Alumni
2020201920182017201620152014201320122011200920082007200620052004200320022001200019991998
2020
Rohith Palli, Ph.D.Executable models of signaling pathways and application to HIV
Advisor: Juilee Thakar, 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 ScottAuxiliary 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 SmithUnderstanding 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 FuRNA 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 LinThermodynamics 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 OzgencDNA 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 WojciechowskiLeukocyte-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 YanMapping 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 SpillmannThe 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 BatoriEngineering 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 CoxStructural 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 EliseevOn 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
Yaqiong LinStructural and Functional Analysis of Mitotic E2 from Human UbcH10
Advisor: Ravi Basavappa, Ph.D.
Now: Senior Research Scientist at Eli Lilly and Company
Dipesh RisalLigand 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 ButlerThe 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 LebedevRole 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 SzekeresIn 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