Frontiers in Genetics | Computational Genomics

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

3,069 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

2,539 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

2,366 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

2,041 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

2,201 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

2,804 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

2,797 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

1,980 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

2,499 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

1,936 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

2,064 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

3,850 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

2,880 views
2 citations

Original Research

Published on 25 Jun 2025

A machine learning framework for predicting cognitive impairment in aging populations using urinary metal and demographic data

in Computational Genomics

Fengchun Ren
Xiao Zhao
Qin Yang
Huaqiang Liao
Yudong Zhang
Xuemei Liu

Frontiers in Genetics

doi 10.3389/fgene.2025.1631228

2,350 views

Original Research

Published on 24 Jun 2025

An analysis of gene expression profiles through machine learning uncovers the new diagnostic signature for diabetic foot ulcers

in Computational Genomics

Yingnan Li
Ning Xiao
Zhuoqun Wang
Wenhai Wang
Fengjiao Li
Jiren Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1620749

3,064 views

Original Research

Published on 23 Jun 2025

CYLD as a key regulator of myocardial infarction-to-heart failure transition revealed by multi-omics integration

in Computational Genomics

Jingya Xu
Zhonghua Dong
Zhaodong Li
Xuan Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1592985

3,083 views

Original Research

Published on 23 Jun 2025

Insights into the evolution and regulation of miRNAs from the view of their DNA replication temporal domains

in Computational Genomics

Xudong Wu
Tingting Liu

Frontiers in Genetics

doi 10.3389/fgene.2025.1544802

1,694 views

Original Research

Published on 20 Jun 2025

Generalized information criteria for personalized gene network inference

in Computational Genomics

Heewon Park
Seiya Imoto
Sadanori Konishi

Frontiers in Genetics

doi 10.3389/fgene.2025.1583756

1,492 views

Original Research

Published on 20 Jun 2025

Integrative bioinformatics analysis of pyroptosis-related genes and immune infiltration patterns in childhood asthma

in Computational Genomics

Di Lian
Chenye Lin
Meiling Xie
JianXing Wei
Xueling Huang
Ke Lian
Qiuyu Tang

Frontiers in Genetics

doi 10.3389/fgene.2025.1557709

2,678 views

Original Research

Published on 20 Jun 2025

Identification of neutrophil extracellular trap-related biomarkers in ulcerative colitis based on bioinformatics and machine learning

in Computational Genomics

Jiao Li
Yupei Liu
Zhiyi Sun
Suqi Zeng
Caisong Zheng

Frontiers in Genetics

doi 10.3389/fgene.2025.1589999

4,069 views
1 citation

Original Research

Published on 19 Jun 2025

Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics

in Computational Genomics

Xiaojuan Yang
Yutao Duan
Lei Qiu
Xia Huang
Fei Li

Frontiers in Genetics

doi 10.3389/fgene.2025.1567173

2,852 views
2 citations

Original Research

Published on 18 Jun 2025

Integrative bioinformatics analysis and experimental validation reveals key genes and regulatory mechanisms in the development of gout

in Computational Genomics

Ye Yuan
Zhiqiang Gao
Jianhong Chen
Yuejing Liu
Jingguo Zhou

Frontiers in Genetics

doi 10.3389/fgene.2025.1598835

2,823 views
1 citation

Original Research

Published on 11 Jun 2025

iKcr-DRC: prediction of lysine crotonylation sites in proteins based on a novel attention module and DenseNet

in Computational Genomics

Xin Wei
Siqin Hu
Jian Tu
Muhammad Akmal Remli

Frontiers in Genetics

doi 10.3389/fgene.2025.1574832

2,279 views

Original Research

Published on 10 Jun 2025

Auto-branch multi-task learning for simultaneous prediction of multiple correlated traits associated with Alzheimer’s disease

in Computational Genomics

Jiaqi Liang
Zhao Xue
Wenchao Zhou
Xiangjie Guo
Yalu Wen

Frontiers in Genetics

doi 10.3389/fgene.2025.1538544

1,881 views

2,653 articles

articles

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

A machine learning framework for predicting cognitive impairment in aging populations using urinary metal and demographic data

An analysis of gene expression profiles through machine learning uncovers the new diagnostic signature for diabetic foot ulcers

CYLD as a key regulator of myocardial infarction-to-heart failure transition revealed by multi-omics integration

Insights into the evolution and regulation of miRNAs from the view of their DNA replication temporal domains

Generalized information criteria for personalized gene network inference

Integrative bioinformatics analysis of pyroptosis-related genes and immune infiltration patterns in childhood asthma

Identification of neutrophil extracellular trap-related biomarkers in ulcerative colitis based on bioinformatics and machine learning

Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics

Integrative bioinformatics analysis and experimental validation reveals key genes and regulatory mechanisms in the development of gout

iKcr-DRC: prediction of lysine crotonylation sites in proteins based on a novel attention module and DenseNet

Auto-branch multi-task learning for simultaneous prediction of multiple correlated traits associated with Alzheimer’s disease