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Previous Next 		Contents: Volume 35, Database issue    January 2007    [Index by Author] 
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Editorial:Back

Alex Batemen
EDITORIAL
Nucl. Acids Res. 2007 35: D1-D2; doi:10.1093/nar/gkl1051 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:Back

Michael Y. Galperin
The Molecular Biology Database Collection: 2007 update
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D3-D4; doi:10.1093/nar/gkl1008 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Database Summaries] [Request Permissions]  

David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Vadim Miller, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, and Eugene Yaschenko
Database resources of the National Center for Biotechnology Information
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D5-D12; doi:10.1093/nar/gkl1031 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hideaki Sugawara, Takashi Abe, Takashi Gojobori, and Yoshio Tateno
DDBJ working on evaluation and classification of bacterial genes in INSDC
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D13-D15; doi:10.1093/nar/gkl908 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Carola Kanz, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Sheila Plaister, Siamak Sobhany, Peter Stoehr, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler
EMBL Nucleotide Sequence Database in 2006
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D16-D20; doi:10.1093/nar/gkl913 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
GenBank
Nucl. Acids Res. 2007 35: D21-D25; doi:10.1093/nar/gkl986 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Donna Maglott, Jim Ostell, Kim D. Pruitt, and Tatiana Tatusova
Entrez Gene: gene-centered information at NCBI
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D26-D31; doi:10.1093/nar/gkl993 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

C. Dieterich, M. W. Franz, and M. Vingron
Developments in CORG: a gene-centric comparative genomics resource
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D32-D35; doi:10.1093/nar/gkl977 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sunil Archak, Eshwar Meduri, P. Sravana Kumar, and J. Nagaraju
InSatDb: a microsatellite database of fully sequenced insect genomes
Nucleic Acids Research Advance Access published on November 1, 2006
Nucl. Acids Res. 2007 35: D36-D39; doi:10.1093/nar/gkl778 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Conrad A. Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J. Benham, and Anne D. Donaldson
OriDB: a DNA replication origin database
Nucleic Acids Research Advance Access published on October 25, 2006
Nucl. Acids Res. 2007 35: D40-D46; doi:10.1093/nar/gkl758 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Byungwook Lee, Taehyung Kim, Seon-Kyu Kim, Kwang H. Lee, and Doheon Lee
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications
Nucleic Acids Research Advance Access published on November 3, 2006
Nucl. Acids Res. 2007 35: D47-D50; doi:10.1093/nar/gkl807 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lei Bao, Mi Zhou, Ligang Wu, Lu Lu, Dan Goldowitz, Robert W. Williams, and Yan Cui
PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D51-D54; doi:10.1093/nar/gkl797 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul Harrrison, and Mark Gerstein
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D55-D60; doi:10.1093/nar/gkl851 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D61-D65; doi:10.1093/nar/gkl842 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cristian Chaparro, Romain Guyot, Andrea Zuccolo, Benoît Piégu, and Olivier Panaud
RetrOryza: a database of the rice LTR-retrotransposons
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2007 35: D66-D70; doi:10.1093/nar/gkl780 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

I. Agrafioti and M. P. H. Stumpf
SNPSTR: a database of compound microsatellite-SNP markers
Nucl. Acids Res. 2007 35: D71-D75; doi:10.1093/nar/gkl806 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gang Wu, Yuanpu Zheng, Imran Qureshi, Htar Thant Zin, Tyler Beck, Blazej Bulka, and Stephen J. Freeland
SGDB: a database of synthetic genes re-designed for optimizing protein over-expression
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2007 35: D76-D79; doi:10.1093/nar/gkl648 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yevgeniy Gelfand, Alfredo Rodriguez, and Gary Benson
TRDB—The Tandem Repeats Database
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D80-D87; doi:10.1093/nar/gkl1013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Axel Visel, Simon Minovitsky, Inna Dubchak, and Len A. Pennacchio
VISTA Enhancer Browser—a database of tissue-specific human enhancers
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D88-D92; doi:10.1093/nar/gkl822 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, and Christopher Lee
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D93-D98; doi:10.1093/nar/gkl884 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yeunsook Lee, Younghee Lee, Bumjin Kim, Youngah Shin, Seungyoon Nam, Pora Kim, Namshin Kim, Won-Hyong Chung, Jaesang Kim, and Sanghyuk Lee
ECgene: an alternative splicing database update
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D99-D103; doi:10.1093/nar/gkl992 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, and Tadashi Imanishi
H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D104-D109; doi:10.1093/nar/gkl854 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tyler S. Alioto
U12DB: a database of orthologous U12-type spliceosomal introns
Nucleic Acids Research Advance Access published on November 1, 2006
Nucl. Acids Res. 2007 35: D110-D115; doi:10.1093/nar/gkl796 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anil G. Jegga, Jing Chen, Sivakumar Gowrisankar, Mrunal A. Deshmukh, RangaChandra Gudivada, Sue Kong, Vivek Kaimal, and Bruce J. Aronow
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
Nucleic Acids Research Advance Access published on December 18, 2006
Nucl. Acids Res. 2007 35: D116-D121; doi:10.1093/nar/gkl1011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, and Mathieu Blanchette
PReMod: a database of genome-wide mammalian cis-regulatory module predictions
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D122-D126; doi:10.1093/nar/gkl879 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mikhail Pachkov, Ionas Erb, Nacho Molina, and Erik van Nimwegen
SwissRegulon: a database of genome-wide annotations of regulatory sites
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D127-D131; doi:10.1093/nar/gkl857 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, and Julio Collado-Vides
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D132-D136; doi:10.1093/nar/gkl800 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

C. Jiang, Z. Xuan, F. Zhao, and M. Q. Zhang
TRED: a transcriptional regulatory element database, new entries and other development
Nucl. Acids Res. 2007 35: D137-D140; doi:10.1093/nar/gkl1041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tao He, Pufeng Du, and Yanda Li
dbRES: a web-oriented database for annotated RNA editing sites
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D141-D144; doi:10.1093/nar/gkl815 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, and Kiyoshi Asai
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D145-D148; doi:10.1093/nar/gkl837 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Molly Megraw, Praveen Sethupathy, Benoit Corda, and Artemis G. Hatzigeorgiou
miRGen: a database for the study of animal microRNA genomic organization and function
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D149-D155; doi:10.1093/nar/gkl904 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yong Zhang, Jiongtang Li, Lei Kong, Ge Gao, Qing-Rong Liu, and Liping Wei
NATsDB: Natural Antisense Transcripts DataBase
Nucleic Acids Research Advance Access published on November 1, 2006
Nucl. Acids Res. 2007 35: D156-D161; doi:10.1093/nar/gkl782 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maciej Szymanski, Volker A. Erdmann, and Jan Barciszewski
Noncoding RNAs database (ncRNAdb)
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D162-D164; doi:10.1093/nar/gkl994 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ju Youn Lee, Ijen Yeh, Ji Yeon Park, and Bin Tian
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes
Nucl. Acids Res. 2007 35: D165-D168; doi:10.1093/nar/gkl870 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. R. Cole, B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, G. M. Garrity, and J. M. Tiedje
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D169-D172; doi:10.1093/nar/gkl889 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ernesto Picardi, Teresa Maria Rosaria Regina, Axel Brennicke, and Carla Quagliariello
REDIdb: the RNA editing database
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D173-D177; doi:10.1093/nar/gkl793 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ken C. Pang, Stuart Stephen, Marcel E. Dinger, Pär G. Engström, Boris Lenhard, and John S. Mattick
RNAdb 2.0—an expanded database of mammalian non-coding RNAs
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D178-D182; doi:10.1093/nar/gkl926 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jun Xie, Ming Zhang, Tao Zhou, Xia Hua, LiSha Tang, and Weilin Wu
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D183-D187; doi:10.1093/nar/gkl873 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, and Matthias Platzer
TassDB: a database of alternative tandem splice sites
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D188-D192; doi:10.1093/nar/gkl762 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

The UniProt Consortium
The Universal Protein Resource (UniProt)
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D193-D197; doi:10.1093/nar/gkl929 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, and Michael K. Gilson
BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D198-D201; doi:10.1093/nar/gkl999 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Di Wu, Feng Cui, Robert Jernigan, and Zhijun Wu
PIDD: database for Protein Inter-atomic Distance Distributions
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D202-D207; doi:10.1093/nar/gkl802 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andea Pierleoni, Pier Luigi Martelli, Piero Fariselli, and Rita Casadio
eSLDB: eukaryotic subcellular localization database
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D208-D212; doi:10.1093/nar/gkl775 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joshua L. Heazlewood, Robert E. Verboom, Julian Tonti-Filippini, Ian Small, and A. Harvey Millar
SUBA: the Arabidopsis Subcellular Database
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2007 35: D213-D218; doi:10.1093/nar/gkl863 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gonzalo Lopez, A. Valencia, and M. Tress
FireDB—a database of functionally important residues from proteins of known structure
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D219-D223; doi:10.1093/nar/gkl897 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Louise Daugherty, Mark Dibley, Robert Finn, Wolfgang Fleischmann, Julian Gough, Daniel Haft, Nicolas Hulo, Sarah Hunter, Daniel Kahn, Alexander Kanapin, Anish Kejariwal, Alberto Labarga, Petra S. Langendijk-Genevaux, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Anastasia N. Nikolskaya, Sandra Orchard, Christine Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, and Corin Yeats
New developments in the InterPro database
Nucl. Acids Res. 2007 35: D224-D228; doi:10.1093/nar/gkl841 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, and Manuela Helmer-Citterich
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D229-D231; doi:10.1093/nar/gkl922 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paolo Sonego, Mircea Pacurar, Somdutta Dhir, Attila Kertész-Farkas, András Kocsor, Zoltán Gáspári, Jack A.M. Leunissen, and Sándor Pongor
A Protein Classification Benchmark collection for machine learning
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D232-D236; doi:10.1093/nar/gkl812 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Aron Marchler-Bauer, John B. Anderson, Myra K. Derbyshire, Carol DeWeese-Scott, Noreen R. Gonzales, Marc Gwadz, Luning Hao, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Dmitri Krylov, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, and Stephen H. Bryant
CDD: a conserved domain database for interactive domain family analysis
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D237-D240; doi:10.1093/nar/gkl951 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Elon Portugaly, Nathan Linial, and Michal Linial
EVEREST: a collection of evolutionary conserved protein domains
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D241-D246; doi:10.1093/nar/gkl850 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Huaiyu Mi, Nan Guo, Anish Kejariwal, and Paul D. Thomas
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D247-D252; doi:10.1093/nar/gkl869 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard, and Alexey G. Murzin
SISYPHUS—structural alignments for proteins with non-trivial relationships
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2007 35: D253-D259; doi:10.1093/nar/gkl746 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-Giglio, William C. Nelson, Alexander R. Richter, and Owen White
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D260-D264; doi:10.1093/nar/gkl1043 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shalin Seebah, Anita Suresh, Shaowei Zhuo, Yong How Choong, Hazel Chua, Danny Chuon, Roger Beuerman, and Chandra Verma
Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D265-D268; doi:10.1093/nar/gkl866 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
REBASE—enzymes and genes for DNA restriction and modification
Nucl. Acids Res. 2007 35: D269-D270; doi:10.1093/nar/gkl891 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mark D'Souza, Elizabeth M. Glass, Mustafa H. Syed, Yi Zhang, Alexis Rodriguez, Natalia Maltsev, and Michael Y. Galperin
Sentra: a database of signal transduction proteins for comparative genome analysis
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D271-D273; doi:10.1093/nar/gkl949 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Qinghu Ren, Kaixi Chen, and Ian T. Paulsen
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D274-D279; doi:10.1093/nar/gkl925 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Philip Toukach, Hiren J Joshi, René Ranzinger, Yuri Knirel, and Claus-W. von der Lieth
Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de
Nucl. Acids Res. 2007 35: D280-D286; doi:10.1093/nar/gkl883 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Frank, T. Lütteke, and C.-W. von der Lieth
GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages
Nucl. Acids Res. 2007 35: 287-290; doi:10.1093/nar/gkl907 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison Cuff, Tim Dallman, Mark Dibley, Oliver Redfern, Frances Pearl, Rekha Nambudiry, Adam Reid, Ian Sillitoe, Corin Yeats, Janet M. Thornton, and Christine A. Orengo
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D291-D297; doi:10.1093/nar/gkl959 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer, Jane He, Siqian He, Shennan Lu, Thomas Madej, Aron Marchler-Bauer, Paul A. Thiessen, Naigong Zhang, and Stephen H. Bryant
MMDB: annotating protein sequences with Entrez's 3D-structure database
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D298-D300; doi:10.1093/nar/gkl952 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Helen Berman, Kim Henrick, Haruki Nakamura, and John L. Markley
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D301-D303; doi:10.1093/nar/gkl971 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kate F. Fulton, Mark A. Bate, Noel G. Faux, Khalid Mahmood, Chris Betts, and Ashley M. Buckle
Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D304-D307; doi:10.1093/nar/gkl1007 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Derek Wilson, Martin Madera, Christine Vogel, Cyrus Chothia, and Julian Gough
The SUPERFAMILY database in 2007: families and functions
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D308-D313; doi:10.1093/nar/gkl910 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Michael Gromiha, Yukimitsu Yabuki, Srinesh Kundu, Sivasundaram Suharnan, and Makiko Suwa
TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D314-D316; doi:10.1093/nar/gkl805 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chesley M. Leslin, Alexej Abyzov, and Valentin A. Ilyin
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
Nucleic Acids Research Advance Access published on October 25, 2006
Nucl. Acids Res. 2007 35: D317-D321; doi:10.1093/nar/gkl809 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gil Alterovitz, Michael Xiang, Mamta Mohan, and Marco F. Ramoni
GO PaD: the Gene Ontology Partition Database
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D322-D327; doi:10.1093/nar/gkl799 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Yuying Tian and Allan W. Dickerman
GeneTrees: a phylogenomics resource for prokaryotes
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D328-D331; doi:10.1093/nar/gkl905 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

T. Ryan Gregory, James A. Nicol, Heidi Tamm, Bellis Kullman, Kaur Kullman, Ilia J. Leitch, Brian G. Murray, Donald F. Kapraun, Johann Greilhuber, and Michael D. Bennett
Eukaryotic genome size databases
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D332-D338; doi:10.1093/nar/gkl828 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, and Hideaki Sugawara
Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: D339-D342; doi:10.1093/nar/gkl1004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ikuo Uchiyama
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D343-D346; doi:10.1093/nar/gkl978 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross Overbeek, and Rick Stevens
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D347-D353; doi:10.1093/nar/gkl947 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Louise Riley, Thorsten Schmidt, Irena I. Artamonova, Christian Wagner, Andreas Volz, Klaus Heumann, Hans-Werner Mewes, and Dmitrij Frishman
PEDANT genome database: 10 years online
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D354-D357; doi:10.1093/nar/gkl1005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christian von Mering, Lars J. Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, and Peer Bork
STRING 7—recent developments in the integration and prediction of protein interactions
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D358-D362; doi:10.1093/nar/gkl825 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christophe Combet, Nicolas Garnier, Céline Charavay, Delphine Grando, Daniel Crisan, Julien Lopez, Alexandre Dehne-Garcia, Christophe Geourjon, Emmanuel Bettler, Chantal Hulo, Philippe Le Mercier, Ralf Bartenschlager, Helmut Diepolder, Darius Moradpour, Jean-Michel Pawlotsky, Charles M. Rice, Christian Trépo, François Penin, and Gilbert Deléage
euHCVdb: the European hepatitis C virus database
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D363-D366; doi:10.1093/nar/gkl970 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Saravanamuttu Gnaneshan, Samreen Ijaz, Joanne Moran, Mary Ramsay, and Jonathan Green
HepSEQ: International Public Health Repository for Hepatitis B
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D367-D370; doi:10.1093/nar/gkl874 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Calvin Pan, Joseph Kim, Lamei Chen, Qi Wang, and Christopher Lee
The HIV positive selection mutation database
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D371-D375; doi:10.1093/nar/gkl855 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Suhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang, Jun Yu, and Jing Wang
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research
Nucleic Acids Research Advance Access published on October 25, 2006
Nucl. Acids Res. 2007 35: D376-D380; doi:10.1093/nar/gkl779 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu, Justin Bo-Kai Hsu, and Hsien-Da Huang
ViTa: prediction of host microRNAs targets on viruses
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D381-D385; doi:10.1093/nar/gkl1009 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luke E. Ulrich and Igor B. Zhulin
MiST: a microbial signal transduction database
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D386-D390; doi:10.1093/nar/gkl932 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

C. E. Zhou, J. Smith, M. Lam, A. Zemla, M. D. Dyer, and T. Slezak
MvirDB—a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D391-D394; doi:10.1093/nar/gkl791 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sung Ho Yoon, Young-Kyu Park, Soohyun Lee, Doil Choi, Tae Kwang Oh, Cheol-Goo Hur, and Jihyun F. Kim
Towards pathogenomics: a web-based resource for pathogenicity islands
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D395-D400; doi:10.1093/nar/gkl790 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

E. E. Snyder, N. Kampanya, J. Lu, E. K. Nordberg, H. R. Karur, M. Shukla, J. Soneja, Y. Tian, T. Xue, H. Yoo, F. Zhang, C. Dharmanolla, N. V. Dongre, J. J. Gillespie, J. Hamelius, M. Hance, K. I. Huntington, D. Jukneliene, J. Koziski, L. Mackasmiel, S. P. Mane, V. Nguyen, A. Purkayastha, J. Shallom, G. Yu, Y. Guo, J. Gabbard, D. Hix, A. F. Azad, S. C. Baker, S. M. Boyle, Y. Khudyakov, X. J. Meng, C. Rupprecht, J. Vinje, O. R. Crasta, M. J. Czar, A. Dickerman, J. D. Eckart, R. Kenyon, R. Will, J. C. Setubal, and B. W. S. Sobral
PATRIC: The VBI PathoSystems Resource Integration Center
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D401-D406; doi:10.1093/nar/gkl858 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexei E. Kazakov, Michael J. Cipriano, Pavel S. Novichkov, Simon Minovitsky, Dmitry V. Vinogradov, Adam Arkin, Andrey A. Mironov, Mikhail S. Gelfand, and Inna Dubchak
RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D407-D412; doi:10.1093/nar/gkl865 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kim Brügger
The Sulfolobus database
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D413-D415; doi:10.1093/nar/gkl847 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chia-Hung Chang, Yu-Chung Chang, Anthony Underwood, Chien-Shun Chiou, and Cheng-Yan Kao
VNTRDB: a bacterial variable number tandem repeat locus database
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D416-D421; doi:10.1093/nar/gkl872 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bradley I. Arshinoff, Garret Suen, Eric M. Just, Sohel M. Merchant, Warren A. Kibbe, Rex L. Chisholm, and Roy D. Welch
Xanthusbase: adapting wikipedia principles to a model organism database
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D422-D426; doi:10.1093/nar/gkl881 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa Rhodes, John Miller, Eileen Kraemer, Christian J. Stoeckert, Jr., David S. Roos, and Jessica C. Kissinger
ApiDB: integrated resources for the apicomplexan bioinformatics resource center
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D427-D430; doi:10.1093/nar/gkl880 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Junichi Watanabe, Hiroyuki Wakaguri, Masahide Sasaki, Yutaka Suzuki, and Sumio Sugano
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D431-D438; doi:10.1093/nar/gkl1039 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Olivier Arnaiz, Scott Cain, Jean Cohen, and Linda Sperling
ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D439-D444; doi:10.1093/nar/gkl777 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Emmet A. O'Brien, Liisa B. Koski, Yue Zhang, LiuSong Yang, Eric Wang, Michael W. Gray, Gertraud Burger, and B. Franz Lang
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)
Nucl. Acids Res. 2007 35: D445-D451; doi:10.1093/nar/gkl770 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Prachi Shah, Gail Binkley, Christopher Lane, Stuart R. Miyasato, and Gavin Sherlock
Sequence resources at the Candida Genome Database
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D452-D456; doi:10.1093/nar/gkl899 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexandre Gattiker, Christa Niederhauser-Wiederkehr, James Moore, Leandro Hermida, and Michael Primig
The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D457-D462; doi:10.1093/nar/gkl957 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Kerstin Glaab, Pär Davidsson, Fabian Nilsson, Graham J. L. Kemp, Olle Nerman, and Anders Blomberg
PROPHECY—a yeast phenome database, update 2006
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D463-D467; doi:10.1093/nar/gkl1029 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Robert Nash, Shuai Weng, Ben Hitz, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Michael S. Livstone, Rose Oughtred, Julie Park, Marek Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Stuart Miyasato, Anand Sethuraman, Mark Schroeder, Kara Dolinski, David Botstein, and J. Michael Cherry
Expanded protein information at SGD: new pages and proteome browser
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D468-D471; doi:10.1093/nar/gkl931 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lisa R. Girard, Tristan J. Fiedler, Todd W. Harris, Felicia Carvalho, Igor Antoshechkin, Michael Han, Paul W. Sternberg, Lincoln D. Stein, and Martin Chalfie
WormBook: the online review of Caenorhabditis elegans biology
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D472-D475; doi:10.1093/nar/gkl894 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Liangjiang Wang, Suzhi Wang, Yonghua Li, Martin S. R. Paradesi, and Susan J. Brown
BeetleBase: the model organism database for Tribolium castaneum
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D476-D479; doi:10.1093/nar/gkl776 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Donald G. Gilbert
DroSpeGe: rapid access database for new Drosophila species genomes
Nucl. Acids Res. 2007 35: D480-D485; doi:10.1093/nar/gkl997 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Madeline A. Crosby, Joshua L. Goodman, Victor B. Strelets, Peili Zhang, William M. Gelbart, and The FlyBase Consortium
FlyBase: genomes by the dozen
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D486-D491; doi:10.1093/nar/gkl827 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thomas Horn, Zeynep Arziman, Juerg Berger, and Michael Boutros
GenomeRNAi: a database for cell-based RNAi phenotypes
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D492-D497; doi:10.1093/nar/gkl906 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christoph Dieterich, Waltraud Roeseler, Patrick Sobetzko, and Ralf J. Sommer
Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2007 35: D498-D502; doi:10.1093/nar/gkl804 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, David Emmert, Martin Hammond, Catherine A. Hill, Ryan C. Kennedy, Neil F. Lobo, M. Robert MacCallum, Greg Madey, Karine Megy, Seth Redmond, Susan Russo, David W. Severson, Eric O. Stinson, Pantelis Topalis, Evgeny M. Zdobnov, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, and Frank H. Collins
VectorBase: a home for invertebrate vectors of human pathogens
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D503-D505; doi:10.1093/nar/gkl960 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tamberlyn Bieri, Darin Blasiar, Philip Ozersky, Igor Antoshechkin, Carol Bastiani, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa Girard, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon McKay, Hans-Michael Müller, Cecilia Nakamura, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, Will Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Richard Durbin, Lincoln D. Stein, Paul W. Sternberg, and John Spieth
WormBase: new content and better access
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D506-D510; doi:10.1093/nar/gkl818 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jens Barthelmes, Christian Ebeling, Antje Chang, Ida Schomburg, and Dietmar Schomburg
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007
Nucl. Acids Res. 2007 35: D511-D514; doi:10.1093/nar/gkl972 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Noel M. O'Boyle, James W. Torrance, Peter Murray-Rust, John B. O. Mitchell, and Janet M. Thornton
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
Nucleic Acids Research Advance Access published on November 1, 2006
Nucl. Acids Res. 2007 35: D515-D520; doi:10.1093/nar/gkl774 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David S. Wishart, Dan Tzur, Craig Knox, Roman Eisner, An Chi Guo, Nelson Young, Dean Cheng, Kevin Jewell, David Arndt, Summit Sawhney, Chris Fung, Lisa Nikolai, Mike Lewis, Marie-Aude Coutouly, Ian Forsythe, Peter Tang, Savita Shrivastava, Kevin Jeroncic, Paul Stothard, Godwin Amegbey, David Block, David. D. Hau, James Wagner, Jessica Miniaci, Melisa Clements, Mulu Gebremedhin, Natalie Guo, Ying Zhang, Gavin E. Duggan, Glen D. MacInnis, Alim M. Weljie, Reza Dowlatabadi, Fiona Bamforth, Derrick Clive, Russ Greiner, Liang Li, Tom Marrie, Brian D. Sykes, Hans J. Vogel, and Lori Querengesser
HMDB: the Human Metabolome Database
Nucl. Acids Res. 2007 35: D521-D526; doi:10.1093/nar/gkl923 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis, Christopher K. Glass, Alfred H. Merrill, Jr, Robert C. Murphy, Christian R. H. Raetz, David W. Russell, and Shankar Subramaniam
LMSD: LIPID MAPS structure database
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D527-D532; doi:10.1093/nar/gkl838 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Claudia Choi, Richard Münch, Stefan Leupold, Johannes Klein, Inga Siegel, Bernhard Thielen, Beatrice Benkert, Martin Kucklick, Max Schobert, Jens Barthelmes, Christian Ebeling, Isam Haddad, Maurice Scheer, Andreas Grote, Karsten Hiller, Boyke Bunk, Kerstin Schreiber, Ida Retter, Dietmar Schomburg, and Dieter Jahn
SYSTOMONAS — an integrated database for systems biology analysis of Pseudomonas
Nucl. Acids Res. 2007 35: D533-D537; doi:10.1093/nar/gkl823 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

H. Craig Mak, Mike Daly, Bianca Gruebel, and Trey Ideker
CellCircuits: a database of protein network models
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D538-D545; doi:10.1093/nar/gkl937 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yoshinobu Igarashi, Alexey Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Jeffrey W. Smith, Andrei L. Osterman, and Adam Godzik
CutDB: a proteolytic event database
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D546-D549; doi:10.1093/nar/gkl813 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fedor Kolpakov, Vladimir Poroikov, Ruslan Sharipov, Yury Kondrakhin, Alexey Zakharov, Alexey Lagunin, Luciano Milanesi, and Alexander Kel
CYCLONET—an integrated database on cell cycle regulation and carcinogenesis
Nucl. Acids Res. 2007 35: D550-D556; doi:10.1093/nar/gkl912 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Arnaud Ceol, Andrew Chatr-aryamontri, Elena Santonico, Roberto Sacco, Luisa Castagnoli, and Gianni Cesareni
DOMINO: a database of domain–peptide interactions
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D557-D560; doi:10.1093/nar/gkl961 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

S. Kerrien, Y. Alam-Faruque, B. Aranda, I. Bancarz, A. Bridge, C. Derow, E. Dimmer, M. Feuermann, A. Friedrichsen, R. Huntley, C. Kohler, J. Khadake, C. Leroy, A. Liban, C. Lieftink, L. Montecchi-Palazzi, S. Orchard, J. Risse, K. Robbe, B. Roechert, D. Thorneycroft, Y. Zhang, R. Apweiler, and H. Hermjakob
IntAct—open source resource for molecular interaction data
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D561-D565; doi:10.1093/nar/gkl958 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David States, and H. V. Jagadish
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D566-D571; doi:10.1093/nar/gkl859 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrew Chatr-aryamontri, Arnaud Ceol, Luisa Montecchi Palazzi, Giuliano Nardelli, Maria Victoria Schneider, Luisa Castagnoli, and Gianni Cesareni
MINT: the Molecular INTeraction database
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D572-D574; doi:10.1093/nar/gkl950 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Petras J. Kundrotas and Emil Alexov
PROTCOM: searchable database of protein complexes enhanced with domain–domain structures
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2007 35: D575-D579; doi:10.1093/nar/gkl768 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Emily R. Jefferson, Thomas P. Walsh, Timothy J. Roberts, and Geoffrey J. Barton
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions
Nucl. Acids Res. 2007 35: D580-D589; doi:10.1093/nar/gkl836 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E. Wanker, and Matthias E. Futschik
UniHI: an entry gate to the human protein interactome
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: D590-D594; doi:10.1093/nar/gkl817 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kieran Hervold, Andrew Martin, Roger A. Kirkpatrick, Paul F. Mc Kenna, and F. A. Ramirez-Weber
Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D595-D598; doi:10.1093/nar/gkl1012 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fiona M. McCarthy, Susan M. Bridges, Nan Wang, G. Bryce Magee, W. Paul Williams, Dawn S. Luthe, and Shane C. Burgess
AgBase: a unified resource for functional analysis in agriculture
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D599-D603; doi:10.1093/nar/gkl936 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhi-Liang Hu, Eric Ryan Fritz, and James M. Reecy
AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D604-D609; doi:10.1093/nar/gkl946 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

T. J. P. Hubbard, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, S. Fitzgerald, J. Fernandez-Banet, S. Graf, S. Haider, M. Hammond, J. Herrero, R. Holland, K. Howe, K. Howe, N. Johnson, A. Kahari, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, C. Melsopp, K. Megy, P. Meidl, B. Ouverdin, A. Parker, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, J. Severin, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, M. Wood, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, A. Kasprzyk, G. Proctor, S. Searle, J. Smith, A. Ureta-Vidal, and E. Birney
Ensembl 2007
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D610-D617; doi:10.1093/nar/gkl996 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and Martin Ringwald
The mouse Gene Expression Database (GXD): 2007 update
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D618-D623; doi:10.1093/nar/gkl1003 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Raquel Egea, Sònia Casillas, Enol Fernández, Miquel Àngel Senar, and Antonio Barbadilla
MamPol: a database of nucleotide polymorphism in the Mammalia class
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D624-D629; doi:10.1093/nar/gkl833 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson, and the Mouse Genome Database Group
The mouse genome database (MGD): new features facilitating a model system
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D630-D637; doi:10.1093/nar/gkl940 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dale A. Begley, Debra M. Krupke, Matthew J. Vincent, John P. Sundberg, Carol J. Bult, and Janan T. Eppig
Mouse Tumor Biology Database (MTB): status update and future directions
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D638-D642; doi:10.1093/nar/gkl983 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Molly A. Bogue, Stephen C. Grubb, Terry P. Maddatu, and Carol J. Bult
Mouse Phenome Database (MPD)
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D643-D649; doi:10.1093/nar/gkl1049 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hirohide Uenishi, Tomoko Eguchi-Ogawa, Hiroki Shinkai, Naohiko Okumura, Kohei Suzuki, Daisuke Toki, Noriyuki Hamasima, and Takashi Awata
PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D650-D653; doi:10.1093/nar/gkl954 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jue Ruan, Yiran Guo, Heng Li, Yafeng Hu, Fei Song, Xin Huang, Karsten Kristiensen, Lars Bolund, and Jun Wang
PigGIS: Pig Genomic Informatics System
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D654-D657; doi:10.1093/nar/gkl808 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Simon N. Twigger, Mary Shimoyama, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob, and the RGD Team
The Rat Genome Database, update 2007—Easing the path from disease to data and back again
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D658-D662; doi:10.1093/nar/gkl988 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, Donna Karolchik, Galt P. Barber, Rachel A. Harte, Jennifer Hillman-Jackson, Robert M. Kuhn, Brooke L. Rhead, Kayla E. Smith, Archana Thakkapallayil, Ann S. Zweig, The ENCODE Project Consortium, David Haussler, and W. James Kent
The ENCODE Project at UC Santa Cruz
Nucleic Acids Research Advance Access published on December 13, 2006
Nucl. Acids Res. 2007 35: D663-D667; doi:10.1093/nar/gkl1017 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

R. M. Kuhn, D. Karolchik, A. S. Zweig, H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke, K. E. Smith, A. Siepel, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, J. S. Pedersen, F. Hsu, A. S. Hinrichs, R. A. Harte, M. Diekhans, H. Clawson, G. Bejerano, G. P. Barber, R. Baertsch, D. Haussler, and W. J. Kent
The UCSC genome browser database: update 2007
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D668-D673; doi:10.1093/nar/gkl928 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alecksandr Kutchma, Nayeem Quayum, and Jan Jensen
GeneSpeed: protein domain organization of the transcriptome
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D674-D679; doi:10.1093/nar/gkl990 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dongmei Zuo, Stephanie E. Mohr, Yanhui Hu, Elena Taycher, Andreas Rolfs, Jason Kramer, Janice Williamson, and Joshua LaBaer
PlasmID: a centralized repository for plasmid clone information and distribution
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D680-D684; doi:10.1093/nar/gkl898 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Koichiro Higasa, Katsuyuki Miyatake, Yoji Kukita, Tomoko Tahira, and Kenshi Hayashi
D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples
Nucleic Acids Research Advance Access published on December 13, 2006
Nucl. Acids Res. 2007 35: D685-D689; doi:10.1093/nar/gkl848 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sjozef van Baal, Polynikis Kaimakis, Manyphong Phommarinh, Daphne Koumbi, Harry Cuppens, Francesca Riccardino, Milan Macek, Jr, Charles R. Scriver, and George P. Patrinos
FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D690-D695; doi:10.1093/nar/gkl934 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Philip Groth, Nadia Pavlova, Ivan Kalev, Spas Tonov, Georgi Georgiev, Hans-Dieter Pohlenz, and Bertram Weiss
PhenomicDB: a new cross-species genotype/phenotype resource
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2007 35: D696-D699; doi:10.1093/nar/gkl662 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anil G. Jegga, Sivakumar Gowrisankar, Jing Chen, and Bruce J. Aronow
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D700-D706; doi:10.1093/nar/gkl826 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shengting Li, Lijia Ma, Heng Li, Søren Vang, Yafeng Hu, Lars Bolund, and Jun Wang
Snap: an integrated SNP annotation platform
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D707-D710; doi:10.1093/nar/gkl969 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jungsun Park, Sohyun Hwang, Yong Seok Lee, Sang-Cheol Kim, and Doheon Lee
SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D711-D715; doi:10.1093/nar/gkl962 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Daryl J. Thomas, Heather Trumbower, Andrew D. Kern, Brooke L. Rhead, Robert M. Kuhn, David Haussler, and W. James Kent
Variation resources at UC Santa Cruz
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D716-D720; doi:10.1093/nar/gkl953 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maureen E. Higgins, Martine Claremont, John E. Major, Chris Sander, and Alex E. Lash
CancerGenes: a gene selection resource for cancer genome projects
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D721-D726; doi:10.1093/nar/gkl811 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Wen-Hui Su, Chuan-Chuan Chao, Shiou-Hwei Yeh, Ding-Shinn Chen, Pei-Jer Chen, and Yuh-Shan Jou
OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D727-D731; doi:10.1093/nar/gkl845 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Suisheng Tang, Zhuo Zhang, Sin Lam Tan, Man-Hung Eric Tang, Arun Prashanth Kumar, Suresh Kumar Ramadoss, and Vladimir B. Bajic
KBERG: KnowledgeBase for Estrogen Responsive Genes
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D732-D736; doi:10.1093/nar/gkl816 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Wuxue Zhang, Yong Zhang, Hui Zheng, Chen Zhang, Wei Xiong, John G. Olyarchuk, Michael Walker, Weifeng Xu, Min Zhao, Shuqi Zhao, Zhuan Zhou, and Liping Wei
SynDB: a Synapse protein DataBase based on synapse ontology
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D737-D741; doi:10.1093/nar/gkl876 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erin M. Hulbert, Luc J. Smink, Ellen C. Adlem, James E. Allen, David B. Burdick, Oliver S. Burren, Christopher C. Cavnor, Geoffrey E. Dolman, Daisy Flamez, Karen F. Friery, Barry C. Healy, Sarah A. Killcoyne, Burak Kutlu, Helen Schuilenburg, Neil M. Walker, Josyf Mychaleckyj, Decio L. Eizirik, Linda S. Wicker, John A. Todd, and Nathan Goodman
T1DBase: integration and presentation of complex data for type 1 diabetes research
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D742-D746; doi:10.1093/nar/gkl933 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

H. Parkinson, M. Kapushesky, M. Shojatalab, N. Abeygunawardena, R. Coulson, A. Farne, E. Holloway, N. Kolesnykov, P. Lilja, M. Lukk, R. Mani, T. Rayner, A. Sharma, E. William, U. Sarkans, and A. Brazma
ArrayExpress—a public database of microarray experiments and gene expression profiles
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D747-D750; doi:10.1093/nar/gkl995 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joan M. Mazzarelli, John Brestelli, Regina K. Gorski, Junmin Liu, Elisabetta Manduchi, Deborah F. Pinney, Jonathan Schug, Peter White, Klaus H. Kaestner, and Christian J. Stoeckert, Jr
EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes
Nucleic Acids Research Advance Access published on October 27, 2006
Nucl. Acids Res. 2007 35: D751-D755; doi:10.1093/nar/gkl748 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fei Pan, Chi-Hsien Chiu, Sudip Pulapura, Michael R. Mehan, Juan Nunez-Iglesias, Kangyu Zhang, Kiran Kamath, Michael S. Waterman, Caleb E. Finch, and Xianghong Jasmine Zhou
Gene Aging Nexus: a web database and data mining platform for microarray data on aging
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D756-D759; doi:10.1093/nar/gkl798 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, and Ron Edgar
NCBI GEO: mining tens of millions of expression profiles—database and tools update
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D760-D765; doi:10.1093/nar/gkl887 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Janos Demeter, Catherine Beauheim, Jeremy Gollub, Tina Hernandez-Boussard, Heng Jin, Donald Maier, John C. Matese, Michael Nitzberg, Farrell Wymore, Zachariah K. Zachariah, Patrick O. Brown, Gavin Sherlock, and Catherine A. Ball
The Stanford Microarray Database: implementation of new analysis tools and open source release of software
Nucleic Acids Research Advance Access published on December 20, 2006
Nucl. Acids Res. 2007 35: D766-D770; doi:10.1093/nar/gkl1019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yanling Zhang, Yong Zhang, Jun Adachi, Jesper V. Olsen, Rong Shi, Gustavo de Souza, Erica Pasini, Leonard J. Foster, Boris Macek, Alexandre Zougman, Chanchal Kumar, Jacek R. Wisniewski, Wang Jun, and Matthias Mann
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D771-D779; doi:10.1093/nar/gkl784 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yi-Bu Chen, Ansuman Chattopadhyay, Phillip Bergen, Cynthia Gadd, and Nancy Tannery
The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System—a one-stop gateway to online bioinformatics databases and software tools
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D780-D785; doi:10.1093/nar/gkl781 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Megan Sickmeier, Justin A. Hamilton, Tanguy LeGall, Vladimir Vacic, Marc S. Cortese, Agnes Tantos, Beata Szabo, Peter Tompa, Jake Chen, Vladimir N. Uversky, Zoran Obradovic, and A. Keith Dunker
DisProt: the Database of Disordered Proteins
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D786-D793; doi:10.1093/nar/gkl893 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

C. J. Zheng, L. Y. Han, B. Xie, C. Y. Liew, S. Ong, J. Cui, H. L. Zhang, Z. Q. Tang, S. H. Gan, L. Jiang, and Y. Z. Chen
PharmGED: Pharmacogenetic Effect Database
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D794-D799; doi:10.1093/nar/gkl853 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexander Loy, Frank Maixner, Michael Wagner, and Matthias Horn
probeBase—an online resource for rRNA-targeted oligonucleotide probes: new features 2007
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D800-D804; doi:10.1093/nar/gkl856 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Wenwu Cui, Dennis D. Taub, and Kevin Gardner
qPrimerDepot: a primer database for quantitative real time PCR
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2007 35: D805-D809; doi:10.1093/nar/gkl767 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nuwee Wiwatwattana, Christopher M. Landau, G. Jamie Cope, Gabriel A. Harp, and Anuj Kumar
Organelle DB: an updated resource of eukaryotic protein localization and function
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D810-D814; doi:10.1093/nar/gkl1000 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Agatha Schlüter, Stéphane Fourcade, Enric Domènech-Estévez, Toni Gabaldón, Jaime Huerta-Cepas, Guillaume Berthommier, Raymond Ripp, Ronald J. A. Wanders, Olivier Poch, and Aurora Pujol
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D815-D822; doi:10.1093/nar/gkl935 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Eduardo Ruiz-Pesini, Marie T. Lott, Vincent Procaccio, Jason C. Poole, Marty C. Brandon, Dan Mishmar, Christina Yi, James Kreuziger, Pierre Baldi, and Douglas C. Wallace
An enhanced MITOMAP with a global mtDNA mutational phylogeny
Nucleic Acids Research Advance Access published on December 18, 2006
Nucl. Acids Res. 2007 35: D823-D828; doi:10.1093/nar/gkl927 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cameron Johnson, Lewis Bowman, Alex T. Adai, Vicki Vance, and Venkatesan Sundaresan
CSRDB: a small RNA integrated database and browser resource for cereals
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D829-D833; doi:10.1093/nar/gkl991 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Manuel Spannagl, Octave Noubibou, Dirk Haase, Li Yang, Heidrun Gundlach, Tobias Hindemitt, Kathrin Klee, Georg Haberer, Heiko Schoof, and Klaus F. X. Mayer
MIPSPlantsDB—plant database resource for integrative and comparative plant genome research
Nucl. Acids Res. 2007 35: D834-D840; doi:10.1093/nar/gkl945 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lorenz Bülow, Martin Schindler, and Reinhard Hehl
PathoPlant®: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D841-D845; doi:10.1093/nar/gkl835 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kevin L. Childs, John P. Hamilton, Wei Zhu, Eugene Ly, Foo Cheung, Hank Wu, Pablo D. Rabinowicz, Chris D. Town, C. Robin Buell, and Agnes P. Chan
The TIGR Plant Transcript Assemblies database
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D846-D851; doi:10.1093/nar/gkl785 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nigel S. Walker, Nicholas Stiffler, and Alice Barkan
POGs/PlantRBP: a resource for comparative genomics in plants
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D852-D856; doi:10.1093/nar/gkl795 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Claudia Galuschka, Martin Schindler, Lorenz Bülow, and Reinhard Hehl
AthaMap web tools for the analysis and identification of co-regulated genes
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D857-D862; doi:10.1093/nar/gkl1006 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, and Hiroyuki Ohta
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D863-D869; doi:10.1093/nar/gkl783 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Timothy A. Erwin, Erica G. Jewell, Christopher G. Love, Geraldine A. C. Lim, Xi Li, Ross Chapman, Jacqueline Batley, Jason E. Stajich, Emmanuel Mongin, Elia Stupka, Bruce Ross, German Spangenberg, and David Edwards
BASC: an integrated bioinformatics system for Brassica research
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D870-D873; doi:10.1093/nar/gkl998 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yong Li, Mario G. Rosso, Prisca Viehoever, and Bernd Weisshaar
GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2007 35: D874-D878; doi:10.1093/nar/gkl753 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Huazong Zeng, Lijun Luo, Weixiong Zhang, Jie Zhou, Zuofeng Li, Hongyan Liu, Tiansheng Zhu, Xiangqian Feng, and Yang Zhong
PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D879-D882; doi:10.1093/nar/gkl814 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shu Ouyang, Wei Zhu, John Hamilton, Haining Lin, Matthew Campbell, Kevin Childs, Françoise Thibaud-Nissen, Renae L. Malek, Yuandan Lee, Li Zheng, Joshua Orvis, Brian Haas, Jennifer Wortman, and C. Robin Buell
The TIGR Rice Genome Annotation Resource: improvements and new features
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D883-D887; doi:10.1093/nar/gkl976 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nathalie Pavy, James J. Johnson, John A. Crow, Charles Paule, Timothy Kunau, John MacKay, and Ernest F. Retzel
ForestTreeDB: a database dedicated to the mining of tree transcriptomes
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D888-D894; doi:10.1093/nar/gkl882 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Carolyn J. Lawrence, Mary L. Schaeffer, Trent E. Seigfried, Darwin A. Campbell, and Lisa C. Harper
MaizeGDB's new data types, resources and activities
Nucl. Acids Res. 2007 35: D895-D900; doi:10.1093/nar/gkl1048 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nunzio D'Agostino, Mario Aversano, Luigi Frusciante, and Maria Luisa Chiusano
TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D901-D905; doi:10.1093/nar/gkl921 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Stefan Günther, Dorothea Hempel, Mathias Dunkel, Kristian Rother, and Robert Preissner
SuperHapten: a comprehensive database for small immunogenic compounds
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D906-D910; doi:10.1093/nar/gkl849 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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