Frontiers in Genetics | Computational Genomics

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

2,149 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

3,234 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

3,566 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

1,702 views
1 citation

Data Report

Published on 10 Feb 2025

Exploring the taxonomical and functional profiles of marine microorganisms in Submarine Groundwater Discharge vent water from Mabini, Batangas, Philippines through metagenome-assembled genomes

in Computational Genomics

Joshua T. Veluz
Laurence Anthony N. Mallari
Paul Christian T. Gloria
Maria Auxilia T. Siringan

Frontiers in Genetics

doi 10.3389/fgene.2025.1522253

3,647 views

Original Research

Published on 06 Feb 2025

Exploring the relationship between sepsis and Golgi apparatus dysfunction: bioinformatics insights and diagnostic marker discovery

in Computational Genomics

Wanli Ma
Xinyi Liu
Ran Yu
Jiannan Song
Lina Hou
Ying Guo
Hongwei Wu
Dandan Feng
Qi Zhou
Haibo Li

Frontiers in Genetics

doi 10.3389/fgene.2025.1483493

3,341 views
1 citation

Editorial

Published on 05 Feb 2025

Editorial: Towards the embedding of artificial intelligence into synthetic organisms: engineering intelligence in microorganisms

in Computational Genomics

Martín Eduardo Gutiérrez
Rafael Lahoz-Beltrá
Alberto J. Donayre-Torres

Frontiers in Genetics

doi 10.3389/fgene.2025.1562092

1,931 views

Original Research

Published on 04 Feb 2025

A structural genomics approach to investigate Dystrophin mutations and their impact on the molecular pathways of Duchenne muscular dystrophy

in Computational Genomics

Abdelbaset Mohamed Elasbali
Farah Anjum
Osama A. AlKhamees
Waleed Abu Al-Soud
Mohd Adnan
Anas Shamsi
Md. Imtaiyaz Hassan

Frontiers in Genetics

doi 10.3389/fgene.2025.1517707

3,700 views

Original Research

Published on 29 Jan 2025

Identifying health risk determinants and molecular targets in patients with idiopathic pulmonary fibrosis via combined differential and weighted gene co-expression analysis

in Computational Genomics

Abu Tayab Moin
Md. Asad Ullah
Jannatul Ferdous Nipa
Mohammad Sheikh Farider Rahman
Afsana Emran
Md. Minhazul Islam
Swapnil Das
Tawsif Al Arian
Mohammad Mahfuz Enam Elahi
Mukta Akter

Frontiers in Genetics

doi 10.3389/fgene.2024.1496462

4,363 views

Original Research

Published on 29 Jan 2025

Quadratic descriptors and reduction methods in a two-layered model for compound inference

in Computational Genomics

Jianshen Zhu
Naveed Ahmed Azam
Shengjuan Cao
Ryota Ido
Kazuya Haraguchi
Liang Zhao
Hiroshi Nagamochi
Tatsuya Akutsu

Frontiers in Genetics

doi 10.3389/fgene.2024.1483490

1,756 views
1 citation

Original Research

Published on 29 Jan 2025

Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers

in Computational Genomics

Rodolfo Brizola Toscan
Wojciech Lesiński
Piotr Stomma
Balakrishnan Subramanian
Paweł P. Łabaj
Witold R. Rudnicki

Frontiers in Genetics

doi 10.3389/fgene.2025.1460508

2,882 views

Brief Research Report

Published on 27 Jan 2025

Characterization of novel human endogenous retrovirus structures on chromosomes 6 and 7

in Computational Genomics

Nicholas Pasternack
Ole Paulsen
Avindra Nath

Frontiers in Genetics

doi 10.3389/fgene.2025.1498978

2,819 views
1 citation

Original Research

Published on 22 Jan 2025

In silico design of an epitope-based vaccine ensemble for fasliolopsiasis

in Computational Genomics

Ruchishree Konhar
Kanhu Charan Das
Aiboklang Nongrum
Rohan Raj Samal
Shailesh Kumar Sarangi
Devendra Kumar Biswal

Frontiers in Genetics

doi 10.3389/fgene.2024.1451853

2,945 views
2 citations

Original Research

Published on 22 Jan 2025

Machine learning potential predictor of idiopathic pulmonary fibrosis

in Computational Genomics

Chenchun Ding
Quan Liao
Renjie Zuo
Shichao Zhang
Zhenzhen Guo
Junjie He
Ziwei Ye
Weibin Chen
Sunkui Ke

Frontiers in Genetics

doi 10.3389/fgene.2024.1464471

4,458 views

Original Research

Published on 15 Jan 2025

Exploring prognosis and therapeutic strategies for HBV-HCC patients based on disulfidptosis-related genes

in Computational Genomics

Chuankuo Zhang
Xing Zhang
Shengjie Dai
Wenjun Yang

Frontiers in Genetics

doi 10.3389/fgene.2024.1522484

4,064 views

Original Research

Published on 08 Jan 2025

Integration of single-cell transcriptomics and bulk transcriptomics to explore prognostic and immunotherapeutic characteristics of nucleotide metabolism in lung adenocarcinoma

in Computational Genomics

Kai Zhang
Luyao Wang
Huili Chen
Lili Deng
Mengling Hu
Ziqiang Wang
Yiluo Xie
Chaoqun Lian
Xiaojing Wang
Jing Zhang

Frontiers in Genetics

doi 10.3389/fgene.2024.1466249

3,008 views

Original Research

Published on 06 Jan 2025

S-DCNN: prediction of ATP binding residues by deep convolutional neural network based on SMOTE

in Computational Genomics

Sixi Hao
Cai-Yan Li
Xiuzhen Hu
Zhenxing Feng
Gaimei Zhang
Caiyun Yang
Huimin Hu

Frontiers in Genetics

doi 10.3389/fgene.2024.1513201

1,330 views

Original Research

Published on 06 Jan 2025

The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer

in Computational Genomics

Yao Yi
Yu Zhong
Lianhua Xie
Shuxian Lu
Yifeng Zhang

Frontiers in Genetics

doi 10.3389/fgene.2024.1505011

3,894 views
1 citation

Original Research

Published on 06 Jan 2025

BIMSSA: enhancing cancer prediction with salp swarm optimization and ensemble machine learning approaches

in Computational Genomics

Pinakshi Panda
Sukant Kishoro Bisoy
Amrutanshu Panigrahi
Abhilash Pati
Bibhuprasad Sahu
Zheshan Guo
Haipeng Liu
Prince Jain

Frontiers in Genetics

doi 10.3389/fgene.2024.1491602

3,587 views
26 citations

Original Research

Published on 06 Jan 2025

TransferBAN-Syn: a transfer learning-based algorithm for predicting synergistic drug combinations against echinococcosis

in Computational Genomics

Haitao Li
Yuanyuan Chu
Liyuan Jiang
Lei Li
GuoDong Lv
Yuansheng Liu
Chunhou Zheng
Yansen Su

Frontiers in Genetics

doi 10.3389/fgene.2024.1465368

1,853 views
2 citations

Original Research

Published on 23 Dec 2024

Integration of gene expression and DNA methylation data using MLA-GNN for liver cancer biomarker mining

in Computational Genomics

Chun-Yu Lu
Zi Liu
Muhammad Arif
Tanvir Alam
Wang-Ren Qiu

Frontiers in Genetics

doi 10.3389/fgene.2024.1513938

2,744 views
5 citations

Review

Published on 16 Dec 2024

Localization is the key to action: regulatory peculiarities of lncRNAs

in Computational Genomics

Joice de Faria Poloni
Fábio Henrique Schuster de Oliveira
Bruno César Feltes

Frontiers in Genetics

doi 10.3389/fgene.2024.1478352

2,995 views
12 citations

Data Report

Published on 16 Dec 2024

SiMul-db: a database of single and multi-target Cas9 guides for hazelnut editing

in Computational Genomics

Ciro Gianmaria Amoroso
Giuseppe Andolfo

Frontiers in Genetics

doi 10.3389/fgene.2024.1467316

1,561 views

Technology and Code

Published on 10 Dec 2024

MMPred: a tool to predict peptide mimicry events in MHC class II recognition

in Computational Genomics

Filippo Guerri
Valentin Junet
Judith Farrés
Xavier Daura

Frontiers in Genetics

doi 10.3389/fgene.2024.1500684

3,153 views
1 citation

2,653 articles

articles

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

Exploring the taxonomical and functional profiles of marine microorganisms in Submarine Groundwater Discharge vent water from Mabini, Batangas, Philippines through metagenome-assembled genomes

Exploring the relationship between sepsis and Golgi apparatus dysfunction: bioinformatics insights and diagnostic marker discovery

Editorial: Towards the embedding of artificial intelligence into synthetic organisms: engineering intelligence in microorganisms

A structural genomics approach to investigate Dystrophin mutations and their impact on the molecular pathways of Duchenne muscular dystrophy

Identifying health risk determinants and molecular targets in patients with idiopathic pulmonary fibrosis via combined differential and weighted gene co-expression analysis

Quadratic descriptors and reduction methods in a two-layered model for compound inference

Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers

Characterization of novel human endogenous retrovirus structures on chromosomes 6 and 7

In silico design of an epitope-based vaccine ensemble for fasliolopsiasis

Machine learning potential predictor of idiopathic pulmonary fibrosis

Exploring prognosis and therapeutic strategies for HBV-HCC patients based on disulfidptosis-related genes

Integration of single-cell transcriptomics and bulk transcriptomics to explore prognostic and immunotherapeutic characteristics of nucleotide metabolism in lung adenocarcinoma

S-DCNN: prediction of ATP binding residues by deep convolutional neural network based on SMOTE

The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer

BIMSSA: enhancing cancer prediction with salp swarm optimization and ensemble machine learning approaches

TransferBAN-Syn: a transfer learning-based algorithm for predicting synergistic drug combinations against echinococcosis

Integration of gene expression and DNA methylation data using MLA-GNN for liver cancer biomarker mining

Localization is the key to action: regulatory peculiarities of lncRNAs

SiMul-db: a database of single and multi-target Cas9 guides for hazelnut editing

MMPred: a tool to predict peptide mimicry events in MHC class II recognition