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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