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A flexible R package for nonnegative matrix factorization

BMC bioinformatics, 2010-07, Vol.11 (1), p.367-367, Article 367

2010

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Controlling for background genetic effects using polygenic scores improves the power of genome-wide association studies

Scientific reports, 2021-10, Vol.11 (1), p.19571-19571, Article 19571

2021

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Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data

PLoS genetics, 2017-01, Vol.13 (1), p.e1006549-e1006549

2017

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Random-effects meta-analysis of effect sizes as a unified framework for gene set analysis

PLoS computational biology, 2022-10, Vol.18 (10), p.e1010278-e1010278

2022

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Bias and inconsistency in the estimation of tumour mutation burden

BMC cancer, 2022-08, Vol.22 (1), p.1-840, Article 840

2022

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Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization

PloS one, 2016-10, Vol.11 (10), p.e0164880-e0164880

2016

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High throughput gene expression measurement with real time PCR in a microfluidic dynamic array

PloS one, 2008-02, Vol.3 (2), p.e1662-e1662

2008

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Gene-set analysis is severely biased when applied to genome-wide methylation data

Bioinformatics, 2013-08, Vol.29 (15), p.1851-1857

2013

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Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data

PloS one, 2019-04, Vol.14 (4), p.e0215987-e0215987

2019

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Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome

Trends in genetics, 2004-10, Vol.20 (10), p.461-464

2004

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Distinctive patterns of microRNA expression associated with karyotype in acute myeloid leukaemia

PloS one, 2008-05, Vol.3 (5), p.e2141-e2141

2008

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vcfView: An Extensible Data Visualization and Quality Assurance Platform for Integrated Somatic Variant Analysis

Cancer Informatics, 2020, Vol.19, p.1176935120972377-1176935120972377

2020

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Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization

BMC bioinformatics, 2024-05, Vol.25 (1), p.179-179, Article 179

2024

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Selection Shapes Synonymous Stop Codon Use in Mammals

Journal of molecular evolution, 2020-09, Vol.88 (7), p.549-561

2020

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Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property

PloS one, 2011-09, Vol.6 (9), p.e25297-e25297

2011

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Differences in the tumor microenvironment between African-American and European-American breast cancer patients

PloS one, 2009-02, Vol.4 (2), p.e4531-e4531

2009

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Mining mammalian transcript data for functional long non-coding RNAs

PloS one, 2010-04, Vol.5 (4), p.e10316

2010

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CellMix: a comprehensive toolbox for gene expression deconvolution

Bioinformatics, 2013-09, Vol.29 (17), p.2211-2212

2013

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A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations

PLoS genetics, 2015-03, Vol.11 (3), p.e1005052-e1005052

2015

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RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

Epigenetics & chromatin, 2015-11, Vol.8 (39), p.46-46, Article 46

2015

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Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis

Epigenetics, 2017-08, Vol.12 (8), p.591-606

2017

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Heritability in the efficiency of nonsense-mediated mRNA decay in humans

PloS one, 2010-07, Vol.5 (7), p.e11657-e11657

2010

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HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC

PLoS pathogens, 2009-05, Vol.5 (5), p.e1000414-e1000414

2009

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Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system

PloS one, 2009-06, Vol.4 (6), p.e5969-e5969

2009

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The hidden geometries of the Arabidopsis thaliana epidermis

PloS one, 2012-09, Vol.7 (9), p.e43546-e43546

2012

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A flexible R package for nonnegative matrix factorization

Controlling for background genetic effects using polygenic scores improves the power of genome-wide association studies

Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data

Random-effects meta-analysis of effect sizes as a unified framework for gene set analysis

Bias and inconsistency in the estimation of tumour mutation burden

Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization

High throughput gene expression measurement with real time PCR in a microfluidic dynamic array

Gene-set analysis is severely biased when applied to genome-wide methylation data

Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data

Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome

Distinctive patterns of microRNA expression associated with karyotype in acute myeloid leukaemia

vcfView: An Extensible Data Visualization and Quality Assurance Platform for Integrated Somatic Variant Analysis

Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization

Selection Shapes Synonymous Stop Codon Use in Mammals

Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property

Differences in the tumor microenvironment between African-American and European-American breast cancer patients

Mining mammalian transcript data for functional long non-coding RNAs

CellMix: a comprehensive toolbox for gene expression deconvolution

A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis

Heritability in the efficiency of nonsense-mediated mRNA decay in humans

HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC

Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system

The hidden geometries of the Arabidopsis thaliana epidermis

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