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Chapter and Conference Paper
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History
Intratumoral heterogeneity arises as a result of genetically distinct subclones emerging during tumor progression. These subclones are characterized by various types of somatic genomic aberrations, with single...
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Article
Open AccessStrain level microbial detection and quantification with applications to single cell metagenomics
Computational identification and quantification of distinct microbes from high throughput sequencing data is crucial for our understanding of human health. Existing methods either use accurate but computationa...
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Article
Open AccessNetwork-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer
Studies of cancer mutations have typically focused on identifying cancer driving mutations that confer growth advantage to cancer cells. However, cancer genomes accumulate a large number of passenger somatic m...
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Chapter and Conference Paper
A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer
The characterization of mutational processes in terms of their signatures of activity relies, to the most part, on the assumption that mutations in a given cancer genome are independent of one another. Recentl...
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Article
Open AccessHarnessing synthetic lethality to predict the response to cancer treatment
While synthetic lethality (SL) holds promise in develo** effective cancer therapies, SL candidates found via experimental screens often have limited translational value. Here we present a data-driven approac...
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Article
Open AccessPutative functional genes in idiopathic dilated cardiomyopathy
Idiopathic dilated cardiomyopathy (DCM) is a complex disorder with a genetic and an environmental component involving multiple genes, many of which are yet to be discovered. We integrate genetic, epigenetic, t...
