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
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  Kate R. Rosenbloom, Joel Armstrong, Galt P. Barber,