Bioinformatics | Research Interests

Name	Email	PhD Program
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.”
Campillo Minano, Beatriz EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Computational Biology, Genetics	“I am interested in developing computational methods and algorithms for solving biological questions. I would like to focus on machine-learning approaches for genetics or structural biology. I am also interested in the development of this approaches as software tools or pipelines to ensure their generalizable usage”
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.
Popov, Konstantin WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Biochemistry & Biophysics, Bioinformatics & Computational Biology RESEARCH INTEREST Biochemistry, Bioinformatics, Biophysics, Drug Discovery	The Popov Lab develops inventive, cutting-edge approaches to solve problems in modern computational structural biology and drug discovery. Their computational research, in collaboration with experimental screening and medicinal chemistry efforts in the Center for Integrative Chemical Biology and Drug Discovery enables the identification of novel chemical probes and drug candidates to advance understanding of biological processes.
Chung, Kay WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Cell Biology & Physiology RESEARCH INTEREST Bioinformatics, Cancer Biology, Cancer Immunology, Cancer Signaling & Biochemistry, Chemical Biology, Computational Biology, Gene Therapy, Immunology, Molecular Biology, Signal Transduction, Systems Biology, Translational Medicine, Virology	The Chung lab is engineering immune cells, particularly T cells, to achieve maximum therapeutic efficacy at the right place and timing. We explore the crossroads of synthetic biology, immunology, and cancer biology. Particularly, we are employing protein engineering, next-gen sequencing, CRISPR screening, and bioinformatics to achieve our objectives: (1) Combinatorial recipes of transcription factors for T cell programming. (2) Technologies for temporal regulation and/or rewiring of tumor and immune signal activation (chemokine, nuclear, inhibitor receptors). (3) Synthetic oncolytic virus for engineering tumor-T cell crosstalk.
Pruitt, Kevin WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Pharmacology RESEARCH INTEREST Bioinformatics, Cancer Biology, Cancer Genomics, Cell Biology, Cell Signaling, Epigenetics & Chromatin Biology, Immunology, Pharmacology	Pruitt lab research involves 3 broad areas. Interest in the first area (cancer epigenetics) stemmed from discoveries made during postdoctoral training assessing how tumor progression disrupts epigenetic mechanisms of control. The second area (Wnt pathway regulation) was the result of early screens as an Assistant Professor at LSU Health Sciences Center. We uncovered novel regulators of oncogenic Wnt signaling and published the first observation that epigenetic enzymes regulate a critical mediator of Wnt signaling (Dishevelled). The third project involves elucidating mechanisms of aromatase regulation which emerged from the obsession of early trainees in the lab with understanding mechanisms cancer-associated estrogen biosynthesis. Within the context of these three projects, I have mentored and guided multiple trainees at every level over the course of 17 years.
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.
Stanley, Natalie WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Bioinformatics & Computational Biology RESEARCH INTEREST Bioinformatics, Computational Biology, Immunology, Medical Imaging, Vaccine Development	We are a computational biology lab jointly located between the department of computer science and the computational medicine program. We develop new methods for automated, efficient, and unbiased analysis of immune profiling data, such as, flow cytometry, mass cytometry, and imaging mass cytometry. Our work specifically seeks to link particular immune cell-types and their functional responses to clinical or experimental phenotypes. Application areas of interest include, vaccine development, T-cell differentiation and designing more effective immunotherapies, neurodegenerative diseases, sexually transmitted diseases, and pregnancy. To design scalable and automated tools for these data, we develop and apply new methods using machine learning and graph signal processing.
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.
Brunk, Elizabeth WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Bioinformatics & Computational Biology, Chemistry, Pharmacology RESEARCH INTEREST Biochemistry, Bioinformatics, Biophysics, Cancer Biology, Computational Biology, Genomics, Pharmacology, Structural Biology, Systems Biology, Translational Medicine	A growing body of work in the biomedical sciences generates and analyzes omics data; our lab’s work contributes to these efforts by focusing on the integration of different omics data types to bring mechanistic insights to the multi-scale nature of cellular processes. The focus of our research is on developing systems genomics approaches to study the impact of genomic variation on genome function. We have used this focus to study genetic and molecular variation in both natural and engineered cellular systems and approach these topics through the lens of computational biology, machine learning and advanced omics data integration. More specifically, we create methods to reveal functional relationships across genomics, transcriptomics, ribosome profiling, proteomics, structural genomics, metabolomics and phenotype variability data. Our integrative omics methods improve understanding of how cells achieve regulation at multiple scales of complexity and link to genetic and molecular variants that influence these processes. Ultimately, the goal of our research is advancing the analysis of high-throughput omics technologies to empower patient care and clinical trial selections. To this end, we are developing integrative methods to improve mutation panels by selecting more informative genetic and molecular biomarkers that match disease relevance.

Research Interest: Bioinformatics