Biophysics | Research Interests

Name	Email	PhD Program
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.
Miao, Yinglong WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Bioinformatics & Computational Biology, Pharmacology RESEARCH INTEREST Aging/Alzheimer's, Biochemistry, Biophysics, Cardiovascular Disease, Computational Biology, Drug Discovery, Pharmacology, Signal Transduction	Our research is focused on the development of novel theoretical and computational methods and AI techniques, which greatly enhance computer simulations and facilitate simulation analysis, and the application of these methods, making unprecedented contributions to biomolecular modeling and drug discovery. In collaboration with leading experimental groups, we combine complementary simulations and experiments to uncover functional mechanisms and design drugs of important biomolecules, including G-protein-coupled receptors (GPCRs), membrane-embedded proteases, RNA-binding proteins, and RNA. At the interface of computational biology, chemistry, biophysics, bioinformatics and pharmacology, our research aims to address three major topics: (i) development of biomolecular enhanced sampling and AI techniques, (ii) multiscale computational modeling of critical cellular signaling pathways, and (iii) AI-driven drug discovery of medically important proteins and RNA for treatments of neurological disorders, heart failure and cancers.
Leiderman, Karin WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Biochemistry & Biophysics, Bioinformatics & Computational Biology RESEARCH INTEREST Biophysics, Cardiovascular Biology, Cell Signaling, Computational Biology, Enzymology, Hematology, Pharmacology, Quantitative Biology, Systems Biology	I am a mathematical biologist interested in the biochemical and biophysical aspects of blood clotting and emergent behavior in biological fluid-structure interaction problems. I especially love mathematical modeling, where creativity, biological knowledge, and mathematical insight meet. My goal is to use mathematical and computational modeling as a tool to learn something new about a biological system, not just to simply match model output to experimental data. My research paradigm includes an integration of mathematical and experimental approaches, together with statistical analyses and inference, to determine mechanisms underlying complex biological phenomena. This paradigm culminates in the contextualization of my findings to both the mathematical and biological communities. My research program is focused mainly on studying the influence of biochemical and biophysical mechanisms on blood coagulation, clot formation, and bleeding.
Simmons, Jake EMAIL	PHD PROGRAM RESEARCH INTEREST Biochemistry, Biophysics, Molecular Biology	“I find myself loving molecular biology techniques, but I always come back to asking how the chemistry works. For this reason, I maintain a great openness in where I land in my rotations, however, I am confident any sort of mechanistic approach will fill my curiosity. Anywhere between protein and cells, interests me. Biochemistry or molecular biology is where I see myself thriving. Particularly, I recently developed an interest in Cryo-EM, however, I’ll admit I have never researched using it.”
Do, Jamie EMAIL	PHD PROGRAM RESEARCH INTEREST Biochemistry, Biophysics, Chemical Biology	“Building on my previous research experience in thiol redox chemistry, enzymology, and protein design, I am eager to delve deeper into the field of macromolecular structure and dynamics as well as chemical biology. For instance, I want to investigate the conformational changes of macromolecules and develop novel small molecule inhibitors for targeted drug delivery. From my current knowledge, the Biochemistry and Biophysics and Pharmaceutical Sciences programs within BBSP will provide the ideal environment for pursuing these research interests. I am also excited about the opportunity to rotate in a lab whose research focus is beyond what I have mentioned.”
Jimenez, Alli EMAIL	PHD PROGRAM RESEARCH INTEREST Biochemistry, Biophysics, Physiology	“I am interested in using biochemistry and biophysics to investigate mechanisms underlying certain disease states. In particular, I find the mechanics of protein folding and dynamics to be very intriguing.”
Hughes, Jake EMAIL	PHD PROGRAM RESEARCH INTEREST Biophysics, Drug Discovery	“I am interested in exploring the world of novel protein design and development for a variety of applications including disease and drug discovery, novel synthetic methods and environmental impacts.”
Oguche, Solomon EMAIL	PHD PROGRAM RESEARCH INTEREST Biophysics, Computational Biology, Structural Biology	“I am interested in understanding the underlying principles of protein engineering and design (PED). My goal is to utilize computational and experimental tools with the understanding of PED principles in developing novel protein-based therapeutics against human diseases.”
Arango, Camila EMAIL	PHD PROGRAM RESEARCH INTEREST Biophysics, Drug Discovery, Structural Biology	“Interested in pursuing research that focuses on using biophysical methods to answer and elucidate structures of protein/small molecule that can be used a potential therapeutic and has wide applications in medicine. Also interested in protein design and gaining computation skills to potentially design proteins from scratch.”

Research Interest: Biophysics