Frontiers in Genetics | Computational Genomics

Original Research

Published on 10 Dec 2024

DMOIT: denoised multi-omics integration approach based on transformer multi-head self-attention mechanism

in Computational Genomics

Zhe Liu
Taesung Park

Frontiers in Genetics

doi 10.3389/fgene.2024.1488683

3,527 views
12 citations

Original Research

Published on 09 Dec 2024

AnchorFCI: harnessing genetic anchors for enhanced causal discovery of cardiometabolic disease pathways

in Computational Genomics

Adèle H. Ribeiro
Milena Crnkovic
Jaqueline Lopes Pereira
Regina Mara Fisberg
Flavia Mori Sarti
Marcelo Macedo Rogero
Dominik Heider
Andressa Cerqueira

Frontiers in Genetics

doi 10.3389/fgene.2024.1436947

2,293 views
2 citations

Original Research

Published on 04 Dec 2024

Systematic pharmacology-based strategy to investigate the mechanism of beta-sitosterol for the treatment of rheumarthritis

in Computational Genomics

Xiaodong Wang
Jingxin Mao

Frontiers in Genetics

doi 10.3389/fgene.2024.1507606

3,808 views
5 citations

Original Research

Published on 04 Dec 2024

Gene expression ranking change based single sample pre-disease state detection

in Computational Genomics

Zhenshen Bao
Xianbin Li
Peng Xu
Xiangzhen Zan

Frontiers in Genetics

doi 10.3389/fgene.2024.1509769

1,559 views

Methods

Published on 04 Dec 2024

OCRClassifier: integrating statistical control chart into machine learning framework for better detecting open chromatin regions

in Computational Genomics

Xin Lai
Min Liu
Yuqian Liu
Xiaoyan Zhu
Jiayin Wang

Frontiers in Genetics

doi 10.3389/fgene.2024.1400228

1,414 views

Original Research

Published on 29 Nov 2024

Correlating gene expression levels with transcription factor binding sites facilitates identification of key transcription factors from transcriptome data

in Computational Genomics

Tinghua Huang
Siqi Niu
Fanghong Zhang
Binyu Wang
Jianwu Wang
Guoping Liu
Min Yao

Frontiers in Genetics

doi 10.3389/fgene.2024.1511456

2,301 views
4 citations

Original Research

Published on 25 Nov 2024

CAMDA 2023: Finding patterns in urban microbiomes

in Computational Genomics

Haydeé Contreras-Peruyero
Imanol Nuñez
Mirna Vazquez-Rosas-Landa
Daniel Santana-Quinteros
Antón Pashkov
Mario E. Carranza-Barragán
Rafael Perez-Estrada
Shaday Guerrero-Flores
Eugenio Balanzario
Víctor Muñiz Sánchez

Frontiers in Genetics

doi 10.3389/fgene.2024.1449461

2,649 views
2 citations

Original Research

Published on 22 Nov 2024

GCRTcall: a transformer based basecaller for nanopore RNA sequencing enhanced by gated convolution and relative position embedding via joint loss training

in Computational Genomics

Qingwen Li
Chen Sun
Daqian Wang
Jizhong Lou

Frontiers in Genetics

doi 10.3389/fgene.2024.1443532

2,435 views
6 citations

Original Research

Published on 22 Nov 2024

asmbPLS: biomarker identification and patient survival prediction with multi-omics data

in Computational Genomics

Runzhi Zhang
Susmita Datta

Frontiers in Genetics

doi 10.3389/fgene.2024.1444054

2,183 views
2 citations

Original Research

Published on 20 Nov 2024

Genome-wide identification and expression analysis of phosphate-sensing SPX proteins in oats

in Computational Genomics

Yinke Du
Jie Gong
Ziyi Dou
Wei Zheng
Renwei Sun
Shiqing Gao

Frontiers in Genetics

doi 10.3389/fgene.2024.1469704

2,334 views
1 citation

Technology and Code

Published on 20 Nov 2024

DElite: a tool for integrated differential expression analysis

in Computational Genomics

Davide Baldazzi
Michele Doni
Beatrice Valenti
Maria Elena Ciuffetti
Stefano Pezzella
Roberta Maestro

Frontiers in Genetics

doi 10.3389/fgene.2024.1440994

2,913 views
1 citation

Original Research

Published on 15 Nov 2024

Subtyping colorectal cancer based on septic shock-associated genes: prognosis and immune characteristics

in Computational Genomics

Jinkai Zhao
Jiaan Chen
Jiancheng Zhang
Xuming Pan
Buhai Xu
Jinli Miao
Wenmin Wang
Guangjun Jin

Frontiers in Genetics

doi 10.3389/fgene.2024.1468424

1,877 views
1 citation

Original Research

Published on 14 Nov 2024

Multi-fusion strategy network-guided cancer subtypes discovering based on multi-omics data

in Computational Genomics

Jian Liu
Xinzheng Xue
Pengbo Wen
Qian Song
Jun Yao
Shuguang Ge

Frontiers in Genetics

doi 10.3389/fgene.2024.1466825

2,885 views
3 citations

Original Research

Published on 13 Nov 2024

Comprehensive analysis of molecular mechanisms underlying kidney stones: gene expression profiles and potential diagnostic markers

in Computational Genomics

Kaisaier Aji
Aierken Aikebaier
Asimujiang Abula
Guang Lu Song

Frontiers in Genetics

doi 10.3389/fgene.2024.1440774

3,396 views
3 citations

Review

Published on 13 Nov 2024

What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools

in Computational Genomics

Sandy Ingrid Aguiar Alves
Carlos Willian Dias Dantas
Daralyns Borges Macedo
Rommel Thiago Jucá Ramos

Frontiers in Genetics

doi 10.3389/fgene.2024.1474611

11,336 views
10 citations

Original Research

Published on 13 Nov 2024

Integrative analysis of single-cell transcriptomic and multilayer signaling networks in glioma reveal tumor progression stage

in Computational Genomics

Fereshteh Fallah Atanaki
Leila Mirsadeghi
Mohsen Riahi Manesh
Kaveh Kavousi

Frontiers in Genetics

doi 10.3389/fgene.2024.1446903

3,082 views
2 citations

Original Research

Published on 12 Nov 2024

PSATF-6mA: an integrated learning fusion feature-encoded DNA-6 mA methylcytosine modification site recognition model based on attentional mechanisms

in Computational Genomics

Yanmei Kang
Hongyuan Wang
Yubo Qin
Guanlin Liu
Yi Yu
Yongjian Zhang

Frontiers in Genetics

doi 10.3389/fgene.2024.1498884

1,312 views

Original Research

Published on 11 Nov 2024

AI-enabled pipeline for virus detection, validation, and SNP discovery from next-generation sequencing data

in Computational Genomics

Abozar Ghorbani
Mahsa Rostami
Pietro Hiram Guzzi

Frontiers in Genetics

doi 10.3389/fgene.2024.1492752

4,628 views
7 citations

Editorial

Published on 05 Nov 2024

Editorial: Emerging talents in computational genomics

in Computational Genomics

Junichi Iwata
Kenta Nakai

Frontiers in Genetics

doi 10.3389/fgene.2024.1512594

1,233 views

Original Research

Published on 05 Nov 2024

Genome-wide comparative analysis of photosynthetic enzymatic genes provides novel insights into foxtail millet and other cereals

in Computational Genomics

Arpit Raturi
Shivam Shekhar
Ratnesh Kumar Jha
Divya Chauhan
Saurabh Pandey
Sarita Kumari
Ashutosh Singh

Frontiers in Genetics

doi 10.3389/fgene.2024.1449113

2,503 views
2 citations

Original Research

Published on 29 Oct 2024

Number of human protein interactions correlates with structural, but not regulatory conservation of the respective genes

in Computational Genomics

Rijalda Mekic
Marianna A. Zolotovskaia
Maksim Sorokin
Tharaa Mohammad
Nina Shaban
Ivan Musatov
Victor Tkachev
Alexander Modestov
Alexander Simonov
Denis Kuzmin

Frontiers in Genetics

doi 10.3389/fgene.2024.1472638

2,385 views
3 citations

Original Research

Published on 28 Oct 2024

TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering

in Computational Genomics

Meryem Banu Cavlak
Gagandeep Singh
Mohammed Alser
Can Firtina
Joël Lindegger
Mohammad Sadrosadati
Nika Mansouri Ghiasi
Can Alkan
Onur Mutlu

Frontiers in Genetics

doi 10.3389/fgene.2024.1429306

2,383 views
6 citations

Methods

Published on 25 Oct 2024

GTasm: a genome assembly method using graph transformers and HiFi reads

in Computational Genomics

Junwei Luo
Ziheng Zhang
Xinliang Ma
Chaokun Yan
Huimin Luo

Frontiers in Genetics

doi 10.3389/fgene.2024.1495657

3,769 views
1 citation

Original Research

Published on 22 Oct 2024

Dinucleotide composition representation -based deep learning to predict scoliosis-associated Fibrillin-1 genotypes

in Computational Genomics

Sen Zhang
Li-Na Dai
Qi Yin
Xiao-Ping Kang
Dan-Dan Zeng
Tao Jiang
Guang-Yu Zhao
Xiao-He Li
Jing Li

Frontiers in Genetics

doi 10.3389/fgene.2024.1492226

2,365 views

2,653 articles

articles

DMOIT: denoised multi-omics integration approach based on transformer multi-head self-attention mechanism

AnchorFCI: harnessing genetic anchors for enhanced causal discovery of cardiometabolic disease pathways

Systematic pharmacology-based strategy to investigate the mechanism of beta-sitosterol for the treatment of rheumarthritis

Gene expression ranking change based single sample pre-disease state detection

OCRClassifier: integrating statistical control chart into machine learning framework for better detecting open chromatin regions

Correlating gene expression levels with transcription factor binding sites facilitates identification of key transcription factors from transcriptome data

CAMDA 2023: Finding patterns in urban microbiomes

GCRTcall: a transformer based basecaller for nanopore RNA sequencing enhanced by gated convolution and relative position embedding via joint loss training

asmbPLS: biomarker identification and patient survival prediction with multi-omics data

Genome-wide identification and expression analysis of phosphate-sensing SPX proteins in oats

DElite: a tool for integrated differential expression analysis

Subtyping colorectal cancer based on septic shock-associated genes: prognosis and immune characteristics

Multi-fusion strategy network-guided cancer subtypes discovering based on multi-omics data

Comprehensive analysis of molecular mechanisms underlying kidney stones: gene expression profiles and potential diagnostic markers

What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools

Integrative analysis of single-cell transcriptomic and multilayer signaling networks in glioma reveal tumor progression stage

PSATF-6mA: an integrated learning fusion feature-encoded DNA-6 mA methylcytosine modification site recognition model based on attentional mechanisms

AI-enabled pipeline for virus detection, validation, and SNP discovery from next-generation sequencing data

Editorial: Emerging talents in computational genomics

Genome-wide comparative analysis of photosynthetic enzymatic genes provides novel insights into foxtail millet and other cereals

Number of human protein interactions correlates with structural, but not regulatory conservation of the respective genes

TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering

GTasm: a genome assembly method using graph transformers and HiFi reads

Dinucleotide composition representation -based deep learning to predict scoliosis-associated Fibrillin-1 genotypes