Bioinformatics

Bioinformatics

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81-100 of 377 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.52791.3
Software Tool Article metrics
Revised
Sherlock: an open-source data platform to store, analyze and integrate Big Data for computational biologists
[version 3; peer review: 2 approved]
Balazs Bohar, David Fazekas, Matthew Madgwick, Luca Csabai, Marton Olbei, Tamás Korcsmáros, Mate Szalay-Beko
Peer Reviewers John H. Morris; Nadezhda Doncheva
  • Funders
  • Earlham Institute
  • Biotechnology and Biological Sciences Research Council
  • Quadram Institute Bioscience
LATEST VERSION PUBLISHED 12 Jan 2023
https://doi.org/10.12688/f1000research.110492.2
Research Article metrics
Revised
From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)
[version 2; peer review: 2 approved]
Maksim Nesterenko, Aleksei Miroliubov
Peer Reviewers Andreas Hejnol and Ferenc Kagan; Viatcheslav Ivanenko
  • Funder
  • Russian Science Foundation
LATEST VERSION PUBLISHED 09 Jan 2023
https://doi.org/10.12688/f1000research.127647.1
Method Article metrics
Turning any bed into an intensive care unit with the Internet of things and artificial intelligence technology. Presenting the enhanced mechanical ventilator
[version 1; peer review: 1 approved, 2 approved with reservations]
Leidy Lorena Pulido Morales, Juan Sebastian Buitrago Romero, Ismael A. Ardila Sanchez, Fernando Yepes-Calderon
Peer Reviewers Christian Grévisse; Andres Felipe Montaño; Maria Florencia Pollo-Cattaneo
PUBLISHED 23 Dec 2022
https://doi.org/10.12688/f1000research.110903.2
Software Tool Article metrics
Revised
SL-Cloud: A Cloud-based resource to support synthetic lethal interaction discovery
[version 2; peer review: 2 approved]
Bahar Tercan, Guangrong Qin, Taek-Kyun Kim, Boris Aguilar, John Phan, William Longabaugh, David Pot, Christopher J. Kemp, Nyasha Chambwe, Ilya Shmulevich
Peer Reviewers Jane Usher; Nishanth Ulhas Nair
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 22 Dec 2022
https://doi.org/10.12688/f1000research.128354.1
Method Article metrics
BOREALIS: an R/Bioconductor package to detect outlier methylation from bisulfite sequencing data
[version 1; peer review: 2 approved with reservations]
Gavin R. Oliver, W. Garrett Jenkinson, Rory J. Olson, Laura E. Schultz-Rogers, Eric W. Klee
Peer Reviewers Philipp Jurmeister and Maximilian Leitheiser; Vicente Yepez
  • Funder
  • Center for Individualized Medicine, Mayo Clinic
PUBLISHED 20 Dec 2022
https://doi.org/10.12688/f1000research.123384.2
Research Article metrics
Revised
In silico and in vitro analysis of THCA synthase gene in Moroccan Cannabis sativa, L
[version 2; peer review: 1 approved with reservations, 3 not approved]
Fadwa Badrana, El Mostafa El Fahime, Abdelrhani Mokhtari, Abdelmajid Soulaymani, Najete Safini, Bouchra Chaouni, Gabriel Malka, Hamid El Amri
Peer Reviewers Supaart Sirikantaramas; Noureddine Hamamouch; Narayanan Srividya; Yuanyuan Liu
  • Funders
  • Center for Scientific and Technical Research in Rabat
  • University Ibn Tofail
  • Genetics Analysis Institute of the Royal Gendarmerie of Morocco
LATEST VERSION PUBLISHED 15 Dec 2022
https://doi.org/10.12688/f1000research.74395.3
Research Article metrics
Revised
Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces
[version 3; peer review: 2 approved]
Francesco Raimondi, Joshua G. Burkhart, Matthew J. Betts, Robert B. Russell, Guanming Wu
Peer Reviewers Andras Szilagyi; Pier Luigi Martelli
  • Funders
  • Associazione Italiana per la Ricerca sul Cancro
  • Germany Research Foundation
  • Italian Ministry of University and Research
  • Alexander von Humboldt-Stiftung
  • U.S. National Library of Medicine
  • National Human Genome Research Institute
LATEST VERSION PUBLISHED 12 Dec 2022
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.124810.1
Software Tool Article metrics
abmAnimalMovement: An R package for simulating animal movement using an agent-based model
[version 1; peer review: 2 approved with reservations]
Benjamin Michael Marshall, Alexander Bradley Duthie
Peer Reviewers Rocío Joo; Andrea Contina
  • Funder
  • Natural Environment Research Council
PUBLISHED 17 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
81-100 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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