Research Projects


Head shot of Lalit Beura
Lalit Beura, PhD

Local Regulation of T Cell Differentiation and Function in the Reproductive Mucosa

Characterize the transcriptional and epigenetic networks that control FRT TRM identity. Our phenotypic characterization has revealed a significant heterogeneity among the TRM populations. We hypothesize that FRT TRM are transcriptionally diverse and their transcriptional heterogeneity is driven by differential chromatin accessibility.

Ian Wong
Ian Wong, PhD

Profiling Gene Expression and Mechanophenotype in Circulating Tumor Cells Ex Vivo

Primary tumors shed circulating tumor cells (CTCs) into the bloodstream that metastasize preferentially to distant organs, resulting in 90% of cancer related fatalities. For example, estrogen receptor positive (ER+) breast cancers exhibit high rates of metastasis to bone, with decreased rates to liver and lung.

Roberta Devito
Roberta DeVito

Recovering Reproducible and Local Signal in Genomic Data

One of the most important challenge in biological science today is to elucidate the extent to which complex experiments, which measure hundreds of thousands of variables, can be analyzed to generate consistent and global signal when repeated, to identify local signal related to tissues, cancer types or population structure. Importantly, we must include the intrinsic diversity of variation across different studies and control for technical confounders as part of this task.

Sanghyun Lee
Sanghyun Lee

Surfaceome CRISPR Screening for SARS-CoV-2 Virulent Proteins

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 19 (COVID-19). Spike protein is the primary antigenic target for COVID vaccines and interfering with the interface between RBD (Receptor Binding Domain) of spike and ACE2 is the mechanism of action for the majority of existing therapeutic antibodies, indicating the importance of RBD and its binding to the cellular receptor for controlling SARS-CoV-2. It is unclear whether there are any intrinsic cellular proteins that inhibit viral entry of SARS-CoV-2.


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.

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

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

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.

Head shot of George Lisi, PhD
George Lisi, PhD

Mapping Long-range Allosteric Pathways in CRISPR-Cas9

Gene regulatory mechanisms are critical for proper cellular and protein function, and modern molecular biology has linked numerous pathologies to dysregulation of these processes. Although modification of the genome to correct pathogenic mutations is a promising therapeutic approach, these efforts cannot be successful without knowledge of the underlying biochemistry of protein machinery such as CRISPR-Cas9 (Cas9).