Frontiers in Bioinformatics

Brief Research Report

Published on 22 Sep 2025

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

in RNA Bioinformatics

Sofia Ramos
João Gregório
Ana Sofia Fernandes
Nuno Saraiva

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1633494

1,230 views

Original Research

Published on 22 Sep 2025

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

in Integrative Bioinformatics

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

1,647 views
1 citation

Original Research

Published on 19 Sep 2025

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

in Genomic Analysis

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613761

2,178 views

Original Research

Published on 19 Sep 2025

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

in Integrative Bioinformatics

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

2,630 views
2 citations

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

in Integrative Bioinformatics

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

2,945 views

Methods

Published on 18 Sep 2025

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

in Single Cell Bioinformatics

Jie Sun
Robert Morrison
Soyeon Kim
Kairuo Yan
Hyun Jung Park

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630161

2,634 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

in Integrative Bioinformatics

Sangeetha Muthamilselvan
Natarajan Vaithilingam
Ashok Palaniappan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1644695

2,298 views
1 citation

Original Research

Published on 18 Sep 2025

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

in Integrative Bioinformatics

Shuang Zhao
He Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1625664

2,793 views

Original Research

Published on 16 Sep 2025

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

in Drug Discovery in Bioinformatics

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

1,562 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

in Network Bioinformatics

Juan Zhou
Huan Wang
Jin Wang
Fuming Zhou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613136

2,821 views

Original Research

Published on 10 Sep 2025

Single-cell splicing QTL analysis in pancreatic islets

in Genomic Analysis

Jae-Won Cho
Jingyi Cao
Martin Hemberg

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1657895

1,650 views

Technology and Code

Published on 08 Sep 2025

PharmacoForge: pharmacophore generation with diffusion models

in Drug Discovery in Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1628800

3,234 views

FAIR² Data

Published on 08 Sep 2025

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

in Integrative Bioinformatics

Max van den Boom
Erik Schultes
Thomas Hankemeier

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1634111

3,585 views

Technology and Code

Published on 05 Sep 2025

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

in Single Cell Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1641491

2,975 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

in Computational BioImaging

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1619790

2,125 views

Methods

Published on 04 Sep 2025

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

in Integrative Bioinformatics

Anas Al-okaily
Abdelghani Tbakhi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1577324

1,085 views

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

in Protein Bioinformatics

Grigorios Koulouras
Yingrong Xu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1576317

3,741 views

Brief Research Report

Published on 04 Sep 2025

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

in Data Visualization

Tim Breitenbach
Thomas Dandekar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1528515

1,709 views
1 citation

Editorial

Published on 02 Sep 2025

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

in Network Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1685992

1,369 views

Data Report

Published on 02 Sep 2025

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

in Genomic Analysis

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

1,954 views

Original Research

Published on 01 Sep 2025

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

in Protein Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630078

1,908 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

in Integrative Bioinformatics

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

2,518 views

Original Research

Published on 26 Aug 2025

Identifying novel therapeutic targets for non-alcoholic fatty liver disease using bioinformatics approaches: from drug repositioning to traditional Chinese medicine

in Drug Discovery in Bioinformatics

Jingmin Zhang
Tianwei Meng
Weiqi Gao
Xinghua Li
Juan Xu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613985

3,114 views

Original Research

Published on 20 Aug 2025

Using reinforcement learning in genome assembly: in-depth analysis of a Q-learning assembler

in Genomic Analysis

Kleber Padovani
Rafael Cabral Borges
Roberto Xavier
André Carlos Carvalho
Anna Reali
Annie Chateau
Ronnie Alves

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1633623

2,170 views

601 articles

articles

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

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

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

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

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

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

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

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

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

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

Identifying novel therapeutic targets for non-alcoholic fatty liver disease using bioinformatics approaches: from drug repositioning to traditional Chinese medicine

Using reinforcement learning in genome assembly: in-depth analysis of a Q-learning assembler