Biochemistry, Structural & Molecular Biology

At a Glance

  • College

    College of Life Sciences

  • Degree

    Doctor of Philosophy

  • Campus

    Center City

  • Format

    On Campus

  • Duration

    4 - 5 Years

Program Director

Name: Philip Wedegaertner, PhD
Position: Program Director, Biochemistry, Structural & Molecular Biology

Program Director

Name: Edward Winter, PhD
Position: Program Director, Biochemistry, Structural & Molecular Pharmacology

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Contact Admissions

Contact Number(s):

Program Coordinator

Name: Danielle Park
Department: Jefferson College of Life Sciences
Organization: Jefferson

1020 Locust Street
M-46 JAH
Philadelphia, Pennsylvania 19107

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Current Students

Oghenerukevwe Akpoghiran
[email protected]

Matriculation Term: Fall 2020
Thesis Advisor: Kyunghee Koh, PhD
Project: TBD


William Auerbacher
[email protected]

Matriculation Term: Summer 2022
Thesis Advisor: Richard Pomerantz, PhD
Project: TBD


Jenna Aumiller
[email protected]

Matriculation Term: Fall 2020
Thesis Advisor: Philip Wedegaertner, PhD
Project: TBD


Aditya Bajaj
[email protected]

Matriculation Term: Fall 2023
Thesis Advisor: Lin Guo, PhD 
Project: TBD


Sarah Barndt
[email protected]

Matriculation Term: Fall 2022
Thesis Advisor: Anna Plucinneik, PhD
Project: TBD


Candice Bizzaro
[email protected]

Matriculation Term: Summer 2021
Thesis Advisor: Lucia Languino, PhD
Project: TBD


Jenny Carey
[email protected]

Matriculation Term: Fall 2019
Thesis Advisor: Lin Guo, PhD
Project: My project focuses on studying protein phase separation of ALS-associated protein FUS and developing RNAs to reverse aberrant phase transition.


Adi Caspi
[email protected]

Matriculation Term: Fall 2020
Thesis Advisor: Scott Waldman, MD, PhD
Project: I study the guanylyl cyclase C (GCC) signaling axis in the context of colorectal cancer. 


Jacquelyn DePierro
[email protected]

Matriculation Term: Fall 2022
Thesis Advisor: Lin Guo, PhD
Project: TBD


Casey Durso
[email protected]

Matriculation Term: Fall 2022
Thesis Advisor: Diane Merry, PhD
Project: TBD


Morgan Dwyer
[email protected]

Matriculation Term: Fall 2018
Thesis Advisor: Philip Wedegaertner, PhD
Project: TBD


Melanie Goetz
[email protected]

Matriculation Term: Fall 2020
Thesis Advisor: Sara Meyer, PhD
Project: Studying the role of p300 in epigenetic mutant acute myeloid leukemia (AML)


Justin Gumas
[email protected]

Matriculation Term: Fall 2019
Thesis Advisor: Yohei Kirino, PhD
Project: Identification and functional characterization of angiogenin-induced 2’,3’-cyclic phosphate-containing RNAs in the context of ALS


Karl Herbine
[email protected]

Matriculation Term: Summer 2019
Thesis Advisor: Dmitry Temiakov, PhD
Project: The purpose of my thesis project is to understand the underlying molecular mechanisms of transcription initiation and processive elongation in human mitochondria using structural methods.


Eden Hornung
[email protected]

Matriculation Term: Fall 2019
Thesis Advisor: Rajanikanth Vadigepalli, PhD
Project: TBD


Kevin Kim
[email protected]

Matriculation Term: Fall 2023
Thesis Advisor: Lin Guo, PhD
Project: TBD


Emily Kurtyan
[email protected]

Matriculation Term: Summer 2022
Thesis Advisor: Fadia Ibrahim, PhD
Project: TBD


Genevieve Lewis (MD/PhD)
[email protected]

Matriculation Term: Summer 2021
Thesis Advisor: Emad Alnemri, PhD
Project: My project aims to elucidate the role of WNK1 signaling in macrophage inflammasome activation and how deregulation of this pathway leads to various inflammation-mediated pathologies.


Annie Londregan
[email protected]

Matriculation Term: Fall 2021
Thesis Advisor: Scott Waldman, MD, PhD
Project: TBD


Brittany Mahon
[email protected]

Matriculation Term: Fall 2021
Thesis Advisor: Christine Eischen, PhD
Project: TBD


Ian Mawn
[email protected]

Matriculation Term: Fall 2022
Thesis Advisor: Michael Soniat, PhD
Project: TBA


Elizabeth McDuffie
[email protected]

Matriculation Term: Fall 2019
Thesis Advisor: Charles Scott, PhD
Project: TBA


Henri McGuigan
[email protected]

Matriculation Term: Fall 2021
Thesis Advisor: Ya-Ming Hou, PhD
Project: TBA


Anthony Monte Carlo
[email protected]

Matriculation Term: Fall 2022
Thesis Advisor: Anna Plucinneik, PhD
Project: TBA


Quynh Nguyen
[email protected]

Matriculation Term: Fall 2023
Thesis Advisor: Michael Soniat, PhD
Project: TBA


Hailey Shankle
[email protected]

Matriculation Term: Fall 2021
Thesis Advisor: Steven McMahon, PhD
Project: TBA


Viktoriia Sokolova
[email protected]

Matriculation Term: Fall 2021
Thesis Advisor: Dmitry Temiakov, PhD
Project: TBA


Sarah Strock
[email protected]

Matriculation Term: Fall 2023
Thesis Advisor: Dmitry Temiakov, PhD
Project: TBD


Lily Thompson
[email protected]

Matriculation Term: Fall 2020
Thesis Advisor: Elise Fouquerel, PhD
Project: My project involves investigating the effect of oxidative stress at the centromere and how this contributes to chromosomal instability.


Mason Tracewell
[email protected]

Matriculation Term: Fall 2018
Thesis Advisor: Steven McMahon, PhD
Project: Investigating the mechanism behind USP22's impact on activator-driven transcription


Khushali Vyas
[email protected]

Matriculation Term: Summer 2023
Thesis Advisor: Steven McMahon, PhD
Project: TBA


Zhanerjiao (Jeff) Yuan
[email protected]

Matriculation Term: Fall 2023
Thesis Advisor: Fadia Ibrahim, PhD
Project: TBA

Recent Graduates

Gina Buchel
Matriculation Term:
Summer 2018
Thesis Title: "Fidelity of DNA Synthesis by Human Mitochondrial Replication Machinery"
Advisor: Demitry Temiakov, PhD

Victoria Frisbie
Matriculation Term:
Summer 2018
Thesis Title: "Mechanism of Cooperative Histone H3 Lysine 76 Methylation by Two DOT1 Enzymes"
Advisor: Erik Debler, PhD

Stephano Iglesias
Matriculation Term: 
Fall 2020
Thesis Title: "Structural and biochemical studies of phage biomedicines"
Advisor: Gino Cingolani, PhD

Natalie Laspata
Matriculation Term:
Fall 2019
Thesis Title: "Investigating the Role of Poly (ADP-Ribose) Polymerase 1 (PARP1) in the Prevention of R-Loop-Mediated Genomic Instability"
Advisor: Elise Fouquerel, PhD

Allison Lisberg
Matriculation Term: 
Summer 2016
Thesis Title: "IDENTIFYING THE MECHANISM BEHIND THE ROLE OF THE AR N/C INTERACTION IN SBMA"
Advisor: Diane Merry, PhD

Ivana Vukovic
Matriculation Term: 
Fall 2016
Thesis Title: "Non-redundant roles for the human mRNA decapping cofactor paralogs DCP1a and DCP1b"
Advisor: Steven McMahon, PhD

Ruoyu Yang
Matriculation Term:
Fall 2019
Thesis Title: "Multifaceted role of importins in virus nuclear import and antiviral response"
Advisor: Gino Cingolani, PhD

Benjamin Barnhart 
Matriculation Term:
Fall 2017
Thesis Title:
 "Partial hepatectomy as a model of liver regeneration: Network-based profiles"
Advisor: 
Rajanikanth Vadigepalli, PhD

Qingqing Cao 
Matriculation Term:
Fall 2017
Thesis Title:
 "The Role of Type VII Collagen in Mediating Extracellular Matrix Protein Secretion in Recessive Dystrophic Epidermolysis Bullosa"
Advisor: 
Andrew South, PhD

Steven Doll 
Matriculation Term:
Fall 2016
Thesis Title: 
"Recognition of the TDP-43 Nuclear Localization Signal by importin α1/β"
Advisor:
Gino Cingolani, PhD

Clinita Randolph 
Matriculation Term: 
Summer 2014
Thesis Title:
 "Dissecting how interactions at the apex of HIV-1 Env modulate epitope exposure at the distant base of the glycoprotein"
Advisor: 
Philip Wedegaertner, PhD

Abhimannyu Rimal 
Matriculation Term: 
Fall 2018
Thesis Title: 
"ISC10, A Developmentally Regulated Inhibitor Of Non-Canonical MAPK Signaling"
Advisor:
Edward Winter, PhD

Hannah Schapiro 
Matriculation Term: 
Fall 2017
Thesis Title: 
"Dissecting how interactions at the apex of HIV-1 Env modulate epitope exposure at the distant base of the glycoprotein"
Advisor: 
Michael Root, MD, PhD

Current Position: Teaching Assistant Professor, Thomas Jefferson University, College of Life Sciences

Matthew Varney 
Matriculation Term:
Summer 2015
Thesis Title:
 "G Protein-Coupled Receptor Kinase 6 (GRK6) Regulation of Insulin Processing and Secretion"
Advisor:
Jeffrey Benovic, PhD

Emanuela Dylgjeri-Kruser 
Matriculation Term:
Fall 2013
Thesis Title: 
"DNA-PK: Novel Roles in Metabolism and Therapeutic Targeting in Prostate Cancer"
Advisor: 
Karen Knudsen, PhD

Marina Farkas 
Matriculation Term:
Fall 2014
Thesis Title: 
"Elucidating Mechanisms Mediating Genome Recognition and Cell Fate Determination by P53"
Advisor:
 Steven McMahon, PhD

Tyler J. Florio 
Matriculation Term:
Fall 2016
Thesis Title: 
"Mechanisms and Regulation of NF-kB Nuclear Import through Importin Isoforms"
Advisor: 
Gino Cingolani, PhD

Michael Joseph Ippolito 
Matriculation Term:
Fall 2014
Thesis Title: 
"Selective Activation of G Protein Signaling through the B2AR via Novel and Redefined Small Molecule Ligands"
Advisor: 
Jeffrey Benovic, PhD

Dominic J. Lapadula 
Matriculation Term:
Fall 2014
Thesis Title: 
"Direct Inhibition of Oncogenic Gg/11 in Uveal Melanoma"
Advisor:
Jeffrey Benovic, PhD

Amy Catherine Mandigo 
Matriculation Term:
Fall 2014
Thesis Title: 
"E2F1 and Androgen Receptor Dysregulation Drives RB-deficient Cancer Progression"
Advisor: 
Karen Knudsen, PhD

Lindsey Gail Mayes-Hopfinger 
Matriculation Term:
Fall 2015
Thesis Title: 
"Identifying WNK1 as a Negative Regulator of NLRP3 Inflammasome Activation and Pyroptosis"
Advisor: 
Emad Alnemri, PhD

Alison Rachel Moss 
Matriculation Term:
Fall 2015
Thesis Title: 
"Central and Peripheral Transcriptomic Networks Driving Cardiovascular Control"
Advisor: 
Rajanikanth Vadigepalli, PhD

Austin David Parrish 
Matriculation Term: 
Fall 2014
Thesis Title: 
"Systems-Level Analysis of Regulatory Networks Involved in Alcoholic Liver Disease"
Advisor: 
Rajanikanth Vadigepalli, PhD

Azadeh Sarfallah 
Matriculation Term: 
Fall 2018
Thesis Title: 
"Mechanism of Transcription Initiation and Primer Generation at the Mitochondrial Origin of Replication OriL"
Advisor: 
Dmitry Temiakov, PhD

Sarah Sulon 
Matriculation Term: 
Fall 2014
Thesis Title: 
"Regulation of G Protein-Coupled Receptor Kinase 5 by Calmodulin"
Advisor: 
Jeffery Benovic, PhD

Current Position: Postdoctoral Fellow, Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA

Nicholas Anthony Swanson 
Matriculation Term: 
Fall 2017
Thesis Title: 
"Structure of the Prototypical Podophage T7 DNA Ejectosome"
Advisor: 
Gino Cingolani, PhD

Halley Rebecca Washburn 
Matriculation Term: 
Fall 2013
Thesis Title: 
"Molecular Mechanisms of the EphB-NMDA Receptor Extracellular Interaction"
Advisor: 
Matthew Dalva, PhD

Samantha Brown 
Matriculation Term:
Fall 2016
Thesis Title: 
"Beyond transcription: studying Human Antigen R (HuR/ELAVL1) and its role in post-transcriptionally regulating the pancreatic cancer-driver, Yes-associated protein 1 (YAP1)"
Advisor: 
Jonathan Brody, PhD

Mai Nguyen 
Matriculation Term:
Fall 2015
Thesis Title: 
"Optimizing MEK inhibitors in NRAS mutant melanoma - overcoming resistance and combination strategies"
Advisor: 
Andrew Aplin, PhD

Sheera Rosenbaum 
Matriculation Term: 
Fall 2015
Thesis Title: 
"The Role of Lineage-Specific Transcription Factors in Regulating Anti-Tumor Immune Responses in Melanoma"
Advisor: 
Andrew Aplin, PhD

Pravin Patel 
Matriculation Term: 
Fall 2014
Thesis Title: 
"Role of ASK1 in Platelet Activation and Immune-Induced Thrombocytopenia and Thrombosis"
Advisor: 
Ulhas Naik, PhD

Elaine Yang (MD/PhD) 
Matriculation Term: 

Thesis Title: 
"Mechanisms of Voltage-Gated Na+ Channel Inhibition by Propofol"
Advisor: 
Manuel Covarrubias, MD, PhD