Research Interest: Translational Medicine

PHD PROGRAM
Bioinformatics & Computational Biology, Genetics & Molecular Biology

RESEARCH INTEREST
Bioinformatics, Developmental Biology, Developmental Disorders, Genetic Basis of Disease, Genetics, Human Subjects Research, Molecular Mechanisms of Disease, Translational Medicine

The Translational and Integrative Sciences Laboratory (TISLab) aims to weave together healthcare systems, basic science research, and patient generated data through development of data integration technologies and innovative data capture strategies. Our research focuses on the development of semantic technologies for data harmonization and analytics, such as ontologies, knowledge graphs, and data models. We leverage these semantic resources to standardize phenotypic information coming from clinical encounters, model and veterinary species, and directly from patients.

As part of a longstanding international consortium called the Monarch Initiative, we utilize structured phenotype data to integrate of genotype-phenotype data across species to improve rare disease diagnosis, mechanism discovery, and to identify treatments. We work with a number of rare disease communities around the world with the goal of making our data standards available for everyone and translated into different languages so that everyone can have access to the same knowledge and have the same chance for a diagnosis.

We are passionate about environmental health and understanding new ways of making environmental and nutrition data computable alongside clinical data. For example, we have integrated patient nutrition survey data together with basic research knowledge to reveal dietary risk factors of women’s reproductive disorders. We recently obtained funding to create an atlas for toxicological experiments and phenotypic outcomes in the zebrafish. TISLab has also recently created a veterinary One Health program, which focuses on understanding health influences affecting veterinary species together with their pet parents.

During Covid, we led a national initiative to harmonize Electronic Health Record data to aid discovery analytics, called the National Covid Cohort Collaborative (N3C). The N3C is now the largest publicly available HIPAA-limited dataset in US history, and has ~5,000 users. We have studied long-Covid, advised the White House and governor’s offices, and have won the NIH/FASEB DataWorks! Grand prize for our work on N3C. We also lead the Center for Linkage and Aquisition of Data (CLAD) for the All of Us Research Program. The CLAD aims to link passive data streams such as insurance claims, mortality, and environmental data to program participants to provide a more comprehensive picture of their health trajectories.

We have produced several global standards, such as the Human Phenotype Ontology, Phenopackets (Global Alliance for Genomics and Health and ISO certified), Mondo, and LinkML. We regularly attend the American Medical Informatics Association, the American Association of Human Genetics, the International Biocuration Society, and the Bioinformatics Open Source at ISMB conferences. TISLab members come from a wide variety of of scientific backgrounds and interests, making us effective partners in translational science and collaborative analytics.

PHD PROGRAM
Bioinformatics & Computational Biology, Pathobiology & Translational Science

RESEARCH INTEREST
Bioinformatics, Cancer Biology, Cancer Genomics, Computational Biology, Medical Imaging, Pathology, Quantitative Biology, Translational Medicine

My lab builds data driven, computational systems to analyze high-resolution histology images of diseased tissue as well as other clinical data sources to improve clinical decision making and advance basic scientific investigation of disease processes.

Keywords: Artificial intelligence, computer vision/medical image analysis, natural language processing, deep-learning, open-source software, multi-omic analysis, digital pathology, multiplex immunofluorescence, spatial transcriptomics, cancer

PHD PROGRAM
Cell Biology & Physiology

RESEARCH INTEREST
Arthritis, Cell Biology, Gene Therapy, Molecular Mechanisms of Disease, RNA Biology, Regenerative Medicine, Translational Medicine

Dr. Hsueh’s research is at the forefront of translational musculoskeletal and aging biology, utilizing cutting-edge multi-omic technologies to pioneer new therapeutic strategies for regenerating damaged joint tissue, with a particular focus on osteoarthritis (OA). Our lab employs advanced in vitro cell culture and cartilage explant models to delve into the mechanisms driving OA pathogenesis and to evaluate the potential of novel drug therapies. A key area of our research investigates the role of noncoding RNAs in human musculoskeletal tissues. We aim to uncover the intricate signaling pathways and downstream gene networks influenced by these noncoding RNAs. Our ultimate goal is to harness this knowledge to enhance the body’s natural repair mechanisms, providing innovative solutions to combat the progression of OA and restore joint function

PHD PROGRAM

RESEARCH INTEREST
Immunology, Neurobiology, Translational Medicine

“I’m interested in a variety of research topics pertaining to neurodegeneration. In particular I desire to expand our understanding of environmental factors that influence the onset of age related dementias. I’m fascinated by asymptomatic Alzheimer’s disease, particularly what neuroprotective factors maintain cognitive function in these individuals with full plaque and tau pathology. Furthermore, I’m intrigued by lipids, fungi, and mental illness and their roles in neurodegeneration.”

PHD PROGRAM

RESEARCH INTEREST
Computational Biology, Toxicology, Translational Medicine

“I am interested in translational toxicology research, specifically, how environmental exposures can impact human health, genetics, fetal development, and disease progression. In addition, I hope to utilize epigenetic and bioinformatic approaches to better understand chemical exposures and aid in public health research.”

PHD PROGRAM

RESEARCH INTEREST
Cancer Biology, Immunology, Translational Medicine

“I am interested in the interaction between the tumor microenvironment and the immune cells, looking into strategies to avoid or overcome immunosuppression. I am also interested in researching ways to make available immunotherapies more effective depending on the tumor microenvironment ( as it varies depending on the type of cancer.) I would like to work in a translational lab where I have access to patient samples and clinical trials (bench to bedside, and from the bed back to the bench).”

PHD PROGRAM

RESEARCH INTEREST
Gene Therapy, Genetics, Molecular Biology, Neurobiology, Translational Medicine

“Within neuroscience, I am most interested in gene therapy and translational research questions as opposed to basic science questions. I prefer to have access to a clinical population (not necessarily conduct research on this population) whether that be through clinic visits or actual clinical models. I am fine working with animals and am interested in how animal models can be translated to clinical models. I am open to outside of neuroscience such as blood diseases.”

PHD PROGRAM

RESEARCH INTEREST
Chemical Biology, Pharmacology, Translational Medicine

“Being a Biochemistry major, I have had various opportunities to explore different research techniques and areas where I have found great interest. Through industry internships, I found a fascination with high throughput screening, mass spectrometry, protein degraders, and general drug discovery. I currently work in a lab focused on mass spectrometry and the gut microbiome which has been an increasing interest of mine as well.”

PHD PROGRAM

RESEARCH INTEREST
Immunology, Toxicology, Translational Medicine

“I am interested in researching the mechanisms of how exposures to environmental pollutants may contribute to lung epithelial barrier damage and the development of other respiratory diseases. I would like to focus on man-made products and their role(s) in increased disease rates. I am also interested in the area where science meets policy.”

PHD PROGRAM

RESEARCH INTEREST
Molecular Biology, Neurobiology, Translational Medicine

“I am primarily interested in studying cellular and molecular neurobiology of disease. I enjoy researching molecular mechanisms of inherited neurodegenerative diseases and would be interested in investigating the contribution of neuroimmunology and inflammation in disease pathogenesis. I would like to expand my knowledge of disease recapitulation in new stem cell models such as multi-cell type organoid cultures. Finally, I am interested in learning and applying bioinformatics analyses towards uncovering abnormal genetic signatures in inherited diseases.”