Research Projects

Current

Alper Uzun, PhD

Computational Genomics of Preeclampsia

In the post genome era, biological research and genomic medicine have been transformed by high-throughput technologies.  New techniques have enabled researchers to investigate biological systems in great detail.  Nonetheless, the extraordinary amount of information in the large number of emerging high-dimension datasets has not been fully exploited.  Increasingly, pathway analysis and other a priori biological knowledge based approaches have improved success in extraction of valuable information from high-throughput experiments and genome-wide association studies.  Preeclampsia is a complex

Jason Wood, PhD

The Role of Sirtuins in Neurodegenerative Disease

This research seeks to characterize the transcriptome and epigenome of models of Alzheimer’s disease (AD) in Drosophila melanogaster. The project will seek to investigate the role of sirtuins in the development and progression of AD, and to understand the molecular mechanism of their reported neuroprotective effects.

Marco De Cecco, PhD

The Role of LINE-1 in Senescence-Associated Cytoplasmic DNA Accumulation

A large fraction of our genomes (~45%) is composed of retrotransposable elements (RTEs), mutagenic mobile DNA elements that have been implicated in the etiology of several diseases. Retrotransposition of RTEs can be deleterious at multiple levels. To protect against RTEs multiple silencing mechanisms have evolved. We made an interesting discovery: RTEs become activated in senescent cells and in aging tissues. We have proposed that RTE activation may represent a hitherto unappreciated molecular aging process.

Lorin Crawford Head Shot
Lorin Crawford, PhD

Deep Learning Methods for Fine Mapping and Discovery in Genomic Association Studies

Nonlinear genetic effects have been proposed as key contributors to missing heritability – the proportion of heritability is a trait that is not explained by the top associated additive variants in genome-wide association (GWA) studies. To this end, probabilistic machine learning approaches have been shown to be useful tools that exhibit great performance gains in genomic selection-based analyses.

Iuliana Ene Head shot
Iuliana Ene, PhD

Genome Evolution, Commensalism, and Pathogenecity in the Diploid Fungust Candida albicans

Fungal pathogens exhibit considerable genetic plasticity, with both microvariation and chromosome-level rearrangements frequently enabling adaptation to host and environmental pressures.  Several genera of fungi are important human pathogens, with invasive fungal infections responsible for the death of approximately 1.5 to 2 million people worldwide each year. Candida species are the most prominent cause of invasive fungal disease in the US, with the major protagonist being Candida albicans.

Completed

Sohini Ramachandran head shot
Sohini Ramachandran, PhD

Incorporating Ethnic and Gender Disparities in Genomic Studies of Disease

Dr. Sohini Ramachandran will develop new computational and analytical methodologies to identify risk alleles for leukemia that differ in incidence across ethnic groups and genders, and apply these methods to genome wide association studies. Analyses of X-linked factors offer new insights into human genomic variation.

Amanda Jamieson, PhD

Tolerance of Viral/Bacterial Co-infections

While infection biology has largely focused on studying the immune response to a single infection, it is becoming increasingly clear that many infections involve more than one pathogen.

Nicola Neretti, PhD

A Drug Repositioning Strategy for Healthspan Extension

Aging is the single most important risk factor for a wide range of chronic illnesses, including diabetes, heart disease, cancer and neurodegenerative diseases. Hence, interventions that can slow aging have the potential to prevent or at least retard the onset of these debilitating diseases.  It was recently discovered that senescent cell clearance in mouse aging models improves healthspan and extends lifespan.

Shipra Vaishnava, PhD

Spatial and Functional Organization of Intestinal Microbiome

The most prominent diseases of modern times--including inflammatory bowel diseases (IBD) such as Crohn's, ulcerative colitis, and colon cancer as well as metabolic diseases such as diabetes and obesity--are caused as a result of failure to maintain homeostatic interactions with commensal bacteria.  However, at the moment, we do not fully understand the mechanisms that regulate host-microbe interactions.  Moreover, attempts to identifiy common microbiome associated patterns linked with these diseases have either failed or are inconsistent at best.  It is likely that the intestinal flora is s