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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.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.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.15666.3
Research Article metrics
Revised
A systematic performance evaluation of clustering methods for single-cell RNA-seq data
[version 3; peer review: 2 approved]
Angelo Duò, Mark D. Robinson, Charlotte Soneson
Peer Reviewers Jean Fan; Saskia Freytag
  • Funders
  • Swiss National Science Foundation
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 16 Nov 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.25813.1
Review metrics
Recent advances in phenotypic drug discovery
[version 1; peer review: 2 approved]
David C. Swinney, Jonathan A. Lee
Peer Reviewers Jeremy L. Jenkins; Ye Fang
PUBLISHED 07 Aug 2020
https://doi.org/10.12688/f1000research.24143.1
Research Article metrics
In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19
[version 1; peer review: 2 approved]
Bharath BR, Hrishikesh Damle, Shiban Ganju, Latha Damle
Peer Reviewers S.M. Vidya; Raghavendra HL
  • Funder
  • Atrimed Pharmaceuticals Pvt. Ltd
PUBLISHED 01 Jul 2020
https://doi.org/10.12688/f1000research.22584.2
Research Article metrics
Revised
Computationally going where experiments cannot: a dynamical assessment of dendritic ion channel currents during in vivo-like states
[version 2; peer review: 2 approved]
Alexandre Guet-McCreight, Frances K. Skinner
Peer Reviewers Fernando Fernandez; Vijayalakshmi Santhakumar and Andrew Huang
  • Funder
  • Natural Sciences and Engineering Research Council of Canada
LATEST VERSION PUBLISHED 11 Jun 2020
https://doi.org/10.12688/f1000research.24074.1
Research Article metrics
Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
[version 1; peer review: 2 approved, 1 approved with reservations]
Debmalya Barh, Sandeep Tiwari, Bruno Silva Andrade, Marta Giovanetti, Eduardo Almeida Costa, Ranjith Kumavath, Preetam Ghosh, Aristóteles Góes-Neto, Luiz Carlos Junior Alcantara, Vasco Azevedo
Peer Reviewers Candan Hizel; Shailendra Dwivedi; Amjad Ali
  • Funders
  • Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
  • Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro
PUBLISHED 09 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.20715.2
Method Article metrics
Revised
Prediction of cell position using single-cell transcriptomic data: an iterative procedure
[version 2; peer review: 2 approved]
Andrés M. Alonso, Alejandra Carrea, Luis Diambra
Peer Reviewers Roosevelt Alves Da Silva; Pablo Meyer
LATEST VERSION PUBLISHED 09 Apr 2020
https://doi.org/10.12688/f1000research.22639.1
Research Article metrics
Accuracy of short tandem repeats genotyping tools in whole exome sequencing data
[version 1; peer review: 2 approved, 1 approved with reservations]
Andreas Halman, Alicia Oshlack
Peer Reviewers Elizabeth A. Worthey; Jan Radvanszky and Jaroslav Budiš; Maria Anisimova
  • Funder
  • National Health and Medical Research Council
PUBLISHED 23 Mar 2020
https://doi.org/10.12688/f1000research.20873.2
Opinion Article metrics
Revised
The why, when, and how of computing in biology classrooms
[version 2; peer review: 2 approved]
April M. Wright, Rachel S. Schwartz, Jamie R. Oaks, Catherine E. Newman, Sarah P. Flanagan
Peer Reviewers Tiffany Timbers; Thomas Kluyver
  • Funders
  • University of Canterbury
  • National Institute of Food and Agriculture
  • National Institute of General Medical Sciences
  • National Science Foundation
LATEST VERSION PUBLISHED 02 Mar 2020
https://doi.org/10.12688/f1000research.21763.1
Software Tool Article metrics
vhcub: Virus-host codon usage co-adaptation analysis
[version 1; peer review: 2 approved]
Ali Mostafa Anwar, Mohamed Soudy, Radwa Mohamed
Peer Reviewers Raj Kumar Singh; Oscar Leonardo Ramírez Suárez and Adriana Patricia Corredor-Figueroa
PUBLISHED 23 Dec 2019
https://doi.org/10.12688/f1000research.21568.1
Editorial metrics NOT PEER REVIEWED
BOSC 2019, the 20th annual Bioinformatics Open Source Conference
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Peter J.A. Cock, Christopher J. Fields, Bastian Greshake Tzovaras, Michael Heuer, Karsten Hokamp, Monica Munoz-Torres, Alexander Peltzer, Bastian Rieck, Heather Wiencko, Yo Yehudi
PUBLISHED 20 Dec 2019
https://doi.org/10.12688/f1000research.11622.4
Method Article metrics
Revised
CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
[version 4; peer review: 2 approved]
Malgorzata Nowicka, Carsten Krieg, Helena L. Crowell, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Peer Reviewers Aaron T. L. Lun and John C. Marioni; Greg Finak and Raphael Gottardo
  • Funders
  • Swiss National Science Foundation
  • Swiss Institute of Bioinformatics
  • University of Zurich
LATEST VERSION PUBLISHED 17 Dec 2019
https://doi.org/10.12688/f1000research.19481.1
Review metrics
Metabolic phenotyping of the human microbiome
[version 1; peer review: 2 approved]
Wiley Barton, Orla O'Sullivan, Paul D. Cotter
Peer Reviewers Robert E Brown; Jack A Gilbert
  • Funders
  • Department of Agriculture, Food and the Marine
  • Science Foundation Ireland
PUBLISHED 22 Nov 2019
https://doi.org/10.12688/f1000research.18866.2
Software Tool Article metrics
Revised
MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data
[version 2; peer review: 2 approved]
Mike W.C. Thang, Xin-Yi Chua, Gareth Price, Dominique Gorse, Matt A. Field
Peer Reviewers Saskia Hiltemann; Leo Lahti
  • Funder
  • Australian Institute of Tropical Health and Medicine
LATEST VERSION PUBLISHED 18 Oct 2019
https://doi.org/10.12688/f1000research.20136.1
Opinion Article metrics
An intrinsically disordered proteins community for ELIXIR
[version 1; peer review: 2 approved]
Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas, John M. Hancock, Jen Harrow, Desmond Higgins, Cy M. Jeffries, Philippe Le Mercier, Balint Mészáros, Marco Necci, Cedric Notredame, Sandra Orchard, Christos A. Ouzounis, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Vasilis J. Promponas, Patrick Ruch, Gabriella Rustici, Pedro Romero, Sirarat Sarntivijai, Gary Saunders, Benjamin Schuler, Malvika Sharan, Denis C. Shields, Joel L. Sussman, Jonathan A. Tedds, Peter Tompa, Michael Turewicz, Jiri Vondrasek, Wim F. Vranken, Bonnie Ann Wallace, Kanin Wichapong, Silvio C. E. Tosatto
Peer Reviewers Iva Pritisanac and Julie Forman-Kay; Osman Ugur Sezerman
  • Funders
  • Vetenskapsrådet
  • BBSRC
  • European Molecular Biology Laboratory
  • Carlsberg Foundation Distinguished Fellowship
  • National Institutes of Health
  • Israel I-CORE Project
  • ELIXIR
  • Danmarks Grundforskningsfond
  • Instruct-ERIC
  • Swiss Federal Government
  • Marie Skłodowska-Curie
  • COST Action BM1405 NGP-net
  • Wellcome Trust
PUBLISHED 15 Oct 2019
81-100 of 369 ARTICLES
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