Nucleic Acids Research, Volume 34

Volume 34, Database-Issue, January 1 2006

• Alex Bateman:
  EDITORIAL. 1
  Electronic Edition (link) BibTeX

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2006 update. 3-5
  Electronic Edition (link) BibTeX
• Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori, Yoshio Tateno:
  DDBJ in preparation for overview of research activities behind data submissions. 6-9
  Electronic Edition (link) BibTeX
• Guy Cochrane, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Wendy Baker, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Paul Browne, Alexandra van den Broek, Matias Castro, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Carola Kanz, Tamara Kulikova, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Michelle McHale, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Siamak Sobhany, Peter Stoehr, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler:
  EMBL Nucleotide Sequence Database: developments in 2005. 10-15
  Electronic Edition (link) BibTeX
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 16-20
  Electronic Edition (link) BibTeX
• Namshin Kim, Pora Kim, Seungyoon Nam, Seokmin Shin, Sanghyuk Lee:
  ChimerDB - a knowledgebase for fusion sequences. 21-24
  Electronic Edition (link) BibTeX
• K. T. Nishant, Kumar Chetan, M. R. S. Rao:
  HUMHOT: a database of human meiotic recombination hot spots. 25-28
  Electronic Edition (link) BibTeX
• Rivka L. Glaser, Joshua P. Ramsay, Ian M. Morison:
  The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations. 29-31
  Electronic Edition (link) BibTeX
• P. Siguier, J. Perochon, L. Lestrade, J. Mahillon, M. Chandler:
  ISfinder: the reference centre for bacterial insertion sequences. 32-36
  Electronic Edition (link) BibTeX
• Grant H. Jacobs, Peter A. Stockwell, Warren Tate, Chris M. Brown:
  Transterm - extended search facilities and improved integration with other databases. 37-40
  Electronic Edition (link) BibTeX
• Jeremy D. Glasner, Michael Rusch, Paul Liss, Guy Plunkett III, Eric L. Cabot, Aaron E. Darling, Bradley D. Anderson, Paul Infield-Harm, Michael C. Gilson, Nicole T. Perna:
  ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. 41-45
  Electronic Edition (link) BibTeX
• Stefan Stamm, Jean-Jack M. Riethoven, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Yesheng Tang, Nuno L. Barbosa-Morais, Thangavel Alphonse Thanaraj:
  ASD: a bioinformatics resource on alternative splicing. 46-55
  Electronic Edition (link) BibTeX
• Dirk Holste, George Huo, Vivian Tung, Christopher B. Burge:
  HOLLYWOOD: a comparative relational database of alternative splicing. 56-62
  Electronic Edition (link) BibTeX
• Enrique Blanco, Domènec Farré, M. Mar Albà, Xavier Messeguer, Roderic Guigó:
  ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. 63-67
  Electronic Edition (link) BibTeX
• Gordon Robertson, Misha Bilenky, K. Lin, An He, W. Yuen, M. Dagpinar, Richard Varhol, Kevin Teague, Obi L. Griffith, X. Zhang, Y. Pan, Maik Hassel, Monica C. Sleumer, W. Pan, Erin Pleasance, M. Chuang, H. Hao, Yvonne Y. Li, Neil Robertson, C. Fjell, B. Li, Stephen Montgomery, Tamara Astakhova, Jianjun Zhou, Jörg Sander, Asim S. Siddiqui, Steven J. M. Jones:
  cisRED: a database system for genome-scale computational discovery of regulatory elements. 68-73
  Electronic Edition (link) BibTeX
• Sarah K. Kummerfeld, Sarah A. Teichmann:
  DBD: a transcription factor prediction database. 74-81
  Electronic Edition (link) BibTeX
• Christoph D. Schmid, Rouaïda Périer, Viviane Praz, Philipp Bucher:
  EPD in its twentieth year: towards complete promoter coverage of selected model organisms. 82-85
  Electronic Edition (link) BibTeX
• Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano:
  DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. 86-89
  Electronic Edition (link) BibTeX
• Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, Philipp Bucher:
  HTPSELEX - a database of high-throughput SELEX libraries for transcription factor binding sites. 90-94
  Electronic Edition (link) BibTeX
• Dominique Vlieghe, Albin Sandelin, Pieter J. De Bleser, Kris Vleminckx, Wyeth W. Wasserman, Frans van Roy, Boris Lenhard:
  A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. 95-97
  Electronic Edition (link) BibTeX
• Hao Sun, Saranyan K. Palaniswamy, Twyla T. Pohar, Victor X. Jin, Tim Hui-Ming Huang, Ramana V. Davuluri:
  MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. 98-103
  Electronic Edition (link) BibTeX
• Xin Chen, Jian-min Wu, Klaus Hornischer, Alexander E. Kel, Edgar Wingender:
  TiProD: the Tissue-specific Promoter Database. 104-107
  Electronic Edition (link) BibTeX
• V. Matys, Olga V. Kel-Margoulis, Ellen Fricke, Ines Liebich, Sigrid Land, A. Barre-Dirrie, Ingmar Reuter, D. Chekmenev, Mathias Krull, Klaus Hornischer, Nico Voss, P. Stegmaier, Birgit Lewicki-Potapov, H. Saxel, Alexander E. Kel, Edgar Wingender:
  TRANSFAC^® and its module TRANSCompel^®: transcriptional gene regulation in eukaryotes. 108-110
  Electronic Edition (link) BibTeX
• Tala Bakheet, Bryan R. G. Williams, Khalid S. A. Khabar:
  ARED 3.0: the large and diverse AU-rich transcriptome. 111-114
  Electronic Edition (link) BibTeX
• Priyanka Shahi, Serguei Loukianiouk, Andreas Bohne-Lang, Marc Kenzelmann, Stefan Küffer, Sabine Maertens, Roland Eils, Hermann-Josef Gröne, Norbert Gretz, Benedikt Brors:
  Argonaute - a database for gene regulation by mammalian microRNAs. 115-118
  Electronic Edition (link) BibTeX
• Rumen Kostadinov, Nishtha Malhotra, Manuel Viotti, Robert Shine, Lawrence D'Antonio, Paramjeet Bagga:
  GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. 119-124
  Electronic Edition (link) BibTeX
• Martin Mokrejs, Václav Vopálensky, Ondrej Kolenaty, Tomás Masek, Zuzana Feketová, Petra Sekyrová, Barbora Skaloudová, Vítezslav Kríz, Martin Pospísek:
  IRESite: the database of experimentally verified IRES structures (www.iresite.org). 125-130
  Electronic Edition (link) BibTeX
• Liliana R. Stefan, Rui Zhang, Aaron G. Levitan, Donna K. Hendrix, Steven E. Brenner, Stephen R. Holbrook:
  MeRNA: a database of metal ion binding sites in RNA structures. 131-134
  Electronic Edition (link) BibTeX
• Paul Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl, Ivo L. Hofacker:
  miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. 135-139
  Electronic Edition (link) BibTeX
• Sam Griffiths-Jones, Russell J. Grocock, Stijn van Dongen, Alex Bateman, Anton J. Enright:
  miRBase: microRNA sequences, targets and gene nomenclature. 140-144
  Electronic Edition (link) BibTeX
• Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, Janusz M. Bujnicki:
  MODOMICS: a database of RNA modification pathways. 145-149
  Electronic Edition (link) BibTeX
• Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, Runsheng Chen:
  NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. 150-152
  Electronic Edition (link) BibTeX
• A. Olson, N. Sheth, J. S. Lee, G. Hannon, R. Sachidanandam:
  RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs. 153-157
  Electronic Edition (link) BibTeX
• Laurent Lestrade, Michel J. Weber:
  snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. 158-162
  Electronic Edition (link) BibTeX
• Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, Jacek Wower, Jan Gorodkin, Tore Samuelsson, Christian Zwieb:
  The tmRDB and SRPDB resources. 163-168
  Electronic Edition (link) BibTeX
• Hans-Werner Mewes, Dmitrij Frishman, Klaus F. X. Mayer, Martin Münsterkötter, Octave Noubibou, Philipp Pagel, Thomas Rattei, Matthias Oesterheld, Andreas Ruepp, Volker Stümpflen:
  MIPS: analysis and annotation of proteins from whole genomes in 2005. 169-172
  Electronic Edition (link) BibTeX
• 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, Wolfgang Helmberg, Yuri Kapustin, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Stephen T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tugba O. Suzek, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko:
  Database resources of the National Center for Biotechnology Information. 173-180
  Electronic Edition (link) BibTeX
• Milton H. Saier Jr., Can V. Tran, Ravi D. Barabote:
  TCDB: the Transporter Classification Database for membrane transport protein analyses and information. 181-186
  Electronic Edition (link) BibTeX
• Cathy H. Wu, Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Raja Mazumder, Claire O'Donovan, Nicole Redaschi, Baris E. Suzek:
  The Universal Protein Resource (UniProt): an expanding universe of protein information. 187-191
  Electronic Edition (link) BibTeX
• Jason P. Mulvenna, Conan K. L. Wang, David J. Craik:
  CyBase: a database of cyclic protein sequence and structure. 192-194
  Electronic Edition (link) BibTeX
• M. D. Shaji Kumar, M. Michael Gromiha:
  PINT: Protein-protein Interactions Thermodynamic Database. 195-198
  Electronic Edition (link) BibTeX
• Christopher P. Toseland, Helen M. McSparron, Matthew N. Davies, Darren R. Flower:
  PPD v1.0 - an integrated, web-accessible database of experimentally determined protein pK_a values. 199-203
  Electronic Edition (link) BibTeX
• M. D. Shaji Kumar, K. Abdulla Bava, M. Michael Gromiha, Ponraj Prabakaran, Koji Kitajima, Hatsuho Uedaira, Akinori Sarai:
  ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. 204-206
  Electronic Edition (link) BibTeX
• Michelle K. M. Chow, Abdullah A. Amin, Kate F. Fulton, Thushan Fernando, Lawrence Kamau, Chris Batty, Michael Louca, Storm Ho, James C. Whisstock, Stephen P. Bottomley, Ashley M. Buckle:
  The REFOLD database: a tool for the optimization of protein expression and refolding. 207-212
  Electronic Edition (link) BibTeX
• J. Lynn Fink, Rajith N. Aturaliya, Melissa J. Davis, Fasheng Zhang, Kelly Hanson, Melvena S. Teasdale, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Rohan D. Teasdale:
  LOCATE: a mouse protein subcellular localization database. 213-217
  Electronic Edition (link) BibTeX
• Anthony Kar Lun Leung, Laura Trinkle-Mulcahy, Yun Wah Lam, Jens S. Andersen, Matthias Mann, Angus I. Lamond:
  NOPdb: Nucleolar Proteome Database. 218-220
  Electronic Edition (link) BibTeX
• Rainer B. Lanz, Zeljko Jericevic, William J. Zuercher, Chris Watkins, David L. Steffen, Ronald Margolis, Neil J. McKenna:
  Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community. 221-226
  Electronic Edition (link) BibTeX
• Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Marco Pagni, Christian J. A. Sigrist:
  The PROSITE database. 227-230
  Electronic Edition (link) BibTeX
• Nicola D. Gold, Richard M. Jackson:
  SitesBase: a database for structure-based protein-ligand binding site comparisons. 231-234
  Electronic Edition (link) BibTeX
• Aaron Birkland, Golan Yona:
  BIOZON: a hub of heterogeneous biological data. 235-242
  Electronic Edition (link) BibTeX
• V. S. Gowri, O. Krishnadev, C. S. Swamy, Narayanaswamy Srinivasan:
  MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. 243-246
  Electronic Edition (link) BibTeX
• Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
  Pfam: clans, web tools and services. 247-251
  Electronic Edition (link) BibTeX
• Thomas Rattei, Roland Arnold, Patrick Tischler, Dominik Lindner, Volker Stümpflen, Hans-Werner Mewes:
  SIMAP: the similarity matrix of proteins. 252-256
  Electronic Edition (link) BibTeX
• Ivica Letunic, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork:
  SMART 5: domains in the context of genomes and networks. 257-260
  Electronic Edition (link) BibTeX
• Alexander A. Zamyatnin, Alexander S. Borchikov, Michail G. Vladimirov, Olga L. Voronina:
  The EROP-Moscow oligopeptide database. 261-266
  Electronic Edition (link) BibTeX
• Marco Donizelli, Marie-Ange Djite, Nicolas Le Novère:
  LGICdb: a manually curated sequence database after the genomes. 267-269
  Electronic Edition (link) BibTeX
• Neil D. Rawlings, Fraser R. Morton, Alan J. Barrett:
  MEROPS: the peptidase database. 270-272
  Electronic Edition (link) BibTeX
• Chittibabu Guda, Lipika R. Pal, Ilya N. Shindyalov:
  DMAPS: a database of multiple alignments for protein structures. 273-276
  Electronic Edition (link) BibTeX
• Zhanwen Li, Yuzhen Ye, Adam Godzik:
  Flexible Structural Neighborhood - a database of protein structural similarities and alignments. 277-280
  Electronic Edition (link) BibTeX
• Corin Yeats, Michael Maibaum, Russell L. Marsden, Mark Dibley, David Lee, Sarah Addou, Christine A. Orengo:
  Gene3D: modelling protein structure, function and evolution. 281-284
  Electronic Edition (link) BibTeX
• Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
  iMOTdb - a comprehensive collection of spatially interacting motifs in proteins. 285-286
  Electronic Edition (link) BibTeX
• Mohammed Tagari, John G. Tate, G. J. Swaminathan, Richard Newman, Avi Naim, Wim Vranken, A. Kapopoulou, A. Hussain, Joël Fillon, Kim Henrick, Samir S. Velankar:
  E-MSD: improving data deposition and structure quality. 287-290
  Electronic Edition (link) BibTeX
• Ursula Pieper, Narayanan Eswar, Fred P. Davis, Hannes Braberg, Mallur S. Madhusudhan, Andrea Rossi, Marc A. Martí-Renom, Rachel Karchin, Ben M. Webb, David Eramian, Min-Yi Shen, Libusha Kelly, Francisco Melo, Andrej Sali:
  MODBASE: a database of annotated comparative protein structure models and associated resources. 291-295
  Electronic Edition (link) BibTeX
• Samuel Flores, Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating, Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, Mark Gerstein:
  The Database of Macromolecular Motions: new features added at the decade mark. 296-301
  Electronic Edition (link) BibTeX
• Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman:
  The RCSB PDB information portal for structural genomics. 302-305
  Electronic Edition (link) BibTeX
• Tiziana Castrignanò, Paolo D'Onorio De Meo, Domenico Cozzetto, Ivano Giuseppe Talamo, Anna Tramontano:
  The PMDB Protein Model Database. 306-309
  Electronic Edition (link) BibTeX
• Christof Winter, Andreas Henschel, Wan Kyu Kim, Michael Schroeder:
  SCOPPI: a structural classification of protein-protein interfaces. 310-314
  Electronic Edition (link) BibTeX
• Jürgen Kopp, Torsten Schwede:
  The SWISS-MODEL Repository: new features and functionalities. 315-318
  Electronic Edition (link) BibTeX
• Tina A. Eyre, Fabrice Ducluzeau, Tam P. Sneddon, Sue Povey, Elspeth A. Bruford, Michael J. Lush:
  The HUGO Gene Nomenclature Database, 2006 updates. 319-321
  Electronic Edition (link) BibTeX
• The Gene Ontology (GO) project in 2006. 322-326
  Electronic Edition (link) BibTeX
• Simon Whelan, Paul I. W. de Bakker, Emmanuel Quevillon, Nicolas Rodriguez, Nick Goldman:
  PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. 327-331
  Electronic Edition (link) BibTeX
• Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos Kyrpides:
  The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. 332-334
  Electronic Edition (link) BibTeX
• Roy R. Chaudhuri, Mark J. Pallen:
  xBASE, a collection of online databases for bacterial comparative genomics. 335-337
  Electronic Edition (link) BibTeX
• Emmanuel Perrodou, Caroline Deshayes, Jean Muller, Christine Schaeffer, Alain Van Dorsselaer, Raymond Ripp, Olivier Poch, Jean-Marc Reyrat, Odile Lecompte:
  ICDS database: interrupted CoDing sequences in prokaryotic genomes. 338-343
  Electronic Edition (link) BibTeX
• Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Greg Werner, Anu Padki, Xueling Zhao, Inna Dubchak, Philip Hugenholtz, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
  The integrated microbial genomes (IMG) system. 344-348
  Electronic Edition (link) BibTeX
• Ingo Paulsen, Arndt von Haeseler:
  INVHOGEN: a database of homologous invertebrate genes. 349-353
  Electronic Edition (link) BibTeX
• Minoru Kanehisa, Susumu Goto, Masahiro Hattori, Kiyoko F. Aoki-Kinoshita, Masumi Itoh, Shuichi Kawashima, Toshiaki Katayama, Michihiro Araki, Mika Hirakawa:
  From genomics to chemical genomics: new developments in KEGG. 354-357
  Electronic Edition (link) BibTeX
• Shujiro Okuda, Toshiaki Katayama, Shuichi Kawashima, Susumu Goto, Minoru Kanehisa:
  ODB: a database of operons accumulating known operons across multiple genomes. 358-362
  Electronic Edition (link) BibTeX
• Feng Chen, Aaron J. Mackey, Christian J. Stoeckert Jr., David S. Roos:
  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. 363-368
  Electronic Edition (link) BibTeX
• Natalia Maltsev, Elizabeth M. Glass, Dinanath Sulakhe, Alexis A. Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, Mark D'Souza:
  PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways. 369-372
  Electronic Edition (link) BibTeX
• Huiquan Wang, Miroslava Kaloper, Craig J. Benham:
  SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes. 373-378
  Electronic Edition (link) BibTeX
• Sucheta Tripathy, Varun N. Pandey, Bing Fang, Fidel Salas, Brett M. Tyler:
  VMD: a community annotation database for oomycetes and microbial genomes. 379-381
  Electronic Edition (link) BibTeX
• Michael J. Adams, John F. Antoniw:
  DPVweb: a comprehensive database of plant and fungal virus genes and genomes. 382-385
  Electronic Edition (link) BibTeX
• Craig M. Shepherd, Ian A. Borelli, Gabriel Lander, Padmaja Natarajan, Vinay Siddavanahalli, Chandrajit L. Bajaj, John E. Johnson, Charles L. Brooks III, Vijay S. Reddy:
  VIPERdb: a relational database for structural virology. 386-389
  Electronic Edition (link) BibTeX
• Thierry Lombardot, Renzo Kottmann, Hauke Pfeffer, Michael Richter, Hanno Teeling, Christian Quast, Frank Oliver Glöckner:
  Megx.net - database resources for marine ecological genomics. 390-393
  Electronic Edition (link) BibTeX
• Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, Julio Collado-Vides:
  RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. 394-397
  Electronic Edition (link) BibTeX
• Jian Yang, Lihong Chen, Jun Yu, Lilian Sun, Qi Jin:
  ShiBASE: an integrated database for comparative genomics of Shigella. 398-401
  Electronic Edition (link) BibTeX
• Guido Dieterich, Uwe Kärst, Elmar Fischer, Jürgen Wehland, Lothar Jänsch:
  LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species. 402-406
  Electronic Edition (link) BibTeX
• Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, Todd M. Lowe:
  The UCSC Archaeal Genome Browser. 407-410
  Electronic Edition (link) BibTeX
• Gopa R. Mishra, M. Suresh, K. Kumaran, N. Kannabiran, Shubha Suresh, P. Bala, K. Shivakumar, N. Anuradha, Raghunath Reddy, T. Madhan Raghavan, Shalini Menon, G. Hanumanthu, Malvika Gupta, Sapna Upendran, Shweta Gupta, M. Mahesh, Bincy Jacob, Pinky Mathew, Pritam Chatterjee, K. S. Arun, Salil Sharma, K. N. Chandrika, Nandan Deshpande, Kshitish Palvankar, R. Raghavnath, R. Krishnakanth, Hiren Karathia, B. Rekha, Rashmi Nayak, G. Vishnupriya, H. G. Mohan Kumar, M. Nagini, G. S. Sameer Kumar, Rojan Jose, P. Deepthi, S. Sujatha Mohan, T. K. B. Gandhi, H. C. Harsha, Krishna S. Deshpande, Malabika Sarker, T. S. Keshava Prasad, Akhilesh Pandey:
  Human protein reference database - 2006 update. 411-414
  Electronic Edition (link) BibTeX
• Alexander Mehrle, Heiko Rosenfelder, Ingo Schupp, Coral del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, Jeremy Simpson, Oliver Hofmann, Winston Hide, Karl-Heinz Glatting, Wolfgang Huber, Rainer Pepperkok, Annemarie Poustka, Stefan Wiemann:
  The LIFEdb database in 2006. 415-418
  Electronic Edition (link) BibTeX
• Mark Heiges, Haiming Wang, Edward Robinson, Cristina Aurrecoechea, Xin Gao, Nivedita Kaluskar, Philippa Rhodes, Sammy Wang, Cong-Zhou He, Yanqi Su, John A. Miller, Eileen Kraemer, Jessica C. Kissinger:
  CryptoDB: a Cryptosporidium bioinformatics resource update. 419-422
  Electronic Edition (link) BibTeX
• Rex L. Chisholm, Pascale Gaudet, Eric M. Just, Karen E. Pilcher, Petra Fey, Sohel N. Merchant, Warren A. Kibbe:
  dictyBase, the model organism database for Dictyostelium discoideum. 423-427
  Electronic Edition (link) BibTeX
• Fernán Agüero, Wenlong Zheng, D. Brent Weatherly, Pablo N. Mendes, Jessica C. Kissinger:
  TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi. 428-431
  Electronic Edition (link) BibTeX
• David Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet:
  Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. 432-435
  Electronic Edition (link) BibTeX
• Ulrich Güldener, Martin Münsterkötter, Matthias Oesterheld, Philipp Pagel, Andreas Ruepp, Hans-Werner Mewes, Volker Stümpflen:
  MPact: the MIPS protein interaction resource on yeast. 436-441
  Electronic Edition (link) BibTeX
• Jodi E. Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Michael S. Livstone, Robert S. Nash, Julie Park, Rose Oughtred, Marek S. Skrzypek, Barry Starr, Chandra L. Theesfeld, Jennifer Williams, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Mayank K. Thanawala, Shuai Weng, Kara Dolinski, David Botstein, J. Michael Cherry:
  Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. 442-445
  Electronic Edition (link) BibTeX
• Miguel C. Teixeira, Pedro T. Monteiro, Pooja Jain, Sandra Tenreiro, Alexandra R. Fernandes, Nuno P. Mira, Marta Alenquer, Ana T. Freitas, Arlindo L. Oliveira, Isabel Sá-Correia:
  The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. 446-451
  Electronic Edition (link) BibTeX
• Kevin P. Byrne, Kenneth H. Wolfe:
  Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. 452-455
  Electronic Edition (link) BibTeX
• Ulrich Güldener, Gertrud Mannhaupt, Martin Münsterkötter, Dirk Haase, Matthias Oesterheld, Volker Stümpflen, Hans-Werner Mewes, Gerhard Adam:
  FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum. 456-458
  Electronic Edition (link) BibTeX
• Rainer Winnenburg, Thomas K. Baldwin, Martin Urban, Christopher J. Rawlings, Jacob Köhler, Kim E. Hammond-Kosack:
  PHI-base: a new database for pathogen host interactions. 459-464
  Electronic Edition (link) BibTeX
• Kamal Gajendran, Michael D. Gonzales, Andrew D. Farmer, Eric Archuleta, Joe Win, Mark E. Waugh, Sophien Kamoun:
  Phytophthora functional genomics database (PFGD): functional genomics of phytophthora-plant interactions. 465-470
  Electronic Edition (link) BibTeX
• David H. Johnson, Jun Tsao, Ming Luo, Mike Carson:
  SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans. 471-474
  Electronic Edition (link) BibTeX
• Erich M. Schwarz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa R. Girard, Todd W. Harris, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Richard Durbin, John Spieth, Lincoln D. Stein, Paul W. Sternberg:
  WormBase: better software, richer content. 475-478
  Electronic Edition (link) BibTeX
• David Sims, Borisas Bursteinas, Qiong Gao, Marketa Zvelebil, Buzz Baum:
  FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets. 479-483
  Electronic Edition (link) BibTeX
• Gary Grumbling, Victor Strelets:
  FlyBase: anatomical data, images and queries. 484-488
  Electronic Edition (link) BibTeX
• Ian Flockhart, Matthew Booker, Amy Kiger, Michael Boutros, Susan Armknecht, Nadire Ramadan, Kris Richardson, Andrew Xu, Norbert Perrimon, Bernard Mathey-Prevot:
  FlyRNAi: the Drosophila RNAi screening center database. 489-494
  Electronic Edition (link) BibTeX
• James C. Sullivan, Joseph F. Ryan, James A. Watson, Jeramy Webb, James C. Mullikin, Daniel Rokhsar, John R. Finnerty:
  StellaBase: The Nematostella vectensis Genomics Database. 495-499
  Electronic Edition (link) BibTeX
• Nicholas A. Stover, Cynthia J. Krieger, Gail Binkley, Qing Dong, Dianna G. Fisk, Robert S. Nash, Anand Sethuraman, Shuai Weng, J. Michael Cherry:
  Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. 500-503
  Electronic Edition (link) BibTeX
• Gary D. Bader, Michael P. Cary, Chris Sander:
  Pathguide: a Pathway Resource List. 504-506
  Electronic Edition (link) BibTeX
• Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, Shankar Subramaniam:
  LMPD: LIPID MAPS proteome database. 507-510
  Electronic Edition (link) BibTeX
• Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne M. Paley, John Pick, Seung Yon Rhee, Christophe Tissier, Peifen Zhang, Peter D. Karp:
  MetaCyc: a multiorganism database of metabolic pathways and enzymes. 511-516
  Electronic Edition (link) BibTeX
• Lynda B. M. Ellis, Dave Roe, Lawrence P. Wackett:
  The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. 517-521
  Electronic Edition (link) BibTeX
• Peter Block, Christoph A. Sotriffer, Ingo Dramburg, Gerhard Klebe:
  AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. 522-526
  Electronic Edition (link) BibTeX
• Aylwin Ng, Borisas Bursteinas, Qiong Gao, Ewan Mollison, Marketa Zvelebil:
  pSTIING: a "systems" approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. 527-534
  Electronic Edition (link) BibTeX
• Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Mike Tyers:
  BioGRID: a general repository for interaction datasets. 535-539
  Electronic Edition (link) BibTeX
• Anatolij Potapov, Ines Liebich, Jürgen Dönitz, Knut Schwarzer, Nicole Sasse, Torsten Schoeps, Torsten Crass, Edgar Wingender:
  EndoNet: an information resource about endocrine networks. 540-545
  Electronic Edition (link) BibTeX
• Mathias Krull, Susanne Pistor, Nico Voss, Alexander E. Kel, Ingmar Reuter, Deborah Kronenberg, Holger Michael, Knut Schwarzer, Anatolij Potapov, Claudia Choi, Olga V. Kel-Margoulis, Edgar Wingender:
  TRANSPATH^®: an information resource for storing and visualizing signaling pathways and their pathological aberrations. 546-551
  Electronic Edition (link) BibTeX
• Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai:
  DBTGR: a database of tunicate promoters and their regulatory elements. 552-555
  Electronic Edition (link) BibTeX
• Ewan Birney, T. Daniel Andrews, Mario Cáccamo, Yuan Chen, Laura Clarke, G. Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas Down, Richard Durbin, X. M. Fernandez-Suarez, Paul Flicek, Stefan Gräf, Martin Hammond, J. Herrero, Kevin L. Howe, V. Iyer, K. Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Felix Kokocinski, Eugene Kulesha, D. London, I. Longden, Craig Melsopp, Patrick Meidl, B. Overduin, A. Parker, Glenn Proctor, Andreas Prlic, Mark Rae, D. Rios, Seth Redmond, M. Schuster, I. Sealy, Stephen M. J. Searle, J. Severin, Guy Slater, Damian Smedley, James Smith, Arne Stabenau, Jim Stalker, S. Trevanion, Abel Ureta-Vidal, J. Vogel, S. White, Cara Woodwark, Tim J. P. Hubbard:
  Ensembl 2006. 556-561
  Electronic Edition (link) BibTeX
• Judith A. Blake, Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson:
  The Mouse Genome Database (MGD): updates and enhancements. 562-567
  Electronic Edition (link) BibTeX
• Andreas Ruepp, Octave Noubibou Doudieu, Jos van den Oever, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Christine Skornia, Steffi Wanka, Thomas Rattei, Philipp Pagel, M. Louise Riley, Dmitrij Frishman, Dimitrij Surmeli, Igor V. Tetko, Matthias Oesterheld, Volker Stümpflen, Hans-Werner Mewes:
  The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. 568-571
  Electronic Edition (link) BibTeX
• Heng Li, Avril Coghlan, Jue Ruan, Lachlan James M. Coin, Jean-Karim Hériché, Lara Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund, Gane Ka-Shu Wong, Wei-Mou Zheng, Paramvir Dehal, Jun Wang, Richard Durbin:
  TreeFam: a curated database of phylogenetic trees of animal gene families. 572-580
  Electronic Edition (link) BibTeX
• Judy Sprague, Leyla Bayraktaroglu, Dave Clements, Tom Conlin, David Fashena, Ken Frazer, Melissa Haendel, Douglas G. Howe, Prita Mani, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, Sierra Taylor, Ceri E. Van Slyke, Monte Westerfield:
  The Zebrafish Information Network: the zebrafish model organism database. 581-585
  Electronic Edition (link) BibTeX
• Kremena V. Star, Quingbin Song, Andy Zhu, Erwin P. Böttinger:
  QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL. 586-589
  Electronic Edition (link) BibTeX
• Angela S. Hinrichs, Donna Karolchik, Robert Baertsch, Galt P. Barber, Gill Bejerano, Hiram Clawson, Mark Diekhans, Terrence S. Furey, Rachel A. Harte, Fan Hsu, Jennifer Hillman-Jackson, Robert M. Kuhn, J. S. Pedersen, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Adam C. Siepel, Kayla E. Smith, Charles W. Sugnet, A. Sultan-Qurraie, Daryl J. Thomas, Heather Trumbower, R. J. Weber, M. Weirauch, Ann S. Zweig, David Haussler, W. James Kent:
  The UCSC Genome Browser Database: update 2006. 590-598
  Electronic Edition (link) BibTeX
• Johann Lenffer, Frank W. Nicholas, Kao Castle, Arjun Rao, Stefan Gregory, Michael Poidinger, Matthew D. Mailman, Shoba Ranganathan:
  OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI. 599-601
  Electronic Edition (link) BibTeX
• Ghazi O. Tadmouri, Mahmoud Taleb Al Ali, Sarah Al-Haj Ali, Najib Al Khaja:
  CTGA: the database for genetic disorders in Arab populations. 602-606
  Electronic Edition (link) BibTeX
• Xiaosong Wang, Haitao Zhao, Qingwen Xu, Weibo Jin, Changning Liu, Huagang Zhang, Zhibin Huang, Xinyu Zhang, Yu Zhang, Dianqi Xin, Andrew J. G. Simpson, Lloyd J. Old, Yanqun Na, Yi Zhao, Weifeng Chen:
  HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. 607-612
  Electronic Edition (link) BibTeX
• Adil Elfilali, Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, Emmanuel Barillot:
  ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. 613-616
  Electronic Edition (link) BibTeX
• Bernice R. Packer, Meredith Yeager, Laura Burdett, Robert Welch, Michael Beerman, Liqun Qi, Hugues Sicotte, Brian Staats, Mekhala Acharya, Andrew Crenshaw, Andrew Eckert, Vinita Puri, Daniela S. Gerhard, Stephen J. Chanock:
  SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. 617-621
  Electronic Edition (link) BibTeX
• Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, Tzu-Hao Wang:
  dbPTM: an information repository of protein post-translational modification. 622-627
  Electronic Edition (link) BibTeX
• Osamu Ogasawara, Makiko Otsuji, Kouji Watanabe, Takayasu Iizuka, Takuro Tamura, Teruyoshi Hishiki, Shoko Kawamoto, Kousaku Okubo:
  BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. 628-631
  Electronic Edition (link) BibTeX
• Hideya Kawaji, Takeya Kasukawa, Shiro Fukuda, Shintaro Katayama, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki:
  CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. 632-636
  Electronic Edition (link) BibTeX
• Jeffrey H. Christiansen, Yiya Yang, Shanmugasundaram Venkataraman, Lorna Richardson, Peter Stevenson, Nicholas Burton, Richard A. Baldock, Duncan Davidson:
  EMAGE: a spatial database of gene expression patterns during mouse embryo development. 637-641
  Electronic Edition (link) BibTeX
• Alex S. Nord, Patricia J. Chang, Bruce R. Conklin, Antony V. Cox, Courtney A. Harper, Geoffrey G. Hicks, Conrad C. Huang, Susan J. Johns, Michiko Kawamoto, Songyan Liu, Elaine C. Meng, John H. Morris, Janet Rossant, Patricia Ruiz, William C. Skarnes, Philippe Soriano, William L. Stanford, Doug Stryke, Harald von Melchner, Wolfgang Wurst, Ken-ichi Yamamura, Stephen G. Young, Patricia C. Babbitt, Thomas E. Ferrin:
  The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. 642-648
  Electronic Edition (link) BibTeX
• Thomas McLaughlin, Jennifer A. Siepen, Julian Selley, Jennifer A. Lynch, King Wai Lau, Hujun Yin, Simon J. Gaskell, Simon J. Hubbard:
  PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. 649-654
  Electronic Edition (link) BibTeX
• Frank Desiere, Eric W. Deutsch, Nichole L. King, Alexey I. Nesvizhskii, Parag Mallick, Jimmy Eng, Sharon Chen, James Eddes, Sandra N. Loevenich, Ruedi Aebersold:
  The PeptideAtlas project. 655-658
  Electronic Edition (link) BibTeX
• Philip Jones, Richard G. Côté, Lennart Martens,