Bioinformatics

Bioinformatics

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221-240 of 389 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.28330.1
Editorial metrics NOT PEER REVIEWED
4th ISCB Latin American Student Council Symposium: a virtual and inclusive experience during COVID-19 times
[version 1; peer review: not peer reviewed]
Camila Castillo-Vilcahuaman, Catalina Valdivia, Cleidy Osorio-Mogollón, Claudia Silva-Andrade, Rafael Puche-Quiñonez, Sebastián Ayala-Ruano, Yesid Cuesta-Astroz, R. Gonzalo Parra
  • Funder
  • ISCB Student Council
PUBLISHED 15 Dec 2020
https://doi.org/10.12688/f1000research.25413.2
Research Article metrics
Revised
Biocuration - mapping resources and needs
[version 2; peer review: 2 approved]
Alexandra Holinski, Melissa L. Burke, Sarah L. Morgan, Peter McQuilton, Patricia M. Palagi
Peer Reviewers Tanya Berardini; Luana Licata
  • Funder
  • ELIXIR
LATEST VERSION PUBLISHED 02 Dec 2020
https://doi.org/10.12688/f1000research.22242.2
Software Tool Article metrics
Revised
AlignmentViewer: Sequence Analysis of Large Protein Families
[version 2; peer review: 2 approved]
Roc Reguant, Yevgeniy Antipin, Rob Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, Nicholas Paul Gauthier
Peer Reviewers Erik Larsson Lekholm; Alex Bateman
  • Funders
  • Human Frontier Science Program
  • Harvard Medical School
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 15 Oct 2020
https://doi.org/10.12688/f1000research.14880.4
Software Tool Article metrics
Revised
SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
[version 4; peer review: 2 approved, 1 not approved]
Syed Hussain Ather, Olaitan Igbagbo Awe, Thomas J. Butler, Tamiru Denka, Stephen Andrew Semick, Wanhu Tang, Ben Busby
Peer Reviewers Philip Ewels; Norann A. Zaghloul; Xi Chen
  • Funder
  • U.S. National Library of Medicine
LATEST VERSION PUBLISHED 22 Sep 2020
https://doi.org/10.12688/f1000research.24187.2
Software Tool Article metrics
Revised
ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R
[version 2; peer review: 3 approved]
Charlotte Soneson, Federico Marini, Florian Geier, Michael I. Love, Michael B. Stadler
Peer Reviewers Jean Fan; Lucy D'Agostino McGowan; Matthew Ritchie
  • Funders
  • National Institutes of Health
  • German Federal Ministry of Education and Research
LATEST VERSION PUBLISHED 16 Sep 2020
https://doi.org/10.12688/f1000research.23297.2
Software Tool Article metrics
Revised
GFF Utilities: GffRead and GffCompare
[version 2; peer review: 3 approved]
Geo Pertea, Mihaela Pertea
Peer Reviewers Andreas Stroehlein; Michael I. Love; Rob Patro
  • Funders
  • U.S. National Institutes of Health
  • National Science Foundation
LATEST VERSION PUBLISHED 09 Sep 2020
https://doi.org/10.12688/f1000research.22280.2
Software Tool Article metrics
Revised
Visualize omics data on networks with Omics Visualizer, a Cytoscape App
[version 2; peer review: 2 approved]
Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen
Peer Reviewers Magnus Palmblad; Ruth Isserlin
  • Funders
  • Innovationsfonden
  • Novo Nordisk Fonden
LATEST VERSION PUBLISHED 30 Jun 2020
https://doi.org/10.12688/f1000research.24271.1
Research Article metrics
Word embedding mining for SARS-CoV-2 and COVID-19 drug repurposing
[version 1; peer review: 2 approved with reservations]
Finn Kuusisto, David Page, Ron Stewart
Peer Reviewers Quentin Vanhaelen; Nansu Zong
  • Funder
  • Marv Conney
PUBLISHED 10 Jun 2020
https://doi.org/10.12688/f1000research.24101.1
Editorial metrics NOT PEER REVIEWED
Highlights of the 3rd ISCB Africa Student Council Symposium 2019 in Ghana
[version 1; peer review: not peer reviewed]
Wisdom A. Akurugu, Albert Doughan, Abdul-Rahman Adamu Bukari, Mahtaab Hayat, Emmanuel James San, Hannah Nyarkoah Nyarko, John Mogaka, Mwangi Harrison Ndung'u, Farzana Rahman, Sayane Shome
  • Funder
  • International Society of Computational Biology
PUBLISHED 27 May 2020
https://doi.org/10.12688/f1000research.13535.2
Method Article metrics
Revised
StateHub-StatePaintR: rapid and reproducible chromatin state evaluation for custom genome annotation
[version 2; peer review: 3 approved with reservations]
Simon G. Coetzee, Zachary Ramjan, Huy Q. Dinh, Benjamin P. Berman, Dennis J. Hazelett
Peer Reviewers Maxwell W. Libbrecht; Yongjin Park; Guillaume J. Filion
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 07 May 2020
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
221-240 of 389 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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