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2023

Jessica Ciesla, PhD

Mechanisms Through Which Metabolism and the Human Cytomegalovirus UL26 Protein Contribute to Anti-Viral Signaling

Advisor: Joshua Munger, Ph.D.

Omar Hedaya, PhD

uORF-mediated Translational Regulation of GATA4 in the Heart

Advisor: Peng Yao, Ph.D.

Now: Post Doctoral Fellow at Univ. of North Carolina

Feng Jiang, PhD

The Molecular Mechanism and Biological Impact of Cis-acting Elements and Trans-acting Factors in mRNA Translation Regulation

Advisor: Peng Yao, Ph.D.

Now: Post Doctoral Fellow at Stanford Univ.

Isreal Moreno, PhD

Enolase 2: A novel determinant of Human Cytomegalovirus infection

Advisor: Joshua Munger, Ph.D.

Now: Research & Development Scientist II at Maine Molecular Quality Controls, Inc. Saco, Maine

Matthew Raymonda, PhD

Identifying Metabolic Vulnerabilities Associated with Viral Infections

Advisor: Joshua Munger, Ph.D.

Griffin Schroeder, PhD

Structural Basis of Translational Regulation by Bacterial Riboswitches

Advisor: Joseph Wedekind, Ph.D.

2022

Monika Tasak, PhD

The Biology of 1-Methyladenosine and Initiator tRNA in Evolutionarily Distant Yeast Species, and Other Aspects of tRNA Modification Biology

Advisor: Eric Phizicky, Ph.D.

Now: Research Scientist in R & D at hC Bioscience

Arica VanderWal, PhD

The Role of CRISPR-Csx28 in CRISPR-Cas Anti-Phage Immunity

Advisor: Mitchell O'Connell, Ph.D.

Now: Postdoctoral Associate at Molecular Biology Department, University of California-San Diego

Ethan Walker, PhD

Global Analysis of the Interplay Between Protein Folding Stabilities and Methionine Oxidation

Advisor: Sina Ghaemmaghami, Ph.D.

Now: Postdoctoral Associate at Broad Institute

2021

Viktoriya Anokhina, Ph.D.

New methods to improve the efficiency of RNA-targeted compounds: application to HIV

Advisor: Benjamin Miller, Ph.D.

Now: Postdoctoral researcher at Broad Institute of MIT and Harvard

Chen Bao, PhD

Mechanisms of Translation Pausing Induced by mRNA Secondary Structures

Advisor: Dmitri Ermolenko, Ph.D.

Now: Research Investigator at Incyte

Fanfan Hao, Ph.D.

Identifying Molecular Determinants of the Structure of the Intrinsically Disordered H1.0 Carboxyl-Terminal Domain

Advisor: Jeffrey Hayes, Ph.D.

Now: Scientist at Vertex Pharmaceuticals

Lisa Houston, PhD

An Analysis of Factors Involved in Translation Frameshifting and Inhibition due to Inhibitory Codon Pairs in Saccharomyces cerevisiae

Advisor: Elizabeth Grayhack, Ph.D.

Now: Application Scientist at Agilent Technologies

Nazish Jeffery, PhD

Investigating the Roles for Histone H2A Variants in Late-Stage Erythropoietic Nuclear Condensation and Gene Regulation

Advisor: Michael Bulger, Ph.D.

Now: Scientist I/Manager at bluebird bio

Lingfeng Luo, Ph.D.

Roles of Cyclic Nucleotide Phosphodiesterases in Smooth Muscle Cells and the Pathogenesis of Vascular Restenosis

Advisor: Xin Li, Ph.D. & Chen Yan, Ph.D.

Now: Postdoctoral scholar at Stanford Univ.

Luke Marr, Ph.D.

Probing genome-wide native chromatin structure via histone surface accessibilities

Advisor: Jeffrey Hayes, Ph.D.

Now: Associate Product Manager at Thermo Fisher Scientific

2020

Thareendra (Teddy) De Zoysa, Ph.D.

Similarities and differences in tRNA quality control decay pathways in evolutionarily distant yeast species

Advisor: Eric Phizicky, Ph.D.

Now: Postdoctoral Fellow at Harvard Univ.

2019

Meemanage (Dudarshika) De Zoysa, Ph.D.

The Mechanism and Function of RNA-Guided RNA Pseudouridylation

Advisor: Yi-Tao Yu, Ph.D.

Now: Scientist Molecular/Viral Vector Biology at ElevateBio

Sierra Fox, Ph.D.

Investigating the Function of Hyperacetylated Chromatin Domain-Forming Enhancers

Advisor: Michael Bulger, Ph.D.

Now: Postdoctoral researcher at Coriell Institute for Medical Research

Christopher Goodwin, Ph.D.

The intersection of Human Cytomegalovirus infection and innate immune signaling

Advisor: Joshua Munger, Ph.D.

Now: Medical Writer at ApotheCom: A MEDiSTRAVA Company

Wan-Jung (Christine) Lai, Ph.D.

The role of the intrinsic closeness of mRNA ends in translation

Advisor: Dmitri Ermolenko, Ph.D.

Now: Senior Quality Engineer at Amgen

Jiyu Wang, Ph.D.

Reading frame maintenance at translation stalls in yeast involves eukaryotic specific mechanisms

Advisor: Elizabeth Grayhack, Ph.D.

Now: Data Science Analyst at Mayo Clinic

Hong Zhu, Ph.D.

Use of Yeast Surface Display to Identify Variants of HIV Envelope Glycoprotein with Enhanced Affinity for Precursors to Broadly Neutralizing Antibodies

Advisor: Mark Dumont, Ph.D.

Now: Healthcare Strategy Consulting at Fletcher Spaght, Inc.

2018

Amber DiPiazza (Cutter), Ph.D.

Molecular Characterization of Nucleosome Recognition by Linker Histone H1.0

Advisor: Jeffrey Hayes, Ph.D.

Now: Senior Test Engineer at Ginkgo BioWorks, Inc

Lu Han, Ph.D.

The Biology of Anticodon Stem-Loop Modifications of Yeast tRNAs

Advisor: Eric Phizicky, Ph.D.

Now: Scientist, RNA Biology at Arrakis Therapeutics

Bronwyn Lucas, Ph.D.

ER-associated Functions of the Double-stranded RNA-binding Protein Staufen1

Advisor: Lynne Maquat, Ph.D.

Now: Senior Research Scientist at UMass Chan Medical School

Jerry Madukwe, Ph.D.

Insights into G protein βγ Regulation of Phospholipase Cε

Advisor: Alan Smrcka, Ph.D.

Now: Editor at Trends in Pharm. Sciences at Cell Press

Matthew Payea, Ph.D.

Characterization of tRNA Quality Control Pathways in Yeast

Advisor: Eric Phizicky, Ph.D.

Now: Postdoctoral Researcher at National Institute on Aging

Owen Charles Smith, Ph.D.

KNa1.2 as a Cardiac Mitochondrial Potassium Channel with Metabolic Impact on Energy Usage

Advisor: Paul Brookes, Ph.D.

Now: Chief Scientific Officer at CannaMetrix

2017

Christina Brule, Ph.D.

Specific Codon Pairs Inhibit Translation in Yeast and Act by Distinct Mechanisms

Advisor: Elizabeth Grayhack, Ph.D.

Now: Associate at Heslin Rothberg Farley & Mesiti P.C.

Clarence Ling, Ph.D.

Regulation of Ribosome Structural Dynamics by Antibiotics, Translation Factors and mRNA Secondary Structure

Advisor: Dmitri Ermolenko, Ph.D.

Now: Scientific reviewer at FDA

Michael Sloma, Ph.D.

Computational Tools for RNA Structure Prediction

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

Now: Data Scientist at Xometry

2016

Shihao Xu, Ph.D.

The Impact of Oncogenic Signaling on Metabolic Stress Responses and Human Cytomegalovirus Infection

Advisor: Joshua Munger, Ph.D.

Now: Senior Scientist at Merck

2015

Angela Balliano, Ph.D.

Characterization of ATP-Dependent Chromatin Remodeler-Nucleosome Interactions and Analysis of the Role of HMGB1 in Base Excision Repair

Advisor: Jeffrey Hayes, Ph.D.

Now: Senior Molecular Biologist II at Antylia Scientific

Marina Feigenson, Ph.D.

Investigating the Role of Prostaglandin E2 Receptor Subtype 1 in Mesenchymal Stem Cell Differentiation

Advisor: Jeffrey Hayes, Ph.D. & Regis O'Keefe, M.D., Ph.D.

Now: Senior Scientist at Axcella Health

Guangze Jin, Ph.D.

Characterization of PIN-domain Toxin-antitoxins VapBC from Mycobacterium tuberculosis

Advisor: Scott Butler, Ph.D.

Now: Software Engineer at LenelS2

Stefanie Martin (DeVito), Ph.D.

Contributions of Pyrimidine Biosynthesis to Viral Infection

Advisor: Joshua Munger, Ph.D.

Now: Assistant Professor at Department of Biological Sciences, University of Delaware

Morgan Monaghan, Ph.D.

Identification of A2 Inter-Subunit Interactions in Factor VIIIa of the Blood Clotting Pathway

Advisor: Philip Fay, Ph.D.

Now: Clinical Trials Medical Writer at ACM Global Laboratories

Kevin Murphy, Ph.D.

The Non-Histone Protein HMGN1 Alters Core Histone Tail and H1 Interactions to Modify Higher-Order Chromatin Structure

Advisor: Jeffrey Hayes, Ph.D.

Now: Principal Scientist, Bioprocess Development at Zoetis Inc.

Chinmay Surve, Ph.D.

Stimulation of Neutrophil Migration through the Dynamic Regulation of Signaling by the Heterotrimeric G Proteins ai and bgSubunit

Advisor: Alan Smrcka, Ph.D.

Now: Scientific Researcher at Gilead Sciences

Yongchun Zhang, Ph.D.

Beta-catenin signaling integrates with BMP2 and CCN1 signaling to regulate chondrocyte differentiation and cartilage development

Advisor: Regis O'Keefe, M.D., Ph.D.

Now: Associate Research Scientist at Columbia University

2014

Brenda Cadiz-Rivera, Ph.D.

Hyperacetylated Domain Formation and cis-acting Regulatory DNA Sequences within the Murine β-globin Locus

Advisor: Michael Bulger, Ph.D.

Now: Research Associate at University of Puerto Rico

Joshua Dewe, Ph.D.

Characterizing the Role of Elongation Factor 1A and Other Cellular Proteins in the Yeast Rapid tRNA Decay Pathway

Advisor: Eric Phizicky, Ph.D.

Now: Principal Scientist at Nova Rock Biotherapeutics

Joseph Liberman, Ph.D.

Structural and Functional Analysis of Gene Regulatory PreQ1 Riboswitches

Advisor: Joseph Wedekind, Ph.D.

Now: Associate Director, Medical Affairs at uniQure

William McDougall, Ph.D.

Characterization of the APOBEC3G ssDNA Editing Complex and its Regulation by RNA

Advisor: Harold Smith, Ph.D.

Now: Assistant Professor at University of Massachusetts

David Rabayev, Ph.D.

Tissue Specific Gene Activation by a Class of Enhancers in Hyperacetylated Domains of Chromatin

Advisor: Michael Bulger, Ph.D.

Now: Medical Writer at Pfizer

Jiashi Wang, Ph.D.

Investigation of an evolutionarily conserved Staufen-mediated mRNA decay pathway that involves SINEs and lncRNAs

Advisor: Lynne Maquat, Ph.D.

2013

Kimberly Dean, Ph.D.

Selection, Identification, and Characterization of Codon Pairs that Inhibit Translation and the Development of the RNA-ID Method to Measure the Effects of Cis-Regulatory Elements

Advisor: Elizabeth Grayhack, Ph.D.

Now: Clinical Project Manager at Becton Dickinson

Geoffrey Lippa, Ph.D.

Thermodynamic Analysis and Characterization of Viral-Host Protein Interactions as a Preface to HIV Therapeutic Design

Advisor: Joseph Wedekind, Ph.D.

Now: Assistant Professor at Department of Biology, Alfred University

Sharon Pepenella, Ph.D.

Characterization of Intra- and Inter-nucleosomal Interactions of the Histone H4 Tail Domain and the Effects of H4 Acetylation on Chromatin Structure

Advisor: Jeffrey Hayes, Ph.D.

Now: Educator at Cold Spring Harbor Laboratory, DNA Learning Center

Cody Spencer, Ph.D.

Fatty Acid Biosynthesis: Elucidating the Mechanisms Behind the Manipulation and Necessity of a Metabolic Pathway Critical for Viral and Cancer Pathogenesis

Advisor: Joshua Munger, Ph.D.

Now: Senior Research Scientist at Bio X Cell

Jeffrey Zuber, Ph.D.

Identification of Mutations Affecting the Thermal Stability of Ste2p, a G Protein Coupled Receptor in S. cerevisiae

Advisor: Mark Dumont, Ph.D.

Now: Bioinformatics Scientist at Alnylam Pharmaceuticals

2012

Jennifer DeAngelis, Ph.D.

The Mechanisms for Catalytic Inactivation of FVIIIa by APC and Factor Xa

Advisor: Philip Fay, Ph.D.

Now: Photographer at Jennydee Photography

Rozzy Finn, Ph.D.

The Role of Glutamate Receptors in the Pathophysiology and Treatment of Infantile Neuronal Ceroid Lipofuscinosis

Advisor: David Pearce, Ph.D.

Now: Licensing Officer at Virginia Tech

Jason Gloor, Ph.D.

Binding and Cleavage Specificities of Human Dna2 and FEN1 Define Their Enzymatic Activities during DNA Replication and Repair

Advisor: Robert Bambara, Ph.D.

Now: Director Business Relations & Portfolio Management at Excellus BCBS

Chenguang Gong, Ph.D.

Staufen1-Mediated mRNA Decay in Mammalian Cells

Advisor: Lynne Maquat, Ph.D.

Now: Investigator II at Novartis Institutes for Biomedical Research

Adam Miller, Ph.D.

Human Telomere DNA Damage by Oxidation and Direct Effect Ionizing Radiation, and the Promotion of Telomere DNA Repair by Telomere Proteins

Advisor: Robert Bambara, Ph.D.

Now: Senior QC Scientist at Regeneron Pharmaceuticals

Athena Petrides (Kantartzis), Ph.D.

Understanding the Molecular Mechanisms of Genome Maintenance

Advisor: Robert Bambara, Ph.D.

Now: Medical Director of Pathology Informatics at Bingham and Women’s Hospital

Karyn Schmidt, Ph.D.

Air Proteins Control Differential TRAMP Substrate Specificity for Nuclear RNA Surveillance

Advisor: Scott Butler, Ph.D.

Now: Principal Scientist at Alnylam Pharmaceuticals

Wen Shen, Ph.D.

Factors that Promote Strand Transfer Recombination during HIV-1 Reverse Transcription

Advisor: Robert Bambara, Ph.D.

Now: Sr. Principal Scientist, Drug Safety R & D at Pfizer

Jessica Van Allen (McArdle), Ph.D.

Uncovering the Mechanism by Which Human Cytomegalovirus Mediates Glycolytic Activation

Advisor: Joshua Munger, Ph.D.

Now: Manager of QC & Technical Support at Zepto Metrix Corporation

Guowei Wu, Ph.D.

Constitutive and inducible pseudouridylation of S. cerevisiae U2 snRNA

Advisor: Yi-Tao Yu, Ph.D.

Now: Principal Statistical Analyst at Merck

2011

Keith Connolly, Ph.D.

Quality control and organization of small ribosomal subunit biogenesis

Advisor: Gloria Culver, Ph.D. & Eric Phizicky, Ph.D.

Now: Principal Scientist at Modalis Therapeutics

Jennifer Gewandter, Ph.D.

Studies in Oxidative Damage Induced Signaling: A Focus Outside the Nucleus

Advisor: Robert Bambara, Ph.D. & Michael O'Reilly, Ph.D.

Now: Assistant Professor at Department of Anesthesiology, University of Rochester

Ryan Henry, Ph.D.

Multiple Roles for Members of the Long Flap Pathway in Okazaki Fragment Processing

Advisor: Robert Bambara, Ph.D.

Now: Assistant Professor at Department of Chemistry, Wilkes University, PA

Christopher Hine, Ph.D.

Defying and Defeating Cancer: Hyaluronic Acid and the Rad51 Promoter

Advisor: Michael Bulger, Ph.D. & Vera Gorbunova, Ph.D.

Now: Assistant Staff at Learner Research Institute

John Karijolich, Ph.D.

Regulation of Translation Termination by Box H/ACA RNP-mediated Post-transcriptional Modification

Advisor: Yi-Tao Yu, Ph.D.

Now: Associate Professor at Vanderbilt University

Holly Kuzmiak, Ph.D.

Roles of Hho1p, Esc2p, and the post-translational modification of Sir2p in transcriptional silencing in Saccharomyces cerevisiae

Advisor: Jeffrey Hayes, Ph.D. & Xin Bi, Ph.D.

Now: Owner & Head Coach at Run with Holly

Ning Liu, Ph.D.

Mechanism of ySWI/SNF and RSC catalyzed nucleosome sliding

Advisor: Jeffrey Hayes, Ph.D.

Now: Assistant Laboratory Director, Clinical Biochemical Genetics at Baylor Genetics

David Stephenson, Ph.D.

Pseudouridylation of the Branch Site Recognition Region of U2 Affects Spliceosome Structure and Function

Advisor: Yi-Tao Yu, Ph.D.

Now: Chief Intellectual Property Officer at Steuben Foods

Amir Taslimi, Ph.D.

Conformational Changes Associated with Activation of the Yeast Saccharomyces cerevisiae α-factor Receptor Ste2p

Advisor: Mark Dumont, Ph.D.

Now: Postdoctoral Research at Univ. of Colorado Auschutz Medical Campus

Joseph Whipple, Ph.D.

Defining the Substrate Specificity Determinants for the Yeast Rapid tRNA Decay Pathway and the Identification of Factors that Mediate Degradation

Advisor: Eric Phizicky, Ph.D.

Now: Development Scientist I at New England Biolabs

2010

Amanda Benedict (Getty), Ph.D.

Studies of the Cell Biology of CLN3 and Cell Motility Defects in the Cln3-/- Mouse

Advisor: David Pearce, Ph.D.

Now: Biology/Chemistry Teacher at The Taft School

Tamara Caterino, Ph.D.

Molecular Determinants of Linker Histone Binding to Nucleosomes

Advisor: Jeffrey Hayes, Ph.D.

Now: Global Clinical Program Leader at Proctor and Gamble

Michael DeRan, Ph.D.

The Role of NPAT in S-Phase-Dependent Histone Gene Transcription and DNA Double-Strand Break Repair

Advisor: Jeffrey Hayes, Ph.D. & Jiyong Zhao, Ph.D.

Now: Scientific Consultant at Diamond Age Data Science

Suresh DeSilva, Ph.D.

Development of a Bipartite Herpes Simplex Virus Sleeping Beauty Amplicon Vector Platform: Toward Site-Directed Integration of Large Transgenons Within the Human Genome

Advisor: William Bowers, Ph.D.

Now: Vice President of Product Development at Shattuck Labs Inc.

Kriti Gaur, Ph.D.

A novel role for tumor suppressor gene Birt-Hogg-Dubé (BHD) in regulating ribosomal RNA (rRNA) synthesis

Advisor: Jeffrey Hayes, Ph.D. & Willis Li, Ph.D.

Now: Advisor-Grants and Alumni Relations at Christian Medical College & Hospital

Chao Huang, Ph.D.

2'O-methylation of Yeast Telomerase in RNA

Advisor: Yi-Tao Yu, Ph.D.

Now: Associate Director at Ultragenyx Pharmaceutical Inc.

David Johnson, Ph.D.

Mitochondrial membrane fusion, pH homeostasis and ROS signaling in C. elegans

Advisor: Joshua Munger, Ph.D. & Keith Nehrke, Ph.D.

Now: Instructor at Department of Biology, Genesee Community College

Chun Chen Mathers, Ph.D.

Mechanisms and Functional Roles of Pseudouridines in RNAs

Advisor: Yi-Tao Yu, Ph.D.

Now: Physician Assistant at Baylor Scott & White Health

Jason Pike, Ph.D.

Understanding Why Three Pathways are Needed for Synthesis of Eukaryotic Nuclear DNA

Advisor: Robert Bambara, Ph.D.

Now: Health Plan Analytics Consultant at Excellus BCBS

Jason Salter, Ph.D.

Biophysical Characterization of the HIV-1 Viral Infectivity Factor and the Innate-Immunity Factor APOBEC3G

Advisor: Joseph Wedekind, Ph.D.

Now: Scientist at OyaGen Inc

2009

George Fromm, Ph.D.

The Formation and Function of Chromatin Domains at the Murine Beta Globin Locus

Advisor: Michael Bulger, Ph.D.

Now: Vice President of Research and Development at Shattuck Labs, Inc

Chad Galloway, Ph.D.

Metabolic Regulation and Structural Evaluation of APOBEC-1 Complementation Factor

Advisor: Harold Smith, Ph.D.

Now: Associate at Department of Pathology and Laboratory Medicine, University of Rochester

David Hoffman, Ph.D.

The Production of Mitochondrial Reactive Oxygen Species at Steady-state Oxygen Concentrations: Implications for Oxygen Sensing

Advisor: Joshua Munger, Ph.D. & Paul Brookes, Ph.D.

Now: Scientist I - Molecular Screening at Cayman Chemical

Jennifer Newell-Caito, Ph.D.

Contributions of Active Site Docking and Exosite Binding to the Mechanism of Thrombin-Catalyzed Activation of Factor VIII

Advisor: Philip Fay, Ph.D.

Now: Instructor and Lab Coordinator at University of Maine

Juanita Perera, Ph.D.

SYT-SSX1 Regulates PIASy Activity to Cause the Overexpression of NCOA3 in Synovial Sarcoma

Advisor: Yin Sun, Ph.D.

Now: Postdoctoral Research Scientist at German Cancer Research Center

Melanie Preston, Ph.D.

Investigation of the Roles of the Highly Conserved G-1 Residue of tRNAHis and Analysis of Unexpected Modification Changes in tRNAHis Variants in Saccharomyces cerevisiae

Advisor: Eric Phizicky, Ph.D.

Now: Senior Applications Scientist at Promega Corporation

Sean Rigby, Ph.D.

Mechanism Analysis of the Factors that Determine the Efficiency of Recombination Events during HIV-1 Reverse Transcription

Advisor: Robert Bambara, Ph.D.

Now: Category Manager at BASF Corporation

Sabrina Seehafer, Ph.D.

Studies on the Biochemical and Immunological Consequence of Lysosomal Dysfunction in Neuronal Ceroid Lipofuscinoses

Advisor: David Pearce, Ph.D.

Now: DNA Criminalist at Dept. of Criminal Investigation, State of Iowa

Madhavika Serasinghe, Ph.D.

Identification of Novel Molecular Interactions of the Mitochondrial Fission Protein hFis1: Insight into its Action Mechanism and Therapeutic Potential

Advisor: Yisang Yoon, Ph.D.

Now: Assistant Professor at Icahn School of Medicine at Mount Sinai

Jason Stewart, Ph.D.

Functional Interactions between Replication Protein A, Dna2, and Flap Endonuclease 1 during Okazaki Fragment Processing

Advisor: Robert Bambara, Ph.D.

Now: Assistant Professor, Department of Biology at University of South Carolina

Beth Van Winkle, Ph.D.

Monocytes and Their Mitochondria in Alzheimer's Disease

Advisor: Thomas Gunter, Ph.D.

Now: Adjunct Curriculum Writer/Instructor at Rochester Institute of Technology

Devin Wolfe, Ph.D.

The Interrelationship between pH, Btn1p and Phospholipid Regulation

Advisor: David Pearce, Ph.D.

Now: Biology & Genetic Disease Scientist at Relay Therapeutics

2008

Lindsay Burwell, Ph.D.

Identification of Mitochondrial S-nitrosothiols and Determination of the Protective Effect of Mitochondrial S-nitrosation in Cardiac Ischemia Reperfusion Injury

Advisor: Paul Brookes, Ph.D.

Now: Associate Professor at Wells College

Kevin Callahan, Ph.D.

Core exosome independent function of the nuclear exoribonuclease Rrp6p

Advisor: Scott Butler, Ph.D.

Now: Associate Professor at St. John Fisher College

Irina Chernyakov, Ph.D.

Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22, and the 5’-3’ exonucleases Rat1 and Xrn1

Advisor: Eric Phizicky, Ph.D.

Now: Assistant Head of School at Namaste Montessori School

Hope Cole, Ph.D.

Activities of Two Base Excision Repair Enzymes on Nucleosomal Substrates

Advisor: Jeffrey Hayes, Ph.D.

Now: IRTA Fellow, Clark Lab at NIH

Lu Gao, Ph.D.

Factors That Promote Recombination during HIV-1 Reverse Transcription and Properties of M184 Drug Resistant Reverse Transcriptases

Advisor: Robert Bambara, Ph.D.

Now: Researcher at Univ. of Chicago

Min Song, Ph.D.

Unique Mechanisms that Control the Efficiency of HIV-1 Minus Strand Strong Stop Transfer

Advisor: Robert Bambara, Ph.D.

Now: Assistant director of Core Antisense Research at Ionis Pharmaceuticals

Seasson Vitiello, Ph.D.

The Yeast Model for Batten Disease: Genetic and Physical Interactions

Advisor: David Pearce, Ph.D.

Now: Associate Professor, Department of Genetics, Molecular Biology, Cell Biology and Cell Signaling at Augustana University

2007

Jared Benedict, Ph.D.

Elucidating and Characterizing the Interacting Partners of the Neuronal Ceroid Lipofuscinoses Proteins

Advisor: David Pearce, Ph.D.

Now: Transformation Program Manager at Nouryon

Ryan Bennett, Ph.D.

A Functional Analysis of the Domains of APOBEC3G Involved in Dimerization, Anti-viral Activity and Cellular Localization

Advisor: Harold Smith, Ph.D.

Now: Chief Scientific Officer at Oyagen, Inc.

Patrick Brandt, Ph.D.

A Role for the Human Rad9-Rad1-Hus1 DNA Clamp Complex in DNA Repair

Advisor: Robert Bambara, Ph.D.

Now: Director of Career Development and Training at University of North Carolina at Chapel Hill

Jason Hoskins, Ph.D.

Analysis of the Mechanisms of 5-Fluorouracil Toxicity in Saccharomyces cerevisiae

Advisor: Scott Butler, Ph.D.

Now: Staff Scientist at National Cancer Institute

Lakmal Kotelawala, Ph.D.

Identification of Yeast tRNASer Um44 2'-O-Methyltransferase (Trm44) and Demonstration of a Role of Trm44 in Maintaining Levels of Specific tRNASer Species

Advisor: Eric Phizicky, Ph.D.

Now: Postdoctoral Researcher at University of Minnesota-Twin Cities

Celeste MacElrevey, Ph.D.

Crystallographic Analysis of a Small Catalytic RNA and Structural Insights into the Enzymes and Substrates of RNA / DNA Editing

Advisor: Joseph Wedekind, Ph.D.

Now: Senior Pharmacokineticist at Covance

Marie Rossi, Ph.D.

Distinguishing the Pathways of Primer Removal during Eukaryotic Okazaki Fragment Maturation

Advisor: Robert Bambara, Ph.D.

Now: Sr. Director, Corporate Communications & Investor Relations at ViaCyte

Fatbardha Varfaj, Ph.D.

Contributions of Exosite Interactions and Active Site Docking to Activated Protein C-Catalyzed Inactivation of Factor VIIIa

Advisor: Philip Fay, Ph.D.

Now: Hematology Manager at Cerus

Xiaochao Wei, Ph.D.

Studies of Signaling Pathways in Cellular Responses to Titanium Particles: Implications of Cyclooxgenes-2/Prostaglandin E2/RANK Ligand Induction in Fibroblasts During Wear Debris-Induced Osteolysis

Advisor: Regis O'Keefe, M.D., Ph.D.

Now: Associate Professor at Washington University School of Medicine at St. Louis

Chunxing Yang, Ph.D.

Functions and Mechanisms of RNA Pseudouridylation

Advisor: Yi-Tao Yu, Ph.D.

Now: Researcher at Umass Medical School

Chujun Yuan, PhD

G Protein bg Subunit Mediated Signaling Specificity: Implications for bg subtypes and Novel Mechanisms of Activation

Advisor: Alan Smrcka, Ph.D.

Now: Director at Cowin Biosciences, Inc.

2006

Charles Ansong, Ph.D.

Probing Protein-Protein Interactions in Factor VIII: Characterization of Inter-Subunit Interactions and Epitope Mapping of Factor VIII Subunits

Advisor: Philip Fay, Ph.D.

Now: Program Director at NIH

Varuni Jamburuthugoda, Ph.D.

dNTP Interaction Mechanisms of HIV-1 Reverse Transcriptase

Advisor: Baek Kim, Ph.D.

Now: Assistant Professor at SUNY Geneseo

Xiaodong Li, Ph.D.

Functional Dissection of Estrogen Signaling Pathways Conveyed by Estrogen Receptor Homodimers and Heterodimer

Advisor: Russell Hilf, Ph.D.

Now: CEO at Luxena Pharmaceuticals

Craig Menges, Ph.D.

The Human Papillomavirus E7 Oncoprotein Upregulates AKT Activity through the Retinoblastoma Protein (Rb) during Keratinocyte Differentiation

Advisor: Mark Dumont, Ph.D.

Now: CAR-T cell Scientist at Spring House

Huan Frank Wang, Ph.D.

Essential Role of Proteoglycans in Caenorhabditis elegans Early Embryonic Cell Division and Characterization of Sequence Requirement for Proteoglycan Modification Site

Advisor: Fred Hagen, Ph.D.

Now: Analyst, Risk Business Intelligence at Kaiser Permanente

2005

Anshika Bajaj, Ph.D.

Ligand Binding and Receptor Activation in a G Protein Coupled Receptor in Baker’s Yeast Saccharomyces cerevisiae

Advisor: Mark Dumont, Ph.D.

Now: Technical Talent Sourcer at Microsoft

Weifeng Gu, Ph.D.

Identification of the Essential Yeast Gene THG1 Encoding the Unusual tRNAHis Degree Guanylytransferase, and Elucidation of Multiple Consequences of Thg1p Post Depletion in vivo

Advisor: Eric Phizicky, Ph.D.

Now: Assistant Professor, Cell Biology and Neuroscience at University of California Riverside

Edward Petri, Ph.D.

Protein Engineering and Rational Mutagenesis in the Crystallization and Structure Determination of Human Cyclin B1

Advisor: Ravi Basavappa, Ph.D.

Now: Assistant Professor at University of Novi Sad

Michael White, Ph.D.

Expression and Solubilization of Yeast Saccharomyces cerevisiae Integral Membrane Proteins for Functional and Structural Genomics

Advisor: Mark Dumont, Ph.D.

Now: Assistant Professor, Department of Genetics at Washington University in St. Louis

Kefang Xie, Ph.D.

Structural and Functional Analysis of APOBEC-Related Editing Enzymes, and the Structural Basis of Antibody Specificity in Blood Type Recognition

Advisor: Joseph Wedekind, Ph.D.

Now: Lead Chemist at US Army Public Health Command - Region Pacific

2004

Jing Huang, Ph.D.

Design of Estrogen Response Element (ERE) Binding Proteins to Study the Roles of ERE-containing Genes in Cell Proliferation and the Functional Differences Between ER Alpha and ER Beta

Advisor: Robert Bambara, Ph.D.

Now: Principal Investigator at The National Cancer Institute

Peter Klover

Obesity-Associated Interleukin-6 Contributes to Hepatic Insulin Resistance in Mice

Advisor: Robert Mooney, Ph.D. & George Kimmich, Ph.D.

Now: Medical Writer II at Technical Resources International, Inc.

Letian Kuai, Ph.D.

Degradation of mRNA in the nucleus and polyadenylation of noncoding RNA in Saccharomyces cerevisiae

Advisor: Fred Sherman, Ph.D.

Now: Senior Director at Head of DEL Biology WuXi AppTec

Xiaoju Ma, Ph.D.

Identification of Pseudouridylases Responsible for the Formation of Pseudouridines in Yeast U2 snRNA

Advisor: Yi-Tao Yu, Ph.D.

Now: Executive Director, Medical Affairs at Coherus BioSciences

James Roussie

The Transport and Metabolism of the Neurotransmitter Glutamate: Regulation of the Glutamate Transport EAAC1 by Protein Kinase C; and Aminotransferase- Catalyzed Isotope Exchange and its Implications for the Glutamate-Glutamine Shuttle Model

Advisor: George Kimmich, Ph.D.

Now: Chief Scientific Officer at SiMPore

Hui-I Tom

The Mechanism of Minus Strand Stop Transfer during HIV-1 Reverse Transcription

Advisor: Robert Bambara, Ph.D.

Now: Scientific Officer at BioAgilytix

Mingxuan Xia

Cooperation of activated Ras and mutant p53 in control of cell motility and invasion during malignant cell transformation

Advisor: Hartmut Land, Ph.D.

Now: TBC at TBC

Chunyang Zheng, Ph.D.

Intra- and Inter-nucleosomal Protein-DNA Interactions of the Core Histone Tail Domains in a Model Dinucleosome and Oligonucleosome Array

Advisor: Jeffrey Hayes, Ph.D.

Now: President and CEO at Robustnique Corporation

2003

Sayura Aoyagi, Ph.D.

Investigation of the Mechanism of Nucleosome Remodeling by the Human SWI?SNF and Xenopus Mi-2 Chromatin Remodeling Complexes

Advisor: Jeffrey Hayes, Ph.D.

Now: Principal Editor for Benign Hematology at EBSCO Information Services

Xi Chen

Investigation of Mitochondrial Protein Degradation Using Mutationally Altered Forms of Yeast Chromosome

Advisor: Robert Bambara, Ph.D. & Fred Sherman, Ph.D.

Now: Assistant Professor (tenure Track) at University of Pittsburg

Yuan Liu

Study on Roles of Eukaryotic Flap Endonuclease 1 (FEN1) in Maintaining Stability of Repeat Sequences During RNA Replication

Advisor: Robert Bambara, Ph.D.

Now: Associate Professor, Department of Chemistry & Biochemistry at Florida International University

Mujib Rahman

Studying the Roles of Androgen Receptor (AR) Coactivators in Prostate Cancer Progression using Dominant-negative Mutants and RNA Interference

Advisor: Chawnshang Chang, Ph.D. & Fred Sherman, Ph.D.

Now: Scientist at Pfizer

Ricardo Roda

The Mechanism of Recombination of HIV-1

Advisor: Robert Bambara, Ph.D.

Now: Assistant Professor of Neurology at John Hopkins Medicine

Stephen Tajc, Ph.D.

The molecular recognition of carbohydrates and ions in aqueous solution.

Advisor: Benjamin Miller, Ph.D.

Now: Associate Professor at Nazareth College

Feng Xing, Ph.D.

A Family of Dihydrouridine Synthases with Different Specificities Responsible for Modification of Cytoplasmic tRNAs of Saccharomyces cerevisiae

Advisor: Eric Phizicky, Ph.D.

Now: Research Fellow at Memorial Sloan Kettering Cancer Center

2002

Tamara Ranalli

Analysis of Mammalian Base Excision Repair: Role of AP Endonuclease and Replication Protein A

Advisor: Robert Bambara, Ph.D.

Now: Senior Vice President at Quidel

Ping Yi

Studies on Mechanisms of Estrogen Receptor Subtype-Specific Transcription Regulation

Advisor: Robert Bambara, Ph.D.

Now: Assistant Professor at Baylor College of Medicine

2000

Negin Martin, Ph.D.

Intramolecular Interactions among Transmembrane Regions of STE2, a G Protein Coupled Receptor in Yeast Saccharomyces cerevisiae

Advisor: Mark Dumont, Ph.D.

Now: Director, Viral Vector Care at National Institute of Environmental Health and Sciences

1999

LuAnn Leavitt, Ph.D.

Dominant Negative Mutations of the a-Factor Receptor Encoded by the STE2 Gene of the Yeast Saccharomyces cerevisiae

Advisor: Mark Dumont, Ph.D.

Now: TBC at TBC

Ganesan Sathya

Characterization of Estrogen-induced Synergistic Response at Multiple EstrogenResponsive Elements (EREs)

Advisor: Robert Bambara, Ph.D.

Now: US Regulatory Science Lead at UCB