Bioinformatics

Bioinformatics

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41-60 of 377 ARTICLES
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 in 
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
https://doi.org/10.12688/f1000research.126839.3
Method Article metrics
Revised
Manual annotation of Drosophila genes: a Genomics Education Partnership protocol
[version 3; peer review: 2 approved]
Chinmay P. Rele, Katie M. Sandlin, Wilson Leung, Laura K. Reed
Peer Reviewers Terence D. Murphy; Madeline Crosby
  • Funders
  • National Institute of General Medical Sciences of the National Institutes of Health
  • National Science Foundation
LATEST VERSION PUBLISHED 13 Oct 2023
https://doi.org/10.12688/f1000research.139488.1
Software Tool Article metrics
Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation.
[version 1; peer review: 2 approved, 1 approved with reservations]
Felipe Marques de Almeida, Tatiana Amabile de Campos, Georgios Joannis Pappas Jr
Peer Reviewers Abdolrahman Khezri; Abhinav Sharma and Emilyn Costa Conceição; Austin G Davis-Richardson
  • Funders
  • Scholarship by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
  • Grant by Fundação de Amparo à Pesquisa do Distrito Federal (FAP-DF)
PUBLISHED 25 Sep 2023
https://doi.org/10.12688/f1000research.130458.2
Software Tool Article metrics
Revised
Numerical Scheme for Compartmental Models: New Matlab Software Codes for Numerical Simulation
[version 2; peer review: 2 approved]
Samuel Okyere, Joseph Ackora-Prah, Ebenezer Bonyah, Samuel Akwasi Adarkwa
Peer Reviewers Belela Samuel Kotola; Shewafera Wondimagegnhu Teklu
LATEST VERSION PUBLISHED 25 Sep 2023
https://doi.org/10.12688/f1000research.138618.1
Research Article metrics AWAITING PEER REVIEW
Choice of bead-beater instrument can result in significant differences in the outcome of host-associated microbiome studies
[version 1; peer review: awaiting peer review]
Ashvini Chauhan, Christian Chukwujindu, Ashish Pathak
Peer Reviewers Invited
  • Funders
  • Department of Energy Minority Serving Institution Partnership Program (MSIPP)
  • Department of Defense
  • National Energy Technology Laboratory
  • National Science Foundation
PUBLISHED 01 Sep 2023
https://doi.org/10.12688/f1000research.134526.1
Research Article metrics
Benchmarking graph representation learning algorithms for detecting modules in molecular networks
[version 1; peer review: 1 approved, 1 approved with reservations]
Zhiwei Song, Brittany Baur, Sushmita Roy
Peer Reviewers Claude Pasquier and Nina Singlan; Renming Liu
  • Funders
  • James S. McDonnell Foundation
  • National Human Genome Research Institute
PUBLISHED 07 Aug 2023
https://doi.org/10.12688/f1000research.53453.2
Software Tool Article metrics
Revised
multiomics: A user-friendly multi-omics data harmonisation R pipeline
[version 2; peer review: 1 approved, 4 not approved]
Tyrone Chen, Al J Abadi, Kim-Anh Lê Cao, Sonika Tyagi
Peer Reviewers Javad Zahiri; Arjun Krishnan; Giri Narasimhan and Parshatd Govindasamy; Junyi Chen; Prashanth Suravajhala
  • Funders
  • Australian Women Research Success Grant - Monash University
  • Monash Faculty of Science Dean’s Postgraduate Research Scholarship - Monash University
  • Australian Government Research Training Program Scholarship
  • National Health and Medical Research Council
  • Australia-India Strategic Research Fund Early- and Mid-Career Researcher Fellowship
LATEST VERSION PUBLISHED 02 Aug 2023
https://doi.org/10.12688/f1000research.131861.2
Research Article metrics
Revised
Single-cell transcriptional uncertainty landscape of cell differentiation
[version 2; peer review: 2 approved]
Nan Papili Gao, Olivier Gandrillon, András Páldi, Ulysse Herbach, Rudiyanto Gunawan
Peer Reviewers Alessandro Giuliani; Geneviève Dupont
  • Funders
  • Swiss National Science Foundation
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 20 Jul 2023
41-60 of 377 ARTICLES
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    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
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    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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