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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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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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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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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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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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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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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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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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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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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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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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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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Deep generative neural network for accurate drug response imputation

Nature communications, 2021-03, Vol.12 (1), p.1740-16, Article 1740

2021

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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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TissGDB: tissue-specific gene database in cancer

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

2018

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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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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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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

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

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

Gene2vec: distributed representation of genes based on co-expression

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

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

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

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

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

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

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

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

Deep generative neural network for accurate drug response imputation

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

TissGDB: tissue-specific gene database in cancer

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

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

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