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
Sherry Chao
Bridging single-cell genomics and tissue spatial organization in health and cancerAdvisors: Michael Brenner and Nir Hacohen Eduardo Maury Somatic mutations in the human brain: Tracing the origins of cancer and schizophrenia Advisor: Christopher 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 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 Sam Freeman Approaches for understanding relationships between cancer genomes and clinical cancer features Advisor: Gad Getz 2020 Alexander Garruss 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