Bioinformatics

Bioinformatics

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101-120 of 377 ARTICLES
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 in 
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.75471.3
Correspondence metrics
Revised
Positional weight matrices have sufficient prediction power for analysis of noncoding variants
[version 3; peer review: 2 approved]
Alexandr Boytsov, Sergey Abramov, Vsevolod J. Makeev, Ivan V. Kulakovskiy
Peer Reviewers Victor G. Levitsky; Philip Machanick
  • Funder
  • Russian Science Foundation
LATEST VERSION PUBLISHED 04 Jul 2022
https://doi.org/10.12688/f1000research.53842.2
Opinion Article metrics
Revised
Python for gene expression
[version 2; peer review: 2 approved]
Leonid Bystrykh
Peer Reviewers Sergio Peignier; Yasha Hasija
LATEST VERSION PUBLISHED 23 Jun 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.18553.2
Research Article metrics
Revised
Impact of pathogenic mutations of the GLUT1 glucose transporter on solute carrier dynamics using ComDYN enhanced sampling
[version 2; peer review: 2 approved, 1 approved with reservations]
Halima Mouhib, Akiko Higuchi, Sanne Abeln, Kei Yura, K. Anton Feenstra
Peer Reviewers Lucie Delemotte; Jocelyne Vreede; Lívia Maria Ferreira Sobrinho
  • Funders
  • European Molecular Biology Organization
  • Ministry of Education, Culture, Sports, Science and Technology
LATEST VERSION PUBLISHED 13 Jun 2022
https://doi.org/10.12688/f1000research.109895.4
Research Article metrics
Revised
Duration of dry and humidified incubation of single-step embryo culture medium and oxygen tension during sham culture do not alter medium composition.
[version 4; peer review: 2 approved]
Aswathi Cheredath, Shubhashree Uppangala, Gitanjali Asampille, Vani Lakshmi R., David Joseph, Keyur Raval, Nagana Gowda G. A., Guruprasad Kalthur, Satish Kumar Adiga
Peer Reviewers Erode N. Prabhakaran; Borut Kovačič and Peter Slatinšek
  • Funders
  • Science and Engineering Research Board
  • Manipal Academy of Higher Education
LATEST VERSION PUBLISHED 30 May 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
101-120 of 377 ARTICLES
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    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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