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Alumni

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2020

Rohith Palli, Ph.D.

Executable models of signaling pathways and application to HIV

Advisor: Juilee Thakar, Ph.D.

Louis Smith, Ph.D.

Hydrogen Bond Model Selection for RNA Force Fields

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

2019

Debapratim Dave Dutta, Ph.D.

Relating Riboswitch Structure to Gene Regulation in Live Cells

Advisor: Joseph Wedekind, Ph.D.

Now: Postdoctoral Fellow, Department of Biophysics at Department of Biophysics at Johns Hopkins

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.

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, M.S.

Modeling RNA Secondary Structure Using Structure Conservation

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

Now: Postdoctoral Researcher at Yale University

2017

Mallory Scott

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

Advisor: Paul Kammermeier, Ph.D.

Now: CMC Manager at Regulatory Compliance and Information Excellence, Bayer Pharma AG, NJ

Karl Smith

Understanding Sieving and Clogging in Ultrathin Membrane Filtration

Advisor: James McGrath, Ph.D.

Now: Knowledge Engineer at Amazon

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: Postdoctoral Scholar at Perelman School of Medicine, University of Pennsylvania, Philadelphia

He Fang, Ph.D.

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

Advisor: Jeffrey Hayes, Ph.D.

Now: Post Doctoral Fellow, Researcher in Pathology at University of Washington, Seattle

Yinghan Fu

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

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

Now: Data Scientist at Yelp

Thomas Hilimire, Ph.D.

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

Advisor: Benjamin Miller, Ph.D.

Sarah Loerch, Ph.D.

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

Advisor: Clara Kielkopf, Ph.D.

Now: Postdoctoral Researcher at Howard Hughes Medical Institute

2015

Dejun Lin

Thermodynamics of Antimicrobial Lipopeptides Interaction with Lipid Membranes”

Advisor: Alan Grossfield, Ph.D.

Now: Post Doctoral Fellow, Researcher 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: Senior Scientist at Atlas Venture NewCo

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: Senior System Engineer at Raytheon

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.

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: Director of Outreach 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: William Bernhard, Ph.D. & Thomas Gunter, Ph.D.

Now: Medical Physicist at Novant 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: Scientist II at Arcellx, BioHealth Innovation, 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: Computational Structural Biologist at Ambry Genetics (California)

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: Senior Manager at T2 Biosystems

Keith Van Nostrand, Ph.D.

Computational Investigation of RNA Conformational Change

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

Now: Technical Support Consultant at Sutherland Global Services

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: Principal Scientist at Pfizer (California)

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: Biotechnology Associate at Yale Center for Molecular Discovery

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: Assistant Professor at Tufts University Department of Chemistry

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: Staff Scientist at Washington University in St. Louis

2007

Nathan Ross, Ph.D.

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

Advisor: Benjamin Miller, Ph.D.

Now: Sr. Director - 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 Attorney at Morgan, Lewis and Bockius LLP

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: Senior Research Investigator 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: Assistant Professor at National Training Institute for the Deaf, 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: Field Application Scientist at ForteBio

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: Professor, Department of Chemistry 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: Joseph Wedekind, Ph.D. & Barry Goldstein, M.D., Ph.D.

Now: Principal Scientist at Aptevo 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: Director of New Product and Venture Development at Drummond Scientific Co

2004

Soumya Mitra, Ph.D.

Photodynamic Therapy: Biophysical Mechanisms and Molecular Responses

Advisor: Thomas Foster, Ph.D.

Now: Senior Scientist II 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: Senior Market Development Manager at Oncology, Illumina

Joel Wojciechowski

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

Advisor: Ingrid Sarelius, Ph.D.

Now: Intellectual Asset Manager at Science & Technology- Corning Incorporated

Shude Yan

Mapping the Rugged Folding Energy Landscape of a Sheet Protein

Advisor: Shohei Koide, Ph.D.

Now: Director, External Research & Strategic Alliances at Hengrui Medicine

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 at NanoTemper Technologies, Germany

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: Assistant Professor at University of Rochester, Department of Orthopaedics

Andreia Ionescu

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

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

Now: Assistant Professor at Harvard Medical School

Yaqiong Lin

Structural and Functional Analysis of Mitotic E2 from Human UbcH10

Advisor: Ravi Basavappa, Ph.D.

Now: Senior 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: Marketing and Product Management Consultant at Clinical Genomics and Biotech Consultancy

2001

James Butler

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

Advisor: Richard Waugh, Ph.D.

Now: Manager of OEM Camera Products at Hamamatsu Photonics, San Francisco Bay

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: Director of Software Development, DNA Services at PerkinElmer

1998

Michael Milano, M.D., Ph.D.

Migration of electrons and holes in DNA exposed to low LET irradiation: a study of free radical trapping in DNA and DNA model systems

Advisor: William Bernhard, Ph.D.

Now: Assistant Professor, Radiation Oncology at University of Rochester/Strong Memorial Hospital