Nucleic Acids Research, Volume 35

Volume 35, Number Database-Issue, January 2007

• Alex Bateman:
  Editorial. 1-2
  

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2007 update. 3-4
  
• 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, Eugene Yaschenko:
  Database resources of the National Center for Biotechnology Information. 5-12
  
• Hideaki Sugawara, Takashi Abe, Takashi Gojobori, Yoshio Tateno:
  DDBJ working on evaluation and classification of bacterial genes in INSDC. 13-15
  
• 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, Rolf Apweiler:
  EMBL Nucleotide Sequence Database in 2006. 16-20
  
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 21-25
  
• Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
  Entrez Gene: gene-centered information at NCBI. 26-31
  
• Christoph Dieterich, M. W. Franz, Martin Vingron:
  Developments in CORG: a gene-centric comparative genomics resource. 32-35
  
• Sunil Archak, Eshwar Meduri, P. Sravana Kumar, Javaregowda Nagaraju:
  InSatDb: a microsatellite database of fully sequenced insect genomes. 36-39
  
• Conrad A. Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J. Benham, Anne D. Donaldson:
  OriDB: a DNA replication origin database. 40-46
  
• Byungwook Lee, Taehyung Kim, Seon-Kyu Kim, Kwang Hyung Lee, Doheon Lee:
  Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. 47-50
  
• Lei Bao, Mi Zhou, Ligang Wu, Lu Lu, Dan Goldowitz, Robert W. Williams, Yan Cui:
  PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. 51-54
  
• John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul M. Harrison, Mark Gerstein:
  Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. 55-60
  
• Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
  NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. 61-65
  
• Cristian Chaparro, Romain Guyot, Andrea Zuccolo, Benoît Piégu, Olivier Panaud:
  RetrOryza: a database of the rice LTR-retrotransposons. 66-70
  
• I. Agrafioti, Michael P. H. Stumpf:
  SNPSTR: a database of compound microsatellite-SNP markers. 71-75
  
• Gang Wu, Yuanpu Zheng, Imran Qureshi, Htar Thant Zin, Tyler Beck, Blazej Bulka, Stephen J. Freeland:
  SGDB: a database of synthetic genes re-designed for optimizing protein over-expression. 76-79
  
• Yevgeniy Gelfand, Alfredo Rodriguez, Gary Benson:
  TRDB - The Tandem Repeats Database. 80-87
  
• Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio:
  VISTA Enhancer Browser - a database of tissue-specific human enhancers. 88-92
  
• Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, Christopher Lee:
  The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. 93-98
  
• Yeunsook Lee, Younghee Lee, Bumjin Kim, Youngah Shin, Seungyoon Nam, Pora Kim, Namshin Kim, Won-Hyong Chung, Jaesang Kim, Sanghyuk Lee:
  ECgene: an alternative splicing database update. 99-103
  
• Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi:
  H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. 104-109
  
• Tyler S. Alioto:
  U12DB: a database of orthologous U12-type spliceosomal introns. 110-115
  
• Anil G. Jegga, Jing Chen, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Ranga Chandra Gudivada, Sue Kong, Vivek Kaimal, 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. 116-121
  
• Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, Mathieu Blanchette:
  PReMod: a database of genome-wide mammalian cis-regulatory module predictions. 122-126
  
• Mikhail Pachkov, Ionas Erb, Nacho Molina, Erik van Nimwegen:
  SwissRegulon: a database of genome-wide annotations of regulatory sites. 127-131
  
• Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides:
  Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. 132-136
  
• C. Jiang, Zhenyu Xuan, Fang Zhao, Michael Q. Zhang:
  TRED: a transcriptional regulatory element database, new entries and other development. 137-140
  
• Tao He, Pufeng Du, Yanda Li:
  dbRES: a web-oriented database for annotated RNA editing sites. 141-144
  
• Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, Kiyoshi Asai:
  fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. 145-148
  
• Molly Megraw, Praveen Sethupathy, Benoit Corda, Artemis G. Hatzigeorgiou:
  miRGen: a database for the study of animal microRNA genomic organization and function. 149-155
  
• Yong Zhang, Jiongtang Li, Lei Kong, Ge Gao, Qing-Rong Liu, Liping Wei:
  NATsDB: Natural Antisense Transcripts DataBase. 156-161
  
• Maciej Szymanski, Volker A. Erdmann, Jan Barciszewski:
  Noncoding RNAs database (ncRNAdb). 162-164
  
• Ju Youn Lee, Ijen Yeh, Ji Yeon Park, Bin Tian:
  PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. 165-168
  
• James R. Cole, B. Chai, Ryan J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, George M. Garrity, James M. Tiedje:
  The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. 169-172
  
• Ernesto Picardi, Teresa Maria Rosaria Regina, Axel Brennicke, Carla Quagliariello:
  REDIdb: the RNA editing database. 173-177
  
• Ken C. Pang, Stuart Stephen, Marcel E. Dinger, Pär G. Engström, Boris Lenhard, John S. Mattick:
  RNAdb 2.0 - an expanded database of mammalian non-coding RNAs. 178-182
  
• Jun Xie, Ming Zhang, Tao Zhou, Xia Hua, LiSha Tang, Weilin Wu:
  Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. 183-187
  
• Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer:
  TassDB: a database of alternative tandem splice sites. 188-192
  
• The Universal Protein Resource (UniProt). 193-197
  
• Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, Michael K. Gilson:
  BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. 198-201
  
• Di Wu, Feng Cui, Robert L. Jernigan, Zhijun Wu:
  PIDD: database for Protein Inter-atomic Distance Distributions. 202-207
  
• Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
  eSLDB: eukaryotic subcellular localization database. 208-212
  
• Joshua L. Heazlewood, Robert E. Verboom, Julian Tonti-Filippini, Ian Small, A. Harvey Millar:
  SUBA: the Arabidopsis Subcellular Database. 213-218
  
• Gonzalo López, Alfonso Valencia, Michael L. Tress:
  FireDB - a database of functionally important residues from proteins of known structure. 219-223
  
• Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise Daugherty, Mark Dibley, Robert D. Finn, Wolfgang Fleischmann, Julian Gough, Daniel H. 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 E. Orchard, Christine A. Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats:
  New developments in the InterPro database. 224-228
  
• Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich:
  Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. 229-231
  
• Paolo Sonego, Mircea Pacurar, Somdutta Dhir, Attila Kertész-Farkas, András Kocsor, Zoltán Gáspári, Jack A. M. Leunissen, Sándor Pongor:
  A Protein Classification Benchmark collection for machine learning. 232-236
  
• 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 M. 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, Stephen H. Bryant:
  CDD: a conserved domain database for interactive domain family analysis. 237-240
  
• Elon Portugaly, Nathan Linial, Michal Linial:
  EVEREST: a collection of evolutionary conserved protein domains. 241-246
  
• Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul D. Thomas:
  PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. 247-252
  
• Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard, Alexey G. Murzin:
  SISYPHUS - structural alignments for proteins with non-trivial relationships. 253-259
  
• Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-Giglio, William C. Nelson, Alexander R. Richter, Owen White:
  TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. 260-264
  
• Shalin Seebah, Anita Suresh, Shaowei Zhuo, Yong How Choong, Hazel Chua, Danny Chuon, Roger Beuerman, Chandra Verma:
  Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. 265-268
  
• Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
  REBASE - enzymes and genes for DNA restriction and modification. 269-270
  
• Mark D'Souza, Elizabeth M. Glass, Mustafa H. Syed, Yi Zhang, Alexis A. Rodriguez, Natalia Maltsev, Michael Y. Galperin:
  Sentra: a database of signal transduction proteins for comparative genome analysis. 271-273
  
• Qinghu Ren, Kaixi Chen, Ian T. Paulsen:
  TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. 274-279
  
• Philip Toukach, Hiren J. Joshi, René Ranzinger, Yuri Knirel, Claus-Wilhelm von der Lieth:
  Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de. 280-286
  
• M. Frank, T. Lütteke, C.-W. von der Lieth:
  GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. 287-290
  
• Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison L. Cuff, Timothy Dallman, Mark Dibley, Oliver Redfern, Frances M. G. Pearl, Rekha Nambudiry, Adam Reid, Ian Sillitoe, Corin Yeats, Janet M. Thornton, Christine A. Orengo:
  The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. 291-297
  
• 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, Stephen H. Bryant:
  MMDB: annotating protein sequences with Entrez's 3D-structure database. 298-300
  
• Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley:
  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. 301-303
  
• Kate F. Fulton, Mark A. Bate, Noel G. Faux, Khalid Mahmood, Chris Betts, Ashley M. Buckle:
  Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. 304-307
  
• Derek Wilson, Martin Madera, Christine Vogel, Cyrus Chothia, Julian Gough:
  The SUPERFAMILY database in 2007: families and functions. 308-313
  
• M. Michael Gromiha, Yukimitsu Yabuki, Srinesh Kundu, Sivasundaram Suharnan, Makiko Suwa:
  TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences. 314-316
  
• Chesley M. Leslin, Alexej Abyzov, Valentin A. Ilyin:
  TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. 317-321
  
• Gil Alterovitz, Michael Xiang, Mamta Mohan, Marco Ramoni:
  GO PaD: the Gene Ontology Partition Database. 322-327
  
• Yuying Tian, Allan W. Dickerman:
  GeneTrees: a phylogenomics resource for prokaryotes. 328-331
  
• T. Ryan Gregory, James A. Nicol, Heidi Tamm, Bellis Kullman, Kaur Kullman, Ilia J. Leitch, Brian G. Murray, Donald F. Kapraun, Johann Greilhuber, Michael D. Bennett:
  Eukaryotic genome size databases. 332-338
  
• Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, Hideaki Sugawara:
  Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes. 339-342
  
• Ikuo Uchiyama:
  MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. 343-346
  
• 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 D. Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross A. Overbeek, Rick Stevens:
  The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. 347-353
  
• M. Louise Riley, Thorsten Schmidt, Irena I. Artamonova, Christian Wagner, Andreas Volz, Klaus Heumann, Hans-Werner Mewes, Dmitrij Frishman:
  PEDANT genome database: 10 years online. 354-357
  
• Christian von Mering, Lars Juhl Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, Peer Bork:
  STRING 7 - recent developments in the integration and prediction of protein interactions. 358-362
  
• 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, Gilbert Deléage:
  euHCVdb: the European hepatitis C virus database. 363-366
  
• Saravanamuttu Gnaneshan, Samreen Ijaz, Joanne Moran, Mary Ramsay, Jonathan Green:
  HepSEQ: International Public Health Repository for Hepatitis B. 367-370
  
• Calvin Pan, Joseph Kim, Lamei Chen, Qi Wang, Christopher Lee:
  The HIV positive selection mutation database. 371-375
  
• 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, Jing Wang:
  Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. 376-380
  
• Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu, Justin Bo-Kai Hsu, Hsien-Da Huang:
  ViTa: prediction of host microRNAs targets on viruses. 381-385
  
• Luke E. Ulrich, Igor B. Zhulin:
  MiST: a microbial signal transduction database. 386-390
  
• Carol Ecale Zhou, Jason Smith, Marisa Lam, Adam Zemla, Matthew D. Dyer, Tom Slezak:
  MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. 391-394
  
• Sung Ho Yoon, Young-Kyu Park, Soohyun Lee, Doil Choi, Tae Kwang Oh, Cheol-Goo Hur, Jihyun F. Kim:
  Towards pathogenomics: a web-based resource for pathogenicity islands. 395-400
  
• E. E. Snyder, N. Kampanya, J. Lu, Eric K. Nordberg, H. R. Karur, M. Shukla, Jeetendra Soneja, Y. Tian, Tian 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, Oswald Crasta, M. J. Czar, Allan Dickerman, J. Dana Eckart, Ron Kenyon, Rebecca Will, J. C. Setubal, Bruno W. S. Sobral:
  PATRIC: The VBI PathoSystems Resource Integration Center. 401-406
  
• Alexei E. Kazakov, Michael J. Cipriano, Pavel S. Novichkov, Simon Minovitsky, Dmitry V. Vinogradov, Adam Arkin, Andrey A. Mironov, Mikhail S. Gelfand, Inna Dubchak:
  RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. 407-412
  
• Kim Brügger:
  The Sulfolobus database. 413-415
  
• Chia-Hung Chang, Yu-Chung Chang, Anthony Underwood, Chien-Shun Chiou, Cheng-Yan Kao:
  VNTRDB: a bacterial variable number tandem repeat locus database. 416-421
  
• Bradley I. Arshinoff, Garret Suen, Eric M. Just, Sohel M. Merchant, Warren A. Kibbe, Rex L. Chisholm, Roy D. Welch:
  Xanthusbase: adapting wikipedia principles to a model organism database. 422-426
  
• Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa Rhodes, John A. Miller, Eileen Kraemer, Christian J. Stoeckert Jr., David S. Roos, Jessica C. Kissinger:
  ApiDB: integrated resources for the apicomplexan bioinformatics resource center. 427-430
  
• Junichi Watanabe, Hiroyuki Wakaguri, Masahide Sasaki, Yutaka Suzuki, Sumio Sugano:
  Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs. 431-438
  
• Olivier Arnaiz, Scott Cain, Jean Cohen, Linda Sperling:
  ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. 439-444
  
• Emmet A. O'Brien, Liisa B. Koski, Yue Zhang, LiuSong Yang, Eric Wang, Michael W. Gray, Gertraud Burger, B. Franz Lang:
  TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). 445-451
  
• Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Prachi Shah, Gail Binkley, Christopher Lane, Stuart R. Miyasato, Gavin Sherlock:
  Sequence resources at the Candida Genome Database. 452-456
  
• Alexandre Gattiker, Christa Niederhauser-Wiederkehr, James Moore, Leandro Hermida, Michael Primig:
  The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction. 457-462
  
• Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Kerstin Glaab, Pär Davidsson, Fabian Nilsson, Graham J. L. Kemp, Olle Nerman, Anders Blomberg:
  PROPHECY - a yeast phenome database, update 2006. 463-467
  
• Robert S. Nash, Shuai Weng, Benjamin C. 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 S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Kara Dolinski, David Botstein, J. Michael Cherry:
  Expanded protein information at SGD: new pages and proteome browser. 468-471
  
• Lisa R. Girard, Tristan J. Fiedler, Todd W. Harris, Felicia Carvalho, Igor Antoshechkin, Michael Han, Paul W. Sternberg, Lincoln D. Stein, Martin Chalfie:
  WormBook: the online review of Caenorhabditis elegans biology. 472-475
  
• Liangjiang Wang, Suzhi Wang, Yonghua Li, Martin S. R. Paradesi, Susan J. Brown:
  BeetleBase: the model organism database for Tribolium castaneum. 476-479
  
• Donald G. Gilbert:
  DroSpeGe: rapid access database for new Drosophila species genomes. 480-485
  
• Madeline A. Crosby, Joshua L. Goodman, Victor B. Strelets, Peili Zhang, William M. Gelbart:
  FlyBase: genomes by the dozen. 486-491
  
• Thomas Horn, Zeynep Arziman, Juerg Berger, Michael Boutros:
  GenomeRNAi: a database for cell-based RNAi phenotypes. 492-497
  
• Christoph Dieterich, Waltraud Roeseler, Patrick Sobetzko, Ralf J. Sommer:
  Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus. 498-502
  
• 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, Robert M. MacCallum, Gregory R. Madey, Karine Megy, Seth Redmond, Susan Russo, David W. Severson, Eric O. Stinson, Pantelis Topalis, Evgeni M. Zdobnov, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins:
  VectorBase: a home for invertebrate vectors of human pathogens. 503-505
  
• 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 R. Girard, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon J. McKay, Hans-Michael Müller, Cecilia Nakamura, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Richard Durbin, Lincoln D. Stein, Paul W. Sternberg, John Spieth:
  WormBase: new content and better access. 506-510
  
• Jens Barthelmes, Christian Ebeling, Antje Chang, Ida Schomburg, Dietmar Schomburg:
  BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. 511-514
  
• Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Noel M. O'Boyle, James W. Torrance, Peter Murray-Rust, John B. O. Mitchell, Janet M. Thornton:
  MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. 515-520
  
• David S. Wishart, Dan Tzur, Craig Knox, Roman Eisner, Anchi Guo, Nelson Young, Dean Cheng, Kevin Jewell, David Arndt, Summit Sawhney, Chris Fung, Lisa Nikolai, Mike Lewis, Marie-Aude Coutouly, Ian J. 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, Russell Greiner, Liang Li, Tom Marrie, Brian D. Sykes, Hans J. Vogel, Lori Querengesser:
  HMDB: the Human Metabolome Database. 521-526
  
• 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, Shankar Subramaniam:
  LMSD: LIPID MAPS structure database. 527-532
  
• 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, Dieter Jahn:
  SYSTOMONAS - an integrated database for systems biology analysis of Pseudomonas. 533-537
  
• H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker:
  CellCircuits: a database of protein network models. 538-545
  
• Yoshinobu Igarashi, Alexey M. Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Jeffrey W. Smith, Andrei Osterman, Adam Godzik:
  CutDB: a proteolytic event database. 546-549
  
• Fedor Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel:
  CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. 550-556
  
• Arnaud Ceol, Andrew Chatr-aryamontri, Elena Santonico, Roberto Sacco, Luisa Castagnoli, Gianni Cesareni:
  DOMINO: a database of domain-peptide interactions. 557-560
  
• Samuel Kerrien, Y. Alam-Faruque, B. Aranda, I. Bancarz, A. Bridge, C. Derow, Emily Dimmer, M. Feuermann, A. Friedrichsen, Rachael P. Huntley, C. Kohler, J. Khadake, C. Leroy, A. Liban, C. Lieftink, Luisa Montecchi-Palazzi, Sandra E. Orchard, J. Risse, K. Robbe, Bernd Roechert, David Thorneycroft, Y. Zhang, Rolf Apweiler, Henning Hermjakob:
  IntAct - open source resource for molecular interaction data. 561-565
  
• Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian D. Athey, David J. States, H. V. Jagadish:
  Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. 566-571
  
• Andrew Chatr-aryamontri, Arnaud Ceol, Luisa Montecchi-Palazzi, Giuliano Nardelli, Maria Victoria Schneider, Luisa Castagnoli, Gianni Cesareni:
  MINT: the Molecular INTeraction database. 572-574
  
• Petras J. Kundrotas, Emil Alexov:
  PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. 575-579
  
• Emily R. Jefferson, Thomas P. Walsh, Timothy J. Roberts, Geoffrey J. Barton:
  SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. 580-589
  
• Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E. Wanker, Matthias E. Futschik:
  UniHI: an entry gate to the human protein interactome. 590-594
  
• Kieran Hervold, Andrew Martin, Roger A. Kirkpatrick, Paul F. Mc Kenna, F. A. Ramirez-Weber:
  Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community. 595-598
  
• Fiona M. McCarthy, Susan M. Bridges, Nan Wang, G. Bryce Magee, W. Paul Williams, Dawn S. Luthe, Shane C. Burgess:
  AgBase: a unified resource for functional analysis in agriculture. 599-603
  
• Zhi-Liang Hu, Eric Ryan Fritz, James M. Reecy:
  AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. 604-609
  
• Tim J. P. Hubbard, B. L. Aken, Kathryn Beal, Benoit Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, G. Coates, Fiona Cunningham, Tim Cutts, Thomas Down, S. C. Dyer, S. Fitzgerald, J. Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Javier Herrero, Richard C. G. Holland, Kevin L. Howe, K. Howe, N. Johnson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, I. Longden, Craig Melsopp, Karine Megy, Patrick Meidl, B. Overduin, A. Parker, Andreas Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, J. Severin, Guy Slater, Damian Smedley, G. Spudich, S. Trevanion, Albert J. Vilella, J. Vogel, S. White, M. Wood, Tony Cox, Val Curwen, Richard Durbin, X. M. Fernandez-Suarez, Paul Flicek, Arek Kasprzyk, Glenn Proctor, Stephen M. J. Searle, James Smith, Abel Ureta-Vidal, Ewan Birney:
  Ensembl 2007. 610-617
  
• Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
  The mouse Gene Expression Database (GXD): 2007 update. 618-623
  
• Raquel Egea, Sònia Casillas, Enol Fernández, Miquel Àngel Senar, Antonio Barbadilla:
  MamPol: a database of nucleotide polymorphism in the Mammalia class. 624-629
  
• Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
  The mouse genome database (MGD): new features facilitating a model system. 630-637
  
• Dale A. Begley, Debra M. Krupke, Matthew J. Vincent, John P. Sundberg, Carol J. Bult, Janan T. Eppig:
  Mouse Tumor Biology Database (MTB): status update and future directions. 638-642
  
• Molly A. Bogue, Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult:
  Mouse Phenome Database (MPD). 643-649
  
• Hirohide Uenishi, Tomoko Eguchi-Ogawa, Hiroki Shinkai, Naohiko Okumura, Kohei Suzuki, Daisuke Toki, Noriyuki Hamasima, Takashi Awata:
  PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. 650-653
  
• Jue Ruan, Yiran Guo, Heng Li, Yafeng Hu, Fei Song, Xin Huang, Karsten Kristiansen, Lars Bolund, Jun Wang:
  PigGIS: Pig Genomic Informatics System. 654-657
  
• Simon N. Twigger, Mary Shimoyama, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob:
  The Rat Genome Database, update 2007 - Easing the path from disease to data and back again. 658-662
  
• 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, David Haussler, W. James Kent:
  The ENCODE Project at UC Santa Cruz. 663-667
  
• Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Heather Trumbower, Daryl J. Thomas, Archana Thakkapallayil, Charles W. Sugnet, Mario Stanke, Kayla E. Smith, Adam C. Siepel, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, J. S. Pedersen, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Mark Diekhans, Hiram Clawson, Gill Bejerano, Galt P. Barber, Robert Baertsch, David Haussler, W. James Kent:
  The UCSC genome browser database: update 2007. 668-673
  
• Alecksandr Kutchma, Nayeem Quayum, Jan Jensen:
  GeneSpeed: protein domain organization of the transcriptome. 674-679
  
• Dongmei Zuo, Stephanie E. Mohr, Yanhui Hu, Elena Taycher, Andreas Rolfs, Jason Kramer, Janice Williamson, Joshua LaBaer:
  PlasmID: a centralized repository for plasmid clone information and distribution. 680-684
  
• Koichiro Higasa, Katsuyuki Miyatake, Yoji Kukita, Tomoko Tahira, Kenshi Hayashi:
  D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples. 685-689
  
• Sjozef van Baal, Polynikis Kaimakis, Manyphong Phommarinh, Daphne Koumbi, Harry Cuppens, Francesca Riccardino, Milan Macek Jr., Charles R. Scriver, George P. Patrinos:
  FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide. 690-695
  
• Philip Groth, Nadia Pavlova, Ivan Kalev, Spas Tonov, Georgi Georgiev, Hans-Dieter Pohlenz, Bertram Weiss:
  PhenomicDB: a new cross-species genotype/phenotype resource. 696-699
  
• Anil G. Jegga, Sivakumar Gowrisankar, Jing Chen, Bruce J. Aronow:
  PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. 700-706
  
• Shengting Li, Lijia Ma, Heng Li, Søren Vang, Yafeng Hu, Lars Bolund, Jun Wang:
  Snap: an integrated SNP annotation platform. 707-710
  
• Jungsun Park, Sohyun Hwang, Yong Seok Lee, Sang-Cheol Kim, Doheon Lee:
  SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. 711-715
  
• Daryl J. Thomas, Heather Trumbower, Andrew D. Kern, Brooke L. Rhead, Robert M. Kuhn, David Haussler, W. James Kent:
  Variation resources at UC Santa Cruz. 716-720
  
• Maureen E. Higgins, Martine Claremont, John E. Major, Chris Sander, Alex E. Lash:
  CancerGenes: a gene selection resource for cancer genome projects. 721-726
  
• Wen-Hui Su, Chuan-Chuan Chao, Shiou-Hwei Yeh, Ding-Shinn Chen, Pei-Jer Chen, Yuh-Shan Jou:
  OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci. 727-731
  
• Suisheng Tang, Zhuo Zhang, Sin Lam Tan, Man-Hung Eric Tang, Arun Prashanth Kumar, Suresh Kumar Ramadoss, Vladimir B. Bajic:
  KBERG: KnowledgeBase for Estrogen Responsive Genes. 732-736
  
• Wuxue Zhang, Yong Zhang, Hui Zheng, Chen Zhang, Wei Xiong, John G. Olyarchuk, Michael Walker, Weifeng Xu, Min Zhao, Shuqi Zhao, Zhuan Zhou, Liping Wei:
  SynDB: a Synapse protein DataBase based on synapse ontology. 737-741
  
• 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, Nathan Goodman:
  T1DBase: integration and presentation of complex data for type 1 diabetes research. 742-746
  
• Helen E. Parkinson, Misha Kapushesky, Mohammadreza Shojatalab, Niran Abeygunawardena, Richard Coulson, Anna Farne, Ele Holloway, N. Kolesnykov, P. Lilja, Margus Lukk, Roby Mani, Tim F. Rayner, Anjan Sharma, E. William, Ugis Sarkans, Alvis Brazma:
  ArrayExpress - a public database of microarray experiments and gene expression profiles. 747-750
  
• Joan M. Mazzarelli, John Brestelli, Regina K. Gorski, Junmin Liu, Elisabetta Manduchi, Deborah F. Pinney, Jonathan Schug, Peter White, Klaus H. Kaestner, Christian J. Stoeckert Jr.:
  EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. 751-755
  
• Fei Pan, Chi-Hsien Chiu, Sudip Pulapura, Michael R. Mehan, Juan Nunez-Iglesias, Kangyu Zhang, Kiran Kamath, Michael S. Waterman, Caleb E. Finch, Xianghong Jasmine Zhou:
  Gene Aging Nexus: a web database and data mining platform for microarray data on aging. 756-759
  
• Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, Ron Edgar:
  NCBI GEO: mining tens of millions of expression profiles - database and tools update. 760-765
  
• 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, Catherine A. Ball:
  The Stanford Microarray Database: implementation of new analysis tools and open source release of software. 766-770
  
• 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, Jan Wang, Matthias Mann:
  MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. 771-779
  
• Yi-Bu Chen, Ansuman Chattopadhyay, Phillip Bergen, Cynthia Gadd, 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. 780-785
  
• 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, A. Keith Dunker:
  DisProt: the Database of Disordered Proteins. 786-793
  
• 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, Yu Zong Chen:
  PharmGED: Pharmacogenetic Effect Database. 794-799
  
• Alexander Loy, Frank Maixner, Michael Wagner, Matthias Horn:
  probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. 800-804
  
• Wenwu Cui, Dennis D. Taub, Kevin Gardner:
  qPrimerDepot: a primer database for quantitative real time PCR. 805-809
  
• Nuwee Wiwatwattana, Christopher M. Landau, G. Jamie Cope, Gabriel A. Harp, Anuj Kumar:
  Organelle DB: an updated resource of eukaryotic protein localization and function. 810-814
  
• Agatha Schlüter, Stéphane Fourcade, Enric Domènech-Estévez, Toni Gabaldón, Jaime Huerta-Cepas, Guillaume Berthommier, Raymond Ripp, Ronald J. A. Wanders, Olivier Poch, Aurora Pujol:
  PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. 815-822
  
• Eduardo Ruiz-Pesini, Marie T. Lott, Vincent Procaccio, Jason C. Poole, Marty C. Brandon, Dan Mishmar, Christina Yi, James Kreuziger, Pierre Baldi, Douglas C. Wallace:
  An enhanced MITOMAP with a global mtDNA mutational phylogeny. 823-828
  
• Cameron Johnson, Lewis Bowman, Alex T. Adai, Vicki Vance, Venkatesan Sundaresan:
  CSRDB: a small RNA integrated database and browser resource for cereals. 829-833
  
• Manuel Spannagl, Octave Noubibou, Dirk Haase, Li Yang, Heidrun Gundlach, Tobias Hindemitt, Kathrin Klee, Georg Haberer, Heiko Schoof, Klaus F. X. Mayer:
  MIPSPlantsDB - plant database resource for integrative and comparative plant genome research. 834-840
  
• Lorenz Bülow, Martin Schindler, Reinhard Hehl:
  PathoPlant^®: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. 841-845
  
• Kevin L. Childs, John P. Hamilton, Wei Zhu, Eugene Ly, Foo Cheung, Hank Wu, Pablo D. Rabinowicz, Chris D. Town, C. Robin Buell, Agnes P. Chan:
  The TIGR Plant Transcript Assemblies database. 846-851
  
• Nigel S. Walker, Nicholas Stiffler, Alice Barkan:
  POGs/PlantRBP: a resource for comparative genomics in plants. 852-856
  
• Claudia Galuschka, Martin Schindler, Lorenz Bülow, Reinhard Hehl:
  AthaMap web tools for the analysis and identification of co-regulated genes. 857-862
  
• Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta:
  ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. 863-869
  
• 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 C. Spangenberg, David Edwards:
  BASC: an integrated bioinformatics system for Brassica research. 870-873
  
• Yong Li, Mario G. Rosso, Prisca Viehoever, Bernd Weisshaar:
  GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions. 874-878
  
• Huazong Zeng, Lijun Luo, Weixiong Zhang, Jie Zhou, Zuofeng Li, Hongyan Liu, Tiansheng Zhu, Xiangqian Feng, Yang Zhong:
  PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information. 879-882