Genomics | Research Interests

Name	Email	PhD Program
Miller, Colette WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Toxicology RESEARCH INTEREST Cardiovascular Biology, Cardiovascular Disease, Developmental Biology, Epigenetics & Chromatin Biology, Genomics, Metabolism, Molecular Biology, Molecular Mechanisms of Disease, Physiology, Pulmonary Research, Toxicology	Our research investigates the effects of air pollutants on maternal health, paternal health, and the health of their children. Through the use of genomics, metabolomics, and proteomics, we investigate the molecular underpinnings of diseases following exposures to pollutants during sensitive life stages. We have broad interests across many tissue systems and diseases relevant to fertility and pregnancy. Our work also explores the Developmental Origins of Health and Disease hypothesis, investigating risks of metabolic diseases in offspring following maternal or paternal exposures to pollutants.
Zhang, Weiwei EMAIL	PHD PROGRAM RESEARCH INTEREST Cardiovascular Biology, Drug Discovery, Genomics	“My research interests involve investigating the pathogenesis of cardiovascular diseases using methods such as single-cell sequencing, metabolomics, and transcriptomics to identify potential intervention targets for mitigating the progression of these diseases.”
Ulloa Avila, Tatiana EMAIL	PHD PROGRAM RESEARCH INTEREST Genetics, Genomics, Neurobiology	“I am interested in studying chromatin architecture and the role that it plays on gene regulation in the context of neurodegenerative and neuropsychiatric disorders. Moreover, I would like to generate an impact with my research by applying my findings to the area of therapeutics.”
Martin, Carmen EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Computational Biology, Gene Therapy, Genetic Basis of Disease, Genomics	“Research the relationship between genetic variation and genetic disease with different computational tools. Understanding the genetic basis of the disease and how the variations can be manipulated to find areas for gene therapy and increase human health.”
Deal, Milena EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Genetics, Genomics	“I am interested in examining the heritability of complex disease using genomics. I want to use both bioinformatics and experimental techniques to work toward this goal. I have interest in other subject areas as well, such as microbiology, but do want to focus on labs that have computational PhD students.”
Anderson, Ashlyn (Ash) EMAIL	PHD PROGRAM RESEARCH INTEREST Evolutionary Biology, Genetics, Genomics, Molecular Biology, Pathogenesis & Infection	“I have broad equal interest in pathogenesis/infection (new to me but has always captivated my interests) and in basic science questions related to chromatin, genetics, and evolution (familiar to me + I already know I love researching these kinds of questions!) I am hoping to narrow down and explore my interests between these further with rotations in virology, genetics-genomics, or bacteriology labs. “
Schrank, Travis EMAIL PUBLICATIONS	PHD PROGRAM Pathobiology & Translational Science RESEARCH INTEREST Bioinformatics, Biophysics, Cancer Biology, Cancer Signaling & Biochemistry, Chemical Biology, Computational Biology, Evolutionary Biology, Genetics, Genomics, Molecular Biology, Molecular Mechanisms of Disease, Translational Medicine, Virology	I am a surgeon-scientist specialized in head and neck cancers. My goal is to address translationalquestions with genomic data and bioinformatic methods, as well as benchtop experimentation. My clinical practice as a head and neck cancer surgeon also influences my research by helping me seek solutions to problems that will directly inform gaps in the current treatment protocols. I have developed a strong interest in HPV genomics as well as HPV/host genome integrations, as these factors are intrinsically related to transcriptional diversity and patient outcomes in HPV-associated head and neck cancers. Our work has helped to demonstrate that a novel mechanism of HPV-mediated oncogenesis requiring NF-kB activation is present in nearly 50% of oropharyngeal tumors. In this vein, we are aggressively investigating the cellular interplay between the NF-kB pathway and persistent HPV infection, tumor radiation response, NRF2 signaling, and more. Another outgrowth of this work has been investigating APOBEC3B and its non-canonical roles in regulating transcription. Our preliminary work has demonstrated that APOBEC3B has surprisingly strong transcriptional effects in HPV+ HNSCC cells and may promote oncogenesis and tumor maintenance by suppressing the innate immune response and influencing the HPV viral lifecycle. Our group also have a strong interest in translational genomic studies. Our group is working to develop methods that will make gene expression-based biomarkers more successful in the clinic, as well as studying many aspects of genomic alterations that contribute to the development of squamous cell carcinomas.
Liu, Qingyun WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Genetics & Molecular Biology, Microbiology & Immunology RESEARCH INTEREST Bacteriology, Bioinformatics, Ecology, Evolutionary Biology, Genetics, Genomics, Microscopy/Imaging, Molecular Biology, Molecular Mechanisms of Disease, Pathogenesis & Infection	Infectious diseases due to highly pathogenic microbes continue to pose a persistent and evolving threat to humans. In this laboratory, we study the evolutionary mechanisms underlying drug resistance and transmissibility in bacterial pathogens, including Mycobacterium tuberculosis and Mycobacterium abscessus, among others.
Johri, Parul WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Bioinformatics & Computational Biology RESEARCH INTEREST Computational Biology, Evolutionary Biology, Genomics	Our research interests broadly span population genetics, statistical inference, and evolutionary genomics. We are interested in how evolutionary processes like changes in population size, recombination, mutation, selection and factors such as genome architecture shape patterns of genomic variation. Work in the lab involves employing computational and theoretical approaches, statistical method development, or using an empirical approach to perform evolutionary inference and ask fundamental questions in population genetics.
Wang, Jeremy WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Bioinformatics & Computational Biology, Pathobiology & Translational Science RESEARCH INTEREST Bioinformatics, Cancer Genomics, Computational Biology, Genomics, Microbiome	Our research focuses on long-read (single-molecule) sequencing and informatics. We develop novel methods to enable more efficient *omic analysis and apply carefully architected high-performance computing approaches to improve the utility of genomics in studies of human diseases, including infectious disease, cancer, and GI. Ongoing work includes genomic epidemiology of SARS-CoV-2, MPXV, and antibiotic resistance; classification of pediatric leukemias and solid tumors in low-resource settings using nanopore transcriptome sequencing; and metagenomics/metataxonomics of mucosa-associated microbiota in inflammatory bowel diseases.

Research Interest: Genomics