Volume 2009

2009

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EISSN 1758-0463

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Volume 2009, 2009

Editorial

DATABASE: A new forum for biological databases and curation

David Landsman, Robert Gentleman, Janet Kelso, B. F. Francis Ouellette

Database, Volume 2009, 2009, bap002, https://doi.org/10.1093/database/bap002

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Original Articles

Cildb: a knowledgebase for centrosomes and cilia

Olivier Arnaiz, Agata Malinowska, Catherine Klotz, Linda Sperling, Michal Dadlez, France Koll, Jean Cohen

Database, Volume 2009, 2009, bap022, https://doi.org/10.1093/database/bap022

MaizeGDB becomes ‘sequence-centric’

Taner Z. Sen, Carson M. Andorf, Mary L. Schaeffer, Lisa C. Harper, Michael E. Sparks, Jon Duvick, Volker P. Brendel, Ethalinda Cannon, Darwin A. Campbell, Carolyn J. Lawrence

Database, Volume 2009, 2009, bap020, https://doi.org/10.1093/database/bap020

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Understanding PubMed^® user search behavior through log analysis

Rezarta Islamaj Dogan, G. Craig Murray, Aurélie Névéol, Zhiyong Lu

Database, Volume 2009, 2009, bap018, https://doi.org/10.1093/database/bap018

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MicroScope: a platform for microbial genome annotation and comparative genomics

D. Vallenet, S. Engelen, D. Mornico, S. Cruveiller, L. Fleury, A. Lajus, Z. Rouy, D. Roche, G. Salvignol, C. Scarpelli, C. Médigue

Database, Volume 2009, 2009, bap021, https://doi.org/10.1093/database/bap021

Integrating text mining into the MGI biocuration workflow

K.G. Dowell, M.S. McAndrews-Hill, D.P. Hill, H.J. Drabkin, J.A. Blake

Database, Volume 2009, 2009, bap019, https://doi.org/10.1093/database/bap019

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A large and accurate collection of peptidase cleavages in the MEROPS database

Neil D. Rawlings

Database, Volume 2009, 2009, bap015, https://doi.org/10.1093/database/bap015

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Models for financial sustainability of biological databases and resources

Christina Chandras, Thomas Weaver, Michael Zouberakis, Damian Smedley, Klaus Schughart, Nadia Rosenthal, John M. Hancock, George Kollias, Paul N. Schofield, Vassilis Aidinis

Database, Volume 2009, 2009, bap017, https://doi.org/10.1093/database/bap017

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Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase

P. Gaudet, L. Lane, P. Fey, A. Bridge, S. Poux, A. Auchincloss, K. Axelsen, S. Braconi Quintaje, E. Boutet, P. Brown, E. Coudert, R.S. Datta, W.C. de Lima, T. de Oliveira Lima, S. Duvaud, N. Farriol-Mathis, S. Ferro Rojas, M. Feuermann, A. Gateau … A. Bairoch

Database, Volume 2009, 2009, bap016, https://doi.org/10.1093/database/bap016

A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki

Lope A. Flórez, Sebastian F. Roppel, Arne G. Schmeisky, Christoph R. Lammers, Jörg Stülke

Database, Volume 2009, 2009, bap012, https://doi.org/10.1093/database/bap012

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The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases

Nils Gehlenborg, Daehee Hwang, Inyoul Y. Lee, Hyuntae Yoo, David Baxter, Brianne Petritis, Rose Pitstick, Bruz Marzolf, Stephen J. DeArmond, George A. Carlson, Leroy Hood

Database, Volume 2009, 2009, bap011, https://doi.org/10.1093/database/bap011

Differential direct coding: a compression algorithm for nucleotide sequence data

Gregory Vey

Database, Volume 2009, 2009, bap013, https://doi.org/10.1093/database/bap013

miRò: a miRNA knowledge base

A. Laganà, S. Forte, A. Giudice, M. R. Arena, P. L. Puglisi, R. Giugno, A. Pulvirenti, D. Shasha, A. Ferro

Database, Volume 2009, 2009, bap008, https://doi.org/10.1093/database/bap008

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Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs

L. Wissler, E. Dattolo, A. D. Moore, T. B. H. Reusch, J. L. Olsen, M. Migliaccio, E. Bornberg-Bauer, G. Procaccini

Database, Volume 2009, 2009, bap009, https://doi.org/10.1093/database/bap009

Radiation Genes: a database devoted to microarrays screenings revealing transcriptome alterations induced by ionizing radiation in mammalian cells

Francesco Chiani, Camilla Iannone, Rodolfo Negri, Daniele Paoletti, Mattia D’Antonio, Paolo D’onorio De Meo, Tiziana Castrignanò

Database, Volume 2009, 2009, bap007, https://doi.org/10.1093/database/bap007

DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels

Hui Yu, Fu-Dong Yu, Guo-Qing Zhang, Xiang Shen, Yun-Qin Chen, Yuan-Yuan Li, Yi-Xue Li

Database, Volume 2009, 2009, bap006, https://doi.org/10.1093/database/bap006

Gramene QTL database: development, content and applications

Junjian Ni, Anuradha Pujar, Ken Youens-Clark, Immanuel Yap, Pankaj Jaiswal, Isaak Tecle, Chih-Wei Tung, Liya Ren, William Spooner, Xuehong Wei, Shuly Avraham, Doreen Ware, Lincoln Stein, Susan McCouch

Database, Volume 2009, 2009, bap005, https://doi.org/10.1093/database/bap005

The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family

R. Travis Moreland, Joseph F. Ryan, Christopher Pan, Andreas D. Baxevanis

Database, Volume 2009, 2009, bap004, https://doi.org/10.1093/database/bap004

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Analysis of CASP8 targets, predictions and assessment methods

ShuoYong Shi, Jimin Pei, Ruslan I. Sadreyev, Lisa N. Kinch, Indraneel Majumdar, Jing Tong, Hua Cheng, Bong-Hyun Kim, Nick V. Grishin

Database, Volume 2009, 2009, bap003, https://doi.org/10.1093/database/bap003

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New mutant phenotype data curation system in the Saccharomyces Genome Database

Maria C. Costanzo, Marek S. Skrzypek, Robert Nash, Edith Wong, Gail Binkley, Stacia R. Engel, Benjamin Hitz, Eurie L. Hong, J. Michael Cherry, the Saccharomyces Genome Database Project

Database, Volume 2009, 2009, bap001, https://doi.org/10.1093/database/bap001