PennCHOP Microbiome Staff Members


Center Directors

Robert Baldassano, MD

Robert Baldassano, MD

Robert N. Baldassano is the Colman Professor of Pediatrics at the Perelman School of Medicine at the University of Pennsylvania and the Director of the Center for Pediatric Inflammatory Bowel Disease at The Children’s Hospital of Philadelphia (CHOP). He completed his Pediatric Residency and Pediatric Gastroenterology and Nutrition Fellowship at CHOP.  Dr. Baldassano’s research focuses on improving the care of children suffering from Inflammatory Bowel Disease. He has been instrumental in developing an international consortium for the study of the gene responsible for causing pediatric inflammatory bowel disease (IBD) and has chaired multiple national and international programs relating to pediatric IBD.

Dr. Baldassano is on the editorial advisory board for five journals. He has published greater than 150 papers on pediatric IBD and is editor of 2 pediatric IBD textbooks.


Frederic Bushman, PhD

Frederic Bushman, PhD

Frederic Bushman is the W.M. Measey Chair of Microbiology and Professor of Microbiology at the Perelman School of Medicine at the University of Pennsylvania and Adjunct Faculty at CHOP. He received his PhD in cellular and developmental biology from Harvard University. His research focuses on host/microbe interactions, with specific projects focusing on the human microbiome, HIV pathogenesis, and human genome therapy.  Many recent projects in the laboratory involve developing new methods for studying microbiology using deep sequencing and bioinformatics. Dr. Bushman has published over 250 papers and two books.


Gary Wu, MD

Gary Wu, MD

Gary Wu is the Ferdinand G. Weisbrod Professor in Gastroenterology at the Perelman School of Medicine at the University of Pennsylvania where he the Associate Director of the Center for Molecular Studies in Digestive and Liver Disease. He is currently Director and Chair of the Scientific Advisory Board for the American Gastroenterological Association Center for Gut Microbiome Research and Education and is an elected member of both the American Society for Clinical Investigation and the American Association of Physicians. The current research programs in his laboratory focus on the mutualistic interactions between the gut microbiota and the host with a particular focus on metabolism.



Administrative Director

Jessi Erlichman, MPH

Jessi Erlichman, MPH


April Weakley

April Weakley
Program Coordinator



Sequencing Core

Lisa Mattei, PhD

Lisa Mattei, PhD
Laboratory Manager


Casey Hofstaedter

Casey Hofstaedter
Technician


Dorothy Kim

Dorothy Kim
Technician



Analytical Core

Kyle Bittinger, PhD

Kyle Bittinger, PhD
Lab Core Director

Kyle Bittinger is a Senior Research Investigator and leads the data analysis group for the PennCHOP Microbiome Program.  After receiving his PhD in physical chemistry from MIT in 2009, he began to investigate the human microbiome at the University of Pennsylvania.  He is a co-author of the QIIME software, which is widely used for analysis of DNA sequencing data.


Ceylan Tanes, PhD

Ceylan Tanes, PhD
Bioinformatics Scientist


Chunyu Zhao, PhD

Chunyu Zhao, PhD
Bioinformatics Scientist


Yue Joy Ren, MA

Yue Joy Ren, MA
Statistician



Acute Care Biobanking Core

Ayannah Fitzgerald, BSN

Ayannah Fitzgerald, BSN
Clinical Coordinator
 ayannah@mail.med.upenn.edu


Layla Khatib, BS

Layla Khatib, BS
Clinical Coordinator
 Layla.Khatib@uphs.upenn.edu


Ize Imai, MS

Ize Imai, MS
Core Technical Coordinator
 imaii@mail.med.upenn.edu


Vincent Knecht, BS

Vincent Knecht, BS
Core Technician



Human Intervention Core

Charlene Compher, PhD/RD

Charlene Compher, PhD/RD
Director, Microbiome-related Diet Assessment Research & Professor of Nutrition Science

Charlene Compher, PhD, RD is Professor of Nutrition Science  and Shearer Chair in Healthy Family Practices at the University of Pennsylvania School of Nursing in Philadelphia, Pennsylvania. Dr. Compher also leads the nutrition research staff in the Penn Clinical Translational Research Center where diet-focused interventions and intake assessment are conducted.  Dr. Compher has been actively involved for 15 years in clinical research in patients with severe gastrointestinal disease,  primarily short bowel syndrome. She has used a range of dietary assessment methods, from in-patient nutrient balance studies to remotely collected dietary intake data, to answer key questions linking diet and disease, as impacted by the gut microbiome.


Lisa Nessel, MSS, MLSP

Lisa Nessel, MSS, MLSP
Project Manager

Lisa Nessel is a Senior Research Project Manager in the Center for Clinical Epidemiology and Biostatisics in the Perelman School of Medicine.  Ms. Nessel has nearly 20 years of experience managing and implementing research protocols focusing primarily on Gastroenterology and Nephrology in both inpatient and outpatient settings.  Ms. Nessel has extensive experience with study planning and start up, budgeting, training study personnel, study management and implementation, and study closure.  She provides oversight of regulatory compliance on a variety of studies including randomized clinical trials.  Ms. Nessel supervises a staff of full-time project managers and research coordinators.  Ms. Nessel is active in the Society for Clinical Research Coordination and Management, serving on committees and presenting course material on the topic of study operations.   Ms. Nessel has a Master’s degree in Social Service and a Master’s degree in Law and Social Policy from Bryn Mawr College.  


Unmesha Roy Paladhi, BS

Unmesha Roy Paladhi, BS
Research Coordinator

Unmesha Roy Paladhi is a Clinical Research Coordinator in the Center for Clinical Epidemiology and Biostatistics at the University of Pennsylvania’s Perelman School of Medicine. She has a Bachelor of Science in Biological Sciences from Drexel University. She has prior experience in clinical research both at the Hospital of the University of Pennsylvania and the Children’s Hospital of Philadelphia. 



Microbial Culture & Metabolomics Core

Elliot Friedman, PhD

Elliot Friedman, PhD
Technical Director

Elliot Friedman is the Technical Director of the Microbial Culture & Metabolomics Core. After studying the role of microbial communities in soil biogeochemical cycles for his Ph.D. in biological & environmental engineering from Cornell University in 2013, he has been focused on the microbial ecology of the gut microbiome.



PennCHOP Microbiome Internal Advisory Board

Yongwon Choi, PhD

Yongwon Choi, PhD
Director, Gnotobiotic Mouse Core & Leonard Jarett Professor of Pathology and Laboratory Medicine


Ronald Collman, MD

Ronald Collman, MD
Director, Acute Care Biobanking Core & Professor of Medicine
 collmanr@upenn.edu


Robert Doms, MD, PhD

Robert Doms, MD, PhD
Professor of Pathology and Laboratory Medicine


Joseph W. St. Geme III, MD

Joseph W. St. Geme III, MD
Chairman of the Department of Pediatrics & Leonard and Madlyn Abramson Professor


Mark Goulian, PhD

Mark Goulian, PhD
Edmund J. and Louise W. Kahn Endowed Term Professor of Biology


Elizabeth Grice, PhD

Elizabeth Grice, PhD
Assistant Professor of Dermatology


Chris Hunter, PhD

Chris Hunter, PhD
Professor & Chairman, Department of Pathobiology


James Lewis, MD, MSCE

James Lewis, MD, MSCE
Director, Microbiome Human Intervention Core & Professor of Medicine

James Lewis, MD, MSCE, is Professor of Medicine and Epidemiology and Senior Scholar in the Center for Clinical Epidemiology and Biostatistics at the University of Pennsylvania’s Perelman School of Medicine in Philadelphia, Pennsylvania. A member of the American Society for Clinical investigation and the Association of American Physicians, Dr. Lewis has been actively involved in clinical research related to inflammatory bowel diseases (IBD), medication safety, and optimizing medical therapies for nearly 20 years. He has employed a wide range of research methods to address these questions, ranging from mathematical modeling to placebo controlled randomized trials and controlled feeding experiments focused on the relationship between diet, inflammation and the gut microbiome. 


Hongzhe Li, PhD

Hongzhe Li, PhD
Professor of Biostatistics and Statistics


John Wherry, PhD

John Wherry, PhD
Professor of Microbiology & Director of the Institute for Immunology


Babette Zemel, PhD

Babette Zemel, PhD
Research Professor of Pediatrics


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