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https://doi.org/10.12688/f1000research.24345.2
Software Tool Article metrics
Update
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
[version 2; peer review: 3 approved]
Justin Wagner, Jayaram Kancherla, Domenick Braccia, James Matsumara, Victor Felix, Jonathan Crabtree, Anup Mahurkar, Héctor Corrada Bravo
Peer Reviewers Ekaterina Smirnova; Edoardo Pasolli; Levi Waldron
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 21 Jun 2021
https://doi.org/10.12688/f1000research.27395.2
Software Tool Article metrics
Revised
GeNePy3D: a quantitative geometry python toolbox for bioimaging
[version 2; peer review: 2 approved]
Minh-Son Phan, Anatole Chessel
Peer Reviewers Virginie Uhlmann; Yizhi Wang
  • Funder
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 17 Jun 2021
https://doi.org/10.12688/f1000research.51613.2
Data Note metrics
Revised
A draft reference assembly of the Psilocybe cubensis genome
[version 2; peer review: 2 approved]
Kevin McKernan, Liam T. Kane, Seth Crawford, Chen-Shan Chin, Aaron Trippe, Stephen McLaughlin
Peer Reviewers Jason C. Slot; Anders Goncalves da Silva and Philippe Henry
LATEST VERSION PUBLISHED 15 Jun 2021
https://doi.org/10.12688/f1000research.20446.2
Method Article metrics
Revised
Unsupervised gene selection for predicting cell spatial positions in the Drosophila embryo
[version 2; peer review: 1 approved, 1 approved with reservations, 3 not approved]
Yang Chen, Disheng Mao, Yuping Zhang, Zhengqing Ouyang
Peer Reviewers Xianwen Ren; Mark S. Cembrowski and Larissa Kraus; Yen-Chung Chen; Saumitra Dey Choudhury; Komal Kumar Bollepogu Raja
  • Funder
  • Univerisity of Connecitcut
LATEST VERSION PUBLISHED 07 Jun 2021
https://doi.org/10.12688/f1000research.53408.1
Editorial metrics NOT PEER REVIEWED
Highlights from the 16th International Society for Computational Biology Student Council Symposium 2020
[version 1; peer review: not peer reviewed]
Wim L. Cuypers, Handan Melike Dönertaş, Jasleen K. Grewal, Nazeefa Fatima, Chase Donnelly, Arvind Singh Mer, Spencer Krieger, Bart Cuypers, Farzana Rahman
PUBLISHED 04 Jun 2021
https://doi.org/10.12688/f1000research.52549.1
Method Article metrics
Supervised topic modeling for predicting molecular substructure from mass spectrometry
[version 1; peer review: 2 approved with reservations]
Gabriel K. Reder, Adamo Young, Jaan Altosaar, Jakub Rajniak, Noémie Elhadad, Michael Fischbach, Susan Holmes
Peer Reviewers Joe Wandy; Hunter N B Moseley
  • Funder
  • National Institutes of Health
PUBLISHED 19 May 2021
https://doi.org/10.12688/f1000research.52954.1
Retraction metrics NOT PEER REVIEWED
RETRACTED: A low-cost in-house HIV integrase strand transfer inhibitor drug resistance test for resource-limited settings
[version 1; peer review: not peer reviewed]
Vera M. Onwong'a, Rachael W. Gachogo, Moses M. Masika, Graeme B. Jacobs, Frank G. Onyambu
  • Funder
  • Interhealth Networks Africa scholarship INA-001
PUBLISHED 20 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.26486.3
Research Article metrics
Revised
Neurons with dendrites can perform linearly separable computations with low resolution synaptic weights
[version 3; peer review: 3 approved]
Romain D. Cazé, Marcel Stimberg
Peer Reviewers Sacha van Albada; Fleur Zeldenrust; Alexandra Tzilivaki and Panayiota Poirazi
  • Funders
  • IHU FOReSIGHT
  • LabEx LIFESENSES
LATEST VERSION PUBLISHED 18 Apr 2021
https://doi.org/10.12688/f1000research.28404.1
Research Article metrics RETRACTED
RETRACTED:  A low-cost in-house HIV integrase strand transfer inhibitor drug resistance test for resource-limited settings
[version 1; peer review: awaiting peer review]
Vera M. Onwong'a, Rachael W. Gachogo, Moses M. Masika, Graeme B. Jacobs, Frank G. Onyambu
  • Funder
  • Interhealth Networks Africa
PUBLISHED 31 Mar 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.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.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.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.27112.2
Software Tool Article metrics
Revised
MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy
[version 2; peer review: 2 approved]
Sébastien Tosi, Lídia Bardia, Maria Jose Barallobre, Arrate Muñoz-Barrutia, María Luisa Soto-Montenegro, Julien Colombelli
Peer Reviewers Stephan Preibisch; Francesco Pampaloni
  • Funders
  • Instituto de Salud Carlos III
  • Ministerio de Ciencia, Innovación y Universidades
  • Ministerio de Economía y Competitividad
  • European Regional Development Fund
LATEST VERSION PUBLISHED 04 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
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