Bioinformatics

Bioinformatics

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101-120 of 389 ARTICLES
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https://doi.org/10.12688/f1000research.128391.1
Research Article metrics
Evaluation of cytosine conversion methods for whole-genome DNA methylation profiling
[version 1; peer review: 2 not approved]
Shyaron Poudel, Brett Hale, Asela J. Wijeratne
Peer Reviewers Aaron John Stevens; Sadaruddin Chachar
  • Funders
  • Arkansas State University
  • Arkansas Biosciences Institute
PUBLISHED 07 Dec 2022
https://doi.org/10.12688/f1000research.109027.2
Software Tool Article metrics
Revised
Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App
[version 2; peer review: 1 approved, 1 approved with reservations]
Pritam Saha, Özgun Babur, Chris Sander, Augustin Luna
Peer Reviewers Ruth Isserlin; Katsuyuki Yugi
  • Funders
  • Google
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 14 Nov 2022
https://doi.org/10.12688/f1000research.78195.2
Research Article metrics
Revised
Research Software vs. Research Data I: Towards a Research Data definition in the Open Science context
[version 2; peer review: 3 approved]
Teresa Gomez-Diaz, Tomas Recio
Peer Reviewers Tibor Koltay; Remedios Melero; Joachim Schöpfel
  • Funder
  • Centre National de la Recherche Scientifique
LATEST VERSION PUBLISHED 01 Nov 2022
https://doi.org/10.12688/f1000research.73420.2
Software Tool Article metrics
Revised
PDBrt: A free database of complexes with measured drug-target residence time
[version 2; peer review: 1 approved, 1 approved with reservations]
Magdalena Ługowska, Marcin Pacholczyk
Peer Reviewers Wiesław Nowak; Marian Novotny
  • Funders
  • European Social Fund
  • Polish National Science Centre
  • Silesian University of Technology
LATEST VERSION PUBLISHED 31 Oct 2022
https://doi.org/10.12688/f1000research.19426.2
Software Tool Article metrics
Revised
Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads
[version 2; peer review: 2 approved]
Andrian Yang, Joshua Y. S. Tang, Michael Troup, Joshua W. K. Ho
Peer Reviewers Quan Nguyen; Marco Previtali and Luca Denti
  • Funders
  • National Heart Foundation of Australia
  • Amazon Web Services
  • National Health and Medical Research Council
  • Department of Education, Australian Governement
LATEST VERSION PUBLISHED 13 Oct 2022
https://doi.org/10.12688/f1000research.78459.2
Research Article metrics
Revised
Research Software vs. Research Data II: Protocols for Research Data dissemination and evaluation in the Open Science context
[version 2; peer review: 2 approved]
Teresa Gomez-Diaz, Tomas Recio
Peer Reviewers Charles Romain and Henry S. Rzepa; Mark Leggott
  • Funder
  • Centre National de la Recherche Scientifique
LATEST VERSION PUBLISHED 07 Oct 2022
https://doi.org/10.12688/f1000research.125381.1
Editorial metrics NOT PEER REVIEWED
Highlights of the 1st Ecuadorian-Venezuelan Symposium of Young Researchers in Bioinformatics (1SEVJIB)
[version 1; peer review: not peer reviewed]
Sebastian Ayala-Ruano, Fernando Hernandez, Arantxa Ortega, Deliana Infante, Daniela Carrascal, Karen Sánchez-Luquez, Rafael Puche-Quiñonez
PUBLISHED 22 Sep 2022
https://doi.org/10.12688/f1000research.123934.1
Software Tool Article metrics
ENA Source Attribute Helper: An Application Programming Interface to facilitate accurate reference to biological source data
[version 1; peer review: 1 approved, 1 not approved]
Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane
Peer Reviewers Sujeevan Ratnasingham; Begoña Aguado and Sandra Gonzalez
  • Funder
  • Horizon 2020 Research and Innovation Action
PUBLISHED 13 Sep 2022
https://doi.org/10.12688/f1000research.125043.1
Editorial metrics NOT PEER REVIEWED
BOSC 2022: the first hybrid and 23rd annual Bioinformatics Open Source Conference
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Karsten Hokamp, Hervé Ménager, Monica C. Munoz-Torres, Deepak Unni, Nicole Vasilevsky, Jason Williams
  • Funders
  • DBI-1265383
  • RM1 HG010860
  • R24 OD011883
  • DBI-0735191
  • DBI-1743442
PUBLISHED 12 Sep 2022
https://doi.org/10.12688/f1000research.122775.1
Method Article metrics
Spatial transcriptomics dimensionality reduction using wavelet bases
[version 1; peer review: 3 approved with reservations, 1 not approved]
Zhuoyan Xu, Kris Sankaran
Peer Reviewers Ben Fulcher; André F Rendeiro; Nguyen Quoc Khanh Le; Shixiong Zhang
  • Funders
  • Office of Science
  • National Science Foundation
PUBLISHED 12 Sep 2022
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
101-120 of 389 ARTICLES
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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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