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
•