This dissertation investigates an old and fundamental question in evolutionary biology: how is adaptation maintained in highly heterogeneous environments? Adaptation in variable environments poses a …
Genome-wide association (GWA) studies identify statistical associations between individual variants and a phenotype of interest. By independently testing the correlation between the allelic state at …
The growing interest in genealogy for African Americans is one expression of a longstanding desire to find answers to questions about ancestors, family, and heritage …
This study introduces Biologically Annotated Neural Networks (BANNs) for identifying causal Single Nucleotide Polymorphisms (SNPs) linked to complex traits. BANNs combine neural network flexibility with …
Age is a fundamental aspect of biology that underlies the efficacy of a broad range of functions. Identifying determinants for how quickly or slowly we …
Background: Cancer, the second leading cause of death in the United States, is a complex disease where multiple genes contribute to the development of the …
Statistical and computational methods for detecting evolutionary processes in human genomic data have been going through rapid advances across multiple fields of study and timescales. …
Defining diverse roles of a single transcription factor on the cellular level is key to understanding its role in the context of an organism. However, …
Biological systems must regulate complex gene transcriptional programs to mediate phenotypic response to diverse stimuli. Control of gene expression requires specific DNA sequence patterns called …
Reciprocal recombinant F2 populations of the fruitfly were created and analyzed using a pooled whole-genome sequencing approach to investigate the effects of divergent mitochondrial DNA …
Cellular senescence and aging are associated with extensive chromatin and transcriptional changes. We examined cell-free DNA (cfDNA) in individuals of different age groups to elucidate …
Idiopathic pulmonary fibrosis (IPF) is a devastating interstitial lung disease involving the uncontrolled scarring of the alveolar epithelium and lethal reduction in ability to breathe. …
Genome Assembly by Bayesian Inference (GABI) is a prototype of a Bayesian framework for sequence assembly. Most genome assemblers construct point estimates, choosing only a …
Since the completion of the Human Genome Project and the first whole human genome sequence in 2003, the number of whole human genome sequences available …
Cancer is characterized by heterogeneity at multiple scales, with implications for diagnosis, prognosis, and treatment. Major advances in genomics have led to a proliferation of …
Antimicrobial resistance is a major problem and according to Centers for Disease Control and Prevention (CDC) it causes about 2.8 million antimicrobial-resistant infections every year …
Human beings are diploid organisms, and it is of great medical and biological interest to accurately obtain the sequences of each chromosome as it aids …
Advances in sequencing technologies in the last decade have enabled us to profile various genomic features at the single-cell resolution, such as gene expression and …
Endemic Burkitt’s lymphoma (eBL) is a malaria- and Epstein-Barr virus (EBV)-associated clonal B-cell lymphoma. eBL is the most common childhood cancer in sub-Saharan Africa, and …
Precision Medicine proposes to revolutionize the delivery of healthcare by tailoring treatments and interventions to an individual’s unique set of characteristics. Since the completion of …