Nucleic Acids Research, Volume 43

Volume 43, Number Database-Issue, January 2015

I. Nucleic acid sequence, structure, and regulation

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  Michael Y. Galperin, Daniel J. Rigden, Xosé M. Fernández-Suárez:
  The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection. 1-5
• 
  Database resources of the National Center for Biotechnology Information. 6-17
• 
  Yuichi Kodama, Jun Mashima, Takehide Kosuge, Toshiaki Katayama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura:
  The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. 18-22
• 
  Nicole Silvester, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Simon Kay, Rasko Leinonen, Weizhong Li, Xin Liu, Rodrigo Lopez, Nima Pakseresht, Swapna Pallreddy, Sheila Plaister, Rajesh Radhakrishnan, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane:
  Content discovery and retrieval services at the European Nucleotide Archive. 23-29
• 
  Dennis A. Benson, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
  GenBank. 30-35
• 
  Garth R. Brown, Vichet Hem, Kenneth S. Katz, Michael Ovetsky, Craig Wallin, Olga D. Ermolaeva, Igor Tolstoy, Tatiana A. Tatusova, Kim D. Pruitt, Donna R. Maglott, Terence D. Murphy:
  Gene: a gene-centered information resource at NCBI. 36-42
• 
  Ashfaq A. Mir, Claude Philippe, Gaël Cristofari:
  euL1db: the European database of L1HS retrotransposon insertions in humans. 43-47
• 
  Corey M. Hudson, Britney Y. Lau, Kelly P. Williams:
  Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes. 48-53
• 
  Dong Zou, Shixiang Sun, Rujiao Li, Jiang Liu, Jing Zhang, Zhang Zhang:
  MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data. 54-58
• 
  Leiming You, Jiexin Wu, Yuchao Feng, Yonggui Fu, Yanan Guo, Liyuan Long, Hui Zhang, Yijie Luan, Peng Tian, Liangfu Chen, Guangrui Huang, Shengfeng Huang, Yuxin Li, Jie Li, Chengyong Chen, Yaqing Zhang, Shangwu Chen, Anlong Xu:
  APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals. 59-67
• 
  Milana Frenkel-Morgenstern, Alessandro Gorohovski, Dunja Vucenovic, Lorena Maestre, Alfonso Valencia:
  ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. 68-75
• 
  Hong-Mei Zhang, Teng Liu, Chun-Jie Liu, Shuangyang Song, Xiantong Zhang, Wei Liu, Haibo Jia, Yu Xue, An-Yuan Guo:
  AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. 76-81
• 
  Yasunobu Okamura, Yuichi Aoki, Takeshi Obayashi, Shu Tadaka, Satoshi Ito, Takafumi Narise, Kengo Kinoshita:
  COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. 82-86
• 
  Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
  DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. 87-91
• 
  René Dreos, Giovanna Ambrosini, Rouaïda Cavin Périer, Philipp Bucher:
  The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. 92-96
• 
  Edgar Wingender, Torsten Schoeps, Martin Haubrock, Jürgen Dönitz:
  TFClass: a classification of human transcription factors and their rodent orthologs. 97-102
• 
  Tsu-Pei Chiu, Lin Yang, Tianyin Zhou, Bradley J. Main, Stephen C. J. Parker, Sergey V. Nuzhdin, Thomas D. Tullius, Remo Rohs:
  GBshape: a genome browser database for DNA shape annotations. 103-109
• 
  Piroon Jenjaroenpun, Chee Siang Chew, Tai Pang Yong, Kiattawee Choowongkomon, Wimada Thammasorn, Vladimir A. Kuznetsov:
  The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome. 110-116
• 
  Maxwell A. Hume, Luis A. Barrera, Stephen S. Gisselbrecht, Martha L. Bulyk:
  UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. 117-122
• 
  RNAcentral: an international database of ncRNA sequences. 123-129
• 
  Eric P. Nawrocki, Sarah W. Burge, Alex Bateman, Jennifer Daub, Ruth Y. Eberhardt, Sean R. Eddy, Evan W. Floden, Paul P. Gardner, Thomas A. Jones, John G. Tate, Robert D. Finn:
  Rfam 12.0: updates to the RNA families database. 130-137
• 
  Corey M. Hudson, Kelly P. Williams:
  The tmRNA website. 138-140
• 
  Pankaj Kumar, Suresh B. Mudunuri, Jordan Anaya, Anindya Dutta:
  tRFdb: a database for transfer RNA fragments. 141-145
• 
  Nathan Wong, Xiaowei Wang:
  miRDB: an online resource for microRNA target prediction and functional annotations. 146-152
• 
  Ioannis S. Vlachos, Maria D. Paraskevopoulou, Dimitra Karagkouni, Georgios K. Georgakilas, Thanasis Vergoulis, Ilias Kanellos, Ioannis-Laertis Anastasopoulos, Sofia Maniou, Konstantina Karathanou, Despina Kalfakakou, Athanasios Fevgas, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
  DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA: mRNA interactions. 153-159
• 
  Kai Blin, Christoph Dieterich, Ricardo Wurmus, Nikolaus Rajewsky, Markus Landthaler, Altuna Akalin:
  DoRiNA 2.0 - upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. 160-167
• 
  Xiu Cheng Quek, Daniel W. Thomson, Jesper L. V. Maag, Nenad Bartonicek, Bethany Signal, Michael B. Clark, Brian S. Gloss, Marcel E. Dinger:
  lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. 168-173
• 
  Pieter-Jan Volders, Kenneth Verheggen, Gerben Menschaert, Klaas Vandepoele, Lennart Martens, Jo Vandesompele, Pieter Mestdagh:
  An update on LNCipedia: a database for annotated human lncRNA sequences. 174-180
• 
  Jing Gong, Wei Liu, Jiayou Zhang, Xiaoping Miao, An-Yuan Guo:
  lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. 181-186
• 
  Lina Ma, Ang Li, Dong Zou, Xingjian Xu, Lin Xia, Jun Yu, Vladimir B. Bajic, Zhang Zhang:
  LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. 187-192
• 
  Qinghua Jiang, Jixuan Wang, Xiaoliang Wu, Rui Ma, Tianjiao Zhang, Shuilin Jin, Zhijie Han, Renjie Tan, Jiajie Peng, Guiyou Liu, Yu Li, Yadong Wang:
  LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression. 193-196
• 
  Hui Liu, Mario A. Flores, Jia Meng, Lin Zhang, Xinyu Zhao, Manjeet K. Rao, Yidong Chen, Yufei Huang:
  MeT-DB: a database of transcriptome methylation in mammalian cells. 197-203

II. Protein sequence and structure, motifs and domains

• 
  UniProt: a hub for protein information. 204-212
• 
  Alex L. Mitchell, Hsin-Yu Chang, Louise C. Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex Bateman, Marco Punta, Teresa K. Attwood, Christian J. A. Sigrist, Nicole Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork, Ivica Letunic, Julian Gough, Matt E. Oates, Daniel H. Haft, Hongzhan Huang, Darren A. Natale, Cathy H. Wu, Christine A. Orengo, Ian Sillitoe, Huaiyu Mi, Paul D. Thomas, Robert D. Finn:
  The InterPro protein families database: the classification resource after 15 years. 213-221
• 
  Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y. Geer, Renata C. Geer, Jane He, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Zhouxi Wang, Roxanne A. Yamashita, Dachuan Zhang, Chanjuan Zheng, Stephen H. Bryant:
  CDD: NCBI's conserved domain database. 222-226
• 
  Matt E. Oates, Jonathan Stahlhacke, Dimitrios V. Vavoulis, Ben Smithers, Owen J. L. Rackham, Adam J. Sardar, Jan Zaucha, Natalie Thurlby, Hai Fang, Julian Gough:
  The SUPERFAMILY 1.75 database in 2014: a doubling of data. 227-233
• 
  Erik L. L. Sonnhammer, Gabriel Östlund:
  InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. 234-239
• 
  Adrian M. Altenhoff, Nives Skunca, Natasha M. Glover, Clément-Marie Train, Anna Sueki, Ivana Pilizota, Kevin Gori, Bartlomiej Tomiczek, Steven Müller, Henning Redestig, Gaston H. Gonnet, Christophe Dessimoz:
  The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. 240-249
• 
  Evgenia V. Kriventseva, Fredrik Tegenfeldt, Tom J. Petty, Robert M. Waterhouse, Felipe A. Simão, Igor A. Pozdnyakov, Panagiotis Ioannidis, Evgeny M. Zdobnov:
  OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. 250-256
• 
  Ivica Letunic, Tobias Doerks, Peer Bork:
  SMART: recent updates, new developments and status in 2015. 257-260
• 
  Michael Y. Galperin, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin:
  Expanded microbial genome coverage and improved protein family annotation in the COG database. 261-269
• 
  Ikuo Uchiyama, Motohiro Mihara, Hiroyo Nishide, Hirokazu Chiba:
  MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. 270-276
• 
  Mathew Mani, Chang Chen, Vaishak Amblee, Haipeng Liu, Tanu Mathur, Grant Zwicke, Shadi Zabad, Bansi Patel, Jagravi Thakkar, Constance J. Jeffery:
  MoonProt: a database for proteins that are known to moonlight. 277-282
• 
  László Dobson, Tamás Langó, István Reményi, Gábor E. Tusnády:
  Expediting topology data gathering for the TOPDB database. 283-289
• 
  Nikolaus Fortelny, Sharon Yang, Paul Pavlidis, Philipp F. Lange, Christopher M. Overall:
  Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. 290-297
• 
  Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
  REBASE - a database for DNA restriction and modification: enzymes, genes and genomes. 298-299
• 
  Richa Mudgal, Sankaran Sandhya, Gayatri Kumar, Ramanathan Sowdhamini, Nagasuma R. Chandra, Narayanaswamy Srinivasan:
  NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. 300-305
• 
  Michal Jamróz, Wanda Niemyska, Eric J. Rawdon, Andrzej Stasiak, Kenneth C. Millett, Piotr Sulkowski, Joanna I. Sulkowska:
  KnotProt: a database of proteins with knots and slipknots. 306-314
• 
  Emilio Potenza, Tomás Di Domenico, Ian Walsh, Silvio C. E. Tosatto:
  MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. 315-320
• 
  Guillaume Launay, R. Salza, D. Multedo, Nicolas Thierry-Mieg, Sylvie Ricard-Blum:
  MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. 321-327
• 
  Zhengnan Huang, Lili Ma, Yongbo Wang, Zhicheng Pan, Jian Ren, Zexian Liu, Yu Xue:
  MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. 328-334
• 
  Anup Shah, David Chen, Akash R. Boda, Leonard J. Foster, Melissa J. Davis, Michelle M. Hill:
  RaftProt: mammalian lipid raft proteome database. 335-338
• 
  Yang Wang, Xue-Jia Hu, Xudong Zou, Xian-Hui Wu, Zhi-Qiang Ye, Yun-Dong Wu:
  WDSPdb: a database for WD40-repeat proteins. 339-344
• 
  Peter W. Rose, Andreas Prlic, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, John D. Westbrook, Jesse Woo, Jasmine Young, Christine Zardecki, Helen M. Berman, Philip E. Bourne, Stephen K. Burley:
  The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. 345-356
• 
  Erica Valentini, Alexey G. Kikhney, Gianpietro Previtali, Cy M. Jeffries, Dmitri I. Svergun:
  SASBDB, a repository for biological small-angle scattering data. 357-363
• 
  Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek, Elmar Krieger, Robbie P. Joosten, Gert Vriend:
  A series of PDB-related databanks for everyday needs. 364-368
• 
  David Sehnal, Radka Svobodová Vareková, Lukás Pravda, Crina-Maria Ionescu, Stanislav Geidl, Vladimír Horský, Deepti Jaiswal Kundu, Michaela Wimmerová, Jaroslav Koca:
  ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. 369-375
• 
  Ian Sillitoe, Tony E. Lewis, Alison L. Cuff, Sayoni Das, Paul Ashford, Natalie L. Dawson, Nicholas Furnham, Roman A. Laskowski, David A. Lee, Jonathan G. Lees, Sonja Lehtinen, Romain A. Studer, Janet M. Thornton, Christine A. Orengo:
  CATH: comprehensive structural and functional annotations for genome sequences. 376-381
• 
  Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Domenico Cozzetto, Jose M. Dana, Ioannis Filippis, Julian Gough, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Jaina Mistry, Alexey G. Murzin, Bernardo Ochoa-Montaño, Matt E. Oates, Marco Punta, Owen J. L. Rackham, Jonathan Stahlhacke, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo:
  Genome3D: exploiting structure to help users understand their sequences. 382-386
• 
  Douglas E. V. Pires, Tom L. Blundell, David B. Ascher:
  Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. 387-391
• 
  Jun-Ichi Ito, Kazuyoshi Ikeda, Kazunori D. Yamada, Kenji Mizuguchi, Kentaro Tomii:
  PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. 392-398
• 
  Jérémy Desaphy, Guillaume Bret, Didier Rognan, Esther Kellenberger:
  sc-PDB: a 3D-database of ligandable binding sites - 10 years on. 399-404
• 
  Randi Vita, James A. Overton, Jason A. Greenbaum, Julia V. Ponomarenko, Jason D. Clark, Jason R. Cantrell, Daniel K. Wheeler, Joseph L. Gabbard, Deborah Hix, Alessandro Sette, Bjoern Peters:
  The immune epitope database (IEDB) 3.0. 405-412
• 
  Marie-Paule Lefranc, Véronique Giudicelli, Patrice Duroux, Joumana Jabado-Michaloud, Géraldine Folch, Safa Aouinti, Emilie Carillon, Hugo Duvergey, Amélie Houles, Typhaine Paysan-Lafosse, Saida Hadi-Saljoqi, Souphatta Sasorith, Gérard Lefranc, Sofia Kossida:
  IMGT^®, the international ImMunoGeneTics information system^® 25 years on. 413-422
• 
  James Robinson, Jason A. Halliwell, James D. Hayhurst, Paul Flicek, Peter Parham, Steven G. E. Marsh:
  The IPD and IMGT/HLA database: allele variant databases. 423-431
• 
  Jared Adolf-Bryfogle, Qifang Xu, Benjamin North, Andreas Lehmann, Roland L. Dunbrack Jr.:
  PyIgClassify: a database of antibody CDR structural classifications. 432-438

III. Metabolic and signalling pathways, enzymes

• 
  Antje Chang, Ida Schomburg, Sandra Placzek, Lisa Jeske, Marcus Ulbrich, Mei Xiao, Christoph W. Sensen, Dietmar Schomburg:
  BRENDA in 2015: exciting developments in its 25th year of existence. 439-446
• 
  Damian Szklarczyk, Andrea Franceschini, Stefan Wyder, Kristoffer Forslund, Davide Heller, Jaime Huerta-Cepas, Milan Simonovic, Alexander Roth, Alberto Santos, Kalliopi Tsafou, Michael Kuhn, Peer Bork, Lars Juhl Jensen, Christian von Mering:
  STRING v10: protein-protein interaction networks, integrated over the tree of life. 447-452
• 
  Nozomi Nagano, Naoko Nakayama, Kazuyoshi Ikeda, Masaru Fukuie, Kiyonobu Yokota, Takuo Doi, Tsuyoshi Kato, Kentaro Tomii:
  EzCatDB: the enzyme reaction database, 2015 update. 453-458
• 
  Anne Morgat, Kristian B. Axelsen, Thierry Lombardot, Rafael Alcántara, Lucila Aimo, Mohamed Zerara, Anne Niknejad, Eugeni Belda, Nevila Hyka-Nouspikel, Elisabeth Coudert, Nicole Redaschi, Lydie Bougueleret, Christoph Steinbeck, Ioannis Xenarios, Alan J. Bridge:
  Updates in Rhea - a manually curated resource of biochemical reactions. 459-464
• 
  Aqeel Ahmed, Richard D. Smith, Jordan J. Clark, James B. Dunbar Jr., Heather A. Carlson:
  Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. 465-469
• 
  Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Rose Oughtred, Lorrie Boucher, Sven Heinicke, Daici Chen, Chris Stark, Ashton Breitkreutz, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Julie Nixon, Lindsay Ramage, Andrew G. Winter, Adnane Sellam, Christie S. Chang, Jodi E. Hirschman, Chandra L. Theesfeld, Jennifer M. Rust, Michael S. Livstone, Kara Dolinski, Mike Tyers:
  The BioGRID interaction database: 2015 update. 470-478
• 
  Birgit H. M. Meldal, Oscar Forner-Martinez, Maria C. Costanzo, Jose M. Dana, Janos Demeter, Marine Dumousseau, Selina S. Dwight, Anna Gaulton, Luana Licata, Anna N. Melidoni, Sylvie Ricard-Blum, Bernd Roechert, Marek S. Skrzypek, Manu Tiwari, Sameer Velankar, Edith D. Wong, Henning Hermjakob, Sandra E. Orchard:
  The complex portal - an encyclopaedia of macromolecular complexes. 479-484
• 
  Dániel V. Veres, Dávid M. Gyurkó, Benedek Thaler, Kristof Z. Szalay, Dávid Fazekas, Tamás Korcsmáros, Peter Csermely:
  ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. 485-493
• 
  Pablo Minguez, Ivica Letunic, Luca Parca, Luz Garcia-Alonso, Joaquín Dopazo, Jaime Huerta-Cepas, Peer Bork:
  PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. 494-502
• 
  Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Kai-Yao Huang, Wei-Chieh Ching, Hsiao-Hsiang Yang, Yen-Chen Liao, Yu-Ju Chen, Tzong-Yi Lee:
  dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. 503-511
• 
  Peter V. Hornbeck, Bin Zhang, Beth Murray, Jon M. Kornhauser, Vaughan Latham, Elzbieta Skrzypek:
  PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. 512-520
• 
  Matthew K. Matlock, Alex S. Holehouse, Kristen M. Naegle:
  ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. 521-530
• 
  Guangyou Duan, Xun Li, Maja Köhn:
  The human DEPhOsphorylation database DEPOD: a 2015 update. 531-535
• 
  Philippe Ortet, David E. Whitworth, Catherine Santaella, Wafa Achouak, Mohamed Barakat:
  P2CS: updates of the prokaryotic two-component systems database. 536-541
• 
  Vijayalakshmi Chelliah, Nick S. Juty, Ishan Ajmera, Raza Ali, Marine Dumousseau, Mihai Glont, Michael Hucka, Gaël Jalowicki, Sarah M. Keating, Vincent Knight-Schrijver, Audald Lloret-Villas, Kedar Nath Natarajan, Jean-Baptiste Pettit, Nicolas Rodriguez, Michael Schubert, Sarala M. Wimalaratne, Yangyang Zhao, Henning Hermjakob, Nicolas Le Novère, Camille Laibe:
  BioModels: ten-year anniversary. 542-548
• 
  Zhengdong Zhang, Tie Shen, Bin Rui, Wenwei Zhou, Xiangfei Zhou, Chuanyu Shang, Chenwei Xin, Xiaoguang Liu, Gang Li, Jiansi Jiang, Chao Li, Ruiyuan Li, Mengshu Han, Shanping You, Guojun Yu, Yin Yi, Han Wen, Zhijie Liu, Xiaoyao Xie:
  CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics. 549-557
• 
  Cheng Zhang, Lin Tao, Chu Qin, Peng Zhang, Shangying Chen, Xian Zeng, Feng Xu, Zhe Chen, Sheng-Yong Yang, Yuzong Chen:
  CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. 558-565

IV. Viruses, bacteria, protozoa, and fungi

• 
  Danso Ako-Adjei, William Fu, Craig Wallin, Kenneth S. Katz, Guangfeng Song, Dakshesh Darji, J. Rodney Brister, Roger G. Ptak, Kim D. Pruitt:
  HIV-1, human interaction database: current status and new features. 566-570
• 
  J. Rodney Brister, Danso Ako-Adjei, Yiming Bao, Olga Blinkova:
  NCBI Viral Genomes Resource. 571-577
• 
  Yanhui Li, Changliang Wang, Zhengqiang Miao, Xiaoman Bi, Deng Wu, Nana Jin, Liqiang Wang, Hao Wu, Kun Qian, Chunhua Li, Ting Zhang, Chunrui Zhang, Ying Yi, Hongyan Lai, Yongfei Hu, Lixin Cheng, Kwong-Sak Leung, Xiaobo Li, Fengmin Zhang, Kongning Li, Xia Li, Dong Wang:
  ViRBase: a resource for virus-host ncRNA-associated interactions. 578-582
• 
  Thibaut Guirimand, Stéphane Delmotte, Vincent Navratil:
  VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. 583-587
• 
  Alberto Calderone, Luana Licata, Gianni Cesareni:
  VirusMentha: a new resource for virus-host protein interactions. 588-592
• 
  Steven F. Stoddard, Byron J. Smith, Robert Hein, Benjamin R. K. Roller, Thomas M. Schmidt:
  rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. 593-598
• 
  Tatiana A. Tatusova, Stacy Ciufo, Scott Federhen, Boris Fedorov, Richard McVeigh, Kathleen O'Neill, Igor Tolstoy, Leonid Zaslavsky:
  Update on RefSeq microbial genomes resources. 599-605
• 
  Yuta Otsuka, Ai Muto, Rikiya Takeuchi, Chihiro Okada, Motokazu Ishikawa, Koichiro Nakamura, Natsuko Yamamoto, Hitomi Dose, Kenji Nakahigashi, Shigeki Tanishima, Sivasundaram Suharnan, Wataru Nomura, Toru Nakayashiki, Walid G. Aref, Barry R. Bochner, Tyrrell Conway, Michael Gribskov, Daisuke Kihara, Kenneth E. Rudd, Yukako Tohsato, Barry L. Wanner, Hirotada Mori:
  GenoBase: comprehensive resource database of Escherichia coli K-12. 606-617
• 
  Judith A. H. Wodke, Andreu Alibés, Luca Cozzuto, Antonio Hermoso, Eva Yus, Maria Lluch-Senar, Luis Serrano, Guglielmo Roma:
  MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. 618-623
• 
  Sung Ho Yoon, Young-Kyu Park, Jihyun F. Kim:
  PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands. 624-630
• 
  Marcin Jakalski, Hiroyuki Wakaguri, Tabea G. Kischka, Yoshifumi Nishikawa, Shin-ichiro Kawazu, Makoto Matsubayashi, Fumiya Kawahara, Naotoshi Tsuji, Shinuo Cao, Fujiko Sunaga, Xuenan Xuan, Kazuhiro Okubo, Ikuo Igarashi, Josef Tuda, Arthur E. Mongan, Yuki Eshita, Ryuichiro Maeda, Wojciech Makalowski, Yutaka Suzuki, Junya Yamagishi:
  DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites. 631-636
• 
  Sanu Shameer, Flora J. Logan-Klumpler, Florence Vinson, Ludovic Cottret, Benjamin Merlet, Fiona Achcar, Michael Boshart, Matthew Berriman, Rainer Breitling, Frédéric Bringaud, Peter Bütikofer, Amy M. Cattanach, Bridget Bannerman-Chukualim, Darren J. Creek, Kathryn Crouch, Harry P. de Koning, Hubert Denise, Charles Ebikeme, Alan H. Fairlamb, Michael A. J. Ferguson, Michael L. Ginger, Christiane Hertz-Fowler, Eduard J. Kerkhoven, Pascal Mäser, Paul A. M. Michels, Archana Nayak, David W. Nes, Derek P. Nolan, Christian Olsen, Fatima Silva-Franco, Terry K. Smith, Martin C. Taylor, Aloysius G. M. Tielens, Michael D. Urbaniak, Jaap J. van Hellemond, Isabel M. Vincent, Shane R. Wilkinson, Susan Wyllie, Fred R. Opperdoes, Michael P. Barrett, Fabien Jourdan:
  TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. 637-644
• 
  Martin Urban, Rashmi Pant, Arathi Raghunath, Alistair G. Irvine, Helder Pedro, Kim E. Hammond-Kosack:
  The Pathogen-Host Interactions database (PHI-base): additions and future developments. 645-655
• 
  Mark D. McDowall, Midori A. Harris, Antonia Lock, Kim Rutherford, Daniel M. Staines, Jürg Bähler, Paul J. Kersey, Stephen G. Oliver, Valerie Wood:
  PomBase 2015: updates to the fission yeast database. 656-661

V. Human genome, model organisms, comparative genomics

• 
  Fiona Cunningham, 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, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Andreas K. Kähäri, Stephen Keenan, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Anne Parker, Mateus Patricio, Emily Perry, Miguel Pignatelli, Harpreet Singh Riat, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Jennifer L. Harrow, Rhoda Kinsella, Matthieu Muffato, Magali Ruffier, Stephen M. J. Searle, Giulietta Spudich, Stephen J. Trevanion, Andy Yates, Daniel R. Zerbino, Paul Flicek:
  Ensembl 2015. 662-669
• 
  Kate R. Rosenbloom, Joel Armstrong, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steven G. Heitner, Glenn Hickey, Angie S. Hinrichs, Robert Hubley, Donna Karolchik, Katrina Learned, Brian T. Lee, Chin H. Li, Karen H. Miga, Ngan Nguyen, Benedict Paten, Brian J. Raney, Arian F. A. Smit, Matthew L. Speir, Ann S. Zweig, David Haussler, Robert M. Kuhn, W. James Kent:
  The UCSC Genome Browser database: 2015 update. 670-681
• 
  Alexandra Louis, Nga Thi Thuy Nguyen, Matthieu Muffato, Hugues Roest Crollius:
  Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics. 682-689
• 
  Gilberto dos Santos, Andrew J. Schroeder, Joshua L. Goodman, Victor B. Strelets, Madeline A. Crosby, Jim Thurmond, David B. Emmert, William M. Gelbart:
  FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. 690-697
• 
  John C. Martin, Bruce A. Rosa, Philip Ozersky, Kymberlie Hallsworth-Pepin, Xu Zhang, Veena Bhonagiri-Palsikar, Rahul Tyagi, Qi Wang, Young-Jun Choi, Xin Gao, Samantha N. McNulty, Paul J. Brindley, Makedonka Dautova Mitreva:
  Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. 698-706
• 
  Gloria I. Giraldo-Calderón, Scott J. Emrich, Robert M. MacCallum, Gareth Maslen, Emmanuel Dialynas, Pantelis Topalis, Nicholas Ho, Sandra Gesing, Gregory R. Madey, Frank H. Collins, Daniel Lawson:
  VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. 707-713
• 
  Monica Poelchau, Christopher P. Childers, Gary Moore, Vijaya Tsavatapalli, Jay D. Evans, Chien-Yueh Lee, Han Lin, Jun-Wei Lin, Kevin Hackett:
  The i5k Workspace@NAL - enabling genomic data access, visualization and curation of arthropod genomes. 714-719
• 
  Jürgen Dönitz, Christian Schmitt-Engel, Daniela Grossmann, Lizzy Gerischer, Maike Tech, Michael Schoppmeier, Martin Klingler, Gregor Bucher:
  iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum. 720-725
• 
  Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
  The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. 726-736
• 
  Xinxia Peng, Jean Thierry-Mieg, Danielle Thierry-Mieg, Andrew Nishida, Lenore Pipes, Marjan Bozinoski, Matthew J. Thomas, Sara Kelly, Jeffrey M. Weiss, Muthuswamy Raveendran, Donna M. Muzny, Richard A. Gibbs, Jeffrey Rogers, Gary P. Schroth, Michael G. Katze, Christopher E. Mason:
  Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). 737-742
• 
  Mary Shimoyama, Jeff de Pons, G. Thomas Hayman, Stanley J. F. Laulederkind, Weisong Liu, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Shur-Jen Wang, Elizabeth A. Worthey, Melinda R. Dwinell, Howard J. Jacob:
  The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. 743-750
• 
  Damjan Cicin-Sain, Antonio Hermoso Pulido, Anton Crombach, Karl R. Wotton, Eva Jiménez-Guri, Jean-François Taly, Guglielmo Roma, Johannes Jaeger:
  SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos. 751-755
• 
  J. Brad Karpinka, Joshua D. Fortriede, Kevin A. Burns, Christina James-Zorn, Virgilio G. Ponferrada, Jacqueline Lee, Kamran Karimi, Aaron M. Zorn, Peter D. Vize:
  Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. 756-763
• 
  Pascale Gaudet, Pierre-André Michel, Monique Zahn-Zabal, Isabelle Cusin, Paula Duek Roggli, Olivier Evalet, Alain Gateau, Anne Gleizes, Mario Pereira, Daniel Dinis Teixeira, Ying Zhang, Lydie Lane, Amos Bairoch:
  The neXtProt knowledgebase on human proteins: current status. 764-770
• 
  Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi, Kenta Nakai:
  DBTMEE: a database of transcriptome in mouse early embryos. 771-776
• 
  Bing Bai, Wen-Ming Zhao, Bixia Tang, Yanqing Wang, Lu Wang, Zhang Zhang, He-Chuan Yang, Yan-Hu Liu, Jun-Wei Zhu, David M. Irwin, Guo-Dong Wang, Ya-Ping Zhang:
  DoGSD: the dog and wolf genome SNP database. 777-783

VI. Genomic variation, diseases and drugs

• 
  Faviel F. Gonzalez-Galarza, Louise Y. C. Takeshita, Eduardo José Melo dos Santos, Felicity Kempson, Maria Helena Thomaz Maia, Andrea Luciana Soares da Silva, André Luiz Teles e Silva, Gurpreet S. Ghattaoraya, Ana Alfirevic, Andrew R. Jones, Derek Middleton:
  Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations. 784-788
• 
  Joanna S. Amberger, Carol A. Bocchini, François Schiettecatte, Alan F. Scott, Ada Hamosh:
  OMIM.org: Online Mendelian Inheritance in Man (OMIM^®), an online catalog of human genes and genetic disorders. 789-798
• 
  John D. Eicher, Christa Landowski, Brian Stackhouse, Arielle Sloan, Wenjie Chen, Nicole Jensen, Ju-Ping Lien, Richard Leslie, Andrew D. Johnson:
  GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. 799-804
• 
  Simon A. Forbes, David Beare, Prasad Gunasekaran, Kenric Leung, Nidhi Bindal, Harry Boutselakis, Minjie Ding, Sally Bamford, Charlotte Cole, Sari Ward, Chai Yin Kok, Mingming Jia, Tisham De, Jon W. Teague, Michael R. Stratton, Ultan McDermott, Peter J. Campbell:
  COSMIC: exploring the world's knowledge of somatic mutations in human cancer. 805-811
• 
  Mary Goldman, Brian Craft, Teresa Swatloski, Melissa S. Cline, Olena Morozova, Mark Diekhans, David Haussler, Jingchun Zhu:
  The UCSC Cancer Genomics Browser: update 2015. 812-817
• 
  Carol J. Bult, Debra M. Krupke, Dale A. Begley, Joel E. Richardson, Steven B. Neuhauser, John P. Sundberg, Janan T. Eppig:
  Mouse Tumor Biology (MTB): a database of mouse models for human cancer. 818-824
• 
  Haoyang Cai, Saumya Gupta, Prisni Rath, Ni Ai, Michael Baudis:
  arrayMap 2014: an updated cancer genome resource. 825-830
• 
  Rosalind J. Cutts, José Afonso Guerra-Assunção, Emanuela Gadaleta, Abu Z. Dayem Ullah, Claude Chelala:
  BCCTBbp: the Breast Cancer Campaign Tissue Bank bioinformatics portal. 831-836
• 
  Atul Tyagi, Abhishek Tuknait, Priya Anand, Sudheer Gupta, Minakshi Sharma, Deepika Mathur, Anshika Joshi, Sandeep Singh, Ankur Gautam, Gajendra P. S. Raghava:
  CancerPPD: a database of anticancer peptides and proteins. 837-843
• 
  Kenneth L. Abbott, Erik T. Nyre, Juan Abrahante, Yen-Yi Ho, Rachel Isaksson Vogel, Timothy K. Starr:
  The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice. 844-848
• 
  Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Lichieh Julie Chu, Ting-Wen Chen, Kai-Ping Chang, Cheng-Yang Lee, Richie Ruei-Chi Gan, Hsuan Liu, Petrus Tang:
  CMPD: cancer mutant proteome database. 849-855
• 
  Wei-Yun Huang, Sheng-Da Hsu, Hsi-Yuan Huang, Yi-Ming Sun, Chih-Hung Chou, Shun-Long Weng, Hsien-Da Huang:
  MethHC: a database of DNA methylation and gene expression in human cancer. 856-861
• 
  Wei-Chung Cheng, I-Fang Chung, Cheng-Fong Tsai, Tse-Shun Huang, Chen-Yang Chen, Shao-Chuan Wang, Ting-Yu Chang, Hsing-Jen Sun, Jeffrey Yung-Chuan Chao, Cheng-Chung Cheng, Cheng-Wen Wu, Hsei-Wei Wang:
  YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research. 862-867
• 
  Yoko Nagai, Yasuko Takahashi, Tadashi Imanishi:
  VaDE: a manually curated database of reproducible associations between various traits and human genomic polymorphisms. 868-872
• 
  Thomas Craig, Chris Smelick, Robi Tacutu, Daniel Wuttke, Shona H. Wood, Henry Stanley, Georges Janssens, Ekaterina Savitskaya, Alexey Moskalev, Robert Arking, João Pedro de Magalhães:
  The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource. 873-878
• 
  Arwa Bin Raies, Hicham Mansour, Roberto Incitti, Vladimir B. Bajic:
  DDMGD: the database of text-mined associations between genes methylated in diseases from different species. 879-886
• 
  Xiaobo Yang, Ming Li, Qi Liu, Yabing Zhang, Junyan Qian, Xueshuai Wan, Anqiang Wang, Haohai Zhang, Chengpei Zhu, Xin Lu, Yilei Mao, Xinting Sang, Haitao Zhao, Yi Zhao, Xiaoyan Zhang:
  Dr.VIS v2.0: an updated database of human disease-related viral integration sites in the era of high-throughput deep sequencing. 887-892
• 
  Xia Ran, Jinchen Li, Qianzhi Shao, Huiqian Chen, Zhongdong Lin, Zhongsheng Sun, Jinyu Wu:
  EpilepsyGene: a genetic resource for genes and mutations related to epilepsy. 893-899
• 
  Deepthi Mannil, Ingo Vogt, Jeanette Prinz, Monica Campillos:
  Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level. 900-906
• 
  Mei-Chun Cai, Quan Xu, Yan-Jing Pan, Wen Pan, Nan Ji, Yin-Bo Li, Hai-Jing Jin, Ke Liu, Zhi-Liang Ji:
  ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms. 907-913
• 
  Allan Peter Davis, Cynthia J. Grondin, Kelley Lennon-Hopkins, Cynthia A. Saraceni-Richards, Daniela Sciaky, Benjamin L. King, Thomas C. Wiegers, Carolyn J. Mattingly:
  The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. 914-920
• 
  Yoshinobu Igarashi, Noriyuki Nakatsu, Tomoya Yamashita, Atsushi Ono, Yasuo Ohno, Tetsuro Urushidani, Hiroshi Yamada:
  Open TG-GATEs: a large-scale toxicogenomics database. 921-927
• 
  David S. Wishart, David Arndt, Allison Pon, Tanvir Sajed, Anchi Guo, Yannick Djoumbou, Craig Knox, Michael Wilson, Yongjie Liang, Jason R. Grant, Yifeng Liu, Seyed Ali Goldansaz, Stephen M. Rappaport:
  T3DB: the toxic exposome database. 928-934
• 
  Priyanka Banerjee, Jevgeni Erehman, Björn-Oliver Gohlke, Thomas Wilhelm, Robert Preissner, Mathias Dunkel:
  Super Natural II - a database of natural products. 935-939
• 
  Kasper Jensen, Gianni Panagiotou, Irene Kouskoumvekaki:
  NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods. 940-945
• 
  Yang Liu, Dafei Xie, Lu Han, Hui Bai, Fei Li, Shengqi Wang, Xiaochen Bo:
  EHFPI: a database and analysis resource of essential host factors for pathogenic infection. 946-955
• 
  Ravi Kumar, Kumardeep Chaudhary, Minakshi Sharma, Gandharva Nagpal, Jagat Singh Chauhan, Sandeep Singh, Ankur Gautam, Gajendra P. S. Raghava:
  AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides. 956-962
• 
  Peng Li, Yongrui Liu, Huan Wang, Yuan He, Xue Wang, Yundong He, Fang Lv, Huaqing Chen, Xiufeng Pang, Mingyao Liu, Tieliu Shi, Zhengfang Yi:
  PubAngioGen: a database and knowledge for angiogenesis and related diseases. 963-967
• 
  Eduard Porta-Pardo, Thomas Hrabe, Adam Godzik:
  Cancer3D: understanding cancer mutations through protein structures. 968-973

VII. Plant databases

• 
  Sebastian Proost, Michiel Van Bel, Dries Vaneechoutte, Yves Van de Peer, Dirk Inzé, Bernd Mueller-Roeber, Klaas Vandepoele:
  PLAZA 3.0: an access point for plant comparative genomics. 974-981
• 
  Xin Yi, Zhenhai Zhang, Yi Ling, Wenying Xu, Zhen Su:
  PNRD: a plant non-coding RNA database. 982-989
• 
  Dapeng Wang, Jun Yu:
  Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. 990-995
• 
  Tak Lee, Sunmo Yang, Eiru Kim, Younhee Ko, Sohyun Hwang, Junha Shin, Jung Eun Shim, Hongseok Shim, Hyojin Kim, Chanyoung Kim, Insuk Lee:
  AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. 996-1002
• 
  Vivek Krishnakumar, Matthew R. Hanlon, Sergio Contrino, Erik S. Ferlanti, Svetlana Karamycheva, Maria Kim, Benjamin D. Rosen, Chia-Yi Cheng, Walter Moreira, Stephen A. Mock, Joseph Stubbs, Julie M. Sullivan, Konstantinos Krampis, Jason R. Miller, Gos Micklem, Matthew Vaughn, Christopher D. Town:
  Araport: the Arabidopsis Information Portal. 1003-1009
• 
  Rim Zaag, Jean-Philippe Tamby, Cécile Guichard, Zakia Tariq, Guillem Rigaill, Etienne Delannoy, Jean-Pierre Renou, Sandrine Balzergue, Tristan Mary-Huard, Sébastien Aubourg, Marie-Laure Martin-Magniette, Véronique Brunaud:
  GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. 1010-1017
• 
  Hu Zhao, Wen Yao, Yidan Ouyang, Wanneng Yang, Gongwei Wang, Xingming Lian, Yongzhong Xing, Lingling Chen, Weibo Xie:
  RiceVarMap: a comprehensive database of rice genomic variations. 1018-1022
• 
  Nickolai Alexandrov, Shuaishuai Tai, Wensheng Wang, Locedie Mansueto, Kevin Palis, Roven Rommel Fuentes, Victor Jun M. Ulat, Dmytro Chebotarov, Gengyun Zhang, Zhikang Li, Ramil Mauleon, Ruaraidh Sackville Hamilton, Kenneth L. McNally:
  SNP-Seek database of SNPs derived from 3000 rice genomes. 1023-1027
• 
  Alexis Dereeper, Stéphanie Bocs, Mathieu Rouard, Valentin Guignon, Sébastien Ravel, Christine Tranchant-Dubreuil, Valérie Poncet, Olivier Garsmeur, Philippe Lashermes, Gaëtan Droc:
  The coffee genome hub: a resource for coffee genomes. 1028-1035
• 
  Noé Fernández-Pozo, Naama Menda, Jeremy D. Edwards, Surya Saha, Isaak Y. Tecle, Susan R. Strickler, Aureliano Bombarely, Thomas Fisher-York, Anuradha Pujar, Hartmut Foerster, Aimin Yan, Lukas A. Mueller:
  The Sol Genomics Network (SGN) - from genotype to phenotype to breeding. 1036-1041

VIII. Other databases

• 
  Europe PMC: a full-text literature database for the life sciences and platform for innovation. 1042-1048
• 
  Gene Ontology Consortium: going forward. 1049-1056
• 
  Rachael P. Huntley, Tony Sawford, Prudence Mutowo-Meullenet, Aleksandra Shypitsyna, Carlos Bonilla, Maria Jesus Martin, Claire O'Donovan:
  The GOA database: Gene Ontology annotation updates for 2015. 1057-1063
• 
  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 2015: updates to the protein family classification and annotation system. 1064-1070
• 
  Warren A. Kibbe, Cesar Arze, Victor Felix, Elvira Mitraka, Evan Bolton, Gang Fu, Christopher J. Mungall, Janos X. Binder, James Malone, Drashtti Vasant, Helen E. Parkinson, Lynn M. Schriml:
  Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. 1071-1078
• 
  Kristian A. Gray, Bethan Yates, Ruth L. Seal, Mathew W. Wright, Elspeth A. Bruford:
  Genenames.org: the HGNC resources in 2015. 1079-1085
• 
  Scott Federhen:
  Type material in the NCBI Taxonomy Database. 1086-1098
• 
  T. B. K. Reddy, Alex D. Thomas, Dimitri Stamatis, Jon Bertsch, Michelle Isbandi, Jakob Jansson, Jyothi Mallajosyula, Ioanna Pagani, Elizabeth A. Lobos, Nikos Kyrpides:
  The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. 1099-1106
• 
  Martin Kollmar, Lotte Kollmar, Björn Hammesfahr, Dominic Simm:
  diArk - the database for eukaryotic genome and transcriptome assemblies in 2014. 1107-1112
• 
  Nikolay Kolesnikov, Emma Hastings, Maria Keays, Olga Melnichuk, Y. Amy Tang, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova, Marco Brandizi, Tony Burdett, Karyn Megy, Ekaterina Pilicheva, Gabriella Rustici, Andrew Tikhonov, Helen E. Parkinson, Robert Petryszak, Ugis Sarkans, Alvis Brazma:
  ArrayExpress update - simplifying data submissions. 1113-1116
• 
  Manuel Sánchez-Castillo, David Ruau, Adam C. Wilkinson, Felicia S. L. Ng, Rebecca Hannah, Evangelia Diamanti, Patrick Lombard, Nicola K. Wilson, Berthold Göttgens:
  CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. 1117-1123
• 
  Sipko van Dam, Thomas Craig, João Pedro de Magalhães:
  GeneFriends: a human RNA-seq-based gene and transcript co-expression database. 1124-1132
• 
  Pingzhang Wang, Huiying Qi, Shibin Song, Shuang Li, Ningyu Huang, Wenling Han, Dalong Ma:
  ImmuCo: a database of gene co-expression in immune cells. 1133-1139
• 
  Alberto Santos, Rasmus Wernersson, Lars Juhl Jensen:
  Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes. 1140-1144
• 
  Elizabeth Montague, Imre Janko, Larissa Stanberry, Elaine Lee, John Choiniere, Nathaniel Anderson, Elizabeth Stewart, William Broomall, Roger Higdon, Natali Kolker, Eugene Kolker:
  Beyond protein expression, MOPED goes multi-omics. 1145-1151

Resource Collection

• 
  Joanne Kamens:
  The Addgene repository: an international nonprofit plasmid and data resource. 1152-1157
• 
  Joakim Galli, Johan Oelrich, Michael J. Taussig, Ulrika Andreasson, Eva Ortega-Paino, Ulf Landegren:
  The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples. 1158-1162
• 
  E. A. Howe, Andrea de Souza, David L. Lahr, S. Chatwin, Philip Montgomery, B. R. Alexander, Dac-Trung Nguyen, Yasel Cruz, D. A. Stonich, G. Walzer, J. T. Rose, Shaita C. Picard, Zihan Liu, Jamie N. Rose, X. Xiang, Jacob K. Asiedu, D. Durkin, J. Levine, J. J. Yang, Stephan C. Schürer, John C. Braisted, Noel Southall, Mark R. Southern, T. D. Y. Chung, Steve Brudz, C. Tanega, Stuart L. Schreiber, Joshua A. Bittker, Rajarshi Guha, Paul A. Clemons:
  BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. 1163-1170
• 
  INFRAFRONTIER - providing mutant mouse resources as research tools for the international scientific community. 1171-1175
• 
  Frank Schwach, Ellen Bushell, Ana Rita Gomes, Burcu Anar, Gareth Girling, Colin Herd, Julian C. Rayner, Oliver Billker:
  PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites. 1176-1182
• 
  Esteban Martínez-García, Tomás Aparicio, Ángel Goñi-Moreno, Sofía Fraile, Víctor de Lorenzo:
  SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities. 1183-1189

Volume 43, Number Webserver-Issue, July 2015

Editorial

• 
  Gary Benson:
  Editorial: Nucleic Acids Research annual Web Server Issue in 2015. W1-W2

Articles

• 
  Jia-Ming Chang, Paolo Di Tommaso, Vincent Lefort, Olivier Gascuel, Cédric Notredame:
  TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. W3-W6
• 
  Itamar Sela, Haim Ashkenazy, Kazutaka Katoh, Tal Pupko:
  GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. W7-W14
• 
  Jamie J. Cannone, Blake A. Sweeney, Anton I. Petrov, Robin Ray Gutell, Craig L. Zirbel, Neocles Leontis:
  R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server. W15-W23
• 
  Panu Somervuo, Liisa Holm:
  SANSparallel: interactive homology search against Uniprot. W24-W29
• 
  Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy:
  HMMER web server: 2015 update. W30-W38
• 
  Timothy L. Bailey, James Johnson, Charles E. Grant, William S. Noble:
  The MEME Suite. W39-W49
• 
  Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime Abraham Castro-Mondragón, Jeremy Delerce, Sébastien Jaeger, Christophe Blanchet, Pierre Vincens, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira, Marie Artufel, Lucie Charbonnier-Khamvongsa, Céline Hernandez, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden:
  RSAT 2015: Regulatory Sequence Analysis Tools. W50-W56
• 
  Hana Imrichová, Gert Hulselmans, Zeynep Kalender Atak, Delphine Potier, Stein Aerts:
  i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. W57-W64
• 
  Bin Liu, Fule Liu, Xiaolong Wang, Junjie Chen, Longyun Fang, Kuo-Chen Chou:
  Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences. W65-W71
• 
  José P. Pinto, Ravi Kiran Reddy Kalathur, Daniel V. Oliveira, Tânia Barata, Rui S. R. Machado, Susana Machado, Ivette Pacheco-Leyva, Isabel Duarte, Matthias E. Futschik:
  StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. W72-W77
• 
  Yi Wang, Devin Coleman-Derr, Guoping Chen, Yong Qiang Gu:
  OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. W78-W84
• 
  Zhigang Hua, Yan Lin, Yazhou Yuan, Dechang Yang, Wen Wei, Feng-Biao Guo:
  ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes. W85-W90
• 
  Junha Shin, Sunmo Yang, Eiru Kim, Chan Yeong Kim, Hongseok Shim, Ara Cho, Hyojin Kim, Sohyun Hwang, Jung Eun Shim, Insuk Lee:
  FlyNet: a versatile network prioritization server for the Drosophila community. W91-W97
• 
  Matthias Munz, Sascha Tönnies, Wolf-Tilo Balke, Eric Simon:
  Multidimensional gene search with Genehopper. W98-W103
• 
  Bhavjinder K. Dhillon, Matthew R. Laird, Julie A. Shay, Geoffrey L. Winsor, Raymond Lo, Fazmin Nizam, Sheldon K. Pereira, Nicholas Waglechner, Andrew G. McArthur, Morgan G. I. Langille, Fiona S. L. Brinkman:
  IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. W104-W108
• 
  Thomas A. Darde, Olivier Sallou, Emmanuelle Becker, Bertrand Evrard, Cyril Monjeaud, Yvan Le Bras, Bernard Jégou, Olivier Collin, Antoine D. Rolland, Frédéric Chalmel:
  The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. W109-W116
• 
  Roberto Alonso, Francisco Salavert, Francisco García-García, José Carbonell-Caballero, Marta Bleda, Luz Garcia-Alonso, Alba Sanchis-Juan, Daniel Perez-Gil, Pablo Marín-García, Rubén Sánchez, Cankut Çubuk, Marta R. Hidalgo, Alicia Amadoz, Rosa D. Hernansaiz-Ballesteros, Alejandro Alemán, Joaquín Tárraga, David Montaner, Ignacio Medina, Joaquín Dopazo:
  Babelomics 5.0: functional interpretation for new generations of genomic data. W117-W121
• 
  Tak Lee, Taeyun Oh, Sunmo Yang, Junha Shin, Sohyun Hwang, Chan Yeong Kim, Hyojin Kim, Hongseok Shim, Jung Eun Shim, Pamela C. Ronald, Insuk Lee:
  RiceNet v2: an improved network prioritization server for rice genes. W122-W127
• 
  Aaron K. Wong, Arjun Krishnan, Victoria Yao, Alicja Tadych, Olga G. Troyanskaya:
  IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. W128-W133
• 
  Damiano Piovesan, Manuel Giollo, Emanuela Leonardi, Carlo Ferrari, Silvio C. E. Tosatto:
  INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. W134-W140
• 
  Sayed M. Sahraeian, Kevin R. Luo, Steven E. Brenner:
  SIFTER search: a web server for accurate phylogeny-based protein function prediction. W141-W147
• 
  Sayoni Das, Ian Sillitoe, David A. Lee, Jonathan G. Lees, Natalie L. Dawson, John Ward, Christine A. Orengo:
  CATH FunFHMMer web server: protein functional annotations using functional family assignments. W148-W153
• 
  Ilyas R. Sadreyev, Fei Ji, Emiliano Cohen, Gary Ruvkun, Yuval Tabach:
  PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles. W154-W159
• 
  Yiming Cheng, Fabiana Perocchi:
  ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. W160-W168
• 
  Liam J. McGuffin, Jennifer D. Atkins, Bajuna R. Salehe, Ahmad N. Shuid, Daniel B. Roche:
  IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences. W169-W173
• 
  Jianyi Yang, Yang Zhang:
  I-TASSER server: new development for protein structure and function predictions. W174-W181
• 
  Jonathan Goya, Aaron K. Wong, Victoria Yao, Arjun Krishnan, Max Homilius, Olga G. Troyanskaya:
  FNTM: a server for predicting functional networks of tissues in mouse. W182-W187
• 
  Mario Lauria, Petros Moyseos, Corrado Priami:
  SCUDO: a tool for signature-based clustering of expression profiles. W188-W192
• 
  Javier Setoain, Mònica Franch, Marta Martínez, Daniel Tabas-Madrid, Carlos Oscar Sánchez Sorzano, Annette Bakker, Eduardo Gonzalez-Couto, Juan Elvira, Alberto D. Pascual-Montano:
  NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning. W193-W199
• 
  David Lagorce, Olivier Sperandio, Jonathan B. Baell, Maria A. Miteva, Bruno O. Villoutreix:
  FAF-Drugs3: a web server for compound property calculation and chemical library design. W200-W207
• 
  Griet Laenen, Amin Ardeshirdavani, Yves Moreau, Lieven Thorrez:
  Galahad: a web server for drug effect analysis from gene expression. W208-W212
• 
  Hyejin Yoon, Jennifer Macke, Anthony P. West Jr., Brian T. Foley, Pamela J. Bjorkman, Bette T. Korber, Karina Yusim:
  CATNAP: a tool to compile, analyze and tally neutralizing antibody panels. W213-W219
• 
  Xiaofeng Yu, Michael Martinez, Annika L. Gable, Jonathan C. Fuller, Neil J. Bruce, Stefan Richter, Rebecca C. Wade:
  webSDA: a web server to simulate macromolecular diffusional association. W220-W224
• 
  Christopher J. Knight, Jochen S. Hub:
  WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics. W225-W230
• 
  Thomas Hrabe:
  Localize.pytom: a modern webserver for cryo-electron tomography. W231-W236
• 
  Tilmann Weber, Kai Blin, Srikanth Duddela, Daniel Krug, Hyun Uk Kim, Robert E. Bruccoleri, Sang Yup Lee, Michael A. Fischbach, Rolf Müller, Wolfgang Wohlleben, Rainer Breitling, Eriko Takano, Marnix H. Medema:
  antiSMASH 3.0 - a comprehensive resource for the genome mining of biosynthetic gene clusters. W237-W243
• 
  Dries De Maeyer, Bram Weytjens, Joris Renkens, Luc De Raedt, Kathleen Marchal:
  PheNetic: network-based interpretation of molecular profiling data. W244-W250
• 
  Jianguo Xia, Igor Sinelnikov, Beomsoo Han, David S. Wishart:
  MetaboAnalyst 3.0 - making metabolomics more meaningful. W251-W257
• 
  Omer Basha, Dvir Flom, Ruth Barshir, Ilan Y. Smoly, Shoval Tirman, Esti Yeger Lotem:
  MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. W258-W263
• 
  Panwen Wang, Jing Qin, Yiming Qin, Yun Zhu, Lily Yan Wang, Mulin Jun Li, Michael Q. Zhang, Junwen Wang:
  ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. W264-W269
• 
  Rosa D. Hernansaiz-Ballesteros, Francisco Salavert, Patricia Sebastián-León, Alejandro Alemán, Ignacio Medina, Joaquín Dopazo:
  Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. W270-W275
• 
  Evangelia Petsalaki, Andreas O. Helbig, Anjali Gopal, Adrian Pasculescu, Frederick P. Roth, Tony Pawson:
  SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets. W276-W282
• 
  Mohamed Hamed, Christian Spaniol, Maryam Nazarieh, Volkhard Helms:
  TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. W283-W288
• 
  Yuanwei Zhang, Zhenhua Yu, Rongjun Ban, Huan Zhang, Furhan Iqbal, Aiwu Zhao, Ao Li, Qinghua Shi:
  DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data. W289-W294
• 
  Alexis Dereeper, Felix Homa, Gwendoline Andres, Guilhem Sempéré, Gautier Sarah, Yann Hueber, Jean-François Dufayard, Manuel Ruiz:
  SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations. W295-W300
• 
  Ali May, Sanne Abeln, Mark J. Buijs, Jaap Heringa, Wim Crielaard, Bernd W. Brandt:
  NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL. W301-W305
• 
  Rafael Zambrano, Michal Jamróz, Agata Szczasiuk, Jordi Pujols, Sebastian Kmiecik, Salvador Ventura:
  AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures. W306-W313
• 
  Eugene Krissinel:
  Stock-based detection of protein oligomeric states in jsPISA. W314-W319
• 
  Javier Iserte, Franco L. Simonetti, Diego J. Zea, Elin Teppa, Cristina Marino Buslje:
  I-COMS: Interprotein-COrrelated Mutations Server. W320-W325
• 
  Sven Degroeve, Davy Maddelein, Lennart Martens:
  MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation. W326-W330
• 
  Rafael Zambrano, Oscar Conchillo-Solé, Valentin Iglesias, Ricard Illa, Frederic Rousseau, Joost Schymkowitz, Raimon Sabate, Xavier Daura, Salvador Ventura:
  PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores. W331-W337
• 
  Tsun-Tsao Huang, Jenn-Kang Hwang, Chu-Huang Chen, Chih-Sheng Chu, Chi-Wen Lee, Chih-Chieh Chen:
  (PS)2: protein structure prediction server version 3.0. W338-W342
• 
  Mahmoud Mabrouk, Ines Putz, Tim Werner, Michael Schneider, Moritz Neeb, Philipp Bartels, Oliver Brock:
  RBO Aleph: leveraging novel information sources for protein structure prediction. W343-W348
• 
  Michael Schantz Klausen, Mads Valdemar Anderson, Martin Closter Jespersen, Morten Nielsen, Paolo Marcatili:
  LYRA, a webserver for lymphocyte receptor structural modeling. W349-W355
• 
  Brian Jiménez-García, Carles Pons, Dmitri I. Svergun, Pau Bernadó, Juan Fernández-Recio:
  pyDockSAXS: protein-protein complex structure by SAXS and computational docking. W356-W361
• 
  Maximilian Grimm, Tomasz Zimniak, Abdullah Kahraman, Franz Herzog:
  xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints. W362-W369
• 
  Noor E. Hafsa, David Arndt, David S. Wishart:
  CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. W370-W377
• 
  Frédéric Guyon, François Martz, Marek Vavrusa, Jérôme Bécot, Julien Rey, Pierre Tufféry:
  BCSearch: fast structural fragment mining over large collections of protein structures. W378-W382
• 
  David Sehnal, Lukás Pravda, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca:
  PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. W383-W388
• 
  Alexey Drozdetskiy, Christian Cole, James B. Procter, Geoffrey J. Barton:
  JPred4: a protein secondary structure prediction server. W389-W394
• 
  Vincent Frappier, Matthieu Chartier, Rafael J. Najmanovich:
  ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. W395-W400
• 
  Konstantinos D. Tsirigos, Christoph Peters, Nanjiang Shu, Lukas Käll, Arne Elofsson:
  The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. W401-W407
• 
  László Dobson, István Reményi, Gábor E. Tusnády:
  CCTOP: a Consensus Constrained TOPology prediction web server. W408-W412
• 
  Jae-Kwan Kim, Youngsong Cho, Mokwon Lee, Roman A. Laskowski, Seong Eon Ryu, Kokichi Sugihara, Deok-Soo Kim:
  BetaCavityWeb: a webserver for molecular voids and channels. W413-W418
• 
  Mateusz Kurcinski, Michal Jamróz, Maciej Blaszczyk, Andrzej Kolinski, Sebastian Kmiecik:
  CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site. W419-W424
• 
  Irina Tuszynska, Marcin Magnus, Katarzyna Jonak, Wayne Dawson, Janusz M. Bujnicki:
  NPDock: a web server for protein-nucleic acid docking. W425-W430
• 
  Hasup Lee, Lim Heo, Myeong Sup Lee, Chaok Seok:
  GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization. W431-W435
• 
  Hiba Abi Hussein, Alexandre Borrel, Colette Geneix, Michel Petitjean, Leslie Regad, Anne-Claude Camproux:
  PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins. W436-W442
• 
  Sebastian Salentin, Sven Schreiber, V. Joachim Haupt, Melissa F. Adasme, Michael Schroeder:
  PLIP: fully automated protein-ligand interaction profiler. W443-W447
• 
  Céline M. Labbé, Julien Rey, David Lagorce, Marek Vavrusa, Jérôme Bécot, Olivier Sperandio, Bruno O. Villoutreix, Pierre Tufféry, Maria A. Miteva:
  MTiOpenScreen: a web server for structure-based virtual screening. W448-W454
• 
  Jose Manuel Rodriguez, Angel Carro, Alfonso Valencia, Michael L. Tress:
  APPRIS WebServer and WebServices. W455-W459
• 
  Ioannis S. Vlachos, Konstantinos Zagganas, Maria D. Paraskevopoulou, Georgios K. Georgakilas, Dimitra Karagkouni, Thanasis Vergoulis, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
  DIANA-miRPath v3.0: deciphering microRNA function with experimental support. W460-W466
• 
  Antonio Rueda, Guillermo Barturen, Ricardo Lebrón, Cristina Gómez-Martín, Ángel M. Alganza, José L. Oliver, Michael Hackenberg:
  sRNAtoolbox: an integrated collection of small RNA research tools. W467-W473
• 
  Miroslav Sulc, Ray M. Marín, Harlan S. Robins, Jirí Vanícek:
  PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences. W474-W479
• 
  Shun Liu, Jun-Hao Li, Jie Wu, Keren Zhou, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu:
  StarScan: a web server for scanning small RNA targets from degradome sequencing data. W480-W486
• 
  Raoul Jean Pierre Bonnal, Riccardo L. Rossi, Donatella Carpi, Valeria Ranzani, Sergio Abrignani, Massimiliano Pagani:
  miRiadne: a web tool for consistent integration of miRNA nomenclature. W487-W492
• 
  Eugenio Mattei, Marco Pietrosanto, Fabrizio Ferrè, Manuela Helmer-Citterich:
  Web-Beagle: a web server for the alignment of RNA secondary structures. W493-W497
• 
  Joseph D. Yesselman, Rhiju Das:
  RNA-Redesign: a web server for fixed-backbone 3D design of RNA. W498-W501
• 
  Piotr Lukasiak, Maciej Antczak, Tomasz Ratajczak, Marta Szachniuk, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz:
  RNAssess - a web server for quality assessment of RNA 3D structures. W502-W506
• 
  Matan Drory Retwitzer, Maya Polishchuk, Elena Churkin, Ilona Kifer, Zohar Yakhini, Danny Barash:
  RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps. W507-W512
• 
  Juan Antonio García-Martín, Iván Dotú, Peter Clote:
  RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules. W513-W521
• 
  Siqi Tian, Joseph D. Yesselman, Pablo Cordero, Rhiju Das:
  Primerize: automated primer assembly for transcribing non-coding RNA domains. W522-W526
• 
  Piroon Jenjaroenpun, Thidathip Wongsurawat, Surya Pavan Yenamandra, Vladimir A. Kuznetsov:
  QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences. W527-W534
• 
  Yifeng Liu, Yongjie Liang, David S. Wishart:
  PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. W535-W542
• 
  Davy Maddelein, Niklaas Colaert, Iain Buchanan, Niels Hulstaert, Kris Gevaert, Lennart Martens:
  The iceLogo web server and SOAP service for determining protein consensus sequences. W543-W546
• 
  Nicholas Nolte, Nils Kurzawa, Roland Eils, Carl Herrmann:
  MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences. W547-W551
• 
  Allison Pon, Timothy Jewison, Yilu Su, Yongjie Liang, Craig Knox, Adam Maciejewski, Michael Wilson, David S. Wishart:
  Pathways with PathWhiz. W552-W559
• 
  Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David P. A. Cohen, Emmanuel Barillot, Andrei Yu. Zinovyev:
  NaviCell Web Service for network-based data visualization. W560-W565
• 
  Tauno Metsalu, Jaak Vilo:
  ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. W566-W570
• 
  Lu Zhu, Apostolos Malatras, Matthew Thorley, Idonnya Aghoghogbe, Arvind Mer, Stéphanie Duguez, Gillian Butler-Browne, Thomas Voit, William Duddy:
  CellWhere: graphical display of interaction networks organized on subcellular localizations. W571-W575
• 
  Alexander S. Rose, Peter W. Hildebrand:
  NGL Viewer: a web application for molecular visualization. W576-W579
• 
  Weizhong Li, Andrew Peter Cowley, Mahmut Uludag, Tamer Gur, Hamish McWilliam, Silvano Squizzato, Young Mi Park, Nicola Buso, Rodrigo Lopez:
  The EMBL-EBI bioinformatics web and programmatic tools framework. W580-W584
• 
  Silvano Squizzato, Young Mi Park, Nicola Buso, Tamer Gur, Andrew Peter Cowley, Weizhong Li, Mahmut Uludag, Sangya Pundir, Jennifer A. Cham, Hamish McWilliam, Rodrigo Lopez:
  The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. W585-W588
• 
  Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James E. Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard A. Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J. Brookes, Gabriele Bucci, Iwan Buetti, Sarah W. Burge, Cédric Cabau, Joseph W. Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J. Cutts, Erik Dassi, Alex Di Génova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon A. Forbes, Robert C. Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M. Garcia-Manteiga, David M. Goodstein, Kristian A. Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dongjin Han, Byungwoo Han, Todd W. Harris, Jayson Harshbarger, Robert K. Hastings, Richard D. Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie N. Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah-Olivia Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Liò, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jérôme Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, François Moreews, Nabihoudine Ibouniyamine, Nelson Ndegwa, Céline Noirot, Christian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James M. Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M. Staines, Delphine Steinbach, Kevin R. Stone, Elia Stupka, Jon W. Teague, Abu Z. Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk:
  The BioMart community portal: an innovative alternative to large, centralized data repositories. W589-W598
• 
  Florian Reisinger, Noemi del-Toro, Tobias Ternent, Henning Hermjakob, Juan Antonio Vizcaíno:
  Introducing the PRIDE Archive RESTful web services. W599-W604
• 
  Sunghwan Kim, Paul A. Thiessen, Evan Bolton, Stephen H. Bryant:
  PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. W605-W611
• 
  Mark Davies, Michal Nowotka, George Papadatos, Nathan Dedman, Anna Gaulton, Francis Atkinson, Louisa J. Bellis, John P. Overington:
  ChEMBL web services: streamlining access to drug discovery data and utilities. W612-W620