2024
Nicita Mehta
Integrated Molecular and Histopathological Study of Germ Cell Tumors
Integrated Molecular and Histopathological Study of Germ Cell Tumors
Advisor: Eliezer Van Allen
Richard Chen
Multimodal & Context-Aware Computational Pathology
Advisor: Faisal Mahmood
Multimodal & Context-Aware Computational Pathology
Advisor: Faisal Mahmood
2023
Laurie Rumker
Modeling inter-individual variation in single-cell datasets to detect cell state abundance associations to clinical features and genetic variants
Advisor: Soumya Raychaudhuri
Modeling inter-individual variation in single-cell datasets to detect cell state abundance associations to clinical features and genetic variants
Advisor: Soumya Raychaudhuri
Raehoon Jeong
The effects of trait-associated variation on transcription factor binding and other regulatory phenotypes
Advisor: Martha Bulyk
Andrew Liu
Design and simulation of quarantine policy and wastewater early detection against future pandemics
Advisor: Michael Springer
Anika Gupta
Systematically inferring directional effects within cell states from single-cell data
Advisors: Soumya Raychaudhuri and Eric Lander
Eric Bartell
Polygenic architecture of human body size and proportion
Advisor: Joel Hirschhorn
Vinayak Venkatasesha Viswanadham
Origins, patterns, and consequences of somatic mutations in engineered, normal, and diseased cells
Advisor: Peter Park
Joyce Kang
Integrative analysis of large-scale single-cell genomics data in immune-mediated diseases
Advisor: Soumya Raychaudhuri
2022
Dan Weiner
Integration of common and rare genetic variation across complex traits and neuropsychiatric disorders
Advisor: Elise Robinson
Benjamin Kompa
New methods for representation learning, uncertainty quantification, and causal inference in biomedical machine learning
Advisor: Andrew Beam
Ryan Collins
The Landscape and Consequences of Structural Variation in the Human Genome
Advisor: Michael Talkowski
Zachary Chiang
In situ epigenomics across length scales
Advisor: Jason Buenrostro
Aparna Nathan
Integration of multimodal single-cell data to characterize T cell phenotypes, gene regulation, and disease associations
Advisor: Soumya Raychaudhuri
Masahiro Kanai
Fine-mapping complex traits in large-scale biobanks across diverse populations
Advisor: Mark Daly
Alison Barton
Investigating the contribution of rare coding variants to phenotypes in human complex traits
Advisor: Po-Ru Loh
Sherry Chao
Bridging single-cell genomics and tissue spatial organization in health and cancer
Advisors: Michael Brenner and Nir Hacohen
Advisors: Michael Brenner and Nir Hacohen
Eduardo Maury
Somatic mutations in the human brain: Tracing the origins of cancer and schizophrenia
Advisor: Chrisopher Walsh
Benjamin DeMeo
Mathematical Methods for Single-cell Analysis
Advisor: Bonnie Berger
Yixuan He
Cumulative effect of multi-exposures on complex traits and diseases: derivation and applications of the polyexposure risk score Advisor: Chirag Patel
2021
Jake Conway
Novel computational frameworks for driver gene identification and evolutionary informed genomics analysis in melanoma and prostate cancer
Advisor: Eliezer Van Allen
Joe Luquette
Methods for Single-Cell DNA Sequencing Analysis with Application to the Human Brain
Advisor: Peter Park
Rebeca Borges Monroy
Transposable Elements in Health and Disease
Advisor: Christopher Walsh
Gaurav Luthria
Quantitative analysis of dynamic tumor cell phenotypes regulated by tumor associated macrophages
Advisor: Miles Miller
Advisor: Miles Miller
Qingbo Wang
Integrating large-scale genomics data to improve variant interpretation in coding and non-coding regions
Advisor: Mark Daly
Sam Freeman
Approaches for understanding relationships between cancer genomes and clinical cancer features
Advisor: Gad Getz
2020
Kate Lachance
Gene expression regulation from the nucleus to the mitochondria
Advisor: Stirling Churchman
Alexander Garrus
Accelerating the Understanding and Design of Intracellular Biosensors by Massively Multiplexed Experimentation and Machine Leaning
Advisor: George Church
Jacob Mayne Luber
Systems Interrogation of Host-Microbiome Immunomodulation and Metabolism
Advisor: Meromit Singer
Tiffany Amariuta
Functional characterization of genetic variation with in silico predictions of cell-type-specific regulatory elements
Advisor: Soumya Raychaudhuri
Danielle Rasooly
Prioritizing Observational Associations with Family History of Disease and Mendelian Randomization
Advisor: Chirag Patel
Surojit Biswas
Principles of machine learning-guided protein engineering
Advisor: George Church
Craig Lambert Bohrson
Discovery and analysis of somatic mutations in aging neurons using single-cell DNA sequencing
Advisor: Peter Park
2019
Siranush Sarkizova
Learning and modeling the rules of endogenous antigen presentation of MHC class I
Advisor: Nir Hacohen
Amaro Taylor-Weiner
Development and application of methods for cancer genome analysis
Advisor: Gad Getz
Luke O’Connor
Genetic Architecture of common diseases and complex traits
Advisor: Alkes Price
Jeffrey Gerold
Evolution and Immunity in Cancer and HIV
Advisor: Martin Nowak
Kamil Slowikowski
Transcriptomics of the synovium in rheumatoid arthritis
Advisor: Soumya Raychaudhuri
Jack Kosmicki
The contribution of rare de novo and inherited coding variants in neurodevelopmental disorders
Advisor: Mark Daly
2018
Adam Riesselman, Building maps from genetic sequences to biological function
Advisor: Debora Marks
Peter Palmedo, Extending the Reach of Coevolution-Based Protein Residue-Residue Contact Prediction
Advisor: Bonnie Berger
Yu-Han Hsu, Developing Computational Methods for Analyzing Metabolomics Data and Applications to Study Obesity
Advisor: Joel Hirschhorn
Jean Fan, Computational and Statistical Methods for Characterizing Single-cell Heterogeneity
Advisor: Peter Kharchenko
2017
Dustin Griesemer, Assaying 3-Prime Untranslated Region Variants in a Massively Parallel Fashion
Advisor: Pardis Sabeti
Jeremiah Wala, Genome-wide detection of structural variants and signatures of their selection in cancer
Advisor: Rameen Beroukhim