- 2012
- Pravech Ajawatanawong, Gemma Catherine Atkinson, Nathan S. Watson-Haigh, Bryony MacKenzie, Sandra L. Baldauf:
SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments. Nucleic Acids Res. 40(Web-Server-Issue): 340-347 (2012) - Rafael Alcántara, Kristian B. Axelsen, Anne Morgat, Eugeni Belda, Elisabeth Coudert, Alan J. Bridge, Hong Cao, Paula de Matos, Marcus Ennis, Steve Turner, Gareth I. Owen, Lydie Bougueleret, Ioannis Xenarios, Christoph Steinbeck:
Rhea - a manually curated resource of biochemical reactions. Nucleic Acids Res. 40(Database-Issue): 754-760 (2012) - Andrey Alexeyenko, Thomas Schmitt, Andreas Tjärnberg, Dimitri Guala, Oliver Frings, Erik L. L. Sonnhammer:
Comparative interactomics with Funcoup 2.0. Nucleic Acids Res. 40(Database-Issue): 821-828 (2012) - Alix Boc, Alpha Boubacar Diallo, Vladimir Makarenkov:
T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res. 40(Web-Server-Issue): 573-579 (2012) - Takayuki Amemiya, Ryotaro Koike, Akinori Kidera, Motonori Ota:
PSCDB: a database for protein structural change upon ligand binding. Nucleic Acids Res. 40(Database-Issue): 554-558 (2012) - Clara Amid, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Richard Gibson, Neil Goodgame, Christopher I. Hunter, Mikyung Jang, Rasko Leinonen, Xin Liu, Arnaud Oisel, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Stéphane Rivière, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Petra ten Hoopen, Daniel Vaughan, Robert Vaughan, Vadim Zalunin, Guy Cochrane:
Major submissions tool developments at the European nucleotide archive. Nucleic Acids Res. 40(Database-Issue): 43-47 (2012) - Praveen Anand, Kalidas Yeturu, Nagasuma R. Chandra:
PocketAnnotate: towards site-based function annotation. Nucleic Acids Res. 40(Web-Server-Issue): 400-408 (2012) - Ramu Anandakrishnan, Boris Aguilar, Alexey Onufriev:
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 40(Web-Server-Issue): 537-541 (2012) - Gerd Anders, Sebastian D. Mackowiak, Marvin Jens, Jonas Maaskola, Andreas Kuntzagk, Nikolaus Rajewsky, Markus Landthaler, Christoph Dieterich:
doRiNA: a database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res. 40(Database-Issue): 180-186 (2012) - Martha B. Arnaud, Gustavo C. Cerqueira, Diane O. Inglis, Marek S. Skrzypek, Jonathan Binkley, Marcus C. Chibucos, Jonathan Crabtree, Clinton Howarth, Joshua Orvis, Prachi Shah, Farrell Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock, Jennifer R. Wortman:
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Res. 40(Database-Issue): 653-659 (2012) - David Arndt, Jianguo Xia, Yifeng Liu, You Zhou, Anchi Guo, Joseph A. Cruz, Igor Sinelnikov, Karen Budwill, Camilla L. Nesbø, David S. Wishart:
METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res. 40(Web-Server-Issue): 88-95 (2012) - Panu Artimo, Manohar Jonnalagedda, Konstantin Arnold, Delphine Baratin, Gábor Csárdi, Edouard De Castro, Severine Duvaud, Volker Flegel, Arnaud Fortier, Elisabeth Gasteiger, Aurélien Grosdidier, Céline Hernandez, Vassilios Ioannidis, Dmitri Kuznetsov, Robin Liechti, Sébastien Moretti, Khaled Mostaguir, Nicole Redaschi, Grégoire Rossier, Ioannis Xenarios, Heinz Stockinger:
ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 40(Web-Server-Issue): 597-603 (2012) - Haim Ashkenazy, Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer, Tal Pupko:
FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res. 40(Web-Server-Issue): 580-584 (2012) - Greet De Baets, Joost J. J. van Durme, Joke Reumers, Sebastian Maurer-Stroh, Peter Vanhee, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau:
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res. 40(Database-Issue): 935-939 (2012) - Preeti Bais, Stephanie M. Moon-Quanbeck, Basil J. Nikolau, Julie A. Dickerson:
Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics - database and tools update. Nucleic Acids Res. 40(Database-Issue): 1216-1220 (2012) - Erich J. Baker, Jeremy J. Jay, Jason A. Bubier, Michael A. Langston, Elissa J. Chesler:
GeneWeaver: a web-based system for integrative functional genomics. Nucleic Acids Res. 40(Database-Issue): 1067-1076 (2012) - Amita Barik, Abhishek Mishra, Ranjit Prasad Bahadur:
PRince: a web server for structural and physicochemical analysis of Protein-RNA interface. Nucleic Acids Res. 40(Web-Server-Issue): 440-444 (2012) - Tanya Barrett, Karen Clark, Robert Gevorgyan, Vyatcheslav Gorelenkov, Eugene Gribov, Ilene Karsch-Mizrachi, Michael Kimelman, Kim D. Pruitt, Sergei Resenchuk, Tatiana A. Tatusova, Eugene Yaschenko, James Ostell:
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res. 40(Database-Issue): 57-63 (2012) - Gary Benson:
Editorial. Nucleic Acids Res. 40(Web-Server-Issue): 1-2 (2012) - Dennis A. Benson, Ilene Karsch-Mizrachi, Karen Clark, David J. Lipman, James Ostell, Eric W. Sayers:
GenBank. Nucleic Acids Res. 40(Database-Issue): 48-53 (2012) - Karel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka:
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40(Web-Server-Issue): 222-227 (2012) - Aadil H. Bhat, Homchoru Mondal, Jagat Singh Chauhan, Gajendra P. S. Raghava, Amrish Methi, Alka Rao:
ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins. Nucleic Acids Res. 40(Database-Issue): 388-393 (2012) - Dexi Bi, Zhen Xu, Ewan M. Harrison, Cui Tai, Yiqing Wei, Xinyi He, Shiru Jia, Zixin Deng, Kumar Rajakumar, Hong-Yu Ou:
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res. 40(Database-Issue): 621-626 (2012) - Dawid Bielewicz, Jakub Dolata, Andrzej Zielezinski, Sylwia Alaba, Bogna Szarzynska, Michal Wojciech Szczesniak, Artur Jarmolowski, Zofia Szweykowska-Kulinska, Wojciech M. Karlowski:
mirEX: a platform for comparative exploration of plant pri-miRNA expression data. Nucleic Acids Res. 40(Database-Issue): 191-197 (2012) - Andrea Bisognin, Gabriele Sales, Alessandro Coppe, Stefania Bortoluzzi, Chiara Romualdi:
MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Res. 40(Web-Server-Issue): 13-21 (2012) - Marta Bleda, Ignacio Medina, Roberto Alonso, Alejandro de María, Francisco Salavert, Joaquín Dopazo:
Inferring the regulatory network behind a gene expression experiment. Nucleic Acids Res. 40(Web-Server-Issue): 168-172 (2012) - Marta Bleda, Joaquín Tárraga, Alejandro de María, Francisco Salavert, Luz Garcia-Alonso, Matilde Celma, Ainoha Martín, Joaquín Dopazo, Ignacio Medina:
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res. 40(Web-Server-Issue): 609-614 (2012) - Carl G. de Boer, Timothy R. Hughes:
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res. 40(Database-Issue): 169-179 (2012) - Dan M. Bolser, Pierre-Yves Chibon, Nicolas Palopoli, Sungsam Gong, Daniel Jacob, Victoria Dominguez Del Angel, Daniel Swan, Sebastian Bassi, Virginia González, Prashanth Suravajhala, Seungwoo Hwang, Paolo Romano, Rob Edwards, Bryan Bishop, John Eargle, Timur Shtatland, Nicholas J. Provart, Dave Clements, Daniel P. Renfro, Daeui Park, Jong Bhak:
MetaBase - the wiki-database of biological databases. Nucleic Acids Res. 40(Database-Issue): 1250-1254 (2012) - Stephen R. Bond, Christian C. Naus:
RF-Cloning.org: an online tool for the design of restriction-free cloning projects. Nucleic Acids Res. 40(Web-Server-Issue): 209-213 (2012)