Frontiers in Genetics | Computational Genomics

Original Research

Published on 09 Apr 2025

A novel end-to-end learning framework for inferring lncRNA-disease associations based on convolution neural network

in Computational Genomics

Shunxian Zhou
Sisi Chen
Jinhai Le
Yangtai Xu
Lei Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1580512

1,774 views
1 citation

Original Research

Published on 04 Apr 2025

Hypergraph-based analysis of weighted gene co-expression hypernetwork

in Computational Genomics

Libing Bai
Zongjin Li
Chunyang Tang
Changxin Song
Feng Hu

Frontiers in Genetics

doi 10.3389/fgene.2025.1560841

3,459 views
4 citations

Original Research

Published on 03 Apr 2025

Role of lactylation and immune infiltration in atherosclerosis: novel insights from bioinformatics analyses

in Computational Genomics

Jintao Qian
Qing Zhou

Frontiers in Genetics

doi 10.3389/fgene.2025.1520325

4,755 views
2 citations

Original Research

Published on 01 Apr 2025

Endoplasmic reticulum stress-related prognosis signature characterizes the immune landscape and predicts the prognosis of colon adenocarcinoma

in Computational Genomics

Lichao Cao
Haoyang Dai
Shangqing Wei
Ying Ba
Fang Chen
Yingying Chen
Chendi Yu
Shenrui Zhang
Erfei Chen
Hezi Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1516232

2,770 views

Original Research

Published on 31 Mar 2025

De novo KCNK4 variant caused epilepsy with febrile seizures plus, neurodevelopmental abnormalities, and hypertrichosis

in Computational Genomics

Hong-Jun Yan
Wen-Hui Liu
Min-Xing Xu
Peng-Yu Wang
Yu-Jie Gu
Hua Li
Jing Guo
Sheng Luo

Frontiers in Genetics

doi 10.3389/fgene.2025.1499716

2,818 views
4 citations

Technology and Code

Published on 27 Mar 2025

CirclizePlus: using ggplot2 feature to write readable R code for circular visualization

in Computational Genomics

Zheyu Zhang
Tianze Cao
Yuexia Huang
Yu Xia

Frontiers in Genetics

doi 10.3389/fgene.2025.1535368

4,017 views
7 citations

Original Research

Published on 21 Mar 2025

A semi-supervised weighted SPCA- and convolution KAN-based model for drug response prediction

in Computational Genomics

Rui Miao
Bing-Jie Zhong
Xin-Yue Mei
Xin Dong
Yang-Dong Ou
Yong Liang
Hao-Yang Yu
Ying Wang
Zi-Han Dong

Frontiers in Genetics

doi 10.3389/fgene.2025.1532651

2,578 views
1 citation

Original Research

Published on 21 Mar 2025

Profiling X chromosome genes expression relevant to sex dimorphism in stroke: insights from transcriptomics landscape analysis

in Computational Genomics

Xiu-De Qin
Yue-Rong Li
Qian Cai
Jia-Ye Liu
Zhao-Hui Dang
Li-Ling Li
Jia-Wei Min
Shao-Hua Qi
Fan Bu

Frontiers in Genetics

doi 10.3389/fgene.2025.1479270

5,044 views

Original Research

Published on 21 Mar 2025

Cancer classification in high dimensional microarray gene expressions by feature selection using eagle prey optimization

in Computational Genomics

Swetha Dhamercherla
Damodar Reddy Edla
Suresh Dara

Frontiers in Genetics

doi 10.3389/fgene.2025.1528810

1,943 views
5 citations

Original Research

Published on 20 Mar 2025

MDNN-DTA: a multimodal deep neural network for drug-target affinity prediction

in Computational Genomics

Xu Gao
Mengfan Yan
Chengwei Zhang
Gang Wu
Jiandong Shang
Congxiang Zhang
Kecheng Yang

Frontiers in Genetics

doi 10.3389/fgene.2025.1527300

2,715 views
2 citations

Original Research

Published on 19 Mar 2025

Identification of key genes in periodontitis

in Computational Genomics

Xianyang Cheng
Shan Shen

Frontiers in Genetics

doi 10.3389/fgene.2025.1579848

3,062 views
5 citations

Original Research

Published on 19 Mar 2025

Mechanism of action and experimental validation of key genes common to diabetic retinopathy and coronary heart disease based on multiple bioinformatics investigations

in Computational Genomics

Fanli Jiang
Shi Yin
Xinjin Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1548147

2,160 views

Original Research

Published on 17 Mar 2025

Exploring the oncogenic role and prognostic value of CKS1B in human lung adenocarcinoma and squamous cell carcinoma

in Computational Genomics

Md. Solayman Hossain
Tariqul Islam Tusar
Nairita Ahsan Faruqui
Tanjim Ishraq Rahaman
Yasin Arafath Sharker
Shimran Saharia Santo
Abu Tayab Moin
Yusha Araf
Ibrahim Khalil Afif
Shoaib Saikat

Frontiers in Genetics

doi 10.3389/fgene.2025.1449466

2,814 views
4 citations

Technology and Code

Published on 17 Mar 2025

weIMPUTE: a user-friendly web-based genotype imputation platform

in Computational Genomics

Mingliang Li
Zhuo Li
Defu Liu
Qi Li
Xiaodong Hu
Jun Yu
Jian Lin
Chunguang Bi
Guanshi Ye
Helong Yu

Frontiers in Genetics

doi 10.3389/fgene.2025.1532464

2,557 views

Original Research

Published on 12 Mar 2025

CLMT: graph contrastive learning model for microbe-drug associations prediction with transformer

in Computational Genomics

Liqi Xiao
Junlong Wu
Liu Fan
Lei Wang
Xianyou Zhu

Frontiers in Genetics

doi 10.3389/fgene.2025.1535279

1,936 views

Original Research

Published on 12 Mar 2025

Identification and validation of key biomarkers associated with immune and oxidative stress for preeclampsia by WGCNA and machine learning

in Computational Genomics

Tiantian Yu
Guiying Wang
Xia Xu
Jianying Yan

Frontiers in Genetics

doi 10.3389/fgene.2025.1500061

4,344 views
2 citations

Editorial

Published on 05 Mar 2025

Editorial: The role of genes and network pharmacology in new drug discovery

in Computational Genomics

Jingxin Mao

Frontiers in Genetics

doi 10.3389/fgene.2025.1578094

2,566 views
3 citations

Methods

Published on 03 Mar 2025

STsisal: a reference-free deconvolution pipeline for spatial transcriptomics data

in Computational Genomics

Yinghao Fu
Leqi Tian
Weiwei Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1512435

3,083 views

Original Research

Published on 24 Feb 2025

Exploring the underlying molecular connections: a bioinformatics approach to link melanoma and Parkinson’s disease

in Computational Genomics

Limei Zhang
Dailin Li
Xu Zheng
Moli Wu
Qijun Yao
Haoran Chen
Zhiqiang Ye
Bo Yuan

Frontiers in Genetics

doi 10.3389/fgene.2025.1526018

2,781 views

Editorial

Published on 21 Feb 2025

Editorial: Integrative genetics and multi-omics of complex human disorders

in Computational Genomics

Hongsheng Gui
Christopher J. Lessard
Jinhui Liu
Miaoxin Li
Indra Adrianto

Frontiers in Genetics

doi 10.3389/fgene.2025.1574431

2,292 views

Original Research

Published on 21 Feb 2025

Comprehensive analysis of non-coding RNA-mediated endothelial cell-specific regulatory circuits in coronary artery disease risk

in Computational Genomics

Boshui Huang
Zhijie Lai
Xiaoyu Wang
Qinhao Zhang
Tingting Hu
Fulong Yu
Shuxian Zhou
Yan Zhang
Juan Meng

Frontiers in Genetics

doi 10.3389/fgene.2025.1559798

2,088 views
1 citation

Original Research

Published on 20 Feb 2025

EDN1 and NTF3 in keloid pathogenesis: computational and experimental evidence as novel diagnostic biomarkers for fibrosis and inflammation

in Computational Genomics

Hui Gong
Jing Liu
Nanji Chen
Hengguang Zhao
Bailin He
Hongpei Zhang
Wenping Wang
Yi Tian

Frontiers in Genetics

doi 10.3389/fgene.2025.1516451

3,148 views
2 citations

Methods

Published on 17 Feb 2025

WCSGNet: a graph neural network approach using weighted cell-specific networks for cell-type annotation in scRNA-seq

in Computational Genomics

Yi-Ran Wang
Pu-Feng Du

Frontiers in Genetics

doi 10.3389/fgene.2025.1553352

3,465 views
2 citations

Original Research

Published on 11 Feb 2025

Dual graph-embedded fusion network for predicting potential microbe-disease associations with sequence learning

in Computational Genomics

Junlong Wu
Liqi Xiao
Liu Fan
Lei Wang
Xianyou Zhu

Frontiers in Genetics

doi 10.3389/fgene.2025.1511521

1,643 views
1 citation

2,649 articles

articles

A novel end-to-end learning framework for inferring lncRNA-disease associations based on convolution neural network

Hypergraph-based analysis of weighted gene co-expression hypernetwork

Role of lactylation and immune infiltration in atherosclerosis: novel insights from bioinformatics analyses

Endoplasmic reticulum stress-related prognosis signature characterizes the immune landscape and predicts the prognosis of colon adenocarcinoma

De novo KCNK4 variant caused epilepsy with febrile seizures plus, neurodevelopmental abnormalities, and hypertrichosis

CirclizePlus: using ggplot2 feature to write readable R code for circular visualization

A semi-supervised weighted SPCA- and convolution KAN-based model for drug response prediction

Profiling X chromosome genes expression relevant to sex dimorphism in stroke: insights from transcriptomics landscape analysis

Cancer classification in high dimensional microarray gene expressions by feature selection using eagle prey optimization

MDNN-DTA: a multimodal deep neural network for drug-target affinity prediction

Identification of key genes in periodontitis

Mechanism of action and experimental validation of key genes common to diabetic retinopathy and coronary heart disease based on multiple bioinformatics investigations

Exploring the oncogenic role and prognostic value of CKS1B in human lung adenocarcinoma and squamous cell carcinoma

weIMPUTE: a user-friendly web-based genotype imputation platform

CLMT: graph contrastive learning model for microbe-drug associations prediction with transformer

Identification and validation of key biomarkers associated with immune and oxidative stress for preeclampsia by WGCNA and machine learning

Editorial: The role of genes and network pharmacology in new drug discovery

STsisal: a reference-free deconvolution pipeline for spatial transcriptomics data

Exploring the underlying molecular connections: a bioinformatics approach to link melanoma and Parkinson’s disease

Editorial: Integrative genetics and multi-omics of complex human disorders

Comprehensive analysis of non-coding RNA-mediated endothelial cell-specific regulatory circuits in coronary artery disease risk

EDN1 and NTF3 in keloid pathogenesis: computational and experimental evidence as novel diagnostic biomarkers for fibrosis and inflammation

WCSGNet: a graph neural network approach using weighted cell-specific networks for cell-type annotation in scRNA-seq

Dual graph-embedded fusion network for predicting potential microbe-disease associations with sequence learning