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https://doi.org/10.12688/f1000research.129958.4
Research Article metrics
Revised
The first released available genome of the common ice plant (Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C3-CAM photosynthetic conversion, and halophilism
[version 4; peer review: 2 approved, 1 approved with reservations]
Ryoma Sato, Yuri Kondo, Sakae Agarie
Peer Reviewers Qijie Guan; Xin-Guang Zhu; Zbigniew Miszalski
  • Funder
  • JSPS KAKENHI
LATEST VERSION PUBLISHED 04 Jan 2024
https://doi.org/10.12688/f1000research.142165.1
Research Article metrics AWAITING PEER REVIEW
A survey into the contribution of regional/national pathogen data platforms and on the resources needed to develop and maintain them
[version 1; peer review: awaiting peer review]
Aitana Neves, Nils P Willassen, Erik Hjerde, Isabel Cuesta, Corinne S Martin, Heleri Inno, Diana Pilvar, Kim Ng, David Salgado, Jacques van Helden, Wei Gu, Marina Popleteeva, Joaquin Dopazo, Timotej Šuri, Jan Pačes, Cezary Mazurek, Krzysztof Kurowski, Natalia Koralewska, Gunter Maier, ELIXIR CONVERGE WP9 community
Peer Reviewers Invited
  • Funder
  • Horizon 2020
PUBLISHED 14 Dec 2023
https://doi.org/10.12688/f1000research.143015.1
Editorial metrics NOT PEER REVIEWED
BOSC 2023, the 24th annual Bioinformatics Open Source Conference
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Christopher J. Fields, Karsten Hokamp, Jérémy Just, Radhika Khetani, Jessica Maia, Hervé Ménager, Monica C. Munoz-Torres, Deepak Unni, Jason Williams
  • Funders
  • IXXI/MSH-LSE/BIOSYL 2023
  • Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy
  • National Human Genome Research Institute
PUBLISHED 07 Dec 2023
https://doi.org/10.12688/f1000research.134078.2
Method Article metrics
Revised
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data
[version 2; peer review: 2 approved, 1 approved with reservations]
Jinming Cheng, Gordon K. Smyth, Yunshun Chen
Peer Reviewers Michael D Morgan; Koen Van den berge; Anna Alemany, Xuan Quy Nguyen and Noëlle Dommann
  • Funders
  • National Health and Medical Research Council
  • Chan Zuckerberg Initiative
  • Medical Research Future Fund
LATEST VERSION PUBLISHED 10 Nov 2023
https://doi.org/10.12688/f1000research.123714.2
Research Article metrics
Revised
Identification of prognostic biomarkers of invasive ductal carcinoma by an integrated bioinformatics approach
[version 2; peer review: 1 approved, 1 approved with reservations]
Albeiro Marrugo-Padilla, Johana Márquez-Lázaro, Antistio Álviz-Amador
Peer Reviewers Xingxin Pan; Russell Hamilton
LATEST VERSION PUBLISHED 30 Oct 2023
https://doi.org/10.12688/f1000research.23805.2
Brief Report metrics
Revised
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India
[version 2; peer review: 2 approved, 1 approved with reservations]
Feroza Begum, Debica Mukherjee, Dluya Thagriki, Sandeepan Das, Prem Prakash Tripathi, Arup Kumar Banerjee, Upasana Ray
Peer Reviewers Pawan Kumar Maurya; Jalaj Gupta; Nicolas Cuburu
LATEST VERSION PUBLISHED 27 Sep 2023
https://doi.org/10.12688/f1000research.139488.1
Software Tool Article metrics
Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation.
[version 1; peer review: 2 approved, 1 approved with reservations]
Felipe Marques de Almeida, Tatiana Amabile de Campos, Georgios Joannis Pappas Jr
Peer Reviewers Abdolrahman Khezri; Abhinav Sharma and Emilyn Costa Conceição; Austin G Davis-Richardson
  • Funders
  • Scholarship by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
  • Grant by Fundação de Amparo à Pesquisa do Distrito Federal (FAP-DF)
PUBLISHED 25 Sep 2023
https://doi.org/10.12688/f1000research.131861.2
Research Article metrics
Revised
Single-cell transcriptional uncertainty landscape of cell differentiation
[version 2; peer review: 2 approved]
Nan Papili Gao, Olivier Gandrillon, András Páldi, Ulysse Herbach, Rudiyanto Gunawan
Peer Reviewers Alessandro Giuliani; Geneviève Dupont
  • Funders
  • Swiss National Science Foundation
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 20 Jul 2023
https://doi.org/10.12688/f1000research.132106.2
Research Article metrics
Revised
Nigella sativa L. seed extracts promote wound healing progress by activating VEGF and PDGF signaling pathways: An in vitro and in silico study
[version 2; peer review: 3 approved, 1 approved with reservations]
Chella Perumal Palanisamy, Phaniendra Alugoju, Selvaraj Jayaraman, Sirilux Poompradub
Peer Reviewers Balasubramani Ravindran; Monica Mironescu; Viji Rajendran; Vinothkannan Ravichandran
  • Funders
  • Center of Excellence in Green Materials for Industrial Application
  • Chulalongkorn University
LATEST VERSION PUBLISHED 21 Jun 2023
https://doi.org/10.12688/f1000research.132587.2
Software Tool Article metrics
Revised
CRUMB: a shiny-based app to analyze rhythmic feeding in Drosophila using the FLIC system
[version 2; peer review: 2 approved]
Sergio Hidalgo, Joanna C Chiu
Peer Reviewers Abhilash Lakshman; Daniel J. Cavanaugh
  • Funders
  • Pew Charitable Trusts
  • National Institute of Diabetes and Digestive and Kidney Diseases
LATEST VERSION PUBLISHED 19 Jun 2023
https://doi.org/10.12688/f1000research.132538.1
Research Article metrics
Discordant results among major histocompatibility complex binding affinity prediction tools
[version 1; peer review: 2 approved with reservations, 1 not approved]
Austin Nguyen, Abhinav Nellore, Reid F. Thompson
Peer Reviewers André Leier; Michael E Birnbaum; Nikolaos G Sgourakis and Sagar Gupta
PUBLISHED 07 Jun 2023
https://doi.org/10.12688/f1000research.122949.2
Software Tool Article metrics
Revised
DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data
[version 2; peer review: 2 approved]
Miriam Riquelme-Perez, Fernando Perez-Sanz, Jean-François Deleuze, Carole Escartin, Eric Bonnet, Solène Brohard
Peer Reviewers Hélène Hirbec; Wenbin Guo
  • Funder
  • PhD fellowship from the CEA (Amont-Aval).
LATEST VERSION PUBLISHED 24 Mar 2023
https://doi.org/10.12688/f1000research.130024.1
Research Article metrics
Identification of potential compounds for the management of multidrug-resistant tuberculosis using computational methods
[version 1; peer review: 2 not approved]
Winnie Gatwiri, Richard Kagia
Peer Reviewers Manish Dwivedi; Grace Mugumbate
PUBLISHED 17 Mar 2023
https://doi.org/10.12688/f1000research.128091.2
Software Tool Article metrics
Revised
SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes
[version 2; peer review: 2 approved]
Nachida Tadrent, Franck Dedeine, Vincent Hervé
Peer Reviewers Célio Dias Santos Júnior; Aram Mikaelyan
  • Funders
  • Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
  • Université de Tours
  • Centre National de la Recherche Scientifique
  • European Regional Development Fund
LATEST VERSION PUBLISHED 27 Feb 2023
https://doi.org/10.12688/f1000research.129161.1
Software Tool Article metrics
AMAW: automated gene annotation for non-model eukaryotic genomes
[version 1; peer review: 3 approved with reservations, 1 not approved]
Loïc Meunier, Denis Baurain, Luc Cornet
Peer Reviewers B. Franz Lang; Guifré Torruella; James Titus-McQuillan; Laura Ruiz Torres and Bruno Contreras-Moreira
  • Funders
  • BELSPO
  • F.R.S.-FNRS
PUBLISHED 16 Feb 2023
https://doi.org/10.12688/f1000research.128982.1
Software Tool Article metrics
Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE)
[version 1; peer review: 2 approved]
Yuda Munarko, Anand Rampadarath, David Nickerson
Peer Reviewers Socrates Dokos; Garima Malik
  • Funders
  • National Institutes of Health
  • Aotearoa Foundation
  • Auckland Bioengineering Institute
PUBLISHED 10 Feb 2023
https://doi.org/10.12688/f1000research.126840.2
Software Tool Article metrics
Revised
Gene expression data visualization tool on the o²S²PARC platform
[version 2; peer review: 2 approved]
Hiba Ben Aribi, Mengyuan Ding, Anmol Kiran
Peer Reviewers Joost B. M. Wagenaar; Esra Neufeld
LATEST VERSION PUBLISHED 06 Feb 2023
https://doi.org/10.12688/f1000research.129945.1
Editorial metrics NOT PEER REVIEWED
ISCB Student Council Symposium 2021, a virtual global venue: challenges and lessons learned
[version 1; peer review: not peer reviewed]
Cleidy Osorio-Mogollon, Victor Grentzinger, Gabriel J. Olguin-Orellana, Sebastian Ayala-Ruano, Shruti Gupta, Pradeep Eranti, Aayush Grover, Bart Cuypers, Nazeefa Fatima, Sayane Shome, Farzana Rahman, R. Gonzalo Parra
PUBLISHED 12 Jan 2023
https://doi.org/10.12688/f1000research.52791.3
Software Tool Article metrics
Revised
Sherlock: an open-source data platform to store, analyze and integrate Big Data for computational biologists
[version 3; peer review: 2 approved]
Balazs Bohar, David Fazekas, Matthew Madgwick, Luca Csabai, Marton Olbei, Tamás Korcsmáros, Mate Szalay-Beko
Peer Reviewers John H. Morris; Nadezhda Doncheva
  • Funders
  • Earlham Institute
  • Biotechnology and Biological Sciences Research Council
  • Quadram Institute Bioscience
LATEST VERSION PUBLISHED 12 Jan 2023
https://doi.org/10.12688/f1000research.110492.2
Research Article metrics
Revised
From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)
[version 2; peer review: 2 approved]
Maksim Nesterenko, Aleksei Miroliubov
Peer Reviewers Andreas Hejnol and Ferenc Kagan; Viatcheslav Ivanenko
  • Funder
  • Russian Science Foundation
LATEST VERSION PUBLISHED 09 Jan 2023
61-80 of 630 ARTICLES
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