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https://doi.org/10.12688/f1000research.122949.2
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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.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.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.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
https://doi.org/10.12688/f1000research.52791.3
Software Tool Article metrics
Revised
Sherlock: an open-source data platform to store, analyze and integrate Big Data for computational biologists
[version 3; peer review: 2 approved]
Balazs Bohar, David Fazekas, Matthew Madgwick, Luca Csabai, Marton Olbei, Tamás Korcsmáros, Mate Szalay-Beko
Peer Reviewers John H. Morris; Nadezhda Doncheva
  • Funders
  • Earlham Institute
  • Biotechnology and Biological Sciences Research Council
  • Quadram Institute Bioscience
LATEST VERSION PUBLISHED 12 Jan 2023
https://doi.org/10.12688/f1000research.110492.2
Research Article metrics
Revised
From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)
[version 2; peer review: 2 approved]
Maksim Nesterenko, Aleksei Miroliubov
Peer Reviewers Andreas Hejnol and Ferenc Kagan; Viatcheslav Ivanenko
  • Funder
  • Russian Science Foundation
LATEST VERSION PUBLISHED 09 Jan 2023
https://doi.org/10.12688/f1000research.110903.2
Software Tool Article metrics
Revised
SL-Cloud: A Cloud-based resource to support synthetic lethal interaction discovery
[version 2; peer review: 2 approved]
Bahar Tercan, Guangrong Qin, Taek-Kyun Kim, Boris Aguilar, John Phan, William Longabaugh, David Pot, Christopher J. Kemp, Nyasha Chambwe, Ilya Shmulevich
Peer Reviewers Jane Usher; Nishanth Ulhas Nair
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 22 Dec 2022
https://doi.org/10.12688/f1000research.128354.1
Method Article metrics
BOREALIS: an R/Bioconductor package to detect outlier methylation from bisulfite sequencing data
[version 1; peer review: 2 approved with reservations]
Gavin R. Oliver, W. Garrett Jenkinson, Rory J. Olson, Laura E. Schultz-Rogers, Eric W. Klee
Peer Reviewers Philipp Jurmeister and Maximilian Leitheiser; Vicente Yepez
  • Funder
  • Center for Individualized Medicine, Mayo Clinic
PUBLISHED 20 Dec 2022
https://doi.org/10.12688/f1000research.123384.2
Research Article metrics
Revised
In silico and in vitro analysis of THCA synthase gene in Moroccan Cannabis sativa, L
[version 2; peer review: 1 approved with reservations, 3 not approved]
Fadwa Badrana, El Mostafa El Fahime, Abdelrhani Mokhtari, Abdelmajid Soulaymani, Najete Safini, Bouchra Chaouni, Gabriel Malka, Hamid El Amri
Peer Reviewers Supaart Sirikantaramas; Noureddine Hamamouch; Narayanan Srividya; Yuanyuan Liu
  • Funders
  • Center for Scientific and Technical Research in Rabat
  • University Ibn Tofail
  • Genetics Analysis Institute of the Royal Gendarmerie of Morocco
LATEST VERSION PUBLISHED 15 Dec 2022
https://doi.org/10.12688/f1000research.74395.3
Research Article metrics
Revised
Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces
[version 3; peer review: 2 approved]
Francesco Raimondi, Joshua G. Burkhart, Matthew J. Betts, Robert B. Russell, Guanming Wu
Peer Reviewers Andras Szilagyi; Pier Luigi Martelli
  • Funders
  • Associazione Italiana per la Ricerca sul Cancro
  • Germany Research Foundation
  • Italian Ministry of University and Research
  • Alexander von Humboldt-Stiftung
  • U.S. National Library of Medicine
  • National Human Genome Research Institute
LATEST VERSION PUBLISHED 12 Dec 2022
https://doi.org/10.12688/f1000research.128391.1
Research Article metrics
Evaluation of cytosine conversion methods for whole-genome DNA methylation profiling
[version 1; peer review: 2 not approved]
Shyaron Poudel, Brett Hale, Asela J. Wijeratne
Peer Reviewers Aaron John Stevens; Sadaruddin Chachar
  • Funders
  • Arkansas State University
  • Arkansas Biosciences Institute
PUBLISHED 07 Dec 2022
https://doi.org/10.12688/f1000research.109027.2
Software Tool Article metrics
Revised
Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App
[version 2; peer review: 1 approved, 1 approved with reservations]
Pritam Saha, Özgun Babur, Chris Sander, Augustin Luna
Peer Reviewers Ruth Isserlin; Katsuyuki Yugi
  • Funders
  • Google
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 14 Nov 2022
https://doi.org/10.12688/f1000research.73420.2
Software Tool Article metrics
Revised
PDBrt: A free database of complexes with measured drug-target residence time
[version 2; peer review: 1 approved, 1 approved with reservations]
Magdalena Ługowska, Marcin Pacholczyk
Peer Reviewers Wiesław Nowak; Marian Novotny
  • Funders
  • European Social Fund
  • Polish National Science Centre
  • Silesian University of Technology
LATEST VERSION PUBLISHED 31 Oct 2022
https://doi.org/10.12688/f1000research.124160.1
Research Article metrics
Polypharmacological drug design opportunities against Parkinson's disease
[version 1; peer review: 1 approved, 1 approved with reservations]
Ezra Michelet Garcia-Romero, Edgar López-López, Catalina Soriano-Correa, José L. Medina-Franco, Carolina Barrientos-Salcedo
Peer Reviewers Giulio Rastelli; Yassir Boulaamane and Iman Touati
PUBLISHED 17 Oct 2022
https://doi.org/10.12688/f1000research.19426.2
Software Tool Article metrics
Revised
Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads
[version 2; peer review: 2 approved]
Andrian Yang, Joshua Y. S. Tang, Michael Troup, Joshua W. K. Ho
Peer Reviewers Quan Nguyen; Marco Previtali and Luca Denti
  • Funders
  • National Heart Foundation of Australia
  • Amazon Web Services
  • National Health and Medical Research Council
  • Department of Education, Australian Governement
LATEST VERSION PUBLISHED 13 Oct 2022
https://doi.org/10.12688/f1000research.125381.1
Editorial metrics NOT PEER REVIEWED
Highlights of the 1st Ecuadorian-Venezuelan Symposium of Young Researchers in Bioinformatics (1SEVJIB)
[version 1; peer review: not peer reviewed]
Sebastian Ayala-Ruano, Fernando Hernandez, Arantxa Ortega, Deliana Infante, Daniela Carrascal, Karen Sánchez-Luquez, Rafael Puche-Quiñonez
PUBLISHED 22 Sep 2022
https://doi.org/10.12688/f1000research.125043.1
Editorial metrics NOT PEER REVIEWED
BOSC 2022: the first hybrid and 23rd annual Bioinformatics Open Source Conference
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Karsten Hokamp, Hervé Ménager, Monica C. Munoz-Torres, Deepak Unni, Nicole Vasilevsky, Jason Williams
  • Funders
  • DBI-1265383
  • RM1 HG010860
  • R24 OD011883
  • DBI-0735191
  • DBI-1743442
PUBLISHED 12 Sep 2022
81-100 of 638 ARTICLES
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