Frontiers in Bioinformatics | Integrative Bioinformatics

Original Research

Accepted on 19 Dec 2025

Cross-Disease Transcriptomic Meta-Analysis and Network Pharmacology Reveal Key Therapeutic Targets in Rheumatoid Arthritis, Systemic Lupus Erythematosus and Multiple Sclerosis

in Integrative Bioinformatics

Lakshmi K
Vino Sundararajan

Frontiers in Bioinformatics

Methods

Accepted on 15 Dec 2025

Genetic Risk Predictions Using Deep Learning Models with Summary Data

in Integrative Bioinformatics

Angela Wang
Elena Xiao
Jason Cheng
Xiaoxi Shen

Frontiers in Bioinformatics

Original Research

Published on 10 Dec 2025

Neurogenic locus notch homolog protein 1 (NOTCH 1) SNP informatics coupled with intrinsically disordered regions and post-translational modifications reveals the complex structural crosstalk of Lung Adenocarcinoma (LUAD)

in Integrative Bioinformatics

Pearl John
C. Sudandiradoss

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1641521

507 views

Original Research

Published on 04 Dec 2025

Predicting GD2 expression across cancer types by the integration of pathway topology and transcriptome data

in Integrative Bioinformatics

Arsenij Ustjanzew
Federico Marini
Saskia Wagner
Arthur Wingerter
Roger Sandhoff
Jörg Faber
Claudia Paret

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1705930

811 views

Correction

Published on 03 Dec 2025

Correction: Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer

in Integrative Bioinformatics

Tianle Xue
Yunpeng Chen
Xiaomeng Li
Zhixiang Zhou
Qiyang Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1750582

380 views

Original Research

Published on 03 Nov 2025

Identification of ordinal relations and alternative suborders within high-dimensional molecular data

in Integrative Bioinformatics

Ana Stolnicu
Peter Eckhardt-Bellmann
Angelika M. R. Kestler
Hans A. Kestler

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1665892

838 views

Original Research

Published on 22 Oct 2025

Inferred global dense residue transition graphs from primary structure sequences enable protein interaction prediction via directed graph convolutional neural networks

in Integrative Bioinformatics

Islam Akef Ebeid
Haoteng Tang
Pengfei Gu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1651623

1,236 views

Original Research

Accepted on 20 Oct 2025

Identification of Multiple Prognostic Biomarker Sets for Risk Stratification in SKCM

in Integrative Bioinformatics

Shivani Malik
Ritu Tomer
Akanksha Arora
Gajendra PS Raghava

Frontiers in Bioinformatics

233 views

Original Research

Published on 15 Oct 2025

Multimodal knowledge expansion widget powered by plant protein phosphorylation database and ChatGPT

in Integrative Bioinformatics

Chunhui Xu
Yang Yu
Govardhan Khadakkar
Jiacheng Xie
Dong Xu
Qiuming Yao

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1687687

1,410 views

Brief Research Report

Published on 02 Oct 2025

Optimizing clustering of CDR3 sequences using natural language processing, Word2Vec, and KMeans

in Integrative Bioinformatics

Sanskriti Baranwal
Ricardo Avila Sanchez
Clement-Andi Edet
Erick Chastain
Inimary Toby

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1623488

1,769 views

Technology and Code

Published on 30 Sep 2025

EPheClass: ensemble-based phenotype classifier from 16S rRNA gene sequences

in Integrative Bioinformatics

Lara Vázquez-González
Carlos Peña-Reyes
Alba Regueira-Iglesias
Carlos Balsa-Castro
Inmaculada Tomás
María J. Carreira

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1514880

1,251 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

1,446 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

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

2,401 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

2,120 views
2 citations

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

1,965 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

2,371 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

2,939 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

924 views

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

2,067 views

Original Research

Published on 18 Aug 2025

Spatial heterogeneity reveals an evolutionary signature predicting therapeutic response and clinical outcomes in hepatocellular carcinoma

in Integrative Bioinformatics

Shangyi Luo
Li Liu
Yang Sun
Jian Shi
Yajing Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1669236

2,077 views

Original Research

Published on 05 Aug 2025

In silico analysis of CSF2RB from cancer genomic databases reveals a heterogeneous role in different breast cancer subtypes

in Integrative Bioinformatics

Raghad Alshelaiel
Abdulmohsen Alkushi
Lolwah Abdullah Alriyees
Abir Abdullah Alamro
Humidah Alanazi
Areej Alhareeri
Bader AlMuzzaini
Mamoon Rashid

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1606828

2,029 views

Original Research

Published on 28 Jul 2025

Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer

in Integrative Bioinformatics

Tianle Xue
Yunpeng Chen
Xiaomeng Li
Zhixiang Zhou
Qiyang Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1599098

3,164 views

Original Research

Published on 21 Jul 2025

NeSyDPP-4: discovering DPP-4 inhibitors for diabetes treatment with a neuro-symbolic AI approach

in Integrative Bioinformatics

Delower Hossain
Ehsan Saghapour
Jake Y. Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1603133

3,163 views

Original Research

Published on 08 Jul 2025

Using deep neural networks and LASSO regression to predict miRNA expression changes based on mRNA data

in Integrative Bioinformatics

Franz Leonard Böge
Helena U. Zacharias
Stefanie C. Becker
Klaus Jung

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1566162

1,773 views

82 articles

articles

Cross-Disease Transcriptomic Meta-Analysis and Network Pharmacology Reveal Key Therapeutic Targets in Rheumatoid Arthritis, Systemic Lupus Erythematosus and Multiple Sclerosis

Genetic Risk Predictions Using Deep Learning Models with Summary Data

Neurogenic locus notch homolog protein 1 (NOTCH 1) SNP informatics coupled with intrinsically disordered regions and post-translational modifications reveals the complex structural crosstalk of Lung Adenocarcinoma (LUAD)

Predicting GD2 expression across cancer types by the integration of pathway topology and transcriptome data

Correction: Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer

Identification of ordinal relations and alternative suborders within high-dimensional molecular data

Inferred global dense residue transition graphs from primary structure sequences enable protein interaction prediction via directed graph convolutional neural networks

Identification of Multiple Prognostic Biomarker Sets for Risk Stratification in SKCM

Multimodal knowledge expansion widget powered by plant protein phosphorylation database and ChatGPT

Optimizing clustering of CDR3 sequences using natural language processing, Word2Vec, and KMeans

EPheClass: ensemble-based phenotype classifier from 16S rRNA gene sequences

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

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

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

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

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

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

Spatial heterogeneity reveals an evolutionary signature predicting therapeutic response and clinical outcomes in hepatocellular carcinoma

In silico analysis of CSF2RB from cancer genomic databases reveals a heterogeneous role in different breast cancer subtypes

Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer

NeSyDPP-4: discovering DPP-4 inhibitors for diabetes treatment with a neuro-symbolic AI approach

Using deep neural networks and LASSO regression to predict miRNA expression changes based on mRNA data