Bioinformatics

Bioinformatics

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81-100 of 389 ARTICLES
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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
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
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.127647.1
Method Article metrics
Turning any bed into an intensive care unit with the Internet of things and artificial intelligence technology. Presenting the enhanced mechanical ventilator
[version 1; peer review: 1 approved, 2 approved with reservations]
Leidy Lorena Pulido Morales, Juan Sebastian Buitrago Romero, Ismael A. Ardila Sanchez, Fernando Yepes-Calderon
Peer Reviewers Christian Grévisse; Andres Felipe Montaño; Maria Florencia Pollo-Cattaneo
PUBLISHED 23 Dec 2022
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.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.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
81-100 of 389 ARTICLES
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  • 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
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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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    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
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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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