Frontiers in Genetics | Computational Genomics

Original Research

Published on 03 Sep 2025

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.2025.1614254

3,733 views
1 citation

Correction

Published on 29 Aug 2025

Correction: Engineering novel features for diabetes complication prediction using synthetic electronic health records

in Computational Genomics

Daniel Voskergian
Burcu Bakir-Gungor
Malik Yousef

Frontiers in Genetics

doi 10.3389/fgene.2025.1687832

1,094 views

Original Research

Published on 25 Aug 2025

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.2025.1622899

1,788 views

Original Research

Published on 22 Aug 2025

Multi-omic insights into mitochondrial dysfunction and prostatic disease: evidence from transcriptomics, proteomics, and methylomics

in Computational Genomics

Binbin Gong
Feixiang Yang
Ning Zhang
Zhengyang Wu
Tianrui Liu
Kun Wang
Xiangyu Zhang
Yangyang Zhang
Zhengyao Song
Chaozhao Liang

Frontiers in Genetics

doi 10.3389/fgene.2025.1609933

3,390 views

Correction

Published on 21 Aug 2025

Correction: Analysis and validation of novel biomarkers related to palmitoylation in adenomyosis

in Computational Genomics

Hongyu Zhang
Yufeng Li
Huijuan Cao
Yiling Zhao
Hongwen Zhu
Tiansheng Qin

Frontiers in Genetics

doi 10.3389/fgene.2025.1683914

1,153 views

Original Research

Published on 15 Aug 2025

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.2025.1646032

2,350 views

Methods

Published on 08 Aug 2025

BANSMDA: a computational model for predicting potential microbe-disease associations based on bilinear attention networks and sparse autoencoders

in Computational Genomics

Xianzhi Liu
Mingmin Liang
Ge Yu
Shichang Tang
Ouxiang Wu
Bin Zeng
Lei Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1618472

1,337 views
1 citation

Original Research

Published on 05 Aug 2025

The role of mitochondria-related genes and immune infiltration in carotid atherosclerosis: identification of hub targets through bioinformatics and machine learning approaches

in Computational Genomics

Dan Liu
Kun Guo
Min Li
Xiaochen Yu
Xue Guan
Xiuru Guan

Frontiers in Genetics

doi 10.3389/fgene.2025.1597445

3,194 views
1 citation

Original Research

Published on 04 Aug 2025

Analysis and validation of novel biomarkers related to palmitoylation in adenomyosis

in Computational Genomics

Hongyu Zhang
Yufeng Li
Huijuan Cao
Yiling Zhao
Hongwen Zhu
Tiansheng Qin

Frontiers in Genetics

doi 10.3389/fgene.2025.1614573

3,006 views

Original Research

Published on 01 Aug 2025

Research on the diagnosis model of osteoarthritis based on methylation-related genes using machine learning algorithms

in Computational Genomics

Xu Cui
Houlin Ji
Shengyang Guo
Ju Liu
Linyuan Zhang
Yongwei Jia
Yin Cui
Xiaoxiao Zhou

Frontiers in Genetics

doi 10.3389/fgene.2025.1595676

1,818 views

Original Research

Published on 31 Jul 2025

Identification of key ferroptosis-related genes and therapeutic target in nasopharyngeal carcinoma

in Computational Genomics

Yuanyuan Gu
Yaozhuang Zhou
Chunhua Xie
Guangyao He
Maosheng Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1595456

3,109 views
1 citation

Original Research

Published on 30 Jul 2025

SLC38A1 and STX11 are mitochondria-related biomarkers associated with immune infiltration in osteoarthritis

in Computational Genomics

Wenxue Lv
Mingxiu Yu
Wenhai Yan
Yuli Cai
Weiguo Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1585775

2,698 views
1 citation

Original Research

Published on 29 Jul 2025

Commonalities and differences in gene expression patterns in major depressive disorder and chronic spontaneous urticaria: implications for comorbidity

in Computational Genomics

Yibo Jiang
Wen Li
Lihao Zheng
Nan Ba

Frontiers in Genetics

doi 10.3389/fgene.2025.1560832

2,216 views

Review

Published on 29 Jul 2025

Decoding circRNA translation: challenges and advances in computational method development

in Computational Genomics

Jingjing Zhang
Rui Zhou
Huiling Zhang
Yin Peng
Jintao Meng
Wenhui Xi
Yanjie Wei

Frontiers in Genetics

doi 10.3389/fgene.2025.1654305

1,978 views
2 citations

Original Research

Published on 24 Jul 2025

A bioinformatics analysis of the correlation between hepatic ischemia–reperfusion injury and postoperative cognitive dysfunction

in Computational Genomics

Qing Hu
Haijie Liu
Yunfei Bao
Zhihao Feng
Hongbo Zhang
Jianling Li

Frontiers in Genetics

doi 10.3389/fgene.2025.1607446

1,790 views

Original Research

Published on 23 Jul 2025

EPI-DynFusion: enhancer-promoter interaction prediction model based on sequence features and dynamic fusion mechanisms

in Computational Genomics

Ao Zhang
Jianhua Jia
Mingwei Sun
Xin Wei

Frontiers in Genetics

doi 10.3389/fgene.2025.1614222

1,859 views

Methods

Published on 23 Jul 2025

A likelihood ratio framework for inferring close kinship from dynamically selected SNPs

in Computational Genomics

Jianye Ge
Bruce Budowle
Michael Cariaso
Kristen Mittelman
David Mittelman

Frontiers in Genetics

doi 10.3389/fgene.2025.1635734

2,474 views
1 citation

Original Research

Published on 17 Jul 2025

Identification of biomarkers between coronary artery disease and non-alcoholic steatohepatitis: a combination of bioinformatics and machine learning

in Computational Genomics

Yihong Lin
Jingmei Song
Xiaohong Li

Frontiers in Genetics

doi 10.3389/fgene.2025.1573621

2,448 views

Original Research

Published on 17 Jul 2025

Incorporating graph representation and mutual attention mechanism for MiRNA-MRNA interaction prediction

in Computational Genomics

Tai-Long Shi
Lei Wang
Leon Wong
Zhu-Hong You
Chang-Qing Yu
Chen Jiang
Si-Zhe Liang

Frontiers in Genetics

doi 10.3389/fgene.2025.1637427

1,714 views
1 citation

Methods

Published on 15 Jul 2025

Robust consensus nuclear and cell segmentation

in Computational Genomics

Melis O. Irfan
Eduardo A. González-Solares
Tristan Whitmarsh
Alireza Molaeinezhad
Mohammad Al Sa’d
Claire M. Mulvey
Marta Páez Ribes
Atefeh Fatemi
Dario Bressan
Nicholas A. Walton

Frontiers in Genetics

doi 10.3389/fgene.2025.1547788

2,031 views

Original Research

Published on 14 Jul 2025

Identification and characterization of signature genes related to fetoplacental vascular endothelial cell programming in gestational diabetes mellitus using bioinformatics analysis

in Computational Genomics

Chunhong Liu
Caicheng Wei
Yulan Lu
Fu Chai
Chunfang Wang
Yonglong Zeng
Huatuo Huang

Frontiers in Genetics

doi 10.3389/fgene.2025.1600756

1,689 views

Original Research

Published on 07 Jul 2025

Geometry-enhanced graph neural networks accelerate circRNA therapeutic target discovery

in Computational Genomics

Zhen Li
Mingming Qi
Juyuan Huang
Wei Zhang
Xu Tan
Yifan Chen

Frontiers in Genetics

doi 10.3389/fgene.2025.1633391

1,793 views
1 citation

Original Research

Published on 02 Jul 2025

Exploration of biomarkers associated with histone lactylation modification in spinal cord injury

in Computational Genomics

Yisong Sun
Jie Gao
Juehua Jing

Frontiers in Genetics

doi 10.3389/fgene.2025.1609439

3,448 views

Original Research

Published on 26 Jun 2025

HyenaCircle: a HyenaDNA-based pretrained large language model for long eccDNA prediction

in Computational Genomics

Fuyu Li
Wenxiang Lu
Yunfei Bai

Frontiers in Genetics

doi 10.3389/fgene.2025.1641162

2,417 views
1 citation

2,640 articles

articles

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

Correction: Engineering novel features for diabetes complication prediction using synthetic electronic health records

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

Multi-omic insights into mitochondrial dysfunction and prostatic disease: evidence from transcriptomics, proteomics, and methylomics

Correction: Analysis and validation of novel biomarkers related to palmitoylation in adenomyosis

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

BANSMDA: a computational model for predicting potential microbe-disease associations based on bilinear attention networks and sparse autoencoders

The role of mitochondria-related genes and immune infiltration in carotid atherosclerosis: identification of hub targets through bioinformatics and machine learning approaches

Analysis and validation of novel biomarkers related to palmitoylation in adenomyosis

Research on the diagnosis model of osteoarthritis based on methylation-related genes using machine learning algorithms

Identification of key ferroptosis-related genes and therapeutic target in nasopharyngeal carcinoma

SLC38A1 and STX11 are mitochondria-related biomarkers associated with immune infiltration in osteoarthritis

Commonalities and differences in gene expression patterns in major depressive disorder and chronic spontaneous urticaria: implications for comorbidity

Decoding circRNA translation: challenges and advances in computational method development

A bioinformatics analysis of the correlation between hepatic ischemia–reperfusion injury and postoperative cognitive dysfunction

EPI-DynFusion: enhancer-promoter interaction prediction model based on sequence features and dynamic fusion mechanisms

A likelihood ratio framework for inferring close kinship from dynamically selected SNPs

Identification of biomarkers between coronary artery disease and non-alcoholic steatohepatitis: a combination of bioinformatics and machine learning

Incorporating graph representation and mutual attention mechanism for MiRNA-MRNA interaction prediction

Robust consensus nuclear and cell segmentation

Identification and characterization of signature genes related to fetoplacental vascular endothelial cell programming in gestational diabetes mellitus using bioinformatics analysis

Geometry-enhanced graph neural networks accelerate circRNA therapeutic target discovery

Exploration of biomarkers associated with histone lactylation modification in spinal cord injury

HyenaCircle: a HyenaDNA-based pretrained large language model for long eccDNA prediction