Nucleic Acids Research, Volume 44

Volume 44, Number Database-Issue, January 2016

Nucleic acid sequence, structure, and regulation

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  Daniel J. Rigden, Xosé M. Fernández-Suárez, Michael Y. Galperin:
  The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. 1-6
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  Database resources of the National Center for Biotechnology Information. 7-19
• 
  Charles E. Cook, Mary Todd Bergman, Robert D. Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler:
  The European Bioinformatics Institute in 2016: Data growth and integration. 20-26
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  The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. 27-37
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  Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak:
  Tools and data services registry: a community effort to document bioinformatics resources. 38-47
• 
  Guy Cochrane, Ilene Karsch-Mizrachi, Toshihisa Takagi:
  The International Nucleotide Sequence Database Collaboration. 48-50
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  Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi:
  DNA data bank of Japan (DDBJ) progress report. 51-57
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  Richard Gibson, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Swapna Pallreddy, Nima Pakseresht, Jeena Rajan, Marc Rossello, Nicole Silvester, Dimitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane:
  Biocuration of functional annotation at the European nucleotide archive. 58-66
• 
  Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
  GenBank. 67-72
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  Paul A. Kitts, Deanna M. Church, Françoise Thibaud-Nissen, Jinna Choi, Vichet Hem, Victor Sapojnikov, Robert G. Smith, Tatiana A. Tatusova, Charlie Xiang, Andrey Zherikov, Michael DiCuccio, Terence D. Murphy, Kim D. Pruitt, Avi Kimchi:
  Assembly: a resource for assembled genomes at NCBI. 73-80
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  Robert Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler:
  The Dfam database of repetitive DNA families. 81-89
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  Jörg Fallmann, Vitaly Sedlyarov, Andrea Tanzer, Pavel Kovarik, Ivo L. Hofacker:
  AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements. 90-95
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  Aline Dousse, Thomas Junier, Evgeny M. Zdobnov:
  CEGA - a catalog of conserved elements from genomic alignments. 96-100
• 
  Michal Chorev, Lotem Guy, Liran Carmel:
  JuncDB: an exon-exon junction database. 101-109
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  Anthony Mathelier, Oriol Fornes, David J. Arenillas, Chih-Yu Chen, Grégoire Denay, Jessica J. Y. Lee, Wenqiang Shi, Casper Shyr, Ge Tan, Rebecca Worsley-Hunt, Allen W. Zhang, François Parcy, Boris Lenhard, Albin Sandelin, Wyeth W. Wasserman:
  JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. 110-115
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  Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Anastasiia V. Soboleva, Artem S. Kasianov, Haitham Ashoor, Wail Ba-alawi, Vladimir B. Bajic, Yulia A. Medvedeva, Fedor A. Kolpakov, Vsevolod J. Makeev:
  HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. 116-125
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  Robert Lesurf, Kelsy C. Cotto, Grace Wang, Malachi Griffith, Katayoon Kasaian, Steven J. M. Jones, Stephen B. Montgomery, Obi L. Griffith:
  ORegAnno 3.0: a community-driven resource for curated regulatory annotation. 126-132
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  Socorro Gama-Castro, Heladia Salgado, Alberto Santos-Zavaleta, Daniela Ledezma-Tejeida, Luis Muñiz-Rascado, Jair Santiago García-Sotelo, Kevin Alquicira-Hernández, Irma Martínez-Flores, Lucia Pannier, Jaime Abraham Castro-Mondragón, Alejandra Medina-Rivera, Hilda Solano-Lira, César Bonavides-Martínez, Ernesto Pérez-Rueda, Shirley Alquicira-Hernández, Liliana Porrón-Sotelo, Alejandra López-Fuentes, Anastasia Hernández-Koutoucheva, Victor del Moral-Chávez, Fabio Rinaldi, Julio Collado-Vides:
  RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. 133-143
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  Olga Zanegina, Dmitry D. Kirsanov, Eugene Baulin, Anna S. Karyagina, Andrei Alexeevski, Sergei A. Spirin:
  An updated version of NPIDB includes new classifications of DNA-protein complexes and their families. 144-153
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  Fengbiao Mao, Luoyuan Xiao, Xianfeng Li, Jialong Liang, Huajing Teng, Wanshi Cai, Zhongsheng Sun:
  RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins. 154-163
• 
  Aziz Khan, Xuegong Zhang:
  dbSUPER: a database of super-enhancers in mouse and human genome. 164-171
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  Yanjun Wei, Shumei Zhang, Shipeng Shang, Bin Zhang, Song Li, Xinyu Wang, Fang Wang, Jianzhong Su, Qiong Wu, Hongbo Liu, Yan Zhang:
  SEA: a super-enhancer archive. 172-179
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  Maciej Szymanski, Andrzej Zielezinski, Jan Barciszewski, Volker A. Erdmann, Wojciech M. Karlowski:
  5SRNAdb: an information resource for 5S ribosomal RNAs. 180-183
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  Patricia P. Chan, Todd M. Lowe:
  GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. 184-189
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  Georgios K. Georgakilas, Ioannis S. Vlachos, Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ilias Kanellos, Panayiotis Tsanakas, Dimitris Dellis, Athanasios Fevgas, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
  DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. 190-195
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  Ling-Ling Zheng, Jun-Hao Li, Jie Wu, Wen-Ju Sun, Shun Liu, Ze-Lin Wang, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu:
  deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. 196-202
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  Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q. Zhang, Runsheng Chen:
  NONCODE 2016: an informative and valuable data source of long non-coding RNAs. 203-208
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  Yu-Chen Liu, Jianrong Li, Chuan-Hu Sun, Erik Andrews, Rou-Fang Chao, Feng-Mao Lin, Shun-Long Weng, Sheng-Da Hsu, Chieh-Chen Huang, Chao Cheng, Chun-Chi Liu, Hsien-Da Huang:
  CircNet: a database of circular RNAs derived from transcriptome sequencing data. 209-215
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  Yuk Yee Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, Li-San Wang:
  DASHR: database of small human noncoding RNAs. 216-222
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  David Rosenkranz:
  piRNA cluster database: a web resource for piRNA producing loci. 223-230
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  Maria D. Paraskevopoulou, Ioannis S. Vlachos, Dimitra Karagkouni, Georgios K. Georgakilas, Ilias Kanellos, Thanasis Vergoulis, Konstantinos Zagganas, Panayiotis Tsanakas, Evangelos Floros, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
  DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. 231-238
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  Chih-Hung Chou, Nai-Wen Chang, Sirjana Shrestha, Sheng-Da Hsu, Yu-Ling Lin, Wei-Hsiang Lee, Chi-Dung Yang, Hsiao-Chin Hong, Ting-Yen Wei, Siang-Jyun Tu, Tzi-Ren Tsai, Shu-Yi Ho, Ting-Yan Jian, Hsin-Yi Wu, Pin-Rong Chen, Nai-Chieh Lin, Hsin-Tzu Huang, Tzu-Ling Yang, Chung-Yuan Pai, Chun-San Tai, Wen-Liang Chen, Chia-Yen Huang, Chun-Chi Liu, Shun-Long Weng, Kuang-Wen Liao, Wen-Lian Hsu, Hsien-Da Huang:
  miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. 239-247
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  Jiang Wang, Tao Liu, Bo Zhao, Qixuan Lu, Zheng Wang, Yuan Cao, Wuju Li:
  sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria. 248-253
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  Shang-Qian Xie, Peng Nie, Yan Wang, Hongwei Wang, Hongyu Li, Zhilong Yang, Yizhi Liu, Jian Ren, Zhi Xie:
  RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling. 254-258
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  Wen-Ju Sun, Jun-Hao Li, Shun Liu, Jie Wu, Hui Zhou, Liang-Hu Qu, Jian-Hua Yang:
  RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data. 259-265
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  Sri Devan Appasamy, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus Raih:
  InterRNA: a database of base interactions in RNA structures. 266-271
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  Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codó, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Josep Ramón Goñi, Modesto Orozco, Josep Lluis Gelpí:
  BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. 272-278

Protein sequence and structure, motifs, and domains

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  Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John G. Tate, Alex Bateman:
  The Pfam protein families database: towards a more sustainable future. 279-285
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  Jaime Huerta-Cepas, Damian Szklarczyk, Kristoffer Forslund, Helen Cook, Davide Heller, Mathias C. Walter, Thomas Rattei, Daniel R. Mende, Shinichi Sunagawa, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, Peer Bork:
  eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. 286-293
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  Holger Dinkel, Kim Van Roey, Sushama Michael, Manjeet Kumar, Bora Uyar, Brigitte Altenberg, Vladislava Milchevskaya, Melanie Schneider, Helen Kühn, Annika Behrendt, Sophie Luise Dahl, Victoria Damerell, Sandra Diebel, Sara Kalman, Steffen Klein, Arne C. Knudsen, Christina Mäder, Sabina Merrill, Angelina Staudt, Vera Thiel, Lukas Welti, Norman E. Davey, Francesca Diella, Toby J. Gibson:
  ELM 2016 - data update and new functionality of the eukaryotic linear motif resource. 294-300
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  Zejun Zheng, Alexander Goncearenco, Igor N. Berezovsky:
  Nucleotide binding database NBDB - a collection of sequence motifs with specific protein-ligand interactions. 301-307
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  Rhonald C. Lua, Stephen J. Wilson, Daniel M. Konecki, Angela D. Wilkins, Eric Venner, Daniel H. Morgan, Olivier Lichtarge:
  UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. 308-312
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  Chunlei Wu, Xuefeng Jin, Ginger Tsueng, Cyrus Afrasiabi, Andrew I. Su:
  BioGPS: building your own mash-up of gene annotations and expression profiles. 313-316
• 
  Ian Sillitoe, Nicholas Furnham:
  FunTree: advances in a resource for exploring and contextualising protein function evolution. 317-323
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  Volodimir Olexiouk, Jeroen Crappé, Steven Verbruggen, Kenneth Verheggen, Lennart Martens, Gerben Menschaert:
  sORFs.org: a repository of small ORFs identified by ribosome profiling. 324-329
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  Yi-Chien Chang, Zhenjun Hu, John Rachlin, Brian P. Anton, Simon Kasif, Richard J. Roberts, Martin Steffen:
  COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. 330-335
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  Huaiyu Mi, Sagar Poudel, Anushya Muruganujan, John T. Casagrande, Paul D. Thomas:
  PANTHER version 10: expanded protein families and functions, and analysis tools. 336-342
• 
  Neil D. Rawlings, Alan J. Barrett, Robert D. Finn:
  Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. 343-350
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  José G. Pérez-Silva, Yaiza Español, Gloria Velasco, Víctor Quesada:
  The Degradome database: expanding roles of mammalian proteases in life and disease. 351-355
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  Vignir Ísberg, Stefan Mordalski, Christian Munk, Krzysztof Rataj, Kasper Harpsøe, Alexander S. Hauser, Bas Vroling, Andrzej J. Bojarski, Gert Vriend, David E. Gloriam:
  GPCRdb: an information system for G protein-coupled receptors. 356-364
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  Albert J. Kooistra, Georgi K. Kanev, Oscar P. J. van Linden, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
  KLIFS: a structural kinase-ligand interaction database. 365-371
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  Milton H. Saier Jr., Vamsee S. Reddy, Brian V. Tsu, Muhammad Saad Ahmed, Chun Li, Gabriel Moreno-Hagelsieb:
  The Transporter Classification Database (TCDB): recent advances. 372-379
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  Damian Szklarczyk, Alberto Santos, Christian von Mering, Lars Juhl Jensen, Peer Bork, Michael Kuhn:
  STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. 380-384
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  Sameer Velankar, Glen van Ginkel, Younes Alhroub, Gary M. Battle, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Ingvar C. Lagerstedt, Saqib Mir, Manuel A. Fernandez Montecelo, Abhik Mukhopadhyay, Thomas J. Oldfield, Ardan Patwardhan, Eduardo Sanz-García, Sanchayita Sen, Robert A. Slowley, Michael E. Wainwright, Mandar S. Deshpande, Andrii Iudin, Gaurav Sahni, José Salavert Torres, Miriam Hirshberg, Lora Mak, Nurul Nadzirin, David R. Armstrong, Alice R. Clark, Oliver S. Smart, Paul K. Korir, Gerard J. Kleywegt:
  PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. 385-395
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  Catherine L. Lawson, Ardan Patwardhan, Matthew L. Baker, Corey Hryc, Eduardo Sanz-García, Brian P. Hudson, Ingvar C. Lagerstedt, Steven J. Ludtke, Grigore Pintilie, Raul Sala, John D. Westbrook, Helen M. Berman, Gerard J. Kleywegt, Wah Chiu:
  EMDataBank unified data resource for 3DEM. 396-403
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  Su Datt Lam, Natalie L. Dawson, Sayoni Das, Ian Sillitoe, Paul Ashford, David A. Lee, Sonja Lehtinen, Christine A. Orengo, Jonathan G. Lees:
  Gene3D: expanding the utility of domain assignments. 404-409
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  Arumugam Gandhimathi, Pritha Ghosh, Sridhar Hariharaputran, Oommen K. Mathew, Ramanathan Sowdhamini:
  PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. 410-414
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  Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang, Ivet Bahar:
  iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. 415-422
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  Thomas Hrabe, Zhanwen Li, Mayya Sedova, Piotr Rotkiewicz, Lukasz Jaroszewski, Adam Godzik:
  PDBFlex: exploring flexibility in protein structures. 423-428
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  Rita Pancsa, Mihaly Varadi, Peter Tompa, Wim F. Vranken:
  Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. 429-434
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  Kai-Yao Huang, Min-Gang Su, Hui-Ju Kao, Yun-Chung Hsieh, Jhih-Hua Jhong, Kuang-Hao Cheng, Hsien-Da Huang, Tzong-Yi Lee:
  dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. 435-446
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  Juan Antonio Vizcaíno, Attila Csordas, Noemi del-Toro, José A. Dianes, Johannes Griss, Ilias Lavidas, Gerhard Mayer, Yasset Pérez-Riverol, Florian Reisinger, Tobias Ternent, Qing-Wei Xu, Rui Wang, Henning Hermjakob:
  2016 update of the PRIDE database and its related tools. 447-456

Metabolic and signalling pathways, enzymes

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  Minoru Kanehisa, Yoko Sato, Masayuki Kawashima, Miho Furumichi, Mao Tanabe:
  KEGG as a reference resource for gene and protein annotation. 457-462
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  Manish Sud, Eoin Fahy, Dawn Cotter, Kenan Azam, Ilango Vadivelu, Charles F. Burant, Arthur Edison, Oliver Fiehn, Richard M. Higashi, K. Sreekumaran Nair, Susan Sumner, Shankar Subramaniam:
  Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. 463-470
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  Ron Caspi, Richard Billington, Luciana Ferrer, Hartmut Foerster, Carol A. Fulcher, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne M. Paley, Pallavi Subhraveti, Daniel S. Weaver, Peter D. Karp:
  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. 471-480
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  Antonio Fabregat, Konstantinos Sidiropoulos, Phani V. Garapati, Marc Gillespie, Kerstin Hausmann, Robin Haw, Bijay Jassal, Steven Jupe, Florian Korninger, Sheldon J. McKay, Lisa Matthews, Bruce May, Marija Milacic, Karen Rothfels, Veronica Shamovsky, Marissa Webber, Joel Weiser, Mark Williams, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
  The Reactome pathway Knowledgebase. 481-487
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  Martina Kutmon, Anders Riutta, Nuno Nunes, Kristina Hanspers, Egon L. Willighagen, Anwesha Bohler, Jonathan Mélius, Andra Waagmeester, Sravanthi R. Sinha, Ryan A. Miller, Susan L. Coort, Elisa Cirillo, Bart Smeets, Chris T. A. Evelo, Alexander R. Pico:
  WikiPathways: capturing the full diversity of pathway knowledge. 488-494
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  Tanvir Sajed, Ana Marcu, Miguel Ramirez-Gaona, Allison Pon, An Chi Guo, Craig Knox, Michael Wilson, Jason R. Grant, Yannick Djoumbou, David S. Wishart:
  ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. 495-501
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  Jörg Wicker, Tim Lorsbach, Martin Gütlein, Emanuel Schmid, Diogo Latino, Stefan Kramer, Kathrin Fenner:
  enviPath - The environmental contaminant biotransformation pathway resource. 502-508
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  Dennis Klementz, Kersten Döring, Xavier Lucas, Kiran K. Telukunta, Anika Erxleben, Denise Deubel, Astrid Erber, Irene Santillana, Oliver S. Thomas, Andreas Bechthold, Stefan Günther:
  StreptomeDB 2.0 - an extended resource of natural products produced by streptomycetes. 509-514
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  Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis:
  BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. 515-522
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  Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan J. Bridge, Anne Morgat, Marco Pagni:
  MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. 523-526
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  Qiancheng Shen, Guanqiao Wang, Shuai Li, Xinyi Liu, Shaoyong Lu, Zhongjie Chen, Kun Song, Junhao Yan, Lv Geng, Zhimin Huang, Wenkang Huang, Guoqiang Chen, Jian Zhang:
  ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks. 527-535
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  Max Kotlyar, Chiara Pastrello, Nicholas Sheahan, Igor Jurisica:
  Integrated interactions database: tissue-specific view of the human and model organism interactomes. 536-541
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  Céline M. Labbé, Mélaine A. Kuenemann, Barbara Zarzycka, Gert Vriend, Gerry A. F. Nicolaes, David Lagorce, Maria A. Miteva, Bruno O. Villoutreix, Olivier Sperandio:
  iPPI-DB: an online database of modulators of protein-protein interactions. 542-547
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  Livia Perfetto, Leonardo Briganti, Alberto Calderone, Andrea Cerquone Perpetuini, Marta Iannuccelli, Francesca Langone, Luana Licata, Milica Marinkovic, Anna Mattioni, Theodora Pavlidou, Daniele Peluso, Lucia Lisa Petrilli, Stefano Pirrò, Daniela Posca, Elena Santonico, Alessandra Silvestri, Filomena Spada, Luisa Castagnoli, Gianni Cesareni:
  SIGNOR: a database of causal relationships between biological entities. 548-554
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  Erich J. Baker, Jason A. Bubier, Timothy Reynolds, Michael A. Langston, Elissa J. Chesler:
  GeneWeaver: data driven alignment of cross-species genomics in biology and disease. 555-559
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  Yoav D. Shaul, Bingbing Yuan, Prathapan Thiru, Andy Nutter-Upham, Scott McCallum, Carolyn Lanzkron, George W. Bell, David M. Sabatini:
  MERAV: a tool for comparing gene expression across human tissues and cell types. 560-566
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  Radek Szklarczyk, Wout Megchelenbrink, Pavel Cizek, Marie Ledent, Gonny Velemans, Damian Szklarczyk, Martijn A. Huynen:
  WeGET: predicting new genes for molecular systems by weighted co-expression. 567-573

Viruses, bacteria, protozoa and fungi

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  Paul Julian Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Jay C. Humphrey, Arnaud Kerhornou, Julia Khobova, Naveen K. Aranganathan, Nicholas Langridge, Ernesto Lowy-Gallego, Mark D. McDowall, Uma Maheswari, Michael Nuhn, Chuang Kee Ong, Bert Overduin, Michael Paulini, Helder Pedro, Emily Perry, Giulietta Spudich, Electra Tapanari, Brandon Walts, Gareth Williams, Marcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Doreen Ware, Daniel M. Bolser, Kevin L. Howe, Eugene Kulesha, Daniel Lawson, Gareth Maslen, Daniel M. Staines:
  Ensembl Genomes 2016: more genomes, more complexity. 574-580
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  Carola Söhngen, Adam Podstawka, Boyke Bunk, Dorothea Gleim, Anna Vetcininova, Lorenz Christian Reimer, Christian Ebeling, Cezar Pendarovski, Jörg Overmann:
  BacDive - The Bacterial Diversity Metadatabase in 2016. 581-585
• 
  Daniel Greuter, Alexander Loy, Matthias Horn, Thomas Rattei:
  probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016. 586-589
• 
  Andreas Wilke, Jared Bischof, Wolfgang Gerlach, Elizabeth M. Glass, Travis Harrison, Kevin P. Keegan, Tobias Paczian, William L. Trimble, Saurabh Bagchi, Ananth Grama, Somali Chaterji, Folker Meyer:
  The MG-RAST metagenomics database and portal in 2015. 590-594
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  Alex L. Mitchell, François Bucchini, Guy Cochrane, Hubert Denise, Petra ten Hoopen, Matthew Fraser, Sebastien Pesseat, Simon C. Potter, Maxim Scheremetjew, Peter Sterk, Robert D. Finn:
  EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data. 595-603
• 
  Samuel C. Forster, Hilary P. Browne, Nitin Kumar, Martin Hunt, Hubert Denise, Alex L. Mitchell, Robert D. Finn, Trevor D. Lawley:
  HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. 604-609
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  Hyeonsoo Jeong, Samsun Sung, Taehyung Kwon, Minseok Seo, Kelsey Caetano-Anollés, Sang Ho Choi, Seoae Cho, Arshan Nasir, Heebal Kim:
  HGTree: database of horizontally transferred genes determined by tree reconciliation. 610-619
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  Marco Moretto, Paolo Sonego, Nicolas Dierckxsens, Matteo Brilli, Luca Bianco, Daniela Ledezma-Tejeida, Socorro Gama-Castro, Marco Galardini, Chiara Romualdi, Kris Laukens, Julio Collado-Vides, Pieter Meysman, Kristof Engelen:
  COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. 620-623
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  Adil Salhi, Magbubah Essack, Aleksandar Radovanovic, Benoit Marchand, Salim Bougouffa, André Antunes, Marta Filipa Simões, Feras F. Lafi, Olaa A. Motwalli, Ameerah Bokhari, Tariq Malas, Soha Al Amoudi, Ghofran Othum, Intikhab Alam, Katsuhiko Mineta, Xin Gao, Robert Hoehndorf, John A. C. Archer, Takashi Gojobori, Vladimir B. Bajic:
  DESM: portal for microbial knowledge exploration systems. 624-633
• 
  Akanksha Rajput, Karambir Kaur, Manoj Kumar:
  SigMol: repertoire of quorum sensing signaling molecules in prokaryotes. 634-639
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  Keren Lasker, Jared M. Schrader, Yifei Men, Tyler Marshik, David L. Dill, Harley H. McAdams, Lucy Shapiro:
  CauloBrowser: A systems biology resource for Caulobacter crescentus. 640-645
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  Geoffrey L. Winsor, Emma J. Griffiths, Raymond Lo, Bhavjinder K. Dhillon, Julie A. Shay, Fiona S. L. Brinkman:
  Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. 646-653
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  Raphael H. Michna, Bingyao Zhu, Ulrike Mäder, Jörg Stülke:
  SubtiWiki 2.0 - an integrated database for the model organism Bacillus subtilis. 654-662
• 
  Michael A. Peabody, Matthew R. Laird, Caitlyn Vlasschaert, Raymond Lo, Fiona S. L. Brinkman:
  PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures. 663-668
• 
  Valerie Eichinger, Thomas Nussbaumer, Alexander Platzer, Marc-André Jehl, Roland Arnold, Thomas Rattei:
  EffectiveDB - updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. 669-674
• 
  Bharathi Reddy Kunduru, Sanjana Anilkumar Nair, Thenmalarchelvi Rathinavelan:
  EK3D: an E. coli K antigen 3-dimensional structure database. 675-681
• 
  Zhi Ruan, Ye Feng:
  BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. 682-687
• 
  Helder Pedro, Uma Maheswari, Martin Urban, Alistair George Irvine, Alayne Cuzick, Mark D. McDowall, Daniel M. Staines, Eugene Kulesha, Kim Elizabeth Hammond-Kosack, Paul Julian Kersey:
  PhytoPath: an integrative resource for plant pathogen genomics. 688-693
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