Bioinformatics

Bioinformatics

track_changes Track Tracking Be alerted when new articles are added in this gateway (manage your tracking alerts via your account) Stop tracking this gateway
Home Gateways Bioinformatics
61-80 of 384 ARTICLES
Previous Next
 in 
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
https://doi.org/10.12688/f1000research.132106.2
Research Article metrics
Revised
Nigella sativa L. seed extracts promote wound healing progress by activating VEGF and PDGF signaling pathways: An in vitro and in silico study
[version 2; peer review: 3 approved, 1 approved with reservations]
Chella Perumal Palanisamy, Phaniendra Alugoju, Selvaraj Jayaraman, Sirilux Poompradub
Peer Reviewers Balasubramani Ravindran; Monica Mironescu; Viji Rajendran; Vinothkannan Ravichandran
  • Funders
  • Center of Excellence in Green Materials for Industrial Application
  • Chulalongkorn University
LATEST VERSION PUBLISHED 21 Jun 2023
https://doi.org/10.12688/f1000research.135767.1
Editorial metrics NOT PEER REVIEWED
1st ASCS: Expanding the ISCB Student Council Symposia to Asia
[version 1; peer review: not peer reviewed]
Aayush Grover, Arsalan Riaz, Syed Muktadir Al Sium, Fatma B. Dincaslan, Sanjana Fatema Chowdhury, Gabriel J Olguin-Orellana, R. Gonzalo Parra, Pradeep Eranti
PUBLISHED 20 Jun 2023
https://doi.org/10.12688/f1000research.132587.2
Software Tool Article metrics
Revised
CRUMB: a shiny-based app to analyze rhythmic feeding in Drosophila using the FLIC system
[version 2; peer review: 2 approved]
Sergio Hidalgo, Joanna C Chiu
Peer Reviewers Abhilash Lakshman; Daniel J. Cavanaugh
  • Funders
  • Pew Charitable Trusts
  • National Institute of Diabetes and Digestive and Kidney Diseases
LATEST VERSION PUBLISHED 19 Jun 2023
https://doi.org/10.12688/f1000research.132538.1
Research Article metrics
Discordant results among major histocompatibility complex binding affinity prediction tools
[version 1; peer review: 2 approved with reservations, 1 not approved]
Austin Nguyen, Abhinav Nellore, Reid F. Thompson
Peer Reviewers André Leier; Michael E Birnbaum; Nikolaos G Sgourakis and Sagar Gupta
PUBLISHED 07 Jun 2023
https://doi.org/10.12688/f1000research.125579.1
Research Article metrics
Cell-type classification of cancer single-cell RNA-seq data using the Subsemble ensemble-based machine learning classifier
[version 1; peer review: 3 approved with reservations]
David Chen, Parisa Shooshtari
Peer Reviewers Saskia Freytag; Yue Cao; Zhixiang Ren
  • Funders
  • Children's Health Research Institute
  • Ontario Institute for Cancer Research
  • Natural Sciences and Engineering Research Council of Canada
  • NSERC Undergraduate Student Research Award
PUBLISHED 14 Apr 2023
https://doi.org/10.12688/f1000research.111658.2
Software Tool Article metrics
Revised
GRAPE: genomic relatedness detection pipeline
[version 2; peer review: 2 approved]
Alexander Medvedev, Mikhail Lebedev, Andrew Ponomarev, Mikhail Kosaretskiy, Dmitriy Osipenko, Alexander Tischenko, Egor Kosaretskiy, Hui Wang, Dmitry Kolobkov, Vitalina Chamberlain-Evans, Ruslan Vakhitov, Pavel Nikonorov
Peer Reviewers Ying Zhou; Ardalan Naseri
  • Funder
  • GenX Global Limited
LATEST VERSION PUBLISHED 13 Apr 2023
https://doi.org/10.12688/f1000research.126463.2
Software Tool Article metrics
Revised
A2TEA: Identifying trait-specific evolutionary adaptations
[version 2; peer review: 2 approved]
Tyll Stöcker, Carolin Uebermuth-Feldhaus, Florian Boecker, Heiko Schoof
Peer Reviewers Manuel Aranda and Octavio Salazar Moya; Rahul Siddharthan
LATEST VERSION PUBLISHED 12 Apr 2023
https://doi.org/10.12688/f1000research.128656.1
Method Article metrics
Phylogenetic placement of whole genome duplications in yeasts through quantitative analysis of hierarchical orthologous groups
[version 1; peer review: 1 approved with reservations, 1 not approved]
Samuel Moix, Natasha Glover, Sina Majidian
Peer Reviewers Xinyi Guo; Gavin Conant
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
PUBLISHED 12 Apr 2023
https://doi.org/10.12688/f1000research.130443.1
Research Article metrics
Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning
[version 1; peer review: 2 approved]
Margaux Aubel, Lars Eicholt, Erich Bornberg-Bauer
Peer Reviewers Caroline Weisman; Isabelle Callebaut
  • Funder
  • Volkswagen Foundation
PUBLISHED 29 Mar 2023
https://doi.org/10.12688/f1000research.122949.2
Software Tool Article metrics
Revised
DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data
[version 2; peer review: 2 approved]
Miriam Riquelme-Perez, Fernando Perez-Sanz, Jean-François Deleuze, Carole Escartin, Eric Bonnet, Solène Brohard
Peer Reviewers Hélène Hirbec; Wenbin Guo
  • Funder
  • PhD fellowship from the CEA (Amont-Aval).
LATEST VERSION PUBLISHED 24 Mar 2023
https://doi.org/10.12688/f1000research.130024.1
Research Article metrics
Identification of potential compounds for the management of multidrug-resistant tuberculosis using computational methods
[version 1; peer review: 2 not approved]
Winnie Gatwiri, Richard Kagia
Peer Reviewers Manish Dwivedi; Grace Mugumbate
PUBLISHED 17 Mar 2023
https://doi.org/10.12688/f1000research.131522.1
Research Article metrics
Seasonal effects decouple SARS-CoV-2 haplotypes worldwide
[version 1; peer review: 2 approved]
Tre Tomaszewski, Muhammad Asif Ali, Kelsey Caetano-Anollés, Gustavo Caetano-Anollés
Peer Reviewers Francisco Solano Muñoz; Kyung Mo Kim
  • Funders
  • National Centre for Supercomputing Applications
  • Office of Research and Office of International Programs, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign
  • National Institute of Food and Agriculture
PUBLISHED 13 Mar 2023
https://doi.org/10.12688/f1000research.128091.2
Software Tool Article metrics
Revised
SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes
[version 2; peer review: 2 approved]
Nachida Tadrent, Franck Dedeine, Vincent Hervé
Peer Reviewers Célio Dias Santos Júnior; Aram Mikaelyan
  • Funders
  • Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
  • Université de Tours
  • Centre National de la Recherche Scientifique
  • European Regional Development Fund
LATEST VERSION PUBLISHED 27 Feb 2023
61-80 of 384 ARTICLES
Previous Next
Gateway Areas
  • Methods and Tools
    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
  • Genetics and Genomics
    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
  • Transcriptomics
    By curating all outputs related to the analysis of the RNA transcripts produced by a genotype, the Transcriptomics Gateway Area will allow readers to easily access content pertinent to this research. Read more keyboard_arrow_right
  • Proteomics
    The Proteomics Gateway Area has been established to allow authors to access and publish research content related to the large-scale study of entire sets of proteins as proteomes. Read more keyboard_arrow_right
  • Metagenomics
    This Gateway Area will allow members of the bioinformatics community to collate all research related to the collection of genomes from an environmental sample. Read more keyboard_arrow_right
ISCB News and Announcements open_in_new
Our Links
Sign In
If you've forgotten your password, please enter your email address below and we'll send you instructions on how to reset your password.

The email address should be the one you originally registered with F1000.
Email address not valid, please try again

You registered with F1000 via Google, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Google account password, please click here.

You registered with F1000 via Facebook, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Facebook account password, please click here.

Code not correct, please try again
Email us for further assistance.
Server error, please try again.