Bioinformatics

Bioinformatics

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1-20 of 397 ARTICLES
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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.173901.1
Method Article metrics AWAITING PEER REVIEW
From Quality Control to Visualization: scToolkit for Reproducible Single-Cell RNA-Seq
[version 1; peer review: awaiting peer review]
Christopher Krolla, Tonmoy Das, Ariane Metzger, Melanie Boerries, Sajib Chakraborty, Geoffroy Andrieux
Peer Reviewers Invited
  • 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: 1 approved, 1 approved with reservations]
Nasar Alwahaibi
Peer Reviewers Marie-Liesse Asselin-Labat; Da-Wei Yang
  • Funder
  • None
LATEST VERSION PUBLISHED 19 Jan 2026
https://doi.org/10.12688/f1000research.176780.1
Review metrics AWAITING PEER REVIEW
Understanding Protein–Protein Interactions in Biology: Applications of NMR Spectroscopy and Isothermal Titration Calorimetry
[version 1; peer review: awaiting peer review]
Nihel Ammous-Boukhris, Ali Gargouri, Raja Mokdad-Gargouri
Peer Reviewers Invited
  • 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 AWAITING PEER REVIEW
MorphoCloud: Democratizing Access to High-Performance Computing for Morphological Data Analysis
[version 1; peer review: awaiting peer review]
A. Murat Maga, Jean-Christophe Fillion-Robin
Peer Reviewers Invited
  • 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 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.175457.1
Brief Report metrics
lncRNA CHASERR Integrates Transcriptional and Post-Transcriptional Gene Regulation
[version 1; peer review: 1 not approved]
Anna Budkina, Anatoliy Zubritskiy, Yulia A. Medvedeva
Peer Reviewers Anna M Krichevsky and Evgeny Deforzh
  • 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: 1 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
  • 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.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.172440.1
Research Article metrics
A Novel Particle Marine Predator Optimizer for Gene Selection Health Problem
[version 1; peer review: 1 approved with reservations, 1 not approved]
Rizik Al-Sayyed, AlMuatasim Billah Rizik AlSayyed, Sharif Naser Makhadmeh, Yousef Sanjalawe, Barihan M. Khasawneh
Peer Reviewers Tao Huang; Hossein Nematzadeh
  • 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
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.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.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.163212.2
Data Note metrics
Revised
CD4+ T-cell transcription factors as early predictors of phenoconversion in idiopathic rapid eye movement sleep behaviour disorder
[version 2; peer review: 2 approved]
Monica Pinoli, Michele Terzaghi, Franca Marino, Cristoforo Comi, Maurizio Versino, Marco Cosentino
Peer Reviewers Tommaso Schirinzi; Adawiya J. Haider
LATEST VERSION PUBLISHED 06 Oct 2025
https://doi.org/10.12688/f1000research.157465.2
Research Article metrics
Revised
Exploring acenocoumarol and silodosin in non-small cell lung cancer: Insights into EGFR-linked signaling mechanisms
[version 2; peer review: 1 approved, 3 approved with reservations, 1 not approved]
Swastika Maity, Krishnaprasad Baby, Bharath Harohalli Byregowda, Megh Pravin Vithalkar, Usha Y Nayak, K Sreedhara Ranganath Pai, Yogendra Nayak
Peer Reviewers Tyler Beyett; Chandan Shivamallu; Jigna Samir Shah; Navjot Kanwar; Abhijeet Rajendra Joshi
  • Funders
  • Science and Engineering Research Board
  • Indian Council of Medical Research
LATEST VERSION PUBLISHED 23 Sep 2025
https://doi.org/10.12688/f1000research.29032.3
Method Article metrics
Revised
Sustainable data analysis with Snakemake
[version 3; peer review: 2 approved]
Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Peter C. van Dyken, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Filipe G. Vieira, Christian Meesters, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Jake VanCampen, Venkat Malladi, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
Peer Reviewers Michael Reich; Caroline C. Friedel
  • Funders
  • Netherlands Organisation for Scientific Research (NWO)
  • Deutsche Stiftung für Herzforschung
  • Google LLC
  • United States National Science Foundation Graduate Research Fellowship Program (NSF-GRFP)
LATEST VERSION PUBLISHED 23 Sep 2025
1-20 of 397 ARTICLES
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Gateway Areas
  • Methods and Tools
    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
  • Genetics and Genomics
    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
  • Transcriptomics
    By curating all outputs related to the analysis of the RNA transcripts produced by a genotype, the Transcriptomics Gateway Area will allow readers to easily access content pertinent to this research. Read more keyboard_arrow_right
  • Proteomics
    The Proteomics Gateway Area has been established to allow authors to access and publish research content related to the large-scale study of entire sets of proteins as proteomes. Read more keyboard_arrow_right
  • Metagenomics
    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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