Gillian Chu

Princeton University | PU

Phylogenetic placement is the problem of placing “query” sequences into an existing tree (called a “backbone tree”). One of the most accurate phylogenetic placement methods to date is the maximum likelihood-based method pplacer, using RAxML to estimate numeric parameters on the backbone tree and then adding the given query sequence to the edge that...

Motivation Multiple sequence alignment (MSA) is a basic step in many bioinformatics pipelines. However, achieving highly accurate alignments on large datasets, especially those with sequence length heterogeneity, is a challenging task. UPP (Ultra-large multiple sequence alignment using Phylogeny-aware Profiles) is a method for MSA estimation that b...

Copy-number aberrations (CNAs) are genetic alterations that amplify or delete the number of copies of large genomic segments. Although they are ubiquitous in cancer and, thus, a critical area of current cancer research, CNA identification from DNA sequencing data is challenging because it requires partitioning of the genome into complex segments wi...

Founder events play a critical role in shaping genetic diversity, fitness and disease risk in a population. Yet our understanding of the prevalence and distribution of founder events in humans and other species remains incomplete, as most existing methods require large sample sizes or phased genomes. Thus, we developed ASCEND that measures the corr...

Phylogenetic placement is the problem of placing 'query' sequences into an existing tree (called a 'backbone tree') whose leaves are aligned sequences, and has applications to updating large trees and microbiome analysis. While substantial advances have been made in developing methods for phylogenetic placement, to date the most accurate approaches...

Motivation Multiple sequence alignment (MSA) is a basic step in many bioinformatics pipelines. However, achieving highly accurate alignments on large datasets, especially those with sequence length heterogeneity, is a challenging task. UPP (Ultra-large multiple sequence alignment using Phylogeny-aware Profiles) is a method for MSA estimation that b...

Motivation Copy-number aberrations (CNA) are genetic alterations that amplify or delete the number of copies of large genomic segments. Although they are ubiquitous in cancer and subsequently a critical area of current cancer research, CNA identification from DNA sequencing data is challenging because it requires partitioning of the genome into com...

Founder events play a critical role in shaping genetic diversity, impacting the fitness of a species and disease risk in humans. Yet our understanding of the prevalence and distribution of founder events in humans and other species remains incomplete, as most existing methods for characterizing founder events require large sample sizes or phased ge...

In this work, we present our framework with applications to various novel gene-drive systems such as: reciprocal chromosomal translocations, toxin-antidote-based underdominant systems. In doing so, we show how our model can be used to answer relevant questions in the field of mosquito-borne diseases elimination, such as: how to make fair comparison...