Using integrated photonic ring resonators to detect cytokine secretion in a human tendon microphysiological system

Advisor: Benjamin Miller, Ph.D.

Improving the Align-Then-Fold Approach for RNA Secondary Structure Prediction

Advisor: David Mathews, M.D., Ph.D.

Free Energy Landscapes of Phase Separating Lipid Bilayers from Molecular Dynamics Simulations

Advisor: Alan Grossfield, Ph.D.

A Bioinformatics Pipeline for Identifying Structurally Conserved ncRNAs: From Prediction to Validation

Advisor: David Mathews, M.D., Ph.D.

Now: Computational Scientist at Moderna, Inc

Nano for Neuro: Developing Hybrid Quantum Dot Nano-Bio Assemblies to Probe Neuroinflammatory Activation

Advisor: Todd Krauss, Ph.D.

Now: Postdoctoral Associate at Univ. of Rochester

Understanding vaccine antibody response: high throughput measurements of equilibrium affinity constants for influenza, cross-reactivity of SARS antibodies, and asthmatic response

Advisor: Benjamin Miller, Ph.D.

Now: Life Science Data Science Consultant at Booz Allen Hamilton

Functional Analysis of Transcriptomic Data Utilizing Prior Biological Knowledge

Advisor: Juilee Thakar, Ph.D.

Now: Senior Bioinformatics Analyst/Programmer at University of Rochester

Executable models of signaling pathways built using omics data

Advisor: Juilee Thakar, Ph.D.

Now: Postdoctoral Research Fellow at Brigham and Women’s Hospital & Harvard Medical School

Integrated Photonics for Point-of-Care Diagnostics

Advisor: Benjamin Miller, Ph.D.

Now: Postdoctoral Associate at University of Rochester

Capturing the influence of solvent and local structure in a fixed-charge force field for RNA

Advisor: David Mathews, M.D., Ph.D.

Now: Postdoctoral Fellow at UC San Diego

Use of Lab-Evolved Proteins to Guide Development of Inhibitors that Target HIV-1 TAR RNA

Advisor: Joseph Wedekind, Ph.D.

Now: Postdoctoral Associate at Dept. of Molecular Biophysics & Biochemistry, Yale University

The Influence of Disease-Associated Mutations on the Structure and Function of U2AF2

Advisor: Clara Kielkopf, Ph.D.

Now: Postdoctoral Associate at Yale University

Development of Photonics-Enabled Point-of-Care Diagnostics: 1) Detection methods for Surveying SARS-CoV-2 - Research-to-Clinic 2) Photonic approaches to quantifying lateral flow assays

Advisor: Benjamin Miller, Ph.D.

Now: Postdoctoral Associate at University of Rochester

Executable models of signaling pathways and application to HIV

Advisor: Juilee Thakar, Ph.D.

Now: Resident at Internal Medicine, University of Rochester Medical Center

Hydrogen Bond Model Selection for RNA Force Fields

Advisor: David Mathews, M.D., Ph.D.

Now: Postdoctoral Research Associate at Washington University at St. Louis

Relating Riboswitch Structure to Gene Regulation in Live Cells

Advisor: Joseph Wedekind, Ph.D.

Now: Research Scientist at Vertex

Study of Rhodopsin's Conformational Equilibrium and Activation Dynamics using Multi-scale Molecular Dynamics Simulations

Advisor: Alan Grossfield, Ph.D.

Now: Postdoctoral Fellow at Icahn School of Medicine at Mount Sinai

Thermodynamic and Structural Studies of RNA Internal Loops Closed by GU Pairs

Advisor: Douglas Turner, Ph.D.

Now: Post Doctoral Fellow at MacLean's Lab Unviersity of Rochester

Modeling RNA Secondary Structure Using Structure Conservation

Advisor: David Mathews, M.D., Ph.D.

Now: Research Analyst at Indus Capital Partners

Auxiliary α2𝜹 Subunits Confer Selectivity of Recombinant CaV2 Channel Subtype Membrane Expression in Rat Sympathetic Ganglia.

Advisor: Paul Kammermeier, Ph.D.

Now: Associate Director Regulatory Chemistry Manufacturing & Control at Legend Biotech

Understanding Sieving and Clogging in Ultrathin Membrane Filtration

Advisor: James McGrath, Ph.D.

Now: Python Developer at US Tech Solutions

Structure and Function of a Phosphorylated Complex Containing the Myelodysplasia-Relevant Pre-mRNA Splicing Factor U2AF35

Advisor: Clara Kielkopf, Ph.D.

Now: Research Scientist at Massachusetts General Hospital

Structural Transition of the Carboxyl-Terminal Domain of Xenopus Linker Histone H1.0

Advisor: Jeffrey Hayes, Ph.D.

Now: ACGME Laboratory Genetics & Genomics Fellow at University of Washington, Seattle

RNA Secondary Structure Comparative Analysis: Method Development and Application to Genomics

Advisor: David Mathews, M.D., Ph.D.

Now: Senior Data Scientist at Instacart

Strategies for Targeting the Frameshift Stimulatory RNA of HIV-1 with Synthetic Molecules

Advisor: Benjamin Miller, Ph.D.

Now: Senior Scientist at Senex Biotechnology

Investigating an SF3b155 Scaffold for UHM-Containing Pre-mRNA Splicing Factors

Advisor: Clara Kielkopf, Ph.D.

Now: Assistant Professor at Univ. of California Santa Cruz

Thermodynamics of Antimicrobial Lipopeptides Interaction with Lipid Membranes”

Advisor: Alan Grossfield, Ph.D.

Now: Senior Fellow at University of Washington

Structural Basis of Splice Site Recognition by U2AF65 and its Relationship to Human Genetic Disease

Advisor: Clara Kielkopf, Ph.D.

Now: Director at Remix Therapeutics

Exploiting the Self-assembly of Hydrogel Nanoparticles for Novel Applications in Biosensor Design and Cell Patterning

Advisor: Benjamin Miller, Ph.D.

Now: Postdoctoral Research Fellow at Fellow at City of Hope

Allostery and Activation in the G Protein-Coupled Receptor, Rhodopsin

Advisor: Alan Grossfield, Ph.D.

Now: System Engineer at L3 Harris Technologies

Relationship between Receptor Occupancy and Signaling Responses in Ste2p, a G Protein Coupled Receptor in Saccharomyces cerevisiae

Advisor: Mark Dumont, Ph.D.

Now: Postdoctoral Associate at University at Buffalo

Computational Prediction of RNA Secondary Structure with Applications to RNA Viruses

Advisor: David Mathews, M.D., Ph.D.

Now: Resident, Academic Surgery at University of Maryland Medical Center, Baltimore, MD

Exploring Lipid-Peptide Interactions Through Computer Simulation of Antimicrobial Lipopeptides and a G Protein-Coupled Receptor

Advisor: Alan Grossfield, Ph.D.

Now: Executive Outreach Director at Northridge Church, Rochester, NY

Structural and Functional Investigation of Phosphorylated Splicing Factor

Advisor: Clara Kielkopf, Ph.D.

Now: Staff Scientist at Regeneron Pharmaceuticals, Inc.

Distribution and Evolution of Free Radicals in DNA and Protein Powders: Multiple-Track Radiation Chemistry

Advisor: Thomas Gunter, Ph.D. & William Bernhard, Ph.D.

Now: Assistant Professor at Wake Forest Baptist Health

Advances in the Mechanistic Understanding of Damage Formation in Single-Stranded and Duplex DNA due to the Direct Effects of Ionizing Radiation

Advisor: William Bernhard, Ph.D.

Now: Research Assistant Professor at Huntsman Cancer Institute at University of Utah

Biophysical Characterization of the Oxalate Transporter OxlT

Advisor: Mark Dumont, Ph.D.

Now: Postdoctoral Research Fellow at University of California-San Diego

Non-Coding RNA: From Structure Prediction to Discovery in Genomes

Advisor: David Mathews, M.D., Ph.D.

Now: Professor at State Key Lab of Food Science and Technology,Nanchang University

Role of a Novel Domain in SF1/U2AF65 Complex Formation and 3' Splice Site Recognition

Advisor: Clara Kielkopf, Ph.D.

Now: Associate Principal Scientist at Arcellx, Inc.

A systematic analysis of codon effects on translation efficiency: Identification and mechanistic examination of the inhibitory effects of the arginine codon CGA

Advisor: Eric Phizicky, Ph.D. & Elizabeth Grayhack, Ph.D.

Now: Forensic Biologist at Monroe County Crime Lab, Rochester, NY

Structural and Thermodynamic Analysis of Protein-Nucleic Acid Interactions Involved in Gene Regulation

Advisor: Clara Kielkopf, Ph.D.

Now: Assistant Professor at Vassar College, Hudson Valley, NY

Computational Studies of Protein Dynamics and Their Interactions with Small Molecules

Advisor: Harry Stern, Ph.D.

Now: Staff Scientist at 1859 Inc.

RNA Structure Prediction: Advancing both Secondary and Tertiary Structure Prediction

Advisor: David Mathews, M.D., Ph.D.

Now: Scientist II, Field Applications Support at Pacific Biosciences, Redwood, California

Porous Nanocrystalline Silicon Membranes as Sieves and Pumps

Advisor: James McGrath, Ph.D.

Now: Associate Director, Molecular Sciences at T2 Biosystems

Computational Investigation of RNA Conformational Change

Advisor: David Mathews, M.D., Ph.D.

Now: Server Infrastructure Support Engineer at Proofpoint

Exploring Small Molecules as Receptors in Carbohydrate Recognition and as Ligands Targeting RNA Sequences Relevant to HIV-1

Advisor: Benjamin Miller, Ph.D.

Now: Senior Principal Scientist at Pfizer

Small Molecule Evolution: Dynamic Combinatorial Selection Applied to the Discovery of Novel RNA-Binding Small Molecules

Advisor: Benjamin Miller, Ph.D.

Now: Research Investigator at Arvinas

Secondary Structure Prediction of Non-coding RNA

Advisor: David Mathews, M.D., Ph.D.

Now: Assistant Professor at Tsinghua University, Beijing, China

Development of Arrayed Imaging Reflectometry as a Tool to Monitor Human Immunological Responses to Pathogens

Advisor: Benjamin Miller, Ph.D.

Now: Associate Professor of Chemistry at Tufts University

Structural Studies of Transition-State Stabilization by a Small Catalytic RNA, Metabolite-Binding by a Regulatory RNA Sequence and the Mechanism of Action of Activation Induced Deaminase

Advisor: Joseph Wedekind, Ph.D.

Now: Assistant Professor of Biochemistry at Ithaca College

Predicting RNA Structure and Discovering Functional RNA Sequences in Genomes Using Folding Thermodynamics

Advisor: David Mathews, M.D., Ph.D.

Now: Senior Scientist at NewCo

Understanding Protein-Protein Interactions as a Prerequisite to Small Molecule Inhibitor Design

Advisor: Benjamin Miller, Ph.D.

Now: Executive Director - Project Leader & Head of Human Assay Technologies at Vertex Pharmaceuticals

NMR studies of two conserved RNA internal loops found in ribosomes

Advisor: Douglas Turner, Ph.D.

Now: Associate VP, Assistant General Patent Counsel at Eli Lilly

The Effect of Acetylation on Interactions of the Histone N-terminal Tail Domain with DNA in Nucleosome Core Particles and Nucleosome Arrays

Advisor: Jeffrey Hayes, Ph.D.

Now: Research Scientist at Dana-Farber Cancer Institute

Fragment Complementation of a Fibronectin Type III Domain and Its Applications in High-Throughput Protein Stability Analysis

Advisor: Shohei Koide, Ph.D.

Now: Principal Scientist at Bristol-Myers Squibb

Understanding the Mechanisms of Dominant Negative Effects on Pheromone Signaling by Mutant Ste2p Receptors in Saccharomyces cerevisiae

Advisor: Mark Dumont, Ph.D.

Now: Associate Professor at Rochester Institute of technology

Effects of Conformational Dynamics on Bacterial Cytochrome c Function

Advisor: Kara Bren, Ph.D.

Now: Associate Professor, School Chemistry and Materials Science at Rochester Institute of Technology

Construction of a Saccharomyces cerevisiae proteomic library and the identification and characterization of a novel 2'-O-methyltransferase that acts on position 4 of tRNA in yeast

Advisor: Eric Phizicky, Ph.D.

Now: Director of Marketing at Unchained Labs

Oxidative Damage to DNA by Ionizing Radiation: Chemical Pathways and Radioprotection

Advisor: William Bernhard, Ph.D.

Now: Associate Professor, Department of Chemistry at East Tennessee State University

Determination and Decomposition of the Factors Affecting the pKa of the Catalytic Cysteine Residue of the Ubiquitin Conjugating Enzymes (E2s): Insight into the Chemical Basis of E2 Function

Advisor: Douglas Turner, Ph.D. & Ravi Basavappa, Ph.D.

Now: Vice Dean of Diversity and Inclusion at Case Western Reserve University

Identification and Functional Analysis of Residues Involved in Activation of the Yeast Saccharomyces cerevisiae G Protein Coupled Receptor Ste2p

Advisor: Mark Dumont, Ph.D.

Now: Faculty at Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia

Folding Studies of Outer Surface Protein A Fragments from Borrellia burgdorferi: a Model Beta Sheet and Structural Investigation of the Catalytic Domain of Human Type II Inosine 5'-Monophosphate Dehydrogenase

Advisor: Barry Goldstein, M.D., Ph.D. & Joseph Wedekind, Ph.D.

Now: Director of Membrane Protein Biochemistry at Tectonic Therapeutics Inc.

Physico-Chemical Mechanisms of Direct Effect Damage in DNA Exposed to Ionizing Radiation

Advisor: William Bernhard, Ph.D.

Now: Research Consultant & Technical Advisor at Independent

The Role of Secondary Structure in DNA Recognition as Applied to Pathogen Detection

Advisor: Benjamin Miller, Ph.D.

Now: Vice President at Drummond Scientific Co

Photodynamic Therapy: Biophysical Mechanisms and Molecular Responses

Advisor: Thomas Foster, Ph.D.

Now: Principal Scientist at AbbVie, Worcester, MA

DNA Damage Tolerance in Escherichia coli by RecA-independent Recombination

Advisor: Christopher Lawrence, Ph.D.

Now: Senior Fellow at University of Washington

Illuminating Conformational Changes in Human Erythrocyte Anion Exchanger 1 (hAE1) by Fluorescence Energy Transfer Methods

Advisor: Philip Knauf,

Now: Associate Director of Global Marketing at Illumina

Leukocyte-Endothelial Cell Interactions Following Firm Adhesion During the Inflammatory Response In Situ

Advisor: Ingrid Sarelius, Ph.D.

Now: Clinical Science Manager at CSI Solutions

Mapping the Rugged Folding Energy Landscape of a Sheet Protein

Advisor: Shohei Koide, Ph.D.

Now: Vice President of Biologics at Everest Medicines

The Design and Synthesis of Novel Receptors for Use in Bacterial Pathogen Detection

Advisor: Benjamin Miller, Ph.D.

Now: Managing Director at Middleland Capital

The Role of Force and Cell Rheology in Neutrophil Adhesion Mediated by B2-Integrin

Advisor: Richard Waugh, Ph.D.

Now: Research Physicist at Center for Bio/Molecular Science and Engineering Naval Research Laboratory, Washington DC

Engineering of a Fibronectin Type III Domain as an Improved Scaffold for Novel Binding Proteins

Advisor: Shohei Koide, Ph.D.

Now: Application Specialist and Account Manager at Biotage

Structural Studies of the N-terminal Region of Cyclin B and Pds1, and Calcium Coordination and Backbone Dynamics of the Metastasis Associated Protein, Mts1

Advisor: Ravi Basavappa, Ph.D.

Now: Adjunct Faculty at Monroe Community College & SUNY Geneseo

On the Mechanisms of Cytochrome C Release from Mitochondria in Apoptosis

Advisor: Thomas Gunter, Ph.D.

Now: Associate Professor at University of Rochester

A Role for Transcription Factors CREB and ATF-2 in Modulation of Chondrocyte Differentation

Advisor: J. Edward Puzas, Ph.D. & Regis O'Keefe, M.D., Ph.D.

Now: Assistant Professor at Northeastern University

Structural and Functional Analysis of Mitotic E2 from Human UbcH10

Advisor: Ravi Basavappa, Ph.D.

Now: Principal Research Scientist at Eli Lilly and Company

Ligand Binding in Human Inosine 5’-Monophosphate Dehydrogenase Type I and Type II: Crystallographic and Kinetic Studies

Advisor: Barry Goldstein, M.D., Ph.D.

Now: Senior Marketing Manager at Bio Legend

The Contribution of Integral Membrane Proteins to the Bilayer-Skeletal Separation Energy in Erythrocytes

Advisor: Richard Waugh, Ph.D.

Now: Manager, Business Development Group at Hamamatsu Photonics

The Transfer and Trapping of Electrons and Holes in Crystals of Oligodeoxynucleotides initiated by the Direct Effects of Ionizing Radiation

Advisor: William Bernhard, Ph.D.

Now: Assistant Professor at Eindhoven University of Technology Energy Cluster

Role of Volume-Sensitive Anion and Amino Acid Flexes in Regulatory Volume Decrease in HL-60 Cells and Fluorescence Energy Transfer Studies of the Human Band 3 Anion Exchange Protein after Fluorescein Maleimide Labeling

Advisor: Philip Knauf,

Now: TBD at TBD

In Vivo Analysis of Damage Tolerance Pathways of Escherichia coli Using Single- and Double-Stranded Specific-Lesion Constructs

Advisor: Christopher Lawrence, Ph.D.

Now: Senior Director of Software Development at Mission Bio