Frontiers in Genetics | Computational Genomics

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

5,200 views
4 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

3,969 views
2 citations

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

2,922 views

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

2,042 views

Original Research

Published on 30 May 2025

Identification of biomarkers for the diagnosis of chronic kidney disease (CKD) with dilated cardiomyopathy (DCM) by bioinformatics analysis and machine learning

in Computational Genomics

Yuhang Liu
Yong Wang
Wenyang Nie
Zhen Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1562891

4,076 views
1 citation

Editorial

Published on 29 May 2025

Editorial: Computational genomic and precision medicine

in Computational Genomics

Zeeshan Ahmed
Ramkumar Thirunavukarasu
Atlas Khan

Frontiers in Genetics

doi 10.3389/fgene.2025.1631668

2,412 views

Original Research

Published on 26 May 2025

Prediction of mild cognitive impairment using blood multi-omics data

in Computational Genomics

Daniel Frank Zhang
Cigdem Sevim Bayrak
Qi Zeng
Minghui Wang
Bin Zhang

Frontiers in Genetics

doi 10.3389/fgene.2025.1552063

2,792 views

Methods

Published on 22 May 2025

stGuide advances label transfer in spatial transcriptomics through attention-based supervised graph representation learning

in Computational Genomics

Yupeng Xu
Hao Dai
Jinwang Feng
Keren Xu
Qiu Wang
Pingting Gao
Chunman Zuo

Frontiers in Genetics

doi 10.3389/fgene.2025.1566675

2,831 views
1 citation

Opinion

Published on 16 May 2025

From bites to bytes: understanding how and why individual malaria risk varies using artificial intelligence and causal inference

in Computational Genomics

Adèle Helena Ribeiro
Júlia M. P. Soler
Rodrigo M. Corder
Marcelo U. Ferreira
Dominik Heider

Frontiers in Genetics

doi 10.3389/fgene.2025.1599826

3,032 views
1 citation

Original Research

Published on 09 May 2025

Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly

in Computational Genomics

Andrey Eremin
Alexander Sergeev
Arthur Kopylov
Vladimir Rodin
Daniil Malyshev
Tatiana Panova
Igor Polyakov
Maria Zvereva

Frontiers in Genetics

doi 10.3389/fgene.2025.1574332

2,297 views
1 citation

Technology and Code

Published on 02 May 2025

TCGADownloadHelper: simplifying TCGA data extraction and preprocessing

in Computational Genomics

Alexandra Anke Baumann
Olaf Wolkenhauer
Markus Wolfien

Frontiers in Genetics

doi 10.3389/fgene.2025.1569290

5,885 views
1 citation

Original Research

Published on 30 Apr 2025

Impact of nonsynonymous single nucleotide polymorphisms in PROCR gene on protein stability and thrombotic risk: a molecular dynamic approach

in Computational Genomics

Hytham Ahmed Abuagla
Khalid Mohamed Adam
Mohamed E. Elangeeb
Elsadig Mohamed Ahmed
Elshazali W. Ali
Ali M. Edris
Abubakr Ali Elamin MohamedAhmed
Elmoiz Idris Eltieb
Tarig Babikir Algak Khalid
Bahaeldin K. Elamin

Frontiers in Genetics

doi 10.3389/fgene.2025.1580993

2,239 views

Original Research

Published on 30 Apr 2025

High-precision lung cancer subtype diagnosis on imbalanced exosomal data via Exo-LCClassifier

in Computational Genomics

Siyu Zhan
Hao Yu
Shuang Liu
Ke Qin
Lu Guo

Frontiers in Genetics

doi 10.3389/fgene.2025.1583081

2,175 views
1 citation

Original Research

Published on 29 Apr 2025

Constructing ancestral recombination graphs through reinforcement learning

in Computational Genomics

Mélanie Raymond
Marie-Hélène Descary
Cédric Beaulac
Fabrice Larribe

Frontiers in Genetics

doi 10.3389/fgene.2025.1569358

2,651 views

Original Research

Published on 29 Apr 2025

The identification of a blood circular RNA signature that differentiates Chikungunya virus infection

in Computational Genomics

Xue Bai
Hanlin Yan
Guoxia Wen
Shaoxun Yuan
Wanjun Gu

Frontiers in Genetics

doi 10.3389/fgene.2025.1602177

2,751 views

Original Research

Published on 29 Apr 2025

Potential common mechanisms between primary Sjögren’s syndrome and Hashimoto’s thyroiditis: a public databases-based study

in Computational Genomics

Yanjun Lin
Shupin Tang
Yan Lin
Rihui Wang
Yifeng Xing
Zonghe Xu
Yan Li
Qingxia Fang
Wenwei Wei
Dong Wu

Frontiers in Genetics

doi 10.3389/fgene.2025.1520332

3,498 views
1 citation

Original Research

Published on 28 Apr 2025

Shared genetic features inference among hypoxia-ischemia diseases in the presence of heterogenous omics data based on a novel risk assessment method

in Computational Genomics

Yifan Zhang
Jianfeng Liu
Zhuoma Basang
Qianxun Yang
Hongce Chen
Shuo Chen
Shaogang Li
Changgui Lei
Mingyan Fang
Huanhuan Liu

Frontiers in Genetics

doi 10.3389/fgene.2025.1587854

4,325 views
2 citations

Original Research

Published on 28 Apr 2025

Single-cell transcriptomic construction of fibroblast score for analysis of immune infiltration in primary and metastatic ovarian cancer

in Computational Genomics

Qian Guo
Hongmei Ding
Qinlin Zheng

Frontiers in Genetics

doi 10.3389/fgene.2025.1549541

2,288 views

Original Research

Published on 28 Apr 2025

Exploring WNT pathway dysregulation in serrated colorectal cancer for improved diagnostic and therapeutic strategies

in Computational Genomics

Fengzhi Zhu
Helen Hoi Ning Yan
Yin Tong
Yueliang Zhao

Frontiers in Genetics

doi 10.3389/fgene.2025.1586867

2,479 views
1 citation

Original Research

Published on 24 Apr 2025

Key gene screening and diagnostic model establishment for acute type a aortic dissection

in Computational Genomics

Yue Pan
Zhiming Yu
Xiaoyu Qian
Xuesong Zhang
Qun Xue
Weizhang Xiao

Frontiers in Genetics

doi 10.3389/fgene.2025.1586880

3,640 views

Original Research

Published on 24 Apr 2025

Integration of bulk RNA-seq and scRNA-seq reveals transcriptomic signatures associated with deep vein thrombosis

in Computational Genomics

Bao-ze Pan
Ming-jun Jiang
Li-ming Deng
Jie Chen
Xian-peng Dai
Zi-xuan Wu
Zhi-he Deng
Dong-yang Luo
Yang-yi-jing Wang
Dan Ning

Frontiers in Genetics

doi 10.3389/fgene.2025.1551879

4,309 views
1 citation

Methods

Published on 24 Apr 2025

MSI expresso: a software for determining MSI status and detecting MSI-related transcription events from RNA sequencing data

in Computational Genomics

Emmanuel Tubacher
Alexandre How-Kit
Mourad Sahbatou
Alex Duval
Victor Renault
Jean-François Deleuze

Frontiers in Genetics

doi 10.3389/fgene.2025.1523278

3,094 views

Original Research

Published on 16 Apr 2025

The potential crosstalk genes and molecular mechanisms between systemic lupus erythematosus and periodontitis

in Computational Genomics

Kai Zhao
Xiaolong Li
Qingmiao Zhu
Mengyu Zhu
Jinge Huang
Ting Zhao

Frontiers in Genetics

doi 10.3389/fgene.2025.1527713

3,445 views
1 citation

Original Research

Published on 15 Apr 2025

Association prediction of lncRNAs and diseases using multiview graph convolution neural network

in Computational Genomics

Wei Zhang
Yifu Zeng
Xiaowen Xiang
Bihai Zhao
Sai Hu
Limiao Li
Xiaoyu Zhu
Lei Wang

Frontiers in Genetics

doi 10.3389/fgene.2025.1568270

2,656 views
1 citation

2,653 articles

articles

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

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

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

Identification of biomarkers for the diagnosis of chronic kidney disease (CKD) with dilated cardiomyopathy (DCM) by bioinformatics analysis and machine learning

Editorial: Computational genomic and precision medicine

Prediction of mild cognitive impairment using blood multi-omics data

stGuide advances label transfer in spatial transcriptomics through attention-based supervised graph representation learning

From bites to bytes: understanding how and why individual malaria risk varies using artificial intelligence and causal inference

Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly

TCGADownloadHelper: simplifying TCGA data extraction and preprocessing

Impact of nonsynonymous single nucleotide polymorphisms in PROCR gene on protein stability and thrombotic risk: a molecular dynamic approach

High-precision lung cancer subtype diagnosis on imbalanced exosomal data via Exo-LCClassifier

Constructing ancestral recombination graphs through reinforcement learning

The identification of a blood circular RNA signature that differentiates Chikungunya virus infection

Potential common mechanisms between primary Sjögren’s syndrome and Hashimoto’s thyroiditis: a public databases-based study

Shared genetic features inference among hypoxia-ischemia diseases in the presence of heterogenous omics data based on a novel risk assessment method

Single-cell transcriptomic construction of fibroblast score for analysis of immune infiltration in primary and metastatic ovarian cancer

Exploring WNT pathway dysregulation in serrated colorectal cancer for improved diagnostic and therapeutic strategies

Key gene screening and diagnostic model establishment for acute type a aortic dissection

Integration of bulk RNA-seq and scRNA-seq reveals transcriptomic signatures associated with deep vein thrombosis

MSI expresso: a software for determining MSI status and detecting MSI-related transcription events from RNA sequencing data

The potential crosstalk genes and molecular mechanisms between systemic lupus erythematosus and periodontitis

Association prediction of lncRNAs and diseases using multiview graph convolution neural network