Frontiers in Bioinformatics | Integrative Bioinformatics

Original Research

Accepted on 02 Oct 2025

Multimodal Knowledge Expansion Widget Powered by Plant Protein Phosphorylation Database and ChatGPT

in Integrative Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1687687

206 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

708 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

522 views

Original Research

Accepted on 22 Sep 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

450 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

822 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

1,214 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

1,031 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

862 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

in Integrative Bioinformatics

Shuang Zhao
He Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1625664

954 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

1,805 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

675 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

1,245 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

1,264 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

1,371 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

2,005 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

2,068 views