Bioinformatics

Bioinformatics

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1-20 of 403 ARTICLES
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https://doi.org/10.12688/f1000research.172407.3
Research Article metrics
Revised
Bioinformatics-based Investigation to Unveiling The miRNA-Immunity Axis in The Tumor Microenvironment of Pancreatic Cancer
[version 3; peer review: 1 approved with reservations, 1 not approved]
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; Jörg Kleeff
  • Funder
  • The authors received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
LATEST VERSION PUBLISHED 22 May 2026
https://doi.org/10.12688/f1000research.94159.2
Software Tool Article metrics
Revised
miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies
[version 2; peer review: 3 approved]
Andreas Diendorfer, Kseniya Khamina, Marianne Pultar, Matthias Hackl
Peer Reviewers Kristian Almstrup, Nina Mørup and Ailsa Maria Main; Francisco J. Enguita, Nina Mørup and Ailsa Maria Main; Iddo Magen
  • Funder
  • Innovative Medicines Initiative 2
LATEST VERSION PUBLISHED 09 May 2026
https://doi.org/10.12688/f1000research.178855.1
Brief Report metrics
Understanding the Inner Workings of Large Language Models in Medicine
[version 1; peer review: 1 approved with reservations, 1 not approved]
Georg Fuellen, Hans Jarchow, Johann-Christian Põder
Peer Reviewers Yavuz Selim Kıyak; Craig S Webster
PUBLISHED 05 May 2026
https://doi.org/10.12688/f1000research.178199.1
Research Article metrics AWAITING PEER REVIEW
Insights into the Mechanistic Actions of Vitamin D3 in Colorectal Cancer Through Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation
[version 1; peer review: awaiting peer review]
Muhammad Iqbal Rivai, Muhammad Iqbal
Peer Reviewers Invited
PUBLISHED 30 Apr 2026
https://doi.org/10.12688/f1000research.179899.1
Software Tool Article metrics AWAITING PEER REVIEW
TagGen: High-Performance Barcode Generator and Demultiplexer for High-Throughput and Long-Read Sequencing Applications
[version 1; peer review: awaiting peer review]
Faiza Chowdhury, Tessa Swain, Roderik Shirokikh, Danielle Rudler, Archa Fox, Alice Cleynen, Nikolay Shirokikh
Peer Reviewers Invited
  • Funders
  • National Health and Medical Research Council of Australia (NHMRC)
  • Australian Research Council (ARC)
  • European Union’s Horizon 2020
  • Bootes Foundation
PUBLISHED 30 Apr 2026
https://doi.org/10.12688/f1000research.178750.1
Research Article metrics AWAITING PEER REVIEW
Bioinformatic identification of abiotic stress tolerance genes in actinomycetes isolated from Lomas Cerro Campana, Peru
[version 1; peer review: awaiting peer review]
Bertha Soriano-Bernilla, Gary Steve Silva-Quipan, David Zavaleta-Verde, Claudio Quiñones Cerna, Carlos Quijano-Jara, Yesenia Melissa Santa Cruz-Vásquez
Peer Reviewers Invited
  • Funder
  • PROCIENCIA/CONCYTEC
PUBLISHED 19 Apr 2026
https://doi.org/10.12688/f1000research.178873.1
Research Article metrics AWAITING PEER REVIEW
INFLUENCE OF WATER ENVIRONMENT ON PROTEIN FOLDING AND COMPLEXATION
[version 1; peer review: awaiting peer review]
Irena Roterman, Katarzyna Stapor, Dawid Dulak, Leszek Konieczny
Peer Reviewers Invited
  • Funder
  • Jagiellonian University – Medical College
PUBLISHED 16 Apr 2026
https://doi.org/10.12688/f1000research.176414.1
Editorial metrics NOT PEER REVIEWED
3rd ISCB Asian Student Council Symposium: from virtual roots to in-person networks
[version 1; peer review: not peer reviewed]
Nilay Yönet, Govinda Rao Dabburu, Shahriar Hossain, Susanna R. Grigson, Ashita Washington, Pradeep Eranti
PUBLISHED 27 Mar 2026
https://doi.org/10.12688/f1000research.175540.1
Software Tool Article metrics
Workflow graphical editor and translator to Nextflow
[version 1; peer review: 2 approved with reservations]
Ilya Kiselev, Anna Ryabova, Fedor Kolpakov
Peer Reviewers Poonam Bansal; Vasilis Bountris
  • Funder
  • «Sirius» Federal Territory
PUBLISHED 29 Jan 2026
https://doi.org/10.12688/f1000research.173901.1
Method Article metrics
From Quality Control to Visualization: scToolkit for Reproducible Single-Cell RNA-Seq
[version 1; peer review: 3 approved with reservations]
Christopher Krolla, Tonmoy Das, Ariane Metzger, Melanie Boerries, Sajib Chakraborty, Geoffroy Andrieux
Peer Reviewers Martin Hemberg and Pranay Ammula; Johannes Köster; Pedro L Baldoni
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Deutsche Forschungsgemeinschaft
PUBLISHED 28 Jan 2026
https://doi.org/10.12688/f1000research.170680.2
Review metrics
Revised
Integrating spatial omics with routine haematoxylin and eosin in formalin-fixed paraffin-embedded: a step-by-step clinical workflow
[version 2; peer review: 2 approved, 1 approved with reservations]
Nasar Alwahaibi
Peer Reviewers Marie-Liesse Asselin-Labat; Da-Wei Yang; Xu Xun
  • Funder
  • None
LATEST VERSION PUBLISHED 19 Jan 2026
https://doi.org/10.12688/f1000research.176780.1
Review metrics
Understanding Protein–Protein Interactions in Biology: Applications of NMR Spectroscopy and Isothermal Titration Calorimetry
[version 1; peer review: 1 not approved]
Nihel Ammous-Boukhris, Ali Gargouri, Raja Mokdad-Gargouri
Peer Reviewers Barbara Zambelli
  • Funder
  • Tunisian Ministry of Higher Education and Scientific Research
PUBLISHED 16 Jan 2026
https://doi.org/10.12688/f1000research.176328.1
Software Tool Article metrics
MorphoCloud: Democratizing Access to High-Performance Computing for Morphological Data Analysis
[version 1; peer review: 2 approved]
A. Murat Maga, Jean-Christophe Fillion-Robin
Peer Reviewers Richard Carter; Brian Metscher
  • Funders
  • Directorate for Biological Sciences
  • National Institutes of Health
PUBLISHED 14 Jan 2026
https://doi.org/10.12688/f1000research.175162.1
Software Tool Article metrics
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem
[version 1; peer review: 2 approved with reservations]
Xingyi Chen, Michael Totty, Stephanie Hicks
Peer Reviewers Patrick Murigu Kamau Njage; Ayshwarya Subramanian and Adam Zuchowski
  • 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, 2 approved with reservations]
Florian Röckl, Caroline C. Friedel
Peer Reviewers Dóra Tombácz; Anuj Kumar; Daniel P Depledge
  • Funder
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 31 Dec 2025
https://doi.org/10.12688/f1000research.175457.1
Brief Report metrics
lncRNA CHASERR Integrates Transcriptional and Post-Transcriptional Gene Regulation
[version 1; peer review: 2 not approved]
Anna Budkina, Anatoliy Zubritskiy, Yulia A. Medvedeva
Peer Reviewers Anna M Krichevsky and Evgeny Deforzh; Hober Nelson Núñez-Martínez
  • Funder
  • Russian Science Foundation
PUBLISHED 30 Dec 2025
https://doi.org/10.12688/f1000research.173844.1
Research Article metrics
Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024
[version 1; peer review: 3 approved with reservations]
Kathryn J. Isaac, Katherine E. L. Cox, Kai Yin Ho, Elizabeth M. Humphries, Natalie Kucher, Jeffrey T. Leek, Stephen Mosher, Michael C. Schatz, Frederick J. Tan, Ava M. Hoffman
Peer Reviewers Hassan Rehan; Matthew D Wilkerson; Alenka Hafner
  • Funder
  • National Institutes of Health, National Human Genome Research Institute
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.172440.1
Research Article metrics
A Novel Particle Marine Predator Optimizer for Gene Selection Health Problem
[version 1; peer review: 1 approved with reservations, 2 not approved]
Rizik Al-Sayyed, AlMuatasim Billah Rizik AlSayyed, Sharif Naser Makhadmeh, Yousef Sanjalawe, Barihan M. Khasawneh
Peer Reviewers Tao Huang; Hossein Nematzadeh; Nimisha Ghosh
  • Funder
  • n/a
PUBLISHED 18 Nov 2025
https://doi.org/10.12688/f1000research.165281.1
Software Tool Article metrics
DataMap: A Browser-based App for Visualizing High-Dimensional Data
[version 1; peer review: 1 approved with reservations]
Xijin Ge
Peer Reviewers Guangchuang Yu
  • Funders
  • National Institute of General Medical Sciences
  • National Human Genome Research Institute
PUBLISHED 10 Nov 2025
1-20 of 403 ARTICLES
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    The Methods and Tools Gateway Area will allow researchers to publish outputs concerning both the application and research into the use of various computational methods to analyse quantities of biological data for a range of different results, including predictions and discoveries. Read more keyboard_arrow_right
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    The Genetics & Genomics Gateway Area will enable researchers to publish content related to the analysis, storage and accessibility of DNA, RNA and protein sequences. This analysis can be conducted in a variety of ways, including comparison of sequences and relationships, identification of functions, and recognition of patterns across the samples. Read more keyboard_arrow_right
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    This Gateway Area will allow members of the bioinformatics community to collate all research related to the collection of genomes from an environmental sample. Read more keyboard_arrow_right
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