Frontiers in Genetics | Computational Genomics

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

552 views

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

830 views

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

671 views

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

646 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

1,035 views

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

897 views

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

751 views

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

1,127 views

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

473 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

524 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

553 views
1 citation

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

748 views

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

777 views
1 citation

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

678 views

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

835 views

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

852 views

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Articles

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

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