#  BIG Defenses 

 



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##  BIG Defenses 

 



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###    BIG Defenses 2026  expand\_more  

**Shandukani Mulaudzi**  
Sifting Through the Noise: Minority Variant Detection in Mycobacterium tuberculosis and Clinical Implications in Bedaquiline Resistance  
Advisor: Maha Farhat

**Brandon M. Sie**  
Antibody repertoire profiling during pregnancy and proteome-wide internal degron mapping  
Advisor: Stephen Elledge

**Arya Kaul**  
Studies in Bacterial Genome Dynamics  
Advisor: Michael Baym

**Danielle Denisko**  
Non-canonical roles of transposable elements in human evolution and disease  
Advisor: Eunjung Lee

**Michael Poeschla**   
Genetic Variation and Hematopoiesis  
Advisor: Vijay Sankaran

 

 



###    2025 Defenses  expand\_more  

**Ruitong Li**  
Integrative analysis of transcriptomics, epigenetics, and copy number to assess lineage and dynamics of tumor clones during cancer progression  
Advisor: Gad Getz

**Nolan Kamitaki**   
Generation of genotypes and phenotypes from sequencing data  
Advisor: Po-Ru Loh, Steven A. McCarroll  
  
**Maha Shady**  
From Cancer Initiation to Clinical Insight: Computational and Machine Learning Approaches to Tumor Dynamics and Precision Oncology  
Advisor: Shamil Sunyaev, Eliezer Van Allen

**Guanlan Dong**  
Single-cell Genomics of Post-mitotic Human Tissues in Aging and Disease  
Advisor: E.Alice Lee

**Maya Talukdar**  
Convergent and Sex-Differential Genetic Underpinnings of Autism  
Advisors: David Page & Christopher Walsh

**Mark S. Keller**  
Visual analytics at the atlas scale for multimodal and spatial single-cell data  
Advisor: Nils Gehlenborg

**Jayoung Ryu**  
Cross-modality data integration for precision perturbation  
Advisor: Luca Pinello

**Yasha Ektefaie**  
Foundations for Genome-Scale Artificial Intelligence  
Advisor: Maha Farhat

**Kathryn Weinand**  
Integration of single-cell multimodal data to define the chromatin landscape of rheumatoid arthritis  
Advisor: Soumya Raychaudhuri

**Tessa Han**  
Trustworthy Machine Learning for Medicine  
Advisor: Hima Lakkaraju

**Kaitlyn Anne Lagattuta**  
Investigating how sequence variation in T cell receptors and human leukocyte antigens shapes T cell development   
Advisor: Soumya Raychaudhuri

**Ajay Nadig**  
Integrative statistical methods for human biology, from biobanks to perturbation atlases  
Advisor: Elise Robinson

 

 



###    2024 Defenses  expand\_more  

**Trevor Manz**  
Composable visualization systems for biological data  
Advisor: Nils Gehlenborg

**Daniel Jaewon Lee**  
A mutation rate model at the basepair resolution and selection metric using deviation of multinomial site-frequency spectrum  
Advisor: Shamil Sunyaev

**Steffanie Paul**   
Modelling Sequence and Structure Towards Functional Protein Design  
Advisor: Debora Marks

**Michelle Li**   
Contextual Learning on Graphs for Precision Medicine  
Advisor: Marinka Zitnik

**Luke Sagers**  
Augmenting Medical Image Classifiers with Synthetic Data across Populations  
Advisor: Arjun Manrai

**Teng Gao**  
Somatic genome evolution in cancer and aging through the lens of transcription  
Advisor: Peter Park, Peter Kharchenko

**Nicita Mehta**  
Integrated Molecular and Histopathological Study of Germ Cell Tumors  
Advisor: Eliezer Van Allen

**Richard Chen**  
Multimodal & Context-Aware Computational Pathology  
Advisor: Faisal Mahmood

 

 



###    2023 Defenses  expand\_more  

**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

**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 Defenses  expand\_more  

**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

**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 Defenses  expand\_more  

**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

**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 Defenses  expand\_more  

**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 Defenses  expand\_more  

**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 Defenses  expand\_more  

**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 Defenses  expand\_more  

**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