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https://doi.org/10.12688/f1000research.171468.1
Software Tool Article metrics AWAITING PEER REVIEW
DTAShiny: An Interactive R Shiny Application for Diagnostic Test Accuracy Analysis and Visualization
[version 1; peer review: awaiting peer review]
Syed Faizaan Shah Quadri, Mahmood Ahmad, Joanne Lac
Peer Reviewers Invited
PUBLISHED 30 Oct 2025
https://doi.org/10.12688/f1000research.162353.2
Research Article metrics
Revised
Optimizing Cardiovascular Treatment in Non-Small Cell Lung Cancer: A Comprehensive Computational Approach for Assessment of Drug-Drug Interactions Between Tyrosine Kinase Inhibitors and Cardiovascular Drugs
[version 2; peer review: 1 approved, 1 approved with reservations]
Prajakta Patil, Mrunal Desai, Gayathri Baburaj, Levin Thomas, Viswam Subeesh, Sumit Birangal, Mahadev Rao, Gurupur Gautham Shenoy, Jagadish P. C.
Peer Reviewers Fahrul Nurkolis; Uday Venkat Mateti
LATEST VERSION PUBLISHED 22 Oct 2025
https://doi.org/10.12688/f1000research.170810.1
Software Tool Article metrics AWAITING PEER REVIEW
DirectRepeateR: An R package for annotating direct repeats in genome assemblies
[version 1; peer review: awaiting peer review]
Megan Copeland, Andres Barboza, Joseph S. Romanowski, Zach N. Adelman, Heath Blackmon
Peer Reviewers Invited
  • Funders
  • National Institute of Allergies and Infectious Diseases, National Institutes of Health
  • National Institute of General Medical Sciences at the National Institutes of Health
PUBLISHED 21 Oct 2025
https://doi.org/10.12688/f1000research.171282.1
Research Article metrics AWAITING PEER REVIEW
’Spanscriptomics’: towards bioinformatics training materials in Spanish.
[version 1; peer review: awaiting peer review]
Jurgi Giraud, Stefana Dreptate, Wendi Bacon, The Galaxy Community
Peer Reviewers Invited
  • Funder
  • Company of Biologists
PUBLISHED 20 Oct 2025
https://doi.org/10.12688/f1000research.129581.2
Software Tool Article metrics
Revised
AmpSeqR: an R package for amplicon deep sequencing data analysis
[version 2; peer review: 1 approved, 2 approved with reservations]
Jiru Han, Jacob E. Munro, Melanie Bahlo
Peer Reviewers Eduardo Castro-Nallar; Cristian Koepfli and Gustavo Da Silva; Patrick Murigu Kamau Njage
  • Funders
  • Institute Infrastructure Support Scheme (IRIISS)
  • National Health and Medical Research Council
LATEST VERSION PUBLISHED 17 Oct 2025
https://doi.org/10.12688/f1000research.166678.1
Research Article metrics
Exploring the Potential of Peptides Derived from the Coelomic Fluid of Echinometra lucunter Targeting Inflammatory Cytokines in Placental Syndromes: In Silico Study
[version 1; peer review: 1 approved with reservations]
Defrin Defrin, Arif Birru, Kevin Cuandra, Ratna Puspita, I Widnyana, Nasya Aqilah, Arzita Fadhilla, Winka Suwardjo, Amanda Amalia, Kalaj Haq, Tirza Amaris, Feroz Aldino, Shabrina Ekitasari, Bernice Sirait, Nathania Kristaningtyas, Rizka Wilanda, Made Ananda
Peer Reviewers Aldi Tamara Rahman
PUBLISHED 10 Oct 2025
https://doi.org/10.12688/f1000research.164530.1
Research Article metrics AWAITING PEER REVIEW
Inferring and simulating a gene regulatory network for the sympathoadrenal differentiation from single-cell transcriptomics in human.
[version 1; peer review: awaiting peer review]
Olivier Gandrillon
Peer Reviewers Invited
  • Funder
  • Ligue Contre le Cancer
PUBLISHED 11 Sep 2025
https://doi.org/10.12688/f1000research.169977.1
Editorial metrics NOT PEER REVIEWED
BOSC 2025, the 26th Bioinformatics Open Source Conference
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Karsten Hokamp, Jessica Maia, Hervé Ménager, Monia C Munoz-Torres, Tazro Ohta, Deepak Unni, Jason Williams
  • Funder
  • NA
PUBLISHED 09 Sep 2025
https://doi.org/10.12688/f1000research.168810.1
Software Tool Article metrics
CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks
[version 1; peer review: 1 not approved]
William Choi-Kim, Sayed-Rzgar Hosseini
Peer Reviewers Florian van daalen
  • Funder
  • STPRZG
PUBLISHED 29 Aug 2025
https://doi.org/10.12688/f1000research.163662.2
Research Article metrics
Revised
Health Security inequalities in Non-EU European Countries: A Cross-National Comparative Assessment Using an Integrated MCDM-Machine Learning Approach
[version 2; peer review: 2 approved]
Mijahed Nasser Aljober, Adel A. Nasser, Abed Saif Ahmed Alghawli, Amani A. K. Elsayed
Peer Reviewers Shaimaa Awadh Baha al_Deen; Mohammed S. Abdo
  • Funder
  • Deanship of Scientific Research, Prince Sattam bin Abdulaziz University
LATEST VERSION PUBLISHED 19 Aug 2025
https://doi.org/10.12688/f1000research.168786.1
Software Tool Article metrics
Identification of Viral Variants from Functional Genomics Data
[version 1; peer review: 1 approved, 1 approved with reservations]
Florian Röckl, Caroline C. Friedel
Peer Reviewers Dóra Tombácz; Anuj Kumar
  • Funder
  • Deutsche Forschungsgemeinschaft
PUBLISHED 18 Aug 2025
https://doi.org/10.12688/f1000research.166538.1
Review metrics
White paper: standards for handling and analyzing plant pan-genomes
[version 1; peer review: 2 approved with reservations]
Marc C. Heuermann, Pedro Barros, Sebastian Beier, Heidrun Gundlach, Jorge Alvarez-Jarreta, Keywan Hassani-Pak, Patrick König, Anne Fiebig, Tim Godec, Kristina Gruden, Nadja Nolte, Marko Petek, Uwe Scholz, Maja Zagorščak, Klaas Vandepoele, Michiel Van Bel
Peer Reviewers Sunil Kumar Sahu; Xiaoming Xie
  • Funders
  • ELIXIR under the call for proposals on Biodiversity, Food Safety and Pathogens
  • Federal Ministry of Education and Research
PUBLISHED 28 Jul 2025
https://doi.org/10.12688/f1000research.139476.2
Research Article metrics
Revised
Epigenetic germline variants predict cancer prognosis and risk and distribute uniquely in topologically associating domains
[version 2; peer review: 1 approved, 1 approved with reservations]
Shervin Goudarzi, Meghana Pagadala, Adam Klie, James V Talwar, Hannah Carter
Peer Reviewers Charu Mehta; Chiara Herzog
  • Funders
  • National Institutes of Health, National Cancer Institute
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 24 Jul 2025
https://doi.org/10.12688/f1000research.166855.1
Software Tool Article metrics
KICA: A MATLAB package for high-throughput analysis of calcium and voltage imaging data from cardiac cells
[version 1; peer review: 1 approved with reservations]
Satya N.V Arjunan, Anton Shpak, George W. Parker, Adam P. Hill
Peer Reviewers Amelia S Power and Amanda Groenewald
  • Funders
  • Targeted Translation Research Accelerator
  • New South Wales Office for Health and Medical Research
PUBLISHED 17 Jul 2025
https://doi.org/10.12688/f1000research.163833.1
Software Tool Article metrics
LitSieve: An integrated literature search and triage tool for biocuration
[version 1; peer review: 1 approved with reservations]
Matt Jeffryes, Melissa Harrison, Henning Hermjakob, Johanna McEntyre
Peer Reviewers Kim Rutherford
  • Funders
  • European Molecular Biology Laboratory
  • HORIZON EUROPE Marie Sklodowska-Curie Actions
PUBLISHED 11 Jul 2025
https://doi.org/10.12688/f1000research.164319.1
Software Tool Article metrics
Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip
[version 1; peer review: 1 approved, 1 approved with reservations]
Viktoria Haghani, Aditi Goyal, Alan Zhang, Osman Sharifi, Natasha Mariano, Dag Yasui, Ian Korf, Janine LaSalle
Peer Reviewers Zhengyao Shao; Karol Bomsztyk
  • Funders
  • Rett Syndrome Research Trust
  • Autism Science Foundation
  • National Institutes of Health
PUBLISHED 25 Jun 2025
https://doi.org/10.12688/f1000research.164583.1
Software Tool Article metrics
Assembly and quantification of transcripts from noisy long reads with NIFFLR
[version 1; peer review: 1 approved with reservations, 2 not approved]
Alina Guo, Mihaela Pertea, Aleksey V Zimin
Peer Reviewers Colin Dewey; Fairlie Reese; Yuan Gao
  • Funders
  • Directorate for Biological Sciences
  • NIH
PUBLISHED 20 Jun 2025
https://doi.org/10.12688/f1000research.155223.2
Review metrics
Revised
Selecting differential splicing methods: Practical considerations for short-read RNA sequencing
[version 2; peer review: 2 approved, 3 approved with reservations]
Ben J. Draper, Mark J. Dunning, David C. James
Peer Reviewers Stefano Donega; Charlotte Capitanchik; Julia Olivieri; Zhaoqi Liu; Monica Salinas and Juan Valcarcel
  • Funders
  • Lonza Biologics plc
  • University of Sheffield
LATEST VERSION PUBLISHED 30 May 2025
https://doi.org/10.12688/f1000research.158264.3
Method Article metrics
Revised
Using text-mining to measure the scientific impact and legacy of ELIXIR, a distributed research infrastructure for life science data
[version 3; peer review: 2 approved, 1 approved with reservations]
Francesca De Leo, Erika Balsyte, Robert Petryszak, Marilena D’Ambrosio, Chiara Bruno, Martin Cook, Ivan Mičetić, Corinne S. Martin
Peer Reviewers Helen M. Berman; Shuichi Kawashima; Alfonso Valencia
  • Funders
  • Italian Ministry for Universities and Research (National Recovery and Resilience Plan M4C2)
  • European Union (Horizon Programmes)
  • ELIXIR, the research infrastructure for life science data
LATEST VERSION PUBLISHED 22 Apr 2025
https://doi.org/10.12688/f1000research.163516.1
Method Article metrics
NAD: Noise-augmented direct sequencing of target nucleic acids by augmenting with noise and selective sampling
[version 1; peer review: 1 approved, 1 approved with reservations]
Hyunjin Shim
Peer Reviewers Ruslan Kalendar; Runsheng Li
PUBLISHED 10 Apr 2025
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