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ORCIDNucleic Acids Research, Volume 40
Volume 40, Number Database-Issue, January 2012
- Michael Y. Galperin
, Xosé M. Fernández-Suárez:
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. 1-8 - Robert D. Finn, Paul P. Gardner, Alex Bateman:
Making your database available through Wikipedia: the pros and cons. 9-12 - 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, Ian M. Fingerman, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Sergey Krasnov, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Karsch-Mizrachi, James Ostell, Anna R. Panchenko, Lon Phan, 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. 13-25 - Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David M. Goodstein, Alan Kuo, Simon Minovitsky, Roman Nikitin, Robin A. Ohm, Robert Otillar, Alexander Poliakov, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak:
The Genome Portal of the Department of Energy Joint Genome Institute. 26-32 - Ilene Karsch-Mizrachi, Yasukazu Nakamura, Guy Cochrane:
The International Nucleotide Sequence Database Collaboration. 33-37 - Yuichi Kodama, Jun Mashima, Eli Kaminuma, Takashi Gojobori, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura:
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. 38-42 - Clara Amid, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Richard Gibson, Neil Goodgame, Christopher I. Hunter, Mikyung Jang, Rasko Leinonen, Xin Liu, Arnaud Oisel, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Stéphane Rivière, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Petra ten Hoopen, Daniel Vaughan, Robert Vaughan, Vadim Zalunin, Guy Cochrane:
Major submissions tool developments at the European nucleotide archive. 43-47 - Dennis A. Benson, Ilene Karsch-Mizrachi, Karen Clark, David J. Lipman, James Ostell, Eric W. Sayers:
GenBank. 48-53 - Yuichi Kodama, Martin Shumway, Rasko Leinonen:
The sequence read archive: explosive growth of sequencing data. 54-56 - Tanya Barrett, Karen Clark, Robert Gevorgyan, Vyatcheslav Gorelenkov, Eugene Gribov, Ilene Karsch-Mizrachi, Michael Kimelman, Kim D. Pruitt, Sergei Resenchuk, Tatiana A. Tatusova, Eugene Yaschenko, James Ostell:
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. 57-63 - Mikhail Gostev, Adam Faulconbridge, Marco Brandizi, Julio Fernandez-Banet, Ugis Sarkans, Alvis Brazma, Helen E. Parkinson:
The BioSample Database (BioSD) at the European Bioinformatics Institute. 64-70 - Reorganizing the protein space at the Universal Protein Resource (UniProt). 71-75
- Lydie Lane, Ghislaine Argoud-Puy, Aurore Britan, Isabelle Cusin, Paula Duek Roggli, Olivier Evalet, Alain Gateau, Pascale Gaudet, Anne Gleizes, Alexandre Masselot, Catherine Zwahlen, Amos Bairoch:
neXtProt: a knowledge platform for human proteins. 76-83 - Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Monika Komorowska, Gautier Koscielny, Eugene Kulesha, Pontus Larsson, Ian Longden, William M. McLaren, Matthieu Muffato, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Y. Amy Tang, Kieron R. Taylor, Stephen J. Trevanion, Jana Vandrovcova, Simon White, Mark Wilson, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates, Amonida Zadissa, Stephen M. J. Searle:
Ensembl 2012. 84-90 - Paul J. Kersey, Daniel M. Staines, Daniel Lawson, Eugene Kulesha, Paul S. Derwent, Jay C. Humphrey, Daniel S. T. Hughes, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Nicholas Langridge, Mark D. McDowall, Karine Megy, Uma Maheswari, Michael Nuhn, Michael Paulini, Helder Pedro, Iliana Toneva, Derek Wilson, Andrew D. Yates, Ewan Birney:
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. 91-97 - Flora J. Logan-Klumpler, Nishadi De Silva, Ulrike Böhme, Matthew B. Rogers, Giles Velarde, Jacqueline A. McQuillan, Tim Carver, Martin Aslett, Christian Olsen, Sandhya Subramanian, Isabelle Phan, Carol Farris, Siddhartha Mitra, Gowthaman Ramasamy, Haiming Wang, Adrian Tivey, Andrew Jackson, Robin Houston, Julian Parkhill, Matthew T. G. Holden, Omar S. Harb, Brian P. Brunk, Peter J. Myler, David S. Roos, Mark Carrington, Deborah F. Smith, Christiane Hertz-Fowler, Matthew Berriman:
GeneDB - an annotation database for pathogens. 98-108 - Minoru Kanehisa, Susumu Goto, Yoko Sato, Miho Furumichi, Mao Tanabe:
KEGG for integration and interpretation of large-scale molecular data sets. 109-114 - Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
IMG: the integrated microbial genomes database and comparative analysis system. 115-122 - Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
IMG/M: the integrated metagenome data management and comparative analysis system. 123-129 - Kim D. Pruitt, Tatiana A. Tatusova, Garth R. Brown, Donna R. Maglott:
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. 130-135 - Scott Federhen:
The NCBI Taxonomy database. 136-143 - Hong-Mei Zhang, Hu Chen, Wei Liu, Hui Liu, Jing Gong, Huili Wang, An-Yuan Guo:
AnimalTFDB: a comprehensive animal transcription factor database. 144-149 - Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. 150-154 - Alberto Riva:
The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites. 155-161 - Aaron T. Spivak, Gary D. Stormo:
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. 162-168 - Carl G. de Boer, Timothy R. Hughes:
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. 169-179 - Gerd Anders, Sebastian D. Mackowiak, Marvin Jens, Jonas Maaskola, Andreas Kuntzagk, Nikolaus Rajewsky, Markus Landthaler, Christoph Dieterich:
doRiNA: a database of RNA interactions in post-transcriptional regulation. 180-186 - Manuel A. Candales, Adrian Duong, Keyar S. Hood, Tony Li, Ryan A. E. Neufeld, Runda Sun, Bonnie A. McNeil, Li Wu, Ashley M. Jarding, Steven Zimmerly:
Database for bacterial group II introns. 187-190 - Dawid Bielewicz, Jakub Dolata, Andrzej Zielezinski, Sylwia Alaba, Bogna Szarzynska, Michal Wojciech Szczesniak, Artur Jarmolowski, Zofia Szweykowska-Kulinska, Wojciech M. Karlowski:
mirEX: a platform for comparative exploration of plant pri-miRNA expression data. 191-197 - Michal Wojciech Szczesniak, Sebastian Deorowicz, Jakub Gapski, Lukasz Kaczynski, Izabela Makalowska:
miRNEST database: an integrative approach in microRNA search and annotation. 198-204 - Alban Ott, Anouar Idali, Antonin Marchais, Daniel Gautheret:
NAPP: the Nucleic Acid Phylogenetic Profile Database. 205-209 - Dechao Bu, Kuntao Yu, Silong Sun, Chaoyong Xie, Geir Skogerbø, Ruoyu Miao, Hui Xiao, Qi Liao, Haitao Luo, Guoguang Zhao, Haitao Zhao, Zhiyong Liu, Changning Liu, Runsheng Chen, Yi Zhao:
NONCODE v3.0: integrative annotation of long noncoding RNAs. 210-215 - Jesse D. Ziebarth, Anindya Bhattacharya, Anlong Chen, Yan Cui:
PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits. 216-221 - Thanasis Vergoulis, Ioannis S. Vlachos, Panagiotis Alexiou, George Georgakilas, Manolis Maragkakis, Martin Reczko, Stefanos Gerangelos, Nectarios Koziris, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. 222-229 - Nishant Thakur, Abid Qureshi, Manoj Kumar:
VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. 230-236 - Ramana Madupu, Alexander R. Richter, Robert J. Dodson, Lauren M. Brinkac, Derek M. Harkins, A. Scott Durkin, Susmita Shrivastava, Granger G. Sutton, Daniel H. Haft:
CharProtDB: a database of experimentally characterized protein annotations. 237-241 - Holger Dinkel, Sushama Michael, Robert J. Weatheritt, Norman E. Davey, Kim Van Roey, Brigitte Altenberg, Grischa Toedt, Bora Uyar, Markus Seiler, Aidan Budd, Lisa Jödicke, Marcel A. Dammert, Christian Schroeter, Maria Hammer, Tobias Schmidt, Peter Jehl, Caroline McGuigan, Magdalena Dymecka, Claudia Chica, Katja Luck, Allegra Via, Andrew Chatr-aryamontri, Niall J. Haslam, Gleb Grebnev, Richard J. Edwards, Michel O. Steinmetz, Heike Meiselbach, Francesca Diella, Toby J. Gibson:
ELM - the database of eukaryotic linear motifs. 242-251 - Tian Mi, Jerlin Camilus Merlin, Sandeep Deverasetty, Michael R. Gryk, Travis J. Bill, Andrew W. Brooks, Logan Y. Lee, Viraj Rathnayake, Christian A. Ross, David P. Sargeant, Christy L. Strong, Paula Watts, Sanguthevar Rajasekaran, Martin R. Schiller:
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. 252-260 - Peter V. Hornbeck, Jon M. Kornhauser, Sasha Tkachev, Bin Zhang, Elzbieta Skrzypek, Beth Murray, Vaughan Latham, Michael Sullivan:
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. 261-270 - Jian Huang, Beibei Ru, Ping Zhu, Fulei Nie, Jun Yang, Xuyang Wang, Ping Dai, Hao Lin, Feng-Biao Guo, Nini Rao:
MimoDB 2.0: a mimotope database and beyond. 271-277 - Irina V. Medvedeva, Pavel Demenkov, Nikolay A. Kolchanov, Vladimir A. Ivanisenko:
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. 278-283 - Sean Powell, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Michael Kuhn, Jean Muller, Roland Arnold, Thomas Rattei, Ivica Letunic, Tobias Doerks, Lars Juhl Jensen, Christian von Mering, Peer Bork:
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. 284-289 - Marco Punta, Penny C. Coggill, Ruth Y. Eberhardt, Jaina Mistry, John G. Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn:
The Pfam protein families database. 290-301 - Ivica Letunic, Tobias Doerks, Peer Bork:
SMART 7: recent updates to the protein domain annotation resource. 302-305 - Sarah Hunter, Philip Jones, Alex L. Mitchell, Rolf Apweiler, Teresa K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge, Edouard De Castro, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Matthew Fraser, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Meullenet, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Sebastien Pesseat, Marco Punta, Antony F. Quinn, Catherine Rivoire, Amaia Sangrador-Vegas, Jeremy D. Selengut, Christian J. A. Sigrist, Maxim Scheremetjew, John G. Tate, Manjulapramila Thimmajanarthanan, Paul D. Thomas, Cathy H. Wu, Corin Yeats, Siew-Yit Yong:
InterPro in 2011: new developments in the family and domain prediction database. 306-312 - Nadav Rappoport, Solange Karsenty, Amos Stern, Nathan Linial, Michal Linial:
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. 313-320 - Fanny Jadeau, Christophe Grangeasse, Lei Shi, Ivan Mijakovic, Gilbert Deléage, Christophe Combet:
BYKdb: the Bacterial protein tYrosine Kinase database. 321-324 - Quentin Kaas, Rilei Yu, Ai-Hua Jin, Sébastien Dutertre, David J. Craik:
ConoServer: updated content, knowledge, and discovery tools in the conopeptide database. 325-330 - Dongseop Kwon, Jong Hwan Yoon, Soo-Yong Shin, Tae-Ho Jang, Hong-Gee Kim, Insuk So, Ju-Hong Jeon, Hyun Ho Park:
A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily. 331-336 - Satyajeet P. Khare, Farhat Habib, Rahul Sharma, Nikhil Gadewal, Sanjay Gupta, Sanjeev Galande:
HIstome - a relational knowledgebase of human histone proteins and histone modifying enzymes. 337-342 - Neil D. Rawlings, Alan J. Barrett, Alex Bateman:
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. 343-350 - Philipp F. Lange, Pitter F. Huesgen, Christopher M. Overall:
TopFIND 2.0 - linking protein termini with proteolytic processing and modifications altering protein function. 351-361 - Anjali Bansal Gupta, Ravi Kumar Verma, Vatsal Agarwal, Manu Vajpai, Vivek Bansal, Ramasubbu Sankararamakrishnan:
MIPModDB: a central resource for the superfamily of major intrinsic proteins. 362-369 - Mikhail A. Lomize, Irina D. Pogozheva, Hyeon Joo, Henry I. Mosberg, Andrei L. Lomize:
OPM database and PPM web server: resources for positioning of proteins in membranes. 370-376 - Bas Vroling, David Thorne, Philip McDermott, Henk-Jan Joosten, Teresa K. Attwood, Steve Pettifer, Gert Vriend:
NucleaRDB: information system for nuclear receptors. 377-380 - Bradley W. Langhorst, William E. Jack, Linda Reha-Krantz, Nicole M. Nichols:
Polbase: a repository of biochemical, genetic and structural information about DNA polymerases. 381-387 - Aadil H. Bhat, Homchoru Mondal, Jagat Singh Chauhan, Gajendra P. S. Raghava, Amrish Methi, Alka Rao:
ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins. 388-393 - Hong Luo, Ke Lin, Audrey David, Harm Nijveen, Jack A. M. Leunissen:
ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins. 394-399 - Yanli Wang, Jewen Xiao, Tugba O. Suzek, Jian Zhang, Jiyao Wang, Zhigang Zhou, Lianyi Han, Karen Karapetyan, Svetlana Dracheva, Benjamin A. Shoemaker, Evan Bolton, Asta Gindulyte, Stephen H. Bryant:
PubChem's BioAssay Database. 400-412 - Ayana Wiener, Marina Shudler, Anat Levit, Masha Y. Niv:
BitterDB: a database of bitter compounds. 413-419 - Saulius Grazulis, Adriana Daskevic, Andrius Merkys, Daniel Chateigner, Luca Lutterotti, Miguel Quirós, Nadezhda R. Serebryanaya, Peter Moeck, Robert T. Downs, Armel Le Bail:
Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration. 420-427 - Abraham Heifets, Igor Jurisica:
SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents. 428-433 - Joachim Schnabl, Pascal Suter, Roland K. O. Sigel:
MINAS - a database of Metal Ions in Nucleic AcidS. 434-438 - Pamela L. Vanegas, Graham A. Hudson, Amber R. Davis, Shannon C. Kelly, Charles C. Kirkpatrick, Brent M. Znosko:
RNA CoSSMos: Characterization of Secondary Structure Motifs - a searchable database of secondary structure motifs in RNA three-dimensional structures. 439-444 - Sameer Velankar, Younes Alhroub, Christoph Best, Ségolène Caboche, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Adel Golovin, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Egon Heuson, Miriam Hirshberg, Melford John, Ingvar C. Lagerstedt, Saqib Mir, Laurence E. Newman, Thomas J. Oldfield, Ardan Patwardhan, Luana Rinaldi, Gaurav Sahni, Eduardo Sanz-García, Sanchayita Sen, Robert A. Slowley, Antonio Suarez-Uruena, G. J. Swaminathan, Martyn F. Symmons, Wim F. Vranken, Michael E. Wainwright, Gerard J. Kleywegt:
PDBe: Protein Data Bank in Europe. 445-452 - Akira R. Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, Atsushi Nakagawa, Haruki Nakamura:
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. 453-460 - Thomas Madej, Kenneth J. Addess, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Christopher J. Lanczycki, Chunlei Liu, Shennan Lu, Aron Marchler-Bauer, Anna R. Panchenko, Jie Chen, Paul A. Thiessen, Yanli Wang, Dachuan Zhang, Stephen H. Bryant:
MMDB: 3D structures and macromolecular interactions. 461-464 - Jonathan G. Lees, Corin Yeats, James Richard Perkins, Ian Sillitoe, Robert Rentzsch, Benoit H. Dessailly, Christine A. Orengo:
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. 465-471 - Darby Tien-Hao Chang, Tsung-Ju Yao, Chen-Yu Fan, Chih-Yun Chiang, Yi-Han Bai:
AH-DB: collecting protein structure pairs before and after binding. 472-478 - Joan Segura, Baldomero Oliva, Narcis Fernandez-Fuentes:
CAPS-DB: a structural classification of helix-capping motifs. 479-485 - Harinder Singh, Jagat Singh Chauhan, M. Michael Gromiha, Gajendra P. S. Raghava:
ccPDB: compilation and creation of data sets from Protein Data Bank. 486-489 - Zong Hong Zhang, Kavitha Bharatham, Sharon M. Q. Chee, Ivana Mihalek:
Cube-DB: detection of functional divergence in human protein families. 490-494 - Alexander Jarasch, Philipp Dziuk, Thomas Becker, Jean-Paul Armache, Andreas Hauser, Daniel N. Wilson, Roland Beckmann:
The DARC site: a database of aligned ribosomal complexes. 495-500 - Xingyan Kuang, Jing Ginger Han, Nan Zhao, Bin Pang, Chi-Ren Shyu, Dmitry Korkin:
DOMMINO: a database of macromolecular interactions. 501-506 - Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Seiko D. Murakami, Takayuki Amemiya, Kazuo Hosoda, Ryotaro Koike, Hidekazu Hiroaki, Motonori Ota:
IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. 507-511 - Zheng Zhang, Cheng Xing, Lushan Wang, Bin Gong, Hui Liu:
IndelFR: a database of indels in protein structures and their flanking regions. 512-518 - Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister:
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. 519-524 - Joshua SungWoo Yang, Ji-han Kim, Sangho Oh, Gukjeong Han, Sanghyuk Lee, Jinhyuk Lee:
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures. 525-530 - Arumugam Gandhimathi, Anu G. Nair, Ramanathan Sowdhamini:
PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies. 531-534 - Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan:
Pocketome: an encyclopedia of small-molecule binding sites in 4D. 535-540 - Jun-Ichi Ito, Yasuo Tabei, Kana Shimizu, Koji Tsuda, Kentaro Tomii:
PoSSuM: a database of similar protein-ligand binding and putative pockets. 541-548 - Olga V. Kalinina, Oliver Wichmann, Gordana Apic, Robert B. Russell:
ProtChemSI: a network of protein-chemical structural interactions. 549-553 - Takayuki Amemiya, Ryotaro Koike, Akinori Kidera, Motonori Ota:
PSCDB: a database for protein structural change upon ligand binding. 554-558 - The Gene Ontology: enhancements for 2011. 559-564
- Emily C. Dimmer, Rachael P. Huntley, Yasmin Alam-Faruque, Tony Sawford, Claire O'Donovan, Maria Jesus Martin, Benoit Bely, Paul Browne, Wei Mun Chan, Ruth Y. Eberhardt, Michael Gardner, Kati Laiho, Duncan Legge, Michele Magrane, Klemens Pichler, Diego Poggioli, Harminder Sehra, Andrea H. Auchincloss, Kristian B. Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi-Quintaje, Lionel Breuza, Alan J. Bridge, Elisabeth Coudert, Anne Estreicher, Maria Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Lydie Bougueleret, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek Roggli, Ioannis Xenarios, Rolf Apweiler:
The UniProt-GO Annotation database in 2011. 565-570 - Ioanna Pagani, Konstantinos Liolios, Jakob Jansson, I-Min A. Chen, Tatyana Smirnova, Bahador Nosrat, Victor M. Markowitz, Nikos Kyrpides:
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. 571-579 - Nick S. Juty, Nicolas Le Novère, Camille Laibe:
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. 580-586 - Carla Kuiken, James Thurmond, Mira Dimitrijevic, Hyejin Yoon:
The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses. 587-592 - Brett E. Pickett, Eva L. Sadat, Yun Zhang, Jyothi Noronha, R. Burke Squires, Victoria Hunt, Mengya Liu, Sanjeev Kumar, Sam Zaremba, Zhiping Gu, Liwei Zhou, Christopher N. Larsen, Jonathan Dietrich, Edward B. Klem, Richard H. Scheuermann:
ViPR: an open bioinformatics database and analysis resource for virology research. 593-598 - Joseph A. Cruz, Yifeng Liu, Yongjie Liang, You Zhou, Michael Wilson, Jonathan J. Dennis, Paul Stothard, Gary H. Van Domselaar, David S. Wishart:
BacMap: an up-to-date electronic atlas of annotated bacterial genomes. 599-604 - Adam A. Witney, Denise E. Waldron, Lucy A. Brooks, Richard H. Tyler, Michael Withers, Neil G. Stoker, Brendan W. Wren, Philip D. Butcher, Jason Hinds:
BμG@Sbase - a microbial gene expression and comparative genomic database. 605-609 - Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Ariston de Carvalho Azevedo, Jan Baumbach:
CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. 610-614 - Abhijit Chakraborty, Sudeshna Ghosh, Garisha Chowdhary, Ujjwal Maulik, Saikat Chakrabarti:
DBETH: A Database of Bacterial Exotoxins for Human. 615-620 - Dexi Bi, Zhen Xu, Ewan M. Harrison, Cui Tai, Yiqing Wei, Xinyi He, Shiru Jia, Zixin Deng, Kumar Rajakumar, Hong-Yu Ou:
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. 621-626 - Blanca Taboada, Ricardo Ciria, Cristian E. Martinez-Guerrero, Enrique Merino:
ProOpDB: Prokaryotic Operon DataBase. 627-631 - Libusha Kelly, Katherine H. Huang, Huiming Ding, Sallie W. Chisholm:
ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. 632-640 - Lihong Chen, Zhaohui Xiong, Lilian Sun, Jian Yang, Qi Jin:
VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. 641-645 - Patricia P. Chan, Andrew D. Holmes, Andrew M. Smith, Danny Tran, Todd M. Lowe:
The UCSC Archaeal Genome Browser: 2012 update. 646-652 - Martha B. Arnaud, Gustavo C. Cerqueira, Diane O. Inglis, Marek S. Skrzypek, Jonathan Binkley, Marcus C. Chibucos, Jonathan Crabtree, Clinton Howarth, Joshua Orvis, Prachi Shah, Farrell Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock, Jennifer R. Wortman:
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. 653-659 - Jane E. Mabey Gilsenan, John Cooley, Paul Bowyer:
CADRE: the Central Aspergillus Data REpository 2012. 660-666 - Diane O. Inglis, Martha B. Arnaud, Jonathan Binkley, Prachi Shah, Marek S. Skrzypek, Farrell Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock:
The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. 667-674 - Jason E. Stajich, Todd W. Harris, Brian P. Brunk, John Brestelli, Steve Fischer, Omar S. Harb, Jessica C. Kissinger, Wei Li, Vishal Nayak, Deborah F. Pinney, Christian J. Stoeckert Jr., David S. Roos:
FungiDB: an integrated functional genomics database for fungi. 675-681 - Cheuk C. Siow, Sian R. Nieduszynska, Carolin A. Müller, Conrad A. Nieduszynski:
OriDB, the DNA replication origin database updated and extended. 682-686 - Ke Jin, Jingjing Li, Frederick S. Vizeacoumar, Zhijian Li, Renqiang Min, Lee Zamparo, Franco J. Vizeacoumar, Alessandro Datti, Brenda J. Andrews, Charles Boone, Zhaolei Zhang:
PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. 687-694 - Valerie Wood, Midori A. Harris, Mark D. McDowall, Kim Rutherford, Brendan W. Vaughan, Daniel M. Staines, Martin Aslett, Antonia Lock, Jürg Bähler, Paul J. Kersey, Stephen G. Oliver:
PomBase: a comprehensive online resource for fission yeast. 695-699 - J. Michael Cherry, Eurie L. Hong, Craig Amundsen, Rama Balakrishnan, Gail Binkley, Esther T. Chan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Kalpana Karra, Cynthia J. Krieger, Stuart R. Miyasato, Robert S. Nash, Julie Park, Marek S. Skrzypek, Matt Simison, Shuai Weng, Edith D. Wong:
Saccharomyces Genome Database: the genomics resource of budding yeast. 700-705 - Peter McQuilton, Susan E. St. Pierre, Jim Thurmond:
FlyBase 101 - the basics of navigating FlyBase. 706-714 - Ian Flockhart, Matthew Booker, Yanhui Hu, Benjamin McElvany, Quentin Gilly, Bernard Mathey-Prevot, Norbert Perrimon, Stephanie E. Mohr:
FlyRNAi.org - the database of the Drosophila RNAi screening center: 2012 update. 715-719 - John C. Martin, Sahar Abubucker, Esley Heizer, Christina M. Taylor, Makedonka Dautova Mitreva:
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. 720-728 - Karine Megy, Scott J. Emrich, Daniel Lawson, David Campbell, Emmanuel Dialynas, Daniel S. T. Hughes, Gautier Koscielny, Christos Louis, Robert M. MacCallum, Seth Redmond, Andrew Sheehan, Pantelis Topalis, Derek Wilson:
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. 729-734 - Karen Yook, Todd W. Harris, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, Norie De La Cruz, Adrian Duong, Ruihua Fang, Uma Ganesan, Christian A. Grove, Kevin L. Howe, Snehalata Kadam, Ranjana Kishore, Raymond Y. N. Lee, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Bill Nash, Philip Ozersky, Michael Paulini, Daniela Raciti, Arun Rangarajan, Gary Schindelman, Xiaoqi Shi, Erich M. Schwarz, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Jonathan Hodgkin, Matthew Berriman, Richard Durbin, Paul J. Kersey, John Spieth, Lincoln Stein, Paul W. Sternberg:
WormBase 2012: more genomes, more data, new website. 735-741 - Ron Caspi, Tomer Altman, Kate Dreher, Carol A. Fulcher, Pallavi Subhraveti, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Anuradha Pujar, Alexander Glennon Shearer, Michael Travers, Deepika Weerasinghe, Peifen Zhang, Peter D. Karp:
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. 742-753 - Rafael Alcántara, Kristian B. Axelsen, Anne Morgat, Eugeni Belda, Elisabeth Coudert, Alan J. Bridge, Hong Cao, Paula de Matos, Marcus Ennis, Steve Turner, Gareth I. Owen, Lydie Bougueleret, Ioannis Xenarios, Christoph Steinbeck:
Rhea - a manually curated resource of biochemical reactions. 754-760 - Anne Morgat, Eric Coissac, Elisabeth Coudert, Kristian B. Axelsen, Guillaume Keller, Amos Bairoch, Alan J. Bridge, Lydie Bougueleret, Ioannis Xenarios, Alain Viari:
UniPathway: a resource for the exploration and annotation of metabolic pathways. 761-769 - Avi I. Flamholz, Elad Noor, Arren Bar-Even, Ron Milo:
eQuilibrator - the biochemical thermodynamics calculator. 770-775 - Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed Asad Rahman, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton:
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. 776-782 - Gemma L. Holliday, Claudia Andreini, Julia D. Fischer, Syed Asad Rahman, Daniel E. Almonacid, Sophie T. Williams, William R. Pearson:
MACiE: exploring the diversity of biochemical reactions. 783-789 - Ulrike Wittig, Renate Kania, Martin Golebiewski, Maja Rey, Lei Shi, Lenneke Jong, Enkhjargal Algaa, Andreas Weidemann, Heidrun Sauer-Danzwith, Saqib Mir, Olga Krebs, Meik Bittkowski, Elina Wetsch, Isabel Rojas, Wolfgang Müller:
SABIO-RK - database for biochemical reaction kinetics. 790-796 - Namhee Yu, Jihae Seo, Kyoohyoung Rho, Yeongjun Jang, Jinah Park, Wan Kyu Kim, Sanghyuk Lee:
hiPathDB: a human-integrated pathway database with facile visualization. 797-802 - Pradeep Kumar Sreenivasaiah, Shilpa Rani, Joseph Cayetano, Novino Arul, Do Han Kim:
IPAVS: Integrated Pathway Resources, Analysis and Visualization System. 803-808 - Masahiro Sugimoto, Satsuki Ikeda, Kanako Niigata, Masaru Tomita, Hideyo Sato, Tomoyoshi Soga:
MMMDB: Mouse Multiple Tissue Metabolome Database. 809-814 - Timothy Jewison, Craig Knox, Vanessa Neveu, Yannick Djoumbou, Anchi Guo, Jacqueline Lee, Philip Liu, Rupasri Mandal, Ram Krishnamurthy, Igor Sinelnikov, Michael Wilson, David S. Wishart:
YMDB: the Yeast Metabolome Database. 815-820 - Andrey Alexeyenko, Thomas Schmitt, Andreas Tjärnberg, Dimitri Guala, Oliver Frings, Erik L. L. Sonnhammer:
Comparative interactomics with Funcoup 2.0. 821-828 - Engin Cukuroglu, Attila Gürsoy, Ozlem Keskin:
HotRegion: a database of predicted hot spot clusters. 829-833 - Benjamin A. Shoemaker, Dachuan Zhang, Manoj Tyagi, Ratna R. Thangudu, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko:
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. 834-840 - Samuel Kerrien, Bruno Aranda, Lionel Breuza, Alan J. Bridge, Fiona Broackes-Carter, Carol Chen, Margaret J. Duesbury, Marine Dumousseau, Marc Feuermann, Ursula Hinz, Christine Jandrasits, Rafael C. Jiménez, Jyoti Khadake, Usha Mahadevan, Patrick Masson, Ivo Pedruzzi, Eric Pfeiffenberger, Pablo Porras, Arathi Raghunath, Bernd Roechert, Sandra E. Orchard, Henning Hermjakob:
The IntAct molecular interaction database in 2012. 841-846 - Guilhem Faure, Jessica Andreani, Raphaël Guérois:
InterEvol database: exploring the structure and evolution of protein complex interfaces. 847-856 - Luana Licata, Leonardo Briganti, Daniele Peluso, Livia Perfetto, Marta Iannuccelli, Eugenia Galeota, Francesca Sacco, Anita Palma, Aurelio Nardozza, Elena Santonico, Luisa Castagnoli, Gianni Cesareni:
MINT, the molecular interaction database: 2012 update. 857-861 - Mark J. Cowley, Mark Pinese, Karin S. Kassahn, Nic Waddell, John V. Pearson, Sean M. Grimmond, Andrew V. Biankin, Sampsa Hautaniemi, Jianmin Wu:
PINA v2.0: mining interactome modules. 862-865 - Benjamin Haibe-Kains, Catharina Olsen, Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton, John Quackenbush:
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. 866-875 - Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Christian von Mering, Lars Juhl Jensen, Peer Bork:
STITCH 3: zooming in on protein-chemical interactions. 876-880 - Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. 881-886 - Terry P. Maddatu, Stephen C. Grubb, Carol J. Bult, Molly A. Bogue:
Mouse Phenome Database (MPD). 887-894 - Marc Bruckskotten, Mario Looso, Richard Reinhardt, Thomas Braun, Thilo Borchardt:
Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens. 895-900 - Wei-Hua Chen, Pablo Minguez, Martin J. Lercher, Peer Bork:
OGEE: an online gene essentiality database. 901-906 - Karl J. Clark, David P. Argue, Andrew M. Petzold, Stephen C. Ekker:
zfishbook: connecting you to a world of zebrafish revertible mutants. 907-911 - Kate R. Rosenbloom, Timothy R. Dreszer, Jeffrey C. Long, Venkat S. Malladi, Cricket A. Sloan, Brian J. Raney, Melissa S. Cline, Donna Karolchik, Galt P. Barber, Hiram Clawson, Mark Diekhans, Pauline A. Fujita, Mary Goldman, Robert C. Gravell, Rachel A. Harte, Angie S. Hinrichs, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Morgan Maddren, Laurence R. Meyer, Andy Pohl, Brooke L. Rhead, Matthew C. Wong, Ann S. Zweig, David Haussler, W. James Kent:
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. 912-917 - Timothy R. Dreszer, Donna Karolchik, Ann S. Zweig, Angie S. Hinrichs, Brian J. Raney, Robert M. Kuhn, Laurence R. Meyer, Matthew C. Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke L. Rhead, Andy Pohl, Venkat S. Malladi, Chin H. Li, Katrina Learned, Vanessa Kirkup, Fan Hsu, Rachel A. Harte, Luvina Guruvadoo, Mary Goldman, Belinda Giardine, Pauline A. Fujita, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
The UCSC Genome Browser database: extensions and updates 2011. 918-923 - Yukio Maruyama, Yoshifumi Kawamura, Tetsuo Nishikawa, Takao Isogai, Nobuo Nomura, Naoki Goshima:
HGPD: Human Gene and Protein Database, 2012 update. 924-929 - Lucas D. Ward, Manolis Kellis:
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. 930-934 - Greet De Baets, Joost J. J. van Durme, Joke Reumers, Sebastian Maurer-Stroh, Peter Vanhee, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau:
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. 935-939 - Lynn M. Schriml, Cesar Arze, Suvarna Nadendla, Yu-Wei Wayne Chang, Mark Mazaitis, Victor Felix, Gang Feng, Warren A. Kibbe:
Disease Ontology: a backbone for disease semantic integration. 940-946 - Mark D. Halling-Brown, Krishna C. Bulusu, Mishal N. Patel, Joe E. Tym, Bissan Al-Lazikani:
canSAR: an integrated cancer public translational research and drug discovery resource. 947-956 - Judice L. Y. Koh, Kevin R. Brown, Azin Sayad, Dahlia Kasimer, Troy Ketela, Jason Moffat:
COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines. 957-963 - Ying He, Menghuan Zhang, Yuanhu Ju, Zhong-Hao Yu, Daqing Lv, Han Sun, Weilan Yuan, Fei He, Jianshe Zhang, Hong Li, Jing Li, Rui Wang-Sattler, Yixue Li, Guoqing Zhang, Lu Xie:
dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. 964-971 - Sen Kao, Cheng-Kai Shiau, De-Leung Gu, Chun-Ming Ho, Wen-Hui Su, Chian-Feng Chen, Chi-Hung Lin, Yuh-Shan Jou:
IGDB.NSCLC: integrated genomic database of non-small cell lung cancer. 972-977 - Matteo D'Antonio, Vera Pendino, Shruti Sinha, Francesca D. Ciccarelli:
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes. 978-983 - Shannan J. Ho Sui, Kimberly Begley, Dorothy Reilly, Brad Chapman, Ray McGovern, Philippe Rocca-Serra, Eamonn Maguire, Gabriel M. Altschuler, Terah A. A. Hansen, Ramakrishna Sompallae, Andrei Krivtsov, Ramesh A. Shivdasani, Scott A. Armstrong, Aedín C. Culhane, Mick Correll, Susanna-Assunta Sansone, Oliver Hofmann, Winston Hide:
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. 984-991 - Sandrine Caputo, Louisa Benboudjema, Olga Sinilnikova, Etienne Rouleau, Christophe Béroud, Rosette Lidereau:
Description and analysis of genetic variants in French hereditary breast and ovarian cancer families recorded in the UMD-BRCA1/BRCA2 databases. 992-1002 - Liuyan Zhang, Suhua Chang, Zhao Li, Kunlin Zhang, Yang Du, Jurg Ott, Jing Wang:
ADHDgene: a genetic database for attention deficit hyperactivity disorder. 1003-1009 - Haseena Rajeevan, Usha Soundararajan, Judith R. Kidd, Andrew J. Pakstis, Kenneth K. Kidd:
ALFRED: an allele frequency resource for research and teaching. 1010-1015 - Li-Ming Xu, Jia-Rui Li, Yue Huang, Min Zhao, Xing Tang, Liping Wei:
AutismKB: an evidence-based knowledgebase of autism genetics. 1016-1022 - Santosh Kumar Patnaik, Wolfgang Helmberg, Olga O. Blumenfeld:
BGMUT: NCBI dbRBC database of allelic variations of genes encoding antigens of blood group systems. 1023-1029 - Jie Lv, Hongbo Liu, Jianzhong Su, Xueting Wu, Hui Liu, Boyan Li, Xue Xiao, Fang Wang, Qiong Wu, Yan Zhang:
DiseaseMeth: a human disease methylation database. 1030-1035 - Albert Pallejà, Heiko Horn, Sabrina Eliasson, Lars Juhl Jensen:
DistiLD Database: diseases and traits in linkage disequilibrium blocks. 1036-1040 - Xin Zhao, Qi Liu, Qingqing Cai, Yanyun Li, Congjian Xu, Yixue Li, Zuofeng Li, Xiaoyan Zhang:
Dr.VIS: a database of human disease-related viral integration sites. 1041-1046 - Mulin Jun Li, Panwen Wang, Xiaorong Liu, Ee Lyn Lim, Zhangyong Wang, Meredith Yeager, Maria P. Wong, Pak Chung Sham, Stephen J. Chanock, Junwen Wang:
GWASdb: a database for human genetic variants identified by genome-wide association studies. 1047-1054 - Juan Wang, Jie Zhang, Kaibo Li, Wei Zhao, Qinghua Cui:
SpliceDisease database: linking RNA splicing and disease. 1055-1059 - Aedín C. Culhane, Markus S. Schröder, Razvan Sultana, Shaita C. Picard, Enzo N. Martinelli, Caroline Kelly, Benjamin Haibe-Kains, Misha Kapushesky, Anne-Alyssa St Pierre, William Flahive, Kermshlise C. Picard, Daniel Gusenleitner, Gerald Papenhausen, Niall O'Connor, Mick Correll, John Quackenbush:
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. 1060-1066 - Erich J. Baker, Jeremy J. Jay, Jason A. Bubier, Michael A. Langston, Elissa J. Chesler:
GeneWeaver: a web-based system for integrative functional genomics. 1067-1076 - Misha Kapushesky, Tomasz Adamusiak, Tony Burdett, Aedín C. Culhane, Anna Farne, Alexey Filippov, Ele Holloway, Andrey Klebanov, Nataliya Kryvych, Natalja Kurbatova, Pavel Kurnosov, James Malone, Olga Melnichuk, Robert Petryszak, Nikolay Pultsin, Gabriella Rustici, Andrew Tikhonov, Ravensara S. Travillian, Eleanor Williams, Andrey Zorin, Helen E. Parkinson, Alvis Brazma:
Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments. 1077-1081 - Sergio Contrino, Richard N. Smith, Daniela Butano, Adrian Carr, Fengyuan Hu, Rachel Lyne, Kim Rutherford, Alex Kalderimis, Julie M. Sullivan, Seth Carbon, Ellen T. Kephart, Paul Lloyd, E. O. Stinson, Nicole L. Washington, Marc D. Perry, Peter Ruzanov, Zheng Zha, Suzanna E. Lewis, Lincoln D. Stein, Gos Micklem:
modMine: flexible access to modENCODE data. 1082-1088 - Edward Wijaya, Martin C. Frith, Kiyoshi Asai, Paul Horton:
RecountDB: a database of mapped and count corrected transcribed sequences. 1089-1092 - Eugene Kolker, Roger Higdon, Winston Haynes, Dean Welch, William Broomall, Doron Lancet, Larissa Stanberry, Natali Kolker:
MOPED: Model Organism Protein Expression Database. 1093-1099 - Anna Gaulton, Louisa J. Bellis, A. Patrícia Bento, Jon Chambers, Mark Davies, Anne Hersey, Yvonne Light, Shaun McGlinchey, David Michalovich, Bissan Al-Lazikani, John P. Overington:
ChEMBL: a large-scale bioactivity database for drug discovery. 1100-1107 - Vijayaraghava Seshadri Sundararajan, Musa Nur Gabere, Ashley Pretorius, Saleem Adam, Alan Christoffels, Minna Lehväslaiho, John A. C. Archer, Vladimir B. Bajic:
DAMPD: a manually curated antimicrobial peptide database. 1108-1112 - Nikolai Hecker, Jessica Ahmed, Joachim von Eichborn, Mathias Dunkel, Karel Macha, Andreas Eckert, Michael K. Gilson, Philip E. Bourne, Robert Preissner:
SuperTarget goes quantitative: update on drug-target interactions. 1113-1117 - María P. Magariños, Santiago J. Carmona, Gregory J. Crowther, Stuart A. Ralph, David S. Roos, Dhanasekaran Shanmugam, Wesley C. Van Voorhis, Fernán Agüero:
TDR Targets: a chemogenomics resource for neglected diseases. 1118-1127 - Feng Zhu, Zhe Shi, Chu Qin, Lin Tao, Xin Liu, Feng Xu, Li Zhang, Yang Song, Xianghui Liu, Jing-Xian Zhang, Bu-Cong Han, Peng Zhang, Yuzong Chen:
Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. 1128-1136 - Daniel E. Newburger, Georges Natsoulis, Sue Grimes, John M. Bell, Ronald W. Davis, Serafim Batzoglou, Hanlee P. Ji:
The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. 1137-1143 - Xiaowei Wang, Athanasia Spandidos, Huajun Wang, Brian Seed:
PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. 1144-1149 - Francesco Rubino, Roberta Piredda, Francesco Maria Calabrese, Domenico Simone, Martin Lang, Claudia Calabrese, Vittoria Petruzzella, Mila Tommaseo Ponzetta, Giuseppe Gasparre, Marcella Attimonelli:
HmtDB, a genomic resource for mitochondrion-based human variability studies. 1150-1159 - Anthony C. Smith, James A. Blackshaw, Alan J. Robinson:
MitoMiner: a data warehouse for mitochondrial proteomics data. 1160-1167 - Paolo D'Onorio De Meo, Mattia D'Antonio, Francesca Griggio, Renato Lupi, Massimiliano Borsani, Giulio Pavesi, Tiziana Castrignanò, Graziano Pesole, Carmela Gissi:
MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa. 1168-1172 - Falk Schreiber, Christian Colmsee, Tobias Czauderna, Eva Grafahrend-Belau, Anja Hartmann, Astrid Junker, Björn H. Junker, Matthias Klapperstück, Uwe Scholz, Stephan Weise:
MetaCrop 2.0: managing and exploring information about crop plant metabolism. 1173-1177 - David M. Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D. Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas H. Putnam, Daniel S. Rokhsar:
Phytozome: a comparative platform for green plant genomics. 1178-1186 - Dijun Chen, Chunhui Yuan, Jian Zhang, Zhao Zhang, Lin Bai, Yijun Meng, Ling-Ling Chen, Ming Chen:
PlantNATsDB: a comprehensive database of plant natural antisense transcripts. 1187-1193 - Sudhansu Dash, John L. Van Hemert, Lu Hong, Roger P. Wise, Julie A. Dickerson:
PLEXdb: gene expression resources for plants and plant pathogens. 1194-1201 - Philippe Lamesch, Tanya Z. Berardini, Donghui Li, David Swarbreck, Christopher Wilks, Rajkumar Sasidharan, Robert J. Muller, Kate Dreher, Debbie L. Alexander, Margarita Garcia-Hernandez, Athikkattuvalasu S. Karthikeyan, Cynthia H. Lee, William D. Nelson, Larry Ploetz, Shanker Singh, April Wensel, Eva Huala:
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. 1202-1210 - Nils Kleinbölting, Gunnar Huep, Andreas Kloetgen, Prisca Viehoever, Bernd Weisshaar:
GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database. 1211-1215 - Preeti Bais, Stephanie M. Moon-Quanbeck, Basil J. Nikolau, Julie A. Dickerson:
Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics - database and tools update. 1216-1220 - Jun Li, Xinbin Dai, Tingsong Liu, Patrick Xuechun Zhao:
LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. 1221-1229 - Anna Chailyan, Anna Tramontano, Paolo Marcatili:
A database of immunoglobulins with integrated tools: DIGIT. 1230-1234 - Krzysztof Kuchta, Daniela Barszcz, Elzbieta Grzesiuk, Pawel Pomorski, Joanna Krwawicz:
DNAtraffic - a new database for systems biology of DNA dynamics during the cell life. 1235-1240 - Suresh Mathivanan, Cassie J. Fahner, Gavin E. Reid, Richard J. Simpson:
ExoCarta 2012: database of exosomal proteins, RNA and lipids. 1241-1244 - Yurong Xin, Benjamin Chanrion, Anne H. O'Donnell, Maria Milekic, Ramiro Costa, Yongchao Ge, Fatemeh G. Haghighi:
MethylomeDB: a database of DNA methylation profiles of the brain. 1245-1249 - Dan M. Bolser, Pierre-Yves Chibon, Nicolas Palopoli, Sungsam Gong, Daniel Jacob, Victoria Dominguez Del Angel, Daniel Swan, Sebastian Bassi, Virginia González, Prashanth Suravajhala, Seungwoo Hwang, Paolo Romano, Rob Edwards, Bryan Bishop, John Eargle, Timur Shtatland, Nicholas J. Provart, Dave Clements, Daniel P. Renfro, Daeui Park, Jong Bhak:
MetaBase - the wiki-database of biological databases. 1250-1254 - Benjamin M. Good, Erik L. Clarke, Luca de Alfaro, Andrew I. Su:
The Gene Wiki in 2011: community intelligence applied to human gene annotation. 1255-1261 - Daniel P. Renfro, Brenley K. McIntosh, Anand Venkatraman, Deborah A. Siegele, James C. Hu:
GONUTS: the Gene Ontology Normal Usage Tracking System. 1262-1269 - Brenley K. McIntosh, Daniel P. Renfro, Gwendowlyn S. Knapp, Chanchala R. Lairikyengbam, Nathan M. Liles, Lili Niu, Amanda M. Supak, Anand Venkatraman, Adrienne E. Zweifel, Deborah A. Siegele, James C. Hu:
EcoliWiki: a wiki-based community resource for Escherichia coli. 1270-1277 - Ulrike Mäder, Arne G. Schmeisky, Lope A. Flórez, Jörg Stülke:
SubtiWiki - a comprehensive community resource for the model organism Bacillus subtilis. 1278-1287 - Philip C. Pratt-Szeliga, Aaron D. Skewes, Jinyuan Yan, Laura G. Welch, Roy D. Welch:
Xanthusbase after five years expands to become Openmods. 1288-1294 - Sujai Kumar, Philipp H. Schiffer, Mark L. Blaxter:
959 Nematode Genomes: a semantic wiki for coordinating sequencing projects. 1295-1300 - Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Martina Kutmon, Bruce R. Conklin, Chris T. A. Evelo, Alexander R. Pico:
WikiPathways: building research communities on biological pathways. 1301-1307 - Michael Cariaso, Greg Lennon:
SNPedia: a wiki supporting personal genome annotation, interpretation and analysis. 1308-1312 - Jing-Woei Li, Keith Robison, Marcel Martin, Andreas Sjödin, Björn Usadel, Matthew Young, Eric C. Olivares, Dan M. Bolser:
The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis. 1313-1317
Volume 40, Number Web-Server-Issue, July 2012
- Gary Benson:
Editorial. 1-2
- Michelle D. Brazas, David S. Yim, Winston Yeung, B. F. Francis Ouellette:
A decade of web server updates at the bioinformatics links directory: 2003-2012. 3-12 - Andrea Bisognin, Gabriele Sales, Alessandro Coppe, Stefania Bortoluzzi, Chiara Romualdi:
MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). 13-21 - Hua-Jun Wu, Ying-Ke Ma, Tong Chen, Meng Wang, Xiu-Jie Wang:
PsRobot: a web-based plant small RNA meta-analysis toolbox. 22-28 - Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu:
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. 29-34 - Hazrina Yusof Hamdani, Sri Devan Appasamy, Peter Willett, Peter J. Artymiuk, Mohd Firdaus Raih:
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. 35-41 - Petr Cech, Daniel Svozil, David Hoksza:
SETTER: web server for RNA structure comparison. 42-48 - Dragos Alexandru Sorescu, Mathias Möhl, Martin Mann, Rolf Backofen, Sebastian Will:
CARNA - alignment of RNA structure ensembles. 49-53 - Ignacio Medina, Alejandro de María, Marta Bleda, Francisco Salavert, Roberto Alonso, Cristina Y. González, Joaquín Dopazo:
VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. 54-58 - Fan Li, Paul Ryvkin, Daniel M. Childress, Otto Valladares, Brian D. Gregory, Li-San Wang:
SAVoR: a server for sequencing annotation and visualization of RNA structures. 59-64 - Abu Z. Dayem Ullah, Nicholas R. Lemoine, Claude Chelala:
SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update). 65-70 - Tien-Dao Luu, Alin Rusu, Vincent Walter, Benjamin Linard, Laetitia Poidevin, Raymond Ripp, Luc Moulinier, Jean Muller, Wolfgang Raffelsberger, Nicolas Wicker, Odile Lecompte, Julie Dawn Thompson, Olivier Poch, Hoan Nguyen:
KD4v: comprehensible knowledge discovery system for missense variant. 71-75 - Yu-Chang Cheng, Fang-Chih Hsiao, Erh-Chan Yeh, Wan-Jia Lin, Cheng-Yang Louis Tang, Huan-Chin Tseng, Hsing-Tsung Wu, Chuan-Kun Liu, Chih-Cheng Chen, Yuan-Tsong Chen, Adam Yao:
VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era. 76-81 - Bernd W. Brandt, Marc J. Bonder, Susan M. Huse, Egija Zaura:
TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage. 82-87 - David Arndt, Jianguo Xia, Yifeng Liu, You Zhou, Anchi Guo, Joseph A. Cruz, Igor Sinelnikov, Karen Budwill, Camilla L. Nesbø, David S. Wishart:
METAGENassist: a comprehensive web server for comparative metagenomics. 88-95 - Camille Menendez, Scott Frees, Paramjeet Singh Bagga:
QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences. 96-103 - Sebastian Luehr, Holger Hartmann, Johannes Söding:
The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences. 104-109 - Gregory K. Taylor, Lucas H. Petrucci, Abigail R. Lambert, Sarah K. Baxter, Jordan Jarjour, Barry L. Stoddard:
LAHEDES: the LAGLIDADG homing endonuclease database and engineering server. 110-116 - Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. VanDyk, Adam J. Bogdanove:
TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. 117-122 - Jun Li, Paul Roebuck, Stefan Grünewald, Han Liang:
SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data. 123-126 - Jianguo Xia, Rupasri Mandal, Igor Sinelnikov, David Broadhurst, David S. Wishart:
MetaboAnalyst 2.0 - a comprehensive server for metabolomic data analysis. 127-133 - Yoan Renaud, Alexandre Baillif, Jean-Baptiste Perez, Marie Agier, Engelbert Mephu Nguifo, Vincent Mirouse:
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. 134-139 - Atanas Kamburov, Ulrich Stelzl, Ralf Herwig:
IntScore: a web tool for confidence scoring of biological interactions. 140-146 - Javier García-García, Sylvia Schleker, Judith Klein-Seetharaman, Baldo Oliva:
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. 147-151 - George C. Linderman, Mark R. Chance, Gürkan Bebek:
MAGNET: MicroArray Gene expression and Network Evaluation Toolkit. 152-156 - Roland A. Pache, Arnaud Céol, Patrick Aloy:
NetAligner - a network alignment server to compare complexes, pathways and whole interactomes. 157-161 - Masaaki Kotera, Yoshihiro Yamanishi, Yuki Moriya, Minoru Kanehisa, Susumu Goto:
GENIES: gene network inference engine based on supervised analysis. 162-167 - Marta Bleda, Ignacio Medina, Roberto Alonso, Alejandro de María, Francisco Salavert, Joaquín Dopazo:
Inferring the regulatory network behind a gene expression experiment. 168-172 - Ting-Ying Chien, Chih-Kang Lin, Chih-Wei Lin, Yi-Zhong Weng, Chien-Yu Chen, Darby Tien-Hao Chang:
DBD2BS: connecting a DNA-binding protein with its binding sites. 173-179 - Razif R. Gabdoulline, Denitsa Eckweiler, Alexander E. Kel, Philip Stegmaier:
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. 180-185 - Shiliang Wang, Jaideep P. Sundaram, Timothy B. Stockwell:
VIGOR extended to annotate genomes for additional 12 different viruses. 186-192 - Anne-Kathrin Schultz, Ingo Bulla, Mariama Abdou-Chekaraou, Emmanuel Gordien, Burkhard Morgenstern, Fabien Zoulim, Paul Dény, Mario Stanke:
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. 193-198 - Nishant Thakur, Abid Qureshi, Manoj Kumar:
AVPpred: collection and prediction of highly effective antiviral peptides. 199-204 - Wubin Qu, Yang Zhou, Yanchun Zhang, Yiming Lu, Xiaolei Wang, Dongsheng Zhao, Yi Yang, Chenggang Zhang:
MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity. 205-208 - Stephen R. Bond, Christian C. Naus:
RF-Cloning.org: an online tool for the design of restriction-free cloning projects. 209-213 - Janez Konc, Dusanka Janezic:
ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins. 214-221 - Karel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka:
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. 222-227 - Yan-Long Lai, Chih-Chieh Chen, Jenn-Kang Hwang:
pKNOT v.2: the protein KNOT web server. 228-231 - Wei-Cheng Lo, Li-Fen Wang, Yen-Yi Liu, Tian Dai, Jenn-Kang Hwang, Ping-Chiang Lyu:
CPred: a web server for predicting viable circular permutations in proteins. 232-237 - Dominique Koua, Age Brauer, Silja Laht, Lauris Kaplinski, Philippe Favreau, Maido Remm, Frédérique Lisacek, Reto Stöcklin:
ConoDictor: a tool for prediction of conopeptide superfamilies. 238-241 - Abhijit Chakraborty, Sapan Mandloi, Christopher J. Lanczycki, Anna R. Panchenko, Saikat Chakrabarti:
SPEER-SERVER: a web server for prediction of protein specificity determining sites. 242-248 - Yao Chi Chen, Jon D. Wright, Carmay Lim:
DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry. 249-256 - Dominik Gront, Maciej Blaszczyk, Piotr Wojciechowski, Andrzej Kolinski:
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles. 257-262 - Chun-Yu Lin, Yi-Wei Lin, Shang-Wen Yu, Yu-Shu Lo, Jinn-Moon Yang:
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. 263-270 - Chi-Ho Ngan, Tanggis Bohnuud, Scott E. Mottarella, Dmitri Beglov, Elizabeth A. Villar, David R. Hall, Dima Kozakov, Sandor Vajda:
FTMAP: extended protein mapping with user-selected probe molecules. 271-275 - Samuel P. Wein, Richard G. Côté, Marine Dumousseau, Florian Reisinger, Henning Hermjakob, Juan Antonio Vizcaíno:
Improvements in the protein identifier cross-reference service. 276-280 - Martin Christen Frølund Thomsen, Morten Nielsen:
Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion. 281-287 - Pierre Thévenet, Yimin Shen, Julien Maupetit, Frédéric Guyon, Philippe Derreumaux, Pierre Tufféry:
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. 288-293 - Junsu Ko, Hahnbeom Park, Lim Heo, Chaok Seok:
GalaxyWEB server for protein structure prediction and refinement. 294-297 - Jiangming Sun, Shengnan Tang, Wenwei Xiong, Peisheng Cong, Tonghua Li:
DSP: a protein shape string and its profile prediction server. 298-302 - Inken Wohlers, Noël Malod-Dognin, Rumen Andonov, Gunnar W. Klau:
CSA: comprehensive comparison of pairwise protein structure alignments. 303-309 - Dennis M. Krüger, Aqeel Ahmed, Holger Gohlke:
NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins. 310-316 - Alexandre G. de Brevern, Aurélie Bornot, Pierrick Craveur, Catherine Etchebest, Jean-Christophe Gelly:
PredyFlexy: flexibility and local structure prediction from sequence. 317-322 - João P. G. L. M. Rodrigues, Michael Levitt, Gaurav Chopra:
KoBaMIN: a knowledge-based minimization web server for protein structure refinement. 323-328 - Dániel Kozma, István Simon, Gábor E. Tusnády:
CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods. 329-333 - James H. Collier, Arthur M. Lesk, Maria Garcia de la Banda, Arun Siddharth Konagurthu:
Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank. 334-339 - Pravech Ajawatanawong, Gemma Catherine Atkinson, Nathan S. Watson-Haigh, Bryony MacKenzie, Sandra L. Baldauf:
SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments. 340-347 - Michael Jenik, R. Gonzalo Parra, Leandro G. Radusky, Adrian Gustavo Turjanski, Peter G. Wolynes, Diego U. Ferreiro:
Protein frustratometer: a tool to localize energetic frustration in protein molecules. 348-351 - Alan Tus, Alen Rakipovic, Goran Peretin, Sanja Tomic, Mile Sikic:
BioMe: biologically relevant metals. 352-357 - Yana Gofman, Turkan Haliloglu, Nir Ben-Tal:
Monte Carlo simulations of peptide-membrane interactions with the MCPep web server. 358-363 - Robert J. Weatheritt, Peter Jehl, Holger Dinkel, Toby J. Gibson:
iELM - a web server to explore short linear motif-mediated interactions. 364-369 - Wing-Cheong Wong, Sebastian Maurer-Stroh, Georg Schneider, Frank Eisenhaber:
Transmembrane helix: simple or complex. 370-375 - Likun Wang, Yipeng Du, Ming Lu, Tingting Li:
ASEB: a web server for KAT-specific acetylation site prediction. 376-379 - Nurul Nadzirin, Eleanor J. Gardiner, Peter Willett, Peter J. Artymiuk, Mohd Firdaus Raih:
SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. 380-386 - David Ryan Koes, Carlos J. Camacho:
PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. 387-392 - Jui-Chih Wang, Pei-Ying Chu, Chung-Ming Chen, Jung-Hsin Lin:
idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. 393-399 - Praveen Anand, Kalidas Yeturu, Nagasuma R. Chandra:
PocketAnnotate: towards site-based function annotation. 400-408 - David Ryan Koes, Carlos J. Camacho:
ZINCPharmer: pharmacophore search of the ZINC database. 409-414 - Alexander A. Kantardjiev:
Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system. 415-422 - Leonardo G. Trabuco, Stefano Lise, Evangelia Petsalaki, Robert B. Russell:
PepSite: prediction of peptide-binding sites from protein surfaces. 423-427 - Bin Pang, Xingyan Kuang, Nan Zhao, Dmitry Korkin, Chi-Ren Shyu:
PBSword: a web server for searching similar protein-protein binding sites. 428-434 - Yan Yuan Tseng, Wen-Hsiung Li:
PSC: protein surface classification. 435-439 - Amita Barik, Abhishek Mishra, Ranjit Prasad Bahadur:
PRince: a web server for structural and physicochemical analysis of Protein-RNA interface. 440-444 - Yanbin Yin, Xizeng Mao, Jincai Yang, Xin Chen, Fenglou Mao, Ying Xu:
dbCAN: a web resource for automated carbohydrate-active enzyme annotation. 445-451 - Ngak-Leng Sim, Prateek Kumar, Jing Hu, Steven Henikoff, Georg Schneider, Pauline C. Ng:
SIFT web server: predicting effects of amino acid substitutions on proteins. 452-457 - Ramona Britto, Olivier Sallou, Olivier Collin, Grégoire Michaux, Michael Primig, Frédéric Chalmel:
GPSy: a cross-species gene prioritization system for conserved biological processes - application in male gamete development. 458-465 - Mark N. Wass, Geraint Barton, Michael J. E. Sternberg:
CombFunc: predicting protein function using heterogeneous data sources. 466-470 - Ambrish Roy, Jianyi Yang, Yang Zhang:
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. 471-477 - Daniel Tabas-Madrid, Rubén Nogales-Cadenas, Alberto D. Pascual-Montano:
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. 478-483 - Aaron K. Wong, Christopher Y. Park, Casey S. Greene, Lars Ailo Bongo, Yuanfang Guan, Olga G. Troyanskaya:
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. 484-490 - Francisco Pereira Lobo, Maíra R. Rodrigues, Gisele O. L. Rodrigues, Heron O. Hilário, Raoni A. Souza, Andreas Tauch, Anderson Miyoshi, Glaura C. Franco, Vasco Ariston de Carvalho Azevedo, Glória R. Franco:
KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa. 491-497 - Ioannis S. Vlachos, Nikos Kostoulas, Thanasis Vergoulis, Georgios K. Georgakilas, Martin Reczko, Manolis Maragkakis, Maria D. Paraskevopoulou, Kostantinos Prionidis, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. 498-504 - Nurcan Tuncbag, Scott McCallum, Shao-Shan Carol Huang, Ernest Fraenkel:
SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. 505-509 - Federico Zambelli, Gian Marco Prazzoli, Graziano Pesole, Giulio Pavesi:
Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. 510-515 - Dominik Seelow, Markus Schuelke:
HomozygosityMapper2012 - bridging the gap between homozygosity mapping and deep sequencing. 516-520 - Vered Kunik, Shaul Ashkenazi, Yanay Ofran:
Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure. 521-524 - Yohan Kim, Julia V. Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E. Bourne, Morten Nielsen, Bjoern Peters:
Immune epitope database analysis resource. 525-530 - Sangjae Seo, Moon Ki Kim:
KOSMOS: a universal morph server for nucleic acids, proteins and their complexes. 531-536 - Ramu Anandakrishnan, Boris Aguilar, Alexey Onufriev:
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. 537-541 - Yuanpeng Janet Huang, Antonio Rosato, Gautam Singh, Gaetano T. Montelione:
RPF: a quality assessment tool for protein NMR structures. 542-546 - D. P. Klose, B. A. Wallace, Robert W. Janes:
DichroMatch: a website for similarity searching of circular dichroism spectra. 547-552 - Matthew A. Kayala, Pierre Baldi:
Cyber-T web server: differential analysis of high-throughput data. 553-559 - Rosalind J. Cutts, Abu Z. Dayem Ullah, Ajanthah Sangaralingam, Emanuela Gadaleta, Nicholas R. Lemoine, Claude Chelala:
O-miner: an integrative platform for automated analysis and mining of -omics data. 560-568 - Huangkai Zhang, Shenghan Gao, Martin J. Lercher, Songnian Hu, Wei-Hua Chen:
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. 569-572 - Alix Boc, Alpha Boubacar Diallo, Vladimir Makarenkov:
T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. 573-579 - Haim Ashkenazy, Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer, Tal Pupko:
FastML: a web server for probabilistic reconstruction of ancestral sequences. 580-584 - Philippe Thomas, Johannes Starlinger, Alexander Vowinkel, Sebastian Arzt, Ulf Leser:
GeneView: a comprehensive semantic search engine for PubMed. 585-591 - Yuki Naito, Hidemasa Bono:
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts. 592-596 - Panu Artimo, Manohar Jonnalagedda, Konstantin Arnold, Delphine Baratin, Gábor Csárdi, Edouard De Castro, Severine Duvaud, Volker Flegel, Arnaud Fortier, Elisabeth Gasteiger, Aurélien Grosdidier, Céline Hernandez, Vassilios Ioannidis, Dmitri Kuznetsov, Robin Liechti, Sébastien Moretti, Khaled Mostaguir, Nicole Redaschi, Grégoire Rossier, Ioannis Xenarios, Heinz Stockinger:
ExPASy: SIB bioinformatics resource portal. 597-603
- Pavel S. Novichkov, Thomas S. Brettin, Elena S. Novichkova, Paramvir S. Dehal, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov:
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. 604-608 - Marta Bleda, Joaquín Tárraga, Alejandro de María, Francisco Salavert, Luz Garcia-Alonso, Matilde Celma, Ainoha Martín, Joaquín Dopazo, Ignacio Medina:
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. 609-614
- Marc Fiume, Eric J. M. Smith, Andrew Brook, Dario Strbenac, Brian Turner, Aziz M. Mezlini, Mark D. Robinson, Shoshana J. Wodak, Michael Brudno:
Savant Genome Browser 2: visualization and analysis for population-scale genomics. 615-621 - Marc Lohse, Anthony M. Bolger, Axel Nagel, Alisdair R. Fernie, John E. Lunn, Mark Stitt, Björn Usadel:
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. 622-627 - Attila Gyenesei, Jonathan Moody, Asta Laiho, Colin A. M. Semple, Chris S. Haley, Wenhua Wei:
BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies. 628-632
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