Bioinformatics

Bioinformatics

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221-240 of 378 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.20590.2
Software Tool Article metrics
Revised
Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps
[version 2; peer review: 2 approved]
Michael C. Ryan, Mark Stucky, Chris Wakefield, James M. Melott, Rehan Akbani, John N. Weinstein, Bradley M. Broom
Peer Reviewers Natasha Caplen and Soumya Sundara Rajan; Melissa Cline
  • Funders
  • Michael and Susan Dell Foundation
  • Mary K. Chapman Foundation
  • National Cancer Institute
LATEST VERSION PUBLISHED 19 Mar 2020
https://doi.org/10.12688/f1000research.17927.4
Software Tool Article metrics
Revised
Biobtree: A tool to search and map bioinformatics identifiers and special keywords
[version 4; peer review: 2 approved]
Tamer Gur
Peer Reviewers Maxim N. Shokhirev; Samuel Lampa
LATEST VERSION PUBLISHED 20 Jan 2020
https://doi.org/10.12688/f1000research.20887.3
Software Tool Article metrics
Revised
RCy3: Network biology using Cytoscape from within R
[version 3; peer review: 3 approved]
Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
Peer Reviewers James Denvir; Krithika Bhuvaneshwar; Ludwig Geistlinger
  • Funders
  • Google
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 04 Dec 2019
https://doi.org/10.12688/f1000research.19994.2
Research Article metrics
Revised
On the evaluation of research software: the CDUR procedure
[version 2; peer review: 2 approved]
Teresa Gomez-Diaz, Tomas Recio
Peer Reviewers Francisco Queiroz; Jean-Pierre Merlet
  • Funder
  • Laboratoire d'informatique Gaspard-Monge
LATEST VERSION PUBLISHED 26 Nov 2019
https://doi.org/10.12688/f1000research.19236.3
Software Tool Article metrics
Revised
Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
[version 3; peer review: 2 approved]
Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J. Davis
Peer Reviewers Marina Lizio; Luiza Handschuh
  • Funder
  • National Health and Medical Research Council
LATEST VERSION PUBLISHED 14 Oct 2019
https://doi.org/10.12688/f1000research.18490.3
Research Article metrics
Revised
Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data
[version 3; peer review: 2 approved, 1 approved with reservations]
J. Javier Diaz-Mejia, Elaine C. Meng, Alexander R. Pico, Sonya A. MacParland, Troy Ketela, Trevor J. Pugh, Gary D. Bader, John H. Morris
Peer Reviewers Saskia Freytag; Jimmy Tsz Hang Lee and Tallulah Andrews; Lindsay Cowell
  • Funders
  • National Resource for Network Biology
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 14 Oct 2019
https://doi.org/10.12688/f1000research.20408.1
Editorial metrics NOT PEER REVIEWED
Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers
[version 1; peer review: not peer reviewed]
Sayane Shome, R. Gonzalo Parra, Nazeefa Fatima, Alexander Miguel Monzon, Bart Cuypers, Yumna Moosa, Nilson Da Rocha Coimbra, Juliana Assis, Carla Giner-Delgado, Handan Melike Dönertaş, Yesid Cuesta-Astroz, Geetha Saarunya, Imane Allali, Shruti Gupta, Ambuj Srivastava, Manisha Kalsan, Catalina Valdivia, Gabriel J. Olguin-Orellana, Sofia Papadimitriou, Daniele Parisi, Nikolaj Pagh Kristensen, Leonor Rib, Marouen Ben Guebila, Eugen Bauer, Gaia Zaffaroni, Amel Bekkar, Efejiro Ashano, Lisanna Paladin, Marco Necci, Nicolás N. Moreyra, Martin Rydén, Jordan Villalobos-Solís, Nikolaos Papadopoulos, Candice Rafael, Tülay Karakulak, Yasin Kaya, Yvonne Gladbach, Sandeep Kumar Dhanda, Nikolina Šoštarić, Aishwarya Alex, Dan DeBlasio, Farzana Rahman
  • Funder
  • International Society for Computational Biology
PUBLISHED 02 Sep 2019
https://doi.org/10.12688/f1000research.16200.2
Research Article metrics
Revised
Predicting transcription factor binding using ensemble random forest models
[version 2; peer review: 2 approved]
Fatemeh Behjati Ardakani, Florian Schmidt, Marcel H. Schulz
Peer Reviewers Jan Grau; Gary D Stormo
  • Funder
  • Cluster of Excellence on Multimodal Computing and Interaction (DFG)
LATEST VERSION PUBLISHED 02 Sep 2019
https://doi.org/10.12688/f1000research.18705.2
Research Article metrics
Revised
Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models
[version 2; peer review: 1 approved, 2 approved with reservations]
Katharina Baum, Jagath C. Rajapakse, Francisco Azuaje
Peer Reviewers Lei Xie and Yue Qiu; Silvia Pineda San Juan; Ana Conesa and Manuel Ugidos
  • Funders
  • Fonds National de la Recherche Luxembourg
  • Joachim Herz Stiftung
LATEST VERSION PUBLISHED 27 Aug 2019
https://doi.org/10.12688/f1000research.19320.1
Opinion Article metrics
Introduction to Genomic Analysis Workshop: A catalyst for engaging life-science researchers in high throughput analysis
[version 1; peer review: 2 approved]
Phillip A. Richmond, Wyeth W. Wasserman
Peer Reviewers Richard Fitzpatrick and Melanie I. Stefan; Michael Springer
  • Funders
  • Natural Sciences and Engineering Research Council
  • BC Children’s Hospital Research Institute
PUBLISHED 30 Jul 2019
https://doi.org/10.12688/f1000research.16454.2
Research Article metrics
Revised
Large-scale analysis of B-cell epitopes of envelope: Implications for Zika vaccine and immunotherapeutic development
[version 2; peer review: 2 approved]
Iman Almansour, Rahaf Alfares, Halah Aljofi
Peer Reviewers Meirong Jia; Sunil K Joshi
  • Funder
  • Imam Abdulrahman Bin Faisal University
LATEST VERSION PUBLISHED 27 Jun 2019
https://doi.org/10.12688/f1000research.18142.2
Software Tool Article metrics
Revised
Visualization of the small RNA transcriptome using seqclusterViz
[version 2; peer review: 2 approved]
Lorena Pantano, Francisco Pantano, Eulalia Marti, Shannan Ho Sui
Peer Reviewers Xavier Bofill-De Ros; Stefan Scholten
LATEST VERSION PUBLISHED 27 Jun 2019
https://doi.org/10.12688/f1000research.19592.1
Software Tool Article metrics
Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
[version 1; peer review: 3 approved]
Aurora S. Blucher, Shannon K. McWeeney, Lincoln Stein, Guanming Wu
Peer Reviewers Fuhai Li; Aritro Nath; Tero Aittokallio and Ziaurrehman Tanoli
  • Funder
  • National Institutes of Health
PUBLISHED 20 Jun 2019
https://doi.org/10.12688/f1000research.19013.1
Method Article metrics
de.NBI Cloud federation through ELIXIR AAI
[version 1; peer review: 2 approved, 1 not approved]
Peter Belmann, Björn Fischer, Jan Krüger, Michal Procházka, Helena Rasche, Manuel Prinz, Maximilian Hanussek, Martin Lang, Felix Bartusch, Benjamin Gläßle, Jens Krüger, Alfred Pühler, Alexander Sczyrba
Peer Reviewers Enol Fernández-del-Castillo; Dixie Baker; Volker P. Brendel
  • Funder
  • Bundesministerium für Bildung und Forschung
PUBLISHED 10 Jun 2019
https://doi.org/10.12688/f1000research.19410.1
Software Tool Article metrics
BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem
[version 1; peer review: 2 approved, 1 approved with reservations]
Shian Su, Vincent J. Carey, Lori Shepherd, Matthew E. Ritchie, Martin T. Morgan, Sean Davis
Peer Reviewers Simina M. Boca; Mike Smith; Henrik Bengtsson
  • Funders
  • EU H2020 Personalizing Health and Care Program
  • Intramural Research Program, National Institutes of Health
  • National Cancer Institute
  • National Human Genome Research Institute
PUBLISHED 29 May 2019
https://doi.org/10.12688/f1000research.15830.2
Software Tool Article metrics
Revised
An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
[version 2; peer review: 2 approved]
Clarence K. Mah, Alexander T. Wenzel, Edwin F. Juarez, Thorin Tabor, Michael M. Reich, Jill P. Mesirov
Peer Reviewers Timothy Tickle; Joshua Batson
  • Funders
  • Silicon Valley Community Foundation
  • National Institutes of Health
LATEST VERSION PUBLISHED 29 May 2019
https://doi.org/10.12688/f1000research.19221.1
Editorial metrics NOT PEER REVIEWED
2019 ISCB Innovator Award recognizes William Stafford Noble
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19220.1
Editorial metrics NOT PEER REVIEWED
2019 ISCB Overton Prize: Christophe Dessimoz
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19219.1
Editorial metrics NOT PEER REVIEWED
Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19218.1
Editorial metrics NOT PEER REVIEWED
2019 Outstanding Contributions to ISCB awarded to Barb Bryant
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
221-240 of 378 ARTICLES
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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
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    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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