Bioinformatics

Bioinformatics

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201-220 of 378 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.25713.2
Software Tool Article metrics
Revised
VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach
[version 2; peer review: 1 approved, 2 approved with reservations]
Priyansh Srivastava, Mehak Talwar, Aishwarya Yadav, Alakto Choudhary, Sabyasachi Mohanty, Samuel Bharti, Priyanka Narad, Abhishek Sengupta
Peer Reviewers Dinesh Gupta; Mitesh Dwivedi and Rasheedunnisa Begum; Animesh A Sinha
LATEST VERSION PUBLISHED 01 Feb 2021
https://doi.org/10.12688/f1000research.21782.4
Research Article metrics
Update
Benchmarking of long-read assemblers for prokaryote whole genome sequencing
[version 4; peer review: 4 approved]
Ryan R. Wick, Kathryn E. Holt
Peer Reviewers Aleksey V. Zimin and Steven Salzberg; Robert Vaser and Mile Šikić; Mikhail Kolmogorov; Olin Silander
  • Funders
  • Department of Education, Employment and Workplace Relations, Australian Government
  • Sylvia and Charles Viertel Charitable Foundation
  • Gates Foundation
LATEST VERSION PUBLISHED 01 Feb 2021
https://doi.org/10.12688/f1000research.21142.2
Software Tool Article metrics
Revised
Falco: high-speed FastQC emulation for quality control of sequencing data
[version 2; peer review: 2 approved]
Guilherme de Sena Brandine, Andrew D. Smith
Peer Reviewers R Henrik Nilsson; Weihong Qi
LATEST VERSION PUBLISHED 27 Jan 2021
https://doi.org/10.12688/f1000research.26429.2
Software Tool Article metrics
Revised
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
[version 2; peer review: 2 approved]
Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Peer Reviewers Kim-Anh Lê Cao; Anais Baudot, Judith Lambert and Laurent Tichit
  • Funders
  • Villum Fonden
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.40666.1
Editorial metrics NOT PEER REVIEWED
6th European Student Council Symposium (ESCS): overcoming obstacles to enhance virtuality, connectivity, inclusivity and community engagement
[version 1; peer review: not peer reviewed]
Gabriel J. Olguín-Orellana, Sofia Papadimitriou, Alberto Langtry Yáñez, Pradeep Eranti, Rosario del Carmen Flores-Vallejo, Ana I. Castillo-Orozco, Kalaumari Mayoral-Peña, R. Gonzalo Parra
  • Funder
  • ISCB Student Council; Information Technology for Translational Medicine (ITTM) Solutions
PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.27268.1
Software Tool Article metrics
rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
[version 1; peer review: 2 approved]
Sebastien Theil, Etienne Rifa
Peer Reviewers Florent Murat; Simon Roux
PUBLISHED 07 Jan 2021
https://doi.org/10.12688/f1000research.28175.1
Research Article metrics
Energy-dependent protein folding: modeling how a protein folding machine may work
[version 1; peer review: 1 approved, 3 approved with reservations]
Harutyun Sahakyan, Karen Nazaryan, Arcady Mushegian, Irina Sorokina
Peer Reviewers Lisa J. Lapidus; Stephen D. Fried; Antonio Trovato; José Arcadio Farías Rico
  • Funders
  • Foundation Armenia (Switzerland)
  • National Academy of Sciences of Armenia
  • Strenic LLC
  • National Science Foundation
PUBLISHED 05 Jan 2021
https://doi.org/10.12688/f1000research.26880.2
Software Tool Article metrics
Revised
Recursive Cluster Elimination based Rank Function (SVM-RCE-R) implemented in KNIME
[version 2; peer review: 3 approved]
Malik Yousef, Burcu Bakir-Gungor, Amhar Jabeer, Gokhan Goy, Rehman Qureshi, Louise C. Showe
Peer Reviewers Marco Chierici; Osman Ugur Sezerman; Abhishek Kumar
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 05 Jan 2021
https://doi.org/10.12688/f1000research.23390.2
Software Tool Article metrics
Revised
Seqpare: a novel metric of similarity between genomic interval sets
[version 2; peer review: 2 approved]
Selena C. Feng, Nathan C. Sheffield, Jianglin Feng
Peer Reviewers Zhaohui Steve Qin; Burcak Otlu
LATEST VERSION PUBLISHED 04 Jan 2021
https://doi.org/10.12688/f1000research.23829.2
Research Article metrics
Revised
Computational screening for potential drug candidates against the SARS-CoV-2 main protease
[version 2; peer review: 2 approved]
Bruno Silva Andrade, Preetam Ghosh, Debmalya Barh, Sandeep Tiwari, Raner José Santana Silva, Wagner Rodrigues de Assis Soares, Tarcisio Silva Melo, Andria Santos Freitas, Patrícia González-Grande, Lucas Sousa Palmeira, Luiz Carlos Junior Alcantara, Marta Giovanetti, Aristóteles Góes-Neto, Vasco Ariston de Carvalho Azevedo
Peer Reviewers Murtaza Tambuwala; Alaa A A Aljabali
  • Funder
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico
LATEST VERSION PUBLISHED 21 Dec 2020
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
201-220 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
  • 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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