumar, Javaregowda Nagaraju:
InSatDb: a microsatellite database of fully sequenced insect genomes.
36-39
Electronic Edition (link) BibTeX
- Conrad A. Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J. Benham, Anne D. Donaldson:
OriDB: a DNA replication origin database.
40-46
Electronic Edition (link) BibTeX
- Byungwook Lee, Taehyung Kim, Seon-Kyu Kim, Kwang Hyung Lee, Doheon Lee:
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications.
47-50
Electronic Edition (link) BibTeX
- Lei Bao, Mi Zhou, Ligang Wu, Lu Lu, Dan Goldowitz, Robert W. Williams, Yan Cui:
PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits.
51-54
Electronic Edition (link) BibTeX
- John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul M. Harrison, Mark Gerstein:
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
55-60
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- Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
61-65
Electronic Edition (link) BibTeX
- Cristian Chaparro, Romain Guyot, Andrea Zuccolo, Benoît Piégu, Olivier Panaud:
RetrOryza: a database of the rice LTR-retrotransposons.
66-70
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- I. Agrafioti, Michael P. H. Stumpf:
SNPSTR: a database of compound microsatellite-SNP markers.
71-75
Electronic Edition (link) BibTeX
- Gang Wu, Yuanpu Zheng, Imran Qureshi, Htar Thant Zin, Tyler Beck, Blazej Bulka, Stephen J. Freeland:
SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.
76-79
Electronic Edition (link) BibTeX
- Yevgeniy Gelfand, Alfredo Rodriguez, Gary Benson:
TRDB - The Tandem Repeats Database.
80-87
Electronic Edition (link) BibTeX
- Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio:
VISTA Enhancer Browser - a database of tissue-specific human enhancers.
88-92
Electronic Edition (link) BibTeX
- Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, Christopher Lee:
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.
93-98
Electronic Edition (link) BibTeX
- Yeunsook Lee, Younghee Lee, Bumjin Kim, Youngah Shin, Seungyoon Nam, Pora Kim, Namshin Kim, Won-Hyong Chung, Jaesang Kim, Sanghyuk Lee:
ECgene: an alternative splicing database update.
99-103
Electronic Edition (link) BibTeX
- Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi:
H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational.
104-109
Electronic Edition (link) BibTeX
- Tyler S. Alioto:
U12DB: a database of orthologous U12-type spliceosomal introns.
110-115
Electronic Edition (link) BibTeX
- Anil G. Jegga, Jing Chen, Sivakumar Gowrisankar, Mrunal A. Deshmukh, RangaChandra Gudivada, Sue Kong, Vivek Kaimal, Bruce J. Aronow:
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
116-121
Electronic Edition (link) BibTeX
- Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, Mathieu Blanchette:
PReMod: a database of genome-wide mammalian cis-regulatory module predictions.
122-126
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- Mikhail Pachkov, Ionas Erb, Nacho Molina, Erik van Nimwegen:
SwissRegulon: a database of genome-wide annotations of regulatory sites.
127-131
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- Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides:
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes.
132-136
Electronic Edition (link) BibTeX
- C. Jiang, Z. Xuan, F. Zhao, M. Q. Zhang:
TRED: a transcriptional regulatory element database, new entries and other development.
137-140
Electronic Edition (link) BibTeX
- Tao He, Pufeng Du, Yanda Li:
dbRES: a web-oriented database for annotated RNA editing sites.
141-144
Electronic Edition (link) BibTeX
- Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, Kiyoshi Asai:
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
145-148
Electronic Edition (link) BibTeX
- Molly Megraw, Praveen Sethupathy, Benoit Corda, Artemis G. Hatzigeorgiou:
miRGen: a database for the study of animal microRNA genomic organization and function.
149-155
Electronic Edition (link) BibTeX
- Yong Zhang, Jiongtang Li, Lei Kong, Ge Gao, Qing-Rong Liu, Liping Wei:
NATsDB: Natural Antisense Transcripts DataBase.
156-161
Electronic Edition (link) BibTeX
- Maciej Szymanski, Volker A. Erdmann, Jan Barciszewski:
Noncoding RNAs database (ncRNAdb).
162-164
Electronic Edition (link) BibTeX
- Ju Youn Lee, Ijen Yeh, Ji Yeon Park, Bin Tian:
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.
165-168
Electronic Edition (link) BibTeX
- James R. Cole, B. Chai, Ryan J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, George M. Garrity, James M. Tiedje:
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.
169-172
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- Ernesto Picardi, Teresa Maria Rosaria Regina, Axel Brennicke, Carla Quagliariello:
REDIdb: the RNA editing database.
173-177
Electronic Edition (link) BibTeX
- Ken C. Pang, Stuart Stephen, Marcel E. Dinger, Pär G. Engström, Boris Lenhard, John S. Mattick:
RNAdb 2.0 - an expanded database of mammalian non-coding RNAs.
178-182
Electronic Edition (link) BibTeX
- Jun Xie, Ming Zhang, Tao Zhou, Xia Hua, LiSha Tang, Weilin Wu:
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.
183-187
Electronic Edition (link) BibTeX
- Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer:
TassDB: a database of alternative tandem splice sites.
188-192
Electronic Edition (link) BibTeX
- The Universal Protein Resource (UniProt).
193-197
Electronic Edition (link) BibTeX
- Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, Michael K. Gilson:
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.
198-201
Electronic Edition (link) BibTeX
- Di Wu, Feng Cui, Robert L. Jernigan, Zhijun Wu:
PIDD: database for Protein Inter-atomic Distance Distributions.
202-207
Electronic Edition (link) BibTeX
- Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
eSLDB: eukaryotic subcellular localization database.
208-212
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- Joshua L. Heazlewood, Robert E. Verboom, Julian Tonti-Filippini, Ian Small, A. Harvey Millar:
SUBA: the Arabidopsis Subcellular Database.
213-218
Electronic Edition (link) BibTeX
- Gonzalo López, Alfonso Valencia, Michael L. Tress:
FireDB - a database of functionally important residues from proteins of known structure.
219-223
Electronic Edition (link) BibTeX
- Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise Daugherty, Mark Dibley, Robert D. Finn, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicolas Hulo, Sarah Hunter, Daniel Kahn, Alexander Kanapin, Anish Kejariwal, Alberto Labarga, Petra S. Langendijk-Genevaux, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Christine A. Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats:
New developments in the InterPro database.
224-228
Electronic Edition (link) BibTeX
- Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich:
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.
229-231
Electronic Edition (link) BibTeX
- Paolo Sonego, Mircea Pacurar, Somdutta Dhir, Attila Kertész-Farkas, András Kocsor, Zoltán Gáspári, Jack A. M. Leunissen, Sándor Pongor:
A Protein Classification Benchmark collection for machine learning.
232-236
Electronic Edition (link) BibTeX
- Aron Marchler-Bauer, John B. Anderson, Myra K. Derbyshire, Carol DeWeese-Scott, Noreen R. Gonzales, Marc Gwadz, Luning Hao, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Dmitri M. Krylov, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant:
CDD: a conserved domain database for interactive domain family analysis.
237-240
Electronic Edition (link) BibTeX
- Elon Portugaly, Nathan Linial, Michal Linial:
EVEREST: a collection of evolutionary conserved protein domains.
241-246
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- Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul D. Thomas:
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.
247-252
Electronic Edition (link) BibTeX
- Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard, Alexey G. Murzin:
SISYPHUS - structural alignments for proteins with non-trivial relationships.
253-259
Electronic Edition (link) BibTeX
- Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-Giglio, William C. Nelson, Alexander R. Richter, Owen White:
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.
260-264
Electronic Edition (link) BibTeX
- Shalin Seebah, Anita Suresh, Shaowei Zhuo, Yong How Choong, Hazel Chua, Danny Chuon, Roger Beuerman, Chandra Verma:
Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides.
265-268
Electronic Edition (link) BibTeX
- Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
REBASE - enzymes and genes for DNA restriction and modification.
269-270
Electronic Edition (link) BibTeX
- Mark D'Souza, Elizabeth M. Glass, Mustafa H. Syed, Yi Zhang, Alexis A. Rodriguez, Natalia Maltsev, Michael Y. Galperin:
Sentra: a database of signal transduction proteins for comparative genome analysis.
271-273
Electronic Edition (link) BibTeX
- Qinghu Ren, Kaixi Chen, Ian T. Paulsen:
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels.
274-279
Electronic Edition (link) BibTeX
- Philip Toukach, Hiren J. Joshi, René Ranzinger, Yuri Knirel, Claus-Wilhelm von der Lieth:
Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de.
280-286
Electronic Edition (link) BibTeX
- M. Frank, T. Lütteke, C.-W. von der Lieth:
GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages.
287-290
Electronic Edition (link) BibTeX
- Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison Cuff, Timothy Dallman, Mark Dibley, Oliver Redfern, Frances M. G. Pearl, Rekha Nambudiry, Adam Reid, Ian Sillitoe, Corin Yeats, Janet M. Thornton, Christine A. Orengo:
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
291-297
Electronic Edition (link) BibTeX
- Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer, Jane He, Siqian He, Shennan Lu, Thomas Madej, Aron Marchler-Bauer, Paul A. Thiessen, Naigong Zhang, Stephen H. Bryant:
MMDB: annotating protein sequences with Entrez's 3D-structure database.
298-300
Electronic Edition (link) BibTeX
- Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley:
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
301-303
Electronic Edition (link) BibTeX
- Kate F. Fulton, Mark A. Bate, Noel G. Faux, Khalid Mahmood, Chris Betts, Ashley M. Buckle:
Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium.
304-307
Electronic Edition (link) BibTeX
- Derek Wilson, Martin Madera, Christine Vogel, Cyrus Chothia, Julian Gough:
The SUPERFAMILY database in 2007: families and functions.
308-313
Electronic Edition (link) BibTeX
- M. Michael Gromiha, Yukimitsu Yabuki, Srinesh Kundu, Sivasundaram Suharnan, Makiko Suwa:
TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences.
314-316
Electronic Edition (link) BibTeX
- Chesley M. Leslin, Alexej Abyzov, Valentin A. Ilyin:
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method.
317-321
Electronic Edition (link) BibTeX
- Gil Alterovitz, Michael Xiang, Mamta Mohan, Marco Ramoni:
GO PaD: the Gene Ontology Partition Database.
322-327
Electronic Edition (link) BibTeX
- Yuying Tian, Allan W. Dickerman:
GeneTrees: a phylogenomics resource for prokaryotes.
328-331
Electronic Edition (link) BibTeX
- T. Ryan Gregory, James A. Nicol, Heidi Tamm, Bellis Kullman, Kaur Kullman, Ilia J. Leitch, Brian G. Murray, Donald F. Kapraun, Johann Greilhuber, Michael D. Bennett:
Eukaryotic genome size databases.
332-338
Electronic Edition (link) BibTeX
- Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, Hideaki Sugawara:
Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes.
339-342
Electronic Edition (link) BibTeX
- Ikuo Uchiyama:
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups.
343-346
Electronic Edition (link) BibTeX
- Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce D. Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross A. Overbeek, Rick Stevens:
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
347-353
Electronic Edition (link) BibTeX
- M. Louise Riley, Thorsten Schmidt, Irena I. Artamonova, Christian Wagner, Andreas Volz, Klaus Heumann, Hans-Werner Mewes, Dmitrij Frishman:
PEDANT genome database: 10 years online.
354-357
Electronic Edition (link) BibTeX
- Christian von Mering, Lars Juhl Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, Peer Bork:
STRING 7 - recent developments in the integration and prediction of protein interactions.
358-362
Electronic Edition (link) BibTeX
- Christophe Combet, Nicolas Garnier, Céline Charavay, Delphine Grando, Daniel Crisan, Julien Lopez, Alexandre Dehne-Garcia, Christophe Geourjon, Emmanuel Bettler, Chantal Hulo, Philippe Le Mercier, Ralf Bartenschlager, Helmut Diepolder, Darius Moradpour, Jean-Michel Pawlotsky, Charles M. Rice, Christian Trépo, François Penin, Gilbert Deléage:
euHCVdb: the European hepatitis C virus database.
363-366
Electronic Edition (link) BibTeX
- Saravanamuttu Gnaneshan, Samreen Ijaz, Joanne Moran, Mary Ramsay, Jonathan Green:
HepSEQ: International Public Health Repository for Hepatitis B.
367-370
Electronic Edition (link) BibTeX
- Calvin Pan, Joseph Kim, Lamei Chen, Qi Wang, Christopher Lee:
The HIV positive selection mutation database.
371-375
Electronic Edition (link) BibTeX
- Suhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang, Jun Yu, Jing Wang:
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.
376-380
Electronic Edition (link) BibTeX
- Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu, Justin Bo-Kai Hsu, Hsien-Da Huang:
ViTa: prediction of host microRNAs targets on viruses.
381-385
Electronic Edition (link) BibTeX
- Luke E. Ulrich, Igor B. Zhulin:
MiST: a microbial signal transduction database.
386-390
Electronic Edition (link) BibTeX
- Carol Ecale Zhou, Jason Smith, Marisa Lam, Adam Zemla, M. D. Dyer, Tom Slezak:
MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications.
391-394
Electronic Edition (link) BibTeX
- Sung Ho Yoon, Young-Kyu Park, Soohyun Lee, Doil Choi, Tae Kwang Oh, Cheol-Goo Hur, Jihyun F. Kim:
Towards pathogenomics: a web-based resource for pathogenicity islands.
395-400
Electronic Edition (link) BibTeX
- E. E. Snyder, N. Kampanya, J. Lu, Eric K. Nordberg, H. R. Karur, M. Shukla, Jeetendra Soneja, Y. Tian, Tian Xue, H. Yoo, F. Zhang, C. Dharmanolla, N. V. Dongre, J. J. Gillespie, J. Hamelius, M. Hance, K. I. Huntington, D. Jukneliene, J. Koziski, L. Mackasmiel, S. P. Mane, V. Nguyen, A. Purkayastha, J. Shallom, G. Yu, Y. Guo, J. Gabbard, D. Hix, A. F. Azad, S. C. Baker, S. M. Boyle, Y. Khudyakov, X. J. Meng, C. Rupprecht, J. Vinje, Oswald Crasta, M. J. Czar, Allan Dickerman, J. Dana Eckart, Ron Kenyon, Rebecca Will, J. C. Setubal, Bruno W. S. Sobral:
PATRIC: The VBI PathoSystems Resource Integration Center.
401-406
Electronic Edition (link) BibTeX
- Alexei E. Kazakov, Michael J. Cipriano, Pavel S. Novichkov, Simon Minovitsky, Dmitry V. Vinogradov, Adam Arkin, Andrey A. Mironov, Mikhail S. Gelfand, Inna Dubchak:
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
407-412
Electronic Edition (link) BibTeX
- Kim Brügger:
The Sulfolobus database.
413-415
Electronic Edition (link) BibTeX
- Chia-Hung Chang, Yu-Chung Chang, Anthony Underwood, Chien-Shun Chiou, Cheng-Yan Kao:
VNTRDB: a bacterial variable number tandem repeat locus database.
416-421
Electronic Edition (link) BibTeX
- Bradley I. Arshinoff, Garret Suen, Eric M. Just, Sohel M. Merchant, Warren A. Kibbe, Rex L. Chisholm, Roy D. Welch:
Xanthusbase: adapting wikipedia principles to a model organism database.
422-426
Electronic Edition (link) BibTeX
- Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa Rhodes, John A. Miller, Eileen Kraemer, Christian J. Stoeckert Jr., David S. Roos, Jessica C. Kissinger:
ApiDB: integrated resources for the apicomplexan bioinformatics resource center.
427-430
Electronic Edition (link) BibTeX
- Junichi Watanabe, Hiroyuki Wakaguri, Masahide Sasaki, Yutaka Suzuki, Sumio Sugano:
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.
431-438
Electronic Edition (link) BibTeX
- Olivier Arnaiz, Scott Cain, Jean Cohen, Linda Sperling:
ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.
439-444
Electronic Edition (link) BibTeX
- Emmet A. O'Brien, Liisa B. Koski, Yue Zhang, LiuSong Yang, Eric Wang, Michael W. Gray, Gertraud Burger, B. Franz Lang:
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs).
445-451
Electronic Edition (link) BibTeX
- Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Prachi Shah, Gail Binkley, Christopher Lane, Stuart R. Miyasato, Gavin Sherlock:
Sequence resources at the Candida Genome Database.
452-456
Electronic Edition (link) BibTeX
- Alexandre Gattiker, Christa Niederhauser-Wiederkehr, James Moore, Leandro Hermida, Michael Primig:
The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.
457-462
Electronic Edition (link) BibTeX
- Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Kerstin Glaab, Pär Davidsson, Fabian Nilsson, Graham J. L. Kemp, Olle Nerman, Anders Blomberg:
PROPHECY - a yeast phenome database, update 2006.
463-467
Electronic Edition (link) BibTeX
- Robert S. Nash, Shuai Weng, Benjamin C. Hitz, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Michael S. Livstone, Rose Oughtred, Julie Park, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Kara Dolinski, David Botstein, J. Michael Cherry:
Expanded protein information at SGD: new pages and proteome browser.
468-471
Electronic Edition (link) BibTeX
- Lisa R. Girard, Tristan J. Fiedler, Todd W. Harris, Felicia Carvalho, Igor Antoshechkin, Michael Han, Paul W. Sternberg, Lincoln D. Stein, Martin Chalfie:
WormBook: the online review of Caenorhabditis elegans biology.
472-475
Electronic Edition (link) BibTeX
- Liangjiang Wang, Suzhi Wang, Yonghua Li, Martin S. R. Paradesi, Susan J. Brown:
BeetleBase: the model organism database for Tribolium castaneum.
476-479
Electronic Edition (link) BibTeX
- Donald G. Gilbert:
DroSpeGe: rapid access database for new Drosophila species genomes.
480-485
Electronic Edition (link) BibTeX
- Madeline A. Crosby, Joshua L. Goodman, Victor B. Strelets, Peili Zhang, William M. Gelbart:
FlyBase: genomes by the dozen.
486-491
Electronic Edition (link) BibTeX
- Thomas Horn, Zeynep Arziman, Juerg Berger, Michael Boutros:
GenomeRNAi: a database for cell-based RNAi phenotypes.
492-497
Electronic Edition (link) BibTeX
- Christoph Dieterich, Waltraud Roeseler, Patrick Sobetzko, Ralf J. Sommer:
Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus.
498-502
Electronic Edition (link) BibTeX
- Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, David Emmert, Martin Hammond, Catherine A. Hill, Ryan C. Kennedy, Neil F. Lobo, M. Robert MacCallum, Gregory R. Madey, Karine Megy, Seth Redmond, Susan Russo, David W. Severson, Eric O. Stinson, Pantelis Topalis, Evgeni M. Zdobnov, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins:
VectorBase: a home for invertebrate vectors of human pathogens.
503-505
Electronic Edition (link) BibTeX
- Tamberlyn Bieri, Darin Blasiar, Philip Ozersky, Igor Antoshechkin, Carol Bastiani, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa R. Girard, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon McKay, Hans-Michael Müller, Cecilia Nakamura, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Richard Durbin, Lincoln D. Stein, Paul W. Sternberg, John Spieth:
WormBase: new content and better access.
506-510
Electronic Edition (link) BibTeX
- Jens Barthelmes, Christian Ebeling, Antje Chang, Ida Schomburg, Dietmar Schomburg:
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
511-514
Electronic Edition (link) BibTeX
- Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Noel M. O'Boyle, James W. Torrance, Peter Murray-Rust, John B. O. Mitchell, Janet M. Thornton:
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
515-520
Electronic Edition (link) BibTeX
- David S. Wishart, Dan Tzur, Craig Knox, Roman Eisner, Anchi Guo, Nelson Young, Dean Cheng, Kevin Jewell, David Arndt, Summit Sawhney, Chris Fung, Lisa Nikolai, Mike Lewis, Marie-Aude Coutouly, Ian J. Forsythe, Peter Tang, Savita Shrivastava, Kevin Jeroncic, Paul Stothard, Godwin Amegbey, David Block, David. D. Hau, James Wagner, Jessica Miniaci, Melisa Clements, Mulu Gebremedhin, Natalie Guo, Ying Zhang, Gavin E. Duggan, Glen D. MacInnis, Alim M. Weljie, Reza Dowlatabadi, Fiona Bamforth, Derrick Clive, Russell Greiner, Liang Li, Tom Marrie, Brian D. Sykes, Hans J. Vogel, Lori Querengesser:
HMDB: the Human Metabolome Database.
521-526
Electronic Edition (link) BibTeX
- Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis, Christopher K. Glass, Alfred H. Merrill Jr., Robert C. Murphy, Christian R. H. Raetz, David W. Russell, Shankar Subramaniam:
LMSD: LIPID MAPS structure database.
527-532
Electronic Edition (link) BibTeX
- Claudia Choi, Richard Münch, Stefan Leupold, Johannes Klein, Inga Siegel, Bernhard Thielen, Beatrice Benkert, Martin Kucklick, Max Schobert, Jens Barthelmes, Christian Ebeling, Isam Haddad, Maurice Scheer, Andreas Grote, Karsten Hiller, Boyke Bunk, Kerstin Schreiber, Ida Retter, Dietmar Schomburg, Dieter Jahn:
SYSTOMONAS - an integrated database for systems biology analysis of Pseudomonas.
533-537
Electronic Edition (link) BibTeX
- H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker:
CellCircuits: a database of protein network models.
538-545
Electronic Edition (link) BibTeX
- Yoshinobu Igarashi, Alexey M. Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Jeffrey W. Smith, Andrei Osterman, Adam Godzik:
CutDB: a proteolytic event database.
546-549
Electronic Edition (link) BibTeX
- Fedor Kolpakov, Vladimir Poroikov, Ruslan Sharipov, Yury Kondrakhin, Alexey Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel:
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis.
550-556
Electronic Edition (link) BibTeX
- Arnaud Ceol, Andrew Chatr-aryamontri, Elena Santonico, Roberto Sacco, Luisa Castagnoli, Gianni Cesareni:
DOMINO: a database of domain-peptide interactions.
557-560
Electronic Edition (link) BibTeX
- Samuel Kerrien, Y. Alam-Faruque, B. Aranda, I. Bancarz, A. Bridge, C. Derow, Emily Dimmer, M. Feuermann, A. Friedrichsen, R. Huntley, C. Kohler, J. Khadake, C. Leroy, A. Liban, C. Lieftink, Luisa Montecchi-Palazzi, Sandra E. Orchard, J. Risse, K. Robbe, Bernd Roechert, David Thorneycroft, Y. Zhang, Rolf Apweiler, Henning Hermjakob:
IntAct - open source resource for molecular interaction data.
561-565
Electronic Edition (link) BibTeX
- Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David J. States, H. V. Jagadish:
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together.
566-571
Electronic Edition (link) BibTeX
- Andrew Chatr-aryamontri, Arnaud Ceol, Luisa Montecchi-Palazzi, Giuliano Nardelli, Maria Victoria Schneider, Luisa Castagnoli, Gianni Cesareni:
MINT: the Molecular INTeraction database.
572-574
Electronic Edition (link) BibTeX
- Petras J. Kundrotas, Emil Alexov:
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures.
575-579
Electronic Edition (link) BibTeX
- Emily R. Jefferson, Thomas P. Walsh, Timothy J. Roberts, Geoffrey J. Barton:
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions.
580-589
Electronic Edition (link) BibTeX
- Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E. Wanker, Matthias E. Futschik:
UniHI: an entry gate to the human protein interactome.
590-594
Electronic Edition (link) BibTeX
- Kieran Hervold, Andrew Martin, Roger A. Kirkpatrick, Paul F. Mc Kenna, F. A. Ramirez-Weber:
Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community.
595-598
Electronic Edition (link) BibTeX
- Fiona M. McCarthy, Susan M. Bridges, Nan Wang, G. Bryce Magee, W. Paul Williams, Dawn S. Luthe, Shane C. Burgess:
AgBase: a unified resource for functional analysis in agriculture.
599-603
Electronic Edition (link) BibTeX
- Zhi-Liang Hu, Eric Ryan Fritz, James M. Reecy:
AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.
604-609
Electronic Edition (link) BibTeX
- Tim J. P. Hubbard, B. L. Aken, K. Beal, B. Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, G. Coates, Fiona Cunningham, Tim Cutts, Thomas Down, S. C. Dyer, S. Fitzgerald, J. Fernandez-Banet, Stefan Gräf, S. Haider, Martin Hammond, J. Herrero, R. Holland, Kevin L. Howe, K. Howe, N. Johnson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, I. Longden, Craig Melsopp, Karine Megy, Patrick Meidl, B. Ouverdin, A. Parker, Andreas Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, J. Severin, Guy Slater, Damian Smedley, G. Spudich, S. Trevanion, Albert J. Vilella, J. Vogel, S. White, M. Wood, Tony Cox, Val Curwen, Richard Durbin, X. M. Fernandez-Suarez, Paul Flicek, Arek Kasprzyk, Glenn Proctor, Stephen M. J. Searle, James Smith, Abel Ureta-Vidal, Ewan Birney:
Ensembl 2007.
610-617
Electronic Edition (link) BibTeX
- Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
The mouse Gene Expression Database (GXD): 2007 update.
618-623
Electronic Edition (link) BibTeX
- Raquel Egea, Sònia Casillas, Enol Fernández, Miquel Àngel Senar, Antonio Barbadilla:
MamPol: a database of nucleotide polymorphism in the Mammalia class.
624-629
Electronic Edition (link) BibTeX
- Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The mouse genome database (MGD): new features facilitating a model system.
630-637
Electronic Edition (link) BibTeX
- Dale A. Begley, Debra M. Krupke, Matthew J. Vincent, John P. Sundberg, Carol J. Bult, Janan T. Eppig:
Mouse Tumor Biology Database (MTB): status update and future directions.
638-642
Electronic Edition (link) BibTeX
- Molly A. Bogue, Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult:
Mouse Phenome Database (MPD).
643-649
Electronic Edition (link) BibTeX
- Hirohide Uenishi, Tomoko Eguchi-Ogawa, Hiroki Shinkai, Naohiko Okumura, Kohei Suzuki, Daisuke Toki, Noriyuki Hamasima, Takashi Awata:
PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences.
650-653
Electronic Edition (link) BibTeX
- Jue Ruan, Yiran Guo, Heng Li, Yafeng Hu, Fei Song, Xin Huang, Karsten Kristiansen, Lars Bolund, Jun Wang:
PigGIS: Pig Genomic Informatics System.
654-657
Electronic Edition (link) BibTeX
- Simon N. Twigger, Mary Shimoyama, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob:
The Rat Genome Database, update 2007 - Easing the path from disease to data and back again.
658-662
Electronic Edition (link) BibTeX
- Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, Donna Karolchik, Galt P. Barber, Rachel A. Harte, Jennifer Hillman-Jackson, Robert M. Kuhn, Brooke L. Rhead, Kayla E. Smith, Archana Thakkapallayil, Ann S. Zweig, David Haussler, W. James Kent:
The ENCODE Project at UC Santa Cruz.
663-667
Electronic Edition (link) BibTeX
- Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Heather Trumbower, Daryl J. Thomas, Archana Thakkapallayil, Charles W. Sugnet, Mario Stanke, Kayla E. Smith, Adam C. Siepel, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, J. S. Pedersen, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Mark Diekhans, Hiram Clawson, Gill Bejerano, Galt P. Barber, Robert Baertsch, David Haussler, W. James Kent:
The UCSC genome browser database: update 2007.
668-673
Electronic Edition (link) BibTeX
- Alecksandr Kutchma, Nayeem Quayum, Jan Jensen:
GeneSpeed: protein domain organization of the transcriptome.
674-679
Electronic Edition (link) BibTeX
- Dongmei Zuo, Stephanie E. Mohr, Yanhui Hu, Elena Taycher, Andreas Rolfs, Jason Kramer, Janice Williamson, Joshua LaBaer:
PlasmID: a centralized repository for plasmid clone information and distribution.
680-684
Electronic Edition (link) BibTeX
- Koichiro Higasa, Katsuyuki Miyatake, Yoji Kukita, Tomoko Tahira, Kenshi Hayashi:
D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples.
685-689
Electronic Edition (link) BibTeX
- Sjozef van Baal, Polynikis Kaimakis, Manyphong Phommarinh, Daphne Koumbi, Harry Cuppens, Francesca Riccardino, Milan Macek Jr., Charles R. Scriver, George P. Patrinos:
FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide.
690-695
Electronic Edition (link) BibTeX
- Philip Groth, Nadia Pavlova, Ivan Kalev, Spas Tonov, Georgi Georgiev, Hans-Dieter Pohlenz, Bertram Weiss:
PhenomicDB: a new cross-species genotype/phenotype resource.
696-699
Electronic Edition (link) BibTeX
- Anil G. Jegga, Sivakumar Gowrisankar,
