Bioinformatics

Bioinformatics

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61-80 of 377 ARTICLES
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 in 
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Editorial metrics NOT PEER REVIEWED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[version 1; peer review: not peer reviewed]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
  • Natural Sciences and Engineering Research Council of Canada
  • Ontario Institute for Cancer Research
  • Children's Health Research Institute
  • 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.129581.1
Software Tool Article metrics
AmpSeqR: an R package for amplicon deep sequencing data analysis
[version 1; peer review: 1 approved, 2 approved with reservations]
Jiru Han, Jacob E. Munro, Melanie Bahlo
Peer Reviewers Eduardo Castro-Nallar; Cristian Koepfli and Gustavo Da Silva; Patrick Murigu Kamau Njage
  • Funders
  • National Health and Medical Research Council
  • Institute Infrastructure Support Scheme (IRIISS)
PUBLISHED 23 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
https://doi.org/10.12688/f1000research.129161.1
Software Tool Article metrics
AMAW: automated gene annotation for non-model eukaryotic genomes
[version 1; peer review: 3 approved with reservations, 1 not approved]
Loïc Meunier, Denis Baurain, Luc Cornet
Peer Reviewers B. Franz Lang; Guifré Torruella; James Titus-McQuillan; Laura Ruiz Torres and Bruno Contreras-Moreira
  • Funders
  • BELSPO
  • F.R.S.-FNRS
PUBLISHED 16 Feb 2023
https://doi.org/10.12688/f1000research.128982.1
Software Tool Article metrics
Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE)
[version 1; peer review: 2 approved]
Yuda Munarko, Anand Rampadarath, David Nickerson
Peer Reviewers Socrates Dokos; Garima Malik
  • Funders
  • National Institutes of Health
  • Aotearoa Foundation
  • Auckland Bioengineering Institute
PUBLISHED 10 Feb 2023
https://doi.org/10.12688/f1000research.130105.1
Research Article metrics
Determination of pharmacological activity of bioactives in Allium sativum using computational analysis
[version 1; peer review: 2 approved with reservations]
Stephen Ouma, Richard Kagia, Faith Kamakia
Peer Reviewers Rahadian Zainul; Sandeep Kumar
PUBLISHED 09 Feb 2023
https://doi.org/10.12688/f1000research.126840.2
Software Tool Article metrics
Revised
Gene expression data visualization tool on the o²S²PARC platform
[version 2; peer review: 2 approved]
Hiba Ben Aribi, Mengyuan Ding, Anmol Kiran
Peer Reviewers Joost B. M. Wagenaar; Esra Neufeld
LATEST VERSION PUBLISHED 06 Feb 2023
https://doi.org/10.12688/f1000research.129490.1
Research Article metrics
Toblerone: detecting exon deletion events in cancer using RNA-seq
[version 1; peer review: 2 approved]
Andrew Lonsdale, Andreas Halman, Lauren Brown, Hansen Kosasih, Paul Ekert, Alicia Oshlack
Peer Reviewers Katherine Pillman; Matt Field
  • Funder
  • National Health and Medical Research Council
PUBLISHED 03 Feb 2023
https://doi.org/10.12688/f1000research.129945.1
Editorial metrics NOT PEER REVIEWED
ISCB Student Council Symposium 2021, a virtual global venue: challenges and lessons learned
[version 1; peer review: not peer reviewed]
Cleidy Osorio-Mogollon, Victor Grentzinger, Gabriel J. Olguin-Orellana, Sebastian Ayala-Ruano, Shruti Gupta, Pradeep Eranti, Aayush Grover, Bart Cuypers, Nazeefa Fatima, Sayane Shome, Farzana Rahman, R. Gonzalo Parra
PUBLISHED 12 Jan 2023
61-80 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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    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
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