Bioinformatics

Bioinformatics

Metagenomics

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1-20 of 20 ARTICLES
 in 
https://doi.org/10.12688/f1000research.154432.2
Research Article metrics
Revised
Deep learning neural network development for the classification of bacteriocin sequences produced by lactic acid bacteria
[version 2; peer review: 4 approved]
Lady L. González, Isaac Arias-Serrano, Fernando Villalba-Meneses, Paulo Navas-Boada, Jonathan Cruz-Varela
Peer Reviewers John J. Georrge; Alaa Kareem Niamah; Ismail Erol; Cristóbal Joel González-Pérez
LATEST VERSION PUBLISHED 20 Jun 2025
https://doi.org/10.12688/f1000research.152290.2
Software Tool Article metrics
Revised
Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG
[version 2; peer review: 2 approved, 1 approved with reservations]
Jeferyd Yepes-García, Laurent Falquet
Peer Reviewers Abraham Gihawi; Fotis Baltoumas; Juliette Hayer
  • Funders
  • Centenary Research Fund of the University of Fribourg
  • Fondation de Recherche en Biochimie, Epalinges, Switzerland
LATEST VERSION PUBLISHED 23 Sep 2024
https://doi.org/10.12688/f1000research.142843.2
Research Article metrics
Revised
In silico analysis of molecular mimicry between human aquaporin 3, Aspergillus fumigatus aquaporin and aquaporins from allergic sources
[version 2; peer review: 2 approved]
Andrés Sánchez, Yaquelin Padilla, Adriana Lorduy, Jorge Sanchez, Marlon Munera, Claudia Baena, Carlos Bernal, Juan Urrego
Peer Reviewers Celso Eduardo Olivier; Elizabeth Garcia
LATEST VERSION PUBLISHED 12 Sep 2024
https://doi.org/10.12688/f1000research.134798.2
Software Tool Article metrics
Revised
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
[version 2; peer review: 1 approved, 3 approved with reservations]
Maxime Borry, Adrian Forsythe, Aida Andrades Valtueña, Alexander Hübner, Anan Ibrahim, Andrea Quagliariello, Anna E. White, Arthur Kocher, Åshild J. Vågene‬, Bjørn Peare Bartholdy, Diāna Spurīte, Gabriel Yaxal Ponce-Soto, Gunnar Neumann, I-Ting Huang, Ian Light, Irina M. Velsko, Iseult Jackson, Jasmin Frangenberg, Javier G. Serrano, Julien Fumey, Kadir T. Özdoğan, Kelly E. Blevins, Kevin G. Daly, Maria Lopopolo, Markella Moraitou, Megan Michel, Meriam van Os, Miriam J. Bravo-Lopez, Mohamed S. Sarhan, Nihan D. Dagtas, Nikolay Oskolkov, Olivia S. Smith, Ophélie Lebrasseur, Piotr Rozwalak, Raphael Eisenhofer, Sally Wasef, Shreya L. Ramachandran, Valentina Vanghi, Christina Warinner, James A. Fellows Yates
Peer Reviewers Timothy Read and Robert Petit III; Jonas Coelho Kasmanas; Intikhab Alam; Emma Griffiths
  • Funders
  • Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
  • Carlsbergfondet
  • H2020 European Research Council
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek
  • Knut och Alice Wallenbergs Stiftelse
  • National Institutes of Health
  • Carl Tryggers Stiftelse för Vetenskaplig Forskning
  • Deutsche Forschungsgemeinschaft
  • Friedrich-Schiller-Universität Jena
  • Science for Life Laboratory National Sequencing Projects
  • Werner Siemens-Stiftung
  • Max-Planck-Gesellschaft
  • National Science Foundation
  • Leverhulme Trust
  • Svenska Forskningsrådet Formas
  • Science Foundation Ireland-Irish Research Council
  • Science Foundation Ireland Centre for Research Training in Genomics Data Science
  • Università degli Studi di Padova
  • Institut Pasteur
  • H2020 Marie Skłodowska-Curie Actions
LATEST VERSION PUBLISHED 28 May 2024
https://doi.org/10.12688/f1000research.134465.2
Research Article metrics
Revised
Spatiotemporal structure and composition of the microbial communities in hypersaline Lake Magadi, Kenya
[version 2; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Alex Kipnyargis, Eucharia Kenya, Fathiya Khamis, Romano Mwirichia
Peer Reviewers Marianne Haines; Srijak Bhatnagar; Cristiano Pedroso-Roussado; Addis Simachew
  • Funder
  • National Research Fund, Kenya
LATEST VERSION PUBLISHED 17 May 2024
https://doi.org/10.12688/f1000research.135151.1
Research Article metrics
Developing potential drugs for insomnia through computational analysis
[version 1; peer review: 1 approved, 1 approved with reservations]
Isaac Oronyi, Richard Kagia
Peer Reviewers Khaled M. Darwish; Yousaf Khan
PUBLISHED 16 Oct 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.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.108835.2
Software Tool Article metrics
Revised
SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline
[version 2; peer review: 2 approved, 1 approved with reservations]
John Krapohl, Brett E. Pickett
Peer Reviewers Tobias Jakobi; Michael J Roach; Lauren Mak
LATEST VERSION PUBLISHED 28 Apr 2022
https://doi.org/10.12688/f1000research.51494.2
Method Article metrics
Revised
The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis
[version 2; peer review: 1 approved, 2 approved with reservations]
Zoey R. Werbin, Briana Hackos, Jorge Lopez-Nava, Michael C. Dietze, Jennifer M. Bhatnagar
Peer Reviewers Naupaka Zimmerman; William Nelson; Olubukola Oluranti Babalola
  • Funder
  • National Science Foundation
LATEST VERSION PUBLISHED 23 Mar 2022
https://doi.org/10.12688/f1000research.26452.1
Software Tool Article metrics
Lessons learned in virulence factor identification and data management from a hackathon on microbial virulence
[version 1; peer review: 1 approved, 1 approved with reservations]
Brett E. Pickett, Ryan Connor, Tamiru Berhanu-Denka, Sherry Bhalla, Vyacheslav Brover, Michael James Chambers, Kumardeep Chaudhary, Ousmane H. Cissé, Allissa Dillman, Moamen M. Elmassry, Michael Feldgarden, Eric Holloway, Xin Huang, William Klimke, Catarina Inês Mendes, S. Elizabeth Norred, Jonathan Parkinson, Samantha Sevilla, Monica Garcia Solache, Defne Surujon, Udana Torian, Vadim Zalunin, Ben Busby
Peer Reviewers Rick Stevens and James Davis; Kevin Tyler
  • Funders
  • Fundação para a Ciência e a Tecnologia
  • Scientific and Technological Research Council of Turkey
  • Intramural Research Program of the National Library of Medicine
PUBLISHED 09 Feb 2022
https://doi.org/10.12688/f1000research.107886.1
Editorial metrics NOT PEER REVIEWED
Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey
[version 1; peer review: not peer reviewed]
Yasin Kaya, Tülay Karakulak, Cemil Can Saylan, E. Ravza Gür, Engin Tatlıdil, Sevilay Güleşen, Fatma Betül Dinçaslan, Handan Melike Dönertaş
  • Funder
  • ISCB Student Council
PUBLISHED 26 Jan 2022
https://doi.org/10.12688/f1000research.53821.2
Software Tool Article metrics
Revised
snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data
[version 2; peer review: 2 approved, 1 approved with reservations]
Christina Vasilopoulou, Benjamin Wingfield, Andrew P. Morris, William Duddy
Peer Reviewers Andries T. Marees; Stephanie M. Gogarten; Anna Ulrich
  • Funders
  • Northern Ireland Public Health Agency (HSC R&D)
  • EU Regional Development Fund (ERDF) EU Sustainable Competitiveness Programme for Northern Ireland
LATEST VERSION PUBLISHED 29 Nov 2021
https://doi.org/10.12688/f1000research.54418.1
Software Tool Article metrics
Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality
[version 1; peer review: 2 approved]
Davide Albanese, Claudio Donati
Peer Reviewers Thomas S. B. Schmidt, Anthony Fullam and Askarbek Orakov; Denis Baurain
  • Funder
  • Autonomous Province of Trento (Accordo di Programma)
PUBLISHED 17 Aug 2021
https://doi.org/10.12688/f1000research.24345.2
Software Tool Article metrics
Update
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
[version 2; peer review: 3 approved]
Justin Wagner, Jayaram Kancherla, Domenick Braccia, James Matsumara, Victor Felix, Jonathan Crabtree, Anup Mahurkar, Héctor Corrada Bravo
Peer Reviewers Ekaterina Smirnova; Edoardo Pasolli; Levi Waldron
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 21 Jun 2021
https://doi.org/10.12688/f1000research.27384.1
Software Tool Article metrics
Meta-Signer: Metagenomic Signature Identifier based onrank aggregation of features
[version 1; peer review: 1 approved with reservations, 1 not approved]
Derek Reiman, Ahmed Metwally, Jun Sun, Yang Dai
Peer Reviewers Braden T Tierney; Boyang JI
PUBLISHED 09 Mar 2021
https://doi.org/10.12688/f1000research.40666.1
Editorial metrics NOT PEER REVIEWED
6th European Student Council Symposium (ESCS): overcoming obstacles to enhance virtuality, connectivity, inclusivity and community engagement
[version 1; peer review: not peer reviewed]
Gabriel J. Olguín-Orellana, Sofia Papadimitriou, Alberto Langtry Yáñez, Pradeep Eranti, Rosario del Carmen Flores-Vallejo, Ana I. Castillo-Orozco, Kalaumari Mayoral-Peña, R. Gonzalo Parra
  • Funder
  • ISCB Student Council; Information Technology for Translational Medicine (ITTM) Solutions
PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.27268.1
Software Tool Article metrics
rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
[version 1; peer review: 2 approved]
Sebastien Theil, Etienne Rifa
Peer Reviewers Florent Murat; Simon Roux
PUBLISHED 07 Jan 2021
https://doi.org/10.12688/f1000research.28330.1
Editorial metrics NOT PEER REVIEWED
4th ISCB Latin American Student Council Symposium: a virtual and inclusive experience during COVID-19 times
[version 1; peer review: not peer reviewed]
Camila Castillo-Vilcahuaman, Catalina Valdivia, Cleidy Osorio-Mogollón, Claudia Silva-Andrade, Rafael Puche-Quiñonez, Sebastián Ayala-Ruano, Yesid Cuesta-Astroz, R. Gonzalo Parra
  • Funder
  • ISCB Student Council
PUBLISHED 15 Dec 2020
https://doi.org/10.12688/f1000research.20408.1
Editorial metrics NOT PEER REVIEWED
Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers
[version 1; peer review: not peer reviewed]
Sayane Shome, R. Gonzalo Parra, Nazeefa Fatima, Alexander Miguel Monzon, Bart Cuypers, Yumna Moosa, Nilson Da Rocha Coimbra, Juliana Assis, Carla Giner-Delgado, Handan Melike Dönertaş, Yesid Cuesta-Astroz, Geetha Saarunya, Imane Allali, Shruti Gupta, Ambuj Srivastava, Manisha Kalsan, Catalina Valdivia, Gabriel J. Olguin-Orellana, Sofia Papadimitriou, Daniele Parisi, Nikolaj Pagh Kristensen, Leonor Rib, Marouen Ben Guebila, Eugen Bauer, Gaia Zaffaroni, Amel Bekkar, Efejiro Ashano, Lisanna Paladin, Marco Necci, Nicolás N. Moreyra, Martin Rydén, Jordan Villalobos-Solís, Nikolaos Papadopoulos, Candice Rafael, Tülay Karakulak, Yasin Kaya, Yvonne Gladbach, Sandeep Kumar Dhanda, Nikolina Šoštarić, Aishwarya Alex, Dan DeBlasio, Farzana Rahman
  • Funder
  • International Society for Computational Biology
PUBLISHED 02 Sep 2019
1-20 of 20 ARTICLES
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
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