Select a group

Program Directors

Photo of Robert N Baldassano, MD
Robert N Baldassano, MD

Robert 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 (IBD). He has been instrumental in developing an international consortium for the study of the gene responsible for causing pediatric 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 3 pediatric IBD textbooks.

Photo of Frederic D Bushman, PhD
Frederic D 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. Visit my lab .

Photo of Gary D Wu, MD
Gary D 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 Staff

Photo of Jessi Erlichman, MPH
Jessi Erlichman, MPH
Administrative Director, CHOP Microbiome Center
Photo of Ariel Myatt
Ariel Myatt
Resource Coordinator, CHOP Microbiome Center
 Photo of Jessica Monkoski
Jessica Monkoski
Program Coordinator, PennCHOP Microbiome Program

Sequencing Core

Ahmed Moustafa, PhD
Ahmed Moustafa, PhD
Sequencing Core Director
Amanda Gonzalez
Amanda Gonzalez
Lab Tech
Steven Mark Jones
Steven Mark Jones
Lab Tech, mARC Project

Human Intervention Core

Photo of 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.

Photo of 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.

Photo of 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.

Photo of 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.

Analytical Core

Photo of Kyle Bittinger, PhD
Kyle Bittinger, PhD

Laboratory Manager

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.

Photo of Ceylan Tanes, PhD
Ceylan Tanes, PhD
Bioinformatics Scientist
Photo of Vincent Tu, PhD, MS
Vincent Tu, PhD, MS
Bioinformatics Scientist
Photo of Scott Daniel, PhD
Scott Daniel, PhD

Bioinformatics Scientist

Weiming Hu, PhD
Weiming Hu, PhD
Bioinformatics Scientist

Acute Care Biobanking Core

Photo of Ronald Collman, MD
Ronald Collman, MD

Director, Acute Care Biobanking Core & Professor of Medicine

collmanr [at] (subject: %5BPennCHOPMicrobiome%20Email%5D) (Email)

Photo of Ayannah Fitzgerald, BSN
Ayannah Fitzgerald, BSN

Clinical Coordinator

ayannah [at] (subject: %5BPennCHOPMicrobiome%20Email%5D) (Email)

Photo of Layla Khatib, BS
Layla Khatib, BS

Clinical Coordinator

Layla.Khatib [at] (subject: %5BPennCHOPMicrobiome%20Email%5D) (Email)

Trivikram Gaddapara

Core Technical Coordinator

Trivikram.Gaddapara [at] (subject: %5BPennCHOPMicrobiome%20Email%5D) (Email)

Microbial Culture & Metobolic Core

Elliot Friedman Headshot
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.

Photo of Dillon Murphy
Dillon Murphy
Technical Assistant

PennCHOP Microbiome Internal Advisory Board

Chris Hunter, PhD Photo
Chris Hunter, PhD
Professor & Chairman, Department of Pathobiology
Yongwon Choi, PhD Photo
Yongwon Choi, PhD
Director, Gnotobiotic Mouse Core & Leonard Jarett Professor of Pathology and Laboratory Medicine
Photo of Robert Doms, MD, PhD
Robert Doms, MD, PhD
Professor of Pathology and Laboratory Medicine
Photo of 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 Photo
Mark Goulian, PhD
Edmund J. and Louise W. Kahn Endowed Term Professor of Biology
Elizabeth Grice, PhD Photo
Elizabeth Grice, PhD
Associate Professor of Dermatology
Hongzhe Li, PhD Photo
Hongzhe Li, PhD
Professor of Biostatistics and Statistics
Mark Goulian, PhD Photo
John Wherry, PhD
Professor of Microbiology & Director of the Institute for Immunology
Photo of  Babette Zemel, PhD
Babette Zemel, PhD
Research Professor of Pediatrics