Bioinformatics

Bioinformatics

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141-160 of 384 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.94159.1
Software Tool Article metrics
miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies
[version 1; peer review: 2 approved with reservations]
Andreas Diendorfer, Kseniya Khamina, Marianne Pultar, Matthias Hackl
Peer Reviewers Kristian Almstrup, Nina Mørup and Ailsa Maria Main; Francisco J. Enguita
  • Funder
  • Innovative Medicines Initiative 2
PUBLISHED 24 Feb 2022
https://doi.org/10.12688/f1000research.28352.2
Method Article metrics
Revised
Methods for sequencing the pandemic: benefits of rapid or high-throughput processing
[version 2; peer review: 2 approved]
Megan L. Folkerts, Darrin Lemmer, Ashlyn Pfeiffer, Danielle Vasquez, Chris French, Amber Jones, Marjorie Nguyen, Brendan Larsen, W. Tanner Porter, Krystal Sheridan, Jolene R. Bowers, David M. Engelthaler
Peer Reviewers Bronwyn MacInnis; Keith Crandall
  • Funders
  • Arizona Department of Health Services
  • The NARBHA institute
LATEST VERSION PUBLISHED 21 Feb 2022
https://doi.org/10.12688/f1000research.75243.1
Software Tool Article metrics
SASCRiP: A Python workflow for preprocessing UMI count-based scRNA-seq data
[version 1; peer review: 2 approved with reservations]
Darisia Moonsamy, Nikki Gentle
Peer Reviewers Fabiola Curion and Luke Zappia; Fangming Xie
  • Funder
  • National Research Foundation
PUBLISHED 15 Feb 2022
https://doi.org/10.12688/f1000research.107925.1
Software Tool Article metrics
NIFtHool: an informatics program for identification of NifH proteins using deep neural networks
[version 1; peer review: 2 approved]
Jefferson Daniel Suquilanda-Pesántez, Evelyn Dayana Aguiar Salazar, Diego Almeida-Galárraga, Graciela Salum, Fernando Villalba-Meneses, Marco Esteban Gudiño Gomezjurado
Peer Reviewers Juan Onofre Orozco-López; Lorena Isabel Barona López
PUBLISHED 09 Feb 2022
https://doi.org/10.12688/f1000research.26452.1
Software Tool Article metrics
Lessons learned in virulence factor identification and data management from a hackathon on microbial virulence
[version 1; peer review: 1 approved, 1 approved with reservations]
Brett E. Pickett, Ryan Connor, Tamiru Berhanu-Denka, Sherry Bhalla, Vyacheslav Brover, Michael James Chambers, Kumardeep Chaudhary, Ousmane H. Cissé, Allissa Dillman, Moamen M. Elmassry, Michael Feldgarden, Eric Holloway, Xin Huang, William Klimke, Catarina Inês Mendes, S. Elizabeth Norred, Jonathan Parkinson, Samantha Sevilla, Monica Garcia Solache, Defne Surujon, Udana Torian, Vadim Zalunin, Ben Busby
Peer Reviewers Rick Stevens and James Davis; Kevin Tyler
  • Funders
  • Fundação para a Ciência e a Tecnologia
  • Scientific and Technological Research Council of Turkey
  • Intramural Research Program of the National Library of Medicine
PUBLISHED 09 Feb 2022
https://doi.org/10.12688/f1000research.28225.2
Research Article metrics
Revised
Human Proteinase 3, an important autoantigen of c-ANCA associated vasculitis, shares cross-reactive epitopes with serine protease allergens from mites: an in silico analysis
[version 2; peer review: 1 approved, 2 approved with reservations]
Emiro Buendía, Múnera Marlon, Orlando Parra, María Sánchez, Andrés Sánchez, Jorge Sánchez, Diego Viasus
Peer Reviewers Chandrabose Selvaraj; Tomas Erban; Hiroshi Tanaka
  • Funder
  • Fondo Nacional de Financiamiento para la Ciencia, la Tecnología y la Innovación
LATEST VERSION PUBLISHED 03 Feb 2022
https://doi.org/10.12688/f1000research.79530.1
Software Tool Article metrics
bit: a multipurpose collection of bioinformatics tools
[version 1; peer review: 2 not approved]
Michael Lee
Peer Reviewers Kai Zhang; Georges Hattab
PUBLISHED 31 Jan 2022
https://doi.org/10.12688/f1000research.107886.1
Editorial metrics NOT PEER REVIEWED
Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey
[version 1; peer review: not peer reviewed]
Yasin Kaya, Tülay Karakulak, Cemil Can Saylan, E. Ravza Gür, Engin Tatlıdil, Sevilay Güleşen, Fatma Betül Dinçaslan, Handan Melike Dönertaş
  • Funder
  • ISCB Student Council
PUBLISHED 26 Jan 2022
https://doi.org/10.12688/f1000research.76828.1
Software Tool Article metrics
The software for interactive evaluation of mass spectrometric imaging heterogeneity
[version 1; peer review: 1 approved with reservations]
Evgeny Zhvansky, Ekaterina Zhdanova, Maxim Belenikin, Maria Shamraeva, Sergei Silkin, Konstantin Bocharov, Anatoly A. Sorokin
Peer Reviewers Jean-Nicolas Audinot
  • Funder
  • Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 25 Jan 2022
https://doi.org/10.12688/f1000research.52785.2
Brief Report metrics
Revised
Global stability analysis of hepatitis B virus dynamics
[version 2; peer review: 2 approved, 1 approved with reservations]
Olajumoke Oludoun, Olukayode Adebimpe, James Ndako, Oluwakemi E. Abiodun, Babatunde Gbadamosi, Benedicta B. Aladeitan
Peer Reviewers Abimbola Abolarinwa; Ran Zhang; Syafruddin Side
LATEST VERSION PUBLISHED 21 Jan 2022
https://doi.org/10.12688/f1000research.52026.2
Method Article metrics
Revised
A deep learning segmentation strategy that minimizes the amount of manually annotated images
[version 2; peer review: 2 approved]
Thierry Pécot, Alexander Alekseyenko, Kristin Wallace
Peer Reviewers Alice Lucas; Romain F Laine
  • Funder
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 17 Jan 2022
https://doi.org/10.12688/f1000research.75321.1
Method Article metrics
Improving prediction of core transcription factors for cell reprogramming and transdifferentiation
[version 1; peer review: 2 not approved]
Mikhail Raevskiy, Anna Kondrashina, Yulia Medvedeva
Peer Reviewers Valentiva Boeva and Samuel Gunz; Erdem B. Dashinimaev
  • Funder
  • Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 13 Jan 2022
https://doi.org/10.12688/f1000research.76004.1
Software Tool Article metrics
skater: an R package for SNP-based kinship analysis, testing, and evaluation
[version 1; peer review: 2 approved, 1 approved with reservations]
Stephen D. Turner, V.P. Nagraj, Matthew Scholz, Shakeel Jessa, Carlos Acevedo, Jianye Ge, August E. Woerner, Bruce Budowle
Peer Reviewers Wei-Min Chen; Magnus Dehli Vigeland; Amy L. Williams
  • Funder
  • National Institute of Justice
PUBLISHED 07 Jan 2022
https://doi.org/10.12688/f1000research.26128.2
Method Article metrics
Revised
Space-log: a novel approach to inferring gene-gene net-works using SPACE model with log penalty
[version 2; peer review: 2 approved, 1 approved with reservations]
Qian (Vicky) Wu, Wei Sun, Li Hsu
Peer Reviewers Yuying Xie and Yuning Hao; Chi Song; Jessie Jeng
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 05 Jan 2022
https://doi.org/10.12688/f1000research.74836.1
Method Article metrics
Slinker: Visualising novel splicing events in RNA-Seq data
[version 1; peer review: 3 approved]
Breon Schmidt, Marek Cmero, Paul Ekert, Nadia Davidson, Alicia Oshlack
Peer Reviewers George Wiggins; Stephen Montgomery; Amy Huei-Yi Lee
  • Funder
  • NHMRC
PUBLISHED 07 Dec 2021
https://doi.org/10.12688/f1000research.53821.2
Software Tool Article metrics
Revised
snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data
[version 2; peer review: 2 approved, 1 approved with reservations]
Christina Vasilopoulou, Benjamin Wingfield, Andrew P. Morris, William Duddy
Peer Reviewers Andries T. Marees; Stephanie M. Gogarten; Anna Ulrich
  • Funders
  • Northern Ireland Public Health Agency (HSC R&D)
  • EU Regional Development Fund (ERDF) EU Sustainable Competitiveness Programme for Northern Ireland
LATEST VERSION PUBLISHED 29 Nov 2021
https://doi.org/10.12688/f1000research.74524.1
Brief Report metrics
An Atlas of Plant Transposable Elements
[version 1; peer review: 2 approved]
Daniel Longhi Fernandes Pedro, Tharcisio Soares Amorim, Alessandro Varani, Romain Guyot, Douglas Silva Domingues, Alexandre Rossi Paschoal
Peer Reviewers Gökhan Karakülah; Adriana Ludwig
  • Funders
  • Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES)
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico
  • NAPI de Bioinformática - Fundação Araucária
  • NVIDIA from the GPU Grant Program 2019 - Accelerated Data Science Call for the GPU Seed Units: Titan V device
  • PROPPG - UTFPR
PUBLISHED 24 Nov 2021
https://doi.org/10.12688/f1000research.73641.1
Software Tool Article metrics
PlotXpress, a webtool for normalization and visualization of reporter expression data
[version 1; peer review: 3 approved]
Elias Brandorff, Marc Galland, Joachim Goedhart
Peer Reviewers Lorena Pantano Rubino; Guillaume Jacquemet; Vincent J. Lynch
PUBLISHED 08 Nov 2021
https://doi.org/10.12688/f1000research.53926.2
Software Tool Article metrics
Revised
PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals
[version 2; peer review: 2 approved]
Peter Briggs, A. Louise Hunter, Shen-hsi Yang, Andrew D. Sharrocks, Mudassar Iqbal
Peer Reviewers Nicolae Radu Zabet; Aziz Khan
  • Funders
  • Medical Research Council (MRC)
  • Wellcome Trust
LATEST VERSION PUBLISHED 02 Nov 2021
https://doi.org/10.12688/f1000research.74074.1
Editorial metrics NOT PEER REVIEWED
BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Peter J. A. Cock, Christopher J. Fields, Karsten Hokamp, Jessica Maia, Monica C. Munoz-Torres, Malvika Sharan, Jason Williams
PUBLISHED 18 Oct 2021
141-160 of 384 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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