Frontiers in Bioinformatics

Original Research

Published on 25 Sep 2025

Integrative machine learning and transcriptomic analysis identifies key molecular targets in MNPN-associated oral squamous cell carcinoma pathogenesis

Xiangjun Wang
Panpan Jin
Juan Xu
Junyi Li
Mengzhen Ji

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1664576

1,553 views

Original Research

Published on 24 Sep 2025

Computational drug repurposing reveals Alectinib as a potential lead targeting Cathepsin S for therapeutic developments against cancer and chronic pain

Mohammed Alrouji
Mohammed S. Alshammari
Sharif Alhajlah
Syed Tasqeeruddin
Khuzin Dinislam
Anas Shamsi
Saleha Anwar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1666573

2,097 views

Brief Research Report

Published on 22 Sep 2025

Association between dysregulated expression of Ca2+ and ROS-related genes and breast cancer patient survival

Sofia Ramos
João Gregório
Ana Sofia Fernandes
Nuno Saraiva

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1633494

1,063 views

Original Research

Published on 22 Sep 2025

Extracting a COVID-19 signature from a multi-omic dataset

Baptiste Bauvin
Thibaud Godon
Guillaume Bachelot
Claudia Carpentier
Riikka Huusaari
Maxime Deraspe
Juho Rousu
Caroline Quach
Jacques Corbeil

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1645785

1,474 views

Original Research

Published on 19 Sep 2025

Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma

Minghao Wang
Yu Wang
Yitong Li
Chengyi Zhang
Canjun Li
Nan Bi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613761

1,917 views

Original Research

Published on 19 Sep 2025

Identification and therapeutic investigation of biomarker genes underpinning hepatocellular carcinoma: an in silico study utilising molecular docking and dynamics simulation

Jishnu Ghosh
Abdullah M. Alshahrani
Aritra Palodhi
Debarghya Bhattacharyya
Subhadip Das
Sunil Kanti Mondal
Abul Kalam
S. Rehan Ahmad
Chittabrata Mal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1567748

2,490 views

Original Research

Published on 19 Sep 2025

Integrated multi-optosis model for pan-cancer candidate biomarker and therapy target discovery

Emanuell Rodrigues de Souza
Higor Almeida Cordeiro Nogueira
Ronaldo da Silva Francisco Junior
Ana Beatriz Garcia
Enrique Medina-Acosta

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630518

2,180 views
2 citations

Methods

Published on 18 Sep 2025

Quantitative measures to assess the quality of cellular indexing of transcriptomes and epitopes by sequencing data

Jie Sun
Robert Morrison
Soyeon Kim
Kairuo Yan
Hyun Jung Park

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630161

2,354 views

Original Research

Published on 18 Sep 2025

Key genes associated with brain metastasis in non-small cell lung cancer: novel insights from bioinformatics analysis

Shuang Zhao
He Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1625664

2,484 views

Original Research

Published on 18 Sep 2025

BC-predict: mining of signal biomarkers and production of models for early-stage breast cancer subtyping and prognosis

Sangeetha Muthamilselvan
Natarajan Vaithilingam
Ashok Palaniappan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1644695

2,033 views
1 citation

Original Research

Published on 16 Sep 2025

Drug discovery for chemotherapeutic resistance based on pathway-responsive gene sets and its application in breast cancer

Dehua Feng
Jingwen Hao
Lingxu Li
Jian Chen
Xinying Liu
Ruijie Zhang
Huirui Han
Tianyi Li
Xuefeng Wang
Xia Li

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1661601

1,334 views

Original Research

Published on 15 Sep 2025

Discovering biomarkers for chronic sinusitis with nasal polyps: a study integrating bioinformatics analysis and experimental validation of macrophage polarization and metabolism-related genes

Juan Zhou
Huan Wang
Jin Wang
Fuming Zhou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613136

2,418 views

Original Research

Published on 10 Sep 2025

Single-cell splicing QTL analysis in pancreatic islets

Jae-Won Cho
Jingyi Cao
Martin Hemberg

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1657895

1,381 views

Technology and Code

Published on 08 Sep 2025

PharmacoForge: pharmacophore generation with diffusion models

Emma L. Flynn
Riya Shah
Ian Dunn
Rishal Aggarwal
David Ryan Koes

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1628800

2,693 views

FAIR² Data

Published on 08 Sep 2025

Structure-based prediction of SARS-CoV-2 variant properties using machine learning on mutational neighborhoods

Max van den Boom
Erik Schultes
Thomas Hankemeier

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1634111

3,072 views

Technology and Code

Published on 05 Sep 2025

TCRscape: a single-cell multi-omic TCR profiling toolkit

Roman Perik-Zavodskii
Olga Perik-Zavodskaia
Marina Volynets
Saleh Alrhmoun
Sergey Sennikov

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1641491

2,537 views
1 citation

Technology and Code

Published on 05 Sep 2025

An image analysis pipeline to quantify the spatial distribution of cell markers in stroma-rich tumors

Antoine A. Ruzette
Nina Kozlova
Kayla A. Cruz
Taru Muranen
Simon F. Nørrelykke

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1619790

1,821 views

Methods

Published on 04 Sep 2025

A novel linear indexing method for strings under all internal nodes in a suffix tree

Anas Al-okaily
Abdelghani Tbakhi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1577324

947 views

Brief Research Report

Published on 04 Sep 2025

Adaptive sampling methods facilitate the determination of reliable dataset sizes for evidence-based modeling

Tim Breitenbach
Thomas Dandekar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1528515

1,470 views
1 citation

Technology and Code

Published on 04 Sep 2025

Protein cleaver: an interactive web interface for in silico prediction and systematic annotation of protein digestion-derived peptides

Grigorios Koulouras
Yingrong Xu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1576317

3,156 views

Editorial

Published on 02 Sep 2025

Editorial: Networks and graphs in biological data: current methods, opportunities and challenges

Derek L. Thompson
Hsiang-Yun Wu
Christopher W. Bartlett
William C. Ray

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1685992

1,170 views

Data Report

Published on 02 Sep 2025

Germline mutation profiling of breast cancer patients using a non-BRCA sequencing panel

Sonar Soni Panigoro
Rafika Indah Paramita
Fadilah Fadilah
Septelia Inawati Wanandi
Aisyah Fitriannisa Prawiningrum
Linda Erlina
Wahyu Dian Utari
Ajeng Megawati Fajrin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1620025

1,742 views

Original Research

Published on 01 Sep 2025

COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices

Rafael Pereira Lemos
Diego Mariano
Sabrina De Azevedo Silveira
Raquel C. de Melo-Minardi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630078

1,640 views
2 citations

Perspective

Published on 29 Aug 2025

Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers–focused program at The Kids Research Institute Australia

Patricia Agudelo-Romero
Talya Conradie
Jose Antonio Caparros-Martin
David Jimmy Martino
Anthony Kicic
Stephen Michael Stick
Christopher Hakkaart
Abhinav Sharma
the Theme Collaboration Group

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1610015

2,136 views

180 Publications

volumes

Integrative machine learning and transcriptomic analysis identifies key molecular targets in MNPN-associated oral squamous cell carcinoma pathogenesis

Computational drug repurposing reveals Alectinib as a potential lead targeting Cathepsin S for therapeutic developments against cancer and chronic pain

Association between dysregulated expression of Ca2+ and ROS-related genes and breast cancer patient survival

Extracting a COVID-19 signature from a multi-omic dataset

Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma

Identification and therapeutic investigation of biomarker genes underpinning hepatocellular carcinoma: an in silico study utilising molecular docking and dynamics simulation

Integrated multi-optosis model for pan-cancer candidate biomarker and therapy target discovery

Quantitative measures to assess the quality of cellular indexing of transcriptomes and epitopes by sequencing data

Key genes associated with brain metastasis in non-small cell lung cancer: novel insights from bioinformatics analysis

BC-predict: mining of signal biomarkers and production of models for early-stage breast cancer subtyping and prognosis

Drug discovery for chemotherapeutic resistance based on pathway-responsive gene sets and its application in breast cancer

Discovering biomarkers for chronic sinusitis with nasal polyps: a study integrating bioinformatics analysis and experimental validation of macrophage polarization and metabolism-related genes

Single-cell splicing QTL analysis in pancreatic islets

PharmacoForge: pharmacophore generation with diffusion models

Structure-based prediction of SARS-CoV-2 variant properties using machine learning on mutational neighborhoods

TCRscape: a single-cell multi-omic TCR profiling toolkit

An image analysis pipeline to quantify the spatial distribution of cell markers in stroma-rich tumors

A novel linear indexing method for strings under all internal nodes in a suffix tree

Adaptive sampling methods facilitate the determination of reliable dataset sizes for evidence-based modeling

Protein cleaver: an interactive web interface for in silico prediction and systematic annotation of protein digestion-derived peptides

Editorial: Networks and graphs in biological data: current methods, opportunities and challenges

Germline mutation profiling of breast cancer patients using a non-BRCA sequencing panel

COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices

Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers–focused program at The Kids Research Institute Australia