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https://doi.org/10.12688/f1000research.108857.2
Research Article metrics
Revised
Diversity and antimicrobial activity of marine nudibranch associated bacteria against tropical human skin pathogens
[version 2; peer review: 1 approved, 1 approved with reservations]
Agus Sabdono, Ocky Radjasa, Agus Trianto, Tatiana Korshunova, Alexander Martynov, Mada Sibero
Peer Reviewers Yi Li; Cristóbal Espinosa-Ruiz
  • Funders
  • MSU Zoological Museum
  • The Research and Public Service Institution, Diponegoro University
  • IDB RAS basic research program
LATEST VERSION PUBLISHED 06 Sep 2022
https://doi.org/10.12688/f1000research.122811.1
Method Article metrics
A training curriculum for retrieving, structuring, and aggregating information derived from the biomedical literature and large-scale data repositories.
[version 1; peer review: 2 approved with reservations]
Darawan Rinchai, Damien Chaussabel
Peer Reviewers Bartholomew N. Ondigo; Ekwaro A. Obuku
PUBLISHED 02 Sep 2022
https://doi.org/10.12688/f1000research.123904.1
Software Tool Article metrics
Peccary, a metaprogramming open-source R platform to improve pharmacometrics efficiency
[version 1; peer review: 1 approved, 1 approved with reservations]
Thibaud Derippe, Xavier Declèves, Sylvain Fouliard
Peer Reviewers Elena Maria Tosca; Sergio Sánchez-Herrero
  • Funder
  • Servier
PUBLISHED 18 Aug 2022
https://doi.org/10.12688/f1000research.74846.2
Method Article metrics
Revised
Hobotnica: exploring molecular signature quality
[version 2; peer review: 2 approved]
Alexey Stupnikov, Alexey Sizykh, Anna Budkina, Alexander Favorov, Bahman Afsari, Sarah Wheelan, Luigi Marchionni, Yulia Medvedeva
Peer Reviewers Roberto Malinverni; Shailesh Tripathi
  • Funders
  • Ministry of Science and Higher Education of the Russian Federation
  • National Institutes of Health
LATEST VERSION PUBLISHED 16 Aug 2022
https://doi.org/10.12688/f1000research.51749.2
Method Article metrics
Revised
satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications
[version 2; peer review: 2 approved]
Jeroen Gilis, Kristoffer Vitting-Seerup, Koen Van den Berge, Lieven Clement
Peer Reviewers Marek Cmero; Alejandro Reyes
  • Funders
  • Belgian American Educational Foundation
  • Fonds Wetenschappelijk Onderzoek
LATEST VERSION PUBLISHED 08 Aug 2022
https://doi.org/10.12688/f1000research.52173.4
Software Tool Article metrics
Revised
target: an R package to predict combined function of transcription factors
[version 4; peer review: 1 approved, 1 approved with reservations]
Mahmoud Ahmed, Deok Ryong Kim
Peer Reviewers Shulan Tian and Yan Huihuang; Mireia Ramos-Rodríguez
  • Funder
  • National Research Foundation of Korea
LATEST VERSION PUBLISHED 03 Aug 2022
https://doi.org/10.12688/f1000research.108804.2
Opinion Article metrics
Revised
Making European performance and impact assessment frameworks for research infrastructures glocal
[version 2; peer review: 2 approved]
Ana M.P. Melo, Sofia Oliveira, Jorge S. Oliveira, Corinne S. Martin, Ricardo B. Leite
Peer Reviewers Eugénio Campos Ferreira; Enrico Guarini and Marialuisa Lavitrano
  • Funders
  • ELIXIR
  • H2020 Research Infrastructures
  • Foundation for Science and Technology - Portugal
LATEST VERSION PUBLISHED 02 Aug 2022
https://doi.org/10.12688/f1000research.122312.1
Opinion Article metrics
Community-driven ELIXIR activities in single-cell omics
[version 1; peer review: 2 approved with reservations]
Paulo Czarnewski, Ahmed Mahfouz, Raffaele A. Calogero, Patricia M. Palagi, Laura Portell-Silva, Asier Gonzalez-Uriarte, Charlotte Soneson, Tony Burdett, Barbara Szomolay, Pavankumar Videm, Hans-Rudolf Hotz, Irene Papatheodorou, John M. Hancock, Björn Grüning, Wilfried Haerty, Roland Krause, Salvador Capella-Gutierrez, Brane Leskošek, Luca Alessandri, Maddalena Arigoni, Tadeja Rezen, Alexander Botzki, Polonca Ferk, Jessica Lindvall, Katharina F. Heil, Naveed Ishaque, Eija Korpelainen
Peer Reviewers Xiao-Yang Zhao; Feng Zhu
  • Funders
  • ELIXIR
  • Knut och Alice Wallenbergs Stiftelse
PUBLISHED 29 Jul 2022
https://doi.org/10.12688/f1000research.111175.2
Software Tool Article metrics
Revised
DSMZCellDive: Diving into high-throughput cell line data
[version 2; peer review: 2 approved]
Julia Koblitz, Wilhelm G. Dirks, Sonja Eberth, Stefan Nagel, Laura Steenpass, Claudia Pommerenke
Peer Reviewers Beate Rinner; Arihiro Kohara
  • Funder
  • Leibniz SAW project DiASPora
LATEST VERSION PUBLISHED 20 Jul 2022
https://doi.org/10.12688/f1000research.122113.1
Method Article metrics
Interactive visualization of spatial omics neighborhoods
[version 1; peer review: 2 approved with reservations]
Tinghui Xu, Kris Sankaran
Peer Reviewers Guangdun Peng and Miao Zhu; Oscar Ospina
PUBLISHED 18 Jul 2022
https://doi.org/10.12688/f1000research.122840.1
Software Tool Article metrics
vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework
[version 1; peer review: 1 approved, 2 approved with reservations]
V.P. Nagraj, Matthew Scholz, Shakeel Jessa, Jianye Ge, August E. Woerner, Meng Huang, Bruce Budowle, Stephen D. Turner
Peer Reviewers Ardalan Naseri; Gianluca Della Vedova; Cristiane Taniguti
  • Funders
  • Center for Human Identification, University of North Texas Health Science Center
  • National Institute of Justice, Office of Justice Programs, U.S. Department of Justice
PUBLISHED 11 Jul 2022
https://doi.org/10.12688/f1000research.118761.1
Software Tool Article metrics
MAFDash: An easy-to-use dashboard builder for mutation data
[version 1; peer review: 2 not approved]
Ashish Jain, Mayank Tandon
Peer Reviewers Sigve Nakken; Heiko Brennenstuhl
  • Funder
  • National Cancer Institute, National Institutes of Health
PUBLISHED 06 Jul 2022
https://doi.org/10.12688/f1000research.53214.4
Research Article metrics
Revised
Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences
[version 4; peer review: 2 approved, 1 approved with reservations]
Onega Ulianova, Yury Saltykov, Sergey Ulyanov, Sergey Zaytsev, Alexander Ulyanov, Valentina Feodorova
Peer Reviewers Oleg Angelsky; Alexey Bashkatov and Claudia Zenkova; Dmitry A. Zimnyakov
  • Funder
  • Russian Foundation for Basic Research
LATEST VERSION PUBLISHED 22 Jun 2022
https://doi.org/10.12688/f1000research.54685.2
Opinion Article metrics
Revised
Introducing R as a smart version of calculators enables beginners to explore it on their own
[version 2; peer review: 3 approved]
Krishna Choudhary, Alexander R. Pico
Peer Reviewers Lex Nederbragt; Yasha Hasija; Rayna M Harris
  • Funders
  • UCSF Bakar Computational Health Sciences Institute
  • Gladstone Institutes
LATEST VERSION PUBLISHED 21 Jun 2022
https://doi.org/10.12688/f1000research.121775.1
Software Tool Article metrics
eXNVerify: coverage analysis for long and short-read sequencing data in clinical context
[version 1; peer review: 2 approved, 1 approved with reservations]
Sebastian Porębski, Tomasz Stokowy
Peer Reviewers Zebin Zhang; Xueyi Dong; Wouter De Coster
  • Funders
  • Bergen Research Foundation
  • Research Council of Norway
  • Silesian University of Technology
PUBLISHED 13 Jun 2022
https://doi.org/10.12688/f1000research.121486.1
Method Article metrics
Ensemble method for cluster number determination and algorithm selection in unsupervised learning
[version 1; peer review: 2 approved with reservations, 1 not approved]
Antoine Zambelli
Peer Reviewers Dong Huang; Ana Estela Antunes da Silva; Luca Coraggio
PUBLISHED 25 May 2022
https://doi.org/10.12688/f1000research.109080.2
Opinion Article metrics
Revised
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
[version 2; peer review: 2 approved]
Sebastian Beier, Anne Fiebig, Cyril Pommier, Isuru Liyanage, Matthias Lange, Paul J. Kersey, Stephan Weise, Richard Finkers, Baron Koylass, Timothee Cezard, Mélanie Courtot, Bruno Contreras-Moreira, Guy Naamati, Sarah Dyer, Uwe Scholz
Peer Reviewers Boas Pucker and Alenka Hafner; Micha M. Bayer
  • Funders
  • ELIXIR
  • Bundesministerium für Bildung und Forschung
  • Horizon 2020 Framework Programme
LATEST VERSION PUBLISHED 19 May 2022
https://doi.org/10.12688/f1000research.51868.3
Method Article metrics
Revised
Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo
[version 3; peer review: 2 approved]
Benjamin Mayer, Meike Schwan, Kai M. Thormann, Peter L. Graumann
Peer Reviewers Massimiliano Lucidi; Janos Kriston-Vizi and Qing Hsuan Ong
  • Funder
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 17 May 2022
https://doi.org/10.12688/f1000research.114698.1
Method Article metrics
DeepReGraph co-clusters temporal gene expression and cis-regulatory elements through heterogeneous graph representation learning
[version 1; peer review: 1 approved, 1 approved with reservations]
Jesús Fernando Cevallos Moreno, Peyman Zarrineh, Aminael Sánchez-Rodríguez, Massimo Mecella
Peer Reviewers Wanding Zhou; Tallulah Andrews and Boris Tchatchoua Ngassam
  • Funders
  • Universidad Técnica Particular de Loja
  • ELIS Innovation Hub
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 13 May 2022
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
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