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2017

Mallory Scott

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

Advisor: Paul J. 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 L. 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 L. 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 J. 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 H. Mathews, M.D., Ph.D.

Now: Data Scientist at Zenefits

Thomas Hilimire, Ph.D.

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

Advisor: Benjamin L. Miller, Ph.D.

Now: Post Doctoral Fellow at NIH in NCI Department

Sarah Loerch, Ph.D.

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

Advisor: Clara L. Kielkopf, Ph.D.

Now: Postdoctoral Researcher at Howard Hughes Medical Institute

2015

Dejun Lin

Thermodynamics of Antimicrobial Lipopeptides Interaction with Lipid Membranes”

Advisor: Alan M. 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 L. Kielkopf, Ph.D.

Now: Investigator, at H3 Biomedicine, Cambridge, MA

Dhrubo Jyoti Basu Roy, Ph.D.

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

Advisor: Benjamin L. Miller, Ph.D.

Nicholas Leioatts, Ph.D.

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

Advisor: Alan M. Grossfield, Ph.D.

Now: Post Doctoral Fellow, Research Assistant at Max Planck Institute for Biophysical Chemistry, Germany

Rajashri Sridharan, Ph.D.

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

Advisor: Mark E. Dumont, Ph.D.

Now: Post Doctoral Fellow 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 H. Mathews, M.D., Ph.D.

Now: Intern and Resident at General Surgery, Research for 2 years at end of residency: University of Maryland Medical Center.

Joshua Horn, Ph.D.

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

Advisor: Alan M. Grossfield, Ph.D.

Now: Outreach Coordinator at Northridge Church, Rochester, NY

Wenhua Wang, Ph.D.

Structural and Functional Investigation of Phosphorylated Splicing Factor

Advisor: Clara L. Kielkopf, Ph.D.

Now: Research Investigator at Bristol Myers Squibb

2012

Paul Black, Ph.D.

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

Advisor: William A. Bernhard, Ph.D.

Now: Medical Physics Resident/ Associate Research Scientist at Columbia Universtiy Medical Center

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 A. Bernhard, Ph.D.

Now: Research Assistant Professor at University of Rochester- Departments of Surgery and Radiation Oncology

Prahnesh Akshayalingam Venkataraman, Ph.D.

Biophysical Characterization of the Oxalate Transporter OxlT

Advisor: Mark E. Dumont, Ph.D.

Now: Post Doctoral Fellow, researcher at University of Michigan Ann Arbor, MI

Zhenjiang Xu, Ph.D.

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

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

Now: Postdoctoral Researcher at University of California-San Diego

2011

Ankit Gupta, Ph.D.

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

Advisor: Clara L. 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.

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 L. 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 A. 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 H. 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 L. McGrath, Ph.D.

Now: Scientist II at T2 Biosystems

Keith Van Nostrand, Ph.D.

Computational Investigation of RNA Conformational Change

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

Now: Computational and Chemical Structural Biophysicist at Rochester Institute of Technology

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 L. 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 L. 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 H. 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 L. 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 E. Wedekind, Ph.D.

Now: Assistant Professor of Biochemistry and Research Lab Director at Bowling Green State University

Rahul Tyagi, Ph.D.

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

Advisor: David H. 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 L. Miller, Ph.D.

Now: Senior Investigator, Chemical Biology & Therapeutics at Novarits

Neelaabh Shankar, Ph.D.

NMR studies of two conserved RNA internal loops found in ribosomes

Advisor: Douglas H. Turner, Ph.D.

Now: Associate at Duane Morris 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 J. 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: Scientist at Janssen Pharmaceuticals , Greater Philadelphia Area

Austin Gehret, Ph.D.

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

Advisor: Mark E. Dumont, Ph.D.

Now: Assistant Professor at National Training Institute for the Deaf, 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: Technical Support Scientist at <a class="link-external" href="http://www.bdbiosciences.com/home.jsp">BD Biosciences</a>

Marina Roginskaya, Ph.D.

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

Advisor: William A. Bernhard, Ph.D.

Now: Assistant Professor at Department of Chemistry, 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 H. Turner, Ph.D.

Now: Assistant Professor at Chemistry Dept. at Case Western University

Lea Vacca, Ph.D.

Effects of Conformational Dynamics on Bacterial Cytochrome c Function

Advisor: Kara L. Bren, Ph.D.

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

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 E. 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 M. 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 A. 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 L. Miller, Ph.D.

Now: Research Assistant Professor at Drexel University

2004

Soumya Mitra, Ph.D.

Photodynamic Therapy: Biophysical Mechanisms and Molecular Responses

Advisor: Thomas H. 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 W. 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 H. 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 L. 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 E. 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 E. 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: J. Edward Puzas, Ph.D.

Now: Instructor 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 M. Goldstein, M.D., Ph.D.

Now: Director , Constellation Platform at Natera

2001

James Butler

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

Advisor: Richard E. 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 A. Bernhard, Ph.D.

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 W. 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 A. Bernhard, Ph.D.

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