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https://doi.org/10.12688/f1000research.26429.2
Software Tool Article metrics
Revised
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
[version 2; peer review: 2 approved]
Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Peer Reviewers Kim-Anh Lê Cao; Anais Baudot, Judith Lambert and Laurent Tichit
  • Funders
  • Villum Fonden
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.44714.1
Data Note metrics
Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus
[version 1; peer review: 2 approved]
Jose De Vega, Iain Donnison, Sarah Dyer, Kerrie Farrar
Peer Reviewers Diego Mauricio Riaño-Pachón; Maria Stefanie Dwiyanti
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 18 Jan 2021
https://doi.org/10.12688/f1000research.28215.1
Brief Report metrics
Evolution of SARS-CoV-2 virus and assessment of the effectiveness of COVID-19 vaccine
[version 1; peer review: 2 approved]
Veljko Veljkovic, Vladimir Perovic, Isabelle Chambers, Slobodan Paessler
Peer Reviewers Ursula Dietrich; Marwa Osama Elgendy
  • Funder
  • Agricultural Department of North Dakota
PUBLISHED 18 Jan 2021
https://doi.org/10.12688/f1000research.26170.2
Research Article metrics
Revised
Development of species-specific SCAR markers for identification and authentication of three rare Peninsular Malaysian endemic Coelogyne (Orchidaceae) orchids
[version 2; peer review: 2 approved]
Yoh Kok Hon, Christina Seok-Yien Yong, Janna Ong Abdullah, Rusea Go
Peer Reviewers Mohd Norfaizal Ghazali; Jean Wan Hong Yong
  • Funder
  • Universiti Putra Malaysia
LATEST VERSION PUBLISHED 05 Jan 2021
https://doi.org/10.12688/f1000research.26880.2
Software Tool Article metrics
Revised
Recursive Cluster Elimination based Rank Function (SVM-RCE-R) implemented in KNIME
[version 2; peer review: 3 approved]
Malik Yousef, Burcu Bakir-Gungor, Amhar Jabeer, Gokhan Goy, Rehman Qureshi, Louise C. Showe
Peer Reviewers Marco Chierici; Osman Ugur Sezerman; Abhishek Kumar
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 05 Jan 2021
https://doi.org/10.12688/f1000research.19080.2
Study Protocol metrics
Revised
A recall-by-genotype study on polymorphisms in the TMPRSS6 gene and oral iron absorption: a study protocol
[version 2; peer review: 1 approved, 1 approved with reservations]
Momodou W. Jallow, Susana Campino, Andrew M. Prentice, Carla Cerami
Peer Reviewers Dale R. Nyholt and Hamzeh MESRIAN TANHA; Alida Melse-Boonstra
  • Funders
  • Department for International Development
  • Medical Research Council UK
LATEST VERSION PUBLISHED 04 Jan 2021
https://doi.org/10.12688/f1000research.26632.1
Research Article metrics
Glibenclamide, ATP and metformin increases the expression of human bile salt export pump ABCB11
[version 1; peer review: 1 approved, 2 approved with reservations]
Nisha Vats, Ravi Chandra Dubey, Madhusudana Girija Sanal, Pankaj Taneja, Senthil Kumar Venugopal
Peer Reviewers Premkumar Kumpati; Jayanta Roy-Chowdhury; Amit Dash
  • Funders
  • Science and Engineering Research Board
  • Department of Biotechnology, Ministry of Science and Technology, India
PUBLISHED 22 Dec 2020
https://doi.org/10.12688/f1000research.20916.2
Method Article metrics
Revised
Fast effect size shrinkage software for beta-binomial models of allelic imbalance
[version 2; peer review: 1 approved, 2 approved with reservations]
Joshua P. Zitovsky, Michael I. Love
Peer Reviewers Matthew Stephens; Jarad Niemi and Ignacio Alvarez-Castro; Ernest Turro
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 14 Dec 2020
https://doi.org/10.12688/f1000research.27262.1
Method Article metrics
A pipeline to analyse time-course gene expression data
[version 1; peer review: 2 approved with reservations]
Nelle Varoquaux, Elizabeth Purdom
Peer Reviewers Michael I. Love; Rodolphe Thiébaut
  • Funders
  • U.S. Department of Energy
  • École Normale Supérieure
  • Gordon and Betty Moore Foundation
  • Alfred P. Sloan Foundation
PUBLISHED 11 Dec 2020
https://doi.org/10.12688/f1000research.27893.1
Method Article metrics
A guide to creating design matrices for gene expression experiments
[version 1; peer review: 2 approved]
Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Peer Reviewers Federico Marini; Jenny Drnevich
  • Funders
  • National Health and Medical Research Council
  • Chan Zuckerberg Initiative
PUBLISHED 10 Dec 2020
https://doi.org/10.12688/f1000research.22021.4
Research Article metrics
Revised
Effects of polyisoprenoids from Avicennia lanata and Avicennia alba leaves on the gene expression of PI3K, Akt1, mTOR, P53, and EGFR in human colorectal adenocarcinoma WiDr cells
[version 4; peer review: 1 approved, 2 not approved]
Taufiq Qurrohman, Poppy Anjelisa Zaitun Hasibuan, Arif Nuryawan, Sumaiyah Sumaiyah, Etti Sartina Siregar, Mohammad Basyuni
Peer Reviewers Ewa Swiezewska and Liliana Surmacz; Aldes Lesbani; Amos Fatokun
  • Funder
  • Ministry of Research, Technology and Higher Education of the Republic of Indonesia
LATEST VERSION PUBLISHED 09 Dec 2020
https://doi.org/10.12688/f1000research.24808.2
Review metrics
Revised
SMARCB1/INI1-deficient tumors of adulthood
[version 2; peer review: 2 approved]
Nathaniel A. Parker, Ammar Al-Obaidi, Jeremy M. Deutsch
Peer Reviewers Conor Patrick Malone; Abdulqadir Nashwan
LATEST VERSION PUBLISHED 09 Dec 2020
https://doi.org/10.12688/f1000research.27681.1
Brief Report metrics
Phylogenetic analysis of the betacoronavirus S1 subunit
[version 1; peer review: 1 approved with reservations, 1 not approved]
Irina Zyrianova
Peer Reviewers Houcemeddine Othman; Peng Zhou
  • Funder
  • The Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 03 Dec 2020
https://doi.org/10.12688/f1000research.27188.1
Software Tool Article metrics
isa4j: a scalable Java library for creating ISA-Tab metadata
[version 1; peer review: 2 approved]
Dennis Psaroudakis, Feng Liu, Patrick König, Uwe Scholz, Astrid Junker, Matthias Lange, Daniel Arend
Peer Reviewers Massimiliano Izzo; Nils Hoffmann
  • Funders
  • ELIXIR
  • German Ministry of Education and Research (BMBF)
PUBLISHED 03 Dec 2020
https://doi.org/10.12688/f1000research.26524.1
Data Note metrics
Complete mitochondrial genome of the endangered species Brycon nattereri (Characiformes, Characidae)
[version 1; peer review: 2 approved with reservations]
Snaydia Viegas Resende, Rubens Pasa, Fabiano Bezerra Menegídio, John Seymour (Pat) Heslop-Harrison, Trude Schwarzacher, Karine Frehner Kavalco
Peer Reviewers Yong Zhang; Dora Davies and Juan José Lauthier
PUBLISHED 18 Nov 2020
https://doi.org/10.12688/f1000research.24956.2
Software Tool Article metrics
Revised
gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
[version 2; peer review: 2 approved]
Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Peer Reviewers Egon L. Willighagen; Ewy Mathe
  • Funders
  • Eesti Teadusagentuur
  • Seventh Framework Programme
  • European Regional Development Fund
LATEST VERSION PUBLISHED 17 Nov 2020
https://doi.org/10.12688/f1000research.23214.2
Software Tool Article metrics
Revised
CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets
[version 2; peer review: 2 approved, 1 not approved]
Sandeep Kasaragod, Varshasnata Mohanty, Ankur Tyagi, Santosh Kumar Behera, Arun H. Patil, Sneha M. Pinto, T. S. Keshava Prasad, Prashant Kumar Modi, Harsha Gowda
Peer Reviewers Suresh Mathivanan; Richard Kumaran Kandasamy; Jorge Duitama and Daniel Mahecha
  • Funders
  • Indian Council of Medical Research
  • Department of Science and Technology, Ministry of Science and Technology, India
  • Department of Biotechnology, Ministry of Science and Technology, India
LATEST VERSION PUBLISHED 16 Nov 2020
https://doi.org/10.12688/f1000research.24654.2
Research Article metrics
Revised
Investigating a novel multiplex proteomics technology for detection of changes in serum protein concentrations that may correlate to tumor burden
[version 2; peer review: 2 approved]
Annie He Ren, Ioannis Prassas, Antoninus Soosaipillai, Stephanie Jarvi, Steven Gallinger, Vathany Kulasingam, Eleftherios P. Diamandis
Peer Reviewers Georgios Pampalakis; Anna E Lokshin
  • Funder
  • Mount Sinai Hospital
LATEST VERSION PUBLISHED 13 Nov 2020
https://doi.org/10.12688/f1000research.22541.1
Research Article metrics
Use of 16s rRNA to identify non-lactose-fermenting bacilli and molecular detection of ESBL resistance genes associated with hospital-acquired infection in Soba University Hospital, Sudan
[version 1; peer review: 1 approved]
Wissam Ahmed Al Hag, Hana Elbadawi, Muzamil Mahdi Abdel Hamid
Peer Reviewers Asim Elnour
PUBLISHED 10 Nov 2020
https://doi.org/10.12688/f1000research.26930.1
Research Article metrics
On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference
[version 1; peer review: 3 approved]
Alexis Criscuolo
Peer Reviewers Brian Ondov; Burkhard Morgenstern; Guy Perrière
PUBLISHED 10 Nov 2020
261-280 of 2,028 ARTICLES
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