Current Students
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Mingyao Li
- Li Shen
Rotations:
- Zhi Huang
- Mingyao Li
- Li Shen
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Brielin Brown
Rotations:
- Brielin Brown
- Ziyue Gao
- Benjamin Voight
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Bo Li
- Nancy Zhang
Rotations:
- Bo Li
- Andy Minn
- Nancy Zhang
Degree: MD/PhD
Matriculation Year: 2024
Project Title: Investigating the effect of genetic variation on mRNA splicing and its implications to disease with long-read RNA sequencing
Advisor(s):
- Yi Xing
Rotations:
- Joel Babdor
- Kai Tan
- Yi Xing
Degree: PhD
Matriculation Year: 2024
Project Title: Genotype–phenotype mapping in complex traits provides high resolution ancestry information and reveals novel associations
Advisor(s):
- Bogdan Pasaniuc
Rotations:
- Bogdan Pasaniuc
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Brielin Brown
- Michael Gandal
Rotations:
- Brielin Brown
- Ophir Shalem
- Yi Xing
Degree: PhD
Matriculation Year: 2024
Project Title: Consideration of diversity and uncertainty in genetic effect estimation improves the utility of genome-wide association studies
Advisor(s):
- Bogdan Pasaniuc
Rotations:
- Bogdan Pasaniuc
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Sokratis Apostolidis
- Dokyoon Kim
Rotations:
- Sokratis Apostolidis
- Dokyoon Kim
- Li Shen
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Joseph Romano
- Shefali Setia Verma
Rotations:
- Sunni Mumford
- Joseph Romano
- Shefali Setia Verma
Degree: MD/PhD
Matriculation Year: 2024
Project Title: White Matter Along-Tract Development and Genetic Risk for Transdiagnostic Psychopathology
Advisor(s):
- Aaron Alexander-Bloch
- Ted Satterthwaite
Rotations:
- Aaron Alexander-Bloch
- Yoseph Barash
- Elizabeth Bhoj
- Ted Satterthwaite
Degree: PhD
Matriculation Year: 2024
Project Title: Integrating genome wide association studies with single cell methylome
Advisor(s):
- Bogdan Pasaniuc
Rotations:
- Bogdan Pasaniuc
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Li Shen
Rotations:
- Dokyoon Kim
- Joseph Romano
- Li Shen
Degree: PhD
Matriculation Year: 2024
Project Title: Understanding the clinical utility of polygenic risk scores
Advisor(s):
- Bogdan Pasaniuc
Rotations:
- Bogdan Pasaniuc
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Kevin Johnson
- Danielle Mowery
Rotations:
- Kevin Johnson
- Danielle Mowery
- Rich Tsui
Degree: PhD
Matriculation Year: 2024
Project Title: The portability of polygenic scores across ancestrally diverse individuals
Advisor(s):
- Bogdan Pasaniuc
Rotations:
- Bogdan Pasaniuc
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Joseph Romano
Rotations:
- Brielin Brown
- Dokyoon Kim
- Joseph Romano
Degree: PhD
Matriculation Year: 2024
Advisor(s):
- Glennis Logsdon
Rotations:
- Gerd Blobel
- Teddy Drivas
- Glennis Logsdon
Degree: PhD
Matriculation Year: 2023
Project Title: Computational Pathology and Three-Dimensional Tumor Modeling for Precision Medicine in Pancreatic Cancer
Advisor(s):
- Ben Stanger
Rotations:
- Jina Ko
- Derek Oldridge
- Ben Stanger
- Yi Xing
Degree: PhD
Matriculation Year: 2023
Project Title: Integrating multi-modal observational health data to enhance patient safety for endometriosis
Advisor(s):
- Joseph Romano
Rotations:
- Lewis Chodosh
- Joseph Romano
- Shefali Setia Verma
Degree: PhD
Matriculation Year: 2023
Project Title: Using knowledge-driven AI to identify uterine fibroid risk factors, etiology, and enhance precision prediction
Advisor(s):
- Joseph Romano
Rotations:
- Kevin Johnson
- Joseph Romano
- Kai Wang
Degree: PhD
Matriculation Year: 2023
Project Title: Decoding Depression: Integrative Modeling Leveraging Genomic Risk and Social Determinants to Predict Treatment Efficacy
Advisor(s):
- Rachel Kember
Rotations:
- Michael Gandal
- Ingo Helbig
- Rachel Kember
- Li Shen
Degree: PhD
Matriculation Year: 2023
Project Title: Machine Learning Approaches to Biological Age Prediction
Advisor(s):
- Qi Long
- Li Shen
Rotations:
- Qi Long
- Joseph Romano
- Li Shen
Degree: PhD
Matriculation Year: 2023
Project Title: Interpreting the Functional Consequences of Small Alternative Splicing Events
Advisor(s):
- Yi Xing
Rotations:
- Pablo G. Camara
- Golnaz Vahedi
- Yi Xing
Degree: PhD
Matriculation Year: 2023
Project Title: Decoding the cellular landscape of atherosclerosis with spatial transcriptomics
Advisor(s):
- Mingyao Li
Rotations:
- Dokyoon Kim
- Mingyao Li
- Taki Shinohara
Degree: PhD
Matriculation Year: 2023
Project Title: Variant Interpretation in the Era of Single-Cell Genomics
Advisor(s):
- Kai Wang
Rotations:
- Ingo Helbig
- Kai Wang
- Wanding Zhou
Degree: PhD
Matriculation Year: 2023
Project Title: Dissecting cellular niches and regulatory mechanisms in Alzheimer's disease by spatial multi-omics
Advisor(s):
- Yanxiang Deng
- Mingyao Li
Rotations:
- Yanxiang Deng
- Mingyao Li
- Katalin Susztak
Degree: PhD
Matriculation Year: 2023
Project Title: Associating Viral Proteins with Responders of Immune Checkpoint Inhibitors in Melanoma
Advisor(s):
- Noam Auslander
- Frederic Bushman
Rotations:
- Noam Auslander
- Frederic Bushman
- Avi Srivastava
Degree: PhD
Matriculation Year: 2023
Project Title: Digital pathology for identification of prognostically relevant morphological and multiomic signatures in pediatric gliomas
Advisor(s):
- Dokyoon Kim
- Derek Oldridge
Rotations:
- Dokyoon Kim
- Derek Oldridge
- Li Shen
Degree: MD/PhD
Matriculation Year: 2023
Project Title: Discovery and characterization of gene regulatory networks in cardiac development and aging
Advisor(s):
- Hao Wu
Rotations:
- Hao Wu
- Zoltan Arany
Degree: PhD
Matriculation Year: 2023
Project Title: Deep Learning Approach to Analyzing Gene Expression and Antigen Presentation in Cancer
Advisor(s):
- Bo Li
Rotations:
- Bo Li
Degree: PhD
Matriculation Year: 2023
Project Title: Deciphering mechanisms driving meningioma progression through high resolution spatial profiling of the tumor microenvironment
Advisor(s):
- Derek Oldridge
Rotations:
- Andy Minn
- Derek Oldridge
- Golnaz Vahedi
Degree: PhD
Matriculation Year: 2023
Project Title: Integrating multi-omics data to improve risk prediction and mechanistic understanding of autoimmune diseases
Advisor(s):
- Dokyoon Kim
Rotations:
- Dokyoon Kim
- Iain Mathieson
- Kai Tan
Degree: MD/PhD
Matriculation Year: 2023
Project Title: Spatiotemporal evolution and ecological dynamics of acute myeloid leukemia upon chemotherapy
Advisor(s):
- Kai Tan
Rotations:
- Kai Tan
- Mingyao Li
- Pablo G. Camara
Degree: PhD
Matriculation Year: 2022
Project Title: Decoding Tumor Heterogeneity and Cell Plasticity in Glioma using High-throughput, Genomic Data and Topologically Driven Methods
Advisor(s):
- Pablo G. Camara
Rotations:
- Yoseph Barash
- Pablo G. Camara
- Ziyue Gao
Degree: PhD
Matriculation Year: 2022
Project Title: Using Electronic Health Records and Multi-Omics Approaches to Improve Understanding of Pharmacogenomics
Advisor(s):
- Marylyn Ritchie
Rotations:
- Marylyn Ritchie
- Yoseph Barash
- Dokyoon Kim
Degree: PhD
Matriculation Year: 2022
Advisor(s):
- Rui Feng
Rotations:
- Rui Feng
- Yi Xing
- Struan Grant
Degree: PhD
Matriculation Year: 2022
Project Title: Identifying genetic and environmental drivers of inter and intra-specific mutation rate spectra evolution
Advisor(s):
- Iain Mathieson
Rotations:
- Iain Mathieson
- Ziyue Gao
- Benjamin Voight
Degree: PhD
Matriculation Year: 2022
Project Title: Modeling local ancestry to detect selection in admixed human populations
Advisor(s):
- Iain Mathieson
Rotations:
- Sarah Tishkoff
- Iain Mathieson
- Ziyue Gao
Degree: PhD
Matriculation Year: 2022
Project Title: Characterizing the Role of Maternal Environmental Exposures on Preeclampsia Using Biomedical Knowledge Graphs
Advisor(s):
- Joseph Romano
Rotations:
- Mary Regina Boland
- Daniel Herman
- Joseph Romano
Degree: PhD
Matriculation Year: 2022
Project Title: Characterizing cell morphology and subcellular protein localization using optimal transport
Advisor(s):
- Pablo G. Camara
Rotations:
- Pablo G. Camara
- Nancy Zhang
- Derek Oldridge
Degree: PhD
Matriculation Year: 2022
Project Title: Generative summarization of autoimmune clinical histories
Advisor(s):
- Dokyoon Kim
Rotations:
- Qi Long
- Kevin Johnson
- Dokyoon Kim
Degree: PhD
Matriculation Year: 2022
Project Title: Improving the functional characterization of gut microbial proteins to enable human disease research
Advisor(s):
- Noam Auslander
Rotations:
- Danielle Mowery
- Noam Auslander
- Dokyoon Kim
Degree: PhD
Matriculation Year: 2022
Project Title: Identification and characterization of hereditary genetic risk factors in hepatocellular carcinoma
Advisor(s):
- Anurag Verma
Rotations:
- Dokyoon Kim
- Danielle Mowery
- Anurag Verma
Degree: PhD
Matriculation Year: 2022
Project Title: Leveraging Deep Clinical Insights and Genomic Integration for Precise Phenotyping and Prognostic Prediction for Endometriosis
Advisor(s):
- Shefali Setia Verma
Rotations:
- Daniel Herman
- Suneeta Senapati
- Shefali Setia Verma
- Anurag Verma
Degree: PhD
Matriculation Year: 2022
Project Title: Characterizing the development of epigenetically encoded inflammatory memory in single cells
Advisor(s):
- Andy Minn
- Nancy Zhang
Rotations:
- Andy Minn
- Derek Oldridge
- Nancy Zhang
Degree: PhD
Matriculation Year: 2022
Project Title: Integrating incomplete multimodal longitudinal imaging and -omics data in Alzheimer’s Disease research
Advisor(s):
- Qi Long
- Li Shen
Rotations:
- Li Shen
- Dokyoon Kim
- Qi Long
Degree: VMD/PhD
Matriculation Year: 2022
Project Title: ESPRESSO-TEA: A long-read RNA sequencing workflow to study locus-specific expression of transposable elements
Advisor(s):
- Yi Xing
Rotations:
- Yi Xing
- Lan Lin
Degree: PhD
Matriculation Year: 2021
Project Title: Multi-modal lineage tracing in single cell and spatial omics data
Advisor(s):
- Nancy Zhang
Rotations:
- Nancy Zhang
- Kai Tan
- Pablo G. Camara
Degree: PhD
Matriculation Year: 2021
Project Title: Investigating the interactions between cancer genomics and host immune responses
Advisor(s):
- Noam Auslander
- Bin Tian
Rotations:
- Wanding Zhou
- Noam Auslander
- Daniel Herman
Degree: PhD
Matriculation Year: 2021
Project Title: Impact of Natural Selection on Disease Phenotypes
Advisor(s):
- Marylyn Ritchie
- Sarah Tishkoff
Rotations:
- Sarah Tishkoff
- Frederic Bushman
- Marylyn Ritchie
Degree: PhD
Matriculation Year: 2021
Project Title: Characterizing the development and functions of tertiary lymphoid structures in human disease
Advisor(s):
- Dokyoon Kim
- John Wherry
Rotations:
- Li Shen
- Dokyoon Kim
- Marylyn Ritchie
Degree: PhD
Matriculation Year: 2021
Project Title: Determining clinical connections between Alzheimer’s Disease and its comorbidities using genetics and electronic health records
Advisor(s):
- Marylyn Ritchie
Rotations:
- Kai Tan
- Dokyoon Kim
- Marylyn Ritchie
- Benjamin Voight
Degree: PhD
Matriculation Year: 2021
Project Title: Long-read RNA Sequencing and Its Applications to Cancer Immunotherapy
Advisor(s):
- Yi Xing
Rotations:
- John Maris
- Yi Xing
- Li Shen
Degree: PhD
Matriculation Year: 2021
Project Title: Characterizing cellular interactions in the acute myeloid leukemia bone marrow microenvironment to overcome therapy resistance
Advisor(s):
- Dana Silverbush
Rotations:
- Kai Tan
- Cesar de la Fuente
- Kai Wang
Degree: PhD
Matriculation Year: 2021
Project Title: Enhancing the risk stratification in Alzheimer’s disease (AD) by augmenting the polygenic risk score (PRS) with rare variants and transcriptome-wide association study (TWAS) data
Advisor(s):
- Dokyoon Kim
Rotations:
- Marylyn Ritchie
- Li Shen
- Dokyoon Kim
Degree: PhD
Matriculation Year: 2021
Project Title: Molecular Determinants of CAR T-cell Therapy Exhaustion and Long-term Persistence
Advisor(s):
- Kai Tan
Rotations:
- Yi Xing
- Kai Tan
- Pablo G. Camara
Degree: PhD
Matriculation Year: 2021
Project Title: Exploring the genetic architecture underlying disease connections with biologically meaningful networks
Advisor(s):
- Dokyoon Kim
Rotations:
- Marylyn Ritchie
- Dokyoon Kim
- Benjamin Voight
Degree: PhD
Matriculation Year: 2021
Project Title: Unraveling Commensal and Pathogen Interactions in Skin Microbial Transplants
Advisor(s):
- Elizabeth Grice
Rotations:
- Frederic Bushman
- Elizabeth Grice
- Li Shen
Degree: PhD
Matriculation Year: 2021
Project Title: Integrating QTL and 3D genomic data for variant-to-gene mapping in liver-related complex disease
Advisor(s):
- Struan Grant
- Laura Almasy
Rotations:
- Dokyoon Kim
- Junhyong Kim
- Christopher Brown
Degree: PhD
Matriculation Year: 2020
Project Title: Incorporating Structured Immunological Knowledge into Graph Data Science Models to Improve Understanding of Autoimmunity
Advisor(s):
- John Wherry
- Marylyn Ritchie
Rotations:
- Jason Moore
- Junhyong Kim
- John Wherry
Degree: PhD
Matriculation Year: 2020
Project Title: Multi-omics data integration for Alzheimer’s disease risk and progression prediction
Advisor(s):
- Dokyoon Kim
Rotations:
- Casey Greene
- Dokyoon Kim
- Jason Moore
Degree: PhD
Matriculation Year: 2020
Project Title: Elucidating Causal Genes for Type 2 Diabetes Risk in the Pancreas
Advisor(s):
- Struan Grant
- Benjamin Voight
Rotations:
- Blanca Himes
- Benjamin Voight
- Struan Grant
Degree: PhD
Matriculation Year: 2020
Project Title: Single cell long read sequencing and perturbation analysis reveals splicing heterogeneity and logic
Advisor(s):
- Nancy Zhang
Rotations:
- Mingyao Li
- Pablo G. Camara
- Nancy Zhang
Degree: PhD
Matriculation Year: 2018
Project Title: Detection and quantification of alternative polyadenylation from RNA-seq to suggest novel regulators in health and disease
Advisor(s):
- Yoseph Barash
- Kristen Lynch
Rotations:
- Christopher Brown
- Zhaolan (Joe) Zhou
- Yoseph Barash
Degree: PhD
Matriculation Year: 2017
Project Title: Pathway Analysis of Recurrent Breast Cancer
Advisor(s):
- Lewis Chodosh
Rotations:
- Lewis Chodosh
- Sarah Tishkoff
- Elizabeth Grice
Degree: PhD
Matriculation Year: 2017
Project Title: Searching for Non-Coding Mechanisms of Disease in Neuroblastoma
Advisor(s):
- John Maris
- Sharon Diskin
Rotations:
- Katherine Nathanson
- Lewis Chodosh
- Sharon Diskin
- John Maris
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