Research Interest: Computational Biology

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.

PHD PROGRAM
Applied Physical Sciences, Biology, Neuroscience

RESEARCH INTEREST
Brain Development, Computational Biology, Microscopy/Imaging, Neurobiology, Neurodevelopmental Disorders, Neuropharmacology, Quantitative Biology

The EnYang Lab explores interdisciplinary fields to unravel the intricate workings of neural networks within the brain, focusing on how they execute computations, foster imagination, and respond to emotional states. Using larval zebrafish as an animal model, the lab observes, decodes, and perturbs the entire neural networks at single-cell resolution during cognitive tasks. Through the integration of whole-brain imaging, brain-machine interface (BMI), Virtual Reality, optogenetic manipulation, deep learning, and other modern technologies, the lab aims to decipher cognitive abilities in the brain and translate findings into engineering solutions, potentially impacting fields like learning disorders and psychiatric management.

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.

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.

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.

PHD PROGRAM

RESEARCH INTEREST
Computational Biology, Neurobiology, Pharmacology

I’m interested to research the neural basis of psychiatric disorders. In particular, the neural mechanisms underlying psychedelic treatments in relation to anxiety and depression.

PHD PROGRAM

RESEARCH INTEREST
Bioinformatics, Computational Biology, Virology

“I am passionate about developing new tools or models for visualizing and analyzing biological data. I am interested in understanding the pathogenesis of cancer-causing viruses through various NGS technologies.”

PHD PROGRAM

RESEARCH INTEREST
Cancer Biology, Computational Biology, Genomics

“I am most interested in computational biology projects! I aim to combine wet and dry lab, as I would love to be involved in both. Although my past experiences center around cancer genomics, I am open to completely new research areas.”

PHD PROGRAM

RESEARCH INTEREST
Bioinformatics, Computational Biology, Genetics

“I would like to focus on developing statistical methods for modeling the effect of genetic variation among immunologic phenotypes in lung diseases, especially asthma.”

PHD PROGRAM

RESEARCH INTEREST
Bioinformatics, Computational Biology, Genomics

“My primary interest is understanding the functions of intronic DNA sequences and noncoding RNA. I’m interested in contributing to the development of methods and algorithms to uncover these functions with respect to their role in human disease. Specific areas of interest include cancer development and women’s health.”