MSTP

Recent MSTP Dissertations

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Biochemistry & Molecular Biophysics

MSTP Trainee Faculty Advisor(s) Thesis Title
Yifei Hu Jun Huang Identifying, Investigating, and Modulating Anti-CD19 CAR T Cells for Large B-Cell Lymphoma
Caraline Sepich Chuan He Location-Dependent Effects of N6-methyladenosine on mRNA Translation and Stability
Andrew Wang Savas Tay Multi-Level Encoding of Inflammatory Memory in the NF-κB Network
Michael Clark Eduardo Perozo Electromechanical Coupling and Gating Polarity in Voltage-Gated Ion Channels
Kathryn Scherpelz Stephen Meredith Alzheimer's Brain and Meninges-Seeded Amyloid Fibrils
Jeremy Treger Francisco Bezanilla Novel Techniques in Optical Electrophysiology Lead to New Biophysical Insights
Ian Roundtree Chuan He Post-Transcriptional Gene Regulation by N 6-Methyladenosine and Selective RNA Binding Proteins
Katherine Zhou Tao Pan RNA Modifications: Impact on Protein Binding, Co-Transcriptional Regulation, and Sequencing Signatures

Biophysical Sciences

MSTP Trainee Faculty Advisor(s) Thesis Title
Hendrik Glauninger Allan Drummond/Tobin Sosnick Insights into Stress-Induced Condensation of mRNA and Protein
Wenli Dai Christopher Weber Role of Transcription Factors and Intercalated Disc Proteins in Arrhythmogenesis
Alan Hutchison Aaron Dinner Improved statistical methods for analyzing circadian rhythms in high-throughput data
Gabe Salzman Demet Arac-Ozkan/Shohei Koide The Extracellular Regions of Adhesion G Protein-Coupled Receptors Regulate Ligand Binding and Intracellular Signaling
Ramya Parameswaran Bozhi Tian Silicon nanowires for the optical modulation of cellular activity

Cancer Biology

MSTP Trainee Faculty Advisor(s) Thesis Title
Matthew Jotte Megan McNerney Defining the Pathogenesis of Del(7q) in Hematopoietic Stem Cells
Allen Zhu Chuan He The Phosphorylation-Dependent Regulation of the RNA N6-Methyladenosine Methyltransferase Complex
Molly Imgruet Megan McNerney The Role of CUX1 in Therapy-Related Myeloid Neoplasms
Adam Gasser Stephen Meredith Synthesis and Assembly of Functionalized Peptide Nanoplatforms for the Targeted Delivery of Molecules to Tumors
Marina Sharifi Kay Macleod Autophagy is Required for Focal Adhesion Dissassembly, Tumor Cell Motility, and Metastasis
Erin Mowers Kay Macleod The role of autophagy in tumor progression and metastasis

Chemistry

MSTP Trainee Faculty Advisor(s) Thesis Title
John Coukos Ray Moellering Defining the Reactivity Landscape of the Clycolytic By-Product Methylglyoxal To Study Cellular Function
Saara-Anne Azizi Bryan Dickinson The Development of Acrylamide-based Inhibitors of DHHC Family Proteins to Regulate ERK Acylation and Activity

Computational Neuroscience

MSTP Trainee Faculty Advisor(s) Thesis Title
Ou (Oliver) Zhu David Freedman Neuronal Encoding of Categorical Decisions Across Primate Oculomotor Networks
Katie Long Sliman Bensmaia Touch Spanning Spatial Scales: Texture Coding along the Somatosensory Neuraxis
Zaina Zayyad Jason MacLean/John Maunsell Visually-Evoked Normalization in Awake Mouse V1
Victoria Okuneye Sarah Keedy Investigating the Relationship of Delusions in Psychosis with the Functional Integration of Prediction Error Neural Networks
Sofija (Sophia) Canavan Daniel Margoliash Avian Sleep Architecture and Motor Replay
Arup Sarma David Freedman Learning-Dependent Plasticity of Visual and Cognitive Encoding in Parieto-Frontal Networks
Sophia Uddin Howard Nusbaum Auditory understanding of speech and non-speech

Development, Regeneration & Stem Cell Biology

MSTP Trainee Faculty Advisor(s) Thesis Title
Rajiv Nadadur Ivan Moskowitz Defining Gene Regulatory Networks of Cardiac Rhythm

Ecology & Evolution

MSTP Trainee Faculty Advisor(s) Thesis Title
Megan Kennedy Eugene Chang/Joy Bergelson Temporal Mechanisms of Population- and Community-Level Microbial Adaptation to Shifting Resource Landscapes
Suraj (Neil) Sheth Luis Bettencourt The Community Human Development Index (CHDI): A Novel Metric for Precision Public Health
Sylvia Ranjeva Sarah Cobey/Greg Dwyer Host heterogeneity and the dynamics of pathogen diversity.
Frank Wen Sarah Cobey Ecological and Evolutionary Dynamics of Influenza Shaped by Human Immunity

Human Genetics

MSTP Trainee Faculty Advisor(s) Thesis Title
David Blair Andrey Rzhetsky Investigating Complex and Mendelian Disease Genetics Through Massive Digital Phenotyping
Samantha Thomas Yoav Gilad Induced Pluripotent Stem Cells as a Model to Study Individual Variation and Comparative Genomics

Genetics, Genomics & Systems Biology

MSTP Trainee Faculty Advisor(s) Thesis Title
Gabriel Casella Marcus Clark/Maryellen Giger Computer Vision and Statistical Methods for the Study of Renal Autoimmunity: The Immune Architecture of Lupus Nephritis and Renal Allograft Rejection
Anthony Hung Yoav Gilad Determining the Genetic Basis of Gene Expression Responses to In Vitro Models of Osteoarthritis
Grace Hansen Marcelo Nobrega Repeat Elements and Novel Genes Contribute to Sex-Specific Mechanisms of Metabolism
Reem Elorbany Yoav Gilad Investigating the Dynamics of Gene Regulation During Cardiomyocyte Differentiation Using Bulk and Single Cell RNA Sequencing
Alex Guzzetta Ivan Moskowitz A Hedgehog-FGF Signaling Cascade Patterns the Anterior-Posterior Axis during Embryonic Development
Justin Chew Mike Rust Vulnerability to Molecular Noise Constrains the Architecture of Bacterial Clocks

Immunology

MSTP Trainee Faculty Advisor(s) Thesis Title
Denis Cipurko Nicolas Chevrier Molecular Cartography of the Mouse In Toto Reveals Mechanisms of Systemic Inflammation
Emily Cullum Tatyana Golovkina  The Role of H2-O and Additional Novel Loci in Antigen Presentation and the Immune Response against Bacteria and Viruses in Mice
Tanner Martinez Megan McNerney Establishing CUX1 as a Determinant of Hematopoietic Stem Cell Heterogeneity
Arpit Panda Chuan He  Multi-omic Urine cfDNA Approaches for Detecting Molecular Residual Disease in Bladder Cancer and Single-Cell Mechanisms of Radiation-Induced Metastasis
Donald Rodriguez Pete Savage Defining the Role of T Cell Receptor - Self-Peptide/MHC Class II Interactions in Directing CD4+ T Cell Fate, Function, and Pathogenic Potential
Kishan Sangani Bana Jabri TET2 Regulates Homeostatic Th2 Immunity in the Small Intestine
Sarah Sun Bana Jabri/Luis Barreiro Mechanisms of Innate Immune Memory in Basic and Clinical Models
Mayuri Viswanathan Erin Adams The T Cell Receptor Guides Development, Polarization, and Peripheral Function of γδ T Cells
Nathaniel Wright Marcus Clark BRWD1 Establishes Epigenetic States for Germinal Center Initiation, Maintenance, and Function
Rebecca Abraham Marcus Clark Interrogating Spatial Features of Renal Inflammation in Human Lupus Nephritis Using Computer Vision
Dustin Shaw Patrick Wilson/Bana Jabri A Unique Adaptive Inflammatory Signature Is Linked to Dysplasia in Primary Sclerosing Cholangitis
Blake Flood Tom Gajewski Tumor Cell-Intrinsic Defects in Sting Pathway Signaling and Type I Interferon Expression
Kaitlin McLean Marcus Clark The Role of GAGA Motif Domains in Chromatin Remodeling of Igκ during B Cell Development
Dan Camacho Anne Sperling Antigen-Presenting Cells in Type 2 Lung Inflammatory Responses
Victoria Lee Pete Savage The Endogenous Repertoire Harbors Self-Reactive CD4+ T Cell Clones That Adopt a T Follicular Helper-like Phenotype at Steady State
Christine Miller Pete Savage Development and Function of Self-Specific Memory-Phenotype CD8+ T Cells
Melissa Tjota Anne Sperling Activation of Antigen Presenting Cells through FCRGamma Drives IL-33 Dependent TH2-Type Responses in the Lungs
Tony Tu Yang-Xin Fu CD160, An Essential Regulator of the Cytokine Response by Natural Killer Cells
Jennifer Jacobsen Barbara Kee EZH2 Regulates the Pre-antigen Receptor Checkpoint and B-2 Lineage Commitment
Ben Casterline Julie Wardenburg Early life acquisition and pathogenesis of maternally inherited Bacteroides fragilis
Jeff Bunker Albert Bendelac Specificity of homeostatic IgA
Phil Hsu Chuan He Roles of mRNA methylations in biology: processing and development

Integrative Neuroscience

MSTP Trainee Faculty Advisor(s) Thesis Title
Anya Bershad Harriet de Wit Effects of Opioids on Social and Emotional Processing in Humans

Microbiology

MSTP Trainee Faculty Advisor(s) Thesis Title
Russell Becker Julie Bubeck-Wardenburg Tissue-Specific Modulation of Innate Immunity by Staphylococcus aureus Alpha-Toxin
Vivian Choi Julie-Bubeck-Wardenburg Characterization of Virulence-Associated Protein Processing Genes in Bacteroides fragilis
Mark Lunderberg Olaf Schneewind Assembly of the Bacillus anthracis vegetative cell envelope
Megan Zilla Dominique Missiakas The Role of LytR-CpsA-Psr Enzymes in the Lifecycle of Bacillus anthracis

Molecular Engineering

MSTP Trainee Faculty Advisor(s) Thesis Title
Andrew Molina Tobin Sosnick/Benoit Roux Uncovering the Mechanism of Potassium Channel Folding and Assembly
Mathew Schnorenberg Matthew Tirrell/James LaBelle Targeted Delivery of Therapeutic Peptides Using Supramolecular Nanomaterials to Drug Intracellular Protein-Protein Interactions in Cancer

Molecular Metabolism and Nutrition

MSTP Trainee Faculty Advisor(s) Thesis Title
Mary Frith Eugene Chang Microbiota-Dependent Early Life Programming of Gastrointestinal Motility

Neurobiology

MSTP Trainee Faculty Advisor(s) Thesis Title
Sarita Deshpande Wim Van Drongelen Spatiotemporal Characterization of Neural Network Activity
Sylvia Edoigiawerie Naoum (Norm) Issa Neurophysiologic Monitoring and Prognostic Algorithms for Neonatal Hypoxic Ischemic Encephalopathy
Somin (Min) Lee Wim Van Drongelen Multiscale Features and Mechanisms of Cortical Epileptiform Activity
Alexis Monical Dan McGehee The Role of the Laterodorsal Tegmental Nucleus in Nicotine Withdrawal
Iboro Umana Dan McGehee Nicotinic Modulation of Descending Pain Control Circuitry
David Koren Wei Wei Dendritic Mechanisms Underlying Retinal Direction Selectivity

Public Health Sciences

MSTP Trainee Faculty Advisor(s) Thesis Title
Meytal Chernoff Brandon Pierce Genes in Context: Understanding How Tissue Type, Ancestry, and Environment Influence the Effects of Genetic Variation on Human Traits

Public Policy

MSTP Trainee Faculty Advisor(s) Thesis Title
Maya Lozinsi (MeSH) David Meltzer/Zarek Brot-Goldberg Essays on the Economics of Scale and Complexity in Healthcare
Nina Gao David Meltzer What Gets Measured (Gets Done): Essays on Healthcare, Policy and Perils of the Subjective made Objective