Bioinformatics

Bioinformatics

Genetics and Genomics

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https://doi.org/10.12688/f1000research.168786.1
Software Tool Article metrics
Identification of Viral Variants from Functional Genomics Data
[version 1; peer review: 1 approved with reservations]
Florian Röckl, Caroline C. Friedel
Peer Reviewers Dóra Tombácz
  • Funder
  • Deutsche Forschungsgemeinschaft
PUBLISHED 18 Aug 2025
https://doi.org/10.12688/f1000research.131134.2
Research Article metrics
Revised
Improving genomic prediction of rhizomania resistance in sugar beet (Beta vulgaris L.) by implementing epistatic effects and feature selection
[version 2; peer review: 1 approved with reservations, 3 not approved]
Thomas Martin Lange, Felix Heinrich, Friedrich Kopisch-Obuch, Harald Keunecke, Mehmet Gültas, Armin O. Schmitt
Peer Reviewers J Mitchell McGrath; Muhammad Massub Tehseen; Daniela Holtgräwe; Chenggen Chu
LATEST VERSION PUBLISHED 28 Aug 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]
Meryem Fakhkhari, Bouabid Badaoui, Hicham Oumzil, Khalid Sadki
Peer Reviewers Gustavo Fioravanti Vieira
PUBLISHED 20 May 2024
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.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.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.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.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.127935.1
Genome Note metrics
Draft genome of a clinical Pseudomonas qingdaonensis isolate from a hospitalized patient at Kenyatta National Hospital, Kenya
[version 1; peer review: 2 approved]
Brian Ogoti, Racheal Gachogo, Frank Onyambu
Peer Reviewers Gerald Mboowa; Aquillah Kanzi
  • Funder
  • Center of Molecular Biosciences
PUBLISHED 21 Dec 2022
https://doi.org/10.12688/f1000research.122113.1
Method Article metrics
Interactive visualization of spatial omics neighborhoods
[version 1; peer review: 2 approved with reservations]
Tinghui Xu, Kris Sankaran
Peer Reviewers Guangdun Peng and Miao Zhu; Oscar Ospina
PUBLISHED 18 Jul 2022
https://doi.org/10.12688/f1000research.53842.2
Opinion Article metrics
Revised
Python for gene expression
[version 2; peer review: 2 approved]
Leonid Bystrykh
Peer Reviewers Sergio Peignier; Yasha Hasija
LATEST VERSION PUBLISHED 23 Jun 2022
https://doi.org/10.12688/f1000research.121775.1
Software Tool Article metrics
eXNVerify: coverage analysis for long and short-read sequencing data in clinical context
[version 1; peer review: 2 approved, 1 approved with reservations]
Sebastian Porębski, Tomasz Stokowy
Peer Reviewers Zebin Zhang; Xueyi Dong; Wouter De Coster
  • Funders
  • Bergen Research Foundation
  • Research Council of Norway
  • Silesian University of Technology
PUBLISHED 13 Jun 2022
https://doi.org/10.12688/f1000research.73600.2
Software Tool Article metrics
Revised
Doublet identification in single-cell sequencing data using scDblFinder
[version 2; peer review: 2 approved]
Pierre-Luc Germain, Aaron Lun, Carlos Garcia Meixide, Will Macnair, Mark D. Robinson
Peer Reviewers Zev J. Gartner and Chris McGinnis; Dennis Kostka and Hannah Schriever
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 16 May 2022
https://doi.org/10.12688/f1000research.114698.1
Method Article metrics
DeepReGraph co-clusters temporal gene expression and cis-regulatory elements through heterogeneous graph representation learning
[version 1; peer review: 1 approved, 1 approved with reservations]
Jesús Fernando Cevallos Moreno, Peyman Zarrineh, Aminael Sánchez-Rodríguez, Massimo Mecella
Peer Reviewers Wanding Zhou; Tallulah Andrews and Boris Tchatchoua Ngassam
  • Funders
  • Universidad Técnica Particular de Loja
  • ELIS Innovation Hub
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 13 May 2022
https://doi.org/10.12688/f1000research.110936.1
Research Article metrics
TReNCo: Topologically associating domain (TAD) aware regulatory network construction
[version 1; peer review: 2 not approved]
Christopher Bennett, Viren Amin, Daehwan Kim, Murat Can Cobanoglu, Venkat Malladi
Peer Reviewers Junbai Wang; Sonika Tyagi
  • Funders
  • National Institute of General Medical Sciences
  • Cancer Prevention and Research Institute of Texas
PUBLISHED 14 Apr 2022
https://doi.org/10.12688/f1000research.84360.1
Review metrics
Automated human chromosome segmentation and feature extraction: Current trends and prospects
[version 1; peer review: 2 approved with reservations]
Umaya Bhashini Balagalla, Jagath Samarabandu, Akila Subasinghe
Peer Reviewers Mousami Munot; Lamiaa Elrefae
PUBLISHED 11 Mar 2022
https://doi.org/10.12688/f1000research.26128.2
Method Article metrics
Revised
Space-log: a novel approach to inferring gene-gene net-works using SPACE model with log penalty
[version 2; peer review: 2 approved, 1 approved with reservations]
Qian (Vicky) Wu, Wei Sun, Li Hsu
Peer Reviewers Yuying Xie and Yuning Hao; Chi Song; Jessie Jeng
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 05 Jan 2022
https://doi.org/10.12688/f1000research.74524.1
Brief Report metrics
An Atlas of Plant Transposable Elements
[version 1; peer review: 2 approved]
Daniel Longhi Fernandes Pedro, Tharcisio Soares Amorim, Alessandro Varani, Romain Guyot, Douglas Silva Domingues, Alexandre Rossi Paschoal
Peer Reviewers Gökhan Karakülah; Adriana Ludwig
  • Funders
  • Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES)
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico
  • NAPI de Bioinformática - Fundação Araucária
  • NVIDIA from the GPU Grant Program 2019 - Accelerated Data Science Call for the GPU Seed Units: Titan V device
  • PROPPG - UTFPR
PUBLISHED 24 Nov 2021
https://doi.org/10.12688/f1000research.53926.2
Software Tool Article metrics
Revised
PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals
[version 2; peer review: 2 approved]
Peter Briggs, A. Louise Hunter, Shen-hsi Yang, Andrew D. Sharrocks, Mudassar Iqbal
Peer Reviewers Nicolae Radu Zabet; Aziz Khan
  • Funders
  • Medical Research Council (MRC)
  • Wellcome Trust
LATEST VERSION PUBLISHED 02 Nov 2021
1-20 of 30 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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