Bioinformatics

Bioinformatics

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181-200 of 384 ARTICLES
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https://doi.org/10.12688/f1000research.27500.2
Opinion Article metrics
Revised
The need for standardisation in life science research - an approach to excellence and trust.
[version 2; peer review: 3 approved]
Susanne Hollmann, Andreas Kremer, Špela Baebler, Christophe Trefois, Kristina Gruden, Witold R. Rudnicki, Weida Tong, Aleksandra Gruca, Erik Bongcam-Rudloff, Chris T. Evelo, Alina Nechyporenko, Marcus Frohme, David Šafránek, Babette Regierer, Domenica D'Elia
Peer Reviewers David Nickerson; Laurent Falquet; Antonella Lanati
  • Funder
  • Horizon 2020
LATEST VERSION PUBLISHED 10 May 2021
https://doi.org/10.12688/f1000research.52141.1
Software Tool Article metrics AWAITING PEER REVIEW
Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design
[version 1; peer review: awaiting peer review]
Kristianne Arielle Gabriel, Maria Rejane Nepacina, Francis Tablizo, Carlo Lapid, Mark Lenczner Mendoza, Daniella Jean Pamulaklakin, Jobeth Domingo, Marc Jermaine Pontiveros, Hannah Mae Magno, Joshua Gregor Dizon, El King Morado, Jan Michael Yap
Peer Reviewers Invited
  • Funder
  • Philippine Council for Industry, Energy and Emerging Technology Research and Development of the Department of Science and Technology
PUBLISHED 07 May 2021
https://doi.org/10.12688/f1000research.25485.1
Opinion Article metrics
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists
[version 1; peer review: 2 approved]
Gabriel G. Martins, Fabrice P. Cordelières, Julien Colombelli, Rocco D’Antuono, Ofra Golani, Romain Guiet, Robert Haase, Anna H. Klemm, Marion Louveaux, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Kota Miura
Peer Reviewers Thorsten Wohland; Kevin Eliceiri
  • Funders
  • Swedish Foundation for Strategic Research
  • Fundação para a Ciência e a Tecnologia
  • COST
  • Luxembourg National Research Fund
  • Cancer Research UK
  • Deutsche Forschungsgemeinschaft
  • Swedish National Microscopy infrastructure
  • UK Medical Research Council
  • France BioImaging national infrastructure
  • Wellcome Trust
PUBLISHED 30 Apr 2021
https://doi.org/10.12688/f1000research.52531.1
Opinion Article metrics
Developing open-source software for bioimage analysis: opportunities and challenges
[version 1; peer review: 2 approved]
Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Peer Reviewers Loïc A. Royer; Nico Stuurman
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Institut National de la Santé et de la Recherche Médicale
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.28608.2
Method Article metrics
Revised
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
[version 2; peer review: 2 approved]
Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap
Peer Reviewers Caitlin Simopoulos; Won Kyong Cho
  • Funders
  • National Cancer Institute
  • University of Minnesota
  • National Science Foundation
LATEST VERSION PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.28439.1
Data Note metrics
CFM: a database of experimentally validated protocols for chemical compound-based direct reprogramming and transdifferentiation
[version 1; peer review: 2 approved with reservations]
Alexey Sizykh, Khalimat Murtazalieva, Yulia Vyshkvorkina, Alexey Stupnikov, Yulia A. Medvedeva
Peer Reviewers Erdem B. Dashinimaev; Stephanie M. Willerth
  • Funder
  • Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 16 Apr 2021
https://doi.org/10.12688/f1000research.27062.2
Software Tool Article metrics
Revised
SAPHIR: a Shiny application to analyze tissue section images
[version 2; peer review: 2 approved]
Elodie Germani, Hugues Lelouard, Mathieu Fallet
Peer Reviewers Mahmoud Ahmed; Seth Winfree
  • Funders
  • Agence Nationale de la Recherche
  • Aix-Marseille University
  • Fondation pour la Recherche Médicale
  • Centre National de la Recherche Scientifique and Institut National de la Santé et de la Recherche Médicale
LATEST VERSION PUBLISHED 08 Apr 2021
https://doi.org/10.12688/f1000research.51794.1
Research Article metrics
Summary of two questionnaires designed to understand the research climate for Bioimage Analysts in the UK between 2016-2019
[version 1; peer review: 1 approved, 2 approved with reservations]
Dominic Waithe
Peer Reviewers Julien Colombelli; Julia Fernandez-Rodriguez; Martin L. Jones
  • Funder
  • UKRI MRC
PUBLISHED 06 Apr 2021
https://doi.org/10.12688/f1000research.28449.1
Opinion Article metrics
Recommendations for the FAIRification of genomic track metadata
[version 1; peer review: 2 approved]
Sveinung Gundersen, Sanjay Boddu, Salvador Capella-Gutierrez, Finn Drabløs, José M. Fernández, Radmila Kompova, Kieron Taylor, Dmytro Titov, Daniel Zerbino, Eivind Hovig
Peer Reviewers Max Haeussler; Granger Sutton
  • Funders
  • ELIXIR
  • ELIXIR Norway
  • ELIXIR Spain
  • INB
  • EMBL-EBI
PUBLISHED 01 Apr 2021
https://doi.org/10.12688/f1000research.27676.2
Research Article metrics
Revised
In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b
[version 2; peer review: 2 approved, 1 approved with reservations]
Shahram Mesdaghi, David L. Murphy, Filomeno Sánchez Rodríguez, J. Javier Burgos-Mármol, Daniel J. Rigden
Peer Reviewers Pradip Panta and William T. Doerrler; Laszlo Dobson and Gábor Tusnády; Claudio Bassot
LATEST VERSION PUBLISHED 25 Mar 2021
https://doi.org/10.12688/f1000research.25447.2
Software Tool Article metrics
Revised
DEVILS: a tool for the visualization of large datasets with a high dynamic range
[version 2; peer review: 2 approved]
Romain Guiet, Olivier Burri, Nicolas Chiaruttini, Olivier Hagens, Arne Seitz
Peer Reviewers Sebastien Tosi; Mehedi Masud
  • Funder
  • Norges Forskningsråd
LATEST VERSION PUBLISHED 22 Mar 2021
https://doi.org/10.12688/f1000research.26771.2
Software Tool Article metrics
Revised
HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas
[version 2; peer review: 3 approved]
Tim O. Nieuwenhuis, Marc K. Halushka
Peer Reviewers Mazdak Salavati; Laurent Gatto; Yasin Kaymaz
  • Funders
  • National Heart, Lung, and Blood Institute
  • National Institutes of Health
LATEST VERSION PUBLISHED 22 Mar 2021
https://doi.org/10.12688/f1000research.51916.1
Software Tool Article metrics
CytoBrowser: a browser-based collaborative annotation platform for whole slide images
[version 1; peer review: 1 approved with reservations, 1 not approved]
Christopher Rydell, Joakim Lindblad
Peer Reviewers Simon Nørrelykke; Peter Bankhead
  • Funder
  • Sweden’s Innovation Agency, VINNOVA
PUBLISHED 22 Mar 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.26669.2
Software Tool Article metrics
Revised
TreeSummarizedExperiment: a S4 class for data with hierarchical structure
[version 2; peer review: 3 approved]
Ruizhu Huang, Charlotte Soneson, Felix G.M. Ernst, Kevin C. Rue-Albrecht, Guangchuang Yu, Stephanie C. Hicks, Mark D. Robinson
Peer Reviewers Leo Lahti; Shila Ghazanfar; Matthew Ritchie
  • Funders
  • University Research Priority Program Evolution in Action at the University of Zurich
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • Chan Zuckerberg Initiative DAF
LATEST VERSION PUBLISHED 02 Mar 2021
https://doi.org/10.12688/f1000research.51192.1
Research Article metrics PEER REVIEW DISCONTINUED
Measure of unevenness in human genomes, described as a self-affine phase transition in a 'spin-chain’ model
[version 1; peer review: 1 not approved]
Sergey Feranchuk
Peer Reviewers Ying Ji
PUBLISHED 25 Feb 2021
https://doi.org/10.12688/f1000research.40668.1
Software Tool Article metrics
RP-REP Ribosomal Profiling Reports: an open-source cloud-enabled framework for reproducible ribosomal profiling data processing, analysis, and result reporting
[version 1; peer review: 2 approved]
Travis L. Jensen, William F. Hooper, Sami R. Cherikh, Johannes B. Goll
Peer Reviewers Molly Hannigan and Christopher Nicchitta; Jordan A. Berg
  • Funders
  • The Emmes Company
  • National Institutes of Allergy and Infectious Disease
PUBLISHED 24 Feb 2021
https://doi.org/10.12688/f1000research.50798.1
Software Tool Article metrics
Interactive biomedical segmentation tool powered by deep learning and ImJoy
[version 1; peer review: 1 approved, 1 approved with reservations]
Wei Ouyang, Trang Le, Hao Xu, Emma Lundberg
Peer Reviewers Jean-Yves Tinevez and Dmitry Ershov; Jan Funke
  • Funders
  • Knut and Alice Wallenberg Foundation
  • Swedish Research Council
  • LST Platform at KTH Royal Institute of Technology
PUBLISHED 24 Feb 2021
https://doi.org/10.12688/f1000research.51143.1
Software Tool Article metrics
periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
[version 1; peer review: 1 approved, 3 approved with reservations]
Jacques Serizay, Julie Ahringer
Peer Reviewers Ilya Ioshikhes; Sabarinathan Radhakrishnan; Eugene Korotkov; Boris Lenhard
  • Funders
  • Wellcome Trust Senior Research Fellowship
  • Medical Research Council DTP studentship
PUBLISHED 24 Feb 2021
https://doi.org/10.12688/f1000research.24714.3
Brief Report metrics
Revised
biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab
[version 3; peer review: 2 approved]
Choumouss Kamoun, Julien Roméjon, Henri de Soyres, Apolline Gallois, Elodie Girard, Philippe Hupé
Peer Reviewers Bernard Pope; Julia Ponomarenko
  • Funder
  • Institut National Du Cancer
LATEST VERSION PUBLISHED 19 Feb 2021
181-200 of 384 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
  • 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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