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NameEmailPhD ProgramResearch InterestPublications
Ferris, Marty
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology, Genetics & Molecular Biology

RESEARCH INTEREST
Bioinformatics, Computational Biology, Genetics, Genomics, Immunology, Pathogenesis & Infection, Systems Biology, Virology

In the Ferris lab, we use genetically diverse mouse strains to better understand the role of genetic variation in immune responses to a variety of insults. We then study these variants mechanistically. We also develop genetic and genomic datasets and resources to better identify genetic features associated with these immunological differences.

Hagood, Jim
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Cell Biology & Physiology

RESEARCH INTEREST
Cell Biology, Molecular Biology, Systems Biology, Translational Medicine

I am a Pediatric Pulmonologist. My lab studies cell phenotype regulation in the context of lung fibrosis and lung development. We use in vitro and ex vivo models, mouse models, human tissue, and multi-omic approaches to explore fibroblast phenotypes in the formation of lung alveoli and in the pathologic modeling of lung fibrosis, and explore novel therapies for lung disease.

Possible Rotation Projects:

Markers of mechanotransduction in lung alveolar formation (immunofluorescence, bioinformatics)
Biological aging of the lung (DNA methylation)
Precision cut lung slice culture to model fibrosis and test therapies ex vivo
Fibroblast phenotype regulation in transgenic mice
Fibroblast-epithelial interactions in lung organoids

Rau, Christoph
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology, Genetics & Molecular Biology

RESEARCH INTEREST
Bioinformatics, Cardiovascular Biology, Computational Biology, Genetics, Genomics, Molecular Biology, Systems Biology, Translational Medicine

Heart failure is an increasingly prevalent cause of death world-wide, but the genetic and epigenetic underpinnings of this disease remain poorly understood. Our laboratory is interested in combining in vitro, in vivo and computational techniques to identify novel markers and predictors of a failing heart. In particular, we leverage mouse populations to perform systems-level analyses with a focus on co-expression network modeling and DNA methylation, following up in primary cell culture and CRISPR-engineered mouse lines to validate our candidate genes and identify potential molecular mechanisms of disease progression and amelioration.

Browne, Edward
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Microbiology & Immunology

RESEARCH INTEREST
Cell Biology, Immunology, Pathogenesis & Infection, Systems Biology, Virology

We study the molecular mechanisms of HIV latency. Transcriptional silencing of HIV is a key mechanism of persistence in patients, and is a barrier to viral eradication, but little is known about the latent reservoir or the molecular mechanisms that regulate it. As such, our repertoire of drugs for targeting latently infected cells is limited. Some latency reversing agents (LRAs) have been developed, but these are typically reactivate only a minor subset of proviruses. This inefficiency is in part due to the reservoir not constituting a uniform target, but instead being a heterogeneous set of cells with diverse characteristics and restrictions to HIV expression. However, most analyses of latency use bulk cell cultures assays in which crucial information about the behavior of individual cells is lost. Also, latently infected cells in patient samples are exceedingly rare, making them very difficult to study directly. New technological breakthroughs in the field of single cell analysis as well as the development of primary cell models for HIV latency now open the possibility of observing how latently infected cells form and are maintained at single cell resolution. Our lab has developed tools to study the establishment, maintenance and reversal of HIV latency at single cell resolution using multi-omics methods. Furthermore, we combine these approaches with genetic perturbation, time-lapse microscopy and novel bioengineering tools to gain insight into how the host cell regulates HIV latency. We have recently discovered using single cell RNAseq (scRNAseq) that latency in primary CD4 T cells is associated with expression of a distinct transcriptional signature (Bradley et al 2018). Our hypothesis is that this signature represents part of a cellular program that regulates latency, and that this program is an exciting novel target for the development of LRAs. Ongoing projects in the lab involve the application of new technologies to our model systems, and testing/validation of the roles of host cell pathways we have identified in HIV latency. Our overall goal is to identify new targets for the development of drugs to clear the HIV reservoir.

Heinzen, Erin
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology, Pharmaceutical Sciences

RESEARCH INTEREST
Genetics, Genomics, Neurobiology, Systems Biology, Translational Medicine

Lu, Zhiyue
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Chemistry

RESEARCH INTEREST
Biomaterials, Biophysics, Cell Signaling, Computational Biology, Drug Delivery, Systems Biology

Button, Brian
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Biochemistry & Biophysics

RESEARCH INTEREST
Biochemistry, Biomaterials, Biophysics, Cell Biology, Cell Signaling, Drug Delivery, Drug Discovery, Nanomedicine, Pathology, Physiology, Systems Biology, Translational Medicine

The Button lab in the Department of Biochemistry and Biophysics is part of the Marsico Lung Institute. Our lab is actively involved in projects that are designed to define the pathogenesis of muco-obstructive pulmonary disorders and to identify therapies that could be used to improve the quality of life in persons afflicted by these diseases. In particular, our research works to understand the biochemical and biophysical properties of mucin biopolymers, which give airway mucus its characteristic gel-like properties, and how they are altered in diseases such as Asthma, COPD, and cystic fibrosis.

Palmer, Adam
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Pharmacology

RESEARCH INTEREST
Cancer Biology, Computational Biology, Pharmacology, Systems Biology, Translational Medicine

The Palmer lab investigates combination cancer therapy: understanding the mechanisms of successful drug combinations to inform the development of combinations with new cancer therapies. Our approach is a synthesis of experiments, analysis of clinical data, and modeling. Students can pursue projects that are experimental, computational, or a mixture of both. Our goals are to improve the design of drug combinations, the interpretation of clinical trials, and patient stratification to increase rates of response and cure through more precise use of cancer medicines in combinations.

Azcarate-Peril, M. Andrea
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Nutrition

RESEARCH INTEREST
Bacteriology, Bioinformatics, Genomics, Molecular Biology, Systems Biology

We are interested in determining the mechanisms involved in the beneficial modulation of the gut microbiota by prebiotics (functional foods that stimulate growth of gut native beneficial bacteria) and probiotics (live bacteria that benefit their host). Specifically, we aim to develop prebiotic and probiotic interventions as alternatives to traditional treatments for microbiota-health related conditions, and to advance microbiota-based health surveillance methods.

Chorley, Brian
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Toxicology

RESEARCH INTEREST
Cell Biology, Genomics, Molecular Biology, Systems Biology, Toxicology

The long-term goal of my research is to incorporate ‘omic (genomic, epigenomic, proteomic, etc.) measurements into environmental human health hazard identification, prioritization and risk assessment using a quantitative and interpretable biological systems framework. Thus, short-term goals have been to develop the molecular tools to investigate key biological events, and measurable biomarkers linked to those events, related to important disease processes that are impacted by environmental chemical exposures, such as liver and lung toxicity.  We have focused recent efforts on early-in-life genomic and epigenetic alterations and linkages to latent adverse outcome susceptibility due to commons exposures, genetics, and pre-existing conditions. Our laboratory uses cutting edge techniques such as gene editing tools including CRISPR-based methods; next generation nucleic acid-based sequencing to probe the genome and epigenome; advance, high-throughput microscopy; targeted RNA, DNA, and non-coding RNA measurements such as digital drop PCR and Fireplex; and advanced in vitro models.