Cell & Molecular Biology

Cell & Molecular Biology

RNA

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https://doi.org/10.12688/f1000research.103533.2
Method Article metrics
Revised
Laboratory protocol for the digital multiplexed gene expression analysis of nasopharyngeal swab samples using the NanoString nCounter system
[version 2; peer review: 2 approved]
Marilina García Aranda, Inmaculada López-Rodríguez, Susana García-Gutiérrez, Maria Padilla-Ruiz, Vanessa de Luque, Maria Luisa Hortas, Tatiana Diaz, Martina Álvarez, Isabel Barragan-Mallofret, Maximino Redondo, Research Network on Health Services in Chronic Diseases (Red de Investigación en Servicios Sanitarios y Enfermedades Crónicas, REDISSEC)
Peer Reviewers Jan Weber; Tara K. Sigdel
  • Funders
  • Consejería de Economía, Conocimiento, Empresas y Universidad de la Junta de Andalucía
  • Instituto de Salud Carlos III
  • Fundación Fuerte
LATEST VERSION PUBLISHED 30 Sep 2022
https://doi.org/10.12688/f1000research.111175.2
Software Tool Article metrics
Revised
DSMZCellDive: Diving into high-throughput cell line data
[version 2; peer review: 2 approved]
Julia Koblitz, Wilhelm G. Dirks, Sonja Eberth, Stefan Nagel, Laura Steenpass, Claudia Pommerenke
Peer Reviewers Beate Rinner; Arihiro Kohara
  • Funder
  • Leibniz SAW project DiASPora
LATEST VERSION PUBLISHED 20 Jul 2022
https://doi.org/10.12688/f1000research.110936.1
Research Article metrics
TReNCo: Topologically associating domain (TAD) aware regulatory network construction
[version 1; peer review: 2 not approved]
Christopher Bennett, Viren Amin, Daehwan Kim, Murat Can Cobanoglu, Venkat Malladi
Peer Reviewers Junbai Wang; Sonika Tyagi
  • Funders
  • National Institute of General Medical Sciences
  • Cancer Prevention and Research Institute of Texas
PUBLISHED 14 Apr 2022
https://doi.org/10.12688/f1000research.76191.2
Research Article metrics
Revised
Sulfiredoxin-1 blood mRNA expression levels negatively correlate with hippocampal atrophy and cognitive decline
[version 2; peer review: 2 approved]
Catalina Anca Cucos, Ioana Cracana, Maria Dobre, Bogdan Ovidiu Popescu, Catalina Tudose, Luiza Spiru, Gina Manda, Gabriela Niculescu, Elena Milanesi
Peer Reviewers David Gurwitz; Sermin Genc
  • Funder
  • Competitiveness Operational Programme
LATEST VERSION PUBLISHED 21 Mar 2022
https://doi.org/10.12688/f1000research.75677.1
Research Article metrics
Design-of-experiments in vitro transcription yield optimization of self-amplifying RNA
[version 1; peer review: 2 approved with reservations]
Karnyart Samnuan, Anna K Blakney, Paul F McKay, Robin J Shattock
Peer Reviewers Rok Sekirnik; Emily Voigt and Devin Brandt
  • Funders
  • European Commission H2020
  • Engineering and Physical Sciences Research Council
PUBLISHED 18 Mar 2022
https://doi.org/10.12688/f1000research.54864.2
Research Article metrics
Revised
The need to reassess single-cell RNA sequencing datasets: the importance of biological sample processing
[version 2; peer review: 2 approved]
Alex M. Ascensión, Marcos J. Araúzo-Bravo, Ander Izeta
Peer Reviewers Xiao Long and Zhujun Li; (Jo) Huiqing Zhou
  • Funders
  • Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza
  • Instituto de Salud Carlos III
  • Horizon 2020
  • European Regional Development Fund
LATEST VERSION PUBLISHED 08 Mar 2022
https://doi.org/10.12688/f1000research.94159.1
Software Tool Article metrics
miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies
[version 1; peer review: 2 approved with reservations]
Andreas Diendorfer, Kseniya Khamina, Marianne Pultar, Matthias Hackl
Peer Reviewers Kristian Almstrup, Nina Mørup and Ailsa Maria Main; Francisco J. Enguita
  • Funder
  • Innovative Medicines Initiative 2
PUBLISHED 24 Feb 2022
https://doi.org/10.12688/f1000research.75243.1
Software Tool Article metrics
SASCRiP: A Python workflow for preprocessing UMI count-based scRNA-seq data
[version 1; peer review: 2 approved with reservations]
Darisia Moonsamy, Nikki Gentle
Peer Reviewers Fabiola Curion and Luke Zappia; Fangming Xie
  • Funder
  • National Research Foundation
PUBLISHED 15 Feb 2022
https://doi.org/10.12688/f1000research.108489.1
Research Article metrics
Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly.
[version 1; peer review: 2 approved with reservations]
Raquel Linheiro, John Archer
Peer Reviewers Ben J. Mans; Kun Lu Lu
  • Funder
  • Fundacão para a Ciência e a Tecnologia (FCT)
PUBLISHED 31 Jan 2022
https://doi.org/10.12688/f1000research.75321.1
Method Article metrics
Improving prediction of core transcription factors for cell reprogramming and transdifferentiation
[version 1; peer review: 2 not approved]
Mikhail Raevskiy, Anna Kondrashina, Yulia Medvedeva
Peer Reviewers Valentiva Boeva and Samuel Gunz; Erdem B. Dashinimaev
  • Funder
  • Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 13 Jan 2022
https://doi.org/10.12688/f1000research.26128.2
Method Article metrics
Revised
Space-log: a novel approach to inferring gene-gene net-works using SPACE model with log penalty
[version 2; peer review: 2 approved, 1 approved with reservations]
Qian (Vicky) Wu, Wei Sun, Li Hsu
Peer Reviewers Yuying Xie and Yuning Hao; Chi Song; Jessie Jeng
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 05 Jan 2022
https://doi.org/10.12688/f1000research.73641.1
Software Tool Article metrics
PlotXpress, a webtool for normalization and visualization of reporter expression data
[version 1; peer review: 3 approved]
Elias Brandorff, Marc Galland, Joachim Goedhart
Peer Reviewers Lorena Pantano Rubino; Guillaume Jacquemet; Vincent J. Lynch
PUBLISHED 08 Nov 2021
https://doi.org/10.12688/f1000research.27868.3
Method Article metrics
Revised
WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data
[version 3; peer review: 2 approved]
Konstantinos Geles, Domenico Palumbo, Assunta Sellitto, Giorgio Giurato, Eleonora Cianflone, Fabiola Marino, Daniele Torella, Valeria Mirici Cappa, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, Francesca Rizzo
Peer Reviewers Juan Pablo Tosar; Wen Yao
  • Funders
  • Italian Association for Cancer Research
  • Ministero dell’Istruzione, dell’Università e della Ricerca
  • Horizon 2020
  • Regione Campania
LATEST VERSION PUBLISHED 12 Jul 2021
https://doi.org/10.12688/f1000research.52350.2
Software Tool Article metrics
Revised
RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction
[version 2; peer review: 2 approved]
Thaís A.R. Ramos, Nilbson R.O. Galindo, Raúl Arias-Carrasco, Cecília F. da Silva, Vinicius Maracaja-Coutinho, Thaís G. do Rêgo
Peer Reviewers Gilderlanio Araújo; Andre Yoshiaki Kashiwabara
  • Funders
  • ANID-FONDECYT
  • ACCDiS
  • ANID-PAI
  • ANID-FONDAP
  • CAPES
LATEST VERSION PUBLISHED 08 Jun 2021
https://doi.org/10.12688/f1000research.27532.2
Brief Report metrics
Revised
Genome-wide screening of upstream transcription factors using an expression library
[version 2; peer review: 2 approved]
Naoya Yahagi, Yoshinori Takeuchi
Peer Reviewers Kazuhiko Igarashi; Harukazu Suzuki
  • Funders
  • Suzuken Memorial Foundation
  • SENSHIN Medical Research Foundation
  • Japan Foundation for Applied Enzymology
  • Ministry of Education, Culture, Sports, Science and Technology
  • Uehara Memorial Foundation
  • Naito Foundation
  • Okinaka Memorial Institute for Medical Research
  • Takeda Science Foundation
  • Japan Heart Foundation
  • Kanae Foundation for the Promotion of Medical Science
  • Ono Medical Research Foundation
  • Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering
  • Senri Life Science Foundation
LATEST VERSION PUBLISHED 08 Mar 2021
https://doi.org/10.12688/f1000research.15666.3
Research Article metrics
Revised
A systematic performance evaluation of clustering methods for single-cell RNA-seq data
[version 3; peer review: 2 approved]
Angelo Duò, Mark D. Robinson, Charlotte Soneson
Peer Reviewers Jean Fan; Saskia Freytag
  • Funders
  • Swiss National Science Foundation
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 16 Nov 2020
21-36 of 36 ARTICLES
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