Frontiers in Genetics | Computational Genomics

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

2,120 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

2,704 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

2,693 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

1,908 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

2,404 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

1,880 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

1,984 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

3,775 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

2,734 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

2,279 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

2,962 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

3,001 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

1,663 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

1,465 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

2,584 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

3,952 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

2,757 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

2,735 views

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

2,164 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

1,834 views

Original Research

Published on 04 Jun 2025

MOLUNGN: a multi-omics graph neural network for biomarker discovery and accurate lung cancer classification

in Computational Genomics

Daifeng Zhang
Guoqiang Bian
Yuanbin Zhang
Jiadong Xie
Chenjun Hu

Frontiers in Genetics

doi 10.3389/fgene.2025.1610284

5,026 views
3 citations

Original Research

Published on 02 Jun 2025

From genetic data to kinship clarity: employing machine learning for detecting incestuous relations

in Computational Genomics

Dejan Šorgić
Aleksandra Stefanović
Mladen Popović
Dušan Keckarević

Frontiers in Genetics

doi 10.3389/fgene.2025.1578581

3,814 views
2 citations

Original Research

Published on 30 May 2025

Reference-free deconvolution of complex samples based on cross-cell-type differential analysis: Systematic evaluations with various feature selection options

in Computational Genomics

Weiwei Zhang
Zhonghe Tian
Ling Peng

Frontiers in Genetics

doi 10.3389/fgene.2025.1570781

1,971 views

Original Research

Published on 30 May 2025

Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma

in Computational Genomics

Wanchen Cao
Kai Gao
Yi Zhao

Frontiers in Genetics

doi 10.3389/fgene.2025.1536198

2,817 views

2,649 articles

articles

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

MOLUNGN: a multi-omics graph neural network for biomarker discovery and accurate lung cancer classification

From genetic data to kinship clarity: employing machine learning for detecting incestuous relations

Reference-free deconvolution of complex samples based on cross-cell-type differential analysis: Systematic evaluations with various feature selection options

Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma