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 in 
https://doi.org/10.12688/f1000research.143633.3
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Identification of compounds from natural Peruvian sources as potential inhibitors of SARS-CoV-2 Mpro mutations by virtual screening and computational simulations
[version 3; peer review: 2 approved]
Haruna Luz Barazorda-Ccahuana, Eymi Gladys Cárcamo Rodriguez, Angela Emperatriz Centeno-Lopez, Margot Paco-Chipana, Luis Daniel Goyzueta-Mamani, Miguel Angel Chavez-Fumagalli
Peer Reviewers Tushar Joshi; Mohammed Bouachrine
  • Funder
  • Universidad Catolica de Santa Maria de Arequipa
LATEST VERSION PUBLISHED 22 Nov 2024
https://doi.org/10.12688/f1000research.157679.1
Research Article metrics
Feather keratin in Pavo cristatus: A tentative structure
[version 1; peer review: 1 approved]
Peter Russ, Helmut O.K. Kirchner, Herwig Peterlik, Ingrid M. Weiss
Peer Reviewers Boaz Pokroy
  • Funders
  • Carl-Zeiss-Stiftung
  • Universität Stuttgart
PUBLISHED 07 Nov 2024
https://doi.org/10.12688/f1000research.157160.1
Software Tool Article metrics
BEpipeR: a user-friendly, flexible, and scalable data synthesis pipeline for the Biodiversity Exploratories and other research consortia
[version 1; peer review: 1 approved with reservations, 1 not approved]
Marcel Glück, Oliver Bossdorf, Henri A. Thomassen
Peer Reviewers Elliot Gould; Matthias Grenié
  • Funder
  • Deutsche Forschungsgemeinschaft
PUBLISHED 24 Oct 2024
https://doi.org/10.12688/f1000research.73999.3
Research Article metrics
Revised
A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.
[version 3; peer review: 2 approved, 1 approved with reservations]
Rizone Al Hasib, Md. Chayan Ali, Md. Shahedur Rahman, Md. Mafizur Rahman, Fee Faysal Ahmed, Md. Abdullah Al Mashud, Md. Azizul Islam, Mohammad Abu Hena Mostofa Jamal
Peer Reviewers Thi Thanh Binh Nguyen; Rituraj Purohit; Behrooz sadeghi kalani
  • Funder
  • Ministry of Science and Technology, Government of the People’s Republic of Bangladesh
LATEST VERSION PUBLISHED 07 Oct 2024
https://doi.org/10.12688/f1000research.131508.2
Research Article metrics
Revised
In silico drug repurposing using molecular docking and dynamics to target the protein interaction between the SARS-CoV-2 S-glycoprotein and the ACE2 receptor
[version 2; peer review: 1 approved, 2 approved with reservations]
Dania Hussein, Abdullah Almatrafi, Mohammed Gomaa, AlAnood Alhowsawi, Sarah Almustafa, Hadi Alsaihaty, Manar Alghamdi
Peer Reviewers Prateek Kumar; Dr Manne Munikumar; Vipul Kumar and Vikas Tiwari
LATEST VERSION PUBLISHED 26 Jul 2024
https://doi.org/10.12688/f1000research.133724.2
Opinion Article metrics
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The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity
[version 2; peer review: 3 approved]
Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Bachir Balech, Endre Barta, Physilia Ying Shi Chua, Valeria Di Cola, Katharina F. Heil, Graham M. Hughes, Lars S. Jermiin, Matúš Kalaš, Jerry Lanfear, Evangelos Pafilis, Patricia M. Palagi, Aristotelis C. Papageorgiou, Joana Paupério, Fotis Psomopoulos, Niels Raes, Josephine Burgin, Toni Gabaldón
Peer Reviewers Patrick Comer; Abigail Benson and Stephen Formel; Cher FY Chow
  • Funders
  • Swiss State Secretariat for Education, Research and Innovation (SERI)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 22 May 2024
https://doi.org/10.12688/f1000research.111382.3
Research Article metrics
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Maxillary first premolar shape (and not size) as an indicator of sexual dimorphism: A 2D geomorphometric study
[version 3; peer review: 2 approved, 1 not approved]
Srikant Natarajan, Junaid Ahmed, Nidhin Philip Jose, Shravan Shetty
Peer Reviewers Aman Chowdhry; Julia Aramendi; Choy Ker Woon
  • Funder
  • Science and Engineering Research Board
LATEST VERSION PUBLISHED 16 Feb 2024
https://doi.org/10.12688/f1000research.127061.2
Research Article metrics
Revised
Understanding the high electronic quantum similarity of a series of ligands used as inhibitors of the SARS-CoV-2 virus by molecular mechanics and density functional theory approaches
[version 2; peer review: 1 approved, 2 approved with reservations, 3 not approved]
Alejandro Morales-Bayuelo, Jesús Sánchez-Márquez
Peer Reviewers Ahmed Metwaly; Ramon Carbó-Dorca; Kiran Bharat Lokhande; Vikram Dalal; Mohnad Abdalla; Sharvan Sehrawat
  • Funder
  • Fundación Universitaria Tecnológico Comfenalco
LATEST VERSION PUBLISHED 06 Feb 2024
https://doi.org/10.12688/f1000research.138059.1
Method Article metrics
A tutorial hub for realising the potential of tools within the SPARC ecosystem
[version 1; peer review: 2 approved with reservations]
Niloofar Shahidi, Omkar Athavale, Yuda Munarko, Mathias Roesler, Kenneth Tran
Peer Reviewers Bhavesh Patel; Andrey Andreev
PUBLISHED 08 Jan 2024
https://doi.org/10.12688/f1000research.143062.1
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COverlap: a Fiji toolset for the 3D co-localization of two fluorescent nuclear markers in confocal images
[version 1; peer review: 3 approved with reservations]
Mélodie Ambroset, Bruno Bontempi, Jean-Luc Morel
Peer Reviewers Thomas Boudier; Jean-Karim Heriche; Bijie Bai
  • Funders
  • Agence Nationale de la Recherche
  • Université de Bordeaux
  • Centre National de la Recherche Scientifique
  • Centre National d’Etudes Spatiales
PUBLISHED 03 Jan 2024
https://doi.org/10.12688/f1000research.123550.3
Research Article metrics
Revised
New findings on ligand series used as SARS-CoV-2 virus inhibitors within the frameworks of molecular docking, molecular quantum similarity and chemical reactivity indices
[version 3; peer review: 1 approved, 4 approved with reservations]
Alejandro Morales-Bayuelo, Jesús Sánchez-Márquez
Peer Reviewers Truong Tan Trung; Yogesh Kumar; M. Aravinthraj Aravinthraj; Emmanuel Kitete Mulongo; Naveen Shivalingegowda
  • Funder
  • UNISINU-2022-2
LATEST VERSION PUBLISHED 11 Dec 2023
https://doi.org/10.12688/f1000research.130530.2
Software Tool Article metrics
Revised
scANANSE gene regulatory network and motif analysis of single-cell clusters
[version 2; peer review: 2 approved]
Jos G.A. Smits, Julian A. Arts, Siebren Frölich, Rebecca R. Snabel, Branco M.H. Heuts, Joost H.A. Martens, Simon J. van Heeringen, Huiqing Zhou
Peer Reviewers Kenji Kamimoto; Marouen Ben Guebila
  • Funders
  • NWO grant 016 Vidi
  • NWO-ALW
  • ZonMw Open
LATEST VERSION PUBLISHED 29 Nov 2023
https://doi.org/10.12688/f1000research.125924.3
Method Article metrics
Revised
Gaidai reliability method for long-term coronavirus modelling
[version 3; peer review: 1 approved, 3 approved with reservations]
Oleg Gaidai, Ping Yan, Yihan Xing, JingXiang Xu, Yu Wu
Peer Reviewers Oluwakemi E Abiodun; Adnan Khan; Md. Ashraful Babu; Eduard Campillo-Funollet
LATEST VERSION PUBLISHED 21 Nov 2023
https://doi.org/10.12688/f1000research.132899.1
Research Article metrics
Identification of informative genes and sub-pathways using Improved Differential Expression Analysis for Pathways (iDEAP) for cancer classification
[version 1; peer review: 1 approved, 1 approved with reservations]
Nurul Athirah Nasarudin, Mohd Saberi Mohamad, Zalmiyah Zakaria, Richard O. Sinnott, Fatma Al Jasmi, Noura Al Dhaheri
Peer Reviewers Suhaila Zainudin; Nora Muda
  • Funder
  • Strategic Research Program, United Arab Emirates University
PUBLISHED 06 Nov 2023
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.130458.2
Software Tool Article metrics
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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.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.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
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