Frontiers in Bioinformatics | Integrative Bioinformatics

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

3,255 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

3,276 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

1,795 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

2,783 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

2,689 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

2,694 views
1 citation

Original Research

Published on 19 May 2025

Integrative multi-omics study identifies sex-specific molecular signatures and immune modulation in bladder cancer

in Integrative Bioinformatics

Yizhou Wang
Priyanka Bhandary
Kevin Griffin
Jason H. Moore
Xue Li
Zhiping Paul Wang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1575790

3,684 views
1 citation

Original Research

Published on 28 Mar 2025

Identification of key hub genes in pancreatic ductal adenocarcinoma: an integrative bioinformatics study

in Integrative Bioinformatics

Kankana Bhattacharjee
Avik Sengupta
Rahul Kumar
Aryya Ghosh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1536783

3,770 views

Review

Published on 24 Feb 2025

Reliable machine learning models in genomic medicine using conformal prediction

in Integrative Bioinformatics

Christina Papangelou
Konstantinos Kyriakidis
Pantelis Natsiavas
Ioanna Chouvarda
Andigoni Malousi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1507448

4,560 views
1 citation

Original Research

Published on 28 Jan 2025

DNA methylation biomarker analysis from low-survival-rate cancers based on genetic functional approaches

in Integrative Bioinformatics

Yi-Hsuan Tsai
Prasenjit Mitra
David Taniar
Tun-Wen Pai

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1523524

3,063 views
1 citation

Methods

Published on 23 Jan 2025

A novel lossless encoding algorithm for data compression–genomics data as an exemplar

in Integrative Bioinformatics

Anas Al-okaily
Abdelghani Tbakhi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1489704

2,871 views
1 citation

Original Research

Published on 15 Jan 2025

Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development

in Integrative Bioinformatics

Wang Wenlun
Yu Chaohang
Huang Yan
Li Wenbin
Zhou Nanqing
Hu Qianmin
Wu Shengcai
Yuan Qing
Yu Shirui
Zhang Feng

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1494717

3,935 views
2 citations

Brief Research Report

Published on 09 Jan 2025

Detection of reproducible liver cancer specific ligand-receptor signaling in blood

in Integrative Bioinformatics

Aram Safrastyan
Damian Wollny

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1332782

1,985 views

Editorial

Published on 07 Jan 2025

Editorial: Multi-omics approaches in the study of human disease mechanisms

in Integrative Bioinformatics

Dapeng Wang
Giuseppe Agapito

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1546680

2,846 views
3 citations

Technology and Code

Published on 20 Dec 2024

PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences

in Integrative Bioinformatics

Benjamin Dubois
Mathieu Delitte
Salomé Lengrand
Claude Bragard
Anne Legrève
Frédéric Debode

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1483255

7,677 views
8 citations

Original Research

Published on 04 Oct 2024

Discovery of plasma biomarkers related to blood-brain barrier dysregulation in Alzheimer’s disease

in Integrative Bioinformatics

Yuet Ruh Dan
Keng-Hwee Chiam

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1463001

5,101 views
1 citation

Editorial

Published on 09 Aug 2024

Editorial: Big data and artificial intelligence for genomics and therapeutics – Proceedings of the 19th Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS)

in Integrative Bioinformatics

Huixiao Hong
Inimary Toby-Ogundeji
Robert J. Doerksen
Zhaohui Steve Qin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1470107

1,878 views

Original Research

Published on 26 Jul 2024

Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences

in Integrative Bioinformatics

Abdullahi Tunde Aborode
Neeraj Kumar
Christopher Busayo Olowosoke
Tope Abraham Ibisanmi
Islamiyyah Ayoade
Haruna Isiyaku Umar
Abdullahi Temitope Jamiu
Basit Bolarinwa
Zainab Olapade
Abidemi Ruth Idowu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1411935

4,173 views
6 citations

Original Research

Published on 15 Jul 2024

CAEM-GBDT: a cancer subtype identifying method using multi-omics data and convolutional autoencoder network

in Integrative Bioinformatics

Jiquan Shen
Xuanhui Guo
Hanwen Bai
Junwei Luo

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1403826

2,231 views
2 citations

Original Research

Published on 19 Jun 2024

A comprehensive multi-omics analysis reveals unique signatures to predict Alzheimer’s disease

in Integrative Bioinformatics

Michael Vacher
Rodrigo Canovas
Simon M. Laws
James D. Doecke

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1390607

5,931 views
12 citations

Original Research

Published on 14 May 2024

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation

in Integrative Bioinformatics

Xihaier Luo
Seyednami Niyakan
Patrick Johnstone
Sean McCorkle
Gilchan Park
Vanessa López-Marrero
Shinjae Yoo
Edward R. Dougherty
Xiaoning Qian
Francis J. Alexander

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1280971

4,986 views
3 citations

Original Research

Published on 16 Apr 2024

PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis

in Integrative Bioinformatics

Fengyuan Huang
Robert S. Welner
Jake Y. Chen
Zongliang Yue

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1336135

3,161 views
1 citation

Original Research

Published on 03 Apr 2024

bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses

in Integrative Bioinformatics

Shamini Hemandhar Kumar
Ines Tapken
Daniela Kuhn
Peter Claus
Klaus Jung

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1380928

3,266 views
3 citations

Brief Research Report

Published on 27 Mar 2024

A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease

in Integrative Bioinformatics

Alban Obel Slabowska
Charles Pyke
Henning Hvid
Leon Eyrich Jessen
Simon Baumgart
Vivek Das

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1352594

6,461 views
9 citations

85 articles

articles

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

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

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

Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization

Integrative multi-omics study identifies sex-specific molecular signatures and immune modulation in bladder cancer

Identification of key hub genes in pancreatic ductal adenocarcinoma: an integrative bioinformatics study

Reliable machine learning models in genomic medicine using conformal prediction

DNA methylation biomarker analysis from low-survival-rate cancers based on genetic functional approaches

A novel lossless encoding algorithm for data compression–genomics data as an exemplar

Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development

Detection of reproducible liver cancer specific ligand-receptor signaling in blood

Editorial: Multi-omics approaches in the study of human disease mechanisms

PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences

Discovery of plasma biomarkers related to blood-brain barrier dysregulation in Alzheimer’s disease

Editorial: Big data and artificial intelligence for genomics and therapeutics – Proceedings of the 19th Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS)

Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences

CAEM-GBDT: a cancer subtype identifying method using multi-omics data and convolutional autoencoder network

A comprehensive multi-omics analysis reveals unique signatures to predict Alzheimer’s disease

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation

PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis

bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses

A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease