Nucleic Acids Research, Volume 45

Volume 45, Number Database-Issue, January 2017

Nucleic acid sequence, structure, and regulation

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  Michael Y. Galperin, Xosé M. Fernández-Suárez, Daniel J. Rigden:
  The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. D1-D11
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  Database Resources of the National Center for Biotechnology Information. D12-D17
• 
  The BIG Data Center: from deposition to integration to translation. D18-D24
• 
  Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi:
  DNA Data Bank of Japan. D25-D31
• 
  Ana Luisa Toribio, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rossello, Nicole Silvester, Dimitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane:
  European Nucleotide Archive in 2016. D32-D36
• 
  Dennis A. Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
  GenBank. D37-D42
• 
  Keren Zhou, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu:
  ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. D43-D50
• 
  René Dreos, Giovanna Ambrosini, Romain Groux, Rouaïda Cavin Périer, Philipp Bucher:
  The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. D51-D55
• 
  Fabrice P. A. David, Jacques Rougemont, Bart Deplancke:
  GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms. D56-D60
• 
  Ivan S. Yevshin, Ruslan N. Sharipov, Tagir F. Valeev, Alexander E. Kel, Fedor A. Kolpakov:
  GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. D61-D67
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  Tobias Penzkofer, Marten Jäger, Marek Figlerowicz, Richard Badge, Stefan Mundlos, Peter N. Robinson, Tomasz Zemojtel:
  L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. D68-D73
• 
  Shangwei Ning, Ming Yue, Peng Wang, Yue Liu, Hui Zhi, Yan Zhang, Jizhou Zhang, Yue Gao, Maoni Guo, Dianshuang Zhou, Xin Li, Xia Li:
  LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs. D74-D78
• 
  Jing Gong, Chun-Jie Liu, Wei Liu, Yu Xiang, Lixia Diao, An-Yuan Guo, Leng Han:
  LNCediting: a database for functional effects of RNA editing in lncRNAs. D79-D84
• 
  Pohao Ye, Yizhao Luan, Kaining Chen, Yizhi Liu, Chuanle Xiao, Zhi Xie:
  MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing. D85-D89
• 
  Christina Backes, Tim Kehl, Daniel Stöckel, Tobias Fehlmann, Lara Schneider, Eckart Meese, Hans-Peter Lenhof, Andreas Keller:
  miRPathDB: a new dictionary on microRNAs and target pathways. D90-D96
• 
  Ricardo Lebrón, Cristina Gómez-Martín, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Michael Hackenberg, José L. Oliver:
  NGSmethDB 2017: enhanced methylomes and differential methylation. D97-D103
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  Boqin Hu, Yu-Cheng T. Yang, Yiming Huang, Yumin Zhu, Zhi John Lu:
  POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. D104-D114
• 
  Ying Yi, Yue Zhao, Chunhua Li, Lin Zhang, Huiying Huang, Yana Li, Lanlan Liu, Ping Hou, Tianyu Cui, Puwen Tan, Yongfei Hu, Ting Zhang, Yan Huang, Xiaobo Li, Jia Yu, Dong Wang:
  RAID v2.0: an updated resource of RNA-associated interactions across organisms. D115-D118
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  Piroon Jenjaroenpun, Thidathip Wongsurawat, Sawannee Sutheeworapong, Vladimir A. Kuznetsov:
  R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops. D119-D127
• 
  The RNAcentral Consortium:
  RNAcentral: a comprehensive database of non-coding RNA sequences. D128-D134
• 
  Ting Zhang, Puwen Tan, Liqiang Wang, Nana Jin, Yana Li, Lin Zhang, Huan Yang, Zhenyu Hu, Lining Zhang, Chunyu Hu, Chunhua Li, Kun Qian, Changjian Zhang, Yan Huang, Kongning Li, Hao Lin, Dong Wang:
  RNALocate: a resource for RNA subcellular localizations. D135-D138
• 
  Sunil Kumar, Giovanna Ambrosini, Philipp Bucher:
  SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity. D139-D144
• 
  Sebastian Schmeier, Tanvir Alam, Magbubah Essack, Vladimir B. Bajic:
  TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. D145-D150
• 
  Dongsheng Chen, Sanjie Jiang, Xiaoyan Ma, Fang Li:
  TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. D151-D157

Protein sequence and structure, motifs, and domains

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  The UniProt Consortium:
  UniProt: the universal protein knowledgebase. D158-D169
• 
  Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria Jesus Martin, Johannes Söding, Martin Steinegger:
  Uniclust databases of clustered and deeply annotated protein sequences and alignments. D170-D176
• 
  Pascale Gaudet, Pierre-André Michel, Monique Zahn-Zabal, Aurore Britan, Isabelle Cusin, Marcin Domagalski, Paula Duek Roggli, Alain Gateau, Anne Gleizes, Valérie Hinard, Valentine Rech de Laval, JinJin Lin, Frédéric Nikitin, Mathieu Schaeffer, Daniel Dinis Teixeira, Lydie Lane, Amos Bairoch:
  The neXtProt knowledgebase on human proteins: 2017 update. D177-D182
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  Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D. Thomas:
  PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. D183-D189
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  Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Young Mi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell:
  InterPro in 2017 - beyond protein family and domain annotations. D190-D199
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  Aron Marchler-Bauer, Bo Yu, Lianyi Han, Jane He, Christopher J. Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Fu Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Zhouxi Wang, Roxanne A. Yamashita, Dachuan Zhang, Chanjuan Zheng, Lewis Y. Geer, Stephen H. Bryant:
  CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. D200-D203
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  Christina A. Vivelo, Ricky Wat, Charul Agrawal, Hui Yi Tee, Anthony Kar Lun Leung:
  ADPriboDB: The database of ADP-ribosylated proteins. D204-D209
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  David M. Kristensen, Yuri I. Wolf, Eugene V. Koonin:
  ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation. D210-D218
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  Damiano Piovesan, Francesco Tabaro, Ivan Micetic, Marco Necci, Federica Quaglia, Christopher J. Oldfield, Maria Cristina Aspromonte, Norman E. Davey, Radoslav Davidovic, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V. Kajava, Lajos Kalmár, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B. Roche, Edoardo Salladini, Éva Schád, Antoine Schramm, Beáta Szabó, Ágnes Tantos, Fiorella Tonello, Konstantinos D. Tsirigos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Per Warholm, Vladimir N. Uversky, A. Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C. E. Tosatto:
  DisProt 7.0: a major update of the database of disordered proteins. D219-D227
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  Márton Miskei, Csaba Antal, Mónika Fuxreiter:
  FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies. D228-D235
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  Hugues Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone:
  JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures. D236-D242
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  Pawel Dabrowski-Tumanski, Aleksandra I. Jarmolinska, Wanda Niemyska, Eric J. Rawdon, Kenneth C. Millett, Joanna I. Sulkowska:
  LinkProt: a database collecting information about biological links. D243-D249
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  Andrei L. Lomize, Mikhail A. Lomize, Shean R. Krolicki, Irina D. Pogozheva:
  Membranome: a database for proteome-wide analysis of single-pass membrane proteins. D250-D255
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  Pora Kim, Junfei Zhao, Pinyi Lu, Zhongming Zhao:
  mutLBSgeneDB: mutated ligand binding site gene DataBase. D256-D263
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  Yang Xu, Shuang Zhang, Shaofeng Lin, Yaping Guo, Wankun Deng, Ying Zhang, Yu Xue:
  WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. D264-D270
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  Peter W. Rose, Andreas Prlic, Ali Altunkaya, Chunxiao Bi, Anthony R. Bradley, Cole H. Christie, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Rachel Kramer Green, David S. Goodsell, Brian P. Hudson, Tara Kalro, Robert Lowe, Ezra Peisach, Christopher Randle, Alexander S. Rose, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D. Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Christine Zardecki, Helen M. Berman, Stephen K. Burley:
  The RCSB protein data bank: integrative view of protein, gene and 3D structural information. D271-D281
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  Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura:
  Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. D282-D288
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  Natalie L. Dawson, Tony E. Lewis, Sayoni Das, Jonathan G. Lees, David A. Lee, Paul Ashford, Christine A. Orengo, Ian Sillitoe:
  CATH: an expanded resource to predict protein function through structure and sequence. D289-D295
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  R. Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V. Grishin:
  ECOD: new developments in the evolutionary classification of domains. D296-D302
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  Lee Whitmore, Andrew John Miles, Lazaros Mavridis, Robert W. Janes, B. A. Wallace:
  PCDDB: new developments at the Protein Circular Dichroism Data Bank. D303-D307
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  Lisanna Paladin, Layla Hirsh, Damiano Piovesan, Miguel A. Andrade-Navarro, Andrey V. Kajava, Silvio C. E. Tosatto:
  RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. D308-D312
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  Stefan Bienert, Andrew Waterhouse, Tjaart A. P. de Beer, Gerardo Tauriello, Gabriel Studer, Lorenza Bordoli, Torsten Schwede:
  The SWISS-MODEL Repository - new features and functionality. D313-D319
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  Liam D. H. Elbourne, Sasha G. Tetu, Karl A. Hassan, Ian T. Paulsen:
  TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. D320-D324
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  Julia Varga, László Dobson, István Reményi, Gábor E. Tusnády:
  TSTMP: target selection for structural genomics of human transmembrane proteins. D325-D330
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  The Gene Ontology Consortium:
  Expansion of the Gene Ontology knowledgebase and resources. D331-D338
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  Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan P. Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman Elsayed, Cathy H. Wu:
  Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. D339-D346
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  Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He:
  Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. D347-D352

Metabolic and signalling pathways, enzymes

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  Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima:
  KEGG: new perspectives on genomes, pathways, diseases and drugs. D353-D361
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  Damian Szklarczyk, John H. Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T. Doncheva, Alexander Roth, Peer Bork, Lars Juhl Jensen, Christian von Mering:
  The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. D362-D368
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  Andrew Chatr-aryamontri, Rose Oughtred, Lorrie Boucher, Jennifer M. Rust, Christie S. Chang, Nadine Kolas, Lara O'Donnell, Sara Oster, Chandra L. Theesfeld, Adnane Sellam, Chris Stark, Bobby-Joe Breitkreutz, Kara Dolinski, Mike Tyers:
  The BioGRID interaction database: 2017 update. D369-D379
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  Sandra Placzek, Ida Schomburg, Antje Chang, Lisa Jeske, Marcus Ulbrich, Jana Tillack, Dietmar Schomburg:
  BRENDA in 2017: new perspectives and new tools in BRENDA. D380-D388
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  Sunmo Yang, Chan Yeong Kim, Sohyun Hwang, Eiru Kim, Hyojin Kim, Hongseok Shim, Insuk Lee:
  COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). D389-D396
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  Shujing Li, Ke Shui, Ying Zhang, Yongqiang Lv, Wankun Deng, Shahid Ullah, Luoying Zhang, Yu Xue:
  CGDB: a database of circadian genes in eukaryotes. D397-D403
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  Katherine Wolstencroft, Olga Krebs, Jacky L. Snoep, Natalie J. Stanford, Finn Bacall, Martin Golebiewski, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, David D. van Niekerk, Alan R. Williams, Lars Malmström, Bernd Rinn, Wolfgang Müller, Carole A. Goble:
  FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. D404-D407
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  Gregorio Alanis-Lobato, Miguel A. Andrade-Navarro, Martin H. Schaefer:
  HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. D408-D414
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  Anne Morgat, Thierry Lombardot, Kristian B. Axelsen, Lucila Aimo, Anne Niknejad, Nevila Hyka-Nouspikel, Elisabeth Coudert, Monica Pozzato, Marco Pagni, Sébastien Moretti, Steven Rosanoff, Joseph Onwubiko, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan J. Bridge:
  Updates in Rhea - an expert curated resource of biochemical reactions. D415-D418
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  Sara Rahmati, Mark Abovsky, Chiara Pastrello, Igor Jurisica:
  pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. D419-D426
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  Omer Basha, Ruth Barshir, Moran Sharon, Eugene Lerman, Binyamin F. Kirson, Idan Hekselman, Esti Yeger Lotem:
  The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. D427-D431
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  Sarah A. Sam, Joelle Teel, Allison N. Tegge, Aditya Bharadwaj, T. M. Murali:
  XTalkDB: a database of signaling pathway crosstalk. D432-D439
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  Miguel Ramirez-Gaona, Ana Marcu, Allison Pon, An Chi Guo, Tanvir Sajed, Noah A. Wishart, Naama Karu, Yannick Djoumbou Feunang, David Arndt, David S. Wishart:
  YMDB 2.0: a significantly expanded version of the yeast metabolome database. D440-D445

Viruses, bacteria, protozoa and fungi

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  Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Olena Verezemska, Michelle Isbandi, Alex D. Thomas, Rida Ali, Kaushal Sharma, Nikos Kyrpides, T. B. K. Reddy:
  Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. D446-D456
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  David Páez-Espino, I-Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, Ernest Szeto, Manoj Pillay, Jinghua Huang, Victor M. Markowitz, Torben Nielsen, Marcel Huntemann, T. B. K. Reddy, Georgios A. Pavlopoulos, Matthew B. Sullivan, Barbara J. Campbell, Feng Chen, Katherine D. McMahon, Steven J. Hallam, Vincent J. Denef, Ricardo Cavicchioli, Sean M. Caffrey, Wolfgang R. Streit, John Webster, Kim M. Handley, Ghasem H. Salekdeh, Nicolas Tsesmetzis, João C. Setubal, Phillip B. Pope, Wen-Tso Liu, Adam R. Rivers, Natalia Ivanova, Nikos Kyrpides:
  IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. D457-D465
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  Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, Sanjeev Kumar, Christopher N. Larsen, Alexandra J. Lee, Xiaomei Li, Catherine Macken, Colin Mahaffey, Brett E. Pickett, Brian Reardon, Thomas Smith, Lucy Stewart, Christian Suloway, Guangyu Sun, Lei Tong, Amy L. Vincent, Bryan Walters, Sam Zaremba, Hongtao Zhao, Liwei Zhou, Christian M. Zmasek, Edward B. Klem, Richard H. Scheuermann:
  Influenza Research Database: An integrated bioinformatics resource for influenza virus research. D466-D474
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  Hyerin Kim, NaNa Kang, Kyuhyeon An, Doyun Kim, Jae Hyung Koo, Min-Soo Kim:
  MRPrimerV: a database of PCR primers for RNA virus detection. D475-D481
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  Eneida Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister:
  Virus Variation Resource - improved response to emergent viral outbreaks. D482-D490
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  Ana Laura Grazziotin, Eugene V. Koonin, David M. Kristensen:
  Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. D491-D498
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  Koenraad Van Doorslaer, Zhiwen Li, Sandhya Xirasagar, Piet Maes, David Kaminsky, David Liou, Qiang Sun, Ramandeep Kaur, Yentram Huyen, Alison A. McBride:
  The Papillomavirus Episteme: a major update to the papillomavirus sequence database. D499-D506
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  I-Min A. Chen, Victor M. Markowitz, Ken Chu, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Evan Andersen, Marcel Huntemann, Neha Varghese, Michalis Hadjithomas, Kristin Tennessen, Torben Nielsen, Natalia Ivanova, Nikos Kyrpides:
  IMG/M: integrated genome and metagenome comparative data analysis system. D507-D516
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  David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoé Rouy, David Roche, Claude Scarpelli, Claudine Médigue:
  MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. D517-D528
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  Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork:
  proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. D529-D534
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  Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas S. Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Hyun Seung Yoo, Rick L. Stevens:
  Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. D535-D542
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  Ingrid M. Keseler, Amanda Mackie, Alberto Santos-Zavaleta, Richard Billington, César Bonavides-Martínez, Ron Caspi, Carol A. Fulcher, Socorro Gama-Castro, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne M. Paley, Martín Peralta-Gil, Pallavi Subhraveti, David A. Velázquez-Ramírez, Daniel S. Weaver, Julio Collado-Vides, Ian T. Paulsen, Peter D. Karp:
  The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. D543-D550
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  Takatomo Fujisawa, Rei Narikawa, Shin-ichi Maeda, Satoru Watanabe, Yu Kanesaki, Koichi Kobayashi, Jiro Nomata, Mitsumasa Hanaoka, Mai Watanabe, Shigeki Ehira, Eiji Suzuki, Koichiro Awai, Yasukazu Nakamura:
  CyanoBase: a large-scale update on its 20th anniversary. D551-D554
• 
  Kai Blin, Marnix H. Medema, Renzo Kottmann, Sang Yup Lee, Tilmann Weber:
  The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters. D555-D559
• 
  Michalis Hadjithomas, I-Min A. Chen, Ken Chu, Jinghua Huang, Anna Ratner, Krishna Palaniappan, Evan Andersen, Victor M. Markowitz, Nikos Kyrpides, Natalia Ivanova:
  IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes. D560-D565
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  Baofeng Jia, Amogelang R. Raphenya, Brian P. Alcock, Nicholas Waglechner, Peiyao Guo, Kara K. Tsang, Briony A. Lago, Biren M. Dave, Sheldon K. Pereira, Arjun N. Sharma, Sachin Doshi, Mélanie Courtot, Raymond Lo, Laura E. Williams, Jonathan G. Frye, Tariq Elsayegh, Daim Sardar, Erin L. Westman, Andrew C. Pawlowski, Timothy A. Johnson, Fiona S. L. Brinkman, Gerard D. Wright, Andrew G. McArthur:
  CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. D566-D573
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  Steven M. Lakin, Christopher J. Dean, Noelle R. Noyes, Adam Dettenwanger, Anne Spencer Ross, Enrique Doster, Pablo Rovira, Zaid Abdo, Kenneth L. Jones, Jaime Ruiz, Keith E. Belk, Paul S. Morley, Christina Boucher:
  MEGARes: an antimicrobial resistance database for high throughput sequencing. D574-D580
• 
  Cristina Aurrecoechea, Ana Barreto, Evelina Y. Basenko, John Brestelli, Brian P. Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C. Kissinger, Cris Lawrence, Wei Li, Deborah F. Pinney, Jane A. Pulman, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J. Stoeckert Jr., Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng:
  EuPathDB: the eukaryotic pathogen genomics database resource. D581-D591
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  Marek S. Skrzypek, Jonathan Binkley, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock:
  The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. D592-D596
• 
  Pedro Tiago Monteiro, Pedro Pais, Catarina Costa, Sauvagya Manna, Isabel Sá-Correia, Miguel Cacho Teixeira:
  The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts. D597-D603
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  Martin Urban, Alayne Cuzick, Kim Rutherford, Alistair G. Irvine, Helder Pedro, Rashmi Pant, Vidyendra Sadanadan, Lokanath Khamari, Santoshkumar Billal, Sagar Mohanty, Kim E. Hammond-Kosack:
  PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database. D604-D610
• 
  Linhuan Wu, Qinglan Sun, Philippe Desmeth, Hideaki Sugawara, Zhenghong Xu, Kevin McCluskey, David Smith, Vasilenko Alexander, Nelson Lima, Moriya Ohkuma, Vincent Robert, Yuguang Zhou, Jianhui Li, Guomei Fan, Supawadee Ingsriswang, Svetlana Ozerskaya, Juncai Ma:
  World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide. D611-D618

Human genome, model organisms, comparative genomics

• 
  Bethan Yates, Bryony Braschi, Kristian A. Gray, Ruth L. Seal, Susan Tweedie, Elspeth A. Bruford:
  Genenames.org: the HGNC and VGNC resources in 2017. D619-D625
• 
  Cath Tyner, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clayton M. Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo, Maximilian Haeussler, Steven G. Heitner, Angie S. Hinrichs, Donna Karolchik, Brian T. Lee, Christopher M. Lee, Parisa Nejad, Brian J. Raney, Kate R. Rosenbloom, Matthew L. Speir, Chris Villarreal, John Vivian, Ann S. Zweig, David Haussler, Michael Kuhn, W. James Kent:
  The UCSC Genome Browser database: 2017 update. D626-D634
• 
  Bronwen L. Aken, Premanand Achuthan, Wasiu A. Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla A. Cummins, Peter Clapham, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Thomas Juettemann, Stephen Keenan, Matthew R. Laird, Ilias Lavidas, Thomas Maurel, William M. McLaren, Benjamin Moore, Daniel N. Murphy, Rishi Nag, Victoria Newman, Michael Nuhn, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Daniel Sheppard, Helen Sparrow, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Steven P. Wilder, Amonida Zadissa, Myrto Kostadima, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Fiona Cunningham, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
  Ensembl 2017. D635-D642
• 
  Yiming Lu, Cheng Quan, Hebing Chen, Xiaochen Bo, Chenggang Zhang:
  3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. D643-D649
• 
  Daniel E. Cook, Stefan Zdraljevic, Joshua P. Roberts, Erik C. Andersen:
  CeNDR, the Caenorhabditis elegans natural diversity resource. D650-D657
• 
  Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing, Tao Liu, Myles Brown, Clifford A. Meyer, Xiaole Shirley Liu:
  Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. D658-D662
• 
  L. Sian Gramates, Steven J. Marygold, Gilberto dos Santos, Jose-Maria Urbano, Giulia Antonazzo, Beverley Matthews, Alix J. Rey, Christopher J. Tabone, Madeline A. Crosby, David B. Emmert, Kathleen Falls, Joshua L. Goodman, Yanhui Hu, Laura Ponting, Andrew J. Schroeder, Victor B. Strelets, Jim Thurmond, Pinglei Zhou, The FlyBase Consortium:
  FlyBase at 25: looking to the future. D663-D671
• 
  Yanhui Hu, Aram Comjean, Charles Roesel, Arunachalam Vinayagam, Ian Flockhart, Jonathan Zirin, Lizabeth Perkins, Norbert Perrimon, Stephanie E. Mohr:
  FlyRNAi.org - the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update. D672-D678
• 
  Benedikt Rauscher, Florian Heigwer, Marco Breinig, Jan Winter, Michael Boutros:
  GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens. D679-D686
• 
  Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L. L. Sonnhammer:
  HieranoiDB: a database of orthologs inferred by Hieranoid. D687-D690
• 
  Ian Streeter, Peter W. Harrison, Adam Faulconbridge, The HipSci Consortium, Paul Flicek, Helen E. Parkinson, Laura Clarke:
  The human-induced pluripotent stem cell initiative - data resources for cellular genetics. D691-D697
• 
  Rosanna Clima, Roberto Preste, Claudia Calabrese, Maria Angela Diroma, Mariangela Santorsola, Gaetano Scioscia, Domenico Simone, Lishuang Shen, Giuseppe Gasparre, Marcella Attimonelli:
  HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor. D698-D706
• 
  Olivier Tassy:
  New data and features for advanced data mining in Manteia. D707-D711
• 
  Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles D. Borromeo, Matthew H. Brush, Seth Carbon, Tom Conlin, Nathan A. Dunn, Mark Engelstad, Erin Foster, Jean-Philippe F. Gourdine, Julius O. B. Jacobsen, Dan Keith, Bryan Laraway, Suzanna E. Lewis, Jeremy NguyenXuan, Kent A. Shefchek, Nicole A. Vasilevsky, Zhou Yuan, Nicole L. Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Melissa A. Haendel:
  The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. D712-D722
• 
  Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Cynthia L. Smith, Carol J. Bult, The Mouse Genome Database Group:
  Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. D723-D729
• 
  Jacqueline H. Finger, Constance M. Smith, Terry F. Hayamizu, Ingeborg J. McCright, Jingxia Xu, Meiyee Law, David R. Shaw, Richard M. Baldarelli, Jon S. Beal, Olin Blodgett, Jeff Campbell, Lori E. Corbani, Jill R. Lewis, Kim L. Forthofer, Pete J. Frost, Sharon C. Giannatto, Lucie N. Hutchins, Dave Miers, Howie Motenko, Kevin R. Stone, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
  The mouse Gene Expression Database (GXD): 2017 update. D730-D736
• 
  Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David J. Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs, Jordan A. Ramilowski, Owen J. L. Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Takeya Kasukawa, Hideya Kawaji:
  Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. D737-D743
• 
  Evgeny M. Zdobnov, Fredrik Tegenfeldt, Dmitry Kuznetsov, Robert M. Waterhouse, Felipe A. Simão, Panagiotis Ioannidis, Mathieu Seppey, Alexis Loetscher, Evgenia V. Kriventseva:
  OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. D744-D749
• 
  Ernesto Picardi, Anna Maria D'Erchia, Claudio Lo Giudice, Graziano Pesole:
  REDIportal: a comprehensive database of A-to-I RNA editing events in humans. D750-D757
• 
  Douglas G. Howe, Yvonne M. Bradford, Anne E. Eagle, David Fashena, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock, Christian Pich, Sridhar Ramachandran, Leyla Ruzicka, Kevin Schaper, Xiang Shao, Amy Singer, Sabrina Toro, Ceri E. Van Slyke, Monte Westerfield:
  The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. D758-D768

Genomic variation, diseases, and drugs

• 
  Dan Wang, Liuhui Yang, Ping Zhang, Joshua LaBaer, Henning Hermjakob, Dong Li, Xiaobo Yu:
  AAgAtlas 1.0: a human autoantigen database. D769-D776
• 
  Simon A. Forbes, David Beare, Harry Boutselakis, Sally Bamford, Nidhi Bindal, John G. Tate, Charlotte Cole, Sari Ward, Elisabeth Dawson, Laura Ponting, Raymund Stefancsik, Bhavana Harsha, Chai Yin Kok, Mingming Jia, Harry Jubb, Zbyslaw Sondka, Sam L. Thompson, Tisham De, Peter J. Campbell:
  COSMIC: somatic cancer genetics at high-resolution. D777-D783
• 
  Myunggyo Lee, Kyubum Lee, Namhee Yu, Insu Jang, Ikjung Choi, Pora Kim, Ye Eun Jang, Byounggun Kim, Sunkyu Kim, Byungwook Lee, Jaewoo Kang, Sanghyuk Lee:
  ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining. D784-D789
• 
  Alessandro Gorohovski, Somnath Tagore, Vikrant Palande, Assaf Malka, Dorith Raviv-Shay, Milana Frenkel-Morgenstern:
  ChiTaRS-3.1 - the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions. D790-D795
• 
  Yi Jiang, Zhongshan Li, Zhenwei Liu, Denghui Chen, Wanying Wu, Yaoqiang Du, Liying Ji, Zi-Bing Jin, Wei Li, Jinyu Wu:
  mirDNMR: a gene-centered database of background de novo mutation rates in human. D796-D803
• 
  Tychele Turner, Qian Yi, Niklas Krumm, John Huddleston, Kendra Hoekzema, Holly A. Stessman, Anna-Lisa Doebley, Raphael A. Bernier, Deborah A. Nickerson, Evan E. Eichler:
  denovo-db: a compendium of human de novo variants. D804-D811
• 
  Zhen Yang, Liangcai Wu, Anqiang Wang, Wei Tang, Yi Zhao, Haitao Zhao, Andrew E. Teschendorff:
  dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers. D812-D818
• 
  Kira M. Wong, Kristofor Langlais, Geoffrey S. Tobias, Colette Fletcher-Hoppe, Donna Krasnewich, Hilary S. Leeds, Laura Lyman Rodriguez, Georgy Godynskiy, Valerie A. Schneider, Erin M. Ramos, Stephen T. Sherry:
  The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data. D819-D826
• 
  Ruifang Cao, Yan Shi, Shuangguan Chen, Yimin Ma, Jiajun Chen, Juan Yang, Geng Chen, Tieliu Shi:
  dbSAP: single amino-acid polymorphism database for protein variation detection. D827-D832
• 
  Janet Piñero González, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I. Furlong:
  DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. D833-D839
• 
  Konrad J. Karczewski, Ben Weisburd, Brett Thomas, Matthew Solomonson, Douglas M. Ruderfer, David Kavanagh, Tymor Hamamsy, Monkol Lek, Kaitlin E. Samocha, Beryl B. Cummings, Daniel Birnbaum, The Exome Aggregation Consortium, Mark J. Daly, Daniel G. MacArthur:
  The ExAC browser: displaying reference data information from over 60 000 exomes. D840-D845
• 
  Emmanouil Viennas, Angeliki Komianou, Clint Mizzi, Maja Stojiljkovic, Christina Mitropoulou, Juha Muilu, Mauno Vihinen, Panagiota Grypioti, Styliani Papadaki, Cristiana Pavlidis, Branka Zukic, Theodora Katsila, Peter J. van der Spek, Sonja Pavlovic, Giannis Tzimas, George P. Patrinos:
  Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies. D846-D853
• 
  Laura Clarke, Susan Fairley, Xiangqun Zheng Bradley, Ian Streeter, Emily Perry, Ernesto Lowy-Gallego, Anne-Marie Tassé, Paul Flicek:
  The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data. D854-D859
• 
  Giuseppe Maccari, James Robinson, Keith Ballingall, Lisbeth A. Guethlein, Unni Grimholt, Jim Kaufman, Chak-Sum Ho, Natasja de Groot, Paul Flicek, Ronald Bontrop, John A. Hammond, Steven G. E. Marsh:
  IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex. D860-D864
• 
  Sebastian Köhler, Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Julie A. McMurry, Ségolène Aymé, Gareth Baynam, Susan M. Bello, Cornelius F. Boerkoel, Kym M. Boycott, Michael Brudno, Orion J. Buske, Patrick F. Chinnery, Valentina Cipriani, Laureen E. Connell, Hugh J. S. Dawkins, Laura E. DeMare, Andrew Devereau, Bert B. A. de Vries, Helen V. Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna Jähn, Roger James, Roland Krause, Stanley J. F. Laulederkind, Hanns Lochmüller, Gholson J. Lyon, Soichi Ogishima, Annie Olry, Willem H. Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H. Scott, Michael Segal, Panagiotis I. Sergouniotis, Richard Sever, Cynthia L. Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W. M. Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O. B. Jacobsen, Tudor Groza, Damian Smedley, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson:
  The Human Phenotype Ontology in 2017. D865-D876
• 
  Noa Rappaport, Michal Twik, Inbar Plaschkes, Ron Nudel, Tsippi Iny Stein, Jacob Levitt, Moran Gershoni, C. Paul Morrey, Marilyn Safran, Doron Lancet:
  MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search. D877-D887
• 
  Yichun Xiong, Yanjun Wei, Yue Gu, Shumei Zhang, Jie Lyu, Bin Zhang, Chuangeng Chen, Jiang Zhu, Yihan Wang, Hongbo Liu, Yan Zhang:
  DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. D888-D895
• 
  Jacqueline A. L. MacArthur, Emily Bowler, Maria Cerezo, Laurent Gil, Peggy Hall, Emma Hastings, Heather Junkins, Aoife McMahon, Annalisa Milano, Joannella Morales, Zoë May Pendlington, Danielle Welter, Tony Burdett, Lucia Hindorff, Paul Flicek, Fiona Cunningham, Helen E. Parkinson:
  The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). D896-D901
• 
  Jianjian Wang, Yuze Cao, Huixue Zhang, Tianfeng Wang, Qinghua Tian, Xiaoyu Lu, Xiaoyan Lu, Xiaotong Kong, Zhaojun Liu, Ning Wang, Shuai Zhang, Heping Ma, Shangwei Ning, Lihua Wang:
  NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases. D902-D907
• 
  Peng Li, Ronald G. Tompkins, Wenzhong Xiao:
  KERIS: kaleidoscope of gene responses to inflammation between species. D908-D914
• 
  Peilin Jia, Guangchun Han, Junfei Zhao, Pinyi Lu, Zhongming Zhao:
  SZGR 2.0: a one-stop shop of schizophrenia candidate genes. D915-D924
• 
  I-Fang Chung, Shing-Jyh Chang, Chen-Yang Chen, Shu-Hsuan Liu, Chia-Yang Li, Chia-Hao Chan, Chuan-Chi Shih, Wei-Chung Cheng:
  YM500v3: a database for small RNA sequencing in human cancer research. D925-D931
• 
  Oleg Ursu, Jayme Holmes, Jeffrey Knockel, Cristian Bologa, Jeremy J. Yang, Stephen L. Mathias, Stuart J. Nelson, Tudor I. Oprea:
  DrugCentral: online drug compendium. D932-D939
• 
  Wei-Hua Chen, Guanting Lu, Xiao Chen, Xing-Ming Zhao, Peer Bork:
  OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. D940-D944
• 
  Anna Gaulton, Anne Hersey, Michal Nowotka, A. Patrícia Bento, Jon Chambers, David Mendez, Prudence Mutowo-Meullenet, Francis Atkinson, Louisa J. Bellis, Elena Cibrián-Uhalte, Mark Davies, Nathan Dedman, Anneli Karlsson, María P. Magariños, John P. Overington, George Papadatos, Ines Smit, Andrew R. Leach:
  The ChEMBL database in 2017. D945-D954
• 
  Yanli Wang, Stephen H. Bryant, Tiejun Cheng, Jiyao Wang, Asta Gindulyte, Benjamin A. Shoemaker, Paul A. Thiessen, Siqian He, Jian Zhang:
  PubChem BioAssay: 2017 update. D955-D963
• 
  Isabel A. Lea, Hui Gong, Anand Paleja, Asif Rashid, Jennifer Fostel:
  CEBS: a comprehensive annotated database of toxicological data. D964-D971
• 
  Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Benjamin L. King, Roy McMorran, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly:
  The Comparative Toxicogenomics Database: update 2017. D972-D978
• 
  Vanessa Neveu, Alice Moussy, Héloïse Rouaix, Roland Wedekind, Allison Pon, Craig Knox, David S. Wishart, Augustin Scalbert:
  Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors. D979-D984
• 
  Gautier Koscielny, Peter An, Denise Carvalho-Silva, Jennifer A. Cham, Luca Fumis, Rippa Gasparyan, Samiul Hasan, Nikiforos Karamanis, Michael Maguire, Eliseo Papa, Andrea Pierleoni, Miguel Pignatelli, Theo Platt, Francis Rowland, Priyanka Wankar, A. Patrícia Bento, Tony Burdett, Antonio Fabregat, Simon A. Forbes, Anna Gaulton, Cristina Yenyxe González, Henning Hermjakob, Anne Hersey, Steven Jupe, Senay Kafkas, Maria Keays, Catherine Leroy, Francisco-Javier Lopez, María P. Magariños, James Malone, Johanna R. McEntyre, Alfonso Muñoz-Pomer Fuentes, Claire O'Donovan, Irene Papatheodorou, Helen E. Parkinson, Barbara Palka, Justin E. Paschall, Robert Petryszak, Naruemon Pratanwanich, Sirarat Sarntivijai, Gary Saunders, Konstantinos Sidiropoulos, Thomas Smith, Zbyslaw Sondka, Oliver Stegle, Y. Amy Tang, Edward Turner, Brendan W. Vaughan, Olga Vrousgou, Xavier Watkins, Maria Jesus Martin, Philippe Sanseau, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham:
  Open Targets: a platform for therapeutic target identification and validation. D985-D994
• 
  Dac-Trung Nguyen, Stephen L. Mathias, Cristian Bologa, Søren Brunak, Nicolas F. Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John P. Overington, Juhee Patel, Andrew D. Rouillard, Stephan C. Schürer, Timothy Sheils, Anton Simeonov, Larry A. Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy J. Yang, Ajit Jadhav, Tudor I. Oprea, Rajarshi Guha:
  Pharos: Collating protein information to shed light on the druggable genome. D995-D1002

Plant databases

• 
  Stephan Weise, Markus Oppermann, Lorenzo Maggioni, Theo J. L. van Hintum, Helmut Knüpffer:
  EURISCO: The European search catalogue for plant genetic resources. D1003-D1008
• 
  Chunhui Yuan, Xianwen Meng, Xue Li, Nicola Illing, Robert A. Ingle, Jingjing Wang, Ming Chen:
  PceRBase: a database of plant competing endogenous RNA. D1009-D1014
• 
  Yi Wang, Ling Xu, Roger Thilmony, Frank M. You, Yong Qiang Gu, Devin Coleman-Derr:
  PIECE 2.0: an update for the plant gene structure comparison and evolution database. 1015-1020
• 
  Daogang Guan, Bin Yan, Christoph J. Thieme, Jingmin Hua, Hailong Zhu, Kenneth R. Boheler, Zhongying Zhao, Friedrich Kragler, Yiji Xia, Shoudong Zhang:
  PlaMoM: a comprehensive database compiles plant mobile macromolecules. D1021-D1028
• 
  Sushma Naithani, Justin Preece, Peter D'Eustachio, Parul Gupta, Vindhya Amarasinghe, Palitha Dharmawardhana, Guanming Wu, Antonio Fabregat, Justin Elser, Joel Weiser, Maria Keays, Alfonso Muñoz-Pomer Fuentes, Robert Petryszak, Lincoln D. Stein, Doreen Ware, Pankaj Jaiswal:
  Plant Reactome: a resource for plant pathways and comparative analysis. D1029-D1039
• 
  Jinpu Jin, Feng Tian, Dechang Yang, Yuqi Meng, Lei Kong, Jingchu Luo, Ge Gao:
  PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. D1040-D1045
• 
  Jingyin Yu, Komivi Dossa, Linhai Wang, Yanxin Zhang, Xin Wei, Boshou Liao, Xiurong Zhang:
  PMDBase: a database for studying microsatellite DNA and marker development in plants. D1046-D1053
• 
  Ümit Seren, Dominik G. Grimm, Joffrey Fitz, Detlef Weigel, Magnus Nordborg, Karsten M. Borgwardt, Arthur Korte:
  AraPheno: a public database for Arabidopsis thaliana phenotypes. D1054-D1059
• 
  Qi Lv, Yiheng Lan, Yan Shi, Huan Wang, Xia Pan, Peng Li, Tieliu Shi:
  AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. D1060-D1063
• 
  Cornelia M. Hooper, Ian R. Castleden, Sandra K. Tanz, Nader Aryamanesh, A. Harvey Millar:
  SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. D1064-D1074
• 
  Locedie Mansueto, Roven Rommel Fuentes, Frances Nikki Borja, Jeffery Detras, Juan Miguel Abriol-Santos, Dmytro Chebotarov, Millicent Sanciangco, Kevin Palis, Dario Copetti, Alexandre Poliakov, Inna Dubchak, Victor V. Solovyev, Rod A. Wing, Ruaraidh Sackville Hamilton, Ramil Mauleon, Kenneth L. McNally, Nickolai Alexandrov:
  Rice SNP-seek database update: new SNPs, indels, and queries. D1075-D1081
• 
  Eiru Kim, Sohyun Hwang, Insuk Lee:
  SoyNet: a database of co-functional networks for soybean Glycine max. D1082-D1089
• 
  Qi You, Wenying Xu, Kang Zhang, Liwei Zhang, Xin Yi, Dongxia Yao, Chun-Chao Wang, Xueyan Zhang, Xinhua Zhao, Nicholas J. Provart, Fuguang Li, Zhen Su:
  ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. D1090-D1099

Other databases

• 
  Eric W. Deutsch, Attila Csordas, Zhi Sun, Andrew F. Jarnuczak, Yasset Pérez-Riverol, Tobias Ternent, David S. Campbell, Manuel Bernal Llinares, Shujiro Okuda, Shin Kawano, Robert L. Moritz, Jeremy Carver, Mingxun Wang, Yasushi Ishihama, Nuno Bandeira, Henning Hermjakob, Juan Antonio Vizcaíno:
  The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. D1100-D1106
• 
  Shujiro Okuda, Yu Watanabe, Yuki Moriya, Shin Kawano, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Naoyuki Sugiyama, Susumu Goto, Yasushi Ishihama:
  jPOSTrepo: an international standard data repository for proteomes. D1107-D1111
• 
  Lukasz Pawel Kozlowski:
  Proteome-pI: proteome isoelectric point database. D1112-D1116
• 
  Etienne Z. Gnimpieba, Menno S. VanDiermen, Shayla M. Gustafson, Bill Conn, Carol M. Lushbough:
  Bio-TDS: bioscience query tool discovery system. D1117-D1122

Erratum

• 
  Erratum: DisProt 7.0: a major update of the database of disordered proteins. D1123-D1124

Volume 45, Number Webserver-Issue, July 2017

Editorial

• 
  Editorial: the 15th annual Nucleic Acids Research Web Server issue 2017. W1-W5

Web Server issue

• 
  Michael Tillich, Pascal Lehwark, Tommaso Pellizzer, Elena S. Ulbricht-Jones, Axel Fischer, Ralph Bock, Stephan Greiner:
  GeSeq - versatile and accurate annotation of organelle genomes. W6-W11
• 
  Yu-Jian Kang, Dechang Yang, Lei Kong, Mei Hou, Yuqi Meng, Liping Wei, Ge Gao:
  CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. W12-W16
• 
  Rosalba Lepore, Pier Paolo Olimpieri, Mario Abdel Messih, Anna Tramontano:
  PIGSPro: prediction of immunoGlobulin structures v2. W17-W23
• 
  Martin Closter Jespersen, Bjoern Peters, Morten Nielsen, Paolo Marcatili:
  BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. W24-W29
• 
  Claire Bertelli, Matthew R. Laird, Kelly P. Williams, Britney Y. Lau, Gemma Hoad, Geoffrey L. Winsor, Fiona S. L. Brinkman:
  IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. W30-W35
• 
  Kai Blin, Thomas Wolf, Marc G. Chevrette, Xiaowen Lu, Christopher J. Schwalen, Satria A. Kautsar, Hernando G. Suarez Duran, Emmanuel L. C. de los Santos, Hyun Uk Kim, Mariana Nave, Jeroen S. Dickschat, Douglas A. Mitchell, Ekaterina Shelest, Rainer Breitling, Eriko Takano, Sang Yup Lee, Tilmann Weber, Marnix H. Medema:
  antiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification. W36-W41
• 
  Mohammad Alanjary, Brent Kronmiller, Martina Adamek, Kai Blin, Tilmann Weber, Daniel H. Huson, Benjamin Philmus, Nadine Ziemert:
  The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. W42-W48
• 
  Michael A. Skinnider, Nishanth J. Merwin, Chad W. Johnston, Nathan A. Magarvey:
  PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. W49-W54
• 
  Satria A. Kautsar, Hernando G. Suarez Duran, Kai Blin, Anne Osbourn, Marnix H. Medema:
  plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. W55-W63
• 
  Paul F. Zierep, Natàlia Padilla, Dimitar G. Yonchev, Kiran K. Telukunta, Dennis Klementz, Stefan Günther:
  SeMPI: a genome-based secondary metabolite prediction and identification web server. W64-W71
• 
  Shradha Khater, Money Gupta, Priyesh Agrawal, Neetu Sain, Jyoti Prava, Priya Gupta, Mansi Grover, Narendra Kumar, Debasisa Mohanty:
  SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases. W72-W79
• 
  Priyesh Agrawal, Shradha Khater, Money Gupta, Neetu Sain, Debasisa Mohanty:
  RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. W80-W88
• 
  Jared M. Sagendorf, Helen M. Berman, Remo Rohs:
  DNAproDB: an interactive tool for structural analysis of DNA-protein complexes. W89-W97
• 
  Zefang Tang, Chenwei Li, Boxi Kang, Ge Gao, Cheng Li, Zemin Zhang:
  GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. W98-W102
• 
  Guanghui Zhu, Hui Yang, Xiao Chen, Jun Wu, Yong Zhang, Xing-Ming Zhao:
  CSTEA: a webserver for the Cell State Transition Expression Atlas. W103-W108
• 
  Simone Puccio, Giorgio Grillo, Flavio Licciulli, Marco Severgnini, Sabino Liuni, Silvio Bicciato, Gianluca De Bellis, Francesco Ferrari, Clelia Peano:
  WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes. W109-W115
• 
  Lefteris Koumakis, Panos Roussos, George Potamias:
  minepath.org: a free interactive pathway analysis web server. W116-W121
• 
  Tian Tian, Yue Liu, Hengyu Yan, Qi You, Xin Yi, Zhou Du, Wenying Xu, Zhen Su:
  agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. W122-W129
• 
  Jing Wang, Suhas V. Vasaikar, Zhiao Shi, Michael Greer, Bing Zhang:
  WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit. W130-W137
• 
  David Gokhman, Guy Kelman, Adir Amartely, Guy Gershon, Shira Tsur, Liran Carmel:
  Gene ORGANizer: linking genes to the organs they affect. W138-W145
• 
  Tim Kehl, Lara Schneider, Florian Schmidt, Daniel Stöckel, Nico Gerstner, Christina Backes, Eckart Meese, Andreas Keller, Marcel H. Schulz, Hans-Peter Lenhof:
  RegulatorTrail: a web service for the identification of key transcriptional regulators. W146-W153
• 
  Jung Eun Shim, Changbae Bang, Sunmo Yang, Tak Lee, Sohyun Hwang, Chan Yeong Kim, Ulf Martin Singh-Blom, Edward M. Marcotte, Insuk Lee:
  GWAB: a web server for the network-based boosting of human genome-wide association data. W154-W161
• 
  Bo Li, Jing Tang, Qingxia Yang, Shuang Li, Xuejiao Cui, Yinghong Li, Yuzong Chen, Weiwei Xue, Xiaofeng Li, Feng Zhu:
  NOREVA: normalization and evaluation of MS-based metabolomics data. W162-W170
• 
  Cedric Christian Laczny, Christina Kiefer, Valentina Galata, Tobias Fehlmann, Christina Backes, Andreas Keller:
  BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation. W171-W179
• 
  Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L. King, Luis B. Agellon, Jianguo Xia:
  MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. W180-W188
• 
  Javier López, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquín Tárraga, Pedro Furió-Tarí, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquín Dopazo, Ignacio Medina:
  HGVA: the Human Genome Variation Archive. W189-W194
• 
  Lidia Mateo, Oriol Guitart-Pla, Carles Pons, Miquel Duran-Frigola, Roberto Mosca, Patrick Aloy:
  A PanorOmic view of personal cancer genomes. W195-W200
• 
  Daniele Raimondi, Ibrahim Tanyalcin, Julien Ferté, Andrea M. Gazzo, Gabriele Orlando, Tom Lenaerts, Marianne Rooman, Wim F. Vranken:
  DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. W201-W206
• 
  Siwei Chen, Juan F. Beltrán, Clara Esteban-Jurado, Sebastià Franch-Expósito, Sergi Castellví-Bel, Steven Lipkin, Xiaomu Wei, Haiyuan Yu:
  GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. W207-W214
• 
  Mulin Jun Li, Hongcheng Yao, Dandan Huang, Huanhuan Liu, Zipeng Liu, Hang Xu, Yiming Qin, Jeanette Prinz, Weiyi Xia, Panwen Wang, Bin Yan, Nhan L. Tran, Jean-Pierre A. Kocher, Pak Chung Sham, Junwen Wang:
  mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers. W215-W221
• 
  Víctor López-Ferrando, Andrea M. Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Lluis Gelpí:
  PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. W222-W228
• 
  Arun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B. Ascher, Tom L. Blundell:
  SDM: a server for predicting effects of mutations on protein stability. W229-W235
• 
  Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto:
  SODA: prediction of protein solubility from disorder and aggregation propensity. W236-W240
• 
  Douglas E. V. Pires, David B. Ascher:
  mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions. W241-W246
• 
  Emidio Capriotti, Piero Fariselli:
  PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. W247-W252
• 
  Janez Konc, Blaz Skrlj, Nika Erzen, Tanja Kunej, Dusanka Janezic:
  GenProBiS: web server for mapping of sequence variants to protein binding sites. W253-W259
• 
  Eli Levy Karin, Haim Ashkenazy, Susann Wicke, Tal Pupko, Itay Mayrose:
  TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. W260-W264
• 
  Aitor Blanco-Míguez, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez:
  P4P: a peptidome-based strain-level genome comparison web tool. W265-W269
• 
  Giorgos Papoutsoglou, Giorgos Athineou, Vincenzo Lagani, Iordanis Xanthopoulos, Angelika Schmidt, Szabolcs Elias, Jesper Tegnér, Ioannis Tsamardinos:
  SCENERY: a web application for (causal) network reconstruction from cytometry data. W270-W275
• 
  Victor Solis-Mezarino, Franz Herzog:
  compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes. W276-W284
• 
  Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio:
  The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. W285-W290
• 
  Chengxin Zhang, Peter L. Freddolino, Yang Zhang:
  COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. W291-W299
• 
  Georgios Efstathiou, Andreas N. Antonakis, Georgios A. Pavlopoulos, Theodosios Theodosiou, Peter Divanach, David C. Trudgian, Benjamin Thomas, Nikolas Papanikolaou, Michalis Aivaliotis, Oreste Acuto, Ioannis Iliopoulos:
  ProteoSign: an end-user online differential proteomics statistical analysis platform. W300-W306
• 
  Francesco Oteri, Francesca Nadalin, Raphaël Champeimont, Alessandra Carbone:
  BIS2Analyzer: a server for co-evolution analysis of conserved protein families. W307-W314
• 
  João P. A. Moraes, Gisele L. Pappa, Douglas E. V. Pires, Sandro C. Izidoro:
  GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms. W315-W319
• 
  Minkyung Baek, Taeyong Park, Lim Heo, Chiwook Park, Chaok Seok:
  GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure. W320-W324
• 
  Antonia Stank, Daria B. Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C. Wade:
  TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. W325-W330
• 
  Leela S. Dodda, Israel Cabeza de Vaca, Julian Tirado-Rives, William L. Jorgensen:
  LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands. W331-W336
• 
  Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, Matthias Rarey:
  ProteinsPlus: a web portal for structure analysis of macromolecules. W337-W343
• 
  Morten Nielsen, Massimo Andreatta:
  NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions. W344-W349
• 
  Céline M. Labbé, Tania Pencheva, Dessislava Jereva, Dimitri Desvillechabrol, Jérôme Bécot, Bruno O. Villoutreix, Ilza Pajeva, Maria A. Miteva:
  AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics. W350-W355
• 
  Xia Wang, Yihang Shen, Shiwei Wang, Shiliang Li, Weilin Zhang, Xiaofeng Liu, Luhua Lai, Jianfeng Pei, Honglin Li:
  PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. W356-W360
• 
  Sjoerd Jacob de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tufféry:
  The pepATTRACT web server for blind, large-scale peptide-protein docking. W361-W364
• 
  Yumeng Yan, Di Zhang, Pei Zhou, Botong Li, Sheng-You Huang:
  HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. W365-W373
• 
  Hongchun Li, Yuan-Yu Chang, Ji Young Lee, Ivet Bahar, Lee-Wei Yang:
  DynOmics: dynamics of structural proteome and beyond. W374-W380
• 
  Bernardo Ochoa-Montaño, Tom L. Blundell:
  XSuLT: a web server for structural annotation and representation of sequence-structure alignments. W381-W387
• 
  Jakub Galgonek, Jirí Vymetal, David Jakubec, Jirí Vondrásek:
  Amino Acid Interaction (INTAA) web server. W388-W392
• 
  Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomás Martínek, David Bednar, Jirí Damborský:
  FireProt: web server for automated design of thermostable proteins. W393-W399
• 
  Yan Wang, Jian Wang, Ruiming Li, Qiang Shi, Zhidong Xue, Yang Zhang:
  ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. W400-W407
• 
  Catherine L. Worth, Franziska Kreuchwig, Johanna K. S. Tiemann, Annika Kreuchwig, Michele Ritschel, Gunnar Kleinau, Peter W. Hildebrand, Gerd Krause:
  GPCR-SSFE 2.0 - a fragment-based molecular modeling web tool for Class A G-protein coupled receptors. W408-W415
• 
  Ali H. A. Maghrabi, Liam J. McGuffin:
  ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models. W416-W421
• 
  Ahmad N. Shuid, Robert Kempster, Liam J. McGuffin:
  ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates. W422-W428
• 
  Yan Wang, Jouko Virtanen, Zhidong Xue, Yang Zhang:
  I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation. W429-W434
• 
  Martin Mann, Patrick R. Wright, Rolf Backofen:
  IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. W435-W439
• 
  Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldispühl:
  RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. W440-W444
• 
  Xiaobo Sun, William S. Pittard, Tianlei Xu, Li Chen, Michael E. Zwick, Xiaoqian Jiang, Fusheng Wang, Zhaohui S. Qin:
  Omicseq: a web-based search engine for exploring omics datasets. W445-W452
• 
  Haim Ashkenazy, Eli Levy Karin, Zach Mertens, Reed A. Cartwright, Tal Pupko:
  SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. W453-W457
• 
  Massimo Andreatta, Bruno Alvarez, Morten Nielsen:
  GibbsCluster: unsupervised clustering and alignment of peptide sequences. W458-W463
• 
  Izabella Krystkowiak, Norman E. Davey:
  SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. W464-W469
• 
  Roman Prytuliak, Michael Volkmer, Markus Meier, Bianca Habermann:
  HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons. W470-W477
• 
  Milena Kraus, Julian Niedermeier, Marcel Jankrift, Sören Tietböhl, Toni Stachewicz, Hendrik Folkerts, Matthias Uflacker, Mariana L. Neves:
  Olelo: a web application for intuitive exploration of biomedical literature. W478-W483
• 
  Andrés Cañada, Salvador Capella-Gutiérrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger:
  LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. W484-W489
• 
  Lukasz Kreft, Arne Soete, Paco Hulpiau, Alexander Botzki, Yvan Saeys, Pieter J. De Bleser:
  ConTra v3: a tool to identify transcription factor binding sites across species, update 2017. W490-W494
• 
  Balaguru Ravikumar, Zaid Alam, Gopal Peddinti, Tero Aittokallio:
  C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms. W495-W500
• 
  Weijun Luo, Gaurav Pant, Yeshvant K. Bhavnasi, Steven G. Blanchard, Cory Brouwer:
  Pathview Web: user friendly pathway visualization and data integration. W501-W508
• 
  Jesper Lund, Markus List, Jan Baumbach:
  Interactive microbial distribution analysis using BioAtlas. W509-W513
• 
  Alexander Goncearenco, Stephanie L. Rager, Minghui Li, Qing-Xiang Sang, Igor B. Rogozin, Anna R. Panchenko:
  Exploring background mutational processes to decipher cancer genetic heterogeneity. W514-W522
• 
  Maoxiang Shi, Juntao Gao, Michael Q. Zhang:
  Web3DMol: interactive protein structure visualization based on WebGL. W523-W527
• 
  Robert M. Hanson, Xiang-Jun Lu:
  DSSR-enhanced visualization of nucleic acid structures in Jmol. W528-W533
• 
  Xuebing Wu, David P. Bartel:
  kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences. W534-W538

Web Services

• 
  Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Jesus Martin:
  The Proteins API: accessing key integrated protein and genome information. W539-W544
• 
  Young Mi Park, Silvano Squizzato, Nicola Buso, Tamer Gur, Rodrigo Lopez:
  The EBI search engine: EBI search as a service - making biological data accessible for all. W545-W549
• 
  Szymon Chojnacki, Andrew Peter Cowley, Joon Lee, Anna Foix, Rodrigo Lopez:
  Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. W550-W553

Stand alone programs

• 
  Yang Young Lu, Kujin Tang, Jie Ren, Jed A. Fuhrman, Michael S. Waterman, Fengzhu Sun:
  CAFE: aCcelerated Alignment-FrEe sequence analysis. W554-W559
• 
  Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen:
  The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. W560-W566
• 
  Heiko Müller, Raúl Jiménez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock:
  VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data. W567-W572

Corrigendum

• 
  Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldispühl:
  RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. W573