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 in 
https://doi.org/10.12688/f1000research.24345.2
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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.53137.1
Research Article metrics
Characterization of SARS-CoV-2 East Java isolate, Indonesia
[version 1; peer review: 2 approved, 1 approved with reservations]
Fedik Abdul Rantam, Cita Rosita Sigit Prakoeswa, Damayanti Tinduh, Jusak Nugraha, Helen Susilowati, Andi Yasmin Wijaya, Ni Nyoman Tri Puspaningsih, Dwiyanti Puspitasari, Dominicus Husada, Neneng Dewi Kurniati, Aryati Aryati
Peer Reviewers Aulanni’am Aulanni'am; Lidia Audrey Rocha Valadas; Marina Derkho
  • Funder
  • Ministry of Research and Technology; Ministry of Health of the Republic of Indonesia
PUBLISHED 16 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.27921.1
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Decaffeinated light-roasted green coffee and green tea extract combination improved metabolic parameters and modulated inflammatory genes in metabolic syndrome rats
[version 1; peer review: 2 approved with reservations]
Mohammad Saifur Rohman, Mifetika Lukitasari, Dwi Adi Nugroho, Risa Ramadhiani, Nashi Widodo, Inggita Kusumastuty, Nur Ida Panca Nugrahini
Peer Reviewers Alex Boye; Nelly Mayulu
  • Funder
  • Universitas Brawijaya
PUBLISHED 14 Jun 2021
https://doi.org/10.12688/f1000research.23471.2
Research Article metrics
Revised
Metformin improves FOXP3 mRNA expression through suppression of interferon gamma levels in pristane-induced murine models of lupus
[version 2; peer review: 3 approved]
Stevent Sumantri, Mochammad Hatta, Rosdiana Natzir, Haerani Rasyid, Iris Rengganis, Muh. Nasrum Massi, Andi Asadul Islam, Gatot Lawrence, Ilhamjaya Patellongi, Andi Fachruddin Benyamin
Peer Reviewers Shuang Ye; Erin B Taylor; Mirza Zaka Pratama
LATEST VERSION PUBLISHED 11 Jun 2021
https://doi.org/10.12688/f1000research.28510.2
Research Article metrics
Revised
Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology
[version 2; peer review: 2 approved, 1 approved with reservations]
Rafael Sebastián Fort, María Ana Duhagon
Peer Reviewers Daniele Hasler; Deepanwita Sengupta; Yong Sun Lee
  • Funders
  • Agencia Nacional de Investigación e Innovación (ANII)
  • Comision Academica de Posgrado, UDELAR
  • Comisión Sectorial de Investigación Científica (CSIC, UDELAR)
  • Programa para el Desarrollo de las Ciencias Basicas (PEDECIBA, MEC)
LATEST VERSION PUBLISHED 09 Jun 2021
https://doi.org/10.12688/f1000research.28022.2
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Revised
BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS
[version 2; peer review: 3 approved]
Caroline Gaud, Bebiana C. Sousa, An Nguyen, Maria Fedorova, Zhixu Ni, Valerie B. O’Donnell, Michael J.O. Wakelam, Simon Andrews, Andrea F. Lopez-Clavijo
Peer Reviewers Amaury Cazenave Gassiot; Phillip Whitfield; Ginger Milne
  • Funders
  • German Federal Ministry of Education and Research
  • Wellcome Trust
LATEST VERSION PUBLISHED 09 Jun 2021
https://doi.org/10.12688/f1000research.25369.1
Opinion Article metrics
Moving forward with forward genetics: A summary of the INFRAFRONTIER Forward Genetics Panel Discussion
[version 1; peer review: 1 approved, 2 approved with reservations]
Asrar Ali Khan, Michael Raess, Martin Hrabe de Angelis
Peer Reviewers Martin S Denzel; Anton Wutz and Corinne Kaufmann; Camron D Bryant
  • Funder
  • Horizon 2020
PUBLISHED 08 Jun 2021
https://doi.org/10.12688/f1000research.52460.1
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scNetViz: from single cells to networks using Cytoscape
[version 1; peer review: 2 approved]
Krishna Choudhary, Elaine C. Meng, J. Javier Diaz-Mejia, Gary D. Bader, Alexander R. Pico, John H. Morris
Peer Reviewers Luca Pinello; Kenji Kamimoto
  • Funders
  • National Resource for Network Biology
  • Chan Zuckerberg Initiative
PUBLISHED 07 Jun 2021
https://doi.org/10.12688/f1000research.50857.2
Brief Report metrics
Revised
Interactive SARS-CoV-2 mutation timemaps
[version 2; peer review: 3 approved]
René L. Warren, Inanc Birol
Peer Reviewers Ingo Ebersberger and Ruben Iruegas; Takahiko Koyama; Jale Moradi
  • Funders
  • National Institute for Health Research
  • Genome Canada
LATEST VERSION PUBLISHED 03 Jun 2021
https://doi.org/10.12688/f1000research.25148.2
Research Article metrics
Revised
First draft genome assembly of the desert locust, Schistocerca gregaria
[version 2; peer review: 3 approved]
Heleen Verlinden, Lieven Sterck, Jia Li, Zhen Li, Anna Yssel, Yannick Gansemans, Rik Verdonck, Michiel Holtof, Hojun Song, Spencer T. Behmer, Gregory A. Sword, Tom Matheson, Swidbert R. Ott, Dieter Deforce, Filip Van Nieuwerburgh, Yves Van de Peer, Jozef Vanden Broeck
Peer Reviewers Uwe Homberg; Surya Saha; Joshua B. Benoit
  • Funders
  • U.S. Department of Agriculture
  • University of Pretoria
  • KU Leuven
  • Fonds Wetenschappelijk Onderzoek
  • Universiteit Gent
  • Biotechnology and Biological Sciences Research Council
  • National Science Foundation
LATEST VERSION PUBLISHED 21 May 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.52178.1
Brief Report metrics
Multi-modality detection of SARS-CoV-2 in faecal donor samples for transplantation and in asymptomatic emergency surgical admissions
[version 1; peer review: 2 approved]
Susan E. Manzoor, Shafquat Zaman, Celina Whalley, David Inglis, Andrew Bosworth, Michael Kidd, Sahida Shabir, Nabil Quraishi, Christopher A. Green, Tariq Iqbal, Andrew D. Beggs
Peer Reviewers Jonathan Landy; James Kinross
  • Funders
  • Cancer Research UK
  • Birmingham Experimental Cancer Medicine Centre
  • CRUK Centre Birmingham
PUBLISHED 11 May 2021
https://doi.org/10.12688/f1000research.51433.1
Case Report metrics
Case Report: Guitarist’s cramp as the initial manifestation of dopa-responsive dystonia with a novel heterozygous GCH1 mutation
[version 1; peer review: 2 approved, 1 approved with reservations]
Takafumi Hasegawa, Tatsuhiko Hosaka, Ryuhei Harada, Ichiro Kawahata, Kyoko Hoshino, Naoto Sugeno, Akio Kikuchi, Masashi Aoki
Peer Reviewers Hiroshi Ichinose; Taku Hatano; Juei-Jueng Lin
  • Funders
  • The Kawano Masanori Memorial Foundation for Promotion of Pediatrics
  • Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan
PUBLISHED 07 May 2021
https://doi.org/10.12688/f1000research.52141.1
Software Tool Article metrics AWAITING PEER REVIEW
Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design
[version 1; peer review: awaiting peer review]
Kristianne Arielle Gabriel, Maria Rejane Nepacina, Francis Tablizo, Carlo Lapid, Mark Lenczner Mendoza, Daniella Jean Pamulaklakin, Jobeth Domingo, Marc Jermaine Pontiveros, Hannah Mae Magno, Joshua Gregor Dizon, El King Morado, Jan Michael Yap
Peer Reviewers Invited
  • Funder
  • Philippine Council for Industry, Energy and Emerging Technology Research and Development of the Department of Science and Technology
PUBLISHED 07 May 2021
https://doi.org/10.12688/f1000research.51874.1
Research Article metrics
Horizontal transfer and evolution of wall teichoic acid gene cassettes in Bacillus subtilis
[version 1; peer review: 1 approved, 2 approved with reservations]
Granger Sutton, Gary B. Fogel, Bradley Abramson, Lauren Brinkac, Todd Michael, Enoch S. Liu, Sterling Thomas
Peer Reviewers Jeffrey B. Jones; José Escudero; Patrick Eichenberger
  • Funders
  • IARPA
  • Office of the Director of National Intelligence
PUBLISHED 07 May 2021
https://doi.org/10.12688/f1000research.51407.1
Case Report metrics
Case Report: A five-year follow up after pediatric renal transplantation using flow cytometry crossmatch and HLA immunophenotyping based on DNA for screening test
[version 1; peer review: 2 approved, 1 approved with reservations, 1 not approved]
Johanes Dwi Meiyanto, Besut Daryanto, Kurnia Penta Seputra
Peer Reviewers Ali Ersin Zumrutbas; Nur Rasyid; Nicolas Guillaume; Shigeo Horie
PUBLISHED 06 May 2021
https://doi.org/10.12688/f1000research.28187.1
Method Article metrics
Validity and reliability of method used to analyse hair cortisol concentration
[version 1; peer review: 2 approved with reservations]
Jordan Reid, Katy Parker, Lydia Clemens, Matt Bristow
Peer Reviewers Yolanda B. de Rijke; Gabriela Berg and Bibiana Fabre
PUBLISHED 06 May 2021
https://doi.org/10.12688/f1000research.27393.3
Brief Report metrics
Revised
Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer
[version 3; peer review: 3 approved]
Colin L. Hisey, Petr Tomek, Yohanes N.S. Nursalim, Lawrence W. Chamley, Euphemia Leung
Peer Reviewers Nagarajan Kannan; Tracy K. Hale; Bruno M. Simoes
  • Funders
  • New Zealand Breast Cancer Foundation
  • Cancer Research Trust New Zealand
  • Faculty of Medical and Health Sciences, University of Auckland
LATEST VERSION PUBLISHED 04 May 2021
https://doi.org/10.12688/f1000research.51164.1
Brief Report metrics
The feasibility of targeted test-trace-isolate for the control of SARS-CoV-2 variants
[version 1; peer review: 2 approved with reservations]
William Bradshaw, Jonathan Huggins, Alun Lloyd, Kevin Esvelt
Peer Reviewers Akira Endo; Tim C. D. Lucas
  • Funders
  • Drexel Endowment
  • Centers for Disease Control and Prevention
  • Open Philanthropy Project
  • Reid Hoffman Foundation
  • COVID-19 HPC consortium
PUBLISHED 16 Apr 2021
121-140 of 644 ARTICLES
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