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ORCIDNucleic Acids Research, Volume 41
Volume 41, Number Database-Issue, January 2013
- Xosé M. Fernández-Suárez, Michael Y. Galperin
:
The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. 1-7 - Database resources of the National Center for Biotechnology Information. 8-20
- Yasukazu Nakamura, Guy Cochrane, Ilene Karsch-Mizrachi:
The International Nucleotide Sequence Database Collaboration. 21-24 - Osamu Ogasawara, Jun Mashima, Yuichi Kodama, Eli Kaminuma, Yasukazu Nakamura, Kousaku Okubo, Toshihisa Takagi:
DDBJ new system and service refactoring. 25-29 - Guy Cochrane, Blaise T. F. Alako, Clara Amid, Lawrence Bower, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Mikyung Jang, Simon Kay, Rasko Leinonen, Xiu Lin, Rodrigo Lopez, Hamish McWilliam, Arnaud Oisel, Nima Pakseresht, Swapna Pallreddy, Young Mi Park, Sheila Plaister, Rajesh Radhakrishnan, Stéphane Rivière, Marc Rossello, Alexander Senf, Nicole Silvester, Dimitriy Smirnov, Petra ten Hoopen, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin:
Facing growth in the European Nucleotide Archive. 30-35 - Dennis A. Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
GenBank. 36-42 - Update on activities at the Universal Protein Resource (UniProt) in 2013. 43-47
- Paul Flicek, Ikhlak Ahmed, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Thomas Juettemann, Andreas Kähäri, Stephen Keenan, Monika Komorowska, Eugene Kulesha, Ian Longden, Thomas Maurel, William M. McLaren, Matthieu Muffato, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sheppard, Daniel Sobral, Kieron R. Taylor, Anja Thormann, Stephen J. Trevanion, Simon White, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Nathan Johnson, Rhoda Kinsella, Anne Parker, Giulietta Spudich, Andy Yates, Amonida Zadissa, Stephen M. J. Searle:
Ensembl 2013. 48-55 - Kate R. Rosenbloom, Cricket A. Sloan, Venkat S. Malladi, Timothy R. Dreszer, Katrina Learned, Vanessa Kirkup, Matthew C. Wong, Morgan Maddren, Ruihua Fang, Steven G. Heitner, Brian T. Lee, Galt P. Barber, Rachel A. Harte, Mark Diekhans, Jeffrey C. Long, Steven P. Wilder, Ann S. Zweig, Donna Karolchik, Robert M. Kuhn, David Haussler, W. James Kent:
ENCODE Data in the UCSC Genome Browser: year 5 update. 56-63 - Laurence R. Meyer, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Robert M. Kuhn, Matthew C. Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke L. Rhead, Brian J. Raney, Andy Pohl, Venkat S. Malladi, Chin H. Li, Brian T. Lee, Katrina Learned, Vanessa Kirkup, Fan Hsu, Steven G. Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Mary Goldman, Belinda Giardine, Pauline A. Fujita, Timothy R. Dreszer, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
The UCSC Genome Browser database: extensions and updates 2013. 64-69 - Travis J. Wheeler, Jody Clements, Sean R. Eddy, Robert Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit, Robert D. Finn:
Dfam: a database of repetitive DNA based on profile hidden Markov models. 70-82 - Nikita S. Vassetzky, Dmitri A. Kramerov:
SINEBase: a database and tool for SINE analysis. 83-89 - Feng Gao, Hao Luo, Chun-Ting Zhang:
DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. 90-93 - Regina Z. Cer, Duncan E. Donohue, Uma Mudunuri, Nuri A. Temiz, Michael A. Loss, Nathan J. Starner, Goran N. Halusa, Natalia Volfovsky, Ming Yi, Brian T. Luke, Albino Bacolla, Jack R. Collins, Robert M. Stephens:
Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools. 94-100 - Slavica Dimitrieva, Philipp Bucher:
UCNEbase - a database of ultraconserved non-coding elements and genomic regulatory blocks. 101-109 - Jose Manuel Rodriguez, Paolo Maietta, Iakes Ezkurdia, Alessandro Pietrelli, Jan-Jaap Wesselink, Gonzalo López, Alfonso Valencia, Michael L. Tress:
APPRIS: annotation of principal and alternative splice isoforms. 110-117 - Anke Busch, Klemens J. Hertel:
HEXEvent: a database of Human EXon splicing Events. 118-124 - Matteo Giulietti, Francesco Piva, Mattia D'Antonio, Paolo D'Onorio De Meo, Daniele Paoletti, Tiziana Castrignanò, Anna Maria D'Erchia, Ernesto Picardi, Federico Zambelli, Giovanni Principato, Giulio Pavesi, Graziano Pesole:
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. 125-131 - Ivan Cvitkovic, Melissa S. Jurica:
Spliceosome Database: a tool for tracking components of the spliceosome. 132-141 - Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark F. Rogers, Kristina Ibáñez, Cesar Boullosa, Eduardo Andrés León, Asa Ben-Hur, Alfonso Valencia:
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. 142-151 - Ivan Antonov, Pavel V. Baranov, Mark Borodovsky:
GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. 152-156 - René Dreos, Giovanna Ambrosini, Rouaïda Cavin Périer, Philipp Bucher:
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. 157-164 - Edgar Wingender, Torsten Schoeps, Jürgen Dönitz:
TFClass: an expandable hierarchical classification of human transcription factors. 165-170 - Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin-Ying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill Moore, Brian G. Pierce, Xianjun Dong, Daniel Virgil, Ewan Birney, Jui-Hung Hung, Zhiping Weng:
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. 171-176 - Jian-Hua Yang, Jun-Hao Li, Shan Jiang, Hui Zhou, Liang-Hu Qu:
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. 177-187 - Jesse D. Ziebarth, Anindya Bhattacharya, Yan Cui:
CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. 188-194 - Ivan V. Kulakovskiy, Yulia A. Medvedeva, Ulf Schaefer, Artem S. Kasianov, Ilya E. Vorontsov, Vladimir B. Bajic, Vsevolod J. Makeev:
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. 195-202 - Heladia Salgado, Martín Peralta-Gil, Socorro Gama-Castro, Alberto Santos-Zavaleta, Luis Muñiz-Rascado, Jair S. García-Sotelo, Verena Weiss, Hilda Solano-Lira, Irma Martínez-Flores, Alejandra Medina-Rivera, Gerardo Salgado-Osorio, Shirley Alquicira-Hernández, Kevin Alquicira-Hernández, Alejandra López-Fuentes, Liliana Porrón-Sotelo, Araceli M. Huerta, César Bonavides-Martínez, Yalbi Itzel Balderas-Martínez, Lucia Pannier, Maricela Olvera, Aurora Labastida, Verónica Jiménez-Jacinto, Leticia Vega-Alvarado, Victor del Moral-Chávez, Alfredo Hernández-Alvarez, Enrique Morett, Julio Collado-Vides:
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. 203-213 - Mikhail Pachkov, Piotr J. Balwierz, Phil Arnold, Evgeniy A. Ozonov, Erik van Nimwegen:
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. 214-220 - Ian M. Fingerman, Xuan Zhang, Walter Ratzat, Nora Husain, Robert F. Cohen, Gregory D. Schuler:
NCBI Epigenomics: What's new for 2013. 221-225 - Sarah W. Burge, Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, Lars Barquist, Eric P. Nawrocki, Sean R. Eddy, Paul P. Gardner, Alex Bateman:
Rfam 11.0: 10 years of RNA families. 226-232 - Lei Li, Dandan Huang, Man Kit Cheung, Wenyan Nong, Qianli Huang, Hoi Shan Kwan:
BSRD: a repository for bacterial small regulatory RNA. 233-238 - Maria D. Paraskevopoulou, Georgios K. Georgakilas, Nikos Kostoulas, Martin Reczko, Manolis Maragkakis, Theodore M. Dalamagas, Artemis G. Hatzigeorgiou:
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. 239-245 - Pieter-Jan Volders, Kenny Helsens, Xiaowei Wang, Björn Menten, Lennart Martens, Kris Gevaert, Jo Vandesompele, Pieter Mestdagh:
LNCipedia: a database for annotated human lncRNA transcript sequences and structures. 246-251 - Sooyoung Cho, Insu Jang, Yukyung Jun, Suhyeon Yoon, Minjeong Ko, Yeajee Kwon, Ikjung Choi, Hyeshik Chang, Daeun Ryu, Byungwook Lee, V. Narry Kim, Wan Kyu Kim, Sanghyuk Lee:
miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. 252-257 - Anmol M. Kiran, John J. O'Mahony, Komal Sanjeev, Pavel V. Baranov:
Darned in 2013: inclusion of model organisms and linking with Wikipedia. 258-261 - Magdalena A. Machnicka, Kaja Milanowska, Okan Osman Oglou, Elzbieta Purta, Malgorzata Kurkowska, Anna Olchowik, Witold Januszewski, Sebastian Kalinowski, Stanislaw Dunin-Horkawicz, Kristian Rother, Mark Helm, Janusz M. Bujnicki, Henri Grosjean:
MODOMICS: a database of RNA modification pathways - 2013 update. 262-267 - Kaja Milanowska, Katarzyna Mikolajczak, Anna Lukasik, Marcin Skorupski, Zuzanna Balcer, Magdalena A. Machnicka, Martyna Nowacka, Kristian Rother, Janusz M. Bujnicki:
RNApathwaysDB - a database of RNA maturation and decay pathways. 268-272 - Valérie Cognat, Gaël Pawlak, Anne-Marie Duchêne, Magali Daujat, Anaïs Gigant, Thalia Salinas, Morgane Michaud, Bernard Gutmann, Philippe Giegé, Anthony Gobert, Laurence Marechal-Drouard:
PlantRNA, a database for tRNAs of photosynthetic eukaryotes. 273-279 - Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann, Andrean Goede, Kristian Rother, Peter Werner Hildebrand:
Voronoia4RNA - a database of atomic packing densities of RNA structures and their complexes. 280-284 - Wei-Chung Cheng, I-Fang Chung, Tse-Shun Huang, Shih-Ting Chang, Hsing-Jen Sun, Cheng-Fong Tsai, Muh-Lii Liang, Tai-Tong Wong, Hsei-Wei Wang:
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. 285-294 - Cheng-Tsung Lu, Kai-Yao Huang, Min-Gang Su, Tzong-Yi Lee, Neil Arvin Bretaña, Wen-Chi Chang, Yi-Ju Chen, Yu-Ju Chen, Hsien-Da Huang:
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. 295-305 - Pablo Minguez, Ivica Letunic, Luca Parca, Peer Bork:
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. 306-311 - Claudia Andreini, Gabriele Cavallaro, Serena Lorenzini, Antonio Rosato:
MetalPDB: a database of metal sites in biological macromolecular structures. 312-319 - Florian Heinke, Stefan Schildbach, Daniel Stockmann, Dirk Labudde:
eProS - a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles. 320-326 - David Gfeller, Olivier Michielin, Vincent Zoete:
SwissSidechain: a molecular and structural database of non-natural sidechains. 327-332 - Niklaas Colaert, Davy Maddelein, Francis Impens, Petra Van Damme, Kim Plasman, Kenny Helsens, Niels Hulstaert, Joël Vandekerckhove, Kris Gevaert, Lennart Martens:
The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events. 333-337 - Szu-Chin Fu, Hsuan-Cheng Huang, Paul Horton, Hsueh-Fen Juan:
ValidNESs: a database of validated leucine-rich nuclear export signals. 338-343 - Christian J. A. Sigrist, Edouard De Castro, Lorenzo Cerutti, Béatrice A. Cuche, Nicolas Hulo, Alan J. Bridge, Lydie Bougueleret, Ioannis Xenarios:
New and continuing developments at PROSITE. 344-347 - Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Shennan Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Dachuan Zhang, Stephen H. Bryant:
CDD: conserved domains and protein three-dimensional structure. 348-352 - Akihiro Nakaya, Toshiaki Katayama, Masumi Itoh, Kazushi Hiranuka, Shuichi Kawashima, Yuki Moriya, Shujiro Okuda, Michihiro Tanaka, Toshiaki Tokimatsu, Yoshihiro Yamanishi, Akiyasu C. Yoshizawa, Minoru Kanehisa, Susumu Goto:
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. 353-357 - Robert M. Waterhouse, Fredrik Tegenfeldt, Jia Li, Evgeny M. Zdobnov, Evgenia V. Kriventseva:
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. 358-365 - Matthew D. Whiteside, Geoffrey L. Winsor, Matthew R. Laird, Fiona S. L. Brinkman:
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. 366-376 - Huaiyu Mi, Anushya Muruganujan, Paul D. Thomas:
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. 377-386 - Daniel H. Haft, Jeremy D. Selengut, Roland A. Richter, Derek M. Harkins, Malay Kumar Basu, Erin Beck:
TIGRFAMs and Genome Properties in 2013. 387-395 - Anthony Bretaudeau, François Coste, Florian Humily, Laurence Garczarek, Gildas Le Corguillé, Christophe Six, Morgane Ratin, Olivier Collin, Wendy M. Schluchter, Frédéric Partensky:
CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. 396-401 - Kyle R. Conway, Christopher N. Boddy:
ClusterMine360: a database of microbial PKS/NRPS biosynthesis. 402-407 - Natsuko Ichikawa, Machi Sasagawa, Mika Yamamoto, Hisayuki Komaki, Yumi Yoshida, Shuji Yamazaki, Nobuyuki Fujita:
DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters. 408-414 - An Xiao, Yingdan Wu, Zhipeng Yang, Yingying Hu, Weiye Wang, Yutian Zhang, Lei Kong, Ge Gao, Zuoyan Zhu, Shuo Lin, Bo Zhang:
EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering. 415-422 - Nicolas Lenfant, Thierry Hotelier, Eric Velluet, Yves Bourne, Pascale Marchot, Arnaud Chatonnet:
ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions. 423-429 - Yi-Yuan Chiu, Chih-Ta Lin, Jhang-Wei Huang, Kai-Cheng Hsu, Jen-Hu Tseng, Syuan-Ren You, Jinn-Moon Yang:
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. 430-440 - Nizar Fawal, Qiang Li, Bruno Savelli, Marie Brette, Gisele Passaia, Maxime Fabre, Catherine Mathé, Christophe Dunand:
PeroxiBase: a database for large-scale evolutionary analysis of peroxidases. 441-444 - Tianshun Gao, Zexian Liu, Yongbo Wang, Han Cheng, Qing Yang, Anyuan Guo, Jian Ren, Yu Xue:
UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. 445-451 - Fengli Fu, Daniel F. Voytas:
Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C2H2 zinc fingers and engineered zinc finger arrays. 452-455 - Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth I. Owen, Steve Turner, Mark Williams, Christoph Steinbeck:
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. 456-463 - Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau:
ChemProt-2.0: visual navigation in a disease chemical biology database. 464-469 - Sunhwan Jo, Wonpil Im:
Glycan fragment database: a database of PDB-based glycan 3D structures. 470-474 - Peter W. Rose, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, Dimitris Dimitropoulos, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, Andreas Prlic, Martha Quesada, Greg B. Quinn, Alexander G. Ramos, John D. Westbrook, Jasmine Young, Christine Zardecki, Helen M. Berman, Philip E. Bourne:
The RCSB Protein Data Bank: new resources for research and education. 475-482 - Sameer Velankar, Jose M. Dana, Julius O. B. Jacobsen, Glen van Ginkel, Paul J. Gane, Jie Luo, Thomas J. Oldfield, Claire O'Donovan, Maria Jesus Martin, Gerard J. Kleywegt:
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. 483-489 - Ian Sillitoe, Alison L. Cuff, Benoit H. Dessailly, Natalie L. Dawson, Nicholas Furnham, David A. Lee, Jonathan G. Lees, Tony E. Lewis, Romain A. Studer, Robert Rentzsch, Corin Yeats, Janet M. Thornton, Christine A. Orengo:
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. 490-498 - Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Alison L. Cuff, Jose M. Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Alex L. Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen J. L. Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, Christine A. Orengo:
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. 499-507 - Matt E. Oates, Pedro Romero, Takashi Ishida, Mohamed F. Ghalwash, Marcin J. Mizianty, Bin Xue, Zsuzsanna Dosztányi, Vladimir N. Uversky, Zoran Obradovic, Lukasz A. Kurgan, A. Keith Dunker, Julian Gough:
D2P2: database of disordered protein predictions. 508-516 - Dmitry D. Kirsanov, Olga Zanegina, Evgeniy Aksianov, Sergei A. Spirin, Anna S. Karyagina, Andrei Alexeevski:
NPIDB: nucleic acid - protein interaction database. 517-523 - Dániel Kozma, István Simon, Gábor E. Tusnády:
PDBTM: Protein Data Bank of transmembrane proteins after 8 years. 524-529 - Gene Ontology Annotations and Resources. 530-535
- Hai Fang, Julian Gough:
dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. 536-544 - Kristian A. Gray, Louise C. Daugherty, Susan M. Gordon, Ruth L. Seal, Mathew W. Wright, Elspeth A. Bruford:
Genenames.org: the HGNC resources in 2013. 545-552 - Kai Peng, Wei Xu, Jianyong Zheng, Kegui Huang, Huisong Wang, Jiansong Tong, Zhifeng Lin, Jun Liu, Wenqing Cheng, Dong Fu, Pan Du, Warren A. Kibbe, Simon M. Lin, Tian Xia:
The disease and gene annotations (DGA): an annotation resource for human disease. 553-560 - Chunlei Wu, Ian MacLeod, Andrew I. Su:
BioGPS and MyGene.info: organizing online, gene-centric information. 561-565 - Juliette Hayer, Fanny Jadeau, Gilbert Deléage, Alan Kay, Fabien Zoulim, Christophe Combet:
HBVdb: a knowledge database for Hepatitis B Virus. 566-570 - Koenraad Van Doorslaer, Qina Tan, Sandhya Xirasagar, Sandya Bandaru, Vivek Gopalan, Yasmin Mohamoud, Yentram Huyen, Alison A. McBride:
The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis. 571-578 - Patrick Masson, Chantal Hulo, Edouard De Castro, Hans Bitter, Lore Gruenbaum, Laurent Essioux, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier:
ViralZone: recent updates to the virus knowledge resource. 579-583 - Ivo Pedruzzi, Catherine Rivoire, Andrea H. Auchincloss, Elisabeth Coudert, Guillaume Keller, Edouard De Castro, Delphine Baratin, Béatrice A. Cuche, Lydie Bougueleret, Sylvain Poux, Nicole Redaschi, Ioannis Xenarios, Alan J. Bridge:
HAMAP in 2013, new developments in the protein family classification and annotation system. 584-589 - Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner:
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. 590-596 - Laure Guillou, Dipankar Bachar, Stéphane Audic, David Bass, Cédric Berney, Lucie Bittner, Christophe Boutte, Gaétan Burgaud, Colomban de Vargas, Johan Decelle, Javier del Campo, John R. Dolan, Micah Dunthorn, Bente Edvardsen, Maria Holzmann, Wiebe H. C. F. Kooistra, Enrique Lara, Noan Le Bescot, Ramiro Logares, Frédéric Mahé, Ramon Massana, Marina Montresor, Raphael Morard, Fabrice Not, Jan Pawlowski, Ian Probert, Anne-Laure Sauvadet, Raffaele Siano, Thorsten Stoeck, Daniel Vaulot, Pascal Zimmermann, Richard Christen:
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. 597-604 - Ingrid M. Keseler, Amanda Mackie, Martín Peralta-Gil, Alberto Santos-Zavaleta, Socorro Gama-Castro, César Bonavides-Martínez, Carol A. Fulcher, Araceli M. Huerta, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne M. Paley, Imke Schröder, Alexander Glennon Shearer, Pallavi Subhraveti, Michael Travers, Deepika Weerasinghe, Verena Weiss, Julio Collado-Vides, Robert P. Gunsalus, Ian T. Paulsen, Peter D. Karp:
EcoCyc: fusing model organism databases with systems biology. 605-612 - Jindan Zhou, Kenneth E. Rudd:
EcoGene 3.0. 613-624 - Anchi Guo, Timothy Jewison, Michael Wilson, Yifeng Liu, Craig Knox, Yannick Djoumbou, Patrick Lo, Rupasri Mandal, Ram Krishnamurthy, David S. Wishart:
ECMDB: The E. coli Metabolome Database. 625-630 - Ikuo Uchiyama, Motohiro Mihara, Hiroyo Nishide, Hirokazu Chiba:
MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. 631-635 - David Vallenet, Eugeni Belda, Alexandra Calteau, Stéphane Cruveiller, Stefan Engelen, Aurélie Lajus, François Le Fèvre, Cyrille Longin, Damien Mornico, David Roche, Zoé Rouy, Gregory Salvignol, Claude Scarpelli, Adam Alexander Thil Smith, Marion Weiman, Claudine Médigue:
MicroScope - an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. 636-647 - Dylan Chivian, Paramvir S. Dehal, Keith Keller, Adam P. Arkin:
metaMicrobesOnline: phylogenomic analysis of microbial communities. 648-654 - Evelien Wynendaele, Antoon Bronselaer, Joachim Nielandt, Matthias D'Hondt, Sofie Stalmans, Nathalie Bracke, Frederick Verbeke, Christophe Van De Wiele, Guy De Tré, Bart De Spiegeleer:
Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides. 655-659 - Dexi Bi, Linmeng Liu, Cui Tai, Zixin Deng, Kumar Rajakumar, Hong-Yu Ou:
SecReT4: a web-based bacterial type IV secretion system resource. 660-665 - Rafael Silva-Rocha, Esteban Martínez-García, Belén Calles, Max Chavarría, Alejandro Arce-Rodríguez, Aitor de las Heras, A. David Páez-Espino, Gonzalo Durante-Rodríguez, Juhyun Kim, Pablo I. Nikel, Raúl Platero, Victor de Lorenzo:
The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. 666-675 - Siddhartha Basu, Petra Fey, Yogesh Pandit, Robert J. Dodson, Warren A. Kibbe, Rex L. Chisholm:
dictyBase 2013: integrating multiple Dictyostelid species. 676-683 - Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P. Brunk, Shon Cade, Ryan Doherty, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Sufen Hu, John Iodice, Jessica C. Kissinger, Eileen T. Kraemer, Wei Li, Deborah F. Pinney, Brian Pitts, David S. Roos, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Haiming Wang, Susanne Warrenfeltz:
EuPathDB: The Eukaryotic Pathogen database. 684-691 - Marius Felder, Alessandro Romualdi, Andreas Petzold, Matthias Platzer, Jürgen Sühnel, Gernot Glöckner:
GenColors-based comparative genome databases for small eukaryotic genomes. 692-699 - Alexandra Louis, Matthieu Muffato, Hugues Roest Crollius:
Genomicus: five genome browsers for comparative genomics in eukaryota. 700-705 - Achchuthan Shanmugasundram, Faviel F. Gonzalez-Galarza, Jonathan M. Wastling, Olga Vasieva, Andrew R. Jones:
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. 706-713 - Jaeyoung Choi, Kyeong-Chae Cheong, Kyongyong Jung, Jongbum Jeon, Gir-Won Lee, Seogchan Kang, Sangsoo Kim, Yin-Won Lee, Yong-Hwan Lee:
CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. 714-719 - Kristen Fortney, Wing Xie, Max Kotlyar, Joshua Griesman, Yulia Kotseruba, Igor Jurisica:
NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. 720-727 - Adhemar Zerlotini, Eric R. G. R. Aguiar, Fudong Yu, Huayong Xu, Yixue Li, Neil D. Young, Robin B. Gasser, Anna V. Protasio, Matthew Berriman, David S. Roos, Jessica C. Kissinger, Guilherme C. Oliveira:
SchistoDB: an updated genome resource for the three key schistosomes of humans. 728-731 - Koji Kyoda, Eru Adachi, Eriko Masuda, Yoko Nagai, Yoko Suzuki, Taeko Oguro, Mitsuru Urai, Ryoko Arai, Mari Furukawa, Kumiko Shimada, Junko Kuramochi, Eriko Nagai, Shuichi Onami:
WDDD: Worm Developmental Dynamics Database. 732-737 - L. Basten Snoek, K. Joeri van der Velde, Danny Arends, Yang Li, Antje Beyer, Mark Elvin, Jasmin Fisher, Alex Hajnal, Michael O. Hengartner, Gino B. Poulin, Miriam Rodriguez, Tobias Schmid, Sabine Schrimpf, Feng Xue, Ritsert C. Jansen, Jan E. Kammenga, Morris A. Swertz:
WormQTL - public archive and analysis web portal for natural variation data in Caenorhabditis spp. 738-743 - Scott W. Robinson, Pawel Herzyk, Julian A. T. Dow, David P. Leader:
FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster. 744-750 - Steven J. Marygold, Paul C. Leyland, Ruth L. Seal, Joshua L. Goodman, Jim Thurmond, Victor B. Strelets, Robert J. Wilson:
FlyBase: improvements to the bibliography. 751-757 - Shuai Zhan, Steven M. Reppert:
MonarchBase: the monarch butterfly genome database. 758-763 - Ida Schomburg, Antje Chang, Sandra Placzek, Carola Söhngen, Michael Rother, Maren Lang, Cornelia Munaretto, Susanne Ulas, Michael Stelzer, Andreas Grote, Maurice Scheer, Dietmar Schomburg:
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. 764-772 - Rafael Alcántara, Joseph Onwubiko, Hong Cao, Paula de Matos, Jennifer A. Cham, Julius O. B. Jacobsen, Gemma L. Holliday, Julia D. Fischer, Syed Asad Rahman, Bijay Jassal, Mickael Goujon, Francis Rowland, Sameer Velankar, Rodrigo Lopez, John P. Overington, Gerard J. Kleywegt, Henning Hermjakob, Claire O'Donovan, Maria Jesus Martin, Janet M. Thornton, Christoph Steinbeck:
The EBI enzyme portal. 773-780 - Kenneth Haug, Reza M. Salek, Pablo Conesa, Janna Hastings, Paula de Matos, Mark Rijnbeek, Tejasvi Mahendraker, Mark Williams, Steffen Neumann, Philippe Rocca-Serra, Eamonn Maguire, Alejandra N. González-Beltrán, Susanna-Assunta Sansone, Julian L. Griffin, Christoph Steinbeck:
MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data. 781-786 - Jonathan R. Karr, Jayodita C. Sanghvi, Derek N. Macklin, Abhishek Arora, Markus W. Covert:
WholeCellKB: model organism databases for comprehensive whole-cell models. 787-792 - Atanas Kamburov, Ulrich Stelzl, Hans Lehrach, Ralf Herwig:
The ConsensusPathDB interaction database: 2013 update. 793-800 - David S. Wishart, Timothy Jewison, Anchi Guo, Michael Wilson, Craig Knox, Yifeng Liu, Yannick Djoumbou, Rupasri Mandal, Farid Aziat, Edison Dong, Souhaila Bouatra, Igor Sinelnikov, David Arndt, Jianguo Xia, Philip Liu, Faizath Yallou, Trent C. Bjorndahl, Rolando Perez-Pineiro, Roman Eisner, Felicity Allen, Vanessa Neveu, Russell Greiner, Augustin Scalbert:
HMDB 3.0 - The Human Metabolome Database in 2013. 801-807 - Andrea Franceschini, Damian Szklarczyk, Sune Frankild, Michael Kuhn, Milan Simonovic, Alexander Roth, Jianyi Lin, Pablo Minguez, Peer Bork, Christian von Mering, Lars Juhl Jensen:
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. 808-815 - Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Sven Heinicke, Lorrie Boucher, Andrew G. Winter, Chris Stark, Julie Nixon, Lindsay Ramage, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Ashton Breitkreutz, Adnane Sellam, Daici Chen, Christie S. Chang, Jennifer M. Rust, Michael S. Livstone, Rose Oughtred, Kara Dolinski, Mike Tyers:
The BioGRID interaction database: 2013 update. 816-823 - Marie Jeanne Basse, Stéphane Betzi, Raphaël Bourgeas, Sofia Bouzidi, Bernard Chétrit, Véronique Hamon, Xavier Morelli, Philippe Roche:
2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions. 824-827 - Qiangfeng Cliff Zhang, Donald Petrey, José Ignacio Garzón, Lei Deng, Barry Honig:
PrePPI: a structure-informed database of protein-protein interactions. 828-833 - Joachim von Eichborn, Mathias Dunkel, Björn O. Gohlke, Sarah C. Preissner, Michael F. Hoffmann, Jakob M. J. Bauer, J. Douglas Armstrong, Martin H. Schaefer, Miguel A. Andrade-Navarro, Nicolas Le Novère, Michael D. R. Croning, Seth G. N. Grant, Pim van Nierop, August B. Smit, Robert Preissner:
SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. 834-840 - Ruth Barshir, Omer Basha, Amir Eluk, Ilan Y. Smoly, Alexander Lan, Esti Yeger Lotem:
The TissueNet database of human tissue protein-protein interactions. 841-844 - Gemma B. Danks, Coen Campsteijn, Mrutyunjaya Parida, Stephen Butcher, Harsha Doddapaneni, Bolei Fu, Raul Petrin, Raghu Metpally, Boris Lenhard, Patrick Wincker, Daniel Chourrout, Eric M. Thompson, J. Robert Manak:
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. 845-853 - Douglas G. Howe, Yvonne M. Bradford, Tom Conlin, Anne E. Eagle, David Fashena, Ken Frazer, Jonathan Knight, Prita Mani, Ryan Martin, Sierra A. T. Moxon, Holly Paddock, Christian Pich, Sridhar Ramachandran, Barbara J. Ruef, Leyla Ruzicka, Kevin Schaper, Xiang Shao, Amy Singer, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield:
ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. 854-860 - Gaurav K. Varshney, Haigen Huang, Suiyuan Zhang, Jing Lu, Derek E. Gildea, Zhongan Yang, Tyra G. Wolfsberg, Shuo Lin, Shawn M. Burgess:
The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion. 861-864 - Christina James-Zorn, Virgilio G. Ponferrada, Chris Jarabek, Kevin A. Burns, Erik Segerdell, Jacqueline Lee, Kevin A. Snyder, Bishnu Bhattacharyya, J. Brad Karpinka, Joshua D. Fortriede, Jeff B. Bowes, Aaron M. Zorn, Peter D. Vize:
Xenbase: expansion and updates of the Xenopus model organism database. 865-870 - Zhi-Liang Hu, Carissa A. Park, Xiaolin Wu, James M. Reecy:
Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. 871-879 - Eli Kaminuma, Takatomo Fujisawa, Yasuhiro Tanizawa, Naoko Sakamoto, Nori Kurata, Tokurou Shimizu, Yasukazu Nakamura:
H2DB: a heritability database across multiple species by annotating trait-associated genomic loci. 880-884 - Carol J. Bult, Janan T. Eppig, Judith A. Blake, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease. 885-891 - Shi-Jian Zhang, Chu-Jun Liu, Mingming Shi, Lei Kong, Jia-Yu Chen, Wei-Zhen Zhou, Xiaotong Zhu, Peng Yu, Jue Wang, Xinzhuang Yang, Ning Hou, Zhi-Qiang Ye, Rongli Zhang, Ruiping Xiao, Xiuqin Zhang, Chuan-Yun Li:
RhesusBase: a knowledgebase for the monkey research community. 892-905 - Lenore Pipes, Sheng Li, Marjan Bozinoski, Robert Palermo, Xinxia Peng, Philip D. Blood, Sara Kelly, Jeffrey M. Weiss, Jean Thierry-Mieg, Danielle Thierry-Mieg, Paul Zumbo, Ronghua Chen, Gary P. Schroth, Christopher E. Mason, Michael G. Katze:
The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. 906-914 - Jun-ichi Takeda, Chisato Yamasaki, Katsuhiko Murakami, Yoko Nagai, Miho Sera, Yuichiro Hara, Nobuo Obi, Takuya Habara, Takashi Gojobori, Tadashi Imanishi:
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. 915-919 - Jean-Loup Huret, Mohammad Ahmad, Mélanie Arsaban, Alain Bernheim, Jérémy Cigna, François Desangles, Jean-Christophe Guignard, Marie-Christine Jacquemot-Perbal, Maureen Labarussias, Vanessa Leberre, Anne Malo, Catherine Morel-Pair, Hossein Mossafa, Jean-Claude Potier, Guillaume Texier, Franck Viguié, Sylvie Yau Chun Wan-Senon, Alain Zasadzinski, Philippe Dessen:
Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013. 920-924 - Wendy S. Rubinstein, Donna R. Maglott, Jennifer M. Lee, Brandi L. Kattman, Adriana J. Malheiro, Michael Ovetsky, Vichet Hem, Vyatcheslav Gorelenkov, Guangfeng Song, Craig Wallin, Nora Husain, Shanmuga Chitipiralla, Kenneth S. Katz, Douglas Hoffman, Wonhee Jang, Mark Johnson, Fedor Karmanov, Alexander Ukrainchik, Mikhail Denisenko, Cathy Fomous, Kathy Hudson, James Ostell:
The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. 925-935 - Ilkka Lappalainen, John Lopez, Lisa Skipper, Timothy Hefferon, J. Dylan Spalding, John Garner, Chao Chen, Michael Maguire, Matthew Corbett, George Zhou, Justin E. Paschall, Victor Ananiev, Paul Flicek, Deanna M. Church:
dbVar and DGVa: public archives for genomic structural variation. 936-941 - Markus Krupp, Timo Itzel, Thorsten Maass, Andreas Hildebrandt, Peter R. Galle, Andreas Teufel:
CellLineNavigator: a workbench for cancer cell line analysis. 942-948 - Mary Goldman, Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa S. Cline, Mark Diekhans, Singer Ma, Chris Wilks, Joshua M. Stuart, David Haussler, Jingchun Zhu:
The UCSC Cancer Genomics Browser: update 2013. 949-954 - Wanjuan Yang, Jorge Soares, Patricia Greninger, Elena J. Edelman, Howard Lightfoot, Simon A. Forbes, Nidhi Bindal, David Beare, James A. Smith, I. Richard Thompson, Sridhar Ramaswamy, P. Andrew Futreal, Daniel A. Haber, Michael R. Stratton, Cyril Benes, Ultan McDermott, Mathew Garnett:
Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. 955-961 - Bernard Leroy, Jean Louis Fournier, Chikashi Ishioka, Paola Monti, Alberto Inga, Gilberto Fronza, Thierry Soussi:
The TP53 website: an integrative resource centre for the TP53 mutation database and TP53 mutant analysis. 962-969 - Min Zhao, Jingchun Sun, Zhongming Zhao:
TSGene: a web resource for tumor suppressor genes. 970-976 - Anindya Bhattacharya, Jesse D. Ziebarth, Yan Cui:
SomamiR: a database for somatic mutations impacting microRNA function in cancer. 977-982 - Geng Chen, Ziyun Wang, Dongqing Wang, Chengxiang Qiu, Mingxi Liu, Xing Chen, Qipeng Zhang, Guiying Yan, Qinghua Cui:
LncRNADisease: a database for long-non-coding RNA-associated diseases. 983-986 - Gabriella Rustici, Nikolay Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon C. Ison, Maria Keays, Natalja Kurbatova, James Malone, Roby Mani, Annalisa Mupo, Rui Pedro Pereira, Ekaterina Pilicheva, Johan Rung, Anjan Sharma, Y. Amy Tang, Tobias Ternent, Andrew Tikhonov, Danielle Welter, Eleanor Williams, Alvis Brazma, Helen E. Parkinson, Ugis Sarkans:
ArrayExpress update - trends in database growth and links to data analysis tools. 987-990 - Tanya Barrett, Stephen E. Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F. Kim, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Michelle Holko, Andrey Yefanov, Hyeseung Lee, Naigong Zhang, Cynthia L. Robertson, Nadezhda Serova, Sean R. Davis, Alexandra Soboleva:
NCBI GEO: archive for functional genomics data sets - update. 991-995 - Susan Sunkin, Lydia Ng, Christopher Lau, Tim Dolbeare, Terri L. Gilbert, Carol L. Thompson, Michael Hawrylycz, Chinh Dang:
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. 996-1008 - Angel D. Pizarro, Katharina Hayer, Nicholas F. Lahens, John B. Hogenesch:
CircaDB: a database of mammalian circadian gene expression profiles. 1009-1013 - Takeshi Obayashi, Yasunobu Okamura, Satoshi Ito, Shu Tadaka, Ikuko N. Motoike, Kengo Kinoshita:
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. 1014-1020 - Esther E. Schmidt, Oliver Pelz, Svetlana Buhlmann, Grainne Kerr, Thomas Horn, Michael Boutros:
GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. 1021-1026 - Robi Tacutu, Thomas Craig, Arie Budovsky, Daniel Wuttke, Gilad Lehmann, Dmitri Taranukha, Joana Cósta, Vadim E. Fraifeld, João Pedro de Magalhães:
Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing. 1027-1033 - Frederik Otzen Bagger, Nicolas Rapin, Kim Theilgaard-Mönch, Bogumil Kaczkowski, Lina A. Thoren, Johan Jendholm, Ole Winther, Bo T. Porse:
HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis. 1034-1039 - Irina Rusinova, Sam Forster, Simon Yu, Anitha Kannan, Marion Masse, Helen Cumming, Ross Chapman, Paul J. Hertzog:
INTERFEROME v2.0: an updated database of annotated interferon-regulated genes. 1040-1046 - Lars Geffers, Benjamin Tetzlaff, Xiao Cui, Jun Yan, Gregor Eichele:
METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters. 1047-1054 - Yuanwei Zhang, Liangwen Zhong, Bo Xu, Yifan Yang, Rongjun Ban, Jun Zhu, Howard J. Cooke, QiaoMei Hao, Qinghua Shi:
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. 1055-1062 - Juan Antonio Vizcaíno, Richard G. Côté, Attila Csordas, José A. Dianes, Antonio Fabregat, Joseph M. Foster, Johannes Griss, Emanuele Alpi, Melih Birim, Javier Contell, Gavin O'Kelly, Andreas Schoenegger, David Ovelleiro, Yasset Pérez-Riverol, Florian Reisinger, Daniel Rios, Rui Wang, Henning Hermjakob:
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. 1063-1069 - Valerie A. Schneider, Hsiu-Chuan Chen, Cliff Clausen, Peter A. Meric, Zhigang Zhou, Nathan Bouk, Nora Husain, Donna R. Maglott, Deanna M. Church:
Clone DB: an integrated NCBI resource for clone-associated data. 1070-1078 - Aaron David Goldman, Tess M. Bernhard, Egor Dolzhenko, Laura F. Landweber:
LUCApedia: a database for the study of ancient life. 1079-1082 - Joanna L. Sharman, Helen E. Benson, Adam J. Pawson, Veny Lukito, Chidochangu P. Mpamhanga, Vincent Bombail, Anthony P. Davenport, John A. Peters, Michael Spedding, Anthony J. Harmar, NC-IUPHAR:
IUPHAR-DB: updated database content and new features. 1083-1088 - Ruichao Xue, Zhao Fang, Meixia Zhang, Zhenghui Yi, Chengping Wen, Tieliu Shi:
TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis. 1089-1095 - Jianyi Yang, Ambrish Roy, Yang Zhang:
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. 1096-1103 - Allan Peter Davis, Cynthia G. Murphy, Robin J. Johnson, Jean M. Lay, Kelley Lennon-Hopkins, Cynthia A. Saraceni-Richards, Daniela Sciaky, Benjamin L. King, Michael C. Rosenstein, Thomas C. Wiegers, Carolyn J. Mattingly:
The Comparative Toxicogenomics Database: update 2013. 1104-1114 - Qian Li, Jun-Feng Xiang, Qian-Fan Yang, Hong-Xia Sun, Ai-Jiao Guan, Ya-Lin Tang:
G4LDB: a database for discovering and studying G-quadruplex ligands. 1115-1123 - Manu Mangal, Parul Sagar, Harinder Singh, Gajendra P. S. Raghava, Subhash M. Agarwal:
NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database. 1124-1129 - Xavier Lucas, Christian Senger, Anika Erxleben, Björn A. Grüning, Kersten Döring, Johannes Mosch, Stephan Flemming, Stefan Günther:
StreptomeDB: a resource for natural compounds isolated from Streptomyces species. 1130-1136 - Matthias Wirth, Vincent Zoete, Olivier Michielin, Wolfgang H. B. Sauer:
SwissBioisostere: a database of molecular replacements for ligand design. 1137-1143 - Thomas Nussbaumer, Mihaela M. Martis, Stephan K. Roessner, Matthias Pfeifer, Kai Christian Bader, Sapna Sharma, Heidrun Gundlach, Manuel Spannagl:
MIPS PlantsDB: a database framework for comparative plant genome research. 1144-1151 - Tae-Ho Lee, Haibao Tang, Xiyin Wang, Andrew H. Paterson:
PGDD: a database of gene and genome duplication in plants. 1152-1158 - Yi Wang, Frank M. You, Gerard R. Lazo, Ming-Cheng Luo, Roger Thilmony, Sean Gordon, Shahryar F. Kianian, Yong Qiang Gu:
PIECE: a database for plant gene structure comparison and evolution. 1159-1166 - Walter Sanseverino, Antonio Hermoso, Raffaella D'Alessandro, Anna V. Vlasova, Giuseppe Andolfo, Luigi Frusciante, Ernesto Lowy-Gallego, Guglielmo Roma, Maria Raffaella Ercolano:
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. 1167-1171 - Chantal Hamelin, Guilhem Sempéré, Vincent Jouffe, Manuel Ruiz:
TropGeneDB, the multi-tropical crop information system updated and extended. 1172-1175 - Monika Zulawski, Rostyslav Braginets, Waltraud X. Schulze:
PhosPhAt goes kinases - searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. 1176-1184 - Sandra K. Tanz, Ian R. Castleden, Cornelia M. Hooper, Michael A. Vacher, Ian Small, A. Harvey Millar:
SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. 1185-1191 - Bohu Pan, Jia Sheng, Weining Sun, Yinhong Zhao, Pei Hao, Xuan Li:
OrysPSSP: a comparative Platform for Small Secreted Proteins from rice and other plants. 1192-1198 - Dapeng Wang, Yan Xia, Xinna Li, Lixia Hou, Jun Yu:
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. 1199-1205 - Yutaka Sato, Hinako Takehisa, Kaori Kamatsuki, Hiroshi Minami, Nobukazu Namiki, Hiroshi Ikawa, Hajime Ohyanagi, Kazuhiko Sugimoto, Baltazar A. Antonio, Yoshiaki Nagamura:
RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome. 1206-1213 - Yutaka Sato, Nobukazu Namiki, Hinako Takehisa, Kaori Kamatsuki, Hiroshi Minami, Hiroshi Ikawa, Hajime Ohyanagi, Kazuhiko Sugimoto, Jun-ichi Itoh, Baltazar A. Antonio, Yoshiaki Nagamura:
RiceFREND: a platform for retrieving coexpressed gene networks in rice. 1214-1221 - James Robinson, Jason A. Halliwell, Hamish McWilliam, Rodrigo Lopez, Peter Parham, Steven G. E. Marsh:
The IMGT/HLA database. 1222-1227 - Karin Breuer, Amir K. Foroushani, Matthew R. Laird, Carol Chen, Anastasia Sribnaia, Raymond Lo, Geoffrey L. Winsor, Robert E. W. Hancock, Fiona S. L. Brinkman, David J. Lynn:
InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation. 1228-1233 - James Robinson, Jason A. Halliwell, Hamish McWilliam, Rodrigo Lopez, Steven G. E. Marsh:
IPD - the Immuno Polymorphism Database. 1234-1240 - David N. Orloff, Janet H. Iwasa, Maryann E. Martone, Mark H. Ellisman, Caroline M. Kane:
The cell: an image library-CCDB: a curated repository of microscopy data. 1241-1250 - Marilu A. Hoeppner:
NCBI Bookshelf: books and documents in life sciences and health care. 1251-1260
Volume 41, Number Webserver-Issue, July 2013
- Gary Benson:
Editorial. 1-2
- Layal Al Ait, Zaher Yamak, Burkhard Morgenstern:
DIALIGN at GOBICS - multiple sequence alignment using various sources of external information. 3-7 - Franco L. Simonetti, Elin Teppa, Ariel Chernomoretz, Morten Nielsen, Cristina Marino Buslje:
MISTIC: mutual information server to infer coevolution. 8-14 - Ryan R. Rahrig, Anton I. Petrov, Neocles Leontis, Craig L. Zirbel:
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures. 15-21 - Shigehiro Kuraku, Christian M. Zmasek, Osamu Nishimura, Kazutaka Katoh:
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. 22-28 - Grzegorz M. Boratyn, Christiam Camacho, Peter S. Cooper, George Coulouris, Amelia Fong, Ning Ma, Thomas L. Madden, Wayne T. Matten, Scott D. McGinnis, Yuri Merezhuk, Yan Raytselis, Eric W. Sayers, Tao Tao, Jian Ye, Irena Zaretskaya:
BLAST: a more efficient report with usability improvements. 29-33 - Jian Ye, Ning Ma, Thomas L. Madden, James M. Ostell:
IgBLAST: an immunoglobulin variable domain sequence analysis tool. 34-40 - Ignacio Medina, Francisco Salavert, Rubén Sánchez, Alejandro de María, Roberto Alonso, Pablo Escobar, Marta Bleda, Joaquín Dopazo:
Genome Maps, a new generation genome browser. 41-46 - Adam Hospital, Ignacio Faustino, Rosana Collepardo-Guevara, Carlos González, Josep Lluis Gelpí, Modesto Orozco:
NAFlex: a web server for the study of nucleic acid flexibility. 47-55 - Tianyin Zhou, Lin Yang, Yan Lu, Iris Dror, Ana Carolina Dantas Machado, Tahereh Ghane, Rosa Di Felice, Remo Rohs:
DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. 56-62 - Jianguo Xia, Christopher D. Fjell, Matthew L. Mayer, Olga M. Pena, David S. Wishart, Robert E. W. Hancock:
INMEX - a web-based tool for integrative meta-analysis of expression data. 63-70 - Lars M. T. Eijssen, Magali Jaillard, Michiel E. Adriaens, Stan Gaj, Philip J. de Groot, Michael R. Müller, Chris T. A. Evelo:
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. 71-76 - Jing Wang, Dexter T. Duncan, Zhiao Shi, Bing Zhang:
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. 77-83 - Daniel D'Andrea, Luigi Grassi, Mariagiovanna Mazzapioda, Anna Tramontano:
FIDEA: a server for the functional interpretation of differential expression analysis. 84-88 - Gabriele Sales, Enrica Calura, Paolo G. V. Martini, Chiara Romualdi:
Graphite Web: web tool for gene set analysis exploiting pathway topology. 89-97 - Xin Yi, Zhou Du, Zhen Su:
PlantGSEA: a gene set enrichment analysis toolkit for plant community. 98-103 - Tune H. Pers, Piotr Dworzynski, Cecilia Engel Thomas, Kasper Lage, Søren Brunak:
MetaRanker 2.0: a web server for prioritization of genetic variation data. 104-108 - Yuko Makita, Norio Kobayashi, Yuko Yoshida, Koji Doi, Yoshiki Mochizuki, Koro Nishikata, Akihiro Matsushima, Satoshi Takahashi, Manabu Ishii, Terue Takatsuki, Rinki Bhatia, Zolzaya Khadbaatar, Hajime Watabe, Hiroshi Masuya, Tetsuro Toyoda:
PosMed: ranking genes and bioresources based on Semantic Web Association Study. 109-114 - Khalid Zuberi, Max Franz, Harold Rodriguez, Jason Montojo, Christian Tannus Lopes, Gary D. Bader, Quaid Morris:
GeneMANIA Prediction Server 2013 Update. 115-122 - Katharina Jasmin Hoff, Mario Stanke:
WebAUGUSTUS - a web service for training AUGUSTUS and predicting genes in eukaryotes. 123-128 - Bhavjinder K. Dhillon, Terry A. Chiu, Matthew R. Laird, Morgan G. I. Langille, Fiona S. L. Brinkman:
IslandViewer update: improved genomic island discovery and visualization. 129-132 - Geir Kjetil Sandve, Sveinung Gundersen, Morten Johansen, Ingrid Kristine Glad, Krishanthi Gunathasan, Lars Holden, Marit Holden, Knut Liestøl, Ståle Nygård, Vegard Nygaard, Jonas Paulsen, Halfdan Rydbeck, Kai Trengereid, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Matús Kalas, Tonje Lien, Morten Rye, Arnoldo Frigessi, Eivind Hovig:
The Genomic HyperBrowser: an analysis web server for genome-scale data. 133-141 - Javier Arnedo, Coral del Val, Gabriel Alejandro de Erausquin, Rocío Romero-Záliz, Dragan Svrakic, Claude Robert Cloninger, Igor Zwir:
PGMRA: a web server for (phenotype × genotype) many-to-many relation analysis in GWAS. 142-149 - Mulin Jun Li, Lily Yan Wang, Zhengyuan Xia, Pak Chung Sham, Junwen Wang:
GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. 150-158 - Claudia Coronnello, Panayiotis V. Benos:
ComiR: combinatorial microRNA target prediction tool. 159-164 - Charles E. Vejnar, Matthias Blum, Evgeny M. Zdobnov:
miRmap web: comprehensive microRNA target prediction online. 165-168 - Maria D. Paraskevopoulou, Georgios K. Georgakilas, Nikos Kostoulas, Ioannis S. Vlachos, Thanasis Vergoulis, Martin Reczko, Christos Filippidis, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. 169-173 - Limor Leibovich, Inbal Paz, Zohar Yakhini, Yael Mandel-Gutfreund:
DRIMust: a web server for discovering rank imbalanced motifs using suffix trees. 174-179 - Hilal Kazan, Quaid Morris:
RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. 180-186 - Tri Hieu Nim, Jacob K. White, Lisa Tucker-Kellogg:
SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments. 187-191 - Eiru Kim, Hanhae Kim, Insuk Lee:
JiffyNet: a web-based instant protein network modeler for newly sequenced species. 192-197 - Omer Basha, Shoval Tirman, Amir Eluk, Esti Yeger Lotem:
ResponseNet2.0: revealing signaling and regulatory pathways connecting your proteins and genes - now with human data. 198-203 - Kai Blin, Marnix H. Medema, Daniyal Kazempour, Michael A. Fischbach, Rainer Breitling, Eriko Takano, Tilmann Weber:
antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers. 204-212 - Patricia Sebastián-León, José Carbonell, Francisco Salavert, Rubén Sánchez, Ignacio Medina, Joaquín Dopazo:
Inferring the functional effect of gene expression changes in signaling pathways. 213-217 - Christopher K. Wong, Charles J. Vaske, Sam Ng, J. Zachary Sanborn, Stephen C. Benz, David Haussler, Joshua M. Stuart:
The UCSC Interaction Browser: multidimensional data views in pathway context. 218-224 - Zhenjun Hu, Yi-Chien Chang, Yan Wang, Chia-Ling Huang, Yang Liu, Feng Tian, Brian Granger, Charles DeLisi:
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. 225-231 - Ofir Cohen, Haim Ashkenazy, Eli Levy Karin, David Burstein, Tal Pupko:
CoPAP: Coevolution of Presence-Absence Patterns. 232-237 - Timothy I. Shaw, Zheng Ruan, Travis C. Glenn, Liang Liu:
STRAW: Species TRee Analysis Web server. 238-241 - Cyrus Afrasiabi, Bushra Samad, David Dineen, Christopher Meacham, Kimmen Sjölander:
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. 242-248 - Cihan Kaya, Andac Armutlulu, Solen Ekesan, Turkan Haliloglu:
MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues. 249-255 - Daniel A. Kirshner, Jerome P. Nilmeier, Felice C. Lightstone:
Catalytic site identification - a web server to identify catalytic site structural matches throughout PDB. 256-265 - Alexander Goncearenco, Simon Mitternacht, Taipang Yong, Birgit Eisenhaber, Frank Eisenhaber, Igor N. Berezovsky:
SPACER: server for predicting allosteric communication and effects of regulation. 266-272 - Pralay Mitra, David Shultis, Yang Zhang:
EvoDesign: de novo protein design based on structural and evolutionary profiles. 273-280 - Luca Parca, Fabrizio Ferrè, Gabriele Ausiello, Manuela Helmer-Citterich:
Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. 281-285 - Leon Eyrich Jessen, Ilka Hoof, Ole Lund, Morten Nielsen:
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. 286-291 - Zhong-Ru Xie, Chuan-Kun Liu, Fang-Chih Hsiao, Adam Yao, Ming-Jing Hwang:
LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites. 292-296 - Didier Devaurs, Léa Bouard, Marc Vaisset, Christophe Zanon, Ibrahim Al-Bluwi, Romain Iehl, Thierry Siméon, Juan Cortés:
MoMA-LigPath: a web server to simulate protein-ligand unbinding. 297-302 - Daniel B. Roche, Maria T. Buenavista, Liam J. McGuffin:
The FunFOLD2 server for the prediction of protein-ligand interactions. 303-307 - Valerio Bianchi, Iolanda Mangone, Fabrizio Ferrè, Manuela Helmer-Citterich, Gabriele Ausiello:
webPDBinder: a server for the identification of ligand binding sites on protein structures. 308-313 - Kuan Pern Tan, Thanh Binh Nguyen, Siddharth Patel, Raghavan Varadarajan, Mallur S. Madhusudhan:
Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins. 314-321 - Armin Madadkar-Sobhani, Victor Guallar:
PELE web server: atomistic study of biomolecular systems at your fingertips. 322-328 - Xuchang Ouyang, Shuo Zhou, Zemei Ge, Runtao Li, Chee Keong Kwoh:
CovalentDock Cloud: a web server for automated covalent docking. 329-332 - Yves Dehouck, Jean Marc Kwasigroch, Marianne Rooman, Dimitri Gilis:
BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations. 333-339 - Dennis M. Krüger, Prakash Chandra Rathi, Christopher Pfleger, Holger Gohlke:
CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. 340-348 - Daniel W. A. Buchan, Federico Minneci, Tim C. O. Nugent, Kevin Bryson, David T. Jones:
Scalable web services for the PSIPRED Protein Analysis Workbench. 349-357 - Cedrik Magis, Paolo Di Tommaso, Cédric Notredame:
T-RMSD: a web server for automated fine-grained protein structural classification. 358-362 - Rubén Nogales-Cadenas, Slavica Jonic, Florence Tama, A. A. Arteni, Daniel Tabas-Madrid, Miguel Vázquez, Alberto D. Pascual-Montano, Carlos Oscar Sánchez Sorzano:
3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy. 363-367 - Liam J. McGuffin, Maria T. Buenavista, Daniel B. Roche:
The ModFOLD4 server for the quality assessment of 3D protein models. 368-372 - Jeremy Esque, Sylvain Léonard, Alexandre G. de Brevern, Christophe Oguey:
VLDP web server: a powerful geometric tool for analysing protein structures in their environment. 373-378 - Jean-Paul Ebejer, Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane:
Memoir: template-based structure prediction for membrane proteins. 379-383 - Lim Heo, Hahnbeom Park, Chaok Seok:
GalaxyRefine: protein structure refinement driven by side-chain repacking. 384-388 - Marcin Pawlowski, Albert Bogdanowicz, Janusz M. Bujnicki:
QA-RecombineIt: a server for quality assessment and recombination of protein models. 389-397 - Nicolas Palopoli, Esteban Lanzarotti, Gustavo D. Parisi:
BeEP Server: using evolutionary information for quality assessment of protein structure models. 398-405 - Maciej Blaszczyk, Michal Jamróz, Sebastian Kmiecik, Andrzej Kolinski:
CABS-fold: server for the de novo and consensus-based prediction of protein structure. 406-411 - Shu-wen W. Chen, Jean-Luc Pellequer:
Adepth: new representation and its implications for atomic depths of macromolecules. 412-416 - Benjamin Woollett, Lee Whitmore, Robert W. Janes, B. A. Wallace:
ValiDichro: a website for validating and quality control of protein circular dichroism spectra. 417-421 - Christian Margreitter, Drazen Petrov, Bojan Zagrovic:
Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. 422-426 - Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik:
CABS-flex: server for fast simulation of protein structure fluctuations. 427-431 - Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus Raih:
IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank. 432-440 - Shengnan Tang, Tonghua Li, Peisheng Cong, Wenwei Xiong, Zhiheng Wang, Jiangming Sun:
PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif. 441-447 - Auke J. van Heel, Anne de Jong, Manuel Montalbán-López, Jan Kok, Oscar P. Kuipers:
BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. 448-453 - Timothy I. Shaw, Ming Zhang:
HIV N-linked glycosylation site analyzer and its further usage in anchored alignment. 454-458 - Dmitry N. Ivankov, Natalya S. Bogatyreva, Peter Hönigschmid, Bastian Dislich, Sebastian Hogl, Peer-Hendrik Kuhn, Dmitrij Frishman, Stefan F. Lichtenthaler:
QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis. 459-464 - Juan Antonio García-Martín, Peter Clote, Iván Dotú:
RNAiFold: a web server for RNA inverse folding and molecular design. 465-470 - Stanislav Bellaousov, Jessica S. Reuter, Matthew G. Seetin, David H. Mathews:
RNAstructure: web servers for RNA secondary structure prediction and analysis. 471-474 - Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin:
The RNAsnp web server: predicting SNP effects on local RNA secondary structure. 475-479 - Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer, Jérôme Waldispühl:
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. 480-485 - Andrey Chursov, Sebastian J. Kopetzky, Gennady Bocharov, Dmitrij Frishman, Alexander Shneider:
RNAtips: analysis of temperature-induced changes of RNA secondary structure. 486-491 - Hanjoo Kim, Pablo Cordero, Rhiju Das, Sungroh Yoon:
HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis. 492-498 - Florian Eggenhofer, Ivo L. Hofacker, Christian Höner zu Siederdissen:
CMCompare webserver: comparing RNA families via covariance models. 499-503 - Klas Hatje, Björn Hammesfahr, Martin Kollmar:
WebScipio: reconstructing alternative splice variants of eukaryotic proteins. 504-509 - Jeongkyun Kim, Seongeun So, Hee-Jin Lee, Jong-Chan Park, Jung-Jae Kim, Hyunju Lee:
DigSee: disease gene search engine with evidence sentences (version cancer). 510-517 - Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu:
PubTator: a web-based text mining tool for assisting biocuration. 518-522 - Chih-Kang Lin, Chien-Yu Chen:
PiDNA: predicting protein-DNA interactions with structural models. 523-530 - Stefan Broos, Arne Soete, Bart Hooghe, Raymond Moran, Frans van Roy, Pieter J. De Bleser:
PhysBinder: improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties. 531-534 - Federico Zambelli, Graziano Pesole, Giulio Pavesi:
PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. 535-543 - Christopher Fletez-Brant, Dongwon Lee, Andrew S. McCallion, Michael A. Beer:
kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets. 544-556 - Katherine Wolstencroft, Robert Haines, Donal Fellows, Alan R. Williams, David Withers, Stuart Owen, Stian Soiland-Reyes, Ian Dunlop, Aleksandra Nenadic, Paul Fisher, Jiten Bhagat, Khalid Belhajjame, Finn Bacall, Alex R. Hardisty, Abraham Nieva de la Hidalga, Maria P. Balcazar Vargas, Shoaib Sufi, Carole A. Goble:
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. 557-561 - Alexander L. R. Lubbock, Elad Katz, David J. Harrison, Ian M. Overton:
TMA Navigator: network inference, patient stratification and survival analysis with tissue microarray data. 562-568 - Robert Sidney Cox III, Koro Nishikata, Sayoko Shimoyama, Yuko Yoshida, Minami Matsui, Yuko Makita, Tetsuro Toyoda:
PromoterCAD: data-driven design of plant regulatory DNA. 569-574 - Marc Lohse, Oliver Drechsel, Sabine Kahlau, Ralph Bock:
OrganellarGenomeDRAW - a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. 575-581 - Maria D. Paraskevopoulou, Ioannis S. Vlachos, Emmanouil Athanasiadis, George M. Spyrou:
BiDaS: a web-based Monte Carlo BioData Simulator based on sequence/feature characteristics. 582-586
- Harm Nijveen, Martijn van Kaauwen, Danny G. Esselink, Brechtje Hoegen, Ben Vosman:
QualitySNPng: a user-friendly SNP detection and visualization tool. 587-590 - Omar Wagih, Matej Usaj, Anastasia Baryshnikova, Benjamin VanderSluis, Elena Kuzmin, Michael Costanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone, Leopold Parts:
SGAtools: one-stop analysis and visualization of array-based genetic interaction screens. 591-596
- Hamish McWilliam, Weizhong Li, Mahmut Uludag, Silvano Squizzato, Young Mi Park, Nicola Buso, Andrew Peter Cowley, Rodrigo Lopez:
Analysis Tool Web Services from the EMBL-EBI. 597-600 - Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Rafael C. Jiménez, Eugenia Galeota, Guillaume Launay, Johannes Goll, Karin Breuer, Keiichiro Ono, Lukasz Salwínski, Henning Hermjakob:
A new reference implementation of the PSICQUIC web service. 601-606
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