Volume 36, Number Database-Issue, January 2008

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  Alex Bateman: Editorial. 1

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  Michael Y. Galperin: The Molecular Biology Database Collection: 2008 update. 2-4
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  Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James K. Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim J. P. Hubbard, Ewan Birney: Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. 5-12
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  David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Martin Shumway, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko: Database resources of the National Center for Biotechnology Information. 13-21
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  Hideaki Sugawara, Osamu Ogasawara, Kousaku Okubo, Takashi Gojobori, Yoshio Tateno: DDBJ with new system and face. 22-24
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  Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler: GenBank. 25-30
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  Yu Zhou, Chen Lu, Qi-Jia Wu, Yu Wang, Zhi-Tao Sun, Jia-Cong Deng, Yi Zhang: GISSD: Group I Intron Sequence and Structure Database. 31-37
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  Carlos Lloréns, Ricardo Futami, D. Bezemer, Andres Moya: The Gypsy Database (GyDB) of mobile genetic elements. 38-46
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  Asaf Levy, Noa Sela, Gil Ast: TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. 47-52
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  Veenu Aishwarya, P. C. Sharma: UgMicroSatdb: database for mining microsatellites from unigenes. 53-56
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  Marco Mangone, Philip MacMenamin, Charles Zegar, Fabio Piano, Kristin C. Gunsalus: UTRome.org: a platform for 3'UTR biology in C. elegans. 57-62
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  Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, Ralf Zimmer: ProSAS: a database for analyzing alternative splicing in the context of protein structures. 63-68
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  Amrita Pati, Ying Jin, Karsten Klage, Richard F. Helm, Lenwood S. Heath, Naren Ramakrishnan: CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining. 69-76
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  Takeshi Obayashi, Shinpei Hayashi, Masayuki Shibaoka, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita: COXPRESdb: a database of coexpressed gene networks in mammals. 77-82
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  Lei Bao, Mi Zhou, Yan Cui: CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators. 83-87
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  Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, Sarah A. Teichmann: DBD--taxonomically broad transcription factor predictions: new content and functionality. 88-92
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  Nicolas Sierro, Yuko Makita, Michiel J. L. de Hoon, Kenta Nakai: DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. 93-96
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  Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai: DBTSS: database of transcription start sites, progress report 2008. 97-101
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  Jan Christian Bryne, Eivind Valen, Man-Hung Eric Tang, Troels Torben Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin: JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. 102-106
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  Obi L. Griffith, Stephen Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter J. De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth W. Wasserman, Ross C. Hardison, Casey M. Bergman, Steven J. M. Jones: ORegAnno: an open-access community-driven resource for regulatory annotation. 107-113
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  Gang-Qing Hu, Xiaobin Zheng, Yi-Fan Yang, Philippe Ortet, Zhen-Su She, Huaiqiu Zhu: ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. 114-119
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  Socorro Gama-Castro, Verónica Jiménez-Jacinto, Martín Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spínola, Bruno Contreras-Moreira, Juan Segura-Salazar, Luis Muñiz-Rascado, Irma Martínez-Flores, Heladia Salgado, César Bonavides-Martínez, Cei Abreu-Goodger, Carlos Rodríguez Penagos, Juan Miranda-Ríos, Enrique Morett, Enrique Merino, Araceli M. Huerta, Luis Treviño-Quintanilla, Julio Collado-Vides: RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. 120-124
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  Barrett C. Foat, Ronald G. Tepper, Harmen J. Bussemaker: TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. 125-131
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  Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d'Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas: YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. 132-136
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  Anason S. Halees, Rashad El-Badrawi, Khalid S. A. Khabar: ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse. 137-140
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  Oleg Kikin, Zachary Zappala, Lawrence D'Antonio, Paramjeet Singh Bagga: GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs. 141-148
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  Doron Betel, Manda Wilson, Aaron Gabow, Debora S. Marks, Chris Sander: The microRNA.org resource: targets and expression. 149-153
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  Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, Anton J. Enright: miRBase: tools for microRNA genomics. 154-158
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  Seungyoon Nam, Bumjin Kim, Seokmin Shin, Sanghyuk Lee: miRGator: an integrated system for functional annotation of microRNAs. 159-164
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  Sheng-Da Hsu, Chia-Huei Chu, Ann-Ping Tsou, Shu-Jen Chen, Hua-Chien Chen, Paul Wei-Che Hsu, Yung-Hao Wong, Yi-Hsuan Chen, Gian-Hung Chen, Hsien-Da Huang: miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. 165-169
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  Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, Runsheng Chen: NONCODE v2.0: decoding the non-coding. 170-172
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  S. Sai Lakshmi, Shipra Agrawal: piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. 173-177
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  Dorota Piekna-Przybylska, Wayne A. Decatur, Maurille J. Fournier: The 3D rRNA modification maps database: with interactive tools for ribosome analysis. 178-183
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  Sung-Chou Li, Cheng-Kai Shiau, Wen-chang Lin: Vir-Mir db: prediction of viral microRNA candidate hairpins. 184-189
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  The UniProt Consortium: The Universal Protein Resource (UniProt). 190-195
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  Hans-Werner Mewes, Sabine Dietmann, Dmitrij Frishman, Richard Gregory, Gertrud Mannhaupt, Klaus F. X. Mayer, Martin Münsterkötter, Andreas Ruepp, Manuel Spannagl, Volker Stümpflen, Thomas Rattei: MIPS: analysis and annotation of genome information in 2007. 196-201
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  Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, Minoru Kanehisa: AAindex: amino acid index database, progress report 2008. 202-205
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  Conan K. L. Wang, Quentin Kaas, Laurent Chiche, David J. Craik: CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. 206-210
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  Hua Cheng, Bong-Hyun Kim, Nick V. Grishin: MALISAM: a database of structurally analogous motifs in proteins. 211-217
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  Ganesan Pugalenthi, Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Saikat Chakrabarti: MegaMotifBase: a database of structural motifs in protein families and superfamilies. 218-221
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  David S. Wishart, David Arndt, Mark V. Berjanskii, Anchi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou, Guohui Lin: PPT-DB: the protein property prediction and testing database. 222-229
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  Josefine Sprenger, J. Lynn Fink, Seetha Karunaratne, Kelly Hanson, Nicholas A. Hamilton, Rohan D. Teasdale: LOCATE: a mammalian protein subcellular localization database. 230-233
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  Gábor E. Tusnády, Lajos Kalmár, István Simon: TOPDB: topology data bank of transmembrane proteins. 234-239
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  Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson: Phospho.ELM: a database of phosphorylation sites - update 2008. 240-244
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  Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Béatrice A. Cuche, Edouard De Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, Christian J. A. Sigrist: The 20 years of PROSITE. 245-249
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  Lars Juhl Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, Peer Bork: eggNOG: automated construction and annotation of orthologous groups of genes. 250-254
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  Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang, Yixue Li: EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. 255-262
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  Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, Erik L. L. Sonnhammer: InParanoid 6: eukaryotic ortholog clusters with inparalogs. 263-266
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  Andreas Heger, Chris P. Ponting: OPTIC: orthologous and paralogous transcripts in clades. 267-270
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  Evgenia V. Kriventseva, Nazim Rahman, Octavio Espinosa, Evgeni M. Zdobnov: OrthoDB: the hierarchical catalog of eukaryotic orthologs. 271-275
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  Andreas Heger, Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, Liisa Holm: PairsDB atlas of protein sequence space. 276-280
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  Robert D. Finn, John G. Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman: The Pfam protein families database. 281-288
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  Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, Hans-Werner Mewes: SIMAP - structuring the network of protein similarities. 289-292
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  Quan-Yuan He, Quan-Ze He, Xing-Can Deng, Lei Yao, Er Meng, Zhong-Hua Liu, Song-Ping Liang: ATDB: a uni-database platform for animal toxins. 293-297
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  Karla Gendler, Tara Paulsen, Carolyn Napoli: ChromDB: The Chromatin Database. 298-302
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  Jianwen Fang, Yinghua Dong, Nazila Salamat-Miller, C. Russell Middaugh: DB-PABP: a database of polyanion-binding proteins. 303-306
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  Charles J. Reedy, Margaret M. Elvekrog, Brian R. Gibney: Development of a heme protein structure-electrochemical function database. 307-313
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  Jérôme Gracy, Dung Le-Nguyen, Jean-Christophe Gelly, Quentin Kaas, Annie Heitz, Laurent Chiche: KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007. 314-319
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  Neil D. Rawlings, Fraser R. Morton, Chai Yin Kok, Jun Kong, Alan J. Barrett: MEROPS: the peptidase database. 320-325
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  Ségolène Caboche, Maude Pupin, Valérie Leclère, Arnaud Fontaine, Philippe Jacques, Gregory Kucherov: NORINE: a database of nonribosomal peptides. 326-331
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  Sergi Castellano, Vadim N. Gladyshev, Roderic Guigó, Marla J. Berry: SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements. 332-338
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  Joshua D. Podlevsky, Christopher J. Bley, Rebecca V. Omana, Xiaodong Qi, Julian J.-L. Chen: The Telomerase Database. 339-343
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  Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, Michael Ashburner: ChEBI: a database and ontology for chemical entities of biological interest. 344-350
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  Kathleen Petri Seiler, Gregory A. George, Mary Pat Happ, Nicole E. Bodycombe, Hyman A. Carrinski, Stephanie Norton, Steve Brudz, John P. Sullivan, Jeremy Muhlich, Martin Serrano, Paul Ferraiolo, Nicola J. Tolliday, Stuart L. Schreiber, Paul A. Clemons: ChemBank: a small-molecule screening and cheminformatics resource database. 351-359
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  François-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, Piotr Cieplak: R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries. 360-367
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  Taku Nakahara, Ryo Hashimoto, Hiroaki Nakagawa, Kenji Monde, Nobuaki Miura, Shin-Ichiro Nishimura: Glycoconjugate Data Bank: Structures - an annotated glycan structure database and N-glycan primary structure verification service. 368-371
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  Ren Zhang, Yan Lin, Chun-Ting Zhang: Greglist: a database listing potential G-quadruplex regulated genes. 372-376
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  Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, Jörg Schultz: The ITS2 Database II: homology modelling RNA structure for molecular systematics. 377-380
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  Vinod Kumar Yadav, James Kappukalayil Abraham, Prithvi Mani, Rashi Kulshrestha, Shantanu Chowdhury: QuadBase: genome-wide database of G4 DNA - occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes. 381-385
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  Mariusz Popenda, Marek Blazewicz, Marta Szachniuk, Ryszard W. Adamiak: RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. 386-391
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  Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, Bruce A. Shapiro: RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. 392-397
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  Fabian Birzele, Jan E. Gewehr, Ralf Zimmer: AutoPSI: a database for automatic structural classification of protein sequences and structures. 398-401
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  Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, John L. Markley: BioMagResBank. 402-408
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  Hidetoshi Kono, Tomo Yuasa, Shinya Nishiue, Kei Yura: coliSNP database server mapping nsSNPs on protein structures. 409-413
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  Corin Yeats, Jonathan G. Lees, Adam James Reid, Paul Kellam, Nigel J. Martin, Xinhui Liu, Christine A. Orengo: Gene3D: comprehensive structural and functional annotation of genomes. 414-418
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  Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin: Data growth and its impact on the SCOP database: new developments. 419-425
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  Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John M. C. Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard H. Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim Vranken, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman: Remediation of the protein data bank archive. 426-433
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  Andreas Schlicker, Mario Albrecht: FunSimMat: a comprehensive functional similarity database. 434-439
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  The Gene Ontology project in 2008. 440-444
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  Elspeth A. Bruford, Michael J. Lush, Mathew W. Wright, Tam P. Sneddon, Sue Povey, Ewan Birney: The HGNC Database in 2008: a resource for the human genome. 445-448
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  Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Yon Rhee, Martin M. Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, Doreen Ware: The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. 449-454
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  In Seok Yang, Chunsun Ryu, Ki Joon Cho, Jin Kwang Kim, Swee Hoe Ong, Wayne P. Mitchell, Bong Su Kim, Hee-Bok Oh, Kyung Hyun Kim: IDBD: Infectious Disease Biomarker Database. 455-460
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  Nicolas J. Tourasse, Anne-Brit Kolstø: SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis). 461-468
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  Pierre Lechat, Laurence Hummel, Sandrine Rousseau, Ivan Moszer: GenoList: an integrated environment for comparative analysis of microbial genomes. 469-474
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  Konstantinos Liolios, Konstantinos Mavrommatis, Nektarios Tavernarakis, Nikos Kyrpides: The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. 475-479
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  Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi: KEGG for linking genomes to life and the environment. 480-484
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  Emmanuel Courcelle, Yoann Beausse, Sébastien Letort, Olivier Stahl, Romain Fremez, Catherine Ngom-Bru, Jérôme Gouzy, Thomas Faraut: Narcisse: a mirror view of conserved syntenies. 485-490
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  Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, Toni Gabaldón: PhylomeDB: a database for genome-wide collections of gene phylogenies. 491-496
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  Burke Squires, Catherine Macken, Adolfo Garcia-Sastre, Shubhada Godbole, Jyothi Noronha, Victoria Hunt, Roger L. Chang, Christopher N. Larsen, Edward B. Klem, Kevin Biersack, Richard H. Scheuermann: BioHealthBase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence. 497-503
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  Yi Huang, Susanna K. P. Lau, Patrick C. Y. Woo, Kwok-yung Yuen: CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes. 504-511
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  Carla Kuiken, Peter Hraber, James Thurmond, Karina Yusim: The hepatitis C sequence database in Los Alamos. 512-516
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  Inti Pedroso, Gustavo Rivera, Felipe Lazo, Max Chacón, Francisco Ossandón, Felipe A. Veloso, David S. Holmes: AlterORF: a database of alternate open reading frames. 517-518
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  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, Thomas Hampton, Paul Liss, Michael Rusch, Matthew Shaker, Lorie Shaull, Panna Shetty, Silpa Thotakura, Jon Whitmore, Frederick R. Blattner, John M. Greene, Nicole T. Perna: Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. 519-523
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  Pere Puigbò, Antoni Romeu, Santiago Garcia-Vallvé: HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. 524-527
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  Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides: The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. 528-533
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  Victor M. Markowitz, Natalia Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Yuri Grechkin, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Philip Hugenholtz, Nikos Kyrpides: IMG/M: a data management and analysis system for metagenomes. 534-538
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  Jian Yang, Lihong Chen, Lilian Sun, Jun Yu, Qi Jin: VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. 539-542
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  Roy R. Chaudhuri, Nicholas J. Loman, Lori A. S. Snyder, Christopher M. Bailey, Dov J. Stekel, Mark J. Pallen: xBASE2: a comprehensive resource for comparative bacterial genomics. 543-546
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  Alberto M. R. Dávila, Pablo N. Mendes, Glauber Wagner, Diogo A. Tschoeke, Rafael R. C. Cuadrat, Felipe Liberman, Luciana Matos, Thiago S. Satake, Kary A. C. S. Ocaña, Omar Triana, Sérgio M. S. Cruz, Henrique C. L. Jucá, Juliano C. Cury, Fabricio N. Silva, Guilherme A. Geronimo, Margarita Ruiz, Eduardo Ruback, Floriano P. Silva Jr., Christian M. Probst, Edmundo C. Grisard, Marco A. Krieger, Samuel Goldenberg, Maria Cláudia Reis Cavalcanti, Milton O. Moraes, Maria Luiza Machado Campos, Marta Mattoso: ProtozoaDB: dynamic visualization and exploration of protozoan genomes. 547-552
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  Bindu Gajria, Amit Bahl, John Brestelli, Jennifer Dommer, Steve Fischer, Xin Gao, Mark Heiges, John Iodice, Jessica C. Kissinger, Aaron J. Mackey, Deborah F. Pinney, David S. Roos, Christian J. Stoeckert Jr., Haiming Wang, Brian P. Brunk: ToxoDB: an integrated Toxoplasma gondii database resource. 553-556
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  Tristan Rossignol, Pierre Lechat, Christina Cuomo, Qiandong Zeng, Ivan Moszer, Christophe d'Enfert: CandidaDB: a multi-genome database for Candida species and related Saccharomycotina. 557-561
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  Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Kwangyul Yu, Jaeyoung Choi, Sunghyung Kong, Jaejin Park, Seryun Kim, Hyojeong Kim, Soonok Kim, Jihyun F. Kim, Jaime E. Blair, Kwangwon Lee, Seogchan Kang, Yong-Hwan Lee: CFGP: a web-based, comparative fungal genomics platform. 562-571
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  Rainer Winnenburg, Martin Urban, Andrew M. Beacham, Thomas K. Baldwin, Sabrina Holland, Magdalen Lindeberg, Hilde Hansen, Christopher J. Rawlings, Kim E. Hammond-Kosack, Jacob Köhler: PHI-base update: additions to the pathogen-host interaction database. 572-576
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  Eurie L. Hong, Rama Balakrishnan, Qing Dong, Karen R. Christie, Julie Park, Gail Binkley, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kathy K. Zhu, Kara Dolinski, David Botstein, J. Michael Cherry: Gene Ontology annotations at SGD: new data sources and annotation methods. 577-581
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  Alexie Papanicolaou, Steffi Gebauer-Jung, Mark L. Blaxter, W. Owen McMillan, Chris D. Jiggins: ButterflyBase: a platform for lepidopteran genomics. 582-587
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  Robert J. Wilson, Joshua L. Goodman, Victor B. Strelets: FlyBase: integration and improvements to query tools. 588-593
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  Marc S. Halfon, Steven M. Gallo, Casey M. Bergman: REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. 594-598
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  Sofia M. C. Robb, Eric Ross, Alejandro Sánchez Alvarado: SmedGD: the Schmidtea mediterranea genome database. 599-606
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  James C. Sullivan, Adam M. Reitzel, John R. Finnerty: Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis. 607-611
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  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 J. McKay, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, Paul W. Sternberg: WormBase 2007. 612-617
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  Matthew Bashton, Irene Nobeli, Janet M. Thornton: PROCOGNATE: a cognate ligand domain mapping for enzymes. 618-622
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  Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne M. Paley, Seung Yon Rhee, Alexander Glennon Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang, Peter D. Karp: The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. 623-631
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  Chong Su, José M. Peregrin-Alvarez, Gareth Butland, Sadhna Phanse, Vincent Fong, Andrew Emili, John Parkinson: Bacteriome.org - an integrated protein interaction database for E. coli. 632-636
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  Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Michael S. Livstone, Rose Oughtred, Daniel H. Lackner, Jürg Bähler, Valerie Wood, Kara Dolinski, Mike Tyers: The BioGRID Interaction Database: 2008 update. 637-640
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  Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi: The cell cycle DB: a systems biology approach to cell cycle analysis. 641-645
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  Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou Doudieu, Volker Stümpflen, Hans-Werner Mewes: CORUM: the comprehensive resource of mammalian protein complexes. 646-650
• 
  Philipp Pagel, Matthias Oesterheld, Oksana Tovstukhina, Normann Strack, Volker Stümpflen, Dmitrij Frishman: DIMA 2.0 - predicted and known domain interactions. 651-655
• 
  Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, Raja Jothi: DOMINE: a database of protein domain interactions. 656-661
• 
  Emre Guney, Nurcan Tuncbag, Ozlem Keskin, Attila Gürsoy: HotSprint: database of computational hot spots in protein interfaces. 662-666
• 
  Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, Shoshana J. Wodak: LigASite - a database of biologically relevant binding sites in proteins with known apo-structures. 667-673
• 
  Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John E. Beaver, Peter Dresslar, Jason Nerothin, Heather A. Carlson: Binding MOAD, a high-quality protein-ligand database. 674-678
• 
  Wuming Gong, Dihan Zhou, Yongliang Ren, Yejun Wang, Zhixiang Zuo, Yanping Shen, Feifei Xiao, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao, Tongbin Li: PepCyber: P~PEP: a database of human protein-protein interactions mediated by phosphoprotein-binding domains. 679-683
• 
  Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, Peer Bork: STITCH: interaction networks of chemicals and proteins. 684-688
• 
  Jürgen Dönitz, Björn Goemann, Muriel Lizé, Holger Michael, Nicole Sasse, Edgar Wingender, Anatolij Potapov: EndoNet: an information resource about regulatory networks of cell-to-cell communication. 689-694
• 
  Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, Tony Pawson: NetworKIN: a resource for exploring cellular phosphorylation networks. 695-699
• 
  Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, Shankar Subramaniam: The Molecule Pages database. 700-706
• 
  Paul Flicek, Bronwen L. Aken, Kathryn Beal, Benoit Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, Tim Cutts, Thomas A. Down, S. C. Dyer, T. Eyre, Stephen Fitzgerald, Julio Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Kerstin Howe, Nathan Johnson, Andrew M. Jenkinson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Bethan Pritchard, Andreas Prlic, S. Rice, Daniel Rios, Michael Schuster, I. Sealy, Guy Slater, Damian Smedley, Giulietta Spudich, S. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, M. Wood, Ewan Birney, Tony Cox, Val Curwen, Richard Durbin, Xosé M. Fernández-Suarez, Javier Herrero, Tim J. P. Hubbard, Arek Kasprzyk, Glenn Proctor, James Smith, Abel Ureta-Vidal, Stephen M. J. Searle: Ensembl 2008. 707-714
• 
  Ann-Marie Mallon, Andrew Blake, John M. Hancock: EuroPhenome and EMPReSS: online mouse phenotyping resource. 715-718
• 
  Carl J. Schmidt, Michael Romanov, Oliver Ryder, Vincent Magrini, Matthew T. Hickenbotham, Jarret Glasscock, Sean McGrath, Elaine R. Mardis, Lincoln D. Stein: Gallus GBrowse: a unified genomic database for the chicken. 719-723
• 
  Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Judith A. Blake: The Mouse Genome Database (MGD): mouse biology and model systems. 724-728
• 
  Ling V. Sun, Ke Jin, Yiming Liu, Wenwei Yang, Xing Xie, Lin Ye, Li Wang, Lin Zhu, Sheng Ding, Yi Su, Jie Zhou, Min Han, Yuan Zhuang, Tian Xu, Xiaohui Wu, Ning Gu, Yang Zhong: PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice. 729-734
• 
  Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin: TreeFam: 2008 Update. 735-740
• 
  Guglielmo Roma, Marco Sardiello, Gilda Cobellis, Pedro Cruz, Giampiero Lago, Remo Sanges, Elia Stupka: The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones. 741-746
• 
  Budrul Ahsan, Daisuke Kobayashi, Tomoyuki Yamada, Masahiro Kasahara, Shin Sasaki, Taro L. Saito, Yukinobu Nagayasu, Koichiro Doi, Yoichiro Nakatani, Wei Qu, Tomoko Jindo, Atsuko Shimada, Kiyoshi Naruse, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda, Yuji Kohara, Shinichi Morishita: UTGB/medaka: genomic resource database for medaka biology. 747-752
• 
  L. G. Wilming, J. G. R. Gilbert, Kerstin Howe, S. Trevanion, Tim J. P. Hubbard, J. L. Harrow: The vertebrate genome annotation (Vega) database. 753-760
• 
  Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen, Nicolas Pollet, Peter D. Vize: Xenbase: a Xenopus biology and genomics resource. 761-767
• 
  Judy Sprague, Leyla Bayraktaroglu, Yvonne Bradford, Tom Conlin, Nathan Dunn, David Fashena, Ken Frazer, Melissa Haendel, Douglas G. Howe, Jonathan Knight, Prita Mani, Sierra A. T. Moxon, Christian Pich, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Xiang Shao, Amy Singer, Peiran Song, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield: The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. 768-772
• 
  Donna Karolchik, Robert M. Kuhn, Robert Baertsch, Galt P. Barber, Hiram Clawson, Mark Diekhans, Belinda Giardine, Rachel A. Harte, Angela S. Hinrichs, Fan Hsu, Kord M. Kober, Webb Miller, Jakob Skou Pedersen, Andy Pohl, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Kayla E. Smith, Mario Stanke, Archana Thakkapallayil, Heather Trumbower, Ting Wang, Ann S. Zweig, David Haussler, W. James Kent: The UCSC Genome Browser Database: 2008 update. 773-779
• 
  Tim Yates, Michal J. Okoniewski, Crispin J. Miller: X: Map: annotation and visualization of genome structure for Affymetrix exon array analysis. 780-786
• 
  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 Ota, 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, Takeshi Itoh: Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. 787-792
• 
  The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. 793-799
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  Gabrielle C. Nickel, David Tefft, Mark D. Adams: Human PAML browser: a database of positive selection on human genes using phylogenetic methods. 800-808
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  Julian Lange, Helen Skaletsky, George W. Bell, David C. Page: MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome. 809-814
• 
  Arti Singh, Adebayo Olowoyeye, Peter H. Baenziger, Jessica Dantzer, Maricel G. Kann, Predrag Radivojac, Randy Heiland, Sean D. Mooney: MutDB: update on development of tools for the biochemical analysis of genetic variation. 815-819
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  Phil Hyoun Lee, Hagit Shatkay: F-SNP: computationally predicted functional SNPs for disease association studies. 820-824
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  Joke Reumers, Lucía Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost J. J. van Durme, Joaquín Dopazo, Frederic Rousseau, Joost Schymkowitz: Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. 825-829
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  Ilari Scheinin, Samuel Myllykangas, Ioana Borze, Tom Böhling, Sakari Knuutila, Juha Saharinen: CanGEM: mining gene copy number changes in cancer. 830-835
• 
  Ximiao He, Suhua Chang, Jiajie Zhang, Qian Zhao, Haizhen Xiang, Kanthida Kusonmano, Liu Yang, Zhong Sheng Sun, Huanming Yang, Jing Wang: MethyCancer: the database of human DNA methylation and cancer. 836-841
• 
  Maté Ongenaert, Leander Van Neste, Tim De Meyer, Gerben Menschaert, Sofie Bekaert, Wim Van Criekinge: PubMeth: a cancer methylation database combining text-mining and expert annotation. 842-846
• 
  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, Thorsten Henrich: 4DXpress: a database for cross-species expression pattern comparisons. 847-853
• 
  Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, Thomas Skøt Jensen: Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. 854-859
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  Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Lorna Richardson, Nicholas Burton, Thomas P. Perry, Paul Smith, Richard A. Baldock, Duncan Davidson, Jeffrey H. Christiansen: EMAGE - Edinburgh Mouse Atlas of Gene Expression: 2008 update. 860-865
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  Jeremiah J. Faith, Michael E. Driscoll, Vincent A. Fusaro, Elissa J. Cosgrove, Boris Hayete, Frank S. Juhn, Stephen J. Schneider, Timothy S. Gardner: Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. 866-870
• 
  Robert J. Marinelli, Kelli Montgomery, Chih Long Liu, Nigam H. Shah, Wijan Prapong, Michael Nitzberg, Zachariah K. Zachariah, Gavin Sherlock, Yasodha Natkunam, Robert B. West, Matt van de Rijn, Patrick O. Brown, Catherine A. Ball: The Stanford Tissue Microarray Database. 871-877
• 
  Philip Jones, Richard G. Côté, Sang Yun Cho, Sebastian Klie, Lennart Martens, Antony F. Quinn, David Thorneycroft, Henning Hermjakob: PRIDE: new developments and new datasets. 878-883
• 
  C. Zhang, Oswald Crasta, S. Cammer, Rebecca Will, Ron Kenyon, Dan Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, Tian Xue, Y. Zhang, M. Moore, Peter B. McGarvey, Hongzhan Huang, Yongxing Chen, J. Zhang, Raja Mazumder, Cathy H. Wu, Bruno W. S. Sobral: An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. 884-891
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  Michael D. Waters, Stanley Stasiewicz, B. Alex Merrick, Kenneth B. Tomer, Pierre R. Bushel, Richard S. Paules, Nancy Stegman, Gerald Nehls, Kenneth J. Yost III, 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, Jennifer Fostel: CEBS - Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. 892-900
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  David S. Wishart, Craig Knox, Anchi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, Murtaza Hassanali: DrugBank: a knowledgebase for drugs, drug actions and drug targets. 901-906
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  Yasushi Okuno, Akiko Tamon, Hiroaki Yabuuchi, Satoshi Niijima, Yohsuke Minowa, Koichiro Tonomura, Ryo Kunimoto, Chunlai Feng: GLIDA: GPCR - ligand database for chemical genomics drug discovery - database and tools update. 907-912
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  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, Teri E. Klein: The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. 913-918
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  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, Robert Preissner: SuperTarget and Matador: resources for exploring drug-target relationships. 919-922
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  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, Yongqun He: VIOLIN: vaccine investigation and online information network. 923-928
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  Shoji Mano, Tomoki Miwa, Shuh-ichi Nishikawa, Tetsuro Mimura, Mikio Nishimura: The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research. 929-937
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  Yong Seok Lee, Jeongsu Oh, Young Uk Kim, Namchul Kim, Sungjin Yang, Ui Wook Hwang: Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals. 938-942
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  Samart Wanchana, Supat Thongjuea, Victor Jun M. Ulat, Mylah Anacleto, Ramil Mauleon, Matthieu G. Conte, Mathieu Rouard, Manuel Ruiz, Nandini Krishnamurthy, Kimmen Sjölander, Theo van Hintum, Richard M. Bruskiewich: The Generation Challenge Programme comparative plant stress-responsive gene catalogue. 943-946
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  Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry M. Casstevens, Bonnie Hurwitz, Susan McCouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Y. Tecle, Jim Thomason, Chih-Wei Tung, Xuehong Wei, Immanuel Yap, Ken Youens-Clark, Doreen Ware, Lincoln Stein: Gramene: a growing plant comparative genomics resource. 947-953
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  Eva Grafahrend-Belau, Stephan Weise, Dirk Koschützki, Uwe Scholz, Björn H. Junker, Falk Schreiber: MetaCrop: a detailed database of crop plant metabolism. 954-958
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  Jon Duvick, Ann Fu, Usha Muppirala, Mukul Sabharwal, Matthew D. Wilkerson, Carolyn J. Lawrence, Carol Lushbough, Volker Brendel: PlantGDB: a resource for comparative plant genomics. 959-965
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  Anyuan Guo, Xin Chen, Ge Gao, He Zhang, Qihui Zhu, Xiao-Chuan Liu, Yingfu Zhong, Xiaocheng Gu, Kun He, Jingchu Luo: PlantTFDB: a comprehensive plant transcription factor database. 966-969
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  P. Kerr Wall, James Leebens-Mack, Kai F. Müller, Dawn Field, Naomi S. Altman, Claude W. dePamphilis: PlantTribes: a gene and gene family resource for comparative genomics in plants. 970-976
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  Yoshiharu Y. Yamamoto, Junichi Obokata: ppdb: a plant promoter database. 977-981
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  Tyler W. H. Backman, Christopher M. Sullivan, Jason S. Cumbie, Zachary A. Miller, Elisabeth J. Chapman, Noah Fahlgren, Scott A. Givan, James C. Carrington, Kristin D. Kasschau: Update of ASRP: the Arabidopsis Small RNA Project database. 982-985
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  Séverine Gagnot, Jean-Philippe Tamby, Marie-Laure Martin-Magniette, Frédérique Bitton, Ludivine Taconnat, Sandrine Balzergue, Sébastien Aubourg, Jean-Pierre Renou, Alain Lecharny, Véronique Brunaud: CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. 986-990
• 
  Matthieu G. Conte, S. Gaillard, N. Lanau, Mathieu Rouard, Christophe Périn: GreenPhylDB: a database for plant comparative genomics. 991-998
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  Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yi-Xue Li, Tieliu Shi: AtPID: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology. 999-1008
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  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, Eva Huala: The Arabidopsis Information Resource (TAIR): gene structure and function annotation. 1009-1014
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  Joshua L. Heazlewood, Pawel Durek, Jan Hummel, Joachim Selbig, Wolfram Weckwerth, Dirk Walther, Waltraud X. Schulze: PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. 1015-1021
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  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, Emmanuel Guiderdoni: Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library. 1022-1027
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  The Rice Annotation Project Database (RAP-DB): 2008 update. 1028-1033
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  Sook Jung, Margaret Staton, Taein Lee, Anna Blenda, Randall Svancara, Albert Abbott, Dorrie Main: GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. 1034-1040
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  Payan Canaran, Edward S. Buckler, Jeffrey Glaubitz, Lincoln Stein, Qi Sun, Wei Zhao, Doreen Ware: Panzea: an update on new content and features. 1041-1043
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  Guo-Zhang Wu, Qiu-Ming Shi, Ya Niu, Mei-Qing Xing, Hong-Wei Xue: Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica. 1044-1047
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  V. Aidinis, C. Chandras, M. Manoloukos, A. Thanassopoulou, K. Kranidioti, M. Armaka, E. Douni, D. L. Kontoyiannis, Michael Zouberakis, G. Kollias: MUGEN mouse database; Animal models of human immunological diseases. 1048-1054

Volume 36, Number Web-Server-Issue, July 2008

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  Gary Benson: Editorial. 1

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  Michelle D. Brazas, Joanne A. Fox, Timothy Brown, Scott McMillan, B. F. Francis Ouellette: Keeping pace with the data: 2008 update on the Bioinformatics Links Directory. 2-4
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  Mark Johnson, Irena Zaretskaya, Yan Raytselis, Yuri Merezhuk, Scott McGinnis, Thomas L. Madden: NCBI BLAST: a better web interface. 5-9
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  Sébastien Moretti, Andreas Wilm, Desmond G. Higgins, Ioannis Xenarios, Cédric Notredame: R-Coffee: a web server for accurately aligning noncoding RNA sequences. 10-13
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  Arnaud Fontaine, Antoine de Monte, Hélène Touzet: MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences. 14-18
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  Yen-Fu Chang, Yen-Lin Huang, Chin Lung Lu: SARSA: a web tool for structural alignment of RNA using a structural alphabet. 19-24
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  Thomas P. Walsh, Caleb Webber, Stephen M. J. Searle, Shane S. Sturrock, Geoffrey J. Barton: SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. 25-29
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  Jimin Pei, Ming Tang, Nick V. Grishin: PROMALS3D web server for accurate multiple protein sequence and structure alignments. 30-34
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  Maria Garcia-Boronat, Carmen M. Diez-Rivero, Ellis L. Reinherz, Pedro A. Reche: PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. 35-41
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  Roberto Mosca, Thomas R. Schneider: RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes. 42-46
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  Raphael A. Bauer, Philip E. Bourne, Arno Formella, Cornelius Frömmel, Christoph Gille, Andrean Goede, Aysam Guerler, Andreas Hoppe, Ernst-Walter Knapp, Thorsten Pöschel, Burghardt Wittig, Valentin Ziegler, Robert Preissner: Superimposé: a 3D structural superposition server. 47-54
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  Mathias Dunkel, Stefan Günther, Jessica Ahmed, Burghardt Wittig, Robert Preissner: SuperPred: drug classification and target prediction. 55-59
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  Byungwook Lee, Doheon Lee: DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture. 60-64
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  Lars Barquist, Ian Holmes: xREI: a phylo-grammar visualization webserver. 65-69
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  Andreas R. Gruber, Ronny Lorenz, Stephan H. F. Bernhart, Richard Neuböck, Ivo L. Hofacker: The Vienna RNA Websuite. 70-74
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  Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama: Software.ncrna.org: web servers for analyses of RNA sequences. 75-78
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  Elfar Torarinsson, Stinus Lindgreen: WAR: Webserver for aligning structural RNAs. 79-84
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  Vegeir Knudsen, Gustavo Caetano-Anollés: NOBAI: a web server for character coding of geometrical and statistical features in RNA structure. 85-90
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  Tzu-Hao Chang, Jorng-Tzong Horng, Hsien-Da Huang: RNALogo: a new approach to display structural RNA alignment. 91-96
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  Young-Kyu Park, Seong-Min Park, Young-Chul Choi, Doheon Lee, Misun Won, Young Joo Kim: AsiDesigner: exon-based siRNA design server considering alternative splicing. 97-103
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  Zhi John Lu, David H. Mathews: OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. 104-108
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  Brian Tjaden: TargetRNA: a tool for predicting targets of small RNA action in bacteria. 109-113
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  Xinbin Dai, Patrick Xuechun Zhao: pssRNAMiner: a plant short small RNA regulatory cascade analysis server. 114-118
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  Morgane Thomas-Chollier, Olivier Sand, Jean-Valéry Turatsinze, Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohée, Jacques van Helden: RSAT: regulatory sequence analysis tools. 119-127
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  Bart Hooghe, Paco Hulpiau, Frans van Roy, Pieter J. De Bleser: ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. 128-132
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  Valer Gotea, Ivan Ovcharenko: DiRE: identifying distant regulatory elements of co-expressed genes. 133-139
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  Brigitte Waegele, Thorsten Schmidt, Hans-Werner Mewes, Andreas Ruepp: OREST: the online resource for EST analysis. 140-144
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  Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel: CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. 145-148
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  Robert T. Sullivan, Caroline B. Morehouse, James W. Thomas: Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design. 149-153
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  Olivier Croce, François Chevenet, Richard Christen: OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences. 154-156
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  Raquel Egea, Sònia Casillas, Antonio Barbadilla: Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites. 157-162
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  Richard Owczarzy, Andrey V. Tataurov, Yihe Wu, Jeffrey A. Manthey, Kyle A. McQuisten, Hakeem G. Almabrazi, Kent F. Pedersen, Yuan Lin, Justin Garretson, Neil O. McEntaggart, Chris A. Sailor, Robert B. Dawson, Andrew S. Peek: IDT SciTools: a suite for analysis and design of nucleic acid oligomers. 163-169
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  Yuichi Kumaki, Masaaki Oda, Masaki Okano: QUMA: quantification tool for methylation analysis. 170-175
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  Cristian E. Martinez-Guerrero, Ricardo Ciria, Cei Abreu-Goodger, Gabriel Moreno-Hagelsieb, Enrique Merino: GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways. 176-180
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  Jason R. Grant, Paul Stothard: The CGView Server: a comparative genomics tool for circular genomes. 181-184
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  Naoshi Fukuhara, Takeshi Kawabata: HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. 185-189
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  Ian M. Overton, C. A. Johannes van Niekerk, Lester G. Carter, Alice Dawson, David M. A. Martin, Scott Cameron, Stephen A. McMahon, Malcolm F. White, William N. Hunter, James H. Naismith, Geoffrey J. Barton: TarO: a target optimisation system for structural biology. 190-196
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  Christian Cole, Jonathan D. Barber, Geoffrey J. Barton: The Jpred 3 secondary structure prediction server. 197-201
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  Scott Montgomerie, Joseph A. Cruz, Savita Shrivastava, David Arndt, Mark V. Berjanskii, David S. Wishart: PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. 202-209
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  Eitan Yaffe, Dan Fishelovitch, Haim J. Wolfson, Dan Halperin, Ruth Nussinov: MolAxis: a server for identification of channels in macromolecules. 210-215
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  Yann Ponty, R. Istrate, E. Porcelli, Peter Clote: LocalMove: computing on-lattice fits for biopolymers. 216-222
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  Dina Schneidman-Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson: PharmaGist: a webserver for ligand-based pharmacophore detection. 223-228
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  Efrat Mashiach, Dina Schneidman-Duhovny, Nelly Andrusier, Ruth Nussinov, Haim J. Wolfson: FireDock: a web server for fast interaction refinement in molecular docking. 229-232
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  Sergey Lyskov, Jeffrey J. Gray: The RosettaDock server for local protein-protein docking. 233-238
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  Grzegorz Koczyk, Igor N. Berezovsky: Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure. 239-245
• 
  Anshul Nigham, Lisa Tucker-Kellogg, Ivana Mihalek, Chandra Verma, David Hsu: pFlexAna: detecting conformational changes in remotely related proteins. 246-251
• 
  Charles A. Lesburg, José S. Duca: soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts. 252-254
• 
  Bernd W. Brandt, Jaap Heringa, Jack A. M. Leunissen: SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. 255-259
• 
  Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson: MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. 260-264
• 
  Steven J. Darnell, Laura LeGault, Julie C. Mitchell: KFC Server: interactive forecasting of protein interaction hot spots. 265-269
• 
  Sunhwan Jo, Miklós Vargyas, Judit Vasko-Szedlar, Benoît Roux, Wonpil Im: PBEQ-Solver for online visualization of electrostatic potential of biomolecules. 270-275
• 
  Stefan Richter, Anne Wenzel, Matthias Stein, Razif R. Gabdoulline, Rebecca C. Wade: webPIPSA: a web server for the comparison of protein interaction properties. 276-280
• 
  Andrew E. Firth, Wayne M. Patrick: GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries. 281-285
• 
  Neil F. W. Saunders, Bostjan Kobe: The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information. 286-290
• 
  Ting-Ying Chien, Darby Tien-Hao Chang, Chien-Yu Chen, Yi-Zhong Weng, Chen-Ming Hsu: E1DS: catalytic site prediction based on 1D signatures of concurrent conservation. 291-296
• 
  Anna E. Lobley, Timothy Nugent, Christine A. Orengo, David T. Jones: FFPred: an integrated feature-based function prediction server for vertebrate proteomes. 297-302
• 
  Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski: 3D-Fun: predicting enzyme function from structure. 303-307
• 
  Joaquín Tárraga, Ignacio Medina, José Carbonell, Jaime Huerta-Cepas, Pablo Minguez, Eva Alloza, Fátima Al-Shahrour, Susana Vegas-Azcárate, Stefan Götz, Pablo Escobar, Francisco García-García, Ana Conesa, David Montaner, Joaquín Dopazo: GEPAS, a web-based tool for microarray data analysis and interpretation. 308-314
• 
  Filippo Geraci, Marco Pellegrini, M. Elena Renda: AMIC@: All MIcroarray Clusterings @ once. 315-319
• 
  Marek Mutwil, Jens Øbro, William G. T. Willats, Staffan Persson: GeneCAT - novel webtools that combine BLAST and co-expression analyses. 320-326
• 
  Alexander E. Ivliev, Peter A. C. 't Hoen, Michel P. Villerius, Johan T. den Dunnen, Bernd W. Brandt: Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. 327-331
• 
  Igor Segota, Nenad Bartonicek, Kristian Vlahovicek: MADNet: microarray database network web server. 332-335
• 
  Yan-Hau Chen, Chuan-Kun Liu, Shu-Chuan Chang, Yi-Jung Lin, Ming-Fang Tsai, Yuan-Tsong Chen, Adam Yao: GenoWatch: a disease gene mining browser for association study. 336-340
• 
  Fátima Al-Shahrour, José Carbonell, Pablo Minguez, Stefan Götz, Ana Conesa, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo: Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. 341-346
• 
  Alexey V. Antonov, Thorsten Schmidt, Yu Wang, Hans-Werner Mewes: ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. 347-351
• 
  Rocío Romero-Záliz, Coral del Val, J. P. Cobb, Igor Zwir: Onto-CC: a web server for identifying Gene Ontology conceptual clusters. 352-357
• 
  Qi Zheng, Xiu-Jie Wang: GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. 358-363
• 
  Andreu Alibés, Andrés Cañada, Ramón Díaz-Uriarte: PaLS: filtering common literature, biological terms and pathway information. 364-367
• 
  J. L. Mosquera, Alex Sánchez-Pla: SerbGO: searching for the best GO tool. 368-371
• 
  Richard G. Côté, Philip Jones, Lennart Martens, Rolf Apweiler, Henning Hermjakob: The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. 372-376
• 
  Léon-Charles Tranchevent, Roland Barriot, Shi Yu, Steven Van Vooren, Peter Van Loo, Bert Coessens, Bart De Moor, Stein Aerts, Yves Moreau: ENDEAVOUR update: a web resource for gene prioritization in multiple species. 377-384
• 
  J. Lynn Fink, Sergey Kushch, Parker R. Williams, Philip E. Bourne: BioLit: integrating biological literature with databases. 385-389
• 
  Hong-Jie Dai, Chi-Hsin Huang, Ryan T. K. Lin, Richard Tzong-Han Tsai, Wen-Lian Hsu: BIOSMILE web search: a web application for annotating biomedical entities and relations. 390-398
• 
  Dean Cheng, Craig Knox, Nelson Young, Paul Stothard, Sambasivarao Damaraju, David S. Wishart: PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. 399-405
• 
  Raoul Frijters, Bart Heupers, Pieter van Beek, Maurice Bouwhuis, René C. van Schaik, Jacob de Vlieg, Jan Polman, Wynand Alkema: CoPub: a literature-based keyword enrichment tool for microarray data analysis. 406-410
• 
  Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, Byoung-Tak Zhang: PIE: an online prediction system for protein-protein interactions from text. 411-415
• 
  Hodong Lee, Gwan-Su Yi, Jong C. Park: E3Miner: a text mining tool for ubiquitin-protein ligases. 416-422
• 
  Shujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, Minoru Kanehisa: KEGG Atlas mapping for global analysis of metabolic pathways. 423-426
• 
  Lynda B. M. Ellis, Junfeng Gao, Kathrin Fenner, Lawrence P. Wackett: The University of Minnesota pathway prediction system: predicting metabolic logic. 427-432
• 
  Sebastian Oehm, David Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann: Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. 433-437
• 
  Chung-Yen Lin, Chia-Hao Chin, Hsin-Hung Wu, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat Ko: Hubba: hub objects analyzer - a framework of interactome hubs identification for network biology. 438-443
• 
  Sylvain Brohée, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, Jacques van Helden: NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. 444-451
• 
  Jüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler, Jaak Vilo: GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. 452-459
• 
  Johannes Klein, Stefan Leupold, Richard Münch, Claudia Pommerenke, Thorsten Johl, Uwe Kärst, Lothar Jänsch, Dieter Jahn, Ida Retter: ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks. 460-464
• 
  Alexis Dereeper, V. Guignon, G. Blanc, Stéphane Audic, S. Buffet, François Chevenet, Jean-François Dufayard, S. Guindon, Vincent Lefort, M. Lescot, Jean-Michel Claverie, Olivier Gascuel: Phylogeny.fr: robust phylogenetic analysis for the non-specialist. 465-469
• 
  Bas E. Dutilh, Ying He, Maarten L. Hekkelman, Martijn A. Huynen: Signature, a web server for taxonomic characterization of sequence samples using signature genes. 470-474
• 
  Li-Wei Jiang, Kuang-Lun Lin, Chin Lung Lu: OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes. 475-480
• 
  Karsten Suhre, Philippe Schmitt-Kopplin: MassTRIX: mass translator into pathways. 481-484
• 
  Jennifer A. Siepen, Khalid Belhajjame, Julian N. Selley, Suzanne M. Embury, Norman W. Paton, Carole A. Goble, Stephen G. Oliver, Robert Stevens, Lucas Zamboulis, Nigel J. Martin, Alexandra Poulovassilis, Philip Jones, Richard G. Côté, Henning Hermjakob, Melissa M. Pentony, David T. Jones, Christine A. Orengo, Simon J. Hubbard: ISPIDER Central: an integrated database web-server for proteomics. 485-490
• 
  Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Seong-Jin Park, Jong-Soon Choi, Seung Il Kim, Jong Bhak, Sunghoon Lee: MassNet: a functional annotation service for protein mass spectrometry data. 491-495
• 
  David S. Wishart, David Arndt, Mark V. Berjanskii, Peter Tang, Jianjun Zhou, Guohui Lin: CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. 496-502
• 
  Xavier Brochet, Marie-Paule Lefranc, Véronique Giudicelli: IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. 503-508
• 
  Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, Morten Nielsen: NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. 509-512
• 
  Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia V. Ponomarenko, Alessandro Sette, Zhanyang Zhu, Björn Peters: Immune epitope database analysis resource (IEDB-AR). 513-518
• 
  Magdalena Feldhahn, Philipp Thiel, Mathias M. Schuler, Nina Hillen, Stefan Stevanovic, Hans-Georg Rammensee, Oliver Kohlbacher: EpiToolKit - a web server for computational immunomics. 519-522
• 
  E. Mejía-Roa, Pedro Carmona-Saez, Rubén Nogales, Cesar Vicente, Miguel Vázquez, X. Y. Yang, Carlos García, Francisco Tirado, Alberto D. Pascual-Montano: bioNMF: a web-based tool for nonnegative matrix factorization in biology. 523-528

last updated on Sat May 25 06:31:57 2013 by the dblp team
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