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Alumni

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2024

Joseph Bucukovski, PhD

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

Advisor: Benjamin Miller, Ph.D.

Abhinav Mittal, PhD

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

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

Ashlin Poruthoor, PhD

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

Advisor: Alan Grossfield, Ph.D.

2023

Sara Ali, PhD

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

Wesley Chiang, PhD

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

Gabrielle Kosoy, PhD

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

2022

Lauren Benoodt, PhD

Functional Analysis of Transcriptomic Data Utilizing Prior Biological Knowledge

Advisor: Juilee Thakar, Ph.D.

Now: Senior Bioinformatics Analyst/Programmer at University of Rochester

Mukta Palshikar, PhD

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

2021

Michael Bryan, Ph.D.

Integrated Photonics for Point-of-Care Diagnostics

Advisor: Benjamin Miller, Ph.D.

Now: Postdoctoral Associate at University of Rochester

Chapin Cavender, Ph.D.

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

Sai Shashank Chavali, PhD

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

Debanjana Maji, PhD

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

Advisor: Clara Kielkopf, Ph.D.

Now: Postdoctoral Associate at Yale University

Daniel J Steiner, PhD

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

2020

Rohith Palli, M.D., Ph.D.

Executable models of signaling pathways and application to HIV

Advisor: Juilee Thakar, Ph.D.

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

Louis Smith, Ph.D.

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

2019

Debapratim Dave Dutta, Ph.D.

Relating Riboswitch Structure to Gene Regulation in Live Cells

Advisor: Joseph Wedekind, Ph.D.

Now: Research Scientist at Vertex

Letty Leslie Ann Salas Estrada, Ph.D.

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

2018

Kyle Berger, Ph.D.

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

Zhen Tan, Ph.D.

Modeling RNA Secondary Structure Using Structure Conservation

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

Now: Research Analyst at Indus Capital Partners

2017

Mallory Scott, Ph.D.

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

Karl Smith, Ph.D.

Understanding Sieving and Clogging in Ultrathin Membrane Filtration

Advisor: James McGrath, Ph.D.

Now: Python Developer at US Tech Solutions

2016

Rakesh Chatrikhi, Ph.D.

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

He Fang, Ph.D.

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

Yinghan Fu, Ph.D.

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

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

Now: Senior Data Scientist at Instacart

Thomas Hilimire, Ph.D.

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

Advisor: Benjamin Miller, Ph.D.

Now: Senior Scientist at Senex Biotechnology

Sarah Loerch, Ph.D.

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

2015

Dejun Lin, Ph.D.

Thermodynamics of Antimicrobial Lipopeptides Interaction with Lipid Membranes”

Advisor: Alan Grossfield, Ph.D.

Now: Senior Fellow at University of Washington

2014

Anant Akash Agrawal, Ph.D.

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

Dhrubo Jyoti Basu Roy, Ph.D.

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

Nicholas Leioatts, Ph.D.

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

Advisor: Alan Grossfield, Ph.D.

Now: System Engineer at L3 Harris Technologies

Rajashri Sridharan, Ph.D.

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

2013

Laura DiChiacchio, M.D., Ph.D.

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

Joshua Horn, Ph.D.

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

Wenhua Wang, Ph.D.

Structural and Functional Investigation of Phosphorylated Splicing Factor

Advisor: Clara Kielkopf, Ph.D.

Now: Staff Scientist at Regeneron Pharmaceuticals, Inc.

2012

Paul Black, Ph.D.

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

Anita Roselyn Peoples, Ph.D.

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

Prahnesh Akshayalingam Venkataraman, Ph.D.

Biophysical Characterization of the Oxalate Transporter OxlT

Advisor: Mark Dumont, Ph.D.

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

Zhenjiang Xu, Ph.D.

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

2011

Ankit Gupta, Ph.D.

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.

Daniel Letzring, Ph.D.

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

Krystle McLaughlin, Ph.D.

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

Min Sun Park, Ph.D.

Computational Studies of Protein Dynamics and Their Interactions with Small Molecules

Advisor: Harry Stern, Ph.D.

Now: Staff Scientist at 1859 Inc.

Matthew Seetin, Ph.D.

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

Jessica Snyder, Ph.D.

Porous Nanocrystalline Silicon Membranes as Sieves and Pumps

Advisor: James McGrath, Ph.D.

Now: Associate Director, Molecular Sciences at T2 Biosystems

Keith Van Nostrand, Ph.D.

Computational Investigation of RNA Conformational Change

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

Now: Server Infrastructure Support Engineer at Proofpoint

2009

Prakash Palde, Ph.D.

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

2008

Peter Gareiss, Ph.D.

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

Zhi Lu, Ph.D.

Secondary Structure Prediction of Non-coding RNA

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

Now: Assistant Professor at Tsinghua University, Beijing, China

Charles Mace, Ph.D.

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

Andrew Torelli, Ph.D.

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

Rahul Tyagi, Ph.D.

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

2007

Nathan Ross, Ph.D.

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

Neelaabh Shankar, Ph.D.

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

Xiaodong Wang, Ph.D.

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

2006

Sanjib Dutta, Ph.D.

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

Austin Gehret, Ph.D.

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

Lea (Vacca) Michel, Ph.D.

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

Martha Perez (Wilkinson), Ph.D.

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

Marina Roginskaya, Ph.D.

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

Blanton Tolbert, Ph.D.

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

2005

Andjelka Celic, Ph.D.

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

Franz Gruswitz, Ph.D.

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.

Shubhadeep Purkayastha, Ph.D.

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

Christopher Strohsahl, Ph.D.

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

2004

Soumya Mitra, Ph.D.

Photodynamic Therapy: Biophysical Mechanisms and Molecular Responses

Advisor: Thomas Foster, Ph.D.

Now: Principal Scientist at AbbVie, Worcester, MA

Ali Ozgenc

DNA Damage Tolerance in Escherichia coli by RecA-independent Recombination

Advisor: Christopher Lawrence, Ph.D.

Now: Senior Fellow at University of Washington

Prithwish Pal, PhD, M.B.A.

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

Joel Wojciechowski

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

Shude Yan

Mapping the Rugged Folding Energy Landscape of a Sheet Protein

Advisor: Shohei Koide, Ph.D.

Now: Vice President of Biologics at Everest Medicines

2003

Scott R. Horner, Ph.D.

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

Advisor: Benjamin Miller, Ph.D.

Now: Managing Director at Middleland Capital

Christopher Spillmann

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

2002

Vincent Batori

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

Cathleen Cox

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

Roman Eliseev

On the Mechanisms of Cytochrome C Release from Mitochondria in Apoptosis

Advisor: Thomas Gunter, Ph.D.

Now: Associate Professor at University of Rochester

Andreia Ionescu

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

Yaqiong Lin

Structural and Functional Analysis of Mitotic E2 from Human UbcH10

Advisor: Ravi Basavappa, Ph.D.

Now: Principal Research Scientist at Eli Lilly and Company

Dipesh Risal

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

2001

James Butler

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

2000

Michael Debije, Ph.D.

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

Dmitry Lebedev

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

1999

Edward Szekeres

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