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  		Contents: Volume 36, Database issue, January 2008   [Index by Author] 

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Editorial Back

Alex Bateman
Editorial
Nucl. Acids Res. 2008 36: D1; doi:10.1093/nar/gkm1139 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Articles Back

Michael Y. Galperin
The Molecular Biology Database Collection: 2008 update
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D2-D4; doi:10.1093/nar/gkm1037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Database Summaries]  

Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James 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 Hubbard, and Ewan Birney
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
Nucleic Acids Research Advance Access published on November 26, 2007
Nucl. Acids Res. 2008 36: D5-D12; doi:10.1093/nar/gkm1018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Eugene Yaschenko
Database resources of the National Center for Biotechnology Information
Nucleic Acids Research Advance Access published on November 27, 2007
Nucl. Acids Res. 2008 36: D13-D21; doi:10.1093/nar/gkm1000 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

H. Sugawara, O. Ogasawara, K. Okubo, T. Gojobori, and Y. Tateno
DDBJ with new system and face
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D22-D24; doi:10.1093/nar/gkm889 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
GenBank
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: D25-D30; doi:10.1093/nar/gkm929 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yu Zhou, Chen Lu, Qi-Jia Wu, Yu Wang, Zhi-Tao Sun, Jia-Cong Deng, and Yi Zhang
GISSD: Group I Intron Sequence and Structure Database
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D31-D37; doi:10.1093/nar/gkm766 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

C. Lloréns, R. Futami, D. Bezemer, and A. Moya
The Gypsy Database (GyDB) of mobile genetic elements
Nucleic Acids Research Advance Access published on September 25, 2007
Nucl. Acids Res. 2008 36: D38-D46; doi:10.1093/nar/gkm697 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Asaf Levy, Noa Sela, and Gil Ast
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D47-D52; doi:10.1093/nar/gkm949 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Veenu Aishwarya and P. C. Sharma
UgMicroSatdb: database for mining microsatellites from unigenes
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D53-D56; doi:10.1093/nar/gkm811 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marco Mangone, Philip MacMenamin, Charles Zegar, Fabio Piano, and Kristin C. Gunsalus
UTRome.org: a platform for 3'UTR biology in C. elegans
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D57-D62; doi:10.1093/nar/gkm946 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, and Ralf Zimmer
ProSAS: a database for analyzing alternative splicing in the context of protein structures
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D63-D68; doi:10.1093/nar/gkm793 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Amrita Pati, Ying Jin, Karsten Klage, Richard F. Helm, Lenwood S. Heath, and Naren Ramakrishnan
CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D69-D76; doi:10.1093/nar/gkm804 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Takeshi Obayashi, Shinpei Hayashi, Masayuki Shibaoka, Motoshi Saeki, Hiroyuki Ohta, and Kengo Kinoshita
COXPRESdb: a database of coexpressed gene networks in mammals
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D77-D82; doi:10.1093/nar/gkm840 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lei Bao, Mi Zhou, and Yan Cui
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D83-D87; doi:10.1093/nar/gkm875 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, and Sarah A. Teichmann
DBD––taxonomically broad transcription factor predictions: new content and functionality
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: D88-D92; doi:10.1093/nar/gkm964 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nicolas Sierro, Yuko Makita, Michiel de Hoon, and Kenta Nakai
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D93-D96; doi:10.1093/nar/gkm910 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, and Kenta Nakai
DBTSS: database of transcription start sites, progress report 2008
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D97-D101; doi:10.1093/nar/gkm901 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jan Christian Bryne, Eivind Valen, Man-Hung Eric Tang, Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, and Albin Sandelin
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Nucleic Acids Research Advance Access published on November 15, 2007
Nucl. Acids Res. 2008 36: D102-D106; doi:10.1093/nar/gkm955 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Obi L. Griffith, Stephen B. 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 De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J.M. Jones, and The Open Regulatory Annotation Consortium
ORegAnno: an open-access community-driven resource for regulatory annotation
Nucleic Acids Research Advance Access published on November 15, 2007
Nucl. Acids Res. 2008 36: D107-D113; doi:10.1093/nar/gkm967 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gang-Qing Hu, Xiaobin Zheng, Yi-Fan Yang, Philippe Ortet, Zhen-Su She, and Huaiqiu Zhu
ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D114-D119; doi:10.1093/nar/gkm799 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Socorro Gama-Castro, Verónica Jiménez-Jacinto, Martín Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spinola, 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, and Julio Collado-Vides
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
Nucleic Acids Research Advance Access published on December 23, 2007
Nucl. Acids Res. 2008 36: D120-D124; doi:10.1093/nar/gkm994 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Barrett C. Foat, Ronald G. Tepper, and Harmen J. Bussemaker
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D125-D131; doi:10.1093/nar/gkm828 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Ana T. Freitas
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: D132-D136; doi:10.1093/nar/gkm976 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Anason S. Halees, Rashad El-Badrawi, and Khalid S. A. Khabar
ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D137-D140; doi:10.1093/nar/gkm959 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Oleg Kikin, Zachary Zappala, Lawrence D’Antonio, and Paramjeet S. Bagga
GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs
Nucleic Acids Research Advance Access published on November 27, 2007
Nucl. Acids Res. 2008 36: D141-D148; doi:10.1093/nar/gkm982 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Doron Betel, Manda Wilson, Aaron Gabow, Debora S. Marks, and Chris Sander
The microRNA.org resource: targets and expression
Nucleic Acids Research Advance Access published on December 23, 2007
Nucl. Acids Res. 2008 36: D149-D153; doi:10.1093/nar/gkm995 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, and Anton J. Enright
miRBase: tools for microRNA genomics
Nucleic Acids Research Advance Access published on November 8, 2007
Nucl. Acids Res. 2008 36: D154-D158; doi:10.1093/nar/gkm952 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Seungyoon Nam, Bumjin Kim, Seokmin Shin, and Sanghyuk Lee
miRGator: an integrated system for functional annotation of microRNAs
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D159-D164; doi:10.1093/nar/gkm829 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Hsien-Da Huang
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D165-D169; doi:10.1093/nar/gkm1012 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, and Runsheng Chen
NONCODE v2.0: decoding the non-coding
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D170-D172; doi:10.1093/nar/gkm1011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

S. Sai Lakshmi and Shipra Agrawal
piRNABank: a web resource on classified and clustered Piwi-interacting RNAs
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2008 36: D173-D177; doi:10.1093/nar/gkm696 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Dorota Piekna-Przybylska, Wayne A. Decatur, and Maurille J. Fournier
The 3D rRNA modification maps database: with interactive tools for ribosome analysis
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D178-D183; doi:10.1093/nar/gkm855 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sung-Chou Li, Cheng-Kai Shiau, and Wen-chang Lin
Vir-Mir db: prediction of viral microRNA candidate hairpins
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2008 36: D184-D189; doi:10.1093/nar/gkm610 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

The UniProt Consortium
The Universal Protein Resource (UniProt)
Nucleic Acids Research Advance Access published on November 27, 2007
Nucl. Acids Res. 2008 36: D190-D195; doi:10.1093/nar/gkm895 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

H. W. Mewes, S. Dietmann, D. Frishman, R. Gregory, G. Mannhaupt, K. F. X. Mayer, M. Münsterkötter, A. Ruepp, M. Spannagl, V. Stümpflen, and T. Rattei
MIPS: analysis and annotation of genome information in 2007
Nucleic Acids Research Advance Access published on December 23, 2007
Nucl. Acids Res. 2008 36: D196-D201; doi:10.1093/nar/gkm980 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, and Minoru Kanehisa
AAindex: amino acid index database, progress report 2008
Nucleic Acids Research Advance Access published on November 12, 2007
Nucl. Acids Res. 2008 36: D202-D205; doi:10.1093/nar/gkm998 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Conan K. L. Wang, Quentin Kaas, Laurent Chiche, and David J. Craik
CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D206-D210; doi:10.1093/nar/gkm953 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hua Cheng, Bong-Hyun Kim, and Nick V. Grishin
MALISAM: a database of structurally analogous motifs in proteins
Nucleic Acids Research Advance Access published on September 12, 2007
Nucl. Acids Res. 2008 36: D211-D217; doi:10.1093/nar/gkm698 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ganesan Pugalenthi, P. N. Suganthan, R. Sowdhamini, and Saikat Chakrabarti
MegaMotifBase: a database of structural motifs in protein families and superfamilies
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D218-D221; doi:10.1093/nar/gkm794 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David S. Wishart, David Arndt, Mark Berjanskii, An Chi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou, and Guohui Lin
PPT-DB: the protein property prediction and testing database
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2008 36: D222-D229; doi:10.1093/nar/gkm800 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Josefine Sprenger, J. Lynn Fink, Seetha Karunaratne, Kelly Hanson, Nicholas A. Hamilton, and Rohan D. Teasdale
LOCATE: a mammalian protein subcellular localization database
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D230-D233; doi:10.1093/nar/gkm950 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gábor E. Tusnády, Lajos Kalmár, and István Simon
TOPDB: topology data bank of transmembrane proteins
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2008 36: D234-D239; doi:10.1093/nar/gkm751 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, and Toby J. Gibson
Phospho.ELM: a database of phosphorylation sites—update 2008
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D240-D244; doi:10.1093/nar/gkm772 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Béatrice A. Cuche, Edouard de Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, and Christian J. A. Sigrist
The 20 years of PROSITE
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: D245-D249; doi:10.1093/nar/gkm977 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lars Juhl Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, and Peer Bork
eggNOG: automated construction and annotation of orthologous groups of genes
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D250-D254; doi:10.1093/nar/gkm796 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang, and Yixue Li
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D255-D262; doi:10.1093/nar/gkm924 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, and Erik L. L. Sonnhammer
InParanoid 6: eukaryotic ortholog clusters with inparalogs
Nucleic Acids Research Advance Access published on November 30, 2007
Nucl. Acids Res. 2008 36: D263-D266; doi:10.1093/nar/gkm1020 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andreas Heger and Chris P. Ponting
OPTIC: orthologous and paralogous transcripts in clades
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D267-D270; doi:10.1093/nar/gkm852 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Evgenia V. Kriventseva, Nazim Rahman, Octavio Espinosa, and Evgeny M. Zdobnov
OrthoDB: the hierarchical catalog of eukaryotic orthologs
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D271-D275; doi:10.1093/nar/gkm845 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andreas Heger, Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, and Liisa Holm
PairsDB atlas of protein sequence space
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D276-D280; doi:10.1093/nar/gkm879 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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, and Alex Bateman
The Pfam protein families database
Nucleic Acids Research Advance Access published on November 26, 2007
Nucl. Acids Res. 2008 36: D281-D288; doi:10.1093/nar/gkm960 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, and Werner Mewes
SIMAP—structuring the network of protein similarities
Nucleic Acids Research Advance Access published on November 23, 2007
Nucl. Acids Res. 2008 36: D289-D292; doi:10.1093/nar/gkm963 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Quan-Yuan He, Quan-Ze He, Xing-Can Deng, Lei Yao, Er Meng, Zhong-Hua Liu, and Song-Ping Liang
ATDB: a uni-database platform for animal toxins
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D293-D297; doi:10.1093/nar/gkm832 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Karla Gendler, Tara Paulsen, and Carolyn Napoli
ChromDB: The Chromatin Database
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D298-D302; doi:10.1093/nar/gkm768 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jianwen Fang, Yinghua Dong, Nazila Salamat-Miller, and C. Russell Middaugh
DB-PABP: a database of polyanion-binding proteins
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2008 36: D303-D306; doi:10.1093/nar/gkm784 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Charles J. Reedy, Margaret M. Elvekrog, and Brian R. Gibney
Development of a heme protein structure–electrochemical function database
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D307-D313; doi:10.1093/nar/gkm814 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jérôme Gracy, Dung Le-Nguyen, Jean-Christophe Gelly, Quentin Kaas, Annie Heitz, and Laurent Chiche
KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D314-D319; doi:10.1093/nar/gkm939 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Neil D. Rawlings, Fraser R. Morton, Chai Yin Kok, Jun Kong, and Alan J. Barrett
MEROPS: the peptidase database
Nucleic Acids Research Advance Access published on November 8, 2007
Nucl. Acids Res. 2008 36: D320-D325; doi:10.1093/nar/gkm954 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ségolène Caboche, Maude Pupin, Valérie Leclère, Arnaud Fontaine, Philippe Jacques, and Gregory Kucherov
NORINE: a database of nonribosomal peptides
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2008 36: D326-D331; doi:10.1093/nar/gkm792 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sergi Castellano, Vadim N. Gladyshev, Roderic Guigó, and Marla J. Berry
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements
Nucleic Acids Research Advance Access published on January 3, 2008
Nucl. Acids Res. 2008 36: D332-D338; doi:10.1093/nar/gkm731 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Joshua D. Podlevsky, Christopher J. Bley, Rebecca V. Omana, Xiaodong Qi, and Julian J.-L. Chen
The Telomerase Database
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: D339-D343; doi:10.1093/nar/gkm700 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, and Michael Ashburner
ChEBI: a database and ontology for chemical entities of biological interest
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D344-D350; doi:10.1093/nar/gkm791 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, *, and Paul A. Clemons
ChemBank: a small-molecule screening and cheminformatics resource database
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D351-D359; doi:10.1093/nar/gkm843 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

François-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, and Piotr Cieplak
R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D360-D367; doi:10.1093/nar/gkm887 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Taku Nakahara, Ryo Hashimoto, Hiroaki Nakagawa, Kenji Monde, Nobuaki Miura, and Shin-Ichiro Nishimura
Glycoconjugate Data Bank:Structures—an annotated glycan structure database and N-glycan primary structure verification service
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D368-D371; doi:10.1093/nar/gkm833 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ren Zhang, Yan Lin, and Chun-Ting Zhang
Greglist: a database listing potential G-quadruplex regulated genes
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2008 36: D372-D376; doi:10.1093/nar/gkm787 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, and Jörg Schultz
The ITS2 Database II: homology modelling RNA structure for molecular systematics
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D377-D380; doi:10.1093/nar/gkm827 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Vinod Kumar Yadav, James Kappukalayil Abraham, Prithvi Mani, Rashi Kulshrestha, and Shantanu Chowdhury
QuadBase: genome-wide database of G4 DNA—occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D381-D385; doi:10.1093/nar/gkm781 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mariusz Popenda, Marek Blazewicz, Marta Szachniuk, and Ryszard W. Adamiak
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2008 36: D386-D391; doi:10.1093/nar/gkm786 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, and Bruce A. Shapiro
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D392-D397; doi:10.1093/nar/gkm842 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fabian Birzele, Jan E. Gewehr, and Ralf Zimmer
AutoPSI: a database for automatic structural classification of protein sequences and structures
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D398-D401; doi:10.1093/nar/gkm834 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and John L. Markley
BioMagResBank
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D402-D408; doi:10.1093/nar/gkm957 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hidetoshi Kono, Tomo Yuasa, Shinya Nishiue, and Kei Yura
coliSNP database server mapping nsSNPs on protein structures
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2008 36: D409-D413; doi:10.1093/nar/gkm801 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Corin Yeats, Jonathan Lees, Adam Reid, Paul Kellam, Nigel Martin, Xinhui Liu, and Christine Orengo
Gene3D: comprehensive structural and functional annotation of genomes
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: D414-D418; doi:10.1093/nar/gkm1019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin
Data growth and its impact on the SCOP database: new developments
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D419-D425; doi:10.1093/nar/gkm993 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kim Henrick, Zukang Feng, Wolfgang F. Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John 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 Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, and Helen M. Berman
Remediation of the protein data bank archive
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: D426-D433; doi:10.1093/nar/gkm937 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andreas Schlicker and Mario Albrecht
FunSimMat: a comprehensive functional similarity database
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D434-D439; doi:10.1093/nar/gkm806 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

The Gene Ontology Consortium
The Gene Ontology project in 2008
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D440-D444; doi:10.1093/nar/gkm883 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Elspeth A. Bruford, Michael J. Lush, Mathew W. Wright, Tam P. Sneddon, Sue Povey, and Ewan Birney
The HGNC Database in 2008: a resource for the human genome
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D445-D448; doi:10.1093/nar/gkm881 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, and Doreen Ware
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
Nucl. Acids Res. 2008 36: D449-D454; doi:10.1093/nar/gkm908 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

In Seok Yang, Chunsun Ryu, Ki Joon Cho, Jin Kwang Kim, Swee Hoe Ong, Wayne P. Mitchell, Bong Su Kim, Hee-Bok Oh, and Kyung Hyun Kim
IDBD: Infectious Disease Biomarker Database
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D455-D460; doi:10.1093/nar/gkm925 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nicolas J. Tourasse and 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)
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D461-D468; doi:10.1093/nar/gkm877 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Pierre Lechat, Laurence Hummel, Sandrine Rousseau, and Ivan Moszer
GenoList: an integrated environment for comparative analysis of microbial genomes
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: D469-D474; doi:10.1093/nar/gkm1042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis, and Nikos C. Kyrpides
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D475-D479; doi:10.1093/nar/gkm884 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, and Yoshihiro Yamanishi
KEGG for linking genomes to life and the environment
Nucleic Acids Research Advance Access published on December 12, 2007
Nucl. Acids Res. 2008 36: D480-D484; doi:10.1093/nar/gkm882 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Emmanuel Courcelle, Yoann Beausse, Sébastien Letort, Olivier Stahl, Romain Fremez, Catherine Ngom-Bru, Jérôme Gouzy, and Thomas Faraut
Narcisse: a mirror view of conserved syntenies
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D485-D490; doi:10.1093/nar/gkm805 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, and Toni Gabaldón
PhylomeDB: a database for genome-wide collections of gene phylogenies
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D491-D496; doi:10.1093/nar/gkm899 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Burke Squires, Catherine Macken, Adolfo Garcia-Sastre, Shubhada Godbole, Jyothi Noronha, Victoria Hunt, Roger Chang, Christopher N. Larsen, Ed Klem, Kevin Biersack, and Richard H. Scheuermann
BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence
Nucleic Acids Research Advance Access published on October 26, 2007
Nucl. Acids Res. 2008 36: D497-D503; doi:10.1093/nar/gkm905 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yi Huang, Susanna K. P. Lau, Patrick C. Y. Woo, and Kwok-yung Yuen
CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2008 36: D504-D511; doi:10.1093/nar/gkm754 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Carla Kuiken, Peter Hraber, James Thurmond, and Karina Yusim
The hepatitis C sequence database in Los Alamos
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D512-D516; doi:10.1093/nar/gkm962 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Inti Pedroso, Gustavo Rivera, Felipe Lazo, Max Chacón, Francisco Ossandón, Felipe A. Veloso, and David S. Holmes
AlterORF: a database of alternate open reading frames
Nucleic Acids Research Advance Access published on December 20, 2007
Nucl. Acids Res. 2008 36: D517-D518; doi:10.1093/nar/gkm886 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Nicole T. Perna
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D519-D523; doi:10.1093/nar/gkm973 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Pere Puigbò, Antoni Romeu, and Santiago Garcia-Vallvé
HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D524-D527; doi:10.1093/nar/gkm831 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova, and Nikos C. Kyrpides
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions
Nucleic Acids Research Advance Access published on October 12, 2007
Nucl. Acids Res. 2008 36: D528-D533; doi:10.1093/nar/gkm846 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Victor M. Markowitz, Natalia N. Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Yuri Grechkin, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Philip Hugenholtz, and Nikos C. Kyrpides
IMG/M: a data management and analysis system for metagenomes
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D534-D538; doi:10.1093/nar/gkm869 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jian Yang, Lihong Chen, Lilian Sun, Jun Yu, and Qi Jin
VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D539-D542; doi:10.1093/nar/gkm951 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Roy R. Chaudhuri, Nicholas J. Loman, Lori A.S. Snyder, Christopher M. Bailey, Dov J. Stekel, and Mark J. Pallen
xBASE2: a comprehensive resource for comparative bacterial genomics
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D543-D546; doi:10.1093/nar/gkm928 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alberto M. R. Dávila, Pablo N. Mendes, Glauber Wagner, Diogo A. Tschoeke, Rafael R. C. Cuadrat, Felipe Liberman, Luciana Matos, Thiago 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 C. R. Cavalcanti, Milton O. Moraes, Maria L. M. Campos, and Marta Mattoso
ProtozoaDB: dynamic visualization and exploration of protozoan genomes
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D547-D552; doi:10.1093/nar/gkm820 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Brian P. Brunk
ToxoDB: an integrated Toxoplasma gondii database resource
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: D553-D556; doi:10.1093/nar/gkm981 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tristan Rossignol, Pierre Lechat, Christina Cuomo, Qiandong Zeng, Ivan Moszer, and Christophe d’Enfert
CandidaDB: a multi-genome database for Candida species and related Saccharomycotina
Nucleic Acids Research Advance Access published on November 26, 2007
Nucl. Acids Res. 2008 36: D557-D561; doi:10.1093/nar/gkm1010 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Yong-Hwan Lee
CFGP: a web-based, comparative fungal genomics platform
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D562-D571; doi:10.1093/nar/gkm758 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rainer Winnenburg, Martin Urban, Andrew Beacham, Thomas K. Baldwin, Sabrina Holland, Magdalen Lindeberg, Hilde Hansen, Christopher Rawlings, Kim E. Hammond-Kosack, and Jacob Köhler
PHI-base update: additions to the pathogen–host interaction database
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D572-D576; doi:10.1093/nar/gkm858 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and J. Michael Cherry
Gene Ontology annotations at SGD: new data sources and annotation methods
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D577-D581; doi:10.1093/nar/gkm909 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexie Papanicolaou, Steffi Gebauer-Jung, Mark L. Blaxter, W. Owen McMillan, and Chris D. Jiggins
ButterflyBase: a platform for lepidopteran genomics
Nucleic Acids Research Advance Access published on October 12, 2007
Nucl. Acids Res. 2008 36: D582-D587; doi:10.1093/nar/gkm853 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Robert J. Wilson, Joshua L. Goodman, Victor B. Strelets, and The FlyBase Consortium
FlyBase: integration and improvements to query tools
Nucleic Acids Research Advance Access published on December 26, 2007
Nucl. Acids Res. 2008 36: D588-D593; doi:10.1093/nar/gkm930 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marc S. Halfon, Steven M. Gallo, and Casey M. Bergman
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
Nucleic Acids Research Advance Access published on November 26, 2007
Nucl. Acids Res. 2008 36: D594-D598; doi:10.1093/nar/gkm876 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sofia M.C. Robb, Eric Ross, and Alejandro Sánchez Alvarado
SmedGD: the Schmidtea mediterranea genome database
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2008 36: D599-D606; doi:10.1093/nar/gkm684 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

James C. Sullivan, Adam M. Reitzel, and John R. Finnerty
Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D607-D611; doi:10.1093/nar/gkm941 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, Will Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, and Paul W. Sternberg
WormBase 2007
Nucleic Acids Research Advance Access published on November 8, 2007
Nucl. Acids Res. 2008 36: D612-D617; doi:10.1093/nar/gkm975 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Matthew Bashton, Irene Nobeli, and Janet M. Thornton
PROCOGNATE: a cognate ligand domain mapping for enzymes
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2008 36: D618-D622; doi:10.1093/nar/gkm611 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne Paley, Seung Y. Rhee, Alexander G. Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang, and Peter D. Karp
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
Nucleic Acids Research Advance Access published on October 27, 2007
Nucl. Acids Res. 2008 36: D623-D631; doi:10.1093/nar/gkm900 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chong Su, Jose M. Peregrin-Alvarez, Gareth Butland, Sadhna Phanse, Vincent Fong, Andrew Emili, and John Parkinson
Bacteriome.org—an integrated protein interaction database for E. coli
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D632-D636; doi:10.1093/nar/gkm807 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Michael Livstone, Rose Oughtred, Daniel H. Lackner, Jürg Bähler, Valerie Wood, Kara Dolinski, and Mike Tyers
The BioGRID Interaction Database: 2008 update
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D637-D640; doi:10.1093/nar/gkm1001 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Roberta Alfieri, Ivan Merelli, Ettore Mosca, and Luciano Milanesi
The cell cycle DB: a systems biology approach to cell cycle analysis
Nucleic Acids Research Advance Access published on December 26, 2007
Nucl. Acids Res. 2008 36: D641-D645; doi:10.1093/nar/gkm873 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou Doudieu, Volker Stümpflen, and H. Werner Mewes
CORUM: the comprehensive resource of mammalian protein complexes
Nucleic Acids Research Advance Access published on October 26, 2007
Nucl. Acids Res. 2008 36: D646-D650; doi:10.1093/nar/gkm936 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Philipp Pagel, Matthias Oesterheld, Oksana Tovstukhina, Norman Strack, Volker Stümpflen, and Dmitrij Frishman
DIMA 2.0—predicted and known domain interactions
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D651-D655; doi:10.1093/nar/gkm996 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, and Raja Jothi
DOMINE: a database of protein domain interactions
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2008 36: D656-D661; doi:10.1093/nar/gkm761 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Emre Guney, Nurcan Tuncbag, Ozlem Keskin, and Attila Gursoy
HotSprint: database of computational hot spots in protein interfaces
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2008 36: D662-D666; doi:10.1093/nar/gkm813 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, and Shoshana J. Wodak
LigASite—a database of biologically relevant binding sites in proteins with known apo-structures
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D667-D673; doi:10.1093/nar/gkm839 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John Beaver, Peter Dresslar, Jason Nerothin, and Heather A. Carlson
Binding MOAD, a high-quality protein–ligand database
Nucleic Acids Research Advance Access published on November 30, 2007
Nucl. Acids Res. 2008 36: D674-D678; doi:10.1093/nar/gkm911 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Wuming Gong, Dihan Zhou, Yongliang Ren, Yejun Wang, Zhixiang Zuo, Yanping Shen, Feifei Xiao, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao, and Tongbin Li
PepCyber:P~PEP: a database of human protein–protein interactions mediated by phosphoprotein-binding domains
Nucleic Acids Research Advance Access published on December 26, 2007
Nucl. Acids Res. 2008 36: D679-D683; doi:10.1093/nar/gkm854 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, and Peer Bork
STITCH: interaction networks of chemicals and proteins
Nucleic Acids Research Advance Access published on December 15, 2007
Nucl. Acids Res. 2008 36: D684-D688; doi:10.1093/nar/gkm795 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jürgen Dönitz, Björn Goemann, Muriel Lizé, Holger Michael, Nicole Sasse, Edgar Wingender, and Anatolij P. Potapov
EndoNet: an information resource about regulatory networks of cell-to-cell communication
Nucleic Acids Research Advance Access published on November 27, 2007
Nucl. Acids Res. 2008 36: D689-D694; doi:10.1093/nar/gkm940 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, and Tony Pawson
NetworKIN: a resource for exploring cellular phosphorylation networks
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D695-D699; doi:10.1093/nar/gkm902 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, and Shankar Subramaniam
The Molecule Pages database
Nucleic Acids Research Advance Access published on October 26, 2007
Nucl. Acids Res. 2008 36: D700-D706; doi:10.1093/nar/gkm907 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, T. Eyre, S. Fitzgerald, J. Fernandez-Banet, S. Gräf, S. Haider, M. Hammond, R. Holland, K. L. Howe, K. Howe, N. Johnson, A. Jenkinson, A. Kähäri, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. J. Vilella, J. Vogel, S. White, M. Wood, E. Birney, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, T. J. P. Hubbard, A. Kasprzyk, G. Proctor, J. Smith, A. Ureta-Vidal, and S. Searle
Ensembl 2008
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D707-D714; doi:10.1093/nar/gkm988 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ann-Marie Mallon, Andrew Blake, and John M. Hancock
EuroPhenome and EMPReSS: online mouse phenotyping resource
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2008 36: D715-D718; doi:10.1093/nar/gkm728 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Carl J. Schmidt, Michael Romanov, Oliver Ryder, Vincent Magrini, Matthew Hickenbotham, Jarret Glasscock, Sean McGrath, Elaine Mardis, and Lincoln D. Stein
Gallus GBrowse: a unified genomic database for the chicken
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D719-D723; doi:10.1093/nar/gkm783 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Judith A. Blake, and the Mouse Genome Database Group
The Mouse Genome Database (MGD): mouse biology and model systems
Nucleic Acids Research Advance Access published on December 23, 2007
Nucl. Acids Res. 2008 36: D724-D728; doi:10.1093/nar/gkm961 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Yang Zhong
PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D729-D734; doi:10.1093/nar/gkm790 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Richard Durbin
TreeFam: 2008 Update
Nucleic Acids Research Advance Access published on December 1, 2007
Nucl. Acids Res. 2008 36: D735-D740; doi:10.1093/nar/gkm1005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guglielmo Roma, Marco Sardiello, Gilda Cobellis, Pedro Cruz, Giampiero Lago, Remo Sanges, and Elia Stupka
The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D741-D746; doi:10.1093/nar/gkm825 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Shinichi Morishita
UTGB/medaka: genomic resource database for medaka biology
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D747-D752; doi:10.1093/nar/gkm765 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

L. G. Wilming, J. G. R. Gilbert, K. Howe, S. Trevanion, T. Hubbard, and J. L. Harrow
The vertebrate genome annotation (Vega) database
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: D753-D760; doi:10.1093/nar/gkm987 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen, Nicolas Pollet, and Peter D. Vize
Xenbase: a Xenopus biology and genomics resource
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D761-D767; doi:10.1093/nar/gkm826 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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, and Monte Westerfield
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes
Nucleic Acids Research Advance Access published on November 8, 2007
Nucl. Acids Res. 2008 36: D768-D772; doi:10.1093/nar/gkm956 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller, J. S. Pedersen, A. Pohl, B. J. Raney, B. Rhead, K. R. Rosenbloom, K. E. Smith, M. Stanke, A. Thakkapallayil, H. Trumbower, T. Wang, A. S. Zweig, D. Haussler, and W. J. Kent
The UCSC Genome Browser Database: 2008 update
Nucleic Acids Research Advance Access published on December 17, 2007
Nucl. Acids Res. 2008 36: D773-D779; doi:10.1093/nar/gkm966 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tim Yates, Michal J. Okoniewski, and Crispin J. Miller
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D780-D786; doi:10.1093/nar/gkm779 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Akihiro Matsuya, Ryuichi Sakate, Yoshihiro Kawahara, Kanako O. Koyanagi, Yoshiharu Sato, Yasuyuki Fujii, Chisato Yamasaki, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Kaori Yamaguchi, Toshinori Endo, Satoshi OOta, Wojciech Makalowski, Kazuho Ikeo, Yoshiyuki Suzuki, Kousuke Hanada, Katsuyuki Hashimoto, Momoki Hirai, Hisakazu Iwama, Naruya Saitou, Aiko T. Hiraki, Lihua Jin, Yayoi Kaneko, Masako Kanno, Katsuhiko Murakami, Akiko Ogura Noda, Naomi Saichi, Ryoko Sanbonmatsu, Mami Suzuki, Jun-ichi Takeda, Masayuki Tanaka, Takashi Gojobori, Tadashi Imanishi, and Takeshi Itoh
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D787-D792; doi:10.1093/nar/gkm878 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genome Information Integration Project And H-Invitational 2
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
Nucleic Acids Research Advance Access published on December 18, 2007
Nucl. Acids Res. 2008 36: D793-D799; doi:10.1093/nar/gkm999 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gabrielle C. Nickel, David Tefft, and Mark D. Adams
Human PAML browser: a database of positive selection on human genes using phylogenetic methods
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D800-D808; doi:10.1093/nar/gkm764 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Julian Lange, Helen Skaletsky, George W. Bell, and David C. Page
MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome
Nucleic Acids Research Advance Access published on October 26, 2007
Nucl. Acids Res. 2008 36: D809-D814; doi:10.1093/nar/gkm849 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Arti Singh, Adebayo Olowoyeye, Peter H. Baenziger, Jessica Dantzer, Maricel G. Kann, Predrag Radivojac, Randy Heiland, and Sean D. Mooney
MutDB: update on development of tools for the biochemical analysis of genetic variation
Nucleic Acids Research Advance Access published on September 7, 2007
Nucl. Acids Res. 2008 36: D815-D819; doi:10.1093/nar/gkm659 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Phil Hyoun Lee and Hagit Shatkay
F-SNP: computationally predicted functional SNPs for disease association studies
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D820-D824; doi:10.1093/nar/gkm904 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Joke Reumers, Lucia Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost Van Durme, Joaquin Dopazo, Frederic Rousseau, and Joost Schymkowitz
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases
Nucleic Acids Research Advance Access published on December 17, 2007
Nucl. Acids Res. 2008 36: D825-D829; doi:10.1093/nar/gkm979 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ilari Scheinin, Samuel Myllykangas, Ioana Borze, Tom Böhling, Sakari Knuutila, and Juha Saharinen
CanGEM: mining gene copy number changes in cancer
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D830-D835; doi:10.1093/nar/gkm802 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ximiao He, Suhua Chang, Jiajie Zhang, Qian Zhao, Haizhen Xiang, Kanthida Kusonmano, Liu Yang, Zhong Sheng Sun, Huanming Yang, and Jing Wang
MethyCancer: the database of human DNA methylation and cancer
Nucleic Acids Research Advance Access published on September 21, 2007
Nucl. Acids Res. 2008 36: D836-D841; doi:10.1093/nar/gkm730 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Maté Ongenaert, Leander Van Neste, Tim De Meyer, Gerben Menschaert, Sofie Bekaert, and Wim Van Criekinge
PubMeth: a cancer methylation database combining text-mining and expert annotation
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D842-D846; doi:10.1093/nar/gkm788 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yannick Haudry, Hugo Berube, Ivica Letunic, Paul-Daniel Weeber, Julien Gagneur, Charles Girardot, Misha Kapushesky, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, and Thorsten Henrich
4DXpress: a database for cross-species expression pattern comparisons
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2008 36: D847-D853; doi:10.1093/nar/gkm797 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, and Thomas Skøt Jensen
Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D854-D859; doi:10.1093/nar/gkm729 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Lorna Richardson, Nicholas Burton, Thomas P. Perry, Paul Smith, Richard A. Baldock, Duncan R. Davidson, and Jeffrey H. Christiansen
EMAGE—Edinburgh Mouse Atlas of Gene Expression: 2008 update
Nucleic Acids Research Advance Access published on December 12, 2007
Nucl. Acids Res. 2008 36: D860-D865; doi:10.1093/nar/gkm938 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jeremiah J. Faith, Michael E. Driscoll, Vincent A. Fusaro, Elissa J. Cosgrove, Boris Hayete, Frank S. Juhn, Stephen J. Schneider, and Timothy S. Gardner
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D866-D870; doi:10.1093/nar/gkm815 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Robert J. Marinelli, Kelli Montgomery, Chih Long Liu, Nigam H. Shah, Wijan Prapong, Michael Nitzberg, Zachariah K. Zachariah, Gavin J. Sherlock, Yasodha Natkunam, Robert B. West, Matt van de Rijn, Patrick O. Brown, and Catherine A. Ball
The Stanford Tissue Microarray Database
Nucleic Acids Research Advance Access published on November 7, 2007
Nucl. Acids Res. 2008 36: D871-D877; doi:10.1093/nar/gkm861 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Philip Jones, Richard G. Côté, Sang Yun Cho, Sebastian Klie, Lennart Martens, Antony F. Quinn, David Thorneycroft, and Henning Hermjakob
PRIDE: new developments and new datasets
Nucleic Acids Research Advance Access published on November 22, 2007
Nucl. Acids Res. 2008 36: D878-D883; doi:10.1093/nar/gkm1021 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

C. Zhang, O. Crasta, S. Cammer, R. Will, R. Kenyon, D. Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, T. Xue, Y. Zhang, M. Moore, P. McGarvey, H. Huang, Y. Chen, J. Zhang, R. Mazumder, C. Wu, and B. Sobral
An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D884-D891; doi:10.1093/nar/gkm903 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michael Waters, Stanley Stasiewicz, B. Alex Merrick, Kenneth Tomer, Pierre Bushel, Richard Paules, Nancy Stegman, Gerald Nehls, Kenneth J. Yost, C. Harris Johnson, Scott F. Gustafson, Sandhya Xirasagar, Nianqing Xiao, Cheng-Cheng Huang, Paul Boyer, Denny D. Chan, Qinyan Pan, Hui Gong, John Taylor, Danielle Choi, Asif Rashid, Ayazaddin Ahmed, Reese Howle, James Selkirk, Raymond Tennant, and Jennifer Fostel
CEBS—Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D892-D900; doi:10.1093/nar/gkm755 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David S. Wishart, Craig Knox, An Chi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, and Murtaza Hassanali
DrugBank: a knowledgebase for drugs, drug actions and drug targets
Nucleic Acids Research Advance Access published on November 29, 2007
Nucl. Acids Res. 2008 36: D901-D906; doi:10.1093/nar/gkm958 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yasushi Okuno, Akiko Tamon, Hiroaki Yabuuchi, Satoshi Niijima, Yohsuke Minowa, Koichiro Tonomura, Ryo Kunimoto, and Chunlai Feng
GLIDA: GPCR—ligand database for chemical genomics drug discovery—database and tools update
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D907-D912; doi:10.1093/nar/gkm948 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tina Hernandez-Boussard, Michelle Whirl-Carrillo, Joan M. Hebert, Li Gong, Ryan Owen, Mei Gong, Winston Gor, Feng Liu, Chuong Truong, Ryan Whaley, Mark Woon, Tina Zhou, Russ B. Altman, and Teri E. Klein
The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: D913-D918; doi:10.1093/nar/gkm1009 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stefan Günther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo Garcia Urdiales, Andreas Gewiess, Lars Juhl Jensen, Reinhard Schneider, Roman Skoblo, Robert B. Russell, Philip E. Bourne, Peer Bork, and Robert Preissner
SuperTarget and Matador: resources for exploring drug-target relationships
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D919-D922; doi:10.1093/nar/gkm862 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zuoshuang Xiang, Thomas Todd, Kim P. Ku, Bethany L. Kovacic, Charles B. Larson, Fang Chen, Andrew P. Hodges, Yuying Tian, Elizabeth A. Olenzek, Boyang Zhao, Lesley A. Colby, Howard G. Rush, Janet R. Gilsdorf, George W. Jourdian, and Yongqun He
VIOLIN: vaccine investigation and online information network
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D923-D928; doi:10.1093/nar/gkm1039 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shoji Mano, Tomoki Miwa, Shuh-ichi Nishikawa, Tetsuro Mimura, and Mikio Nishimura
The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D929-D937; doi:10.1093/nar/gkm789 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yong Seok Lee, Jeongsu Oh, Young Uk Kim, Namchul Kim, Sungjin Yang, and Ui Wook Hwang
Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D938-D942; doi:10.1093/nar/gkm763 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Samart Wanchana, Supat Thongjuea, Victor Jun Ulat, Mylah Anacleto, Ramil Mauleon, Matthieu Conte, Mathieu Rouard, Manuel Ruiz, Nandini Krishnamurthy, Kimmen Sjolander, Theo van Hintum, and Richard M. Bruskiewich
The Generation Challenge Programme comparative plant stress-responsive gene catalogue
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D943-D946; doi:10.1093/nar/gkm798 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry Casstevens, Bonnie Hurwitz, Susan McCouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Tecle, Jim Thomason, Chih-wei Tung, Xuehong Wei, Immanuel Yap, Ken Youens-Clark, Doreen Ware, and Lincoln Stein
Gramene: a growing plant comparative genomics resource
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D947-D953; doi:10.1093/nar/gkm968 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Eva Grafahrend-Belau, Stephan Weise, Dirk Koschützki, Uwe Scholz, Björn H. Junker, and Falk Schreiber
MetaCrop: a detailed database of crop plant metabolism
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D954-D958; doi:10.1093/nar/gkm835 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jon Duvick, Ann Fu, Usha Muppirala, Mukul Sabharwal, Matthew D. Wilkerson, Carolyn J. Lawrence, Carol Lushbough, and Volker Brendel
PlantGDB: a resource for comparative plant genomics
Nucleic Acids Research Advance Access published on December 6, 2007
Nucl. Acids Res. 2008 36: D959-D965; doi:10.1093/nar/gkm1041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

An-Yuan Guo, Xin Chen, Ge Gao, He Zhang, Qi-Hui Zhu, Xiao-Chuan Liu, Ying-Fu Zhong, Xiaocheng Gu, Kun He, and Jingchu Luo
PlantTFDB: a comprehensive plant transcription factor database
Nucleic Acids Research Advance Access published on October 12, 2007
Nucl. Acids Res. 2008 36: D966-D969; doi:10.1093/nar/gkm841 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

P. Kerr Wall, Jim Leebens-Mack, Kai F. Müller, Dawn Field, Naomi S. Altman, and Claude W. dePamphilis
PlantTribes: a gene and gene family resource for comparative genomics in plants
Nucleic Acids Research Advance Access published on December 10, 2007
Nucl. Acids Res. 2008 36: D970-D976; doi:10.1093/nar/gkm972 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yoshiharu Y. Yamamoto and Junichi Obokata
ppdb: a plant promoter database
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D977-D981; doi:10.1093/nar/gkm785 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tyler W. H. Backman, Christopher M. Sullivan, Jason S. Cumbie, Zachary A. Miller, Elisabeth J. Chapman, Noah Fahlgren, Scott A. Givan, James C. Carrington, and Kristin D. Kasschau
Update of ASRP: the Arabidopsis Small RNA Project database
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D982-D985; doi:10.1093/nar/gkm997 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Séverine Gagnot, Jean-Philippe Tamby, Marie-Laure Martin-Magniette, Frédérique Bitton, Ludivine Taconnat, Sandrine Balzergue, Sébastien Aubourg, Jean-Pierre Renou, Alain Lecharny, and Véronique Brunaud
CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D986-D990; doi:10.1093/nar/gkm757 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

M. G. Conte, S. Gaillard, N. Lanau, M. Rouard, and C. Périn
GreenPhylDB: a database for plant comparative genomics
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D991-D998; doi:10.1093/nar/gkm934 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yixue Li, and Tieliu Shi
AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D999-D1008; doi:10.1093/nar/gkm844 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David Swarbreck, Christopher Wilks, Philippe Lamesch, Tanya Z. Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang, and Eva Huala
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D1009-D1014; doi:10.1093/nar/gkm965 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Joshua L. Heazlewood, Pawel Durek, Jan Hummel, Joachim Selbig, Wolfram Weckwerth, Dirk Walther, and Waltraud X. Schulze
PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D1015-D1021; doi:10.1093/nar/gkm812 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Pierre Larmande, Céline Gay, Mathias Lorieux, Christophe Périn, Matthieu Bouniol, Gaëtan Droc, Christophe Sallaud, Pascual Perez, Isabelle Barnola, Corinne Biderre-Petit, Jérôme Martin, Jean Benoît Morel, Alexander A. T. Johnson, Fabienne Bourgis, Alain Ghesquière, Manuel Ruiz, Brigitte Courtois, and Emmanuel Guiderdoni
Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D1022-D1027; doi:10.1093/nar/gkm762 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rice Annotation Project
The Rice Annotation Project Database (RAP-DB): 2008 update
Nucleic Acids Research Advance Access published on December 17, 2007
Nucl. Acids Res. 2008 36: D1028-D1033; doi:10.1093/nar/gkm978 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sook Jung, Margaret Staton, Taein Lee, Anna Blenda, Randall Svancara, Albert Abbott, and Dorrie Main
GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D1034-D1040; doi:10.1093/nar/gkm803 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Payan Canaran, Edward S. Buckler, Jeffrey C. Glaubitz, Lincoln Stein, Qi Sun, Wei Zhao, and Doreen Ware
Panzea: an update on new content and features
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D1041-D1043; doi:10.1093/nar/gkm1022 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guo-Zhang Wu, Qiu-Ming Shi, Ya Niu, Mei-Qing Xing, and Hong-Wei Xue
Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2008 36: D1044-D1047; doi:10.1093/nar/gkm780 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

V. Aidinis, C. Chandras, M. Manoloukos, A. Thanassopoulou, K. Kranidioti, M. Armaka, E. Douni, D. L. Kontoyiannis, M. Zouberakis, G. Kollias, and the Mugen NoE consortium
MUGEN mouse database; Animal models of human immunological diseases
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D1048-D1054; doi:10.1093/nar/gkm838 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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