BIG Defenses

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
 

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

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

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

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

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

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

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

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

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