Doctoral Dissertations

May 2024
Graduate Student Dissertation Title Advisor(s)
Avnika Bali A “Spicy” Molecular Mechanism of TRPA1 Hyperactivation Conferred by a Disease Mutant and Insights Into C-Terminal Regulatory Components Candie Paulsen
Kathryn Barth Investigating the Sequence Requirements for Specific Ligand Recognition in Variant Riboswitches Scott Strobel
Allison Butt The Duality of Neurons: Co-Transmission of Serotonin and a Neuropeptide, NLP-3, in the Caenorhabditis Elegans Egg-Laying Circuit Michael Koelle 
Kevin Chung Structural Insights Into Group II Intron Splicing and Retrotransposition Anna Marie Pyle
Daisy Duan Regulation of Microtubule Nucleation and Repair by an Abl Family Kinase Anthony Koleske
Luka Maisuradze The Elucidation of Chromatin Structural Properties Through Feature Detection in Hi-C Maps Corey O’Hern
Katelyn Noronha Understanding Vulnerabilities in Metabolism and DNA Repair in Oncometabolite-Producing Cancers Ranjit Bindra

Justin Sanders

Uncovering a Critical Role for Calmodulin in Calcium-Dependent Regulation of the Nociceptor TRPA1 Candie Paulsen 
December 2023
Gabriel Casanova Speúlveda Autoregulation Mechanism of LIM Domain Kinases  Titus Boggon
Ellen Corcoran Disruption of Trio GEF Function and Regulation in Neurodevelopmental Disorders Tony Koleske
Daniel Konstantinovsky Probing Diverse Biological Systems and their Hydration Shells by Modeling Chiral Sum Frequency Generation Spectroscopy Sharon Hammes-Schiffer
May 2023
Carolyn Breckel The Essential Protein Sts1 Facilitates 26S Proteasome Nuclear Import by a Unidirectional Mechanism in Saccharomyces cerevisiae Mark Hochstrasser
Carson Bryant Uncovering Novel Biological Regulators of Human Ribosome Biogenesis Susan Baserga
Peter Dahl Toward Understanding the Mechanism of Charge Transport in Protein Nanowires Nikhil Malvankar
Austin Draycott Canonical and Non-Canonical Functions of Dihydrouridine Synthases in Health and Disease Wendy Gilbert
Mason McCool Novel Protein Regulators of Human Ribosome Biogenesis Susan Baserga
Aldo Salazar Morales  Molecular Mechanism of Assembly and Secretion of Geobacter sulfurreducens Pili and Cytochrome Nanowires for Extracellular Electron Transport Nikhil Malvankar
December 2022
Nakeriah Christie Investigating a Locomotor Neuron that Makes a Potential Sensory Cilium Lying over the C. elegans Egg-laying Apparatus, Designing an Accessible System for Neuron Identifications, and Advancing Imaging and Modeling in the Egg-laying System Michael Koelle
Caroline Focht Monitoring Translation Regulation by Structured RNA Elements Scott Strobel
Shawn Gray Determining the Function and ATPase/RNA Remodeling Cycle of Dbp5 Enrique De La Cruz
Nicholas Huston Identifying Riboregulatory Elements in Long, Single-Stranded, Positive-Sense RNA Viral Genomes Anna Marie Pyle
Wanging Lyu Abl2 Regulates Microtubule Dynamics Through Interaction With Both the Microtubule Lattice and Tubulin Dimers Tony Koleske
Shivali Patel A Pipeline for Discovery and Determination of Functional Tertiary Structures in Large RNAs Anna Marie Pyle
Sarah Prophet Mechanisms of Protein Quality Control at the Nuclear Envelope and During Nuclear Pore Complex Biogenesis Christian Schlieker
Catherine Shipps Electrons on the Move in Proteins: Microbial Cytochrome Nanowires in Extracellular Electron Transfer and as Functional Materials Nikhil Malvankar
Vishok Srikanth Structural Basis for the Assembly of OmcS and OmcS-Like Cytochrome Nanowires in Diverse Microbial Species Nikhil Malvankar
Josh Zimmer The Dynamics of Early Steps in Transcription and Their Dysregulation in X-Linked Dystonia Parkinsonism Matthew Simon

May 2022

Dahyana Arias Escayola Comprehensive Identification and Characterization of Cajal Body Components Karla Neugebauer
Josie Bircher Regulation of Trio GEF1 Activity by the Spectrin Repeats and Cellular Factors Tony Koleske
Megan Brady  Structural Basis of Flagellar Filament Asymmetry and Supercoil Templating by Leptospira Sheath Factors Charles Sindelar
Melanie Horwitz Targeted Nucleic Acid Delivery to the Endothelium Mark W. Saltzman
Clorice Reinhardt Tyrosine Mediated Proton-Coupled Electron Transfer Reactions Sharon Hammes - Schiffer
December 2021
Catherine Amaya Role of NOMO in Determining ER Morphology and Function Christian Schlieker
Sachita Ganesa The DNA Mismatch Repair Pathway Affects ATR Activation Upon Temozolomide Treatment in MGMT-Promoter Methylated Glioblastoma Multiforme Ranjit Bindra
Mengyuan (Helen) Sun Characterizing the Photophysics of Photoconvertible Fluorescent Protein mEos3.2 for Quantitative Fluorescence Microscopy Thomas Pollard & Joerg Bewersdorf
Joshua Temple Structural Studies on Mechanisms of SAMHD1 Function and Dysfunction Yong Xiong
Danielle Widner Novel Functions for Large Noncoding Nucleic Acids in Bacteria Ronald Breaker
May 2021
Rajshekhar Basak Biophysical Characterization of Somatosensory Responses in Drosophila Class IV Dendritic Arborization Neurons Joe Howard
Marth Braun FisB Mediated Membrane Fission During Sporulation in Bacillus Subtilis Erdem Karatekin
Ken Brewer Computational Discovery of Structured Noncoding RNA Motifs in Bacteria Ronald Breaker
Chin Leng Cheng Insights Into the Regulation and Mechanism of 26S Proteasome Base Assembly in Saccharomyces Cerevisiae Mark Hochstrasser
Jennifer Garbarino Loss of ATRX Confers DNA Repair Defects and PARP Inhibitor Sensitivity in Glioma Ranjit Bindra & Ryan Jensen
Lisa McLean Discovering Novel Regulators of Nucleolar Form and Function Susan Baserga
Curran Oi Reversible Peptide-Protein Interactions Inside Cells: Enabling a New Approach for Achieving Super-Resolution Imaging in Live Cells Lynne Regan
Kristen Reimer Co-Transcriptional Splicing in Murine Erythroblasts Karla Neugebauer
Nicole Rosa Mercado Insights Into the Biogenesis of Stress-Induced Readthrough Transcripts Joan Steitz
Meaghan Sullivan A Comparative Approach to Studying RNA Biochemistry Using TimeLapse Chemistry and Labeling in Cell Culture (TILAC) Matthew Simon
Kuanlin Wu Platelet-Derived Growth Factor Receptor Beta Activates Abl2 Through Direct Binding and Phosphorylation Tony Koleske
December 2020
Lea Kiefer Investigating RNA Population Dynamics Through Nucleotide Recoding: Extending the TimeLapse-seq Toolkit to 6-Thioguanosine Matthew Simon
Patrick O’Brien  A Tale of Two Nanowires: The Biochemical and Spectroscopic Characterization of the Conductive Cytochrome OmcS and OmcZ Filaments of Geobacter Sulfurreducens Nikhik Malvankar
May 2020
Tara Alpert Coordination Between Pre-Mrna Splicing And Cleavage In Budding Yeast Karla Neugebauer
Ryan Brecht Regulation And Targeting Of V(D)J Recombination Through Rag Interactome Analysis David Schatz
Hongli Chen A Wolbachia Nuclease And Its Binding Partner Provide A Novel Mechanism For Cytoplasmic Incompatibility Mark Hochstrasser
Edward Courchaine Assembly Mechanisms Of Nuclear Bodies Karla Neugebauer
Garrett Debs Using Cryo-Electron Microscopy To Study Microtubule Heterogeneity Charles Sindelar 
Robert Fernandez An Atlas Of Neurotransmitter Gpcr Cellular Expression Patterns In The C. Elegans Egg-Laying Circuit Michael Koelle 
Pei-Tzu Huang Interactions And Regulation Of The Microtubule System By Viral And Cellular Proteins Yong Xiong  & Joe Howard
Andrew Huehn Structural Studies Of Actin-Binding Proteins Involved In Actin Dynamics, Organization And Force Sensing Charles Sindelar 
Nicole Johnston Fluoride Toxicity And The Cellular Response In Normal, Sensitized, And Resistant Yeast Scott Stobel
Kirsten Knecht Investigating Immune Pathways Involved With Cancer Drug Metabolism & Viral Evasion Yong Xiong
Christopher Lim Structural Elucidation Of A Multifunctional Protein From Orientia Tsutsgamushi Yong Xiong
Nandan Pandit Mechanical Properties Of The Arp2/3 Complex Enrique De La Cruz
Jeremy Schofield Timelapse-Seq: Examining The Dynamics Of The Transcriptome Through 4-Thiouridine Nucleoside Recoding Matthew Simon 
Juliana Shaw Actin Regulation And Functional Interactions In Dendritic Spines Anthony Koleske
December 2019
Lauren Budenholzer The Protein Sts1 Binds Mature Proteasomes And Facilitates Proteasome Nuclear Localization In Saccharomyces Cerevisiae Mark Hochstrasser
Neal Ravindra Molecular Assembly In The Endocytic Pathway Julien Barro
Anthony Schramm Plastic Deformations And Fragmentation Of Deformed Actin And Cofilactin Filaments Enrique De La Cruz
Tyler Smith Reengineering The Uridine-54 Trna Methyltransferase, Trma, To Covalently Capture New Rna Substrates Matthew Simon
May 2019
Ruben Atilho Using Riboswitches To Uncover Hidden Biological Processes And Novel Antibacterial Agents Ronald Breaker 
Kelly Culhane Uncovering The Molecular Mechanisms Of Ligand Binding To Parathyroid Hormone 1 Receptor E. Chui - Ying Yan
Katherine Farley - Barnes Discovery Of New Regulators Of Human Ribosome Biogenesis Susan Baserga
Jimi Miller Canonical And Non-Canonical Plant Heterotrimeric G Proteins In Plant Immunity Nicole Clay
Stephanie Reikine Biophysical Studies On Nucleotide Sensing Proteins In The Immune System Enrique De La Cruz & Yorgo Modis
Michael Rutenberg Schoenberg Development Of Computational Tools To Analyze New Experimental Technologies For The Study Of Noncoding Rna Matthew Simon & Mark Gerstein
Sarah Smaga Examining The Interaction Of The Antiviral Protein Mxb With Hiv Capsid Xiong Yong
Sammie Ziegler Insight Into Interactions Of Apobec3 Proteins With Dna And Hiv Vif Xiong Yong
December 2018
Olga Buzovetsky Protecting The Genome: Preserving Nucleotide Metabolism And Dna Repair, And Defending Against Viral Invaders Yong Xiong
Ethan Laudermilch Elucidating Torsin Atpase Function And Regulation At The Nuclear Envelope Christian Schlieker 
Cary Liptak Investigating Nucleotide Selection Fidelity Mechanisms In Dna Polymerase Beta Patrick J. Loria 
Jimi Miller Non-Canonical Plant G Proteins In Plant Immunity Nicole Clay
Daniel Moonan Design And Construction Of A Recoded Organism Containing 62 Codons Farren Isaacs
Brady Summers Modular Hiv-1 Capsid Assemblies For Investigating Diverse Host Recognition Mechanisms Yong Xiong
Tenaya Vallery Functional Studies On Polyadenylated Nuclear Rna In Kaposi’S Sarcoma-Associated Herpesvirus-Infected Cells Joan Steitz
May 2018
Daniel Bondeson Furthering The Scope, Understanding, And Application Of Proteolysis Targeting Chimera Craig Crews
Erin Duffy Measuring Transcriptional Dynamics Using Mts Chemistry Mathew Simon
Michael Hinrichsen Applying Protein-Peptide Interactions To Fluorescently Label Proteins In S. Cerevisiae Lynne Regan
Michael Lacy Single-Molecule Dynamics In Clathrin-Mediated Endocytosis And Membrane Remodeling Julien Berro
Caroline Reiss Structural Basis for Functional Versatility in Riboswitches  Scott Strobel
Madeline Sherlock Revealing Hidden Biology By Identifying Ligands For The Ykkc Orphan Riboswitches Ronald Breaker
Danielle Williams Engineering Protein-Based Biomaterials Using SpyTag/SpyCatcher Technology Lynne Regan