Karen is a MD and fellow in the Division of Infectious Diseases at the Children’s Hospital of Philadelphia (CHOP). As part of her fellowship, she is spending 2 years in the lab learning about bench research. She has taken the lead on an exciting new project for the lab, which involves testing whether the microbiome may be linked to severe pneumonia in children from lower- and middle-income countries. To address this important question, Karen is using metagenomic profiling of archival samples from the Pneumonia Etiology Research for Child Health (PERCH). Karen is also pursuing a ‘distance-learning’ masters degree in Epidemiology through the London School of Hygiene and Tropical Medicine (LSHTM). These combined efforts underscore her passion for negelected tropical diseases and global health.

Felipe graduated in Dentistry and has a Master’s degree in Biosciences and Biotechnology from the University of São Paulo, in Brazil, where he’s currently a PhD student. Felipe has been working for over 10 years in the characterization of Salmonella serovars of importance in the “One Health” context. He’s currently spending 6-months as a “sandwich” student during his PhD. During his time in the lab, Felipe will learn computational methods to analyze RNA-seq data with the goal of identifying differences in the gene expression of Salmonella Infantis under conditions of stress. In his free time, you’ll probably find Felipe cooking, reading thriller books or watching Marvel movies.

Celine joined the lab in the Summer of 2023 as our first undergraduate through the First Exposure to Research in the Biological Sciences (FERBS). She helped with the early planning stages of a large project the lab began to use metagenomic sequencing and immune profiling of samples from three African sites that participated in the PERCH study.

Samy spent the Fall of 2022 working in the lab to optimize our Selective Whole Genome Amplification work with graduate student, Olivia Pilling

Yirui (pronounced ‘E-Ray) rotated through the lab in the Fall of 2022 and worked on developing methods for carrying out RNA-seq on the model archeaon, H. volcanii. Yirui is now a graduate student in the lab of Mecky Pohlschroder in the Biology Department at UPenn.

Theresa is a rising second-year VMD-PhD student at Penn and a member of the MVP graduate group. She graduated with a BS in Animal Science from the University of Vermont, where she completed an undergraduate research thesis investigating bovine teat skin commensals with antimicrobial activity against pathogens responsible for mastitis. After college, Theresa spent a year teaching English in southern France before returning to the US to work as a research technician at the University of Wisconsin-Madison. There she worked under the direction of Dr. JP van Pijkeren on several projects revolving around ecology of the gut symbiont Lactobacillus reuteri and the development of probiotic bacteria as delivery vehicles for recombinant biotherapeutics. Broadly, she is interested in small animal internal medicine, the link between diet and microbiome health, and targets for therapeutic manipulation of the microbiome. During her Spring independent study and subsequent Summer rotation, Theresa took the lead on assembling a pangenome for elusive, but important, bile acid-producing commensals. She used the Anvi’o suite of computational tools to carry out comparative analysis of different bile acid-producer species, and to identify bacterial factors that might drive host adaptation.

Shelby is an veterinary student at UPenn (Class of ‘26) who spent the summer of 2023 in the lab working jointly with the PennVet Wildlife Futures program. As a ‘WFP’ student, Shelby split her time between bench work and field work. She collected and identified hundreds of ticks recovered from White-tailed Deer (Odocoileus virginianus) in PA state. She extracted DNA from these ticks and ran QPCR tests for a range of pathogens, then used this data to select ticks for metagenomic sequencing.

Erin is an veterinary student at UPenn (Class of ‘26). Prior to coming to PennVet, Erin worked as a consultant/analyst doing extensive market research for pharmaceutical and medical technology products. She also completed her Master’s degree at Yale University in Molecular, Cellular and Developmental Biology, where she used computational methods to study bacterial cell growth. Erin has used a variety command-line and statistical tools for her work, including R, Matlab, Python, SQL, and Stata. She currently works part-time in the lab and has focused her computational skills on optimizing and running a Nextflow workflow for analysis of shotgun metagenomic data from our piglet gut microbiome project.

Dan graduated from Boston University with a B.A. in Biology specializing in Cell Biology, Molecular Biology, and Genetics. After graduation, Dan was commissioned into the U.S. Army as an Infantry Officer, serving in a Dismounted Reconnaissance Troop at Fort Drum, NY. Dan has a fiancee, Michelle, and two cats, Enzo and Luca. He enjoys Formula 1 racing and working on his Land Rover.

Arnav is an undergraduate at UPenn (Class of ‘23) who came to us through the Galapagos Education and Research Alliance (GERA). In the Summers of 2022 and 2023 he joined others in our lab on a research trip to San Cristobol, Galapagos, where he was key in helping to develop portable sequencing methods to monitor natural water sources for potential pathogens. Arnav is currently using computational tools to analyze the data he generated. Arnav was selected for the presitgious Churchill Scholarship – one of only 16 students nationally – which will allow him to complete a 1yr masters program at Churchill College at Cambridge. After completing his masters, Arnav will begin an MD/PhD program at Harvard.