Transcriptome profiling including whole genome bulk and single cell RNA sequencing (RNA-seq) enables the quantitative study of transcript changes at either tissue or single cell level. With the advancement in next generation sequencing technology, it is now part of routine lab practice. More than other high-throughput technologies, computational algorithms are...
Uterine leiomyomas (fibroids) are a major source of gynaecologic morbidity in reproductive age women and are characterised by the excessive deposition of a disorganised extracellular matrix, resulting in rigid benign tumours. Clinically, leiomyoma patients usually present with pelvic pain, urinary incontinence, as well as heavy cyclic and non-cyclic bleeding. Curative...
Understanding the complex genome-phenome associations behind human complex traits will be a primary focus for the practice of precision medicine in the future. Identifying the genetic variants that contribute to the inter- and intra- phenotypic variations of individuals, elucidating pleiotropic architecture of common complex traits, and demonstrating how personal biomedical...
Platelets are circulating anucleate discs derived from megakaryocytes, and play major roles in hemostasis, inflammation, thrombosis, and vascular biology. Multi-phase culture systems for inducing in vitro platelet production from mature megakaryocytes have been explored to allow progenitor expansion, megakaryocyte maturation, and promotion of platelet formation and shedding. In this thesis,...
Wastewater and bioreactors in wastewater treatment plants (WWTPs) are reservoirs for antibiotic resistance genes (ARGs), which can pass through treatment processes and migrate into the environment as they are released in effluent. WWTPs harbor a variety of ARGs that can be spread by horizontal gene transfer facilitated by mobile genetic...
The critical importance of alternative mRNA splicing and the RNA binding proteins that orchestrate this essential layer of post-transcriptional gene regulation is increasingly recognized in gene regulatory programs. We and others have shown that alternative splicing plays a causal role during the Epithelial-Mesenchymal transition, a cell-developmental program that is hijacked...
The embryonic neural crest is a unique vertebrate stem cell population that has the ability to retain its stem attributes while neighboring cells in the embryo undergo lineage restriction. These cells possess multi-germ layer developmental potential and can give rise to a diverse array of derivatives such as components of...
Annual age-adjusted breast cancer incidence rates in the United States have been static for decades. More recently, the development of massively parallel, high throughput DNA sequencing has enabled the cataloging of somatic mutations in cancer. Mutations are non-random and occur within sequence motifs. These motifs provide us with evidence to...
Understanding and controlling microbial community assembly is critical to developing novel bioprocesses for nutrient and energy recovery from wastewater and preparing for global climate change. As molecular biology tools and DNA sequencing improve, microbial ecologists can progress from answering qualitative questions about “who is there, and what are they doing?”...
Recent studies have shown that many high profile studies in biology could not be reproduced, calling into questions the legitimacy of their findings. These reports have the potential to greatly jeopardize the credibility of scientists in the field as well as erode public confidence in the scientific enterprise. Computational research...