Dissertation Library

Our last decade has included the following PhD dissertations, some of the exciting academic accomplishments from students and mentors of the Pulmonary Center:

2026

Gabrielle Grifno
Developing and Utilizing the Crystal Ribcage Platform to Probe Respiratory and Circulatory Functions of the Lung From Whole Organ to Single Alveolus in Helath and Disease
Mentor: Hadi Nia

Roberty Lebourdais
Title
Mentor: Hadi Nia

Yewoo Lee
Title
Mentor: Katrina Traber

Carly Merrit
Gain-of-function Toxicity in Alpha-1 Antitrypsin Deficient Type 2 Alveolar Epithelial Cells
Mentor: Andrew Wilson

Linzheng Shi
Lung-resident immunity governs early pneumonia defense revealed by paracorporeal crystal ribcage
Mentor: Hadi Nia

2025

Kevin Hayes
Impacts of endogenously expressed, heterozygous Nuclear Factor Kappa B Subunit 1 variants on complicated common variable immune deficiency
Mentor: PJ Maglione

Jhonatan Henao Vasquez
Lung airway MIWI2 expressing multiciliated cells and influenza A pathogenesis
Mentors: Matt Jones and Alan Fine

Erik Matson
Molecular and immunological mechanisms of B cell activating factor-driven B cell dysregulation in CVID
Mentor: PJ Maglione

Riley Pihl
Neutrophils respond with pathogen-specific defenses during bacterial pneumonia
Mentor: Katrina Traber

Nathan Sanders
Animal models for investigating coronavirus heterotypic immunity
Mentors: Joseph Mizgerd and Mohsan Saeed
Microbiology PhD

Kara Vasilew
Polyphosphates interfere with the host immunity in Legionella infection
Mentor: Markus Bosmann

2024

Senegal Carty
Pulmonary lymphatic remodeling in response to influenza-induced inflammation
Mentors: Matt Jones and Alan Fine

Carina Cheng 
The Roles of YAP/TAZ signaling in Immune Responses
Mentor:

Jake Le Suer 
SMAD signaling in early foregut development and the basal cell program: mechanisms driving lung competence and airway maintenance
Mentors: Finn Hawkins and Xaralabos Varelas

Táchira Pichardo
Deciphering the immune contexture of premalignancy in a murine model of lung squamous cell carcinoma
Mentor: Sarah Mazzili

Addie Matschulat
Understanding the roles of the Hippo pathway kinases LATS1/2 in the lung epithelium
Mentor: Bob Varelas

Taylor Matte
Investigating the role of NKX2-1 in human lung development
Mentor: Finn Hawkins

Kiloni Quiles
Epithelial remodeling and microbial dysbiosis in the lower respiratory tract of vitamin A-deficient mouse lungs
Mentor: Felicia Chen

Arjun Sharma
Immunity in the context of pathogens: Elucidating the complexity of host defense response mechanisms
Mentor: Markus Bosmann

2023

Claire Burgess
Generation of human alveolar epithelial type I cells from pluripotent stem cells
Mentor: Darrell Kotton
Molecular & Translational Medicine

Neelou Etesami
Dynamics and functions of protective lung B cells after pneumococcal infection
Mentor: Joseph Mizgerd
Microbiology PhD

Bibek Thapa
Cell state changes during compensatory lung regrowth following pneumonectomy
Mentor: Darrell Kotton
Molecular & Translational Medicine

Alex Ysasi

2022

Mike Breen
Extravascular B cell populations in the influenza A virus experienced lung
Mentors: Rachel Fearns and Joseph P. Mizgerd
Microbiology PhD

Carolina Lyon De Ana
Novel subsets of resident lymphocytes in murine lungs recovered from pneumococcal pneumonia
Mentor: Joseph P. Mizgerd
Microbiology PhD

Elim Na
The cytoprotective effects of leukemia inhibitory factor during bacterial pneumonia
Mentor: Lee J. Quinton
Molecular and Translational Medicine PhD

Christine Odom
Liver-dependent lung remodeling during systemic inflammation alters responses to secondary infection
Mentor: Lee J. Quinton
Microbiology PhD

2021

Emad Arafa
Recovery from pneumococcal pneumonia remodels the pool of alveolar macrophages
Mentor: Joseph P. Mizgerd
Molecular and Translational Medicine PhD

Kim Barker
The establishment and function of lung resident memory B cells after bacterial respiratory infection
Mentor: Joseph P. Mizgerd
Microbiology PhD

Elizabeth Becker
Derivation of airway epithelium transcriptomic signatures of COPD phenotypes
Mentor: Katrina Steiling
Bioinformatics GRS PhD

Julia Hicks-Berthet
Roles for YAP and TAZ in Lung Epithelial Biology
Mentor: Bob Varelas
Biochemistry PhD

Xu Ke
Airway Gene Expression Alterations in Association with Radiographic Abnormalities of the Lung
Mentor: Marc Lenburg
Bioinformatics MD/PhD

Nathan Kingston
Roles for Hippo effectors TAZ and YAP in cancer and fibrosis
Mentor: Bob Varelas
Biomedical Sciences (PiBS) PhD

Xingyi Shi
Bronchial Gene Expression Associated with Airway Premalignancy and Lung Cancer Subtypes
Mentor: Marc Lenburg
Bioinformatics PhD

2020

Yuliang (Leon) Sun
The role of ATP binding cassette A3 (ABCA3) in health and disease using pluripotent stem cell-derived type II alveolar epithelial cells
Mentor: Darrell Kotton
Molecular and Translational Medicine PhD

Jiarui Zhang
Genomic biomarker development to impact clinical management of patients at risk for lung cancer
Mentor: Marc Lenburg
Molecular and Translational Medicine PhD

2019

Anant Balijepalli
Design, synthesis, characterization, and evaluation of a cationic poly-amido-saccharide towards biocompatible nucleic acid delivery
Mentor: Mark Grinstaff
Biomedical Engineering PhD

Sean Corbett
Approaches for identifying lung cell type responses to perturbation
Mentor: Marc Lenburg
Bioinformatics PhD

Yuri Kim
Liver-dependent protection during pneumonia and sepsis
Mentor: Lee J. Quinton
Molecular and Translational Medicine PhD

George Kwong
Induced pluripotent stem cell reporter systems for smooth muscle cell sheet engineering
Mentor: Darrell Kotton
Biomedical Engineering PhD

Timothy Norman
Origin and maturation of the pulmonary lymphatic endothelium
Mentor: Alan Fine
Pathology PhD

Alicia Wooten
Pneumococcal phosphodiesterase 2 mutation elicits a unique type I interferon response in macrophages
Mentor: Joseph P. Mizgerd
Molecular and Translational Medicine PhD

2018

Julia Barrios
Neural regulation of the pulmonary neuroendocrine system induce mucus overproduction
Mentor: Xingbin Ai
Molecular and Translational Medicine PhD

Grant Duclos
Characterization of smoking-associated transcriptomic alterations to the human bronchial epithelium
Mentor: Avrum Spira
Molecular and Translational Medicine PhD

Terry Hsieh
Mild traumatic brain injury augments innate immune responses through neurokinin and cholinergic signaling
Mentor: Daniel Remick
Pathology Md/PhD

2017

Ana Brandusa Pavel
Multi-omics data integration for the detection and characterization of smoking related lung diseases
Mentor: Marc Lenburg
Bioinformatics PhD

Katherine Benson McCauley
Pluripotent stem cell modeling of airway epithelial fate
Mentor: Darrell Kotton
Molecular Biology PhD

Anjali Jacob
Generation of mature type II alveolar epithelial cells from human pluripotent stem cells
Mentor: Darrell Kotton
Molecular and Translational Medicine PhD

Jacob Josef Kantrowitz
Transcriptomic alterations underlying pathogenesis and carcinogenesis in COPD
Mentor: Marc Lenburg
Molecular and Translational Medicine MD/PhD

Joseph Perez-Rogers
Development of a minimally invasive molecular biomarker for early detection of lung cancer
Mentor: Marc Lenburg/Avrum Spira
Bioinformatics PhD

Aleksander Szymaniak
Polarity and Hippo signaling in epithelial cell fate regulation
Mentor: Bob Varelas
Biochemistry PhD

2016

Fadie Coleman
Influence of macrophage NF-kappaB activation on pneumococcal pneumonia
Mentor: Joseph P. Mizgerd
Microbiology PhD

Elyse Kozlowski
Functional roles for the terminal uridyltransferase enzymes Zcchc6 and Zcchc11 in mammalian biology
Mentor: Matthew R. Jones
Molecular and Translational Medicine PhD

Nicole Stauffer Smith
Respiratory infections with pneumococci establish multi-pronged heterotypic protection against pneumonia
Mentor: Joseph P. Mizgerd
Pathology and Laboratory Medicine PhD

Greg Wasserman
A discrete population of ciliated cells express the piRNA binding protein MIWI2 to regulate lung inflammation
Mentor: Matthew R. Jones
Microbiology PhD

2015

Kristie Hilliard
The functional significance of the lung-liver axis during pneumonia
Mentor: Lee J. Quinton
Microbiology PhD

Rebecca Kusko
Integrative transcriptomics in smoking related lung diseases
Mentor: Avrum Spira
Genetics & Genomics PhD

Teresa Wang
Transcriptomics of the human airway epithelium reflect the physiologic response to inhaled environmental pollutants
Mentor: Marc Lenburg
Bioinformatics PhD

2014

Joseph Gerrein
Using gene and microRNA expression in the human airway for lung cancer diagnosis
Mentor: Avrum Spira
Bioinformatics PhD

Kahkeshan Hijazi
The airway transcriptome as a measure of injury response to and recovery from smoking and alternative tobacco products
Mentor: Marc Lenburg
Bioinformatics PhD

John Mahoney
The role of Yap in lung development
Mentor: Wellington Cardoso
Pathology & Laboratory Medicine PhD

2013

Linh Aven
Innervation defects as a mechanism of childhood asthma
Mentor: Xingbin Ai
Molecular Medicine, Cell and Molecular Biology PhD

John Brothers
Characterizing and reassembling the COPD and ILD transcriptome using RNA-Seq
Mentor: Marc Lenburg
Bioinformatics PhD

Radhika Dixit
The contribution of mesothelial cells to lung development
Mentor: Alan Fine
Molecular Medicine PhD

2012

Joshua Campbell
Genome-wide characterization of microRNA and gene expression patterns in smoking-related lung disease
Mentor: Marc Lenburg
Bioinformatics PhD

Julie Gil Zeskind
Gene expression alterations associated with progression of emphysema and small airway disease in smokers with COPD
Mentor: Avrum Spira/Marc Lenburg
Bioinformatics PhD

Adam Gower
Discovering biological connections between experimental conditions based on common patterns of differential gene expression
Mentor: Avrum Spira/Marc Lenburg
Bioinformatics PhD