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https://doi.org/10.12688/f1000research.172236.2
Research Article metrics
Revised
Dysregulation of MicroRNA-181a-5p Targets TNFAIP3 to Promote MIF-CXCR4 Signaling and Immune Inflammatory Remodeling in Chronic Myeloid Leukemia
[version 2; peer review: 2 approved with reservations]
Noha Mohammed Saleh, Rawaa AlChalabi, Yasir Issa, Shahad Nassurat
Peer Reviewers Ikhwan Rinaldi; haijiao Zhang and Anna He
LATEST VERSION PUBLISHED 05 Feb 2026
https://doi.org/10.12688/f1000research.175540.1
Software Tool Article metrics AWAITING PEER REVIEW
Workflow graphical editor and translator to Nextflow
[version 1; peer review: awaiting peer review]
Ilya Kiselev, Anna Ryabova, Fedor Kolpakov
Peer Reviewers Invited
  • Funder
  • «Sirius» Federal Territory
PUBLISHED 29 Jan 2026
https://doi.org/10.12688/f1000research.175162.1
Software Tool Article metrics AWAITING PEER REVIEW
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem
[version 1; peer review: awaiting peer review]
Xingyi Chen, Michael Totty, Stephanie Hicks
Peer Reviewers Invited
  • Funders
  • National Institute of Mental Health
  • National Institute of General Medical Sciences
PUBLISHED 09 Jan 2026
https://doi.org/10.12688/f1000research.168786.2
Software Tool Article metrics
Revised
Identification of Viral Variants from Functional Genomics Data
[version 2; peer review: 1 approved, 1 approved with reservations]
Florian Röckl, Caroline C. Friedel
Peer Reviewers Dóra Tombácz; Anuj Kumar
  • Funder
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 31 Dec 2025
https://doi.org/10.12688/f1000research.173116.1
Opinion Article metrics
Strengthening bioinformatics education: e-learning initiatives across ELIXIR Nodes and Communities
[version 1; peer review: 1 approved, 2 approved with reservations]
Monique Zahn-Zabala, Minna Ahokas, Bérénice Batut, Sebastian Beier, Alexander Botzki, Alexia Cardona, Kristina Gruden, Eija Korpelainen, Maria Lehtivaara, Brane Leskosek, Bogdan Mirăuță, Ajay Mishra, Cyril Pommier, Krzysztof Poterlowicz, Helena Rasche, Olivier Sand, Rob Waterhouse, Samantha Wittke, Cătălina Zenoaga-Barbăroșie, Mihail Anton, Daniel Wibberg
Peer Reviewers Michelle D. Brazas; Ming Chen; Gangqing Hu
PUBLISHED 22 Dec 2025
https://doi.org/10.12688/f1000research.171697.1
Research Article metrics
Antibiogram, antibiotic resistance genes and health risks of Listeria species from fruits and vegetables in selected locations in Nigeria
[version 1; peer review: 1 approved]
Anthony Adegoke, Kate O Igoche, Olaniyi Owolawi, Moses Ekpenyong, Aso Joseph Omololu, Olayinka A Aiyegoro
Peer Reviewers Rahul Vashishth
  • Funder
  • National Research Foundation
PUBLISHED 22 Dec 2025
https://doi.org/10.12688/f1000research.124810.2
Software Tool Article metrics
Revised
abmAnimalMovement: An R package for simulating animal movement using an agent-based model
[version 2; peer review: 4 approved with reservations]
Benjamin Michael Marshall, Alexander Bradley Duthie
Peer Reviewers Rocío Joo; Andrea Contina; Pratik Rajan Gupte; Luciano Bosso
  • Funder
  • Natural Environment Research Council
LATEST VERSION PUBLISHED 17 Dec 2025
https://doi.org/10.12688/f1000research.172407.1
Research Article metrics
Bioinformatics-based Investigation to Unveiling The miRNA-Immunity Axis in The Tumor Microenvironment of Pancreatic Cancer
[version 1; peer review: 1 approved with reservations]
Mohammed Salih AL-Janaby, Salah H. Mannoush, Saif S. Al-Janabi, Ahmed AbdulJabbar Suleiman, Ali Hazim Abdulkareem, Anmar Kamil Alalwani, Mustafa M. Fahad
Peer Reviewers Fadehl Lafta
  • Funder
  • The authors received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
PUBLISHED 16 Dec 2025
https://doi.org/10.12688/f1000research.164583.2
Software Tool Article metrics
Revised
Assembly and quantification of transcripts from noisy long reads with NIFFLR
[version 2; 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
LATEST VERSION PUBLISHED 03 Dec 2025
https://doi.org/10.12688/f1000research.171889.1
Software Tool Article metrics
BISCUIT: An Open-Source Platform for Visual Comparison of Segmentation Models in Bioimage Analysis
[version 1; peer review: 2 approved with reservations]
Emmanouela Rantsiou, Franziska Oschmann, Lukas von Ziegler, Thomas Wüst, Andrzej J. Rzepiela, Szymon Stoma
Peer Reviewers Constantin Pape Pape; Peter Bankhead and Laura Nicolás-Sáenz
PUBLISHED 18 Nov 2025
https://doi.org/10.12688/f1000research.166538.2
Review metrics
Revised
White paper: standards for handling and analyzing plant pan-genomes
[version 2; peer review: 2 approved, 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; Rutwik Barmukh; Jianping Xu
  • Funders
  • ELIXIR under the call for proposals on Biodiversity, Food Safety and Pathogens
  • Federal Ministry of Education and Research
LATEST VERSION PUBLISHED 18 Nov 2025
https://doi.org/10.12688/f1000research.170665.1
Software Tool Article metrics
Sixth Annual BCM Hackathon on Structural Variation and Pangenomics
[version 1; peer review: 2 approved with reservations]
Farhang Jaryani, Bishnu Adhikar, Shaghayegh Beheshti, Sarah Fross, Jędrzej Kubica, Jen-Yu Wang, Aanuoluwa Adekoya, Daniel P. Agustinho, Oluwaseun Akinsulire, Francesco Andreace, Abolhassan Bahari, Christian Brueffer, Siyuan Cheng, Jonah Cullen, Kristen Curry, Ryan Doughty, Adam English, Neda Ghohabi Esfahani, Natali Gulbahce, Tina Han, Nha Van Huynh, Michal Izydorczyk, Minal Jamsandekar, Emrah Kacar, Arthur Shem Kasambula, Rupesh K. Kesharwani, Divya Kalra, Shwetha V Kumar, Iva Kotásková, Callum MacPhillamy, Sina Majidian, Mauricio Moldes, Abraham (Jon) Moller, Rajarshi Mondal, Eleni Mourouzidou, Michael Nute, Dmitrii Olisov, Anika Pallapothu, Meghana Ram, Marcus Chan Hua Rui, Philippe Sanio, Russel T. Santos, Michael Olufemi, Narges SangaraniPour, Moustafa Shokrof, Sam Stroupe, Gobikrishnan Subramaniam, Todd J. Treangen, Pankhuri Wanjari, Umran Yaman, Farha zain, Xinchang Zheng, Fritz J Sedlazeck, Ben Busby
Peer Reviewers Istvan Albert; Colin Diesh
  • Funders
  • Shwetha V Kumar is supported by CPRIT grant #RP210037 (PI Aaron Thrift)
  • Ryan Doughty is supported by a training fellowship from the Gulf Coast Consortia, on the NLM Training Program in Biomedical Informatics & Data Science (T15LM007093)
  • Sarah Fross is supported by a training grant from the National Institutes of Health under Award Number 5T32GM135748-04.
  • Sedlazeck NIH grant: 1UG3NS132105-01, 1U01HG011758-01
  • Jędrzej Kubica is supported by the Ministry of Science and Higher Education (Poland) as a project under the program Excellence Initiative – Research University (2020–2026) (decision no.: IV.2.3./30/2024) and the France 2030 state funding managed by the National Research Agency with the reference
  • Shaghayegh Beheshti is supported by a training grant from the National Institutes of Health under Award Number 5T32GM139534-04 and NHGRI U01 HG011758.
  • The research was supported by Cancer Prevention and Research Institute of Texas under grant number: #RP210037
PUBLISHED 07 Nov 2025
https://doi.org/10.12688/f1000research.166678.2
Research Article metrics
Revised
Exploring the Potential of Peptides Derived from the Coelomic Fluid of Echinometra lucunter Targeting Inflammatory Cytokines in Placental Syndromes: In Silico Study
[version 2; peer review: 2 approved]
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; Norbertus Marcell Prayogi
LATEST VERSION PUBLISHED 06 Nov 2025
https://doi.org/10.12688/f1000research.171468.1
Software Tool Article metrics
DTAShiny: An Interactive R Shiny Application for Diagnostic Test Accuracy Analysis and Visualization
[version 1; peer review: 3 approved with reservations]
Syed Faizaan Shah Quadri, Ahmad Mahmood, Joanne Lac
Peer Reviewers Christos Nakas; Budi Sunaryo; Pedro Castaneda
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: 2 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; Janmejay Pant
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
’Spanscriptomics’: towards bioinformatics training materials in Spanish.
[version 1; peer review: 2 approved with reservations]
Jurgi Giraud, Stefana Dreptate, Wendi Bacon, The Galaxy Community
Peer Reviewers Carlos C. Goller; Wei Ruan
  • 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: 3 approved]
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.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
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