Volume 36,
Number Database-Issue,
January 2008
Editorial
Articles
- Michael Y. Galperin:
The Molecular Biology Database Collection: 2008 update.
2-4
Electronic Edition (link) BibTeX
- Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James K. Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim J. P. Hubbard, Ewan Birney:
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.
5-12
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- David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Martin Shumway, 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.
13-21
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- Hideaki Sugawara, Osamu Ogasawara, Kousaku Okubo, Takashi Gojobori, Yoshio Tateno:
DDBJ with new system and face.
22-24
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- Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
GenBank.
25-30
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- Yu Zhou, Chen Lu, Qi-Jia Wu, Yu Wang, Zhi-Tao Sun, Jia-Cong Deng, Yi Zhang:
GISSD: Group I Intron Sequence and Structure Database.
31-37
Electronic Edition (link) BibTeX
- C. Lloréns, R. Futami, D. Bezemer, A. Moya:
The Gypsy Database (GyDB) of mobile genetic elements.
38-46
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- Asaf Levy, Noa Sela, Gil Ast:
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.
47-52
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- Veenu Aishwarya, P. C. Sharma:
UgMicroSatdb: database for mining microsatellites from unigenes.
53-56
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- Marco Mangone, Philip MacMenamin, Charles Zegar, Fabio Piano, Kristin C. Gunsalus:
UTRome.org: a platform for 3'UTR biology in C. elegans.
57-62
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- Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, Ralf Zimmer:
ProSAS: a database for analyzing alternative splicing in the context of protein structures.
63-68
Electronic Edition (link) BibTeX
- Amrita Pati, Ying Jin, Karsten Klage, Richard F. Helm, Lenwood S. Heath, Naren Ramakrishnan:
CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining.
69-76
Electronic Edition (link) BibTeX
- Takeshi Obayashi, Shinpei Hayashi, Masayuki Shibaoka, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita:
COXPRESdb: a database of coexpressed gene networks in mammals.
77-82
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- Lei Bao, Mi Zhou, Yan Cui:
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.
83-87
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- Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, Sarah A. Teichmann:
DBD--taxonomically broad transcription factor predictions: new content and functionality.
88-92
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- Nicolas Sierro, Yuko Makita, Michiel J. L. de Hoon, Kenta Nakai:
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.
93-96
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- Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai:
DBTSS: database of transcription start sites, progress report 2008.
97-101
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- Jan Christian Bryne, Eivind Valen, Man-Hung Eric Tang, Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin:
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
102-106
Electronic Edition (link) BibTeX
- Obi L. Griffith, Stephen Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter J. De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth W. Wasserman, Ross C. Hardison, Casey M. Bergman, Steven J. M. Jones:
ORegAnno: an open-access community-driven resource for regulatory annotation.
107-113
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- Gang-Qing Hu, Xiaobin Zheng, Yi-Fan Yang, Philippe Ortet, Zhen-Su She, Huaiqiu Zhu:
ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes.
114-119
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- Socorro Gama-Castro, Verónica Jiménez-Jacinto, Martín Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spínola, Bruno Contreras-Moreira, Juan Segura-Salazar, Luis Muñiz-Rascado, Irma Martínez-Flores, Heladia Salgado, César Bonavides-Martínez, Cei Abreu-Goodger, Carlos Rodríguez Penagos, Juan Miranda-Ríos, Enrique Morett, Enrique Merino, Araceli M. Huerta, Luis Treviño-Quintanilla, Julio Collado-Vides:
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
120-124
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- Barrett C. Foat, Ronald G. Tepper, Harmen J. Bussemaker:
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors.
125-131
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- Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d'Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas:
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae.
132-136
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- Anason S. Halees, Rashad El-Badrawi, Khalid S. A. Khabar:
ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.
137-140
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- Oleg Kikin, Zachary Zappala, Lawrence D'Antonio, Paramjeet Bagga:
GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs.
141-148
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- Doron Betel, Manda Wilson, Aaron Gabow, Debora S. Marks, Chris Sander:
The microRNA.org resource: targets and expression.
149-153
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- Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, Anton J. Enright:
miRBase: tools for microRNA genomics.
154-158
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- Seungyoon Nam, Bumjin Kim, Seokmin Shin, Sanghyuk Lee:
miRGator: an integrated system for functional annotation of microRNAs.
159-164
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- Sheng-Da Hsu, Chia-Huei Chu, Ann-Ping Tsou, Shu-Jen Chen, Hua-Chien Chen, Paul Wei-Che Hsu, Yung-Hao Wong, Yi-Hsuan Chen, Gian-Hung Chen, Hsien-Da Huang:
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.
165-169
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- Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, Runsheng Chen:
NONCODE v2.0: decoding the non-coding.
170-172
Electronic Edition (link) BibTeX
- S. Sai Lakshmi, Shipra Agrawal:
piRNABank: a web resource on classified and clustered Piwi-interacting RNAs.
173-177
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- Dorota Piekna-Przybylska, Wayne A. Decatur, Maurille J. Fournier:
The 3D rRNA modification maps database: with interactive tools for ribosome analysis.
178-183
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- Sung-Chou Li, Cheng-Kai Shiau, Wen-chang Lin:
Vir-Mir db: prediction of viral microRNA candidate hairpins.
184-189
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- The UniProt Consortium:
The Universal Protein Resource (UniProt).
190-195
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- Hans-Werner Mewes, S. Dietmann, Dmitrij Frishman, Richard Gregory, Gertrud Mannhaupt, Klaus F. X. Mayer, Martin Münsterkötter, Andreas Ruepp, Manuel Spannagl, Volker Stümpflen, Thomas Rattei:
MIPS: analysis and annotation of genome information in 2007.
196-201
Electronic Edition (link) BibTeX
- Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, Minoru Kanehisa:
AAindex: amino acid index database, progress report 2008.
202-205
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- Conan K. L. Wang, Quentin Kaas, Laurent Chiche, David J. Craik:
CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering.
206-210
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- Hua Cheng, Bong-Hyun Kim, Nick V. Grishin:
MALISAM: a database of structurally analogous motifs in proteins.
211-217
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- Ganesan Pugalenthi, Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Saikat Chakrabarti:
MegaMotifBase: a database of structural motifs in protein families and superfamilies.
218-221
Electronic Edition (link) BibTeX
- David S. Wishart, David Arndt, Mark V. Berjanskii, Anchi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou, Guohui Lin:
PPT-DB: the protein property prediction and testing database.
222-229
Electronic Edition (link) BibTeX
- Josefine Sprenger, J. Lynn Fink, Seetha Karunaratne, Kelly Hanson, Nicholas A. Hamilton, Rohan D. Teasdale:
LOCATE: a mammalian protein subcellular localization database.
230-233
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- Gábor E. Tusnády, Lajos Kalmár, István Simon:
TOPDB: topology data bank of transmembrane proteins.
234-239
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- Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson:
Phospho.ELM: a database of phosphorylation sites - update 2008.
240-244
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- Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Béatrice A. Cuche, Edouard De Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, Christian J. A. Sigrist:
The 20 years of PROSITE.
245-249
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- Lars Juhl Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, Peer Bork:
eggNOG: automated construction and annotation of orthologous groups of genes.
250-254
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- Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang, Yixue Li:
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.
255-262
Electronic Edition (link) BibTeX
- Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer:
InParanoid 6: eukaryotic ortholog clusters with inparalogs.
263-266
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- Andreas Heger, Chris P. Ponting:
OPTIC: orthologous and paralogous transcripts in clades.
267-270
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- Evgenia V. Kriventseva, Nazim Rahman, Octavio Espinosa, Evgeni M. Zdobnov:
OrthoDB: the hierarchical catalog of eukaryotic orthologs.
271-275
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- Andreas Heger, Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, Liisa Holm:
PairsDB atlas of protein sequence space.
276-280
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- Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
The Pfam protein families database.
281-288
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- Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, Hans-Werner Mewes:
SIMAP - structuring the network of protein similarities.
289-292
Electronic Edition (link) BibTeX
- Quan-Yuan He, Quan-Ze He, Xing-Can Deng, Lei Yao, Er Meng, Zhong-Hua Liu, Song-Ping Liang:
ATDB: a uni-database platform for animal toxins.
293-297
Electronic Edition (link) BibTeX
- Karla Gendler, Tara Paulsen, Carolyn Napoli:
ChromDB: The Chromatin Database.
298-302
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- Jianwen Fang, Yinghua Dong, Nazila Salamat-Miller, C. Russell Middaugh:
DB-PABP: a database of polyanion-binding proteins.
303-306
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- Charles J. Reedy, Margaret M. Elvekrog, Brian R. Gibney:
Development of a heme protein structure-electrochemical function database.
307-313
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- Jérôme Gracy, Dung Le-Nguyen, Jean-Christophe Gelly, Quentin Kaas, Annie Heitz, Laurent Chiche:
KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007.
314-319
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- Neil D. Rawlings, Fraser R. Morton, Chai Yin Kok, Jun Kong, Alan J. Barrett:
MEROPS: the peptidase database.
320-325
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- Ségolène Caboche, Maude Pupin, Valérie Leclère, Arnaud Fontaine, Philippe Jacques, Gregory Kucherov:
NORINE: a database of nonribosomal peptides.
326-331
Electronic Edition (link) BibTeX
- Sergi Castellano, Vadim N. Gladyshev, Roderic Guigó, Marla J. Berry:
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.
332-338
Electronic Edition (link) BibTeX
- Joshua D. Podlevsky, Christopher J. Bley, Rebecca V. Omana, Xiaodong Qi, Julian J.-L. Chen:
The Telomerase Database.
339-343
Electronic Edition (link) BibTeX
- Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, Michael Ashburner:
ChEBI: a database and ontology for chemical entities of biological interest.
344-350
Electronic Edition (link) BibTeX
- Kathleen Petri Seiler, Gregory A. George, Mary Pat Happ, Nicole E. Bodycombe, Hyman A. Carrinski, Stephanie Norton, Steve Brudz, John P. Sullivan, Jeremy Muhlich, Martin Serrano, Paul Ferraiolo, Nicola J. Tolliday, Stuart L. Schreiber, Paul A. Clemons:
ChemBank: a small-molecule screening and cheminformatics resource database.
351-359
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- François-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, Piotr Cieplak:
R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries.
360-367
Electronic Edition (link) BibTeX
- Taku Nakahara, Ryo Hashimoto, Hiroaki Nakagawa, Kenji Monde, Nobuaki Miura, Shin-Ichiro Nishimura:
Glycoconjugate Data Bank: Structures - an annotated glycan structure database and N-glycan primary structure verification service.
368-371
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- Ren Zhang, Yan Lin, Chun-Ting Zhang:
Greglist: a database listing potential G-quadruplex regulated genes.
372-376
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- Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, Jörg Schultz:
The ITS2 Database II: homology modelling RNA structure for molecular systematics.
377-380
Electronic Edition (link) BibTeX
- Vinod Kumar Yadav, James Kappukalayil Abraham, Prithvi Mani, Rashi Kulshrestha, Shantanu Chowdhury:
QuadBase: genome-wide database of G4 DNA - occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.
381-385
Electronic Edition (link) BibTeX
- Mariusz Popenda, Marek Blazewicz, Marta Szachniuk, Ryszard W. Adamiak:
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures.
386-391
Electronic Edition (link) BibTeX
- Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, Bruce A. Shapiro:
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.
392-397
Electronic Edition (link) BibTeX
- Fabian Birzele, Jan E. Gewehr, Ralf Zimmer:
AutoPSI: a database for automatic structural classification of protein sequences and structures.
398-401
Electronic Edition (link) BibTeX
- Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, John L. Markley:
BioMagResBank.
402-408
Electronic Edition (link) BibTeX
- Hidetoshi Kono, Tomo Yuasa, Shinya Nishiue, Kei Yura:
coliSNP database server mapping nsSNPs on protein structures.
409-413
Electronic Edition (link) BibTeX
- Corin Yeats, Jonathan Lees, Adam Reid, Paul Kellam, Nigel J. Martin, Xinhui Liu, Christine A. Orengo:
Gene3D: comprehensive structural and functional annotation of genomes.
414-418
Electronic Edition (link) BibTeX
- Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin:
Data growth and its impact on the SCOP database: new developments.
419-425
Electronic Edition (link) BibTeX
- Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John M. C. Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim Vranken, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman:
Remediation of the protein data bank archive.
426-433
Electronic Edition (link) BibTeX
- Andreas Schlicker, Mario Albrecht:
FunSimMat: a comprehensive functional similarity database.
434-439
Electronic Edition (link) BibTeX
- The Gene Ontology project in 2008.
440-444
Electronic Edition (link) BibTeX
- Elspeth A. Bruford, Michael J. Lush, Mathew W. Wright, Tam P. Sneddon, Sue Povey, Ewan Birney:
The HGNC Database in 2008: a resource for the human genome.
445-448
Electronic Edition (link) BibTeX
- Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Yon Rhee, Martin M. Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, Doreen Ware:
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.
449-454
Electronic Edition (link) BibTeX
- In Seok Yang, Chunsun Ryu, Ki Joon Cho, Jin Kwang Kim, Swee Hoe Ong, Wayne P. Mitchell, Bong Su Kim, Hee-Bok Oh, Kyung Hyun Kim:
IDBD: Infectious Disease Biomarker Database.
455-460
Electronic Edition (link) BibTeX
- Nicolas J. Tourasse, Anne-Brit Kolstø:
SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis).
461-468
Electronic Edition (link) BibTeX
- Pierre Lechat, Laurence Hummel, Sandrine Rousseau, Ivan Moszer:
GenoList: an integrated environment for comparative analysis of microbial genomes.
469-474
Electronic Edition (link) BibTeX
- Konstantinos Liolios, Konstantinos Mavrommatis, Nektarios Tavernarakis, Nikos Kyrpides:
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.
475-479
Electronic Edition (link) BibTeX
- Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi:
KEGG for linking genomes to life and the environment.
480-484
Electronic Edition (link) BibTeX
- Emmanuel Courcelle, Yoann Beausse, Sébastien Letort, Olivier Stahl, Romain Fremez, Catherine Ngom-Bru, Jérôme Gouzy, Thomas Faraut:
Narcisse: a mirror view of conserved syntenies.
485-490
Electronic Edition (link) BibTeX
- Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, Toni Gabaldón:
PhylomeDB: a database for genome-wide collections of gene phylogenies.
491-496
Electronic Edition (link) BibTeX
- Burke Squires, Catherine Macken, Adolfo Garcia-Sastre, Shubhada Godbole, Jyothi Noronha, Victoria Hunt, Roger Chang, Christopher N. Larsen, Ed Klem, Kevin Biersack, Richard H. Scheuermann:
BioHealthBase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence.
497-503
Electronic Edition (link) BibTeX
- Yi Huang, Susanna K. P. Lau, Patrick C. Y. Woo, Kwok-yung Yuen:
CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes.
504-511
Electronic Edition (link) BibTeX
- Carla Kuiken, Peter Hraber, James Thurmond, Karina Yusim:
The hepatitis C sequence database in Los Alamos.
512-516
Electronic Edition (link) BibTeX
- Inti Pedroso, Gustavo Rivera, Felipe Lazo, Max Chacón, Francisco Ossandón, Felipe A. Veloso, David S. Holmes:
AlterORF: a database of alternate open reading frames.
517-518
Electronic Edition (link) BibTeX
- Jeremy D. Glasner, Guy Plunkett III, Bradley D. Anderson, David J. Baumler, Bryan S. Biehl, Valerie Burland, Eric L. Cabot, Aaron E. Darling, Bob Mau, Eric C. Neeno-Eckwall, David Pot, Yu Qiu, Anna I. Rissman, Sara Worzella, Sam Zaremba, Joel Fedorko, Tom Hampton, Paul Liss, Michael Rusch, Matthew Shaker, Lorie Shaull, Panna Shetty, Silpa Thotakura, Jon Whitmore, Frederick R. Blattner, John M. Greene, Nicole T. Perna:
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria.
519-523
Electronic Edition (link) BibTeX
- Pere Puigbò, Antoni Romeu, Santiago Garcia-Vallvé:
HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.
524-527
Electronic Edition (link) BibTeX
- Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.
528-533
Electronic Edition (link) BibTeX
- Victor M. Markowitz, Natalia Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Yuri Grechkin, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Philip Hugenholtz, Nikos Kyrpides:
IMG/M: a data management and analysis system for metagenomes.
534-538
Electronic Edition (link) BibTeX
- Jian Yang, Lihong Chen, Lilian Sun, Jun Yu, Qi Jin:
VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics.
539-542
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- Roy R. Chaudhuri, Nicholas J. Loman, Lori A. S. Snyder, Christopher M. Bailey, Dov J. Stekel, Mark J. Pallen:
xBASE2: a comprehensive resource for comparative bacterial genomics.
543-546
Electronic Edition (link) BibTeX
- Alberto M. R. Dávila, Pablo N. Mendes, Glauber Wagner, Diogo A. Tschoeke, Rafael R. C. Cuadrat, Felipe Liberman, Luciana Matos, Thiago S. Satake, Kary A. C. S. Ocaña, Omar Triana, Sérgio M. S. Cruz, Henrique C. L. Jucá, Juliano C. Cury, Fabricio N. Silva, Guilherme A. Geronimo, Margarita Ruiz, Eduardo Ruback, Floriano P. Silva Jr., Christian M. Probst, Edmundo C. Grisard, Marco A. Krieger, Samuel Goldenberg, Maria Cláudia Reis Cavalcanti, Milton O. Moraes, Maria Luiza Machado Campos, Marta Mattoso:
ProtozoaDB: dynamic visualization and exploration of protozoan genomes.
547-552
Electronic Edition (link) BibTeX
- Bindu Gajria, Amit Bahl, John Brestelli, Jennifer Dommer, Steve Fischer, Xin Gao, Mark Heiges, John Iodice, Jessica C. Kissinger, Aaron J. Mackey, Deborah F. Pinney, David S. Roos, Christian J. Stoeckert Jr., Haiming Wang, Brian P. Brunk:
ToxoDB: an integrated Toxoplasma gondii database resource.
553-556
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- Tristan Rossignol, Pierre Lechat, Christina Cuomo, Qiandong Zeng, Ivan Moszer, Christophe d'Enfert:
CandidaDB: a multi-genome database for Candida species and related Saccharomycotina.
557-561
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- Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Kwangyul Yu, Jaeyoung Choi, Sunghyung Kong, Jaejin Park, Seryun Kim, Hyojeong Kim, Soonok Kim, Jihyun F. Kim, Jaime E. Blair, Kwangwon Lee, Seogchan Kang, Yong-Hwan Lee:
CFGP: a web-based, comparative fungal genomics platform.
562-571
Electronic Edition (link) BibTeX
- Rainer Winnenburg, Martin Urban, Andrew Beacham, Thomas K. Baldwin, Sabrina Holland, Magdalen Lindeberg, Hilde Hansen, Christopher J. Rawlings, Kim E. Hammond-Kosack, Jacob Köhler:
PHI-base update: additions to the pathogen-host interaction database.
572-576
Electronic Edition (link) BibTeX
- Eurie L. Hong, Rama Balakrishnan, Qing Dong, Karen R. Christie, Julie Park, Gail Binkley, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kathy K. Zhu, Kara Dolinski, David Botstein, J. Michael Cherry:
Gene Ontology annotations at SGD: new data sources and annotation methods.
577-581
Electronic Edition (link) BibTeX
- Alexie Papanicolaou, Steffi Gebauer-Jung, Mark L. Blaxter, W. Owen McMillan, Chris D. Jiggins:
ButterflyBase: a platform for lepidopteran genomics.
582-587
Electronic Edition (link) BibTeX
- Robert J. Wilson, Joshua L. Goodman, Victor B. Strelets, The FlyBase Consortium:
FlyBase: integration and improvements to query tools.
588-593
Electronic Edition (link) BibTeX
- Marc S. Halfon, Steven M. Gallo, Casey M. Bergman:
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.
594-598
Electronic Edition (link) BibTeX
- Sofia M. C. Robb, Eric Ross, Alejandro Sánchez Alvarado:
SmedGD: the Schmidtea mediterranea genome database.
599-606
Electronic Edition (link) BibTeX
- James C. Sullivan, Adam M. Reitzel, John R. Finnerty:
Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.
607-611
Electronic Edition (link) BibTeX
- Anthony Rogers, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Carol Bastiani, Payan Canaran, Juancarlos Chan, Wen J. Chen, Paul Davis, Jolene Fernandes, Tristan J. Fiedler, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon McKay, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, Paul W. Sternberg:
WormBase 2007.
612-617
Electronic Edition (link) BibTeX
- Matthew Bashton, Irene Nobeli, Janet M. Thornton:
PROCOGNATE: a cognate ligand domain mapping for enzymes.
618-622
Electronic Edition (link) BibTeX
- Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne M. Paley, Seung Yon Rhee, Alexander G. Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang, Peter D. Karp:
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
623-631
Electronic Edition (link) BibTeX
- Chong Su, José M. Peregrin-Alvarez, Gareth Butland, Sadhna Phanse, Vincent Fong, Andrew Emili, John Parkinson:
Bacteriome.org - an integrated protein interaction database for E. coli.
632-636
Electronic Edition (link) BibTeX
- Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Michael S. Livstone, Rose Oughtred, Daniel H. Lackner, Jürg Bähler, Valerie Wood, Kara Dolinski, Mike Tyers:
The BioGRID Interaction Database: 2008 update.
637-640
Electronic Edition (link) BibTeX
- Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi:
The cell cycle DB: a systems biology approach to cell cycle analysis.
641-645
Electronic Edition (link) BibTeX
- Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou Doudieu, Volker Stümpflen, Hans-Werner Mewes:
CORUM: the comprehensive resource of mammalian protein complexes.
646-650
Electronic Edition (link) BibTeX
- Philipp Pagel, Matthias Oesterheld, Oksana Tovstukhina, Normann Strack, Volker Stümpflen, Dmitrij Frishman:
DIMA 2.0 - predicted and known domain interactions.
651-655
Electronic Edition (link) BibTeX
- Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, Raja Jothi:
DOMINE: a database of protein domain interactions.
656-661
Electronic Edition (link) BibTeX
- Emre Guney, Nurcan Tuncbag, Ozlem Keskin, Attila Gürsoy:
HotSprint: database of computational hot spots in protein interfaces.
662-666
Electronic Edition (link) BibTeX
- Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, Shoshana J. Wodak:
LigASite - a database of biologically relevant binding sites in proteins with known apo-structures.
667-673
Electronic Edition (link) BibTeX
- Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John Beaver, Peter Dresslar, Jason Nerothin, Heather A. Carlson:
Binding MOAD, a high-quality protein-ligand database.
674-678
Electronic Edition (link) BibTeX
- Wuming Gong, Dihan Zhou, Yongliang Ren, Yejun Wang, Zhixiang Zuo, Yanping Shen, Feifei Xiao, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao, Tongbin Li:
PepCyber: P~PEP: a database of human protein-protein interactions mediated by phosphoprotein-binding domains.
679-683
Electronic Edition (link) BibTeX
- Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, Peer Bork:
STITCH: interaction networks of chemicals and proteins.
684-688
Electronic Edition (link) BibTeX
- Jürgen Dönitz, Björn Goemann, Muriel Lizé, Holger Michael, Nicole Sasse, Edgar Wingender, Anatolij Potapov:
EndoNet: an information resource about regulatory networks of cell-to-cell communication.
689-694
Electronic Edition (link) BibTeX
- Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, Tony Pawson:
NetworKIN: a resource for exploring cellular phosphorylation networks.
695-699
Electronic Edition (link) BibTeX
- Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, Shankar Subramaniam:
The Molecule Pages database.
700-706
Electronic Edition (link) BibTeX
- Paul Flicek, B. L. Aken, K. Beal, B. Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, G. Coates, Fiona Cunningham, Tim Cutts, Thomas A. Down, S. C. Dyer, T. Eyre, S. Fitzgerald, J. Fernandez-Banet, Stefan Gräf, S. Haider, Martin Hammond, R. Holland, Kevin L. Howe, K. Howe, N. Johnson, A. Jenkinson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, I. Longden, Karine Megy, Patrick Meidl, B. Overduin, A. Parker, B. Pritchard, Andreas Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, Guy Slater, Damian Smedley, G. Spudich, S. Trevanion, Albert J. Vilella, J. Vogel, S. White, M. Wood, Ewan Birney, Tony Cox, Val Curwen, Richard Durbin, X. M. Fernandez-Suarez, J. Herrero, Tim J. P. Hubbard, Arek Kasprzyk, Glenn Proctor, James Smith, Abel Ureta-Vidal, Stephen M. J. Searle:
Ensembl 2008.
707-714
Electronic Edition (link) BibTeX
- Ann-Marie Mallon, Andrew Blake, John M. Hancock:
EuroPhenome and EMPReSS: online mouse phenotyping resource.
715-718
Electronic Edition (link) BibTeX
- Carl J. Schmidt, Michael Romanov, Oliver Ryder, Vincent Magrini, Matthew T. Hickenbotham, Jarret Glasscock, Sean McGrath, Elaine R. Mardis, Lincoln D. Stein:
Gallus GBrowse: a unified genomic database for the chicken.
719-723
Electronic Edition (link) BibTeX
- Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Judith A. Blake:
The Mouse Genome Database (MGD): mouse biology and model systems.
724-728
Electronic Edition (link) BibTeX
- Ling V. Sun, Ke Jin, Yiming Liu, Wenwei Yang, Xing Xie, Lin Ye, Li Wang, Lin Zhu, Sheng Ding, Yi Su, Jie Zhou, Min Han, Yuan Zhuang, Tian Xu, Xiaohui Wu, Ning Gu, Yang Zhong:
PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice.
729-734
Electronic Edition (link) BibTeX
- Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin:
TreeFam: 2008 Update.
735-740
Electronic Edition (link) BibTeX
- Guglielmo Roma, Marco Sardiello, Gilda Cobellis, Pedro Cruz, Giampiero Lago, Remo Sanges, Elia Stupka:
The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones.
741-746
Electronic Edition (link) BibTeX
- Budrul Ahsan, Daisuke Kobayashi, Tomoyuki Yamada, Masahiro Kasahara, Shin Sasaki, Taro L. Saito, Yukinobu Nagayasu, Koichiro Doi, Yoichiro Nakatani, Wei Qu, Tomoko Jindo, Atsuko Shimada, Kiyoshi Naruse, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda, Yuji Kohara, Shinichi Morishita:
UTGB/medaka: genomic resource database for medaka biology.
747-752
Electronic Edition (link) BibTeX
- L. G. Wilming, J. G. R. Gilbert, K. Howe, S. Trevanion, Tim J. P. Hubbard, J. L. Harrow:
The vertebrate genome annotation (Vega) database.
753-760
Electronic Edition (link) BibTeX
- Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen, Nicolas Pollet, Peter D. Vize:
Xenbase: a Xenopus biology and genomics resource.
761-767
Electronic Edition (link) BibTeX
- Judy Sprague, Leyla Bayraktaroglu, Yvonne Bradford, Tom Conlin, Nathan Dunn, David Fashena, Ken Frazer, Melissa Haendel, Douglas G. Howe, Jonathan Knight, Prita Mani, Sierra A. T. Moxon, Christian Pich, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Xiang Shao, Amy Singer, Peiran Song, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield:
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.
768-772
Electronic Edition (link) BibTeX
- Donna Karolchik, Robert M. Kuhn, Robert Baertsch, Galt P. Barber, Hiram Clawson, Mark Diekhans, Belinda Giardine, Rachel A. Harte,
