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 in 
https://doi.org/10.12688/f1000research.52460.1
Software Tool Article metrics
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
https://doi.org/10.12688/f1000research.27502.2
Research Article metrics
Revised
Inter-site and interpersonal diversity of salivary and tongue microbiomes, and the effect of oral care tablets
[version 2; peer review: 3 approved]
Hugo Maruyama, Ayako Masago, Takayuki Nambu, Chiho Mashimo, Kazuya Takahashi, Toshinori Okinaga
Peer Reviewers Takuichi Sato; Rohit Kunnath Menon; Priya Nimish Deo
  • Funder
  • Japan Society for the Promotion of Science
LATEST VERSION PUBLISHED 09 Apr 2021
https://doi.org/10.12688/f1000research.24818.3
Research Article metrics
Revised
β-lactamases (bla TEM, bla SHV, bla CTXM-1, bla VEB, bla OXA-1) and class C β-lactamases gene frequency in Pseudomonas aeruginosa isolated from various clinical specimens in Khartoum State, Sudan: a cross sectional study
[version 3; peer review: 2 approved]
Dina N. Abdelrahman, Aya A. Taha, Mazar M. Dafaallah, Alaa Abdelgafoor Mohammed, Abdel Rahim M. El Hussein, Ahmed I. Hashim, Yousif F. Hamedelnil, Hisham N. Altayb
Peer Reviewers Nobumichi Kobayashi; Muhammad Qasim
LATEST VERSION PUBLISHED 01 Apr 2021
https://doi.org/10.12688/f1000research.51213.2
Research Article metrics
Revised
MGMT promoter gene methylation and neurological scale improvement in glioma: a cohort study
[version 2; peer review: 1 approved, 1 not approved]
Pricilla Yani Gunawan, Andi Asadul Islam, Julius July, Ilhamjaya Patelongi, Agussalim Bukhari, Muh. Nasrum Massi
Peer Reviewers Young Zoon Kim; Ery Kus Dwianingsih
LATEST VERSION PUBLISHED 30 Mar 2021
https://doi.org/10.12688/f1000research.27089.2
Research Article metrics
Revised
In silico analysis of cross reactivity among phospholipases from Hymenoptera species
[version 2; peer review: 2 approved]
Yuliana Emiliani, Andrés Sánchez, Marlon Munera, Jorge Sánchez, Dilia Aparicio
Peer Reviewers Anna Pomés; Jose F. Cantillo
LATEST VERSION PUBLISHED 29 Mar 2021
https://doi.org/10.12688/f1000research.51546.1
Research Article metrics
A new method for early detection of latent infection by ‘Candidatus Liberibacter asiaticus’ in citrus trees
[version 1; peer review: 1 approved, 1 approved with reservations]
Kazuki Fujiwara, Kenta Tomimura, Toru Iwanami, Takashi Fujikawa
Peer Reviewers Siti Subandiyah; Madhurababu Kunta
  • Funder
  • This work was supported in part by grants from the Project of the NARO Bio-oriented Technology Research Advancement Institution (Research program on development of innovative technology).
PUBLISHED 29 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.26771.2
Software Tool Article metrics
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.23740.2
Research Article metrics
Revised
Morphological and genetic evaluation of the thumbprint emperor, Lethrinus harak (Forsskål, 1775) in the Pacific and Indian Oceans
[version 2; peer review: 2 approved, 2 approved with reservations]
Muhammad Afrisal, Yukio Iwatsuki, Andi Iqbal Burhanuddin
Peer Reviewers Jayasankar Pallipuram; Femy Mahmud Sahami; Arvind Kumar Dwivedi; Siti Azizah Mohd Nor
  • Funder
  • Direktorat Jenderal Pendidikan Tinggi
LATEST VERSION PUBLISHED 16 Mar 2021
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