Frontiers in Genetics | Computational Genomics

Original Research

Published on 16 Dec 2025

Identification and validation of biomarkers related to nicotinamide metabolic pathway activity in heart failure

in Computational Genomics

Jianping Du
Xiaoyu Yang
Shuxing Wu
Shuli Bi
Peng Wang
Lisong Cheng
Zhuhua Yao

Frontiers in Genetics

doi 10.3389/fgene.2025.1673314

1,315 views

Original Research

Published on 10 Dec 2025

Hyperlipidemia-associated specific modules and hub genes revealed by integrative methods of WGCNA and MetaDE

in Computational Genomics

Zhiyi Zhao
Yin Cao
Anna Gu
Hanxin Yao

Frontiers in Genetics

doi 10.3389/fgene.2025.1592778

1,358 views

Original Research

Published on 04 Dec 2025

Integrating GWAS and machine learning for disease risk prediction in the Taiwanese Hakka population

in Computational Genomics

Jing-Hong Xiao
Hsiao-Yen Kang
Li-Ching Wu
Tien Hsu
Chin-Pyng Wu
Li-Jen Su

Frontiers in Genetics

doi 10.3389/fgene.2025.1694084

1,845 views

Original Research

Published on 01 Dec 2025

Potential prognostic biomarkers in restenosis of peripheral arteries identified through comprehensive ceRNA network analysis

in Computational Genomics

Yulin Miao
Zongxin Li
Qianqian Sun
Gang Zhao
Guohang Shen
Haobo Zhang
Fengli Gao

Frontiers in Genetics

doi 10.3389/fgene.2025.1597644

1,439 views

Methods

Published on 26 Nov 2025

OFGPMA: Optimal frequency graph representation learning for pseudogene and miRNA association prediction

in Computational Genomics

Yongbin Zeng
Lixiang Xiong
Yungui Luo

Frontiers in Genetics

doi 10.3389/fgene.2025.1643921

1,067 views

Original Research

Published on 26 Nov 2025

DMAGCL: A dual-masked adaptive graph contrastive learning framework for predicting circRNA-drug sensitivity

in Computational Genomics

Peng Wang
Yuqi Guo
Zejun Li
Di Tang
Mingming Qi
Zhanyi Zhu
Lichao Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1721716

1,534 views
1 citation

Methods

Published on 20 Nov 2025

A network-based discovery of prognostic markers in recurrent IDH wild-type gliomas

in Computational Genomics

Yang Liu
Jason Huse
Kasthuri Kannan

Frontiers in Genetics

doi 10.3389/fgene.2025.1672015

1,462 views

Review

Published on 20 Nov 2025

Bioinformatics identification of key genes and therapeutic targets for exercise intervention in polycystic ovary syndrome

in Computational Genomics

Xiaodie Yang
Hong Yang
Dongyi Shen
Qiang Zhang
Chan Zhu

Frontiers in Genetics

doi 10.3389/fgene.2025.1634588

1,568 views

Original Research

Published on 19 Nov 2025

Potential diagnostic markers and therapeutic targets for obstructive sleep apnea with comorbid depression based on bioinformatics analysis

in Computational Genomics

Yinfei Lu
Zao Tang
Xiangyu Zhou
Wanting Lin
Xiao Guo

Frontiers in Genetics

doi 10.3389/fgene.2025.1655000

1,624 views

Correction

Published on 12 Nov 2025

Correction: Integrative machine learning and Mendelian randomization identify causal laboratory biomarkers for coronary artery lesions in Kawasaki disease: a prospective study

in Computational Genomics

Hancao Yang
Meng Wu
Keqing Liang
Yi Li
Ran Yang
Beibei Yuan
Ming Wu
Jin Xu

Frontiers in Genetics

doi 10.3389/fgene.2025.1735649

814 views

Mini Review

Published on 10 Nov 2025

Advances in post-processing methods for multiple sequence alignment

in Computational Genomics

Yixiao Zhai
Zitong Zhang
Zhen Li

Frontiers in Genetics

doi 10.3389/fgene.2025.1722317

1,989 views

Original Research

Published on 07 Nov 2025

KSRV: a Kernel PCA-Based framework for inferring spatial RNA velocity at single-cell resolution

in Computational Genomics

Yan He
Jian Jiang
Huahai Qiu
Ya-Zhou Shi
Ben-Gong Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1695803

1,835 views

Correction

Published on 07 Nov 2025

Correction: Identification of shared diagnostic genes between osteoporosis and Crohn’s disease through integrated transcriptomic analysis and machine learning

in Computational Genomics

Guirong Yi
Peng Zhou
Qinxu Yang
Maosheng Zhao
Qiaoqiao Yang
Shensong Li
Chenpo Dang

Frontiers in Genetics

doi 10.3389/fgene.2025.1722642

831 views

Original Research

Published on 06 Nov 2025

Systems biology and experimental validation indicate DDIT4, FOXO1, and STAT3 as shared key genes linking osteoporosis and sarcopenia

in Computational Genomics

Wenjing Li
Yuechen Xing
Lihong Jiang
Jia Meng
Yue Wang
Renjie Tan
Yina Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1630705

1,837 views

Review

Published on 28 Oct 2025

From bench to bytes: a practical guide to RNA sequencing data analysis

in Computational Genomics

Prabin Dawadi
Bivek Pokharel
Anita Shrestha
Dikshya Niraula
Afifa Naeem
Sayaka Miura
Mishal Roy
Saroj Nepal

Frontiers in Genetics

doi 10.3389/fgene.2025.1697922

5,216 views

Original Research

Published on 23 Oct 2025

Multi-omics identification and validation of oxidative phosphorylation–related hub genes in schizophrenia

in Computational Genomics

Yu Zhou
Shuang Zhang
Yao-Xia Liu
Xin Dai
Ting Zhang
Xiao-Tao Xu
Sheng-Nan Deng
Min-Yan Yang
Zhen Fan

Frontiers in Genetics

doi 10.3389/fgene.2025.1690947

2,098 views

Original Research

Published on 16 Oct 2025

CGSDA: inferring snoRNA-disease associations via ChebNetII and GatedGCN

in Computational Genomics

Yongfu Zou
Yusong Lu
Shanghui Lu
Zhanliang Wei
Le Li
Shuilin Liao
Ting Zeng
Yi Zhang
Rui Miao

Frontiers in Genetics

doi 10.3389/fgene.2025.1684484

1,532 views

Original Research

Published on 14 Oct 2025

Identification of key genes for heart failure in dilated cardiomyopathy in different populations

in Computational Genomics

Yue Yu
Chentian Xue
Dong Ji
Wei Sheng
Xiang Gao
Xize Wu
Chengyan Wu

Frontiers in Genetics

doi 10.3389/fgene.2025.1618390

2,857 views

Review

Published on 14 Oct 2025

Gene-LLMs: a comprehensive survey of transformer-based genomic language models for regulatory and clinical genomics

in Computational Genomics

P. Balakrishnan
A. Anny Leema
V. Dhivya Shree
C. Mohammad Saad
A. Mohan Babu

Frontiers in Genetics

doi 10.3389/fgene.2025.1634882

6,562 views

Correction

Published on 13 Oct 2025

Correction: DeepRNAac4C: a hybrid deep learning framework for RNA N4-acetylcytidine site prediction

in Computational Genomics

Guohua Huang
Runjuan Xiao
Chunying Peng
Jinyun Jiang
Weihong Chen

Frontiers in Genetics

doi 10.3389/fgene.2025.1704319

931 views

Original Research

Published on 08 Oct 2025

GTAT-GRN: a graph topology-aware attention method with multi-source feature fusion for gene regulatory network inference

in Computational Genomics

Shuran Wang
Lilian Zhang
Lutao Gao
Yao Rao
Jie Cui
Linnan Yang

Frontiers in Genetics

doi 10.3389/fgene.2025.1668773

2,687 views

Original Research

Published on 07 Oct 2025

Identification of shared diagnostic genes between osteoporosis and Crohn’s disease through integrated transcriptomic analysis and machine learning

in Computational Genomics

Guirong Yi
Peng Zhou
Qinxu Yang
Maosheng Zhao
Qiaoqiao Yang
Shensong Li
Chenpo Dang

Frontiers in Genetics

doi 10.3389/fgene.2025.1609915

2,633 views

Correction

Published on 07 Oct 2025

Correction: Multi-omics integration uncovers key transcriptional regulators in triple-negative breast cancer spatial heterogeneity

in Computational Genomics

Ning Zhang
Ye Zhang
Rui-Fei Yang
Min Tan
Hai-Qing Chu
Abdur Rehman
Lu-Yu Yang
Ya-Yu Li
Fahad M. Alshabrmi
Xin Zhou

Frontiers in Genetics

doi 10.3389/fgene.2025.1701926

1,364 views

Original Research

Published on 03 Oct 2025

HFTC: a hierarchical fungal taxonomic classification model for ITS sequences using low-dimensional embedding features

in Computational Genomics

Jiawei Wang
Shaojie Qiao
Dongsheng Xiang
Yangcheng Liao
Chao Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1650244

2,391 views

2,653 articles

articles

Identification and validation of biomarkers related to nicotinamide metabolic pathway activity in heart failure

Hyperlipidemia-associated specific modules and hub genes revealed by integrative methods of WGCNA and MetaDE

Integrating GWAS and machine learning for disease risk prediction in the Taiwanese Hakka population

Potential prognostic biomarkers in restenosis of peripheral arteries identified through comprehensive ceRNA network analysis

OFGPMA: Optimal frequency graph representation learning for pseudogene and miRNA association prediction

DMAGCL: A dual-masked adaptive graph contrastive learning framework for predicting circRNA-drug sensitivity

A network-based discovery of prognostic markers in recurrent IDH wild-type gliomas

Bioinformatics identification of key genes and therapeutic targets for exercise intervention in polycystic ovary syndrome

Potential diagnostic markers and therapeutic targets for obstructive sleep apnea with comorbid depression based on bioinformatics analysis

Correction: Integrative machine learning and Mendelian randomization identify causal laboratory biomarkers for coronary artery lesions in Kawasaki disease: a prospective study

Advances in post-processing methods for multiple sequence alignment

KSRV: a Kernel PCA-Based framework for inferring spatial RNA velocity at single-cell resolution

Correction: Identification of shared diagnostic genes between osteoporosis and Crohn’s disease through integrated transcriptomic analysis and machine learning

Systems biology and experimental validation indicate DDIT4, FOXO1, and STAT3 as shared key genes linking osteoporosis and sarcopenia

From bench to bytes: a practical guide to RNA sequencing data analysis

Multi-omics identification and validation of oxidative phosphorylation–related hub genes in schizophrenia

CGSDA: inferring snoRNA-disease associations via ChebNetII and GatedGCN

Identification of key genes for heart failure in dilated cardiomyopathy in different populations

Gene-LLMs: a comprehensive survey of transformer-based genomic language models for regulatory and clinical genomics

Correction: DeepRNAac4C: a hybrid deep learning framework for RNA N4-acetylcytidine site prediction

GTAT-GRN: a graph topology-aware attention method with multi-source feature fusion for gene regulatory network inference

Identification of shared diagnostic genes between osteoporosis and Crohn’s disease through integrated transcriptomic analysis and machine learning

Correction: Multi-omics integration uncovers key transcriptional regulators in triple-negative breast cancer spatial heterogeneity

HFTC: a hierarchical fungal taxonomic classification model for ITS sequences using low-dimensional embedding features