Nucleic Acids Research, Volume 42

Volume 42, Number Database-Issue, January 2014

I. Nucleic acid sequence, structure and regulation

• 
  Xosé M. Fernández-Suárez, Daniel J. Rigden, Michael Y. Galperin:
  The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. 1-6
• 
  Database resources of the National Center for Biotechnology Information. 7-17
• 
  Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney, Janet M. Thornton:
  The European Bioinformatics Institute's data resources 2014. 18-25
• 
  Henrik Nordberg, Michael Cantor, Serge Dusheyko, Susan Hua, Alexander Poliakov, Igor Shabalov, Tatyana Smirnova, Igor V. Grigoriev, Inna Dubchak:
  The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. 26-31
• 
  Dennis A. Benson, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
  GenBank. 32-37
• 
  Nima Pakseresht, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Tamer Gur, Mikyung Jang, Simon Kay, Rasko Leinonen, Weizhong Li, Xin Liu, Rodrigo Lopez, Hamish McWilliam, Arnaud Oisel, Swapna Pallreddy, Sheila Plaister, Rajesh Radhakrishnan, Stéphane Rivière, Marc Rossello, Alexander Senf, Nicole Silvester, Dimitriy Smirnov, Silvano Squizzato, Petra ten Hoopen, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane:
  Assembly information services in the European Nucleotide Archive. 38-43
• 
  Takehide Kosuge, Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura:
  DDBJ progress report: a new submission system for leading to a correct annotation. 44-49
• 
  Adam Faulconbridge, Tony Burdett, Marco Brandizi, Mikhail Gostev, Rui Pedro Pereira, Drashtti Vasant, Ugis Sarkans, Alvis Brazma, Helen E. Parkinson:
  Updates to BioSamples database at European Bioinformatics Institute. 50-52
• 
  Stefanie Geisen, Guillermo Barturen, Ángel M. Alganza, Michael Hackenberg, José L. Oliver:
  NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes. 53-59
• 
  Klaus Wethmar, Adriano Barbosa-Silva, Miguel A. Andrade-Navarro, Achim Leutz:
  uORFdb - a comprehensive literature database on eukaryotic uORF biology. 60-67
• 
  Ana Kozomara, Sam Griffiths-Jones:
  miRBase: annotating high confidence microRNAs using deep sequencing data. 68-73
• 
  Michal Wojciech Szczesniak, Izabela Makalowska:
  miRNEST 2.0: a database of plant and animal microRNAs. 74-77
• 
  Sheng-Da Hsu, Yu-Ting Tseng, Sirjana Shrestha, Yu-Ling Lin, Anas Khaleel, Chih-Hung Chou, Chao-Fang Chu, Hsi-Yuan Huang, Ching-Min Lin, Shu-Yi Ho, Ting-Yan Jian, Feng-Mao Lin, Tzu-Hao Chang, Shun-Long Weng, Kuang-Wen Liao, I-En Liao, Chun-Chi Liu, Hsien-Da Huang:
  miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. 78-85
• 
  Anindya Bhattacharya, Jesse D. Ziebarth, Yan Cui:
  PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. 86-91
• 
  Jun-Hao Li, Shun Liu, Hui Zhou, Liang-Hu Qu, Jian-Hua Yang:
  starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. 92-97
• 
  Chaoyong Xie, Jiao Yuan, Hui Li, Ming Li, Guoguang Zhao, Dechao Bu, Weimin Zhu, Wei Wu, Runsheng Chen, Yi Zhao:
  NONCODEv4: exploring the world of long non-coding RNA genes. 98-103
• 
  Jiao Yuan, Wei Wu, Chaoyong Xie, Guoguang Zhao, Yi Zhao, Runsheng Chen:
  NPInter v2.0: an updated database of ncRNA interactions. 104-108
• 
  Gokul Ramaswami, Jin Billy Li:
  RADAR: a rigorously annotated database of A-to-I RNA editing. 109-113
• 
  Buvaneswari Coimbatore Narayanan, John D. Westbrook, Saheli Ghosh, Anton I. Petrov, Blake A. Sweeney, Craig L. Zirbel, Neocles Leontis, Helen M. Berman:
  The Nucleic Acid Database: new features and capabilities. 114-122
• 
  Grzegorz Chojnowski, Tomasz Walen, Janusz M. Bujnicki:
  RNA Bricks - a database of RNA 3D motifs and their interactions. 123-131
• 
  Ankita Mehta, Surabhi Sonam, Isha Gouri, Saurabh Loharch, Deepak K. Sharma, Raman Parkesh:
  SMMRNA: a database of small molecule modulators of RNA. 132-141
• 
  Anthony Mathelier, Xiaobei Zhao, Allen W. Zhang, François Parcy, Rebecca Worsley-Hunt, David J. Arenillas, Sorana Buchman, Chih-Yu Chen, Alice Yi Chou, Hans Ienasescu, Jonathan S. Lim, Casper Shyr, Ge Tan, Michelle Zhou, Boris Lenhard, Albin Sandelin, Wyeth W. Wasserman:
  JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. 142-147
• 
  Lin Yang, Tianyin Zhou, Iris Dror, Anthony Mathelier, Wyeth W. Wasserman, Raluca Gordân, Remo Rohs:
  NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites. 148-155
• 
  Sefa Kiliç, Elliot R. White, Dinara M. Sagitova, Joseph P. Cornish, Ivan Erill:
  CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria. 156-160
• 
  Miguel Cacho Teixeira, Pedro Tiago Monteiro, Joana Fernandes Guerreiro, Joana Pinho Gonçalves, Nuno Pereira Mira, Sandra Costa dos Santos, Tânia Rodrigues Cabrito, Margarida Palma, Catarina Costa, Alexandre Paulo Francisco, Sara Cordeiro Madeira, Arlindo Limede Oliveira, Ana Teresa Freitas, Isabel Sá-Correia:
  The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. 161-166
• 
  Shula Shazman, Hunjoong Lee, Yakov Socol, Richard S. Mann, Barry Honig:
  OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. 167-171
• 
  Diego Chacón, Dominik Beck, Dilmi Perera, Jason W. H. Wong, John E. Pimanda:
  BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells. 172-177
• 
  David T. W. Tzeng, Yu-Ting Tseng, Matthew Ung, I-En Liao, Chun-Chi Liu, Chao Cheng:
  DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data. 178-183
• 
  Serdar Turkarslan, Elisabeth J. Wurtmann, Wei-Ju Wu, Ning Jiang, J. Christopher Bare, Karen Foley, David J. Reiss, Pavel S. Novichkov, Nitin S. Baliga:
  Network portal: a database for storage, analysis and visualization of biological networks. 184-190

II. Protein sequence and structure, motifs and domains

• 
  Activities at the Universal Protein Resource (UniProt). 191-198
• 
  Minoru Kanehisa, Susumu Goto, Yoko Sato, Masayuki Kawashima, Miho Furumichi, Mao Tanabe:
  Data, information, knowledge and principle: back to metabolism in KEGG. 199-205
• 
  Ross A. Overbeek, Robert Olson, Gordon D. Pusch, Gary J. Olsen, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Bruce D. Parrello, Maulik Shukla, Veronika Vonstein, Alice R. Wattam, Fangfang Xia, Rick Stevens:
  The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). 206-214
• 
  Matthew P. Campbell, Robyn Peterson, Julien Mariethoz, Elisabeth Gasteiger, Yukie Akune, Kiyoko F. Aoki-Kinoshita, Frédérique Lisacek, Nicolle H. Packer:
  UniCarbKB: building a knowledge platform for glycoproteomics. 215-221
• 
  Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta:
  Pfam: the protein families database. 222-230
• 
  Sean Powell, Kristoffer Forslund, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Jaime Huerta-Cepas, Toni Gabaldón, Thomas Rattei, Christopher J. Creevey, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, Peer Bork:
  eggNOG v4.0: nested orthology inference across 3686 organisms. 231-239
• 
  Jonathan G. Lees, David A. Lee, Romain A. Studer, Natalie L. Dawson, Ian Sillitoe, Sayoni Das, Corin Yeats, Benoit H. Dessailly, Robert Rentzsch, Christine A. Orengo:
  Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. 240-245
• 
  Eshita Mutt, Oommen K. Mathew, Ramanathan Sowdhamini:
  LenVarDB: database of length-variant protein domains. 246-250
• 
  Milton H. Saier Jr., Vamsee S. Reddy, Dorjee G. Tamang, Åke Västermark:
  The Transporter Classification Database. 251-258
• 
  Holger Dinkel, Kim Van Roey, Sushama Michael, Norman E. Davey, Robert J. Weatheritt, Diana Born, Tobias Speck, Daniel Krüger, Gleb Grebnev, Marta Kuban, Marta Strumillo, Bora Uyar, Aidan Budd, Brigitte Altenberg, Markus Seiler, Lucía B. Chemes, Juliana Glavina, Ignacio E. Sánchez, Francesca Diella, Toby J. Gibson:
  The eukaryotic linear motif resource ELM: 10 years and counting. 259-266
• 
  Paolo Maietta, Gonzalo López, Angel Carro, Benjamin J. Pingilley, Leticia G. Leon, Alfonso Valencia, Michael L. Tress:
  FireDB: a compendium of biological and pharmacologically relevant ligands. 267-272
• 
  Michail Yu. Lobanov, Igor V. Sokolovskiy, Oxana V. Galzitskaya:
  HRaP: database of occurrence of HomoRepeats and patterns in proteomes. 273-278
• 
  Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei:
  SIMAP - the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. 279-284
• 
  Aleksandras Gutmanas, Younes Alhroub, Gary M. Battle, John M. Berrisford, Estelle Bochet, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Swanand P. Gore, Pauline Haslam, Rowan Hatherley, Pieter M. S. Hendrickx, Miriam Hirshberg, Ingvar C. Lagerstedt, Saqib Mir, Abhik Mukhopadhyay, Thomas J. Oldfield, Ardan Patwardhan, Luana Rinaldi, Gaurav Sahni, Eduardo Sanz-García, Sanchayita Sen, Robert A. Slowley, Sameer Velankar, Michael E. Wainwright, Gerard J. Kleywegt:
  PDBe: Protein Data Bank in Europe. 285-291
• 
  Tjaart A. P. de Beer, Karel Berka, Janet M. Thornton, Roman A. Laskowski:
  PDBsum additions. 292-296
• 
  Thomas Madej, Christopher J. Lanczycki, Dachuan Zhang, Paul A. Thiessen, Renata C. Geer, Aron Marchler-Bauer, Stephen H. Bryant:
  MMDB and VAST+: tracking structural similarities between macromolecular complexes. 297-303
• 
  Naomi K. Fox, Steven E. Brenner, John-Marc Chandonia:
  SCOPe: Structural Classification of Proteins - extended, integrating SCOP and ASTRAL data and classification of new structures. 304-309
• 
  Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey G. Murzin:
  SCOP2 prototype: a new approach to protein structure mining. 310-314
• 
  Jaume Bonet, Joan Planas-Iglesias, Javier García-García, Manuel Alejandro Marín-López, Narcis Fernandez-Fuentes, Baldo Oliva:
  ArchDB 2014: structural classification of loops in proteins. 315-319
• 
  Satoshi Fukuchi, Takayuki Amemiya, Shigetaka Sakamoto, Yukiko Nobe, Kazuo Hosoda, Yumiko Kado, Seiko D. Murakami, Ryotaro Koike, Hidekazu Hiroaki, Motonori Ota:
  IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners. 320-325
• 
  Mihaly Varadi, Simone Kosol, Pierre Lebrun, Erica Valentini, Martin Blackledge, A. Keith Dunker, Isabella C. Felli, Julie D. Forman-Kay, Richard W. Kriwacki, Roberta Pierattelli, Joel L. Sussman, Dmitri I. Svergun, Vladimir N. Uversky, Michele Vendruscolo, David S. Wishart, Peter E. Wright, Peter Tompa:
  pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. 326-335
• 
  Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges, Andrej Sali:
  ModBase, a database of annotated comparative protein structure models and associated resources. 336-346
• 
  Alexander S. Rose, Dominic Theune, Andrean Goede, Peter Werner Hildebrand:
  MP: PD - a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins. 347-351
• 
  Tomás Di Domenico, Emilio Potenza, Ian Walsh, R. Gonzalo Parra, Manuel Giollo, Giovanni Minervini, Damiano Piovesan, Awais Ihsan, Carlo Ferrari, Andrey V. Kajava, Silvio C. E. Tosatto:
  RepeatsDB: a database of tandem repeat protein structures. 352-357
• 
  Sandra E. Orchard, Mais G. Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H. Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Eugenia Galeota, Ursula Hinz, Marta Iannuccelli, Sruthi Jagannathan, Rafael C. Jiménez, Jyoti Khadake, Astrid Lægreid, Luana Licata, Ruth C. Lovering, Birgit Meldal, Anna N. Melidoni, Mila Milagros, Daniele Peluso, Livia Perfetto, Pablo Porras, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Andre Stutz, Michael Tognolli, Kim Van Roey, Gianni Cesareni, Henning Hermjakob:
  The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases. 358-363
• 
  Robert D. Finn, Benjamin L. Miller, Jody Clements, Alex Bateman:
  iPfam: a database of protein family and domain interactions found in the Protein Data Bank. 364-373
• 
  Roberto Mosca, Arnaud Céol, Amelie Stein, Roger Olivella, Patrick Aloy:
  3did: a catalog of domain-based interactions of known three-dimensional structure. 374-379
• 
  Thomas Schmitt, Christoph Ogris, Erik L. L. Sonnhammer:
  FunCoup 3.0: database of genome-wide functional coupling networks. 380-388
• 
  Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie:
  KBDOCK 2013: a spatial classification of 3D protein domain family interactions. 389-395
• 
  Philipp Blohm, Goar Frishman, Pawel Smialowski, Florian Goebels, Benedikt Wachinger, Andreas Ruepp, Dmitrij Frishman:
  Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. 396-400
• 
  Michael Kuhn, Damian Szklarczyk, Sune Pletscher-Frankild, Thomas H. Blicher, Christian von Mering, Lars Juhl Jensen, Peer Bork:
  STITCH 4: integration of protein-chemical interactions with user data. 401-407
• 
  Ravi Kiran Reddy Kalathur, José Pedro Pinto, Miguel A. Hernández-Prieto, Rui S. R. Machado, Dulce Almeida, Gautam Chaurasia, Matthias E. Futschik:
  UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. 408-414
• 
  Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Carol J. Bult, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, Olivia Helfer, Hongzhan Huang, Anna Maria Masci, Jia Ren, Natalia V. Roberts, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Meher Shruti Yerramalla, Jian Zhang, Aisha AlJanahi, Irem Çelen, Cynthia Gan, Mengxi Lv, Emily Schuster-Lezell, Cathy H. Wu:
  Protein Ontology: a controlled structured network of protein entities. 415-421
• 
  Vignir Ísberg, Bas Vroling, Rob van der Kant, Kang Li, Gert Vriend, David E. Gloriam:
  GPCRDB: an information system for G protein-coupled receptors. 422-425
• 
  Daiane C. F. Golbert, Eliane Santana-van-Vliet, Alex S. Mundstein, Vicente Calfo, Wilson Savino, Ana T. R. de Vasconcelos:
  Laminin-database v.2.0: an update on laminins in health and neuromuscular disorders. 426-429
• 
  Joao Miguel da Conceiçao Alves-Cruzeiro, Rubén Nogales-Cadenas, Alberto Domingo Pascual-Montano:
  CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. 430-436
• 
  Frédéric Romagné, Didac Santesmasses, Louise White, Gaurab K. Sarangi, Marco Mariotti, Ron Hübler, Antje Weihmann, Genis Parra, Vadim N. Gladyshev, Roderic Guigó, Sergi Castellano:
  SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans. 437-443
• 
  Ankur Gautam, Kumardeep Chaudhary, Sandeep Singh, Anshika Joshi, Priya Anand, Abhishek Tuknait, Deepika Mathur, Grish C. Varshney, Gajendra P. S. Raghava:
  Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. 444-449
• 
  Qixuan Wang, Jinyan Huang, Hanfei Sun, Jing Liu, Juan Wang, Qian Wang, Qian Qin, Shenglin Mei, Chengchen Zhao, Xiaoqin Yang, Xiaole Shirley Liu, Yong Zhang:
  CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. 450-458

III. Metabolic and signalling pathways, enzymes

• 
  Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A. Fulcher, Timothy A. Holland, Ingrid M. Keseler, Anamika Kothari, Aya Kubo, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Pallavi Subhraveti, Daniel S. Weaver, Deepika Weerasinghe, Peifen Zhang, Peter D. Karp:
  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. 459-471
• 
  David Croft, Antonio Fabregat Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani V. Garapati, Marc Gillespie, Maulik R. Kamdar, Bijay Jassal, Steven Jupe, Lisa Matthews, Bruce May, Stanislav Palatnik, Karen Rothfels, Veronica Shamovsky, Heeyeon Song, Mark Williams, Ewan Birney, Henning Hermjakob, Lincoln Stein, Peter D'Eustachio:
  The Reactome pathway knowledgebase. 472-477
• 
  Timothy Jewison, Yilu Su, Fatemeh Miri Disfany, Yongjie Liang, Craig Knox, Adam Maciejewski, Jenna Poelzer, Jessica Huynh, You Zhou, David Arndt, Yannick Djoumbou, Yifeng Liu, Lu Deng, Anchi Guo, Beomsoo Han, Allison Pon, Michael Wilson, Shahrzad Rafatnia, Philip Liu, David S. Wishart:
  SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database. 478-484
• 
  Nicholas Furnham, Gemma L. Holliday, Tjaart A. P. de Beer, Julius O. B. Jacobsen, William R. Pearson, Janet M. Thornton:
  The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. 485-489
• 
  Vincent Lombard, Hemalatha Golaconda Ramulu, Elodie Drula, Pedro M. Coutinho, Bernard Henrissat:
  The carbohydrate-active enzymes database (CAZy) in 2013. 490-495
• 
  Yongbo Wang, Zexian Liu, Han Cheng, Tianshun Gao, Zhicheng Pan, Qing Yang, Anyuan Guo, Yu Xue:
  EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. 496-502
• 
  Neil D. Rawlings, Matthew Waller, Alan J. Barrett, Alex Bateman:
  MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. 503-509
• 
  Zhimin Huang, Linkai Mou, Qiancheng Shen, Shaoyong Lu, Chuangang Li, Xinyi Liu, Guanqiao Wang, Shuai Li, Lv Geng, Yaqin Liu, Jiawei Wu, Guoqiang Chen, Jian Zhang:
  ASD v2.0: updated content and novel features focusing on allosteric regulation. 510-516
• 
  Sergio Hernández, Gabriela Ferragut, Isaac Amela, JosepAntoni Perez-Pons, Jaume Piñol, Angel Mozo-Villarias, Juan Cedano, Enrique Querol:
  MultitaskProtDB: a database of multitasking proteins. 517-520
• 
  Eyal Akiva, Shoshana D. Brown, Daniel E. Almonacid, Alan E. Barber II, Ashley F. Custer, Michael A. Hicks, Conrad C. Huang, Florian Lauck, Susan T. Mashiyama, Elaine C. Meng, David Mischel, John H. Morris, Sunil Ojha, Alexandra M. Schnoes, Doug Stryke, Jeffrey M. Yunes, Thomas E. Ferrin, Gemma L. Holliday, Patricia C. Babbitt:
  The Structure-Function Linkage Database. 521-530
• 
  Zexian Liu, Yongbo Wang, Tianshun Gao, Zhicheng Pan, Han Cheng, Qing Yang, Zhongyi Cheng, Anyuan Guo, Jian Ren, Yu Xue:
  CPLM: a database of protein lysine modifications. 531-536
• 
  Min-Gang Su, Kai-Yao Huang, Cheng-Tsung Lu, Hui-Ju Kao, Ya-Han Chang, Tzong-Yi Lee:
  topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. 537-545

IV. Viruses, bacteria, protozoa and fungi

• 
  Paul Julian Kersey, James E. Allen, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Daniel Seth Toney Hughes, Jay C. Humphrey, Arnaud Kerhornou, Julia Khobova, Nicholas Langridge, Mark D. McDowall, Uma Maheswari, Gareth Maslen, Michael Nuhn, Chuang Kee Ong, Michael Paulini, Helder Pedro, Iliana Toneva, Mary Ann Tuli, Brandon Walts, Gareth Williams, Derek Wilson, Ken Youens-Clark, Marcela K. Monaco, Joshua C. Stein, Xuehong Wei, Doreen Ware, Daniel M. Bolser, Kevin Lee Howe, Eugene Kulesha, Daniel Lawson, Daniel Michael Staines:
  Ensembl Genomes 2013: scaling up access to genome-wide data. 546-552
• 
  Tatiana A. Tatusova, Stacy Ciufo, Boris Fedorov, Kathleen O'Neill, Igor Tolstoy:
  RefSeq microbial genomes database: new representation and annotation strategy. 553-559
• 
  Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Tanja Woyke, Marcel Huntemann, Iain Anderson, Konstantinos Billis, Neha Varghese, Konstantinos Mavrommatis, Amrita Pati, Natalia Ivanova, Nikos Kyrpides:
  IMG 4 version of the integrated microbial genomes comparative analysis system. 560-567
• 
  Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Manoj Pillay, Anna Ratner, Jinghua Huang, Ioanna Pagani, Susannah Tringe, Marcel Huntemann, Konstantinos Billis, Neha Varghese, Kristin Tennessen, Konstantinos Mavrommatis, Amrita Pati, Natalia Ivanova, Nikos Kyrpides:
  IMG/M 4 version of the integrated metagenome comparative analysis system. 568-573
• 
  Hao Luo, Yan Lin, Feng Gao, Chun-Ting Zhang, Ren Zhang:
  DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. 574-580
• 
  Alice R. Wattam, David Abraham, Oral Dalay, Terry Disz, Timothy Driscoll, Joseph L. Gabbard, Joseph J. Gillespie, Roger Gough, Deborah Hix, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Robert Olson, Ross A. Overbeek, Gordon D. Pusch, Maulik Shukla, Julie Schulman, Rick L. Stevens, Daniel E. Sullivan, Veronika Vonstein, Andrew S. Warren, Rebecca Will, Meredith J. C. Wilson, Hyun Seung Yoo, Chengdong Zhang, Yan Zhang, Bruno W. S. Sobral:
  PATRIC, the bacterial bioinformatics database and analysis resource. 581-591
• 
  Carola Söhngen, Boyke Bunk, Adam Podstawka, Dorothea Gleim, Jörg Overmann:
  BacDive - the Bacterial Diversity Metadatabase. 592-599
• 
  Sarah Hunter, Matthew Corbett, Hubert Denise, Matthew Fraser, Alejandra N. González-Beltrán, Christopher I. Hunter, Philip Jones, Rasko Leinonen, Craig McAnulla, Eamonn Maguire, John Maslen, Alex L. Mitchell, Gift Nuka, Arnaud Oisel, Sebastien Pesseat, Rajesh Radhakrishnan, Philippe Rocca-Serra, Maxim Scheremetjew, Peter Sterk, Daniel Vaughan, Guy Cochrane, Dawn Field, Susanna-Assunta Sansone:
  EBI metagenomics - a new resource for the analysis and archiving of metagenomic data. 600-606
• 
  Gabriele Dröge, Katharine Barker, Jonas J. Astrin, Paul Bartels, Carol Butler, David Cantrill, Jonathan Coddington, Félix Forest, Birgit Gemeinholzer, Donald Hobern, Jacqueline Mackenzie-Dodds, Éamonn Ó Tuama, Gitte Petersen, Oris Sanjur, David Schindel, Ole Seberg:
  The Global Genome Biodiversity Network (GGBN) Data Portal. 607-612
• 
  Aidan C. Parte:
  LPSN - list of prokaryotic names with standing in nomenclature. 613-616
• 
  Katherine Huang, Arthur Brady, Anup Mahurkar, Owen White, Dirk Gevers, Curtis Huttenhower, Nicola Segata:
  MetaRef: a pan-genomic database for comparative and community microbial genomics. 617-624
• 
  Yemin Lan, J. Calvin Morrison, Ruth Hershberg, Gail L. Rosen:
  POGO-DB - a database of pairwise-comparisons of genomes and conserved orthologous genes. 625-632
• 
  James R. Cole, Qiong Wang, Jordan A. Fish, Benli Chai, Donna M. McGarrell, Yanni Sun, C. Titus Brown, Andrea Porras-Alfaro, Cheryl R. Kuske, James M. Tiedje:
  Ribosomal Database Project: data and tools for high throughput rRNA analysis. 633-642
• 
  Pelin Yilmaz, Laura Wegener Parfrey, Pablo Yarza, Jan Gerken, Elmar Pruesse, Christian Quast, Timmy Schweer, Jörg Peplies, Wolfgang Ludwig, Frank Oliver Glöckner:
  The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. 643-648
• 
  Pieter Meysman, Paolo Sonego, Luca Bianco, Qiang Fu, Daniela Ledezma-Tejeida, Socorro Gama-Castro, Veerle Liebens, Jan Michiels, Kris Laukens, Kathleen Marchal, Julio Collado-Vides, Kristof Engelen:
  COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. 649-653
• 
  Xizeng Mao, Qin Ma, Chuan Zhou, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu:
  DOOR 2.0: presenting operons and their functions through dynamic and integrated views. 654-659
• 
  J. Rodney Brister, Yiming Bao, Sergey A. Zhdanov, Yuri Ostapchuck, Vyacheslav Chetvernin, Boris Kiryutin, Leonid Zaslavsky, Michael Kimelman, Tatiana A. Tatusova:
  Virus Variation Resource - recent updates and future directions. 660-665
• 
  Takatomo Fujisawa, Shinobu Okamoto, Toshiaki Katayama, Mitsuteru Nakao, Hidehisa Yoshimura, Hiromi Kajiya-Kanegae, Sumiko Yamamoto, Chiyoko Yano, Yuka Yanaka, Hiroko Maita, Takakazu Kaneko, Satoshi Tabata, Yasukazu Nakamura:
  CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes. 666-670
• 
  Sophie Bleves, Irmtraud Dunger, Mathias C. Walter, Dimitrios Frangoulidis, Gabi Kastenmüller, Romé Voulhoux, Andreas Ruepp:
  HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. 671-676
• 
  James C. Hu, Gavin Sherlock, Deborah A. Siegele, Suzanne A. Aleksander, Catherine A. Ball, Janos Demeter, Sushanth Gouni, Timothy A. Holland, Peter D. Karp, John E. Lewis, Nathan M. Liles, Brenley K. McIntosh, Huaiyu Mi, Anushya Muruganujan, Farrell Wymore, Paul D. Thomas:
  PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. 677-684
• 
  Robyn T. Eijlander, Anne de Jong, Antonina O. Krawczyk, Siger Holsappel, Oscar P. Kuipers:
  SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis. 685-691
• 
  Raphael H. Michna, Fabian M. Commichau, Dominik Tödter, Christopher P. Zschiedrich, Jörg Stülke:
  SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information. 692-698
• 
  Igor V. Grigoriev, Roman Nikitin, Sajeet Haridas, Alan Kuo, Robin A. Ohm, Robert Otillar, Robert Riley, Asaf A. Salamov, Xueling Zhao, Frank Korzeniewski, Tatyana Smirnova, Henrik Nordberg, Inna Dubchak, Igor Shabalov:
  MycoCosm portal: gearing up for 1000 fungal genomes. 699-704
• 
  Gustavo C. Cerqueira, Martha B. Arnaud, Diane O. Inglis, Marek S. Skrzypek, Gail Binkley, Matt Simison, Stuart R. Miyasato, Jonathan Binkley, Joshua Orvis, Prachi Shah, Farrell Wymore, Gavin Sherlock, Jennifer R. Wortman:
  The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. 705-710
• 
  Jonathan Binkley, Martha B. Arnaud, Diane O. Inglis, Marek S. Skrzypek, Prachi Shah, Farrell Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock:
  The Candida Genome Database: The new homology information page highlights protein similarity and phylogeny. 711-716
• 
  Maria C. Costanzo, Stacia R. Engel, Edith D. Wong, Paul Lloyd, Kalpana Karra, Esther T. Chan, Shuai Weng, Kelley M. Paskov, Greg R. Roe, Gail Binkley, Benjamin C. Hitz, J. Michael Cherry:
  Saccharomyces genome database provides new regulation data. 717-725
• 
  Michal Breker, Melissa Gymrek, Ofer Moldavski, Maya Schuldiner:
  LoQAtE - Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast. 726-730
• 
  Hanhae Kim, Junha Shin, Eiru Kim, Hyojin Kim, Sohyun Hwang, Jung Eun Shim, Insuk Lee:
  YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. 731-736
• 
  Chandan Pal, Johan Bengtsson-Palme, Christopher Rensing, Erik Kristiansson, D. G. Joakim Larsson:
  BacMet: antibacterial biocide and metal resistance genes database. 737-743
• 
  Marie Chantal Lemfack, Janette Nickel, Mathias Dunkel, Robert Preissner, Birgit Piechulla:
  mVOC: a database of microbial volatiles. 744-748

V. Human genome, model organisms, comparative genomics

• 
  Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Nathan Johnson, Thomas Juettemann, Andreas Kähäri, Stephen Keenan, Eugene Kulesha, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet Singh Riat, Magali Ruffier, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Stephen J. Trevanion, Alessandro Vullo, Steven P. Wilder, Mark Wilson, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Rhoda Kinsella, Matthieu Muffato, Anne Parker, Giulietta Spudich, Andy Yates, Daniel R. Zerbino, Stephen M. J. Searle:
  Ensembl 2014. 749-755
• 
  Kim D. Pruitt, Garth R. Brown, Susan M. Hiatt, Françoise Thibaud-Nissen, Alexander Astashyn, Olga D. Ermolaeva, Catherine M. Farrell, Jennifer Hart, Melissa J. Landrum, Kelly M. McGarvey, Michael R. Murphy, Nuala A. O'Leary, Shashikant Pujar, Bhanu Rajput, Sanjida H. Rangwala, Lillian D. Riddick, Andrei Shkeda, Hanzhen Sun, Pamela Tamez, Raymond E. Tully, Craig Wallin, David Webb, Janet Weber, Wendy Wu, Michael DiCuccio, Paul A. Kitts, Donna R. Maglott, Terence D. Murphy, James M. Ostell:
  RefSeq: an update on mammalian reference sequences. 756-763
• 
  Donna Karolchik, Galt P. Barber, Jonathan Casper, Hiram Clawson, Melissa S. Cline, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steven G. Heitner, Angie S. Hinrichs, Katrina Learned, Brian T. Lee, Chin H. Li, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Cricket A. Sloan, Matthew L. Speir, Ann S. Zweig, David Haussler, Robert M. Kuhn, W. James Kent:
  The UCSC Genome Browser database: 2014 update. 764-770
• 
  Jennifer L. Harrow, Charles A. Steward, Adam Frankish, James G. R. Gilbert, Jose M. Gonzalez, Jane E. Loveland, Jonathan M. Mudge, Daniel Sheppard, Mark Thomas, Stephen J. Trevanion, Laurens G. Wilming:
  NAR Breakthrough Article: The Vertebrate Genome Annotation browser 10 years on. 771-779
• 
  Susan E. St. Pierre, Laura Ponting, Raymund Stefancsik, Peter McQuilton:
  FlyBase 102 - advanced approaches to interrogating FlyBase. 780-788
• 
  Todd W. Harris, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Christian A. Grove, Kevin L. Howe, Ranjana Kishore, Raymond Y. N. Lee, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Michael Paulini, Daniela Raciti, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, J. D. Wong, Karen Yook, Tim Schedl, Jonathan Hodgkin, Matthew Berriman, Paul J. Kersey, John Spieth, Lincoln Stein, Paul W. Sternberg:
  WormBase 2014: new views of curated biology. 789-793
• 
  K. Joeri van der Velde, Mark de Haan, Konrad Zych, Danny Arends, L. Basten Snoek, Jan E. Kammenga, Ritsert C. Jansen, Morris A. Swertz, Yang Li:
  WormQTL^HD - a web database for linking human disease to natural variation data in C. elegans. 794-801
• 
  Gautier Koscielny, Gagarine Yaikhom, Vivek Iyer, Terrence F. Meehan, Hugh Morgan, Julian Atienza-Herrero, Andrew Blake, Chao-Kung Chen, Richard Easty, Armida Di Fenza, Tanja Fiegel, Mark Grifiths, Alan Horne, Natasha A. Karp, Natalja Kurbatova, Jeremy C. Mason, Peter Matthews, Darren J. Oakley, Asfand Qazi, Jack Regnart, Ahmad Retha, Luis A. Santos, Duncan J. Sneddon, Jonathan Warren, Henrik Westerberg, Robert J. Wilson, David G. Melvin, Damian Smedley, Steve D. M. Brown, Paul Flicek, William C. Skarnes, Ann-Marie Mallon, Helen E. Parkinson:
  The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. 802-809
• 
  Judith A. Blake, Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson:
  The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse. 810-817
• 
  Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Jingxia Xu, Joanne Berghout, Jeff Campbell, Lori E. Corbani, Kim L. Forthofer, Pete J. Frost, Dave Miers, David R. Shaw, Kevin R. Stone, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
  The mouse Gene Expression Database (GXD): 2014 update. 818-824
• 
  Stephen C. Grubb, Carol J. Bult, Molly A. Bogue:
  Mouse Phenome Database. 825-834
• 
  Lorna J. Richardson, Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Julie Moss, Liz Graham, Nicholas Burton, Bill Hill, Jianguo Rao, Richard A. Baldock, Chris Armit:
  EMAGE mouse embryo spatial gene expression database: 2014 update. 835-844
• 
  Ji Wan, Shu-Bing Qian:
  TISdb: a database for alternative translation initiation in mammalian cells. 845-850
• 
  Florian Halbritter, Anastasia I. Kousa, Simon R. Tomlinson:
  GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments. 851-858
• 
  Audrey M. Michel, Gearoid Fox, Anmol M. Kiran, Christof De Bo, Patrick B. F. O'Connor, Stephen M. Heaphy, James P. A. Mullan, Claire A. Donohue, Desmond G. Higgins, Pavel V. Baranov:
  GWIPS-viz: development of a ribo-seq genome browser. 859-864
• 
  Catherine M. Farrell, Nuala A. O'Leary, Rachel A. Harte, Jane E. Loveland, Laurens G. Wilming, Craig Wallin, Mark Diekhans, Daniel Barrell, Stephen M. J. Searle, Bronwen L. Aken, Susan M. Hiatt, Adam Frankish, Marie-Marthe Suner, Bhanu Rajput, Charles A. Steward, Garth R. Brown, Ruth Bennett, Michael R. Murphy, Wendy Wu, Mike P. Kay, Jennifer Hart, Jeena Rajan, Janet Weber, Catherine Snow, Lillian D. Riddick, Toby Hunt, David Webb, Mark Thomas, Pamela Tamez, Sanjida H. Rangwala, Kelly M. McGarvey, Shashikant Pujar, Andrei Shkeda, Jonathan M. Mudge, Jose M. Gonzalez, James G. R. Gilbert, Stephen J. Trevanion, Robert Baertsch, Jennifer L. Harrow, Tim J. P. Hubbard, James M. Ostell, David Haussler, Kim D. Pruitt:
  Current status and new features of the Consensus Coding Sequence database. 865-872
• 
  Jacqueline A. L. MacArthur, Joannella Morales, Ray E. Tully, Alex Astashyn, Laurent Gil, Elspeth A. Bruford, Pontus Larsson, Paul Flicek, Raymond Dalgleish, Donna R. Maglott, Fiona Cunningham:
  Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. 873-878
• 
  Aik Aun Khoo, Mario Ogrizek-Tomas, Ana Bulovic, Matija Korpar, Ece Gürler, Ivan Slijepcevic, Mile Sikic, Ivana Mihalek:
  ExoLocator - an online view into genetic makeup of vertebrate proteins. 879-881
• 
  Olivier Tassy, Olivier Pourquié:
  Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. 882-891
• 
  Rolf Hühne, Torsten Thalheim, Jürgen Sühnel:
  AgeFactDB - the JenAge Ageing Factor Database - towards data integration in ageing research. 892-896
• 
  Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, Marina Marcet-Houben, Toni Gabaldón:
  PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. 897-902
• 
  Marc Pybus, Giovanni Marco Dall'Olio, Pierre Luisi, Manu Uzkudun, Angel Carreño-Torres, Pavlos Pavlidis, Hafid Laayouni, Jaume Bertranpetit, Johannes Engelken:
  1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. 903-909
• 
  Mulin Jun Li, Lily Yan Wang, Zhengyuan Xia, Maria P. Wong, Pak Chung Sham, Junwen Wang:
  dbPSHP: a database of recent positive selection across human populations. 910-916
• 
  Sébastien Moretti, Balazs Laurenczy, Walid H. Gharib, Briséïs Castella, Arnold Kuzniar, Hannes Schabauer, Romain A. Studer, Mario Valle, Nicolas Salamin, Heinz Stockinger, Marc Robinson-Rechavi:
  Selectome update: quality control and computational improvements to a database of positive selection. 917-921
• 
  Fabian Schreiber, Mateus Patricio, Matthieu Muffato, Miguel Pignatelli, Alex Bateman:
  TreeFam v9: a new website, more species and orthology-on-the-fly. 922-925
• 
  Robert Petryszak, Tony Burdett, Benedetto Fiorelli, Nuno A. Fonseca, Mar Gonzalez-Porta, Emma Hastings, Wolfgang Huber, Simon Jupp, Maria Keays, Nataliya Kryvych, Julie A. McMurry, John C. Marioni, James Malone, Karine Megy, Gabriella Rustici, Y. Amy Tang, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E. Parkinson, Alvis Brazma:
  Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. 926-932
• 
  Parker B. Antin, Tatiana A. Yatskievych, Sean Davey, Diana K. Darnell:
  GEISHA: an evolving gene expression resource for the chicken embryo. 933-937
• 
  Matthew N. McCall, Harris A. Jaffee, Susan J. Zelisko, Neeraj Sinha, Guido J. E. K. Hooiveld, Rafael A. Irizarry, Michael J. Zilliox:
  The Gene Expression Barcode 3.0: improved data processing and mining tools. 938-943
• 
  Abu Z. Dayem Ullah, Rosalind J. Cutts, Millika Ghetia, Emanuela Gadaleta, Stephan A. Hahn, Tatjana Crnogorac-Jurcevic, Nicholas R. Lemoine, Claude Chelala:
  The pancreatic expression database: recent extensions and updates. 944-949
• 
  Harald Stachelscheid, Stefanie Seltmann, Fritz Lekschas, Jean-Fred Fontaine, Nancy Mah, Mariana L. Neves, Miguel A. Andrade-Navarro, Ulf Leser, Andreas Kurtz:
  CellFinder: a cell data repository. 950-958
• 
  Vishalakshi Nanjappa, Joji Kurian Thomas, Arivusudar Marimuthu, Babylakshmi Muthusamy, Aneesha Radhakrishnan, Rakesh Sharma, Aafaque Ahmad Khan, Lavanya Balakrishnan, Nandini A. Sahasrabuddhe, Satwant Kumar, Binit Nitinbhai Jhaveri, Kaushal Vinaykumar Sheth, Ramesh Kumar Khatana, Patrick G. Shaw, Srinivas Manda Srikanth, Premendu P. Mathur, Subramanian Shankar, Dindagur Nagaraja, Rita Christopher, Suresh Mathivanan, Rajesh Raju, Ravi Sirdeshmukh, Aditi Chatterjee, Richard J. Simpson, H. C. Harsha, Akhilesh Pandey, T. S. Keshava Prasad:
  Plasma Proteome Database as a resource for proteomics research: 2014 update. 959-965

VI. Genomic variation, diseases and drugs

• 
  Sebastian Köhler, Sandra C. Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig, Andrew P. Jackson, Kathleen Freson, Marta Gîrdea, Ingo Helbig, Jane A. Hurst, Johanna Jähn, Laird G. Jackson, Anne M. Kelly, David H. Ledbetter, Sahar Mansour, Christa L. Martin, Celia Moss, Andrew D. Mumford, Willem H. Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H. Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J. Wapner, Andrew O. M. Wilkie, Caroline F. Wright, Anneke T. Vulto-van Silfhout, Nicole de Leeuw, Bert B. A. de Vries, Nicole L. Washington, Cynthia L. Smith, Monte Westerfield, Paul N. Schofield, Barbara J. Ruef, Georgios V. Gkoutos, Melissa A. Haendel, Damian Smedley, Suzanna E. Lewis, Peter N. Robinson:
  The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. 966-974
• 
  Kimberly A. Tryka, Luning Hao, Anne Sturcke, Yumi Jin, Zhen Y. Wang, Lora Ziyabari, Moira Lee, Natalia Popova, Nataliya Sharopova, Masato Kimura, Michael Feolo:
  NCBI's Database of Genotypes and Phenotypes: dbGaP. 975-979
• 
  Melissa J. Landrum, Jennifer M. Lee, George R. Riley, Wonhee Jang, Wendy S. Rubinstein, Deanna M. Church, Donna R. Maglott:
  ClinVar: public archive of relationships among sequence variation and human phenotype. 980-985
• 
  Jeffrey R. MacDonald, Robert Ziman, Ryan K. C. Yuen, Lars Feuk, Stephen W. Scherer:
  The Database of Genomic Variants: a curated collection of structural variation in the human genome. 986-992
• 
  Eugene Bragin, Eleni A. Chatzimichali, Caroline F. Wright, Matthew E. Hurles, Helen V. Firth, A. Paul Bevan, Jawahar Swaminathan:
  DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. 993-1000
• 
  Danielle Welter, Jacqueline A. L. MacArthur, Joannella Morales, Tony Burdett, Peggy Hall, Heather Junkins, Alan Klemm, Paul Flicek, Teri Manolio, Lucia Hindorff, Helen E. Parkinson:
  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. 1001-1006
• 
  Dinanath Sulakhe, Sandhya Balasubramanian, Bingqing Xie, Bo Feng, Andrew Taylor, Sheng Wang, Eduardo Berrocal, Utpal J. Dave, Jinbo Xu, Daniela Börnigen, T. Conrad Gilliam, Natalia Maltsev:
  Lynx: a database and knowledge extraction engine for integrative medicine. 1007-1012
• 
  Sungsam Gong, James S. Ware, Roddy Walsh, Stuart A. Cook:
  NECTAR: a database of codon-centric missense variant annotations. 1013-1019
• 
  Petros Papadopoulos, Emmanouil Viennas, Vassiliki Gkantouna, Cristiana Pavlidis, Marina Bartsakoulia, Zafeiria-Marina Ioannou, Ilham Ratbi, Abdelaziz Sefiani, John Tsaknakis, Konstantinos Poulas, Giannis Tzimas, George P. Patrinos:
  Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies. 1020-1026
• 
  Alexander Martínez-Fundichely, Sònia Casillas, Raquel Egea, Miquel Ràmia, Antonio Barbadilla, Lorena Pantano, Marta Puig, Mario Cáceres:
  InvFEST, a database integrating information of polymorphic inversions in the human genome. 1027-1032
• 
  Liyuan Guo, Yang Du, Suhua Chang, Kunlin Zhang, Jing Wang:
  rSNPBase: a database for curated regulatory SNPs. 1033-1039
• 
  Krishna C. Bulusu, Joseph E. Tym, Elizabeth A. Coker, Amanda C. Schierz, Bissan Al-Lazikani:
  canSAR: updated cancer research and drug discovery knowledgebase. 1040-1047
• 
  Wei-Chung Cheng, I-Fang Chung, Chen-Yang Chen, Hsing-Jen Sun, Jun-Jeng Fen, Wei-Chun Tang, Ting-Yu Chang, Tai-Tong Wong, Hsei-Wei Wang:
  DriverDB: an exome sequencing database for cancer driver gene identification. 1048-1054
• 
  Haoyang Cai, Nitin Kumar, Ni Ai, Saumya Gupta, Prisni Rath, Michael Baudis:
  Progenetix: 12 years of oncogenomic data curation. 1055-1062
• 
  Belinda Giardine, Joseph Borg, Emmanouil Viennas, Cristiana Pavlidis, Kamran Moradkhani, Philippe Joly, Marina Bartsakoulia, Cathy Riemer, Webb Miller, Giannis Tzimas, Henri Wajcman, Ross C. Hardison, George P. Patrinos:
  Updates of the HbVar database of human hemoglobin variants and thalassemia mutations. 1063-1069
• 
  Yang Li, Chengxiang Qiu, Jian Tu, Bin Geng, Jichun Yang, Tianzi Jiang, Qinghua Cui:
  HMDD v2.0: a database for experimentally supported human microRNA and disease associations. 1070-1074
• 
  Yanli Wang, Tugba O. Suzek, Jian Zhang, Jiyao Wang, Siqian He, Tiejun Cheng, Benjamin A. Shoemaker, Asta Gindulyte, Stephen H. Bryant:
  PubChem BioAssay: 2014 update. 1075-1082
• 
  A. Patrícia Bento, Anna Gaulton, Anne Hersey, Louisa J. Bellis, Jon Chambers, Mark Davies, Felix A. Krüger, Yvonne Light, Lora Mak, Shaun McGlinchey, Michal Nowotka, George Papadatos, Rita Santos, John P. Overington:
  The ChEMBL bioactivity database: an update. 1083-1090
• 
  Vivian Law, Craig Knox, Yannick Djoumbou, Timothy Jewison, Anchi Guo, Yifeng Liu, Adam Maciejewski, David Arndt, Michael Wilson, Vanessa Neveu, Alexandra Tang, Geraldine Gabriel, Carol Ly, Sakina Adamjee, Zerihun T. Dame, Beomsoo Han, You Zhou, David S. Wishart:
  DrugBank 4.0: shedding new light on drug metabolism. 1091-1097
• 
  Adam J. Pawson, Joanna L. Sharman, Helen E. Benson, Elena Faccenda, Stephen P. H. Alexander, Oscar Peter Buneman, Anthony P. Davenport, John C. McGrath, John A. Peters, Christopher Southan, Michael Spedding, Wenyuan Yu, Anthony J. Harmar, NC-IUPHAR:
  The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. 1098-1106
• 
  Björn O. Gohlke, Robert Preissner, Saskia Preissner:
  SuperPain - a resource on pain-relieving compounds targeting ion channels. 1107-1112
• 
  Michael F. Hoffmann, Sarah C. Preissner, Janette Nickel, Mathias Dunkel, Robert Preissner, Saskia Preissner:
  The Transformer database: biotransformation of xenobiotics. 1113-1117
• 
  Chu Qin, Cheng Zhang, Feng Zhu, Feng Xu, Shangying Chen, Peng Zhang, Ying Hong Li, Sheng-Yong Yang, Yu-Quan Wei, Lin Tao, Yuzong Chen:
  Therapeutic target database update 2014: a resource for targeted therapeutics. 1118-1123
• 
  Yongqun He, Rebecca Racz, Samantha Sayers, Yu Lin, Thomas E. Todd, Junguk Hur, Xinna Li, Mukti Patel, Boyang Zhao, Monica Chung, Joseph Ostrow, Andrew Sylora, Priya Dungarani, Guerlain Ulysse, Kanika Kochhar, Boris Vidri, Kelsey Strait, George W. Jourdian, Zuoshuang Xiang:
  Updates on the web-based VIOLIN vaccine database and analysis system. 1124-1132
• 
  Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai W. Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik:
  bNAber: database of broadly neutralizing HIV antibodies. 1133-1139
• 
  James Dunbar, Konrad Krawczyk, Jinwoo Leem, Terry Baker, Angelika Fuchs, Guy Georges, Jiye Shi, Charlotte M. Deane:
  SAbDab: the structural antibody database. 1140-1146
• 
  Abid Qureshi, Nishant Thakur, Himani Tandon, Manoj Kumar:
  AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. 1147-1153
• 
  Faiza Hanif Waghu, Lijin Gopi, Ram Shankar Barai, Pranay Ramteke, Bilal Nizami, Susan Idicula-Thomas:
  CAMP: Collection of sequences and structures of antimicrobial peptides. 1154-1158

VII. Plant databases

• 
  Sònia Garcia, Ilia J. Leitch, Alba Anadon-Rosell, Miguel Á. Canela, Francisco Gálvez, Teresa Garnatje, Airy Gras, Oriane Hidalgo, Emmeline Johnston, Gemma Mas de Xaxars, Jaume Pellicer, Sonja Siljak-Yakovlev, Joan Vallès, Daniel Vitales, Michael D. Bennett:
  Recent updates and developments to plant genome size databases. 1159-1166
• 
  Ziva Ramsak, Spela Baebler, Ana Rotter, Matej Korbar, Igor Mozetic, Björn Usadel, Kristina Gruden:
  GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. 1167-1175
• 
  Jiongjiong Chen, Qun Hu, Yu Zhang, Chen Lu, Hanhui Kuang:
  P-MITE: a database for plant miniature inverted-repeat transposable elements. 1176-1181
• 
  Jinpu Jin, He Zhang, Lei Kong, Ge Gao, Jingchu Luo:
  PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. 1182-1187
• 
  Ayaka Hieno, Hushna Ara Naznin, Mitsuro Hyakumachi, Tetsuya Sakurai, Mututomo Tokizawa, Hiroyuki Koyama, Naoki Sato, Tomoaki Nishiyama, Mitsuyasu Hasebe, Andreas D. Zimmer, Daniel Lang, Ralf Reski, Stefan A. Rensing, Junichi Obokata, Yoshiharu Y. Yamamoto:
  ppdb: plant promoter database version 3.0. 1188-1192
• 
  Marcela K. Monaco, Joshua C. Stein, Sushma Naithani, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson, Yinping Jiao, Zhenyuan Lu, Daniel M. Bolser, Arnaud Kerhornou, Daniel M. Staines, Brandon Walts, Guanming Wu, Peter D'Eustachio, Robin Haw, David Croft, Paul J. Kersey, Lincoln Stein, Pankaj Jaiswal, Doreen Ware:
  Gramene 2013: comparative plant genomics resources. 1193-1199
• 
  Zhonghai Li, Yi Zhao, Xiao-Chuan Liu, Jinying Peng, Hongwei Guo, Jingchu Luo:
  LSD 2.0: an update of the leaf senescence database. 1200-1205
• 
  Qiuming Yao, Huangyi Ge, Shangquan Wu, Ning Zhang, Wei Chen, Chunhui Xu, Jianjiong Gao, Jay J. Thelen, Dong Xu:
  P³DB 3.0: From plant phosphorylation sites to protein networks. 1206-1213
• 
  Pratibha Gour, Priyanka Garg, Rashmi Jain, Shaji V. Joseph, Akhilesh K. Tyagi, Saurabh Raghuvanshi:
  Manually curated database of rice proteins. 1214-1221
• 
  Zhang Zhang, Jian Sang, Lina Ma, Gang Wu, Hao Wu, Dawei Huang, Dong Zou, Siqi Liu, Ang Li, Lili Hao, Ming Tian, Chao Xu, Xumin Wang, Jiayan Wu, Jing-Fa Xiao, Lin Dai, Ling-Ling Chen, Songnian Hu, Jun Yu:
  RiceWiki: a wiki-based database for community curation of rice genes. 1222-1228
• 
  Jing Yu, Sook Jung, Chun-Huai Cheng, Stephen P. Ficklin, Taein Lee, Ping Zheng, Don Jones, Richard G. Percy, Dorrie Main:
  CottonGen: a genomics, genetics and breeding database for cotton research. 1229-1236
• 
  Sook Jung, Stephen P. Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Ping Zheng, Jing Yu, Aureliano Bombarely, Ilhyung Cho, Sushan Ru, Kate Evans, Cameron Peace, Albert G. Abbott, Lukas A. Mueller, Mercy A. Olmstead, Dorrie Main:
  The Genome Database for Rosaceae (GDR): year 10 update. 1237-1244
• 
  Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, Dong Xu:
  Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. 1245-1252

VIII. Other databases

• 
  Catherine Y. Seiler, Jin G. Park, Amit Sharma, Preston Hunter, Padmini Surapaneni, Casey Sedillo, James Field, Rhys Algar, Andrea Price, Jason Steel, Andrea Throop, Michael Fiacco, Joshua LaBaer:
  DNASU plasmid and PSI: Biology-Materials repositories: resources to accelerate biological research. 1253-1260
• 
  Joana Damas, João Carneiro, António Amorim, Filipe Pereira:
  MitoBreak: the mitochondrial DNA breakpoints database. 1261-1268
• 
  Janusz Dutkowski, Keiichiro Ono, Michael Kramer, Michael Yu, Dexter Pratt, Barry Demchak, Trey Ideker:
  NeXO Web: the NeXO ontology database and visualization platform. 1269-1274

Volume 42, Number Webserver-Issue, July 2014

Editorial

• 
  Gary Benson:
  Editorial: Nucleic Acids Research annual Web Server Issue in 2014. 1-2

Articles

• 
  Christoph Gille, Michael Fähling, Birgit Weyand, Thomas Wieland, Andreas Gille:
  Alignment-Annotator web server: rendering and annotating sequence alignments. 3-6
• 
  Sebastian Horwege, Sebastian Lindner, Marcus Boden, Klas Hatje, Martin Kollmar, Chris-André Leimeister, Burkhard Morgenstern:
  Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches. 7-11
• 
  Qin Ma, Hanyuan Zhang, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu:
  DMINDA: an integrated web server for DNA motif identification and analyses. 12-19
• 
  Charles Blatti, Saurabh Sinha:
  Motif Enrichment Tool. 20-25
• 
  Janette Nickel, Björn-Oliver Gohlke, Jevgeni Erehman, Priyanka Banerjee, Wen Wei Rong, Andrean Goede, Mathias Dunkel, Robert Preissner:
  SuperPred: update on drug classification and target prediction. 26-31
• 
  David Gfeller, Aurélien Grosdidier, Matthias Wirth, Antoine Daina, Olivier Michielin, Vincent Zoete:
  SwissTargetPrediction: a web server for target prediction of bioactive small molecules. 32-38
• 
  Yoshihiro Yamanishi, Masaaki Kotera, Yuki Moriya, Ryusuke Sawada, Minoru Kanehisa, Susumu Goto:
  DINIES: drug-target interaction network inference engine based on supervised analysis. 39-45
• 
  Heng Luo, Ping Zhang, Hui Huang, Jialiang Huang, Emily Kao, Leming Shi, Lin He, Lun Yang:
  DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. 46-52
• 
  Malgorzata N. Drwal, Priyanka Banerjee, Mathias Dunkel, Martin R. Wettig, Robert Preissner:
  ProTox: a web server for the in silico prediction of rodent oral toxicity. 53-58
• 
  Tao Qi, Tianyi Qiu, Qingchen Zhang, Kailin Tang, Yangyang Fan, Jingxuan Qiu, Dingfeng Wu, Wei Zhang, Yanan Chen, Jun Gao, Ruixin Zhu, Zhiwei Cao:
  SEPPA 2.0 - more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen. 59-63
• 
  Gwo-Yu Chuang, David Liou, Peter D. Kwong, Ivelin Georgiev:
  NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences. 64-71
• 
  W. James Dittmar, Lauren McIver, Pawel Michalak, Harold R. Garner, Gregorio Valdez:
  EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles. 72-75
• 
  Ara Cho, Junha Shin, Sohyun Hwang, Chanyoung Kim, Hongseok Shim, Hyojin Kim, Hanhae Kim, Insuk Lee:
  WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans. 76-82
• 
  Alejandro Alemán, Francisco García-García, Ignacio Medina, Joaquín Dopazo:
  A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. 83-87
• 
  Alejandro Alemán, Francisco García-García, Francisco Salavert, Ignacio Medina, Joaquín Dopazo:
  A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. 88-93
• 
  Felicity Allen, Allison Pon, Michael Wilson, Russell Greiner, David S. Wishart:
  CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. 94-99
• 
  Arnold Kuzniar, Roland Kanaar:
  PIQMIe: a web server for semi-quantitative proteomics data management and analysis. 100-106
• 
  Chao Wu, Eric E. Bardes, Anil G. Jegga, Bruce J. Aronow:
  ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context. 107-113
• 
  William A. Rennie, Chaochun Liu, C. Steven Carmack, Adam Wolenc, Shaveta Kanoria, Jun Lu, Dang D. Long, Ye Ding:
  STarMir: a web server for prediction of microRNA binding sites. 114-118
• 
  Patrick R. Wright, Jens Georg, Martin Mann, Dragos Alexandru Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, Rolf Backofen:
  CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. 119-123
• 
  Mary Beth Kery, Monica Feldman, Jonathan Livny, Brian Tjaden:
  TargetRNA2: identifying targets of small regulatory RNAs in bacteria. 124-129
• 
  Daogang Guan, Jiaofang Shao, Zhongying Zhao, Panwen Wang, Jing Qin, Youping Deng, Kenneth R. Boheler, Junwen Wang, Bin Yan:
  PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. 130-136
• 
  Chun-Chi Liu, Yu-Ting Tseng, Wenyuan Li, Chia-Yu Wu, Ilya Mayzus, Andrey Rzhetsky, Fengzhu Sun, Michael S. Waterman, Jeremy J. W. Chen, Preet M. Chaudhary, Joseph Loscalzo, Edward Crandall, Xianghong Jasmine Zhou:
  DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. 137-146
• 
  Sohyun Hwang, Eiru Kim, Sunmo Yang, Edward M. Marcotte, Insuk Lee:
  MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. 147-153
• 
  José P. Pinto, Ravi Kiran Reddy Kalathur, Rui S. R. Machado, Joana M. Xavier, José Bragança, Matthias E. Futschik:
  StemCellNet: an interactive platform for network-oriented investigations in stem cell biology. 154-160
• 
  Yi Wang, Roger Thilmony, Yong Qiang Gu:
  NetVenn: an integrated network analysis web platform for gene lists. 161-166
• 
  Jianguo Xia, Maia J. Benner, Robert E. W. Hancock:
  NetworkAnalyst - integrative approaches for protein-protein interaction network analysis and visual exploration. 167-174
• 
  Manuel Garcia-Albornoz, Subazini Thankaswamy-Kosalai, Avlant Nilsson, Leif Väremo, Intawat Nookaew, Jens Nielsen:
  BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data. 175-181
• 
  Solange Karsenty, Nadav Rappoport, Dan Ofer, Adva Zair, Michal Linial:
  NeuroPID: a classifier of neuropeptide precursors. 182-186
• 
  Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, Thomas Manke:
  deepTools: a flexible platform for exploring deep-sequencing data. 187-191
• 
  Liran Juan, Mingxiang Teng, Tianyi Zang, Yafeng Hao, Zhenxing Wang, Chengwu Yan, Yongzhuang Liu, Jie Li, Tianjiao Zhang, Yadong Wang:
  The personal genome browser: visualizing functions of genetic variants. 192-197
• 
  Florent Villiers, Olivier Bastien, June M. Kwak:
  R. S. WebTool, a web server for random sampling-based significance evaluation of pairwise distances. 198-204
• 
  Cyrille Pauthenier, Jean-Loup Faulon:
  PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling. 205-209
• 
  Lim Heo, Woong-Hee Shin, Myeong Sup Lee, Chaok Seok:
  GalaxySite: ligand-binding-site prediction by using molecular docking. 210-214
• 
  Janez Konc, Dusanka Janezic:
  ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites. 215-220
• 
  Adrien Saladin, Julien Rey, Pierre Thévenet, Martin Zacharias, Gautier Moroy, Pierre Tufféry:
  PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces. 221-226
• 
  Radka Svobodová Vareková, Deepti Jaiswal Kundu, David Sehnal, Crina-Maria Ionescu, Stanislav Geidl, Lukás Pravda, Vladimír Horský, Michaela Wimmerová, Jaroslav Koca:
  MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. 227-233
• 
  Mahendra Awale, Jean-Louis Reymond:
  A multi-fingerprint browser for the ZINC database. 234-239
• 
  Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe, Adam Godzik:
  POSA: a user-driven, interactive multiple protein structure alignment server. 240-245
• 
  Marcus Stamm, René Staritzbichler, Kamil Khafizov, Lucy R. Forrest:
  AlignMe - a membrane protein sequence alignment web server. 246-251
• 
  Marco Biasini, Stefan Bienert, Andrew Waterhouse, Konstantin Arnold, Gabriel Studer, Tobias Schmidt, Florian Kiefer, Tiziano Gallo Cassarino, Martino Bertoni, Lorenza Bordoli, Torsten Schwede:
  SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. 252-258
• 
  Kliment Olechnovic, Ceslovas Venclovas:
  The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes. 259-263
• 
  Elisa Cilia, Rita Pancsa, Peter Tompa, Tom Lenaerts, Wim F. Vranken:
  The DynaMine webserver: predicting protein dynamics from sequence. 264-270
• 
  José Ramón López-Blanco, José Ignacio Aliaga, Enrique S. Quintana-Ortí, Pablo Chacón:
  iMODS: internal coordinates normal mode analysis server. 271-276
• 
  Kuan Pern Tan, Shruti Khare, Raghavan Varadarajan, Mallur Srivatsan Madhusudhan:
  TSpred: a web server for the rational design of temperature-sensitive mutants. 277-284
• 
  Alper Baspinar, Engin Cukuroglu, Ruth Nussinov, Ozlem Keskin, Attila Gürsoy:
  PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. 285-289
• 
  Lei Deng, Qiangfeng Cliff Zhang, Zhigang Chen, Yang Meng, Jihong Guan, Shuigeng Zhou:
  PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. 290-295
• 
  Chin-Hsien Tai, Rohit Paul, Dukka Kc, Jeffery D. Shilling, Byungkook Lee:
  SymD webserver: a platform for detecting internally symmetric protein structures. 296-300
• 
  Ian Walsh, Flavio Seno, Silvio C. E. Tosatto, Antonio Trovato:
  PASTA 2.0: an improved server for protein aggregation prediction. 301-307
• 
  Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik:
  AIDA: ab initio domain assembly server. 308-313
• 
  Douglas E. V. Pires, David B. Ascher, Tom L. Blundell:
  DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. 314-319
• 
  Xavier Robert, Patrice Gouet:
  Deciphering key features in protein structures with the new ENDscript server. 320-324
• 
  Qi Zhao, Yubin Xie, Yueyuan Zheng, Shuai Jiang, Wenzhong Liu, Weiping Mu, Zexian Liu, Yong Zhao, Yu Xue, Jian Ren:
  GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. 325-330
• 
  Morena Pappalardo, Mark N. Wass:
  VarMod: modelling the functional effects of non-synonymous variants. 331-336
• 
  Guy Yachdav, Edda Kloppmann, László Kaján, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer, Lothar Richter, Haim Ashkenazy, Marco Punta, Avner Schlessinger, Yana Bromberg, Reinhard Schneider, Gerrit Vriend, Chris Sander, Nir Ben-Tal, Burkhard Rost:
  PredictProtein - an open resource for online prediction of protein structural and functional features. 337-343
• 
  Dmitry A. Suplatov, Eugeny M. Kirilin, Mikhail Arbatsky, Vakil Takhaveev, Vytas K. Svedas:
  pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families. 344-349
• 
  Tatyana Goldberg, Maximilian Hecht, Tobias Hamp, Timothy Karl, Guy Yachdav, Nadeem Ahmed, Uwe Altermann, Philipp Angerer, Sonja Ansorge, Kinga Balasz, Michael Bernhofer, Alexander Betz, Laura Cizmadija, Kieu Trinh Do, Julia Gerke, Robert Greil, Vadim Joerdens, Maximilian Hastreiter, Katharina Hembach, Max Herzog, Maria Kalemanov, Michael Kluge, Alice Meier, Hassan Nasir, Ulrich Neumaier, Verena Prade, Jonas Reeb, Aleksandr Sorokoumov, Ilira Troshani, Susann Vorberg, Sonja Waldraff, Jonas Zierer, Henrik Nielsen, Burkhard Rost:
  LocTree3 prediction of localization. 350-355
• 
  Paolo Di Tommaso, Giovanni Bussotti, Carsten Kemena, Emidio Capriotti, Maria Chatzou, Pablo Prieto, Cédric Notredame:
  SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments. 356-360
• 
  Inbal Paz, Idit Kosti, Manuel Ares, Melissa S. Cline, Yael Mandel-Gutfreund:
  RBPmap: a web server for mapping binding sites of RNA-binding proteins. 361-367
• 
  Maciej Antczak, Tomasz Zok, Mariusz Popenda, Piotr Lukasiak, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk:
  RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. 368-372
• 
  Daniel Lai, Irmtraud M. Meyer:
  e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation. 373-376
• 
  Gewen He, Albert Steppi, Jose Laborde, Anuj Srivastava, Peixiang Zhao, Jinfeng Zhang:
  RASS: a web server for RNA alignment in the joint sequence-structure space. 377-381
• 
  Mohd Firdaus Raih, Hazrina Yusof Hamdani, Nurul Nadzirin, Effirul Ikhwan Ramlan, Peter Willett, Peter J. Artymiuk:
  COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures. 382-388
• 
  Pablo Carbonell, Pierre Parutto, Joan Hérisson, Shashi Bhushan Pandit, Jean-Loup Faulon:
  XTMS: pathway design in an eXTended metabolic space. 389-394
• 
  Neil Swainston, Andrew Currin, Philip J. Day, Douglas B. Kell:
  GeneGenie: optimized oligomer design for directed evolution. 395-400
• 
  Tessa G. Montague, José M. Cruz, James A. Gagnon, George M. Church, Eivind Valen:
  CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. 401-407
• 
  Mads Tvillinggaard Bonde, Michael Schantz Klausen, Mads Valdemar Anderson, Annika I. N. Wallin, Harris H. Wang, Morten O. A. Sommer:
  MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. 408-415
• 
  Hee-Jin Lee, Tien Cuong Dang, Hyunju Lee, Jong-Chan Park:
  OncoSearch: cancer gene search engine with literature evidence. 416-421
• 
  José A. Gijón-Correas, Miguel A. Andrade-Navarro, Jean-Fred Fontaine:
  Alkemio: association of chemicals with biomedical topics by text and data mining. 422-429
• 
  Lukasz Jaroszewski, Laszlo Koska, Mayya Sedova, Adam Godzik:
  PubServer: literature searches by homology. 430-435
• 
  Heinz Stockinger, Adrian M. Altenhoff, Konstantin Arnold, Amos Bairoch, Frederic B. Bastian, Sven Bergmann, Lydie Bougueleret, Philipp Bucher, Mauro Delorenzi, Lydie Lane, Philippe Le Mercier, Frédérique Lisacek, Olivier Michielin, Patricia M. Palagi, Jacques Rougemont, Torsten Schwede, Christian von Mering, Erik van Nimwegen, Daniel Walther, Ioannis Xenarios, Mihaela Zavolan, Evgeny M. Zdobnov, Vincent Zoete, Ron D. Appel:
  Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. 436-441
• 
  Shin Kawano, Tsutomu Watanabe, Sohei Mizuguchi, Norie Araki, Toshiaki Katayama, Atsuko Yamaguchi:
  TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model. 442-448
• 
  Qiaonan Duan, Corey Flynn, Mario Niepel, Marc Hafner, Jeremy Muhlich, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Edward Y. Chen, Todd R. Golub, Peter K. Sorger, Aravind Subramanian, Avi Ma'ayan:
  LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. 449-460
• 
  Alina Munteanu, Uwe Ohler, Raluca Gordân:
  COUGER - co-factors associated with uniquely-bound genomic regions. 461-467

Web Services

• 
  Alex Kalderimis, Rachel Lyne, Daniela Butano, Sergio Contrino, Mike Lyne, Joshua Heimbach, Fengyuan Hu, Richard N. Smith, Radek Stepan, Julie M. Sullivan, Gos Micklem:
  InterMine: extensive web services for modern biology. 468-472
• 
  Dinanath Sulakhe, Andrew Taylor, Sandhya Balasubramanian, Bo Feng, Bingqing Xie, Daniela Börnigen, Utpal J. Dave, Ian T. Foster, T. Conrad Gilliam, Natalia Maltsev:
  Lynx web services for annotations and systems analysis of multi-gene disorders. 473-477
• 
  Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin:
  Enhancing UCSF Chimera through web services. 478-484

Stand Alone

• 
  Charles Coulombe, Christian Poitras, Alexei Nordell-Markovits, Mylène Brunelle, Marc-André Lavoie, François Robert, Pierre-Étienne Jacques:
  VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery. 485-493
• 
  Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
  mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. 494-500
• 
  Daniel Becker, Pavlo Lutsik, Peter Ebert, Christoph Bock, Thomas Lengauer, Jörn Walter:
  BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives. 501-507