Frontiers in Genetics | Computational Genomics

Original Research

Published on 18 Sep 2023

ITRPCA: a new model for computational drug repositioning based on improved tensor robust principal component analysis

in Computational Genomics

Mengyun Yang
Bin Yang
Guihua Duan
Jianxin Wang

Frontiers in Genetics

doi 10.3389/fgene.2023.1271311

2,683 views
5 citations

Technology and Code

Published on 15 Sep 2023

ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization

in Computational Genomics

Xiao Liang
Jingyi Zhang
Yoonjin Kim
Josh Ho
Kevin Liu
Ishi Keenum
Suraj Gupta
Benjamin Davis
Shannon L. Hepp
Liqing Zhang

Frontiers in Genetics

doi 10.3389/fgene.2023.1219297

10,563 views
3 citations

Original Research

Published on 13 Sep 2023

Machine learning and bioinformatics analysis to identify autophagy-related biomarkers in peripheral blood for rheumatoid arthritis

in Computational Genomics

Guoqi Dong
Hui Gao
Yingqi Chen
Huayuan Yang

Frontiers in Genetics

doi 10.3389/fgene.2023.1238407

5,094 views
10 citations

Original Research

Published on 08 Sep 2023

Identification and validation of disulfidptosis-associated molecular clusters in non-alcoholic fatty liver disease

in Computational Genomics

Xiaoxiao Yu
Zihao Guo
Zhihao Fang
Kai Yang
Changxu Liu
Zhichao Dong
Chang Liu

Frontiers in Genetics

doi 10.3389/fgene.2023.1251999

5,594 views
7 citations

Original Research

Published on 08 Sep 2023

Comprehensive analysis of mitophagy-related genes in diagnosis and heterogeneous endothelial cells in chronic rhinosinusitis: based on bulk and single-cell RNA sequencing data

in Computational Genomics

Shican Zhou
Kai Fan
Ju Lai
Shiwang Tan
Zimu Zhang
Jingwen Li
Xiayue Xu
Chunyan Yao
BoJin Long
Chuanliang Zhao

Frontiers in Genetics

doi 10.3389/fgene.2023.1228028

5,617 views
5 citations

Editorial

Published on 08 Sep 2023

Editorial: Predicting high-risk individuals for common diseases using multi-omics and epidemiological data, volume II

in Computational Genomics

Werner P. Veldsman
Xin Maizie Zhou
YuanWei Zhang
Bailiang Li
Lu Zhang

Frontiers in Genetics

doi 10.3389/fgene.2023.1280648

1,636 views

Original Research

Published on 07 Sep 2023

MBMethPred: a computational framework for the accurate classification of childhood medulloblastoma subgroups using data integration and AI-based approaches

in Computational Genomics

Edris Sharif Rahmani
Ankita Lawarde
Prakash Lingasamy
Sergio Vela Moreno
Andres Salumets
Vijayachitra Modhukur

Frontiers in Genetics

doi 10.3389/fgene.2023.1233657

7,137 views
12 citations

Methods

Published on 06 Sep 2023

Intra-FCY1: a novel system to identify mutations that cause protein misfolding

in Computational Genomics

N. Quan
Y. Eguchi
K. Geiler-Samerotte

Frontiers in Genetics

doi 10.3389/fgene.2023.1198203

4,159 views
3 citations

Original Research

Published on 05 Sep 2023

A novel marker integrating multiple genetic alterations better predicts platinum sensitivity in ovarian cancer than HRD score

in Computational Genomics

Fan Yang
Wei Wei
Ganghua Li
Qiongyu Lan
Xiwei Liu
Lin Gao
Chao Zhang
Jiangtao Fan
Jundong Li

Frontiers in Genetics

doi 10.3389/fgene.2023.1240068

3,339 views
2 citations

Correction

Published on 05 Sep 2023

Corrigendum: A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration

in Computational Genomics

Wenhao Kuang
Cong Jiang
Cheng Yu
Jinwei Hu
Yang Duan
Zhong Chen

Frontiers in Genetics

doi 10.3389/fgene.2023.1236744

1,996 views
1 citation

Original Research

Published on 31 Aug 2023

Gene network inference from single-cell omics data and domain knowledge for constructing COVID-19-specific ICAM1-associated pathways

in Computational Genomics

Mitsuhiro Odaka
Morgan Magnin
Katsumi Inoue

Frontiers in Genetics

doi 10.3389/fgene.2023.1250545

4,030 views
1 citation

Brief Research Report

Published on 31 Aug 2023

Prediction of distinct populations of innate lymphoid cells by transcriptional profiles

in Computational Genomics

Haiyao Dong
Zhenguang Du
Haoming Ma
Zhicheng Zhou
Haitao Yang
Zhenyuan Wang

Frontiers in Genetics

doi 10.3389/fgene.2023.1227452

2,177 views

Original Research

Published on 29 Aug 2023

A meta-analysis of microarray datasets to identify biological regulatory networks in Alzheimer’s disease

in Computational Genomics

Kimia Sadat Hashemi
Mohadese Koohi Aliabadi
Arian Mehrara
Elham Talebi
Ali Akbar Hemmati
Radin Dabbagh Rezaeiye
Mohammad Javad Ghanbary
Maryam Motealleh
Behnaz Dayeri
Shayan Khalili Alashti

Frontiers in Genetics

doi 10.3389/fgene.2023.1225196

6,652 views
9 citations

Technology and Code

Published on 24 Aug 2023

EasySSR: a user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison

in Computational Genomics

Sandy Ingrid Aguiar Alves
Victor Benedito Costa Ferreira
Carlos Willian Dias Dantas
Artur Luiz da Costa da Silva
Rommel Thiago Jucá Ramos

Frontiers in Genetics

doi 10.3389/fgene.2023.1228552

6,124 views
7 citations

Original Research

Published on 24 Aug 2023

An efficient convolutional neural network-based diagnosis system for citrus fruit diseases

in Computational Genomics

Zhangcai Huang
Xiaoxiao Jiang
Shaodong Huang
Sheng Qin
Su Yang

Frontiers in Genetics

doi 10.3389/fgene.2023.1253934

4,053 views
13 citations

Original Research

Published on 23 Aug 2023

PSF toolkit: an R package for pathway curation and topology-aware analysis

in Computational Genomics

Siras Hakobyan
Ani Stepanyan
Lilit Nersisyan
Hans Binder
Arsen Arakelyan

Frontiers in Genetics

doi 10.3389/fgene.2023.1264656

5,735 views
6 citations

Original Research

Published on 21 Aug 2023

GeNetOntology: identifying affected gene ontology terms via grouping, scoring, and modeling of gene expression data utilizing biological knowledge-based machine learning

in Computational Genomics

Nur Sebnem Ersoz
Burcu Bakir-Gungor
Malik Yousef

Frontiers in Genetics

doi 10.3389/fgene.2023.1139082

6,977 views
20 citations

Brief Research Report

Published on 21 Aug 2023

Comparative evaluation and analysis of DNA N4-methylcytosine methylation sites using deep learning

in Computational Genomics

Hong Ju
Jie Bai
Jing Jiang
Yusheng Che
Xin Chen

Frontiers in Genetics

doi 10.3389/fgene.2023.1254827

2,636 views
3 citations

Original Research

Published on 21 Aug 2023

Identification and verification of novel immune-related ferroptosis signature with excellent prognostic predictive and clinical guidance value in hepatocellular carcinoma

in Computational Genomics

Wenxiu Jiang
Lili Wang
Yajuan Zhang
Hongliang Li

Frontiers in Genetics

doi 10.3389/fgene.2023.1112744

2,545 views

Technology and Code

Published on 17 Aug 2023

Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction

in Computational Genomics

Alexander Freudenberg
Jeremie Vandenplas
Martin Schlather
Torsten Pook
Ross Evans
Jan Ten Napel

Frontiers in Genetics

doi 10.3389/fgene.2023.1220408

3,116 views
2 citations

Original Research

Published on 16 Aug 2023

Identification of shared biological features in four different lung cell lines infected with SARS-CoV-2 virus through RNA-seq analysis

in Computational Genomics

Xiaoxi Zhang
Seungjun Ahn
Peihua Qiu
Somnath Datta

Frontiers in Genetics

doi 10.3389/fgene.2023.1235927

3,005 views
1 citation

Methods

Published on 10 Aug 2023

Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs

in Computational Genomics

Lisa Fiedler
Martin Middendorf
Matthias Bernt

Frontiers in Genetics

doi 10.3389/fgene.2023.1250907

6,330 views
6 citations

Perspective

Published on 10 Aug 2023

Unraveling patient heterogeneity in complex diseases through individualized co-expression networks: a perspective

in Computational Genomics

Verónica Latapiat
Mauricio Saez
Inti Pedroso
Alberto J. M. Martin

Frontiers in Genetics

doi 10.3389/fgene.2023.1209416

5,128 views
9 citations

Original Research

Published on 09 Aug 2023

Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh

in Computational Genomics

Mohammad Tanbir Habib
Saikt Rahman
Mokibul Hassan Afrad
Arif Mahmud Howlader
Manjur Hossain Khan
Farhana Khanam
Ahmed Nawsher Alam
Emran Kabir Chowdhury
Ziaur Rahman
Mustafizur Rahman

Frontiers in Genetics

doi 10.3389/fgene.2023.1220906

5,294 views
3 citations

2,650 articles

articles

ITRPCA: a new model for computational drug repositioning based on improved tensor robust principal component analysis

ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization

Machine learning and bioinformatics analysis to identify autophagy-related biomarkers in peripheral blood for rheumatoid arthritis

Identification and validation of disulfidptosis-associated molecular clusters in non-alcoholic fatty liver disease

Comprehensive analysis of mitophagy-related genes in diagnosis and heterogeneous endothelial cells in chronic rhinosinusitis: based on bulk and single-cell RNA sequencing data

Editorial: Predicting high-risk individuals for common diseases using multi-omics and epidemiological data, volume II

MBMethPred: a computational framework for the accurate classification of childhood medulloblastoma subgroups using data integration and AI-based approaches

Intra-FCY1: a novel system to identify mutations that cause protein misfolding

A novel marker integrating multiple genetic alterations better predicts platinum sensitivity in ovarian cancer than HRD score

Corrigendum: A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration

Gene network inference from single-cell omics data and domain knowledge for constructing COVID-19-specific ICAM1-associated pathways

Prediction of distinct populations of innate lymphoid cells by transcriptional profiles

A meta-analysis of microarray datasets to identify biological regulatory networks in Alzheimer’s disease

EasySSR: a user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison

An efficient convolutional neural network-based diagnosis system for citrus fruit diseases

PSF toolkit: an R package for pathway curation and topology-aware analysis

GeNetOntology: identifying affected gene ontology terms via grouping, scoring, and modeling of gene expression data utilizing biological knowledge-based machine learning

Comparative evaluation and analysis of DNA N4-methylcytosine methylation sites using deep learning

Identification and verification of novel immune-related ferroptosis signature with excellent prognostic predictive and clinical guidance value in hepatocellular carcinoma

Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction

Identification of shared biological features in four different lung cell lines infected with SARS-CoV-2 virus through RNA-seq analysis

Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs

Unraveling patient heterogeneity in complex diseases through individualized co-expression networks: a perspective

Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh