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https://doi.org/10.12688/f1000research.28142.2
Software Tool Article metrics
Revised
MIREyA: a computational approach to detect miRNA-directed gene activation
[version 2; peer review: 1 approved, 2 approved with reservations]
Anna Elizarova, Mumin Ozturk, Reto Guler, Yulia A. Medvedeva
Peer Reviewers Michiel Jan Laurens De Hoon; Xiangfu Zhong; Chaogang Shao
  • Funders
  • European and Developing Countries Clinical Trials Partnership
  • Russian Foundation for Basic Research
  • South Africa National Research Foundation
LATEST VERSION PUBLISHED 26 Aug 2021
https://doi.org/10.12688/f1000research.52412.2
Method Article metrics
Revised
A signaling pathway-driven bioinformatics pipeline for predicting therapeutics against emerging infectious diseases
[version 2; peer review: 2 approved, 1 approved with reservations]
Tiana M. Scott, Sam Jensen, Brett E. Pickett
Peer Reviewers José Pedro Cerón-Carrasco; Babatunde Joseph Oso; Soumya Lipsa Rath
  • Funder
  • Brigham Young University
LATEST VERSION PUBLISHED 20 Aug 2021
https://doi.org/10.12688/f1000research.54418.1
Software Tool Article metrics
Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality
[version 1; peer review: 2 approved]
Davide Albanese, Claudio Donati
Peer Reviewers Thomas S. B. Schmidt, Anthony Fullam and Askarbek Orakov; Denis Baurain
  • Funder
  • Autonomous Province of Trento (Accordo di Programma)
PUBLISHED 17 Aug 2021
https://doi.org/10.12688/f1000research.54258.1
Research Article metrics
Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach
[version 1; peer review: 3 approved]
Fedik Abdul Rantam, Viol Dhea Kharisma, Christrijogo Sumartono, Jusak Nugraha, Andi Yasmin Wijaya, Helen Susilowati, Suryo Kuncorojakti, Alexander Patera Nugraha
Peer Reviewers Mohammad Saifur Rohman; Dur Lashari and Yasmeen Lashari; Hesham Mohammed Al-Sharani
  • Funders
  • Lembaga Pengelola Dana Pendidikan, Ministry of Finance, Republic of Indonesia
  • Ministry of Research and Technology, Republic of Indonesia
PUBLISHED 16 Aug 2021
https://doi.org/10.12688/f1000research.54071.1
Data Note metrics
Organizing knowledge to enable faster data interpretation in COVID-19 research
[version 1; peer review: 2 approved with reservations]
Joseph Hearnshaw, Marco Brandizi, Ajit Singh, Chris Rawlings, Keywan Hassani-Pak
Peer Reviewers Justin Reese; Keith Hall
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 30 Jul 2021
https://doi.org/10.12688/f1000research.19630.2
Software Tool Article metrics
Revised
A strategy for building and using a human reference pangenome
[version 2; peer review: 2 approved]
Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas A. Sibbesen, Charles J. Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael F. Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva L. Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Siren, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki T. Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten, Ben Busby
Peer Reviewers Anna Kuosmanen; Robert A. Beagrie
  • Funders
  • Simons Foundation
  • Carlsbergfondet
  • U.S. National Library of Medicine
  • W. M. Keck Foundation
  • National Institutes of Health
  • Australian Research Council
LATEST VERSION PUBLISHED 29 Jul 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.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.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.28022.2
Software Tool Article metrics
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.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.50850.3
Research Article metrics
Revised
Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches
[version 3; peer review: 3 approved]
Gurudeeban Selvaraj, Satyavani Kaliamurthi, Gilles H. Peslherbe, Dong-Qing Wei
Peer Reviewers Sugunadevi Sakkiah; Dhurvas C. Dinesh; Turanli Beste
  • Funders
  • Natural Sciences and Engineering Research Council of Canada
  • Ministry of Science and Technology of the People's Republic of China
  • Concordia University
  • National Natural Science Foundation of China
  • MITACS Global Research
LATEST VERSION PUBLISHED 17 May 2021
https://doi.org/10.12688/f1000research.27500.2
Opinion Article metrics
Revised
The need for standardisation in life science research - an approach to excellence and trust.
[version 2; peer review: 3 approved]
Susanne Hollmann, Andreas Kremer, Špela Baebler, Christophe Trefois, Kristina Gruden, Witold R. Rudnicki, Weida Tong, Aleksandra Gruca, Erik Bongcam-Rudloff, Chris T. Evelo, Alina Nechyporenko, Marcus Frohme, David Šafránek, Babette Regierer, Domenica D'Elia
Peer Reviewers David Nickerson; Laurent Falquet; Antonella Lanati
  • Funder
  • Horizon 2020
LATEST VERSION PUBLISHED 10 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.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.25485.1
Opinion Article metrics
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists
[version 1; peer review: 2 approved]
Gabriel G. Martins, Fabrice P. Cordelières, Julien Colombelli, Rocco D’Antuono, Ofra Golani, Romain Guiet, Robert Haase, Anna H. Klemm, Marion Louveaux, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Kota Miura
Peer Reviewers Thorsten Wohland; Kevin Eliceiri
  • Funders
  • Swedish Foundation for Strategic Research
  • Fundação para a Ciência e a Tecnologia
  • COST
  • Luxembourg National Research Fund
  • Cancer Research UK
  • Deutsche Forschungsgemeinschaft
  • Swedish National Microscopy infrastructure
  • UK Medical Research Council
  • France BioImaging national infrastructure
  • Wellcome Trust
PUBLISHED 30 Apr 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
141-160 of 638 ARTICLES
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