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https://doi.org/10.12688/f1000research.26771.2
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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.27309.1
Data Note metrics
The complete genome sequences of two species of seventeen-year cicadas: Magicicada septendecim and Magicicada septendecula
[version 1; peer review: 2 approved with reservations]
Harold B. White, Stacy Pirro
Peer Reviewers Hu Li; Shuai Zhan
  • Funder
  • Iridian Genomes
PUBLISHED 16 Mar 2021
https://doi.org/10.12688/f1000research.28133.1
Research Article metrics
Development of a physiologically based pharmacokinetic (PBPK) model of psilocybin and psilocin from magic mushroom in rats and humans
[version 1; peer review: 1 approved with reservations, 1 not approved]
Prinya Musikaphongsakul, Kimheang Ya, Pakpoom Subsoontorn, Manupat Lohitnavy
Peer Reviewers Michael Dzierlenga; Quoc Ba Tran
  • Funder
  • Naresuan University
PUBLISHED 15 Mar 2021
https://doi.org/10.12688/f1000research.51479.1
Brief Report metrics
Most Japanese individuals are genetically predisposed to recognize an immunogenic protein fragment shared between COVID-19 and common cold coronaviruses
[version 1; peer review: 2 approved, 1 approved with reservations]
Johannes M. Dijkstra, Aaron P. Frenette, Brian Dixon
Peer Reviewers Brian M. Baker; Andrea J. Sant; Anna Gil
PUBLISHED 10 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.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
https://doi.org/10.12688/f1000research.27140.2
Software Tool Article metrics
Revised
Effective image visualization for publications – a workflow using open access tools and concepts
[version 2; peer review: 2 approved]
Christopher Schmied, Helena Klara Jambor
Peer Reviewers Guillaume Jacquemet; Georgina Fletcher and David Barry
  • Funder
  • Deutsche Krebshilfe
LATEST VERSION PUBLISHED 18 Feb 2021
https://doi.org/10.12688/f1000research.26872.2
Software Tool Article metrics
Revised
Fiji plugins for qualitative image annotations: routine analysis and application to image classification
[version 2; peer review: 2 approved, 1 approved with reservations]
Laurent S. V. Thomas, Franz Schaefer, Jochen Gehrig
Peer Reviewers Jan Eglinger; Christian Tischer and Aliaksandr Halavatyi; Elisabet Teixido
  • Funder
  • Horizon 2020
LATEST VERSION PUBLISHED 12 Feb 2021
https://doi.org/10.12688/f1000research.26848.2
Software Tool Article metrics
Revised
CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline
[version 2; peer review: 2 approved]
Dustin B. Miller, Stephen R. Piccolo
Peer Reviewers Soohyun Lee; Sushant Patil
LATEST VERSION PUBLISHED 10 Feb 2021
https://doi.org/10.12688/f1000research.24163.2
Method Article metrics
Revised
Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency
[version 2; peer review: 2 approved]
Maryam Zand, Jianhua Ruan
Peer Reviewers Tianci Song and Rui Kuang; Adi Tarca
  • Funders
  • National Institutes of Health
  • National Science Foundation
LATEST VERSION PUBLISHED 09 Feb 2021
https://doi.org/10.12688/f1000research.22391.1
Research Article metrics
Parent-child signals identify candidate cancer driver genes
[version 1; peer review: 2 approved with reservations]
Emilie Ann Ramsahai, Vrijesh Tripathi, Melford John
Peer Reviewers Hilal Kazan; Alexander Lachmann
  • Funder
  • University of the West Indies
PUBLISHED 03 Feb 2021
https://doi.org/10.12688/f1000research.25713.2
Software Tool Article metrics
Revised
VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach
[version 2; peer review: 1 approved, 2 approved with reservations]
Priyansh Srivastava, Mehak Talwar, Aishwarya Yadav, Alakto Choudhary, Sabyasachi Mohanty, Samuel Bharti, Priyanka Narad, Abhishek Sengupta
Peer Reviewers Dinesh Gupta; Mitesh Dwivedi and Rasheedunnisa Begum; Animesh A Sinha
LATEST VERSION PUBLISHED 01 Feb 2021
https://doi.org/10.12688/f1000research.21782.4
Research Article metrics
Update
Benchmarking of long-read assemblers for prokaryote whole genome sequencing
[version 4; peer review: 4 approved]
Ryan R. Wick, Kathryn E. Holt
Peer Reviewers Aleksey V. Zimin and Steven Salzberg; Robert Vaser and Mile Šikić; Mikhail Kolmogorov; Olin Silander
  • Funders
  • Department of Education, Employment and Workplace Relations, Australian Government
  • Sylvia and Charles Viertel Charitable Foundation
  • Gates Foundation
LATEST VERSION PUBLISHED 01 Feb 2021
https://doi.org/10.12688/f1000research.21142.2
Software Tool Article metrics
Revised
Falco: high-speed FastQC emulation for quality control of sequencing data
[version 2; peer review: 2 approved]
Guilherme de Sena Brandine, Andrew D. Smith
Peer Reviewers R Henrik Nilsson; Weihong Qi
LATEST VERSION PUBLISHED 27 Jan 2021
https://doi.org/10.12688/f1000research.36371.1
Research Article metrics
Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2
[version 1; peer review: 2 approved]
Vipul Kumar, Sudhakar Kancharla, Prachetha Kolli, Manoj Jena
Peer Reviewers Sivaraman Natarajan; Tirumala Bharani K. Settypalli
PUBLISHED 23 Jan 2021
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