All Research Articles

41-60 of 630 ARTICLES
https://doi.org/10.12688/f1000research.55370.3
Software Tool Article metrics
Revised
UKB.COVID19: an R package for UK Biobank COVID-19 data processing and analysis
[version 3; peer review: 2 approved, 1 not approved]
Peer Reviewers Thomas Michael Palmer; Virginia Valeria and Annalisa De Silvestri; Edgar Gonzalez-Kozlova
  • Funder
  • Australian Government National Health and Medical Research Council (NHMRC)
LATEST VERSION PUBLISHED 26 Jul 2024
https://doi.org/10.12688/f1000research.139356.2
Research Article metrics
Revised
Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric
[version 2; peer review: 3 approved]
Peer Reviewers Paul Zaharias; Xianzhao Kan; Anthony K. Redmond
  • Funders
  • Norges Forskningsråd
  • Norwegian Metacenter for Computational Science
LATEST VERSION PUBLISHED 10 Jul 2024
https://doi.org/10.12688/f1000research.122924.2
Software Tool Article metrics
Revised
Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics
[version 2; peer review: 2 approved, 2 approved with reservations]
Peer Reviewers Justin M. Wozniak; Iacopo Colonnelli; Denis Yuen; Stephen R. Piccolo
  • Funders
  • JSPS KAKENHI
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan
  • Japan Science and Technology Agency
LATEST VERSION PUBLISHED 24 Jun 2024
https://doi.org/10.12688/f1000research.149494.1
Software Tool Article metrics
sSNAPPY: an R/Bioconductor package for single-sample directional pathway perturbation analysis
[version 1; peer review: 2 approved with reservations]
Peer Reviewers Dario Strbenac; Panagiotis Moulos
  • Funders
  • National Health and Medical Research Council
  • National Breast Cancer Foundation
PUBLISHED 13 Jun 2024
https://doi.org/10.12688/f1000research.123984.2
Research Article metrics
Revised
A potential role of arcadia in conditioned media - umbilical cord derived mesenchymal stem cell on  cartilage repair
[version 2; peer review: 1 approved with reservations, 3 not approved]
Peer Reviewers William Mark Erwin; Girish Pattappa; Rajesh Ramasamy; Jeanne Adiwinata Pawitan
LATEST VERSION PUBLISHED 06 Jun 2024
https://doi.org/10.12688/f1000research.126734.2
Opinion Article metrics
Revised
Systems Biology in ELIXIR: modelling in the spotlight
[version 2; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers Yoram Vodovotz; Herbert Sauro; Ioannis Androulakis
  • Funder
  • EPAnEk-NSRF
LATEST VERSION PUBLISHED 31 May 2024
https://doi.org/10.12688/f1000research.149577.1
Research Article metrics
Easing genomic surveillance: A comprehensive performance evaluation of long-read assemblers across multi-strain mixture data of HIV-1 and Other pathogenic viruses for constructing a user-friendly bioinformatic pipeline
[version 1; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers Udom Sae-Ueng; Rujira Chaysiri; Sira Sriswasdi
  • Funders
  • The Health Systems Research Institute, Thailand
  • The Faculty of Medicine Research Fund, Chiang Mai University,
PUBLISHED 31 May 2024
https://doi.org/10.12688/f1000research.135164.2
Method Article metrics
Revised
On the limits of inferring biophysical parameters of RBP-RNA interactions from in vitro RNA Bind’n Seq data
[version 2; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Peer Reviewers Johannes Söding; Jun Zhang; Junbai Wang; Andreas Schlundt
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 29 May 2024
https://doi.org/10.12688/f1000research.134798.2
Software Tool Article metrics
Revised
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
[version 2; peer review: 1 approved, 3 approved with reservations]
Peer Reviewers Timothy Read and Robert Petit III; Jonas Coelho Kasmanas; Intikhab Alam; Emma Griffiths
  • Funders
  • Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
  • Carlsbergfondet
  • H2020 European Research Council
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek
  • Knut och Alice Wallenbergs Stiftelse
  • National Institutes of Health
  • Carl Tryggers Stiftelse för Vetenskaplig Forskning
  • Deutsche Forschungsgemeinschaft
  • Friedrich-Schiller-Universität Jena
  • Science for Life Laboratory National Sequencing Projects
  • Werner Siemens-Stiftung
  • Max-Planck-Gesellschaft
  • National Science Foundation
  • Leverhulme Trust
  • Svenska Forskningsrådet Formas
  • Science Foundation Ireland-Irish Research Council
  • Science Foundation Ireland Centre for Research Training in Genomics Data Science
  • Università degli Studi di Padova
  • Institut Pasteur
  • H2020 Marie Skłodowska-Curie Actions
LATEST VERSION PUBLISHED 28 May 2024
https://doi.org/10.12688/f1000research.149237.1
Software Tool Article metrics
ZARP: A user-friendly and versatile RNA-seq analysis workflow
[version 1; peer review: 2 approved with reservations]
Peer Reviewers Silvia Liu; Bo Li
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • National Center of Competence in Research RNA & Disease
PUBLISHED 24 May 2024
https://doi.org/10.12688/f1000research.150049.1
Research Article metrics
Design of SARS-CoV-2 protein S peptides recognized by the most frequent HLA alleles in the Moroccan population using an immunoinformatics approach
[version 1; peer review: 1 not approved]
Peer Reviewers Gustavo Fioravanti Vieira
PUBLISHED 20 May 2024
https://doi.org/10.12688/f1000research.74416.2
Software Tool Article metrics
Revised
BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data
[version 2; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers Oliver M. Crook; Andrew McDavid; Michel S Naslavsky
  • Funders
  • Cancer Research UK
  • University of Edinburgh
  • European Molecular Biology Laboratory
LATEST VERSION PUBLISHED 07 May 2024
https://doi.org/10.12688/f1000research.147631.1
Research Article metrics
Analyzing a series of ligands against malaria through the application of molecular docking, molecular quantum similarity, and reactivity indices
[version 1; peer review: 1 approved with reservations, 1 not approved]
Peer Reviewers Tawanda Zininga; Ezekiel Adebiyi and Yagoub Adam
  • Funder
  • Tecnologico
PUBLISHED 02 May 2024
https://doi.org/10.12688/f1000research.127348.2
Software Tool Article metrics
Revised
CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes
[version 2; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers Eric Soler and Mohammad Salma; Xueyi Dong; Alexander Zelikovsky and Bikram Sahoo
  • Funder
  • Japan Society for the Promotion of Science
LATEST VERSION PUBLISHED 30 Apr 2024
https://doi.org/10.12688/f1000research.124059.2
Software Tool Article metrics
Revised
LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies
[version 2; peer review: 2 approved]
Peer Reviewers Adam Frankish; Mark Borodovsky
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 29 Apr 2024
https://doi.org/10.12688/f1000research.136683.2
Software Tool Article metrics
Revised
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2
[version 2; peer review: 2 approved]
Peer Reviewers Wolfgang Maier; Sondes Haddad-Boubaker
  • Funder
  • European Centre for Disease Prevention and Control
LATEST VERSION PUBLISHED 16 Apr 2024
https://doi.org/10.12688/f1000research.126215.2
Method Article metrics
Revised
Bayesian Multi-View Clustering given complex inter-view structure
[version 2; peer review: 2 approved]
Peer Reviewers Sara Mostafavi; Max Moldovan
  • Funders
  • Microsoft
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 29 Feb 2024
https://doi.org/10.12688/f1000research.125325.2
Software Tool Article metrics
Revised
Librarian: A quality control tool to analyse sequencing library compositions
[version 2; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers Andrew Keniry; Konstantin Okonechnikov; Karim Gharbi
  • Funder
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 24 Jan 2024
https://doi.org/10.12688/f1000research.135250.2
Software Tool Article metrics
Revised
DrosOMA: the Drosophila Orthologous Matrix browser
[version 2; peer review: 4 approved]
Peer Reviewers Berend Snel; Daofeng Li; Jung-Wan Mok; Elise Parey
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 16 Jan 2024
https://doi.org/10.12688/f1000research.110072.4
Research Article metrics
Revised
In silico comparison between the mutated and wild-type androgen receptors and their influence on the selection of optimum androgenic receptor blockers for the treatment of prostate cancer
[version 4; peer review: 3 approved]
Peer Reviewers Zarrin Basharat; Ahmed A J Mahmood; Mahmoud A. Al-Sha'er
  • Funder
  • The author(s) declared that no grants were involved in supporting this work.
LATEST VERSION PUBLISHED 11 Jan 2024
41-60 of 630 ARTICLES
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We publish a wide range of article types in science, engineering, medicine, social sciences and humanities, with no editorial biases.
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