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ORCIDNucleic Acids Research, Volume 38
Volume 38, Number Database-Issue, January 2010
- Guy Cochrane
, Michael Y. Galperin:
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. 1-4 - Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna R. Panchenko, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye:
Database resources of the National Center for Biotechnology Information. 5-16 - Catherine Brooksbank, Graham Cameron, Janet M. Thornton:
The European Bioinformatics Institute's data resources. 17-25 - Yukiko Yamazaki, Ryo Akashi, Yutaka Banno, Takashi Endo, Hiroshi Ezura, Kaoru Fukami-Kobayashi, Kazuo Inaba, Tadashi Isa, Katsuhiko Kamei, Fumie Kasai, Masatomo Kobayashi, Nori Kurata, Makoto Kusaba, Tetsuro Matuzawa, Shohei Mitani, Taro Nakamura, Yukio Nakamura, Norio Nakatsuji, Kiyoshi Naruse, Hironori Niki, Eiji Nitasaka, Yuichi Obata, Hitoshi Okamoto, Moriya Okuma, Kazuhiro Sato, Tadao Serikawa, Toshihiko Shiroishi, Hideaki Sugawara, Hideko Urushibara, Masatoshi Yamamoto, Yoshio Yaoita, Atsushi Yoshiki, Yuji Kohara:
NBRP databases: databases of biological resources in Japan. 26-32 - Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura:
DDBJ launches a new archive database with analytical tools for next-generation sequence data. 33-38 - Rasko Leinonen, Ruth Akhtar, Ewan Birney, James K. Bonfield, Lawrence Bower, Matthew Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher I. Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel R. Zerbino, Guy Cochrane:
Improvements to services at the European Nucleotide Archive. 39-45 - Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
GenBank. 46-51 - Weizhong Li, Hamish McWilliam, Ana Richart de la Torre, Adam Grodowski, Irina Benediktovich, Mickael Goujon, Stephane Nauche, Rodrigo Lopez:
Non-redundant patent sequence databases with value-added annotations at two levels. 52-56 - Raphaël Leplae, Gipsi Lima-Mendez, Ariane Toussaint:
ACLAME: A CLAssification of Mobile genetic Elements, update 2010. 57-61 - Pryavahiny Kichenaradja, Patricia Siguier, Jocelyne Pérochon, Michael Chandler:
ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes. 62-68 - Michaël Bekaert, Andrew E. Firth, Yan Zhang, Vadim N. Gladyshev, John F. Atkins, Pavel V. Baranov:
Recode-2: new design, new search tools, and many more genes. 69-74 - Giorgio Grillo, Antonio Turi, Flavio Licciulli, Flavio Mignone, Sabino Liuni, Sandro Banfi, Vincenzo Alessandro Gennarino, David Stephen Horner, Giulio Pavesi, Ernesto Picardi, Graziano Pesole:
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. 75-80 - Pora Kim, Suhyeon Yoon, Namshin Kim, Sanghyun Lee, Minjeong Ko, Haeseung Lee, Hyunjung Kang, Jaesang Kim, Sanghyuk Lee:
ChimerDB 2.0 - a knowledgebase for fusion genes updated. 81-85 - Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Takashi Gojobori, Tadashi Imanishi, Sumio Sugano:
H-DBAS: human-transcriptome database for alternative splicing: update 2010. 86-90 - Bruno Contreras-Moreira:
3D-footprint: a database for the structural analysis of protein-DNA complexes. 91-97 - Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS provides a tissue specific dynamic view of Transcription Start Sites. 98-104 - Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David J. Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin:
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. 105-110 - Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov:
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. 111-118 - Juan Wang, Ming Lu, Chengxiang Qiu, Qinghua Cui:
TransmiR: a transcription factor-microRNA regulation database. 119-122 - Jian-Hua Yang, Peng Shao, Hui Zhou, Yue-Qin Chen, Liang-Hu Qu:
deepBase: a database for deeply annotating and mining deep sequencing data. 123-130 - Martin Mokrejs, Tomás Masek, Václav Vopálenský, Petr Hlubucek, Philippe Delbos, Martin Pospísek:
IRESite - a tool for the examination of viral and cellular internal ribosome entry sites. 131-136 - Panagiotis Alexiou, Thanasis Vergoulis, Martin Gleditzsch, George Prekas, Theodore Dalamagas, Molly Megraw, Ivo Grosse, Timos K. Sellis, Artemis G. Hatzigeorgiou:
miRGen 2.0: a database of microRNA genomic information and regulation. 137-141 - The Universal Protein Resource (UniProt) in 2010. 142-148
- Yan Zhang, Jie Lv, Hongbo Liu, Jiang Zhu, Jianzhong Su, Qiong Wu, Yunfeng Qi, Fang Wang, Xia Li:
HHMD: the human histone modification database. 149-154 - Jian Ren, Zexian Liu, Xinjiao Gao, Changjiang Jin, Mingliang Ye, Hanfa Zou, Longping Wen, Zhaolei Zhang, Yu Xue, Xuebiao Yao:
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. 155-160 - Christian J. A. Sigrist, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Virginie Bulliard, Amos Bairoch, Nicolas Hulo:
PROSITE, a protein domain database for functional characterization and annotation. 161-166 - Cathryn M. Gould, Francesca Diella, Allegra Via, Pål Puntervoll, Christine Gemünd, Sophie Chabanis-Davidson, Sushama Michael, Ahmed Sayadi, Jan Christian Bryne, Claudia Chica, Markus Seiler, Norman E. Davey, Niall J. Haslam, Robert J. Weatheritt, Aidan Budd, Tim Hughes, Jakub Pas, Leszek Rychlewski, Gilles Travé, Rein Aasland, Manuela Helmer-Citterich, Rune Linding, Toby J. Gibson:
ELM: the status of the 2010 eukaryotic linear motif resource. 167-180 - Annalisa Marsico, Kerstin Scheubert, Anne Tuukkanen, Andreas Henschel, Christof Winter, Rainer Winnenburg, Michael Schroeder:
MeMotif: a database of linear motifs in α-helical transmembrane proteins. 181-189 - Jean Muller, Damian Szklarczyk, Philippe Julien, Ivica Letunic, Alexander Roth, Michael Kuhn, Sean Powell, Christian von Mering, Tobias Doerks, Lars Juhl Jensen, Peer Bork:
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. 190-195 - Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, Erik L. L. Sonnhammer:
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. 196-203 - Huaiyu Mi, Qing Dong, Anushya Muruganujan, Pascale Gaudet, Suzanna Lewis, Paul D. Thomas:
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. 204-210 - Robert D. Finn, Jaina Mistry, John G. Tate, Penny C. Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman:
The Pfam protein families database. 211-222 - Thomas Rattei, Patrick Tischler, Stefan Götz, Marc-André Jehl, Jonathan Hoser, Roland Arnold, Ana Conesa, Hans-Werner Mewes:
SIMAP - a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. 223-226 - Neil D. Rawlings, Alan J. Barrett, Alex Bateman:
MEROPS: the peptidase database. 227-233 - Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes. 234-236 - Saskia Preissner, Katharina Kroll, Mathias Dunkel, Christian Senger, Gady Goldsobel, Daniel Kuzman, Stefan Günther, Rainer Winnenburg, Michael Schroeder, Robert Preissner:
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. 237-243 - Andreas Schlicker, Mario Albrecht:
FunSimMat update: new features for exploring functional similarity. 244-248 - Paula de Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, Christoph Steinbeck:
Chemical Entities of Biological Interest: an update. 249-254 - Yanli Wang, Evan Bolton, Svetlana Dracheva, Karen Karapetyan, Benjamin A. Shoemaker, Tugba O. Suzek, Jiyao Wang, Jewen Xiao, Jian Zhang, Stephen H. Bryant:
An overview of the PubChem BioAssay resource. 255-266 - Guohui Zheng, Andrew V. Colasanti, Xiang-Jun Lu, Wilma K. Olson:
3DNALandscapes: a database for exploring the conformational features of DNA. 267-274 - Christian Koetschan, Frank Förster, Alexander Keller, Tina Schleicher, Benjamin Ruderisch, Roland Schwarz, Tobias Müller, Matthias Wolf, Jörg Schultz:
The ITS2 Database III - sequences and structures for phylogeny. 275-279 - Douglas H. Turner, David H. Mathews:
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. 280-282 - Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, Oxana V. Galzitskaya:
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. 283-287 - Yan Yuan Tseng, Z. Jeffrey Chen, Wen-Hsiung Li:
fPOP: footprinting functional pockets of proteins by comparative spatial patterns. 288-295 - Jonathan G. Lees, Corin Yeats, Oliver Redfern, Andrew B. Clegg, Christine A. Orengo:
Gene3D: merging structure and function for a Thousand genomes. 296-300 - François Ehrenmann, Quentin Kaas, Marie-Paule Lefranc:
IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. 301-307 - Samir S. Velankar, Christoph Best, B. Beuth, Harry Boutselakis, N. Cobley, Alan W. Sousa da Silva, Dimitris Dimitropoulos, Adel Golovin, Miriam Hirshberg, Melford John, Evgeny B. Krissinel, Richard H. Newman, Thomas J. Oldfield, Anne Pajon, Christopher J. Penkett, Jorge Pineda-Castillo, Gaurav Sahni, Sanchayita Sen, Robert A. Slowley, Antonio Suarez-Uruena, Jawahar Swaminathan, Glen van Ginkel, Wim F. Vranken, Kim Henrick, Gerard J. Kleywegt:
PDBe: Protein Data Bank in Europe. 308-317 - Sven Griep, Uwe Hobohm:
PDBselect 1992-2009 and PDBfilter-select. 318-319 - Donald S. Berkholz, Peter B. Krenesky, John R. Davidson, P. Andrew Karplus:
Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry. 320-325 - Patrick May, Annika Kreuchwig, Thomas Steinke, Ina Koch:
PTGL: a database for secondary structure-based protein topologies. 326-330 - The Gene Ontology in 2010: extensions and refinements. 331-335
- Johannes Goll, Robert Montgomery, Lauren M. Brinkac, Seth A. Schobel, Derek M. Harkins, Yinong Sebastian, Susmita Shrivastava, A. Scott Durkin, Granger G. Sutton:
The Protein Naming Utility: a rules database for protein nomenclature. 336-339 - Tanja Davidsen, Erin Beck, Anuradha Ganapathy, Robert Montgomery, Nikhat Zafar, Qi Yang, Ramana Madupu, Phil Goetz, Kevin Galinsky, Owen White, Granger G. Sutton:
The comprehensive microbial resource. 340-345 - Konstantinos Liolios, I-Min A. Chen, Konstantinos Mavrommatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, Nikos Kyrpides:
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. 346-354 - Minoru Kanehisa, Susumu Goto, Miho Furumichi, Mao Tanabe, Mika Hirakawa:
KEGG for representation and analysis of molecular networks involving diseases and drugs. 355-360 - Ikuo Uchiyama, Toshio Higuchi, Mikihiko Kawai:
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. 361-365 - Lubos Klucar, Matej Stano, Matus Hajduk:
phiSITE: database of gene regulation in bacteriophages. 366-370 - J. Pellet, Lionel Tafforeau, M. Lucas-Hourani, Vincent Navratil, Laurène Meyniel, Guillaume Achaz, A. Guironnet-Paquet, A. Aublin-Gex, Grégory Caignard, P. Cassonnet, A. Chaboud, T. Chantier, A. Deloire, C. Demeret, M. Le Breton, Gregory Neveu, L. Jacotot, Vaglio Vaglio, Stéphane Delmotte, Christian Gautier, Christophe Combet, Gilbert Deléage, M. Favre, F. Tangy, Yves Jacob, Patrice André, Vincent Lotteau, Chantal Rabourdin-Combe, P. O. Vidalain:
ViralORFeome: an integrated database to generate a versatile collection of viral ORFs. 371-378 - Mitsuteru Nakao, Shinobu Okamoto, Mitsuyo Kohara, Tsunakazu Fujishiro, Takatomo Fujisawa, Shusei Sato, Satoshi Tabata, Takakazu Kaneko, Yasukazu Nakamura:
CyanoBase: the cyanobacteria genome database update 2010. 379-381 - Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
The integrated microbial genomes system: an expanding comparative analysis resource. 382-390 - Renzo Kottmann, Ivaylo Kostadinov, Melissa Beth Duhaime, Pier Luigi Buttigieg, Pelin Yilmaz, Wolfgang Hankeln, Jost Waldmann, Frank Oliver Glöckner:
Megx.net: integrated database resource for marine ecological genomics. 391-395 - Paramvir S. Dehal, Marcin P. Joachimiak, Morgan N. Price, John T. Bates, Jason K. Baumohl, Dylan Chivian, Greg D. Friedland, Katherine H. Huang, Keith Keller, Pavel S. Novichkov, Inna Dubchak, Eric J. Alm, Adam P. Arkin:
MicrobesOnline: an integrated portal for comparative and functional genomics. 396-400 - Luke E. Ulrich, Igor B. Zhulin:
The MiST2 database: a comprehensive genomics resource on microbial signal transduction. 401-407 - Lauren M. Brinkac, Tanja Davidsen, Erin Beck, Anuradha Ganapathy, Elisabet Caler, Robert J. Dodson, A. Scott Durkin, Derek M. Harkins, Hernan Lorenzi, Ramana Madupu, Yinong Sebastian, Susmita Shrivastava, Mathangi Thiagarajan, Joshua Orvis, Jaideep P. Sundaram, Jonathan Crabtree, Kevin Galens, Yongmei Zhao, Jason M. Inman, Robert Montgomery, Seth A. Schobel, Kevin Galinsky, David M. Tanenbaum, Adam Resnick, Nikhat Zafar, Owen White, Granger G. Sutton:
Pathema: a clade-specific bioinformatics resource center for pathogen research. 408-414 - Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen T. Kraemer, Wei Li, John A. Miller, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Ryan Thibodeau, Charles Treatman, Haiming Wang:
EuPathDB: a portal to eukaryotic pathogen databases. 415-419 - Martha B. Arnaud, Marcus C. Chibucos, Maria C. Costanzo, Jonathan Crabtree, Diane O. Inglis, Adil Lotia, Joshua Orvis, Prachi Shah, Marek S. Skrzypek, Gail Binkley, Stuart R. Miyasato, Jennifer R. Wortman, Gavin Sherlock:
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. 420-427 - Marek S. Skrzypek, Martha B. Arnaud, Maria C. Costanzo, Diane O. Inglis, Prachi Shah, Gail Binkley, Stuart R. Miyasato, Gavin Sherlock:
New tools at the Candida Genome Database: biochemical pathways and full-text literature search. 428-432 - Stacia R. Engel, Rama Balakrishnan, Gail Binkley, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Eurie L. Hong, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Julie Park, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kara Dolinski, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database provides mutant phenotype data. 433-436 - Hee Shin Kim, Terence Murphy, Jing Xia, Doina Caragea, Yoonseong Park, Richard W. Beeman, Marcé D. Lorenzen, Stephen Butcher, J. Robert Manak, Susan J. Brown:
BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. 437-442 - Ulrike Pfreundt, Daniel P. James, Susan Tweedie, Derek Wilson, Sarah A. Teichmann, Boris Adryan:
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. 443-447 - Moritz Gilsdorf, Thomas Horn, Zeynep Arziman, Oliver Pelz, Evgeny Kiner, Michael Boutros:
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update. 448-452 - Jun Duan, Ruiqiang Li, Daojun Cheng, Wei Fan, Xingfu Zha, Tingcai Cheng, Yuqian Wu, Jun Wang, Kazuei Mita, Zhonghuai Xiang, Qingyou Xia:
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology. 453-456 - Martin Aslett, Cristina Aurrecoechea, Matthew Berriman, John Brestelli, Brian P. Brunk, Mark Carrington, Daniel P. Depledge, Steve Fischer, Bindu Gajria, Xin Gao, Malcolm J. Gardner, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Robin Houston, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen T. Kraemer, Wei Li, Flora J. Logan, John A. Miller, Siddhartha Mitra, Peter J. Myler, Vishal Nayak, Cary Pennington, Isabelle Phan, Deborah F. Pinney, Gowthaman Ramasamy, Matthew B. Rogers, David S. Roos, Chris Ross, Dhileep Sivam, Deborah F. Smith, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Sandhya Subramanian, Ryan Thibodeau, Adrian Tivey, Charles Treatman, Giles Velarde, Haiming Wang:
TriTrypDB: a functional genomic resource for the Trypanosomatidae. 457-462 - Todd W. Harris, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Juancarlos Chan, Wen J. Chen, Norie De La Cruz, Paul Davis, Margaret J. Duesbury, Ruihua Fang, Jolene Fernandes, Michael Han, Ranjana Kishore, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, 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: a comprehensive resource for nematode research. 463-467 - Vineet K. Sharma, Naveen Kumar, Tulika Prakash, Todd D. Taylor:
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. 468-472 - Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Suzanne M. Paley, Liviu Popescu, Anuradha Pujar, Alexander Glennon Shearer, Peifen Zhang, Peter D. Karp:
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. 473-479 - Alex Frolkis, Craig Knox, Emilia Lim, Timothy Jewison, Vivian Law, David D. Hau, Philip Liu, Bijaya Gautam, Son Ly, Anchi Guo, Jianguo Xia, Yongjie Liang, Savita Shrivastava, David S. Wishart:
SMPDB: The Small Molecule Pathway Database. 480-487 - Junfeng Gao, Lynda B. M. Ellis, Lawrence P. Wackett:
The University of Minnesota Biocatalysis/Biodegradation Database: improving public access. 488-491 - Lewis Y. Geer, Aron Marchler-Bauer, Renata C. Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, Stephen H. Bryant:
The NCBI BioSystems database. 492-496 - Andreas Ruepp, Brigitte Waegele, Martin Lechner, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Hans-Werner Mewes:
CORUM: the comprehensive resource of mammalian protein complexes - 2009. 497-501 - Judice L. Y. Koh, Huiming Ding, Michael Costanzo, Anastasia Baryshnikova, Kiana Toufighi, Gary D. Bader, Chad L. Myers, Brenda J. Andrews, Charles Boone:
DRYGIN: a database of quantitative genetic interaction networks in yeast. 502-507 - Milana Frenkel-Morgenstern, Ariel A. Cohen, Naama Geva-Zatorsky, Eran Eden, Jaime Prilusky, Irina Issaeva, Alex Sigal, Cellina Cohen-Saidon, Yuvalal Liron, Lydia Cohen, Tamar Danon, Natalie Perzov, Uri Alon:
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. 508-512 - Petras J. Kundrotas, Zhengwei Zhu, Ilya A. Vakser:
GWIDD: Genome-wide protein docking database. 513-517 - Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Tom Madej, Anna R. Panchenko:
Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites. 518-524 - Bruno Aranda, P. Achuthan, Yasmin Alam-Faruque, Irina M. Armean, Alan J. Bridge, C. Derow, Marc Feuermann, A. T. Ghanbarian, Samuel Kerrien, Jyoti Khadake, Jules Kerssemakers, C. Leroy, Michael P. Menden, Magali Michaut, Luisa Montecchi-Palazzi, S. N. Neuhauser, Sandra E. Orchard, V. Perreau, Bernd Roechert, K. van Eijk, Henning Hermjakob:
The IntAct molecular interaction database in 2010. 525-531 - Arnaud Céol, Andrew Chatr-aryamontri, Luana Licata, Daniele Peluso, Leonardo Briganti, Livia Perfetto, Luisa Castagnoli, Gianni Cesareni:
MINT, the molecular interaction database: 2009 update. 532-539 - Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman, Andreas Ruepp:
The Negatome database: a reference set of non-interacting protein pairs. 540-544 - Peter Vanhee, Joke Reumers, Francois Stricher, Lies Baeten, Luis Serrano, Joost Schymkowitz, Frederic Rousseau:
PepX: a structural database of non-redundant protein-peptide complexes. 545-551 - Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Monica Campillos, Christian von Mering, Lars Juhl Jensen, Andreas Beyer, Peer Bork:
STITCH 2: an interaction network database for small molecules and proteins. 552-556 - Paul Flicek, Bronwen L. Aken, Benoît Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew M. Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William M. McLaren, Karine Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y. Amy Tang, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, James A. Smith, Stephen M. J. Searle:
Ensembl's 10th year. 557-562 - Paul J. Kersey, Daniel Lawson, Ewan Birney, Paul S. Derwent, Matthias Haimel, Javier Herrero, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Andreas Kähäri, Rhoda Kinsella, Eugene Kulesha, Uma Maheswari, Karine Megy, Michael Nuhn, Glenn Proctor, Daniel M. Staines, Franck Valentin, Albert J. Vilella, Andy Yates:
Ensembl Genomes: Extending Ensembl across the taxonomic space. 563-569 - Phil Wilkinson, Jitka Sengerova, Raffaele Matteoni, Chao-Kung Chen, Gaetan Soulat, Abel Ureta-Vidal, Sabine Fessele, Michael Hagn, Marzia Massimi, Karen Pickford, Richard H. Butler, Susan Marschall, Ann-Marie Mallon, Amanda J. Pickard, Marcello Raspa, Ferdinando Scavizzi, Martin Fray, Vanessa Larrigaldie, Johan Leyritz, Ewan Birney, Glauco P. Tocchini-Valentini, Steve D. M. Brown, Yann Herault, Lluis Montoliu, Martin Hrabé de Angelis, Damian Smedley:
EMMA - mouse mutant resources for the international scientific community. 570-576 - Hugh Morgan, Tim Beck, Andrew Blake, Hilary Gates, Niels C. Adams, Guillaume Debouzy, Sophie Leblanc, Christoph Lengger, Holger Maier, David G. Melvin, Hamid Meziane, Dave Richardson, Sara Wells, Jacqui White, Joe Wood, Martin Hrabé de Angelis, Steve D. M. Brown, John M. Hancock, Ann-Marie Mallon:
EuroPhenome: a repository for high-throughput mouse phenotyping data. 577-585 - Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, Janan T. Eppig:
The Mouse Genome Database: enhancements and updates. 586-592 - Andrew Blake, Karen Pickford, Simon Greenaway, Steve Thomas, Amanda J. Pickard, Christine M. Williamson, Niels C. Adams, Alison Walling, Tim Beck, Martin Fray, Jo Peters, Tom Weaver, Steve D. M. Brown, John M. Hancock, Ann-Marie Mallon:
MouseBook: an integrated portal of mouse resources. 593-599 - Keiko Akagi, Robert M. Stephens, Jingfeng Li, Evgenji Evdokimov, Michael R. Kuehn, Natalia Volfovsky, David E. Symer:
MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains. 600-606 - Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Chris Jarabek, Kenan Azam, Aaron M. Zorn, Peter D. Vize:
Xenbase: gene expression and improved integration. 607-612 - Brooke L. Rhead, Donna Karolchik, Robert M. Kuhn, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Mark Diekhans, Kayla E. Smith, Kate R. Rosenbloom, Brian J. Raney, Andy Pohl, Michael Pheasant, Laurence R. Meyer, Katrina Learned, Fan Hsu, Jennifer Hillman-Jackson, Rachel A. Harte, Belinda Giardine, Timothy R. Dreszer, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
The UCSC Genome Browser database: update 2010. 613-619 - Kate R. Rosenbloom, Timothy R. Dreszer, Michael Pheasant, Galt P. Barber, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Ting Wang, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Katrina Learned, Brooke L. Rhead, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, David Haussler, W. James Kent:
ENCODE whole-genome data in the UCSC Genome Browser. 620-625 - Chisato Yamasaki, Katsuhiko Murakami, Jun-ichi Takeda, Yoshiharu Sato, Akiko Ogura Noda, Ryuichi Sakate, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Akihiro Matsuya, Tadashi Imanishi, Takashi Gojobori:
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. 626-632 - Jon W. Huss III, Pierre Lindenbaum, Michael Martone, Donabel Roberts, Angel D. Pizarro, Faramarz Valafar, John B. Hogenesch, Andrew I. Su:
The Gene Wiki: community intelligence applied to human gene annotation. 633-639 - Samuel Hiard, Carole Charlier, Wouter Coppieters, Michel Georges, Denis Baurain:
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. 640-651 - Simon A. Forbes, Gurpreet W. Tang, Nidhi Bindal, Sally Bamford, Elisabeth Dawson, Charlotte Cole, Chai Yin Kok, Mingming Jia, Rebecca Ewing, Andrew Menzies, Jon W. Teague, Michael R. Stratton, P. Andrew Futreal:
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. 652-657 - Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie, Yixue Li:
dbDEPC: a database of Differentially Expressed Proteins in human Cancers. 658-664 - Lishan Wang, Yuanyuan Xiong, Yihua Sun, Zhaoyuan Fang, Li Li, Hongbin Ji, Tieliu Shi:
HLungDB: an integrated database of human lung cancer research. 665-669 - Adnan S. Syed, Matteo D'Antonio, Francesca D. Ciccarelli:
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. 670-675 - Brian A. Kennedy, Wenqing Gao, Tim Hui-Ming Huang, Victor X. Jin:
HRTBLDb: an informative data resource for hormone receptors target binding loci. 676-681 - Stefan M. Woerner, Yan P. Yuan, Axel Benner, Sebastian Korff, Magnus von Knebel Doeberitz, Peer Bork:
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology. 682-689 - Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen E. Parkinson, Alvis Brazma:
Gene Expression Atlas at the European Bioinformatics Institute. 690-698 - Nicholas Paul Gauthier, Lars Juhl Jensen, Rasmus Wernersson, Søren Brunak, Thomas Skøt Jensen:
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. 699-702 - Lorna J. Richardson, Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Nicholas Burton, Jianguo Rao, Malcolm E. Fisher, Richard A. Baldock, Duncan Davidson, Jeffrey H. Christiansen:
EMAGE mouse embryo spatial gene expression database: 2010 update. 703-709 - Jun Zhao, Graham Klyne, Elizabeth Benson, Elin Gudmannsdottir, Helen White-Cooper, David M. Shotton:
FlyTED: the Drosophila Testis Gene Expression Database. 710-715 - Aedín C. Culhane, Thomas Schwarzl, Razvan Sultana, Kermshlise C. Picard, Shaita C. Picard, Tim H. Lu, Katherine R. Franklin, Simon J. French, Gerald Papenhausen, Mick Correll, John Quackenbush:
GeneSigDB - a curated database of gene expression signatures. 716-725 - Ramil N. Nurtdinov, Mikhail O. Vasiliev, Anna S. Ershova, Ilia S. Lossev, Anna S. Karyagina:
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays. 726-730 - Li Ji, Tanya Barrett, Oluwabukunmi Ayanbule, Dennis B. Troup, Dmitry Rudnev, Rolf N. Muertter, Maxim Tomashevsky, Alexandra Soboleva, Douglas J. Slotta:
NCBI Peptidome: a new repository for mass spectrometry proteomics data. 731-735 - Juan Antonio Vizcaíno, Richard G. Côté, Florian Reisinger, Harald Barsnes, Joseph M. Foster, Jonathan Rameseder, Henning Hermjakob, Lennart Martens:
The Proteomics Identifications database: 2010 update. 736-742 - Catherine Y. Cormier, Stephanie E. Mohr, Dongmei Zuo, Yanhui Hu, Andreas Rolfs, Jason Kramer, Elena Taycher, Fontina Kelley, Michael Fiacco, Greggory Turnbull, Joshua LaBaer:
Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community. 743-749 - Ron Milo, Paul Jorgensen, Uri Moran, Griffin M. Weber, Michael Springer:
BioNumbers - the database of key numbers in molecular and cell biology. 750-753 - Lynn M. Schriml, Cesar Arze, Suvarna Nadendla, Anurhada Ganapathy, Victor Felix, Anup Mahurkar, Katherine H. Phillippy, Aaron Gussman, Samuel V. Angiuoli, Elodie Ghedin, Owen White, Neil Hall:
GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. 754-764 - Liwei Li, Khuchtumur Bum-Erdene, Peter H. Baenziger, Joshua J. Rosen, Jamison R. Hemmert, Joy A. Nellis, Marlon E. Pierce, Samy O. Meroueh:
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome. 765-773 - Shaini Thomas, Shreyas Karnik, Ram Shankar Barai, Vaidyanathan K. Jayaraman, Susan Idicula-Thomas:
CAMP: a useful resource for research on antimicrobial peptides. 774-780 - Emilia Lim, Allison Pon, Yannick Djoumbou, Craig Knox, Savita Shrivastava, Anchi Guo, Vanessa Neveu, David S. Wishart:
T3DB: a comprehensively annotated database of common toxins and their targets. 781-786 - Feng Zhu, Bu-Cong Han, Pankaj Kumar, Xianghui Liu, Xiao Hua Ma, XiaoNa Wei, Lu Huang, Yangfan Guo, Lianyi Han, Chanjuan Zheng, Yuzong Chen:
Update of TTD: Therapeutic Target Database. 787-791 - Athanasia Spandidos, Xiaowei Wang, Huajun Wang, Brian Seed:
PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification. 792-799 - Agatha Schlüter, Alejandro Real-Chicharro, Toni Gabaldón, Francisca Sánchez-Jiménez, Aurora Pujol:
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome. 800-805 - Zhenhai Zhang, Jingyin Yu, Daofeng Li, Zuyong Zhang, Fengxia Liu, Xin Zhou, Tao Wang, Yi Ling, Zhen Su:
PMRD: plant microRNA database. 806-813 - Walter Sanseverino, Guglielmo Roma, Marco De Simone, Luigi Faino, Sara Melito, Elia Stupka, Luigi Frusciante, Maria Raffaella Ercolano:
PRGdb: a bioinformatics platform for plant resistance gene analysis. 814-821 - Paulino Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Corrêa, Stefan A. Rensing, Birgit Kersten, Bernd Mueller-Roeber:
PlnTFDB: updated content and new features of the plant transcription factor database. 822-827 - Pawel Durek, Robert Schmidt, Joshua L. Heazlewood, Alexandra Jones, Daniel MacLean, Axel Nagel, Birgit Kersten, Waltraud X. Schulze:
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. 828-834 - Motohiro Mihara, Takeshi Itoh, Takeshi Izawa:
SALAD database: a motif-based database of protein annotations for plant comparative genomics. 835-842 - David M. Grant, Rex T. Nelson, Steven B. Cannon, Randy C. Shoemaker:
SoyBase, the USDA-ARS soybean genetics and genomics database. 843-846 - Hifzur Rahman Ansari, Darren R. Flower, G. P. S. Raghava:
AntigenDB: an immunoinformatics database of pathogen antigens. 847-853 - Randi Vita, Laura Zarebski, Jason Greenbaum, Hussein Emami, Ilka Hoof, Nima Salimi, Rohini Damle, Alessandro Sette, Björn Peters:
The Immune Epitope Database 2.0. 854-862 - James Robinson, Kavita Mistry, Hamish McWilliam, Rodrigo Lopez, Steven G. E. Marsh:
IPD - the Immuno Polymorphism Database. 863-869 - Martin Shumway, Guy Cochrane, Hideaki Sugawara:
Archiving next generation sequencing data. 870-871
Volume 38, Number Web-Server-Issue, July 2010
- Gary Benson:
Editorial. 1-2
- Michelle D. Brazas, Joseph Tadashi Yamada, B. F. Francis Ouellette:
Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory. 3-6 - Federico Abascal, Rafael Zardoya, Maximilian J. Telford:
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. 7-13 - Daniel Glez-Peña, Daniel Gómez-Blanco, Miguel Reboiro-Jato, Florentino Fdez-Riverola, David Posada:
ALTER: program-oriented conversion of DNA and protein alignments. 14-18 - Amarendran Ramaswami Subramanian, Suvrat Hiran, Rasmus Steinkamp, Peter Meinicke, Eduardo Corel, Burkhard Morgenstern:
DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS. 19-22 - Osnat Penn, Eyal Privman, Haim Ashkenazy, Giddy Landan, Dan Graur, Tal Pupko:
GUIDANCE: a web server for assessing alignment confidence scores. 23-28 - Raffi Hagopian, John R. Davidson, Ruchira S. Datta, Bushra Samad, Glen R. Jarvis, Kimmen Sjölander:
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction. 29-34 - Bernd W. Brandt, K. Anton Feenstra, Jaap Heringa:
Multi-Harmony: detecting functional specificity from sequence alignment. 35-40 - Raffaello Potestio, Tyanko Aleksiev, Francesco Pontiggia, Stefano Cozzini, Cristian Micheletti:
ALADYN: a web server for aligning proteins by matching their large-scale motion. 41-45 - Aysam Guerler, Ernst-Walter Knapp:
GIS: a comprehensive source for protein structure similarities. 46-52 - Chi-Ren Shyu, Bin Pang, Pin-Hao Chi, Nan Zhao, Dmitry Korkin, Dong Xu:
ProteinDBS v2.0: a web server for global and local protein structure search. 53-58 - Satish Chikkagoudar, Dennis R. Livesay, Usman Roshan:
PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences. 59-63 - Zhou Du, Xin Zhou, Yi Ling, Zhenhai Zhang, Zhen Su:
agriGO: a GO analysis toolkit for the agricultural community. 64-70 - Jianguo Xia, David S. Wishart:
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. 71-77 - Alexey V. Antonov, Esther Schmidt, Sabine Dietmann, Maria Krestyaninova, Henning Hermjakob:
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. 78-83 - Nadav Rappoport, Menachem Fromer, Regev Schweiger, Michal Linial:
PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. 84-89 - Kunlin Zhang, Sijia Cui, Suhua Chang, Liuyan Zhang, Jing Wang:
i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. 90-95 - Vivek Kaimal, Eric E. Bardes, Scott C. Tabar, Anil G. Jegga, Bruce J. Aronow:
ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. 96-102 - Choong-Hyun Sun, Taeho Hwang, Kimin Oh, Gwan-Su Yi:
DynaMod: dynamic functional modularity analysis. 103-108 - Jignesh R. Parikh, Bertram Klinger, Yu Xia, Jarrod A. Marto, Nils Blüthgen:
Discovering causal signaling pathways through gene-expression patterns. 109-117 - Sabine Dietmann, Wanseon Lee, Philip Wong, Igor V. Rodchenkov, Alexey V. Antonov:
CCancer: a bird's eye view on gene lists reported in cancer-related studies. 118-123 - Yi-Ting Wang, Yen-Hua Huang, Y.-C. Chen, Chia-Lang Hsu, Ueng-Cheng Yang:
PINT: Pathways INtegration Tool. 124-131 - Ludovic Cottret, David Wildridge, Florence Vinson, Michael P. Barrett, Hubert Charles, Marie-France Sagot, Fabien Jourdan:
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. 132-137 - Yuki Moriya, Daichi Shigemizu, Masahiro Hattori, Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto, Minoru Kanehisa:
PathPred: an enzyme-catalyzed metabolic pathway prediction server. 138-143 - Marija Cvijovic, Roberto Olivares-Hernández, Rasmus Agren, Niklas Dahr, Wanwipa Vongsangnak, Intawat Nookaew, Kiran Raosaheb Patil, Jens Nielsen:
BioMet Toolbox: genome-wide analysis of metabolism. 144-149 - Alptug Dilek, Mehmet E. Belviranli, Ugur Dogrusoz:
VISIBIOweb: visualization and layout services for BioPAX pathway models. 150-154 - Richard G. Côté, Florian Reisinger, Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, Henning Hermjakob:
The Ontology Lookup Service: bigger and better. 155-160 - Barry Moore, Guozhen Fan, Karen Eilbeck:
SOBA: sequence ontology bioinformatics analysis. 161-164 - Divya Sardana, Suresh Vasa, Nishanth Vepachedu, Jing Chen, Ranga Chandra Gudivada, Bruce J. Aronow, Anil G. Jegga:
PhenoHM: human-mouse comparative phenome-genome server. 165-174 - Xin He, Yanen Li, Radhika S. Khetani, Barry Sanders, Yue Lu, Xu Ling, ChengXiang Zhai, Bruce R. Schatz:
BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects. 175-181 - Angel Carro, Daniel Rico, Oscar M. Rueda, Ramón Díaz-Uriarte, David G. Pisano:
waviCGH: a web application for the analysis and visualization of genomic copy number alterations. 182-187 - Jitender Cheema, T. H. Noel Ellis, Jo L. Dicks:
THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps. 188-193 - Yucheng Shao, Xinyi He, Ewan M. Harrison, Cui Tai, Hong-Yu Ou, Kumar Rajakumar, Zixin Deng:
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. 194-200 - Scott F. Saccone, Raphael Bolze, Prasanth Thomas, Jiaxi Quan, Gaurang Mehta, Ewa Deelman, Jay A. Tischfield, John R. Rice:
SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. 201-209 - Ignacio Medina, José Carbonell, Luis Pulido, Sara C. Madeira, Stefan Götz, Ana Conesa, Joaquín Tárraga, Alberto D. Pascual-Montano, Rubén Nogales-Cadenas, Javier Santoyo, Francisco García-García, Martina Marbà, David Montaner, Joaquín Dopazo:
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. 210-213 - David Warde-Farley, Sylva L. Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes, Anson Maitland, Sara Mostafavi, Jason Montojo, Quentin Shao, George Wright, Gary D. Bader, Quaid Morris:
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. 214-220 - Yen-Lin Huang, Chen-Cheng Huang, Chuan Yi Tang, Chin Lung Lu:
SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations. 221-227 - Miguel Vázquez, Rubén Nogales-Cadenas, Javier Arroyo, Pedro Botías, Raul García, José María Carazo, Francisco Tirado, Alberto D. Pascual-Montano, Pedro Carmona-Saez:
MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. 228-232 - Szymon M. Kielbasa, Nils Blüthgen, Michael Fähling, Ralf Mrowka:
Targetfinder.org: a resource for systematic discovery of transcription factor target genes. 233-238 - María José Nueda, José Carbonell, Ignacio Medina, Joaquín Dopazo, Ana Conesa:
Serial Expression Analysis: a web tool for the analysis of serial gene expression data. 239-245 - Taegyun Yun, Taeho Hwang, Kihoon Cha, Gwan-Su Yi:
CLIC: clustering analysis of large microarray datasets with individual dimension-based clustering. 246-253 - Richard C. Stolz, Thomas C. Bishop:
ICM Web: the interactive chromatin modeling web server. 254-261 - Ivan Merelli, Alessandro Guffanti, Marco Fabbri, Andrea Cocito, Laura Furia, Ursula Grazini, Raoul Jean Pierre Bonnal, Luciano Milanesi, Fraser McBlane:
RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes. 262-267 - Michael J. Palumbo, Lee Aaron Newberg:
Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data. 268-274 - Szymon M. Kielbasa, Holger Klein, Helge G. Roider, Martin Vingron, Nils Blüthgen:
TransFind - predicting transcriptional regulators for gene sets. 275-280 - Inbal Paz, Martin Akerman, Iris Dror, Idit Kosti, Yael Mandel-Gutfreund:
SFmap: a web server for motif analysis and prediction of splicing factor binding sites. 281-285 - Laurie Tonon, Hélène Touzet, Jean-Stéphane Varré:
TFM-Explorer: mining cis-regulatory regions in genomes. 286-292 - Vineeth Surendranath, Janet Chusainow, Joachim Hauber, Frank Buchholz, Bianca Habermann:
SeLOX - a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems. 293-298 - Pavel S. Novichkov, Dmitry A. Rodionov, Elena D. Stavrovskaya, Elena S. Novichkova, Alexei E. Kazakov, Mikhail S. Gelfand, Adam P. Arkin, Andrey A. Mironov, Inna Dubchak:
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. 299-307 - Alain L. Gervais, Maud Marques, Luc Gaudreau:
PCRTiler: automated design of tiled and specific PCR primer pairs. 308-312 - Frank M. You, Humphrey Wanjugi, Naxin Huo, Gerard R. Lazo, Ming-Cheng Luo, Olin D. Anderson, Jan Dvorak, Yong Qiang Gu:
RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development. 313-320 - Yann S. Dufour, Gary E. Wesenberg, Andrew J. Tritt, Jeremy D. Glasner, Nicole T. Perna, Julie C. Mitchell, Timothy J. Donohue:
chipD: a web tool to design oligonucleotide probes for high-density tiling arrays. 321-325 - Thomas Weniger, Justina Krawczyk, Philip Supply, Stefan Niemann, Dag Harmsen:
MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria. 326-331 - Thomas Horn, Michael Boutros:
E-RNAi: a web application for the multi-species design of RNAi reagents - 2010 update. 332-339 - Chih-Wei Wang, Kun-Tze Chen, Chin Lung Lu:
iPARTS: an improved tool of pairwise alignment of RNA tertiary structures. 340-347 - Regina Bohnert, Gunnar Rätsch:
rQuant.web: a tool for RNA-Seq-based transcript quantitation. 348-351 - Gabriele Sales, Alessandro Coppe, Andrea Bisognin, Marta Biasiolo, Stefania Bortoluzzi, Chiara Romualdi:
MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. 352-359 - Monica Campillos, Ildefonso Cases, Matthias W. Hentze, Mayka Sanchez:
SIREs: searching for iron-responsive elements. 360-367 - Eckart Bindewald, Tanner Kluth, Bruce A. Shapiro:
CyloFold: secondary structure prediction including pseudoknots. 368-372 - Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen:
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. 373-377 - Andreas Massouras, Frederik Decouttere, Korneel Hens, Bart Deplancke:
WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data. 378-384 - Po-Jung Huang, Yi-Chung Liu, Chi-Ching Lee, Wei-Chen Lin, Richie Ruei-Chi Gan, Ping-Chiang Lyu, Petrus Tang:
DSAP: deep-sequencing small RNA analysis pipeline. 385-391 - Erle Zhu, Fangqing Zhao, Gang Xu, Huabin Hou, LingLin Zhou, Xiaokun Li, Zhongsheng Sun, Jinyu Wu:
mirTools: microRNA profiling and discovery based on high-throughput sequencing. 392-397 - Shandar Ahmad, Ozlem Keskin, Kenji Mizuguchi, Akinori Sarai, Ruth Nussinov:
CCRXP: exploring clusters of conserved residues in protein structures. 398-401 - Nurcan Tuncbag, Ozlem Keskin, Attila Gürsoy:
HotPoint: hot spot prediction server for protein interfaces. 402-406 - Lidio M. C. Meireles, Alexander S. Dömling, Carlos J. Camacho:
ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery. 407-411 - Yoichi Murakami, Ruth V. Spriggs, Haruki Nakamura, Susan Jones:
PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. 412-416 - Pemra Ozbek, Seren Soner, Burak Erman, Turkan Haliloglu:
DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. 417-423 - Yen-Fu Chen, Kai-Cheng Hsu, Shen-Rong Lin, Wen-Ching Wang, Yu-Chi Huang, Jinn-Moon Yang:
SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties. 424-430 - Matthew B. Carson, Robert E. Langlois, Hui Lu:
NAPS: a residue-level nucleic acid-binding prediction server. 431-435 - Janez Konc, Dusanka Janezic:
ProBiS: a web server for detection of structurally similar protein binding sites. 436-440 - Jingyuan Ren, Lei Xie, Wilfred W. Li, Philip E. Bourne:
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. 441-444 - Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie:
HexServer: an FFT-based protein docking server powered by graphics processors. 445-449 - Yoon Sup Choi, Seong Kyu Han, Jinho Kim, Jae-Seong Yang, Jouhyun Jeon, Sung Ho Ryu, Sanguk Kim:
ConPlex: a server for the evolutionary conservation analysis of protein complex structures. 450-456 - Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson:
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. 457-461 - Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, Drena Dobbs:
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. 462-468 - Mark N. Wass, Lawrence A. Kelley, Michael J. E. Sternberg:
3DLigandSite: predicting ligand-binding sites using similar structures. 469-473 - Xihao Hu, Wenjian Zhou, Keiko Udaka, Hiroshi Mamitsuka, Shanfeng Zhu:
MetaMHC: a meta approach to predict peptides binding to MHC molecules. 474-479 - Dennis M. Krüger, Holger Gohlke:
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. 480-486 - Swadha Anand, M. V. R. Prasad, Gitanjali Yadav, Narendra Kumar, Jyoti Shehara, Mohd. Zeeshan Ansari, Debasisa Mohanty:
SBSPKS: structure based sequence analysis of polyketide synthases. 487-496 - Sebastian Briesemeister, Jörg Rahnenführer, Oliver Kohlbacher:
YLoc - an interpretable web server for predicting subcellular localization. 497-502 - Hsuan-Hung Lin, Lin-Yu Tseng:
DBCP: a web server for disulfide bonding connectivity pattern prediction without the prior knowledge of the bonding state of cysteines. 503-507 - Rohit Singh, Daniel Park, Jinbo Xu, Raghavendra Hosur, Bonnie Berger:
Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. 508-515 - Yu-Shu Lo, Chun-Yu Lin, Jinn-Moon Yang:
PCFamily: a web server for searching homologous protein complexes. 516-522 - Gilad Wainreb, Haim Ashkenazy, Yana Bromberg, Alina Starovolsky-Shitrit, Turkan Haliloglu, Eytan Ruppin, Karen B. Avraham, Burkhard Rost, Nir Ben-Tal:
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. 523-528 - Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, Nir Ben-Tal:
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. 529-533 - Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards:
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. 534-539 - Dina Schneidman-Duhovny, Michal Hammel, Andrej Sali:
FoXS: a web server for rapid computation and fitting of SAXS profiles. 540-544 - Liisa Holm, Päivi Rosenström:
Dali server: conservation mapping in 3D. 545-549 - Raquel Norel, Donald Petrey, Barry Honig:
PUDGE: a flexible, interactive server for protein structure prediction. 550-554 - Neil Voss, Mark Gerstein:
3V: cavity, channel and cleft volume calculator and extractor. 555-562 - Daniel W. A. Buchan, S. M. Ward, Anna E. Lobley, Timothy Nugent, Kevin Bryson, David T. Jones:
Protein annotation and modelling servers at University College London. 563-568 - Florian Lauck, Colin A. Smith, Gregory F. Friedland, Elisabeth L. Humphris, Tanja Kortemme:
RosettaBackrub - a web server for flexible backbone protein structure modeling and design. 569-575 - Morten Nielsen, Claus Lundegaard, Ole Lund, Thomas Nordahl Petersen:
CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles. 576-581 - Peter Schmidtke, Vincent Le Guilloux, Julien Maupetit, Pierre Tufféry:
fpocket: online tools for protein ensemble pocket detection and tracking. 582-589 - Zong Hong Zhang, Kavitha Bharatham, Westley A. Sherman, Ivana Mihalek:
deconSTRUCT: general purpose protein database search on the substructure level. 590-594 - Gregory Cipriano, Gary Wesenberg, Tom Grim, George N. Phillips Jr., Michael Gleicher:
GRAPE: GRaphical Abstracted Protein Explorer. 595-601 - Alexander S. Rose, Andrean Goede, Peter Werner Hildebrand:
MPlot - a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins. 602-608 - Xiaofeng Liu, Sisheng Ouyang, Biao Yu, Yabo Liu, Kai Huang, Jiayu Gong, Siyuan Zheng, Zhihua Li, Honglin Li, Hualiang Jiang:
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. 609-614 - Dominique Douguet:
e-LEA3D: a computational-aided drug design web server. 615-621 - Maria A. Miteva, Frédéric Guyon, Pierre Tufféry:
Frog2: Efficient 3D conformation ensemble generator for small compounds. 622-627 - Davide Martin Heller, Alejandro Giorgetti:
NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints. 628-632 - Mark V. Berjanskii, Yongjie Liang, Jianjun Zhou, Peter Tang, Paul Stothard, You Zhou, Joseph A. Cruz, Cam Macdonell, Guohui Lin, Paul Lu, David S. Wishart:
PROSESS: a protein structure evaluation suite and server. 633-640 - Russell S. Hamilton, Richard M. Parton, Raquel Alves Oliveira, Georgia Vendra, Graeme Ball, Kim Nasmyth, Ilan Davis:
ParticleStats: open source software for the analysis of particle motility and cytoskeletal polarity. 641-646 - Anne de Jong, Auke J. van Heel, Jan Kok, Oscar P. Kuipers:
BAGEL2: mining for bacteriocins in genomic data. 647-651 - Masahiro Hattori, Nobuya Tanaka, Minoru Kanehisa, Susumu Goto:
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. 652-656 - Jeffrey K. Noel, Paul C. Whitford, Karissa Y. Sanbonmatsu, José N. Onuchic:
SMOG@ctbp: simplified deployment of structure-based models in GROMACS. 657-661 - Aleksey A. Porollo, Jaroslaw Meller:
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations. 662-666 - Hiren J. Joshi, Claus-Wilhelm von der Lieth, Nicolle H. Packer, Marc R. Wilkins:
GlycoViewer: a tool for visual summary and comparative analysis of the glycome. 667-670 - Sergio Ramírez, Antonio Muñoz-Merida, Tor Johan Mikael Karlsson, Maximiliano García, Antonio J. Pérez-Pulido, M. Gonzalo Claros, Oswaldo Trelles:
MOWServ: a web client for integration of bioinformatic resources. 671-676 - Carole A. Goble, Jiten Bhagat, Sergejs Aleksejevs, Don Cruickshank, Danius T. Michaelides, David R. Newman, Mark Borkum, Sean Bechhofer, Marco Roos, Peter Li, David De Roure:
myExperiment: a repository and social network for the sharing of bioinformatics workflows. 677-682
- Steve Pettifer, Jon C. Ison, Matús Kalas, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, José María Fernández, José Manuel Rodriguez, David G. Pisano, Christophe Blanchet, Mahmut Uludag, Peter M. Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten L. Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B. Clegg, Erik Bongcam-Rudloff, Jean Salzemann, Vincent Breton, Teresa K. Attwood, Graham Cameron, Gert Vriend:
The EMBRACE web service collection. 683-688 - Jiten Bhagat, Franck Tanoh, Eric Nzuobontane, Thomas Laurent, Jerzy Orlowski, Marco Roos, Katy Wolstencroft, Sergejs Aleksejevs, Robert Stevens, Steve Pettifer, Rodrigo Lopez, Carole A. Goble:
BioCatalogue: a universal catalogue of web services for the life sciences. 689-694 - Mickael Goujon, Hamish McWilliam, Weizhong Li, Franck Valentin, Silvano Squizzato, Juri Paern, Rodrigo Lopez:
A new bioinformatics analysis tools framework at EMBL-EBI. 695-699 - Kazuharu Arakawa, Nobuhiro Kido, Kazuki Oshita, Masaru Tomita:
G-language genome analysis environment with REST and SOAP web service interfaces. 700-705 - Toshiaki Katayama, Mitsuteru Nakao, Toshihisa Takagi:
TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services. 706-711 - Achille Zappa, Mariangela Miele, Paolo Romano:
IBWS: IST Bioinformatics Web Services. 712-718 - Maarten L. Hekkelman, Tim A. H. te Beek, Steve Pettifer, David Thorne, Terri K. Attwood, Gert Vriend:
WIWS: a protein structure bioinformatics Web service collection. 719-723 - Jingyuan Ren, Nadya Williams, Luca Clementi, Sriram Krishnan, Wilfred W. Li:
Opal web services for biomedical applications. 724-731
- Huabin Hou, Fangqing Zhao, LingLin Zhou, Erle Zhu, Huajing Teng, Xiaokun Li, Qiyu Bao, Jinyu Wu, Zhongsheng Sun:
MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation. 732-736 - Dhananjai Madhava Rao, J. C. Moler, Mufit Ozden, Y. Zhang, C. Liang, John E. Karro:
PEACE: Parallel Environment for Assembly and Clustering of Gene Expression. 737-742 - Zefeng Zhang, Hao Lin, Bin Ma:
ZOOM Lite: next-generation sequencing data mapping and visualization software. 743-748 - Dougu Nam, Jin Kim, Seon-Young Kim, Sangsoo Kim:
GSA-SNP: a general approach for gene set analysis of polymorphisms. 749-754 - Dorothea Emig, Nathan Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, Mario Albrecht:
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. 755-762
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