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

Kostas Kontodimas
Distinct venous endothelias cells contribute to the fibrotic remodeling of the lung
Mentor: Bob Varelas

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

Robert Lebourdais
Title
Mentor: Hadi Nia

Yewoo Lee
Investigating the Role of Oncostatin M in Host Defense Against Pneumonia
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