Frontiers in Bioinformatics | Integrative Bioinformatics

Original Research

Published on 29 Jan 2026

Benchmarking multiple gene ontology enrichment tools reveals high biological significance, ranking, and stringency heterogeneity among datasets

in Integrative Bioinformatics

Fábio Henrique Schuster de Oliveira
Felipe Acker Gomes
Bruno César Feltes

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1755664

241 views

Original Research

Published on 29 Jan 2026

IRMKD: an application of instance relation matrix in plant disease recognition

in Integrative Bioinformatics

Jinqing Huang
Jian Su
Tengfei Cheng

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1761574

109 views

Original Research

Published on 27 Jan 2026

Identification and bioinformatics analysis of a novel member of the lumbrokinase gene family in earthworms

in Integrative Bioinformatics

Xiong Rongchuan
Li Jianhong
Liu Tingchang
Su Chengyuan
Chen Hong
Chen Zhengpeng
Tang Chaozhi
Zhao Xinxia

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1736746

320 views

Original Research

Published on 21 Jan 2026

Cross-disease transcriptomic meta-analysis and network pharmacology reveal key therapeutic targets in rheumatoid arthritis, systemic lupus erythematosus and multiple sclerosis

in Integrative Bioinformatics

K. Lakshmi
Sundararajan Vino

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1744094

526 views

Original Research

Accepted on 19 Jan 2026

Boolean network and meshless simulations for the comparison of transport and reaction mechanisms arising in one-short tri-exponential and uniform infusion electro-chemotherapeutic treatments

in Integrative Bioinformatics

Fabián Mauricio Vélez Salazar
Iván David Patiño Arcila
Ismael E. Rivera Madrid
Marlon R. Fulla

Frontiers in Bioinformatics

108 views

Original Research

Published on 14 Jan 2026

PreBP: an interpretable, optimized ensemble framework using routine complete blood count for rapid pathogen identification in bacterial pneumonia

in Integrative Bioinformatics

Xiaoxi Hao
Dingjian Liang
Yimin Shen
Cuimin Sun
Wei Lan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1769816

597 views

Original Research

Published on 14 Jan 2026

An integrated subtractive genomics and immunoinformatic approach for designing a multi-epitope peptide vaccine against methicillin-resistant Staphylococcus aureus

in Integrative Bioinformatics

Nandha Kumar Subramani
Subhashree Venugopal
Anand Prem Rajan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1745495

533 views

Original Research

Accepted on 08 Jan 2026

Evaluating Transcriptomic Integration for Cyanobacterial Constraint-based Metabolic Modelling

in Integrative Bioinformatics

Thomas Pugsley
Guy Hanke
Christopher Duffy

Frontiers in Bioinformatics

181 views

Methods

Published on 08 Jan 2026

Genetic risk predictions using deep learning models with summary data

in Integrative Bioinformatics

Angela Wang
Elena Xiao
Jason Cheng
Xiaoxi Shen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1657021

508 views

Original Research

Published on 07 Jan 2026

Identification of multiple prognostic biomarker sets for risk stratification in SKCM

in Integrative Bioinformatics

Shivani Malik
Ritu Tomer
Akanksha Arora
Gajendra P. S. Raghava

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1624329

826 views

Review

Accepted on 24 Dec 2025

Essential Nucleic Acid Omics: A Theoretical Foundation for Early-Stage Users

in Integrative Bioinformatics

Andrew J. Maritan
Frank J. Stewart

Frontiers in Bioinformatics

186 views

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

914 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

1,340 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

746 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

1,062 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

1,430 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

1,621 views
1 citation

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

1,960 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

1,429 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

1,612 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

2,848 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

2,513 views
1 citation

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

2,257 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

2,746 views

90 articles

articles

Benchmarking multiple gene ontology enrichment tools reveals high biological significance, ranking, and stringency heterogeneity among datasets

IRMKD: an application of instance relation matrix in plant disease recognition

Identification and bioinformatics analysis of a novel member of the lumbrokinase gene family in earthworms

Cross-disease transcriptomic meta-analysis and network pharmacology reveal key therapeutic targets in rheumatoid arthritis, systemic lupus erythematosus and multiple sclerosis

Boolean network and meshless simulations for the comparison of transport and reaction mechanisms arising in one-short tri-exponential and uniform infusion electro-chemotherapeutic treatments

PreBP: an interpretable, optimized ensemble framework using routine complete blood count for rapid pathogen identification in bacterial pneumonia

An integrated subtractive genomics and immunoinformatic approach for designing a multi-epitope peptide vaccine against methicillin-resistant Staphylococcus aureus

Evaluating Transcriptomic Integration for Cyanobacterial Constraint-based Metabolic Modelling

Genetic risk predictions using deep learning models with summary data

Identification of multiple prognostic biomarker sets for risk stratification in SKCM

Essential Nucleic Acid Omics: A Theoretical Foundation for Early-Stage Users

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

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