Frontiers in Genetics | Computational Genomics

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

1,414 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

3,534 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

1,765 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

1,317 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

2,222 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

4,475 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

820 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

2,253 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

2,214 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

1,191 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

1,967 views

Original Research

Published on 02 Oct 2025

Analyses of haplotypes of TLR2 and TLR3 genes for COVID-19 prognosis in a cohort of professionals who worked in the first pandemic wave in Belém-PA, Brazil

in Computational Genomics

Marcos Jessé Abrahão Silva
Luiza Raquel Tapajós Figueira
Daniele Melo Sardinha
Eliete Costa da Cruz
Natasha Cristina Oliveira Andrade
Sebastião Kauã De Sousa Bispo
Thiago Augusto Ferreira Dos Anjos
Everaldina Cordeiro Dos Santos
Ana Judith Pires Garcia
Luana Nepomuceno Gondim Costa Lima

Frontiers in Genetics

doi 10.3389/fgene.2025.1659269

1,375 views
1 citation

Data Report

Published on 01 Oct 2025

Annotated genome of Aedes japonicus japonicus using a hybrid-assembly approach

in Computational Genomics

Friederike Reuss
Tilman Schell
Haruhiko Isawa
Shinji Kasai
Sven Klimpel
Ruth Müller
Markus Pfenninger
Judith Kochmann

Frontiers in Genetics

doi 10.3389/fgene.2025.1667262

2,365 views

Original Research

Published on 29 Sep 2025

Immune-molecular nexus in reproductive disorders: mechanisms linking POI and RSA

in Computational Genomics

Chen Chen
Xinyue Zhang
Wenxin Li
Yueqin Liu
Dan Zhao
Subo Zhang
Xiaolan Zhu

Frontiers in Genetics

doi 10.3389/fgene.2025.1652519

2,631 views

Original Research

Published on 25 Sep 2025

Cross-modal predictive modeling of multi-omic data in 3D airway organ tissue equivalents during viral infection

in Computational Genomics

Mostafa Rezapour
Patrick M. McNutt
David A. Ornelles
Stephen J. Walker
Sean V. Murphy
Anthony Atala
Metin Nafi Gurcan

Frontiers in Genetics

doi 10.3389/fgene.2025.1658577

2,819 views

Original Research

Published on 22 Sep 2025

Identification of platelet function-related genes in STEMI patients

in Computational Genomics

Jingjing Zhu
Shuangya Yang
Qing Guo
Yifan Yang
Bei Shi

Frontiers in Genetics

doi 10.3389/fgene.2025.1651794

1,764 views

Original Research

Published on 19 Sep 2025

A hypergraph neural network for prioritizing Alzheimer’s disease risk genes

in Computational Genomics

Meng Ma
Chao Deng
Yan Liu
Qingqing Cao
Fang Liu
Yan Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1668200

1,729 views

Original Research

Published on 17 Sep 2025

Uncovering differential gene expression between mtRNA-positive and -negative osteosarcoma cells: implications beyond mitochondrial function

in Computational Genomics

Xiaoyuan Meng
Zhongcheng Han
Wuerkan Yeerken
Zhigang Wang
Le Ma
Hongbo Liu

Frontiers in Genetics

doi 10.3389/fgene.2025.1588581

1,798 views

Original Research

Published on 17 Sep 2025

Genetic and in silico functional characterization of a novel structural variant in the PAH gene by long-reads sequencing and structural modeling

in Computational Genomics

Viviana Gallardo
Alexis Gaete
Jonathan Maldonado
Paulina Morales
Angela Peña
Valerie Hamilton
Víctor Faundes
Lorena Santa María

Frontiers in Genetics

doi 10.3389/fgene.2025.1669007

2,184 views

Original Research

Published on 17 Sep 2025

BioSemAF-BiLSTM: a protein sequence feature extraction framework based on semantic and evolutionary information

in Computational Genomics

Zihan Zhang
Yixuan Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1616880

1,905 views

Original Research

Published on 12 Sep 2025

Dissecting and validation the biomarker of heart failure progression in patients with atherosclerosis by single-cell sequencing, bioinformatics, and machine learning

in Computational Genomics

Lihua Ni
Huabo Li
Juan Du
Ke Zhou
Fugui Zhang
Liankai Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1587274

2,343 views

Original Research

Published on 10 Sep 2025

Genome-wide evolution and function analysis of ALOG gene family in cotton

in Computational Genomics

Zhen Liu
Siyu Shen
Zhijuan Cui
Tao Wang
Pengtao Li
Yangyang Wei
Renhai Peng

Frontiers in Genetics

doi 10.3389/fgene.2025.1625634

1,620 views

Original Research

Published on 10 Sep 2025

Diphenyl pyridine intervention improves S. aureus-induced pneumonia by globally regulating transcriptome profile

in Computational Genomics

Wei Duan
Qingfeng Zhu
Hai Ci
Jingang Zhang
Zhiwei Tian
Wanyu Li
Zhengfu Yang

Frontiers in Genetics

doi 10.3389/fgene.2025.1624327

1,579 views

Original Research

Published on 05 Sep 2025

Integrative analysis of single-cell and microarray data reveals SPI1-centered macrophage regulatory signatures in ulcerative colitis

in Computational Genomics

Yeqing Yu
Chengwei Yu
Shanshan Dai
Yixu Liu
Lanlan Hu
Weimin Lu

Frontiers in Genetics

doi 10.3389/fgene.2025.1617834

2,760 views

2,640 articles

articles

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

Analyses of haplotypes of TLR2 and TLR3 genes for COVID-19 prognosis in a cohort of professionals who worked in the first pandemic wave in Belém-PA, Brazil

Annotated genome of Aedes japonicus japonicus using a hybrid-assembly approach

Immune-molecular nexus in reproductive disorders: mechanisms linking POI and RSA

Cross-modal predictive modeling of multi-omic data in 3D airway organ tissue equivalents during viral infection

Identification of platelet function-related genes in STEMI patients

A hypergraph neural network for prioritizing Alzheimer’s disease risk genes

Uncovering differential gene expression between mtRNA-positive and -negative osteosarcoma cells: implications beyond mitochondrial function

Genetic and in silico functional characterization of a novel structural variant in the PAH gene by long-reads sequencing and structural modeling

BioSemAF-BiLSTM: a protein sequence feature extraction framework based on semantic and evolutionary information

Dissecting and validation the biomarker of heart failure progression in patients with atherosclerosis by single-cell sequencing, bioinformatics, and machine learning

Genome-wide evolution and function analysis of ALOG gene family in cotton

Diphenyl pyridine intervention improves S. aureus-induced pneumonia by globally regulating transcriptome profile

Integrative analysis of single-cell and microarray data reveals SPI1-centered macrophage regulatory signatures in ulcerative colitis