PhD Dissertations
2025
John Sterrett - Integrated Physiology - PIs: Chris Lowry and Cathy Lozupone
- Novel Multi-Omics Methods Improve Understanding of Host-Microbe Crosstalk in the Mammalian Gut
Clair Huffine - Biochemistry - PI: Jeff Cameron
- Linking Cyanobacterial Carboxysome Maturation, Permeability, and Equilibria via Redox Dynamics
Casey Middleton - Computer Science - PI: Dan Larremore
- Multiscale Infectious Disease Dynamics: Linking Epidemiology and Testing for Outbreak Neutralization
Zach Maas - Computer Science - PI: Robin Dowell
- Supervised and Unsupervised Methods for Transcriptional Sequencing Data
Sharon Wu - Molecular Cellular and Developmental Biology - PI: Sara Sawyer
- Exploring The Diversity of Virus-Host Compatibility: Cell Entry Receptor Usage by Clade D Arenaviruses
Jack Gugel - Molecular Cellular and Developmental Biology - PI: Leslie Leinwand
Liam Friar - Geology - PI: Boswell Wing
Kathleen Murphy - Molecular Cellular and Developmental Biology - PI: Zoe Donaldson
2024
Payton Martinez - Biomedical Engineering - PI: Mark Borden
- Enhancing Drug Delivery in Diffuse Midline Gliomas Using Focused Ultrasound Mediated BBB Opening: Optimization of Acoustic and Microbubble Parameters
Lukas Buecherl - Biomedical Engineering - PI: Chris Myers
- Decoding Genetic Circuit Failures: Analyzing Static and Dynamic Failures in Genetic Circuitry
Alison Leonard - Chemical and Biological Engineering - PI: Tim Whitehead
- Engineering Protein Folds for Enhanced Stability and Molecular Recognition of Diverse Drug-Like Small Molecules
Adam Dziulko - Computer Science - PI: Ed Chuong
- Retroviral Dysregulation of an Immune Chromatin Regulator
Tristan Caro - Geology - PI: Alexis Templeton
- From Soil to Subsurface: Tracking Microbial Growth Under Energy Limitation
Kate Bubar - Computer Science - PI: Dan Larremore
- Quantifying the Effectiveness of Infectious Disease Interventions in Heterogeneous Populations
Karl Widney - Biochemistry - PI: Shelley Copley
- Evolution of Novel Metabolic Pathways
Kristen Schneider - Computer Science - PI: Ryan Layer
- Supporting Efficient Investigation of Biobank-Scale Human Genomic Data for Application in Precision Medicine
Sierra Jech - Ecology and Evolutionary Biology - PI: Nicole Bargar
- Inoculation as a Biocrust Rehabilitation Strategy
Peter Innes - Ecology and Evolutionary Biology - PI: Nolan Kane
- Evolution, Diversity, and Domestication of North American Blue Flax
Andrea Halling - Geology - PIs: Carl Simpson and Patrick Kociolek
- Evolutionary and Ecological Significance of Multicellularity: Insights From Experimental, Fitness, and Isotopic Perspectives
Sukuan Liu - Ecology and Evolutionary Biology - PI: Stacey Smith
Using South American Pitcher Plants Heliamphora as Study System to Investigate the Convergent and Divergent Evolution of Plant Carnivory in Angiosperms
2023
Corinne Walsh - Ecology and Evolutionary Biology - PI: Noah Fierer
- Building a Predictive Understanding of Plant, Soil, and Microbe Associations
Grant Vagle - Ecology and Evolutionary Biology - PI: Christy McCain
- Diversity Mechanisms and Rarity: How Rare Species Contribute to Biodiversity Patterns
Scott Nordstrom - Ecology and Evolutionary Biology - PI: Brett Melbourne
Within-Population Environmental and Genetic Variation and Its Demographic and Evolutionary Consequences
2022
Michael Smallegan - Molecular, Cellular, and Developmental Biology - PI: John Rinn
- The Role of RNA in Transcriptional Regulation
Dieu My Nguyen - Computer Science - PI: Orit Peleg
- Flow-Mediated Collective Olfactory Communication in Honey Bee Swarms
Kaitlin McCreery - Mechanical Engineering - PI: Corey Neu
- Multiscale Biophysical Signaling Regulates Tissue Morphogenesis and Degeneration
Courtney Van Den Elzen - Ecology and Evolutionary Biology - PI: Nancy Emery
- On the Evolution of Seed Dispersal and Seed Dormancy in Variable Environments
Daniel Ramirez - Molecular, Cellular, and Developmental Biology - PIs: Robin Dowell and Ed Chuong
- On the Evolution of Gene Transcription Regulation in Metazoans
Kelsey Dahlgren - Biochemistry - PI: Jeff Cameron
- Development and Use of Proximity-Based Proteomics to Determine Subcellular Localization of Proteins in Cyanobacteria
Jennifer Coulombe - Biomedical Engineering - PI: Virginia Ferguson
Diminished Bone Structural Quality in Aging and Microgravity Follow Impairments of the Osteocyte Lacunar-Canalicular System
2021
Audrey Watson - Biochemistry - PI: John Rinn
- Coding and Noncoding Modalities of LncRNA Function
Kristin Calahan - Mechanical Engineering - PIs: Mark Renschler and Rong Long
- Soft Tribology of Micropatterned Surfaces: Friction Mechanism Discovery for Informed Design
Cierra Walker - Material Science and Engineering - PIs: Kristi Anseth and Leslie Leinwand
- Signaling from Matrix Stiffness to the Cells of the Heart
Andrew Kavran - Computer Science - PI: Natalie Ahn
- Intermittent Drug Treatment of BRAFV600E Melanoma Cells Delays Resistance by Adaptive Resensitization to Drug Rechallenge
April Goebl - Ecology and Environmental Biology - PIs: Dan Doak and Nolan Kane
- Factors Affecting Establishment, Adaptation, and Persistence of Small Populations in Variable Environments
Chris Smith - Ecology and Evolutionary Biology - PIs: Sam Flaxman and Nolan Kane
- Investigating Population History and Diversification Using Genome-Scale Data
Kyle Keepers - Ecology and Evolutionary Biology - PI: Nolan Kane
Harnessing Genomic and Bioinformatic Tools to Inform Conservation Decisions of Species that Are Vulnerable to Human-Driven Impacts of Climate Change
2020
Ignacio Tripodi - Computer Science - PIs: Robin Dowell and Larry Hunter
- Inferring Mechanisms of Toxicity from Differential Genomics and Semantic Knowledge Representations
Jacqueline Wentz - Applied Math - PI: David Bortz
- Spatial-Temporal Effects of Diffusion in Complex Biochemical Networks
Taisa Kusher - Computer Science - PI: Sriram Sankaranarayanan
- Data-Driven Modeling and Verification for Artificial Pancreas Systems
Carter Tillquist - Computer Science - PI: Manual Lladser
- Low-Dimensional Embeddings for Symbolic Data Science
Antony Pearson - Applied Math - PI: Manual Lladser
On Hidden Structures in Contaminated Symbolic Data
2019
Lynn Sanford - Biochemistry - PI: Amy Palmer
- Characterization of Intracellular Zn2+ Dynamics and Zn2+-Dependent Gene Expression in Primary Dissociated Hippocampal Neurons
Patrick Heenan - Physics - PIs: Tom Perkins and Tom Cech
- Improved Energy Landscape Reconstruction and Imaging of Nucleic and Amino Acids via Atomic Force Microscopy
Katia Tarasava - Material Science and Engineering - PI: Ryan Gill
- Development of Novel CRISPR-Based Methods for Transcriptional Control Over Bacterial Gene Expression
Eric Kightley - Applied Math - PI: David Bortz
- Stokes, Gauss, and Bayes walk into a bar...
Kathryn Palma Wall - Biochemistry - PI: Loren Hough and Debora Wuttke
- Investigating the Role of the Disordered C-Terminal Tails in Tubulin Dynamics
Anna Broido - Applied Math - PI: Aaron Clauset
Characterizing the Tails of Degree Distributions in Real-World Networks
2018
Cloe Pogoda - Molecular, Cellular, and Developmental Biology _ PIs: Nolan Kane and Robin Dowell
- Mitochondrial Genomes as Tools for Analysis and Teaching of Comparative Genomics, Evolution, and Ecology
John Nardini - Applied Math - PI: David Bortz
- Partial Differential Equation Models of Collective Migration During Wound Healing
David Brazel - Molecular, Cellular, and Developmental Biology - PI: Kenneth Krauter and Scott Vrieze
- Understanding the Genetics of Substance Use: Novel Phenotypic and Large-scale Genomic Approaches
Ryan Langendorf - Environmental Studies - PI: Dan Doak
- Mechanical Inference in Dynamic Ecosystems
Carlos Vera - Molecular Cellular and Developmental Biology - PI: Leslie Leinwand
Christopher Weiss-Lehman - Environmental Biology - PI: Brett Melbourne
- Spatial Structure in Extinction and Range Expansion: Models and Experiments
Nora Connor - Computer Science - PI: Aaron Clauset
- Using Data Science to Find Interpretable Answers for Problems in Ecology and Political Science
Aaron Aziz - Chemical and Biological Engineering - PI: Stephanie Bryant
Biomimetic Hydrogels to Support Bone Development for Osteochondral Tissue Engineering Applications
2017
Sam Way - Computer Science - PI: Aaron Clauset
- Systematic inequalities in the composition and productivity of computer science faculty
Aaron Wacholder - Ecology and Evolutionary Biology - PI: David Pollock
- Evolutionary Inference in Transposable Elements
Joey Azofeifa - Computer Science - PI: Robin Dowell
- Stochastic modeling of RNA polymerase predicts transcription factor activity
Lauren Shoemaker - Environmental Biology - PIs: Brett Melbourne and Aaron Clauset
Stabilizing and Equalizing Mechanisms Alter Community Coexistence and Macroevolutionary Diversity Patterns
2016
Hui-Shun Kuan - Physics - PIs: Meredith Betterton and Matthew Glaser
Active pattern formation in one and two dimensions
2015
Adam Robbins-Pianka - Computer Science - PI: Rob Knight
- Advanced Computational Tools for Analyzing Microbial Communities for Energy Production Environments
Daniel McDonald - Computer Science - PI: Rob Knight
The development of a microbiome reference that spans thousands of individuals
2012
Dan Knights - Biochemistry - PIs: Rob Knight and Michael Mozer
- Predictive Modeling of Metagenomes