Frontiers in Bioinformatics | Integrative Bioinformatics

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

556 views

Technology and Code

Accepted on 28 Aug 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 CARMONA
Maria J Carreira

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1514880

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

631 views

Original Research

Accepted on 15 Aug 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
Dr Abdullah Alshahrani
Aritra Palodhi
Debarghya Bhattacharyya
Subhadip Das
Sunil Kanti Mondal
Abul Kalam
S Rehan Ahmad
Dr. Chittabrata Mal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1567748

263 views

Original Research

Accepted on 13 Aug 2025

Extracting a COVID-19 Signature from a Multi-Omic Dataset

in Integrative Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1645785

311 views

Original Research

Accepted on 12 Aug 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

302 views

Original Research

Accepted on 11 Aug 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
Prof. Enrique Medina-Acosta, M.Sc., Ph.D.

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630518

289 views

Methods

Accepted on 07 Aug 2025

A Novel Linear Indexing 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

198 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

837 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

1,310 views

FAIR² Data

Accepted on 24 Jul 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

495 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

1,419 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

926 views

Original Research

Published on 26 Jun 2025

Identification of immune and major depressive disorder-related diagnostic markers for early nonalcoholic fatty liver disease by WGCNA and machine learning

in Integrative Bioinformatics

Yuyun Jia
Yanping Cao
Qin Yin
Xueqian Li
Xiu Wen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1594971

1,339 views

Original Research

Published on 25 Jun 2025

Integrated single-cell and bulk RNA dequencing to identify and validate prognostic genes related to T Cell senescence in acute myeloid leukemia

in Integrative Bioinformatics

Mengyao Sha
Jun Chen
Haifeng Hou
Huaihui Dou
Yan Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1606284

1,314 views

Original Research

Published on 18 Jun 2025

Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization

in Integrative Bioinformatics

Ehsan Saghapour
Rahul Sharma
Delower Hossain
Kevin Song
Zhandos Sembay
Jake Y. Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1602850

1,477 views
1 citation