- Rosalind J. Cutts, Abu Z. Dayem Ullah, Ajanthah Sangaralingam, Emanuela Gadaleta, Nicholas R. Lemoine, Claude Chelala:
O-miner: an integrative platform for automated analysis and mining of -omics data. Nucleic Acids Res. 40(Web-Server-Issue): 560-568 (2012) - Matteo D'Antonio, Vera Pendino, Shruti Sinha, Francesca D. Ciccarelli:
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes. Nucleic Acids Res. 40(Database-Issue): 978-983 (2012) - Sudhansu Dash, John L. Van Hemert, Lu Hong, Roger P. Wise, Julie A. Dickerson:
PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Res. 40(Database-Issue): 1194-1201 (2012) - Emily C. Dimmer, Rachael P. Huntley, Yasmin Alam-Faruque, Tony Sawford, Claire O'Donovan, Maria Jesus Martin, Benoit Bely, Paul Browne, Wei Mun Chan, Ruth Y. Eberhardt, Michael Gardner, Kati Laiho, Duncan Legge, Michele Magrane, Klemens Pichler, Diego Poggioli, Harminder Sehra, Andrea H. Auchincloss, Kristian B. Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi-Quintaje, Lionel Breuza, Alan J. Bridge, Elisabeth Coudert, Anne Estreicher, Maria Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Lydie Bougueleret, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek-Roggli, Ioannis Xenarios, Rolf Apweiler:
The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 40(Database-Issue): 565-570 (2012) - Holger Dinkel, Sushama Michael, Robert J. Weatheritt, Norman E. Davey, Kim Van Roey, Brigitte Altenberg, Grischa Toedt, Bora Uyar, Markus Seiler, Aidan Budd, Lisa Jödicke, Marcel A. Dammert, Christian Schroeter, Maria Hammer, Tobias Schmidt, Peter Jehl, Caroline McGuigan, Magdalena Dymecka, Claudia Chica, Katja Luck, Allegra Via, Andrew Chatr-aryamontri, Niall J. Haslam, Gleb Grebnev, Richard J. Edwards, Michel O. Steinmetz, Heike Meiselbach, Francesca Diella, Toby J. Gibson:
ELM - the database of eukaryotic linear motifs. Nucleic Acids Res. 40(Database-Issue): 242-251 (2012) - Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister:
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 40(Database-Issue): 519-524 (2012) - Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. VanDyk, Adam J. Bogdanove:
TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res. 40(Web-Server-Issue): 117-122 (2012) - Timothy R. Dreszer, Donna Karolchik, Ann S. Zweig, Angie S. Hinrichs, Brian J. Raney, Robert M. Kuhn, Laurence R. Meyer, Matthew C. Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke L. Rhead, Andy Pohl, Venkat S. Malladi, Chin H. Li, Katrina Learned, Vanessa Kirkup, Fan Hsu, Rachel A. Harte, Luvina Guruvadoo, Mary Goldman, Belinda Giardine, Pauline A. Fujita, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent:
The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 40(Database-Issue): 918-923 (2012) - Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res. 40(Database-Issue): 881-886 (2012) - Guilhem Faure, Jessica Andreani, Raphaël Guérois:
InterEvol database: exploring the structure and evolution of protein complex interfaces. Nucleic Acids Res. 40(Database-Issue): 847-856 (2012) - Scott Federhen:
The NCBI Taxonomy database. Nucleic Acids Res. 40(Database-Issue): 136-143 (2012) - Robert D. Finn, Paul P. Gardner, Alex Bateman:
Making your database available through Wikipedia: the pros and cons. Nucleic Acids Res. 40(Database-Issue): 9-12 (2012) - Marc Fiume, Eric J. M. Smith, Andrew Brook, Dario Strbenac, Brian Turner, Aziz M. Mezlini, Mark D. Robinson, Shoshana J. Wodak, Michael Brudno:
Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res. 40(Web-Server-Issue): 615-621 (2012) - Avi I. Flamholz, Elad Noor, Arren Bar-Even, Ron Milo:
eQuilibrator - the biochemical thermodynamics calculator. Nucleic Acids Res. 40(Database-Issue): 770-775 (2012) - Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Monika Komorowska, Gautier Koscielny, Eugene Kulesha, Pontus Larsson, Ian Longden, William M. McLaren, Matthieu Muffato, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Y. Amy Tang, Kieron R. Taylor, Stephen J. Trevanion, Jana Vandrovcova, Simon White, Mark Wilson, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates, Amonida Zadissa, Stephen M. J. Searle:
Ensembl 2012. Nucleic Acids Res. 40(Database-Issue): 84-90 (2012) - Ian Flockhart, Matthew Booker, Yanhui Hu, Benjamin McElvany, Quentin Gilly, Bernard Mathey-Prevot, Norbert Perrimon, Stephanie E. Mohr:
FlyRNAi.org - the database of the Drosophila RNAi screening center: 2012 update. Nucleic Acids Res. 40(Database-Issue): 715-719 (2012) - Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Seiko D. Murakami, Takayuki Amemiya, Kazuo Hosoda, Ryotaro Koike, Hidekazu Hiroaki, Motonori Ota:
IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. Nucleic Acids Res. 40(Database-Issue): 507-511 (2012) - Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Syed Asad Rahman, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton:
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Res. 40(Database-Issue): 776-782 (2012) - Razif R. Gabdoulline, Denitsa Eckweiler, Alexander E. Kel, Philip Stegmaier:
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. Nucleic Acids Res. 40(Web-Server-Issue): 180-185 (2012) - Michael Y. Galperin, Xosé M. Fernández-Suárez:
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res. 40(Database-Issue): 1-8 (2012) - Arumugam Gandhimathi, Anu G. Nair, Ramanathan Sowdhamini:
PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies. Nucleic Acids Res. 40(Database-Issue): 531-534 (2012) - Javier García-García, Sylvia Schleker, Judith Klein-Seetharaman, Baldo Oliva:
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. Nucleic Acids Res. 40(Web-Server-Issue): 147-151 (2012) - Anna Gaulton, Louisa J. Bellis, A. Patrícia Bento, Jon Chambers, Mark Davies, Anne Hersey, Yvonne Light, Shaun McGlinchey, David Michalovich, Bissan Al-Lazikani, John P. Overington:
ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 40(Database-Issue): 1100-1107 (2012) - Jane E. Mabey Gilsenan, John Cooley, Paul Bowyer:
CADRE: the Central Aspergillus Data REpository 2012. Nucleic Acids Res. 40(Database-Issue): 660-666 (2012) - Yana Gofman, Turkan Haliloglu, Nir Ben-Tal:
Monte Carlo simulations of peptide-membrane interactions with the MCPep web server. Nucleic Acids Res. 40(Web-Server-Issue): 358-363 (2012) - Benjamin M. Good, Erik L. Clarke, Luca de Alfaro, Andrew I. Su:
The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res. 40(Database-Issue): 1255-1261 (2012) - David M. Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D. Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas H. Putnam, Daniel S. Rokhsar:
Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40(Database-Issue): 1178-1186 (2012) - Mikhail Gostev, Adam Faulconbridge, Marco Brandizi, Julio Fernandez-Banet, Ugis Sarkans, Alvis Brazma, Helen E. Parkinson:
The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res. 40(Database-Issue): 64-70 (2012) - Saulius Grazulis, Adriana Daskevic, Andrius Merkys, Daniel Chateigner, Luca Lutterotti, Miguel Quirós, Nadezhda R. Serebryanaya, Peter Moeck, Robert T. Downs, Armel Le Bail:
Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration. Nucleic Acids Res. 40(Database-Issue): 420-427 (2012) - Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David M. Goodstein, Alan Kuo, Simon Minovitsky, Roman Nikitin, Robin A. Ohm, Robert Otillar, Alexander Poliakov, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak:
The Genome Portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 40(Database-Issue): 26-32 (2012)