Bioinformatics

Bioinformatics

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301-320 of 384 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.11718.1
Opinion Article metrics
Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action
[version 1; peer review: 3 approved]
Aleksandra Pawlik, Celia W.G. van Gelder, Aleksandra Nenadic, Patricia M. Palagi, Eija Korpelainen, Philip Lijnzaad, Diana Marek, Susanna-Assunta Sansone, John Hancock, Carole Goble
Peer Reviewers Erin A. Becker; Anelda P. van der Walt and Juan Steyn; Laurent Gatto
  • Funders
  • Horizon 2020
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 03 Jul 2017
https://doi.org/10.12688/f1000research.9416.3
Research Article metrics
Revised
Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics
[version 3; peer review: 1 approved, 2 approved with reservations]
Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Peer Reviewers Antonio Rosato; Robert D. Finn; David M. Kristensen
LATEST VERSION PUBLISHED 27 Jun 2017
https://doi.org/10.12688/f1000research.11588.1
Editorial metrics NOT PEER REVIEWED
2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11587.1
Editorial metrics NOT PEER REVIEWED
2017 Outstanding Contributions to ISCB Award: Fran Lewitter
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11586.1
Editorial metrics NOT PEER REVIEWED
2017 ISCB Overton Prize: Christoph Bock
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11585.1
Editorial metrics NOT PEER REVIEWED
2017 ISCB Innovator Award: Aviv Regev
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11837.1
Opinion Article metrics
ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR
[version 1; peer review: 4 approved, 1 approved with reservations]
L. Larcombe, R. Hendricusdottir, T.K. Attwood, F. Bacall, N. Beard, L.J. Bellis, W.B. Dunn, J.M. Hancock, A. Nenadic, C. Orengo, B. Overduin, S-A Sansone, M. Thurston, M.R. Viant, C.L. Winder, C.A. Goble, C.P. Ponting, G. Rustici
Peer Reviewers Michelle D. Brazas; Patricia M. Palagi; Celia W.G. van Gelder; Nicola J. Mulder; Manuel Corpas
  • Funders
  • Horizon 2020
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 21 Jun 2017
https://doi.org/10.12688/f1000research.11407.1
Opinion Article metrics
Four simple recommendations to encourage best practices in research software
[version 1; peer review: 3 approved]
Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch
Peer Reviewers Roberto Di Cosmo; Gregory V. Wilson; Stefanie Betz
  • Funders
  • ELIXIR-EXCELERATE
  • EMBL-ABR
  • Netherlands eScience Center
  • CORBEL
  • Software Sustainability Institute
PUBLISHED 13 Jun 2017
https://doi.org/10.12688/f1000research.11751.1
Opinion Article metrics
A community proposal to integrate proteomics activities in ELIXIR
[version 1; peer review: 2 approved]
Juan Antonio Vizcaíno, Mathias Walzer, Rafael C. Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J.R. Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit Schwämmle, Dirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek, Martin Eisenacher, Lennart Martens, Oliver Kohlbacher
Peer Reviewers Felix Elortza; Chuming Chen
  • Funder
  • Horizon 2020
PUBLISHED 13 Jun 2017
https://doi.org/10.12688/f1000research.9417.3
Research Note metrics
Revised
Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Biochemically-inspired Machine Learning
[version 3; peer review: 2 approved]
Eliseos J. Mucaki, Katherina Baranova, Huy Q. Pham, Iman Rezaeian, Dimo Angelov, Alioune Ngom, Luis Rueda, Peter K. Rogan
Peer Reviewers Elana J. Fertig; Chun-Wei Tung
LATEST VERSION PUBLISHED 12 May 2017
https://doi.org/10.12688/f1000research.11290.1
Research Article metrics
Gene length and detection bias in single cell RNA sequencing protocols
[version 1; peer review: 4 approved]
Belinda Phipson, Luke Zappia, Alicia Oshlack
Peer Reviewers Charlotte Soneson;  Samuel W. Lukowski; Wolfgang Huber; Sam Buckberry and Timothy Stuart
  • Funders
  • National Health and Medical Research Council
  • Australian Federal Government
PUBLISHED 28 Apr 2017
https://doi.org/10.12688/f1000research.10041.1
Software Tool Article metrics
Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data
[version 1; peer review: 2 approved, 1 approved with reservations]
Delasa Aghamirzaie, Karthik Raja Velmurugan, Shuchi Wu, Doaa Altarawy, Lenwood S. Heath, Ruth Grene
Peer Reviewers Nicholas J. Provart; Asa Ben-Hur; Sakiko Okumoto
  • Funder
  • National Science Foundation
PUBLISHED 28 Mar 2017
https://doi.org/10.12688/f1000research.10473.2
Method Article metrics
Revised
An open and transparent process to select ELIXIR Node Services as implemented by ELIXIR-UK
[version 2; peer review: 2 approved, 1 approved with reservations]
John M. Hancock, Alf Game, Chris P. Ponting, Carole A. Goble
Peer Reviewers Christine Durinx; Alfonso Valencia; Janet Kelso
  • Funders
  • Medical Research Council
  • Natural Environment Research Council
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 20 Mar 2017
https://doi.org/10.12688/f1000research.10529.2
Research Article metrics
Revised
Systematic assessment of multi-gene predictors of pan-cancer cell line sensitivity to drugs exploiting gene expression data
[version 2; peer review: 2 approved]
Linh Nguyen, Cuong C Dang, Pedro J. Ballester
Peer Reviewers Marc Poirot; Ronnie Alves
  • Funders
  • Vietnam National International Development
  • A*MIDEX
LATEST VERSION PUBLISHED 14 Mar 2017
https://doi.org/10.12688/f1000research.9656.2
Method Article metrics
Revised
Identifying ELIXIR Core Data Resources
[version 2; peer review: 2 approved]
Christine Durinx, Jo McEntyre, Ron Appel, Rolf Apweiler, Mary Barlow, Niklas Blomberg, Chuck Cook, Elisabeth Gasteiger, Jee-Hyub Kim, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Alfonso Valencia
Peer Reviewers Helen M. Berman; Maryann E. Martone
LATEST VERSION PUBLISHED 09 Mar 2017
https://doi.org/10.12688/f1000research.8290.2
Software Tool Article metrics
Revised
dbVar structural variant cluster set for data analysis and variant comparison
[version 2; peer review: 2 approved]
Lon Phan, Jeffrey Hsu, Le Quang Minh Tri, Michaela Willi, Tamer Mansour, Yan Kai, John Garner, John Lopez, Ben Busby
Peer Reviewers Lihua Julie Zhu; Justin M. Zook
LATEST VERSION PUBLISHED 28 Feb 2017
https://doi.org/10.12688/f1000research.10114.3
Research Note metrics
Revised
Optimal threshold estimation for binary classifiers using game theory
[version 3; peer review: 3 approved]
Ignacio Enrique Sanchez
Peer Reviewers Pieter Meysman; Luis Diambra; Marcel Brun and Arjen ten Have
LATEST VERSION PUBLISHED 08 Feb 2017
https://doi.org/10.12688/f1000research.10443.1
Method Article metrics
ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
[version 1; peer review: 1 approved, 2 approved with reservations]
Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen
Peer Reviewers Marla I. Trindade and Leonardo van Zyl; Takashi Gojobori; Anders Blomberg
  • Funders
  • ELIXIR
  • EMBL-EBI
  • Universitetet i Tromsø
PUBLISHED 23 Jan 2017
https://doi.org/10.12688/f1000research.9909.1
Software Tool Article metrics
The PathLinker app: Connect the dots in protein interaction networks
[version 1; peer review: 1 approved, 2 approved with reservations]
Daniel P. Gil, Jeffrey N. Law, T. M. Murali
Peer Reviewers Barry Demchak; Tamás Korcsmáros and David Fazekas; Stefan Wuchty
  • Funders
  • National Institutes of Health
  • National Science Foundation
PUBLISHED 20 Jan 2017
https://doi.org/10.12688/f1000research.8923.2
Software Tool Article metrics
Revised
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
[version 2; peer review: 1 approved, 2 approved with reservations]
Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Peer Reviewers Kyle Ellrott; Elena Papaleo; Charlotte Soneson
LATEST VERSION PUBLISHED 28 Dec 2016
301-320 of 384 ARTICLES
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  • Methods and Tools
    The Methods and Tools Gateway Area will allow researchers to publish outputs concerning both the application and research into the use of various computational methods to analyse quantities of biological data for a range of different results, including predictions and discoveries. Read more keyboard_arrow_right
  • Genetics and Genomics
    The Genetics & Genomics Gateway Area will enable researchers to publish content related to the analysis, storage and accessibility of DNA, RNA and protein sequences. This analysis can be conducted in a variety of ways, including comparison of sequences and relationships, identification of functions, and recognition of patterns across the samples. Read more keyboard_arrow_right
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    By curating all outputs related to the analysis of the RNA transcripts produced by a genotype, the Transcriptomics Gateway Area will allow readers to easily access content pertinent to this research. Read more keyboard_arrow_right
  • Proteomics
    The Proteomics Gateway Area has been established to allow authors to access and publish research content related to the large-scale study of entire sets of proteins as proteomes. Read more keyboard_arrow_right
  • Metagenomics
    This Gateway Area will allow members of the bioinformatics community to collate all research related to the collection of genomes from an environmental sample. Read more keyboard_arrow_right
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