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Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties

Journal of the American Medical Informatics Association : JAMIA, 2014-10, Vol.21 (e2), p.e278-e286

2014

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Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

BMC bioinformatics, 2013-09, Vol.14 Suppl 11 (Suppl 11), p.S1-S1, Article S1

2013

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Circular RNA expression profiles and features in human tissues: a study using RNA-seq data

BMC genomics, 2017-10, Vol.18 (Suppl 6), p.680-680, Article 680

2017

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Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

Briefings in bioinformatics, 2016-07, Vol.17 (4), p.642-656

2016

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VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data

PLoS computational biology, 2014-02, Vol.10 (2), p.e1003460-e1003460

2014

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deTS: tissue-specific enrichment analysis to decode tissue specificity

Bioinformatics, 2019-10, Vol.35 (19), p.3842-3845

2019

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6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes

Bioinformatics, 2020-05, Vol.36 (10), p.3257-3259

2020

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VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data

PloS one, 2013-05, Vol.8 (5), p.e64465

2013

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Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise

Scientific reports, 2020-12, Vol.10 (1), p.22164-22164, Article 22164

2020

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Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer

BMC bioinformatics, 2022-04, Vol.23 (Suppl 3), p.153-153, Article 153

2022

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Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition

Nature communications, 2017-11, Vol.8 (1), p.1604-12, Article 1604

2017

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Gene2vec: distributed representation of genes based on co-expression

BMC genomics, 2019-02, Vol.20 (Suppl 1), p.82-82, Article 82

2019

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dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks

Bioinformatics, 2011-01, Vol.27 (1), p.95-102

2011

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Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types

Cell reports (Cambridge), 2019-01, Vol.26 (2), p.496-506.e3

2019

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Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma

PLoS computational biology, 2012-07, Vol.8 (7), p.e1002488-e1002488

2012

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Differential Expression of Viral Transcripts From Single-Cell RNA Sequencing of Moderate and Severe COVID-19 Patients and Its Implications for Case Severity

Frontiers in microbiology, 2020-10, Vol.11

2020

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NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes

Genomics, proteomics & bioinformatics, 2022-10, Vol.20 (5), p.1002-1012

2022

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scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies

Genome Biology, 2022-10, Vol.23 (1), p.220-220, Article 220

2022

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TissGDB: tissue-specific gene database in cancer

Nucleic acids research, 2018-01, Vol.46 (D1), p.D1031

2018

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A comparative study of cancer proteins in the human protein-protein interaction network

BMC genomics, 2010-12, Vol.11 Suppl 3 (Suppl 3), p.S5-S5

2010

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scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells

Genes, 2017-12, Vol.8 (12), p.368

2017

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The allergy mediator histamine confers resistance to immunotherapy in cancer patients via activation of the macrophage histamine receptor H1

Cancer cell, 2022-01, Vol.40 (1), p.36-52.e9

2022

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Explanation-Driven Deep Learning Model for Prediction of Brain Tumour Status Using MRI Image Data

Frontiers in genetics, 2022-03, Vol.13, p.822666-822666

2022

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Dimensionality Reduction and Louvain Agglomerative Hierarchical Clustering for Cluster-Specified Frequent Biomarker Discovery in Single-Cell Sequencing Data

Frontiers in genetics, 2022-02, Vol.13, p.828479-828479

2022

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Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours

Epigenetics, 2021-02, Vol.16 (2), p.162-176

2021

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Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

Circular RNA expression profiles and features in human tissues: a study using RNA-seq data

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data

deTS: tissue-specific enrichment analysis to decode tissue specificity

6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes

VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data

Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise

Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer

Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition

Gene2vec: distributed representation of genes based on co-expression

dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks

Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types

Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma

Differential Expression of Viral Transcripts From Single-Cell RNA Sequencing of Moderate and Severe COVID-19 Patients and Its Implications for Case Severity

NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes

scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies

TissGDB: tissue-specific gene database in cancer

A comparative study of cancer proteins in the human protein-protein interaction network

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells

The allergy mediator histamine confers resistance to immunotherapy in cancer patients via activation of the macrophage histamine receptor H1

Explanation-Driven Deep Learning Model for Prediction of Brain Tumour Status Using MRI Image Data

Dimensionality Reduction and Louvain Agglomerative Hierarchical Clustering for Cluster-Specified Frequent Biomarker Discovery in Single-Cell Sequencing Data

Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours

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