Bioinformatics

Bioinformatics

track_changes Track Tracking Be alerted when new articles are added in this gateway (manage your tracking alerts via your account) Stop tracking this gateway
Home Gateways Bioinformatics
261-280 of 384 ARTICLES
Previous Next
 in 
https://doi.org/10.12688/f1000research.16338.1
Software Tool Article metrics
An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays
[version 1; peer review: 2 approved]
Clarence K. Mah, Jill P. Mesirov, Lukas Chavez
Peer Reviewers Robert  Ivanek; Aris Floratos
  • Funder
  • National Institutes of Health
PUBLISHED 05 Dec 2018
https://doi.org/10.12688/f1000research.16301.2
Software Tool Article metrics
Revised
Increasing workflow development speed and reproducibility with Vectools
[version 2; peer review: 2 approved]
Tyler Weirick, Raphael Müller, Shizuka Uchida
Peer Reviewers Yutaka Saito; Dimitar Vassilev
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Gheens Foundation
  • University of Louisville
LATEST VERSION PUBLISHED 23 Oct 2018
https://doi.org/10.12688/f1000research.16605.1
Software Tool Article metrics
KnetMaps: a BioJS component to visualize biological knowledge networks
[version 1; peer review: 3 approved, 1 approved with reservations]
Ajit Singh, Christopher J. Rawlings, Keywan Hassani-Pak
Peer Reviewers Ian Dunham and Gareth Peat; Chia-Yi Cheng; Nicholas J. Provart; Ramil Mauleon
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 17 Oct 2018
https://doi.org/10.12688/f1000research.16290.1
Method Article metrics
A unified GenomeSpace recipe to identify essential genes and associated subnetworks from Genome-Scale CRISPR-Cas9 knockout screens
[version 1; peer review: 2 approved with reservations]
Daniel E. Carlin, Forrest Kim, Trey Ideker, Jill P. Mesirov
Peer Reviewers Shouhong Guang; Xiaowei Wang
  • Funder
  • National Human Genome Research Institute
PUBLISHED 12 Oct 2018
https://doi.org/10.12688/f1000research.16415.1
Method Article metrics
Large-scale protein function prediction using heterogeneous ensembles
[version 1; peer review: 2 approved]
Linhua Wang, Jeffrey Law, Shiv D. Kale, T. M. Murali, Gaurav Pandey
Peer Reviewers Guoxian Yu; Predrag Radivojac
  • Funders
  • International Business Machines Corporation
  • Intelligence Advanced Research Projects Activity
  • National Institutes of Health
PUBLISHED 28 Sep 2018
https://doi.org/10.12688/f1000research.16310.1
Research Article metrics
Design and implementation of semester long project and problem based bioinformatics course
[version 1; peer review: 3 approved with reservations]
Geetha Saarunya, Bert Ely
Peer Reviewers Russell Schwartz; Mark A. Pauley; Allegra Via
PUBLISHED 25 Sep 2018
https://doi.org/10.12688/f1000research.16026.2
Software Tool Article metrics
Revised
DRETools: A tool-suite for differential RNA editing detection
[version 2; peer review: 1 approved, 1 approved with reservations, 1 not approved]
Tyler Weirick, Patrick Trainor, Eric Rouchka, Andrew DeFilippis, Shizuka Uchida
Peer Reviewers Ernesto Picardi; Yicheng Zhao; Graziano Pesole
  • Funders
  • Gheens Foundation
  • National Institutes of Health
  • V.V. Cooke Foundation
  • University of Louisville
LATEST VERSION PUBLISHED 19 Sep 2018
https://doi.org/10.12688/f1000research.15146.2
Software Tool Article metrics
Revised
aMatReader: Importing adjacency matrices via Cytoscape Automation
[version 2; peer review: 2 approved]
Brett Settle, David Otasek, John H Morris, Barry Demchak
Peer Reviewers Hideo Matsuda; Kimberly Glass
  • Funders
  • National Resource for Network Biology
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 10 Aug 2018
https://doi.org/10.12688/f1000research.15144.2
Software Tool Article metrics
Revised
Copycat Layout: Network layout alignment via Cytoscape Automation
[version 2; peer review: 2 approved]
Brett Settle, David Otasek, John H Morris, Barry Demchak
Peer Reviewers Bernhard Mlecnik; Katja Luck
  • Funders
  • National Resource for Network Biology
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 10 Aug 2018
https://doi.org/10.12688/f1000research.15119.1
Software Tool Article metrics
Norwegian e-Infrastructure for Life Sciences (NeLS)
[version 1; peer review: 2 approved]
Kidane M. Tekle, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Wei Zhang, Christian Andreetta, Teshome Dagne Mulugeta, Matúš Kalaš, Morten B. Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen
Peer Reviewers Olivier Collin; Wolfgang Mueller
  • Funders
  • Norges Forskningsråd
  • NordForsk
PUBLISHED 29 Jun 2018
https://doi.org/10.12688/f1000research.12093.2
Software Tool Article metrics
Revised
bcbioRNASeq: R package for bcbio RNA-seq analysis
[version 2; peer review: 1 approved, 1 approved with reservations]
Michael J. Steinbaugh, Lorena Pantano, Rory D. Kirchner, Victor Barrera, Brad A. Chapman, Mary E. Piper, Meeta Mistry, Radhika S. Khetani, Kayleigh D. Rutherford, Oliver Hofmann, John N. Hutchinson, Shannan Ho Sui
Peer Reviewers Charlotte Soneson; Davide Risso
LATEST VERSION PUBLISHED 20 Jun 2018
https://doi.org/10.12688/f1000research.14616.1
Software Tool Article metrics
Automating the PathLinker app for Cytoscape
[version 1; peer review: 2 approved]
Li Jun Huang, Jeffrey N. Law, T. M. Murali
Peer Reviewers Alexander Pico; Stefan Wuchty
  • Funders
  • Intelligence Advanced Research Projects Activity
  • National Science Foundation
PUBLISHED 12 Jun 2018
https://doi.org/10.12688/f1000research.12344.2
Opinion Article metrics
Revised
Best practice data life cycle approaches for the life sciences
[version 2; peer review: 2 approved]
Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew Treloar, Sonika Tyagi, Jeffrey H. Christiansen, Saravanan Dayalan, Simon Gladman, Sandra B. Hangartner, Helen L. Hayden, William W.H. Ho, Gabriel Keeble-Gagnère, Pasi K. Korhonen, Peter Neish, Priscilla R. Prestes, Mark F. Richardson, Nathan S. Watson-Haigh, Kelly L. Wyres, Neil D. Young, Maria Victoria Schneider
Peer Reviewers Johannes Starlinger; Sven Nahnsen
  • Funders
  • Bioplatforms Australia
  • University of Melbourne
LATEST VERSION PUBLISHED 04 Jun 2018
https://doi.org/10.12688/f1000research.14561.1
Software Tool Article metrics
­­­A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants
[version 1; peer review: 2 approved]
Anuj Kumar, Ajay Pandeya, Girik Malik, Mansi Sharma, Hima Kumari P., Anil Kumar S., Vijay Gahlaut, M.N.V. Prasad Gajula, Krishna Pal Singh, Prashanth Suravajhala, Harindra Singh Balyan, Pushpendra K. Gupta
Peer Reviewers Rajib Bandopadhyay; Vishal Acharya
PUBLISHED 29 May 2018
https://doi.org/10.12688/f1000research.14776.2
Software Tool Article metrics
Revised
Automation of ReactomeFIViz via CyREST API
[version 2; peer review: 2 approved]
Fred Loney, Guanming Wu
Peer Reviewers Marina Piccirillo; John H. Morris
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 23 May 2018
https://doi.org/10.12688/f1000research.13049.2
Software Tool Article metrics
Revised
RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting
[version 2; peer review: 2 approved]
Travis L. Jensen, Michael Frasketi, Kevin Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes B. Goll
Peer Reviewers Anup Mahurkar; Ben Busby
  • Funders
  • Emmes Corporation
  • National Institutes of Health
LATEST VERSION PUBLISHED 13 Apr 2018
https://doi.org/10.12688/f1000research.14197.1
Software Tool Article metrics
TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data
[version 1; peer review: 1 approved, 1 approved with reservations]
Tiago Chedraoui Silva, Antonio Colaprico, Catharina Olsen, Tathiane M Malta, Gianluca Bontempi, Michele Ceccarelli, Benjamin P Berman, Houtan Noushmehr
Peer Reviewers Zuguang Gu; Michael Lawrence
  • Funders
  • Fonds De La Recherche Scientifique - FNRS
  • National Cancer Institute
  • Fundação de Amparo à Pesquisa do Estado de São Paulo
  • Henry Ford Hospital
  • Innoviris
PUBLISHED 10 Apr 2018
https://doi.org/10.12688/f1000research.7329.3
Software Tool Article metrics
Revised
MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format
[version 3; peer review: 2 approved, 2 approved with reservations]
Zeeshan Ahmed, Thomas Dandekar
Peer Reviewers Juilee Thakar; M. Julius Hossain; Florencio Pazos; Karin Verspoor
LATEST VERSION PUBLISHED 04 Apr 2018
https://doi.org/10.12688/f1000research.14258.1
Method Article metrics
An unsupervised disease module identification technique in biological networks using novel quality metric based on connectivity, conductance and modularity
[version 1; peer review: 2 approved with reservations]
Raghvendra Mall, Ehsan Ullah, Khalid Kunji, Michele Ceccarelli, Halima Bensmail
Peer Reviewers Eric E Schadt; Yunpeng Liu
PUBLISHED 26 Mar 2018
https://doi.org/10.12688/f1000research.14242.1
Editorial metrics NOT PEER REVIEWED
Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago
[version 1; peer review: not peer reviewed]
Lonnie Welch, Bruno Gaeta, Diane E. Kovats, Milana Frenkel Morgenstern
  • Funder
  • None
PUBLISHED 19 Mar 2018
261-280 of 384 ARTICLES
Previous Next
Gateway Areas
  • 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
  • Transcriptomics
    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
ISCB News and Announcements open_in_new
Our Links
Sign In
If you've forgotten your password, please enter your email address below and we'll send you instructions on how to reset your password.

The email address should be the one you originally registered with F1000.
Email address not valid, please try again

You registered with F1000 via Google, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Google account password, please click here.

You registered with F1000 via Facebook, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Facebook account password, please click here.

Code not correct, please try again
Email us for further assistance.
Server error, please try again.