Frontiers in Genetics | Computational Genomics

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

1,377 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

2,233 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

2,584 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

2,386 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

2,097 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

2,271 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

2,854 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

1,820 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

2,785 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

3,337 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

10,836 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

2,966 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

1,257 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

4,535 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

1,218 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

2,417 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

2,292 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

2,316 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

3,646 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

2,318 views

Original Research

Published on 16 Oct 2024

Identification of potential therapeutic targets for systemic lupus erythematosus based on GEO database analysis and Mendelian randomization analysis

in Computational Genomics

Aishanjiang Apaer
Yanyan Shi
Alimijiang Aobulitalifu
Fujie Wen
Adalaiti Muhetaer
Nuermaimaiti Ajimu
Maierhaba Sulitan
Lei Cheng

Frontiers in Genetics

doi 10.3389/fgene.2024.1454486

8,986 views
5 citations

Original Research

Published on 02 Oct 2024

TCRcost: a deep learning model utilizing TCR 3D structure for enhanced of TCR–peptide binding

in Computational Genomics

Fan Li
Xinyang Qian
Xiaoyan Zhu
Xin Lai
Xuanping Zhang
Jiayin Wang

Frontiers in Genetics

doi 10.3389/fgene.2024.1346784

2,667 views
5 citations

Original Research

Published on 01 Oct 2024

Transparent sparse graph pathway network for analyzing the internal relationship of lung cancer

in Computational Genomics

Zhibin Jin
Yuhu Shi
Lili Zhou

Frontiers in Genetics

doi 10.3389/fgene.2024.1437174

1,596 views
1 citation

Original Research

Published on 20 Sep 2024

Genomic analysis and mechanisms exploration of a stress tolerance and high-yield pullulan producing strain

in Computational Genomics

Jing Yang
Ning Sun
Wenru Wang
Ruihua Zhang
Siqi Sun
Biqi Li
Yue Shi
Junfeng Zeng
Shulei Jia

Frontiers in Genetics

doi 10.3389/fgene.2024.1469600

2,614 views
1 citation

2,649 articles

articles

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

Identification of potential therapeutic targets for systemic lupus erythematosus based on GEO database analysis and Mendelian randomization analysis

TCRcost: a deep learning model utilizing TCR 3D structure for enhanced of TCR–peptide binding

Transparent sparse graph pathway network for analyzing the internal relationship of lung cancer

Genomic analysis and mechanisms exploration of a stress tolerance and high-yield pullulan producing strain