Bioinformatics

Bioinformatics

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41-60 of 384 ARTICLES
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https://doi.org/10.12688/f1000research.145486.1
Research Article metrics
Negligible effects of read trimming on the accuracy of germline short variant calling in the human genome
[version 1; peer review: 2 approved with reservations]
Yury Barbitoff, Alexander Predeus
Peer Reviewers Dharma Varapula; Xihao Li and Muqing Zhou
PUBLISHED 17 May 2024
https://doi.org/10.12688/f1000research.134465.2
Research Article metrics
Revised
Spatiotemporal structure and composition of the microbial communities in hypersaline Lake Magadi, Kenya
[version 2; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Alex Kipnyargis, Eucharia Kenya, Fathiya Khamis, Romano Mwirichia
Peer Reviewers Marianne Haines; Srijak Bhatnagar; Cristiano Pedroso-Roussado; Addis Simachew
  • Funder
  • National Research Fund, Kenya
LATEST VERSION PUBLISHED 17 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]
Alan O'Callaghan, Nils Eling, John C. Marioni, Catalina A. Vallejos
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.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]
Jianqiang Sun, Xi Fu, Wei Cao
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]
Alaina Shumate, Steven Salzberg
Peer Reviewers Adam Frankish; Mark Borodovsky
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 29 Apr 2024
https://doi.org/10.12688/f1000research.140624.3
Opinion Article metrics
Revised
Creating cloud platforms for supporting FAIR data management in biomedical research projects.
[version 3; peer review: 2 approved]
Marcel Jentsch, Valentin Schneider-Lunitz, Ulrike Taron, Martin Braun, Naveed Ishaque, Harald Wagener, Christian Conrad, Sven Twardziok
Peer Reviewers Anna Bernasconi; Joseph Bonello
  • Funders
  • Bundesministerium für Bildung und Forschung
  • HORIZON EUROPE European Research Council
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]
Marie Lataretu, Oliver Drechsel, René Kmiecinski, Kathrin Trappe, Martin Hölzer, Stephan Fuchs
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.140403.2
Brief Report metrics
Revised
Methylation risk score in peripheral blood predictive of conversion from mild cognitive impairment to Alzheimer's Disease
[version 2; peer review: 2 approved with reservations, 1 not approved]
Jarrett D. Morrow
Peer Reviewers Adam Smith; Rachel Cavill; Lily Wang and Wei Zhang
  • Funder
  • National Heart, Lung, and Blood Institute
LATEST VERSION PUBLISHED 15 Mar 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]
Benjamin D. Shapiro, Alexis Battle
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.141786.2
Review metrics
Revised
Models for the retention of duplicate genes and their biological underpinnings
[version 2; peer review: 2 approved]
Raquel Assis, Gavin Conant, Barbara Holland, David A. Liberles, Malgorzata M. O'Reilly, Amanda E. Wilson
Peer Reviewers Nadia El-Mabrouk; Arturo Becerra
LATEST VERSION PUBLISHED 12 Feb 2024
https://doi.org/10.12688/f1000research.127061.2
Research Article metrics
Revised
Understanding the high electronic quantum similarity of a series of ligands used as inhibitors of the SARS-CoV-2 virus by molecular mechanics and density functional theory approaches
[version 2; peer review: 1 approved, 1 approved with reservations, 3 not approved]
Alejandro Morales-Bayuelo, Jesús Sánchez-Márquez
Peer Reviewers Ahmed Metwaly; Ramon Carbó-Dorca; Kiran Bharat Lokhande; Vikram Dalal; Mohnad Abdalla
  • Funder
  • Fundación Universitaria Tecnológico Comfenalco
LATEST VERSION PUBLISHED 06 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]
Kartavya Vashishtha, Caroline Gaud, Simon Andrews, Christel Krueger
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]
Antonin Thiébaut, Adrian M. Altenhoff, Giulia Campli, Natasha Glover, Christophe Dessimoz, Robert M. Waterhouse
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.138059.1
Method Article metrics
A tutorial hub for realising the potential of tools within the SPARC ecosystem
[version 1; peer review: 2 approved with reservations]
Niloofar Shahidi, Omkar Athavale, Yuda Munarko, Mathias Roesler, Kenneth Tran
Peer Reviewers Bhavesh Patel; Andrey Andreev
PUBLISHED 08 Jan 2024
https://doi.org/10.12688/f1000research.129958.4
Research Article metrics
Revised
The first released available genome of the common ice plant (Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C3-CAM photosynthetic conversion, and halophilism
[version 4; peer review: 2 approved, 1 approved with reservations]
Ryoma Sato, Yuri Kondo, Sakae Agarie
Peer Reviewers Qijie Guan; Xin-Guang Zhu; Zbigniew Miszalski
  • Funder
  • JSPS KAKENHI
LATEST VERSION PUBLISHED 04 Jan 2024
https://doi.org/10.12688/f1000research.130530.2
Software Tool Article metrics
Revised
scANANSE gene regulatory network and motif analysis of single-cell clusters
[version 2; peer review: 2 approved]
Jos G.A. Smits, Julian A. Arts, Siebren Frölich, Rebecca R. Snabel, Branco M.H. Heuts, Joost H.A. Martens, Simon J. van Heeringen, Huiqing Zhou
Peer Reviewers Kenji Kamimoto; Marouen Ben Guebila
  • Funders
  • NWO grant 016 Vidi
  • NWO-ALW
  • ZonMw Open
LATEST VERSION PUBLISHED 29 Nov 2023
https://doi.org/10.12688/f1000research.125924.3
Method Article metrics
Revised
Gaidai reliability method for long-term coronavirus modelling
[version 3; peer review: 1 approved, 3 approved with reservations]
Oleg Gaidai, Ping Yan, Yihan Xing, JingXiang Xu, Yu Wu
Peer Reviewers Oluwakemi E Abiodun; Adnan Khan; Md. Ashraful Babu; Eduard Campillo-Funollet
LATEST VERSION PUBLISHED 21 Nov 2023
https://doi.org/10.12688/f1000research.134078.2
Method Article metrics
Revised
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data
[version 2; peer review: 2 approved, 1 approved with reservations]
Jinming Cheng, Gordon K. Smyth, Yunshun Chen
Peer Reviewers Michael D Morgan; Koen Van den berge; Anna Alemany, Xuan Quy Nguyen and Noëlle Dommann
  • Funders
  • National Health and Medical Research Council
  • Chan Zuckerberg Initiative
  • Medical Research Future Fund
LATEST VERSION PUBLISHED 10 Nov 2023
https://doi.org/10.12688/f1000research.123714.2
Research Article metrics
Revised
Identification of prognostic biomarkers of invasive ductal carcinoma by an integrated bioinformatics approach
[version 2; peer review: 1 approved, 1 approved with reservations]
Albeiro Marrugo-Padilla, Johana Márquez-Lázaro, Antistio Álviz-Amador
Peer Reviewers Xingxin Pan; Russell Hamilton
LATEST VERSION PUBLISHED 30 Oct 2023
https://doi.org/10.12688/f1000research.135151.1
Research Article metrics
Developing potential drugs for insomnia through computational analysis
[version 1; peer review: 1 approved, 1 approved with reservations]
Isaac Oronyi, Richard Kagia
Peer Reviewers Khaled M. Darwish; Yousaf Khan
PUBLISHED 16 Oct 2023
41-60 of 384 ARTICLES
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