Qianxuan completed his first of three rotations in the lab and is a member of the Microbiology, Virology and Parasitology (MVP) Graduate group. Qianxuan’s project focused on a bile acid-prodcing commensal, Clostridium hiranonis, which we initially identified as an important factor in modulating GI disease. Due to COVID, Qianxuan has worked virtually to annotate a recently completed genome of C. hiranonis, while exploring published and unpublished shotgun metagenomic datasets to better understand this organism.
Seble spent the Summer of 2020 ‘in the lab’ (virutally, due to COVID) doing a rotation. She is a member of the Immunology Graduate Group (IGG), and her project focused on using bioinformatic tools to analyze single cell RNA sequencing data (scRNA-seq) from 3-dimensional cultures of intestinal epithelial cells in order to understand how these cells might be better poised to response to infection or inflammation.
Lydia spent the Spring of 2020 doing a virutal rotation in the lab during the earliest (and scariest!) phase of the COVID19 pandemic. She is a member of the Microbiology, Virology and Parasitology (MVP) Graduate group. Her rotation was mostly devoted to learning the computationoal methods and principles of RNA-seq.
Cleo was enrolled in the Masters of Biotechnology program at UPenn. As part of the molecular biology track within this program, Cleo did her independent study in the lab working with some of the bacterial isolates from our canine IBD study to try to set-up in vitro systems to study microbe-microbe interactions between bile acid producers and pathobionts. Unfortunately, this work was cut short by the COVID19 pandemic, but Cleo still finished her independent study virtually.
Alyssa spent her Junior and Senior years as an undergraduate researcher working in the lab. During this time, Alyssa simultaneous completed her Master’s degree in Biology, working to develop 3-Dimensional tissue culture models for studying how secondary bile acids impact immunity and barrier function. After graduating with her Bachelor’s and Master’s degrees in 2022 from UPenn, Alyssa started her PhD studies in Microbiology and Immunology at Columbia University.
Eman spent time in the lab when she was a senior at the University of the Sciences Philadelphia (USP), and spent the Spring semester of 2020 working in the lab on an independent study project. Eman was new to bench research and spent her time getting acquainted with fundamental techniques in molecular microbiology. Unfortunately, this work was cut short by the COVID19 pandemic, and Eman was accepted into a Postbac program at WashU.
Wojtek joined the lab in November of 2019 as our first bona fide software developer. He came to us from the Sanger Institute, where he served as the primary developer of Wormbase paraSite. His role on our team is to advance our microbiomeDB project, and he works closely with the larger VEuPathDB team that is our (essential!) partner in this effort. Wojtek moved on to other software development projects with this larger team, but during his time with us he loaded large enteric disease datasets into microbiomeDB, built private user workspaces that allow users to directly upload and analyze their own data, developed an automated workflow that enables handling of shotgun metagenomic data, and built a new software tool (CORRAL) that allows investigators to identify microbial eukaryotes in complex metagenomic datasets.
Camila initially came to spend a year in the lab as a PhD student participating in Brazil’s ‘sandwich’ program. During this time, she fell in love with bioinformatics and returned after her PhD to start a postdoc jointly between our lab and the laboratory of Phil Scott. Since she started her postdoc in January of 2018, she has taken the lead on advancing our understanding of the transcriptional response that drives skin pathology during cutaneous leishmaniasis. Her initial studies identified key biomarkers that predict patient outcomes even before the first treatment has begun, and more recently she demonstrated that localized skin infection with Leishmania elicits a chronic systemic inflammatory response in patients. Currently, she is working to integrate data from multiomic assays generated from patients in Brazil, in an effort improve our understanding of disease development.
Olivia is a PhD student in the lab and is a member of the Microbiology, Virology and Parasitology (MVP) Graduate group. Olivia’s project is focused on the development of Selective Whole Genome Amplification (SWGA) to study the skin-dwelling parasite, Leishmania braziliensis. She will test whether specially designed primer sets are capable of selectively amplifying L. braziliensis DNA even in the presence of substantial human DNA contamination. If successful, this would constitute a breakthrough for the leishmania research field that would allow researchers to amplify whole L. braziliensis genomes directly from patient material to carry out population genetic studies of this important pathogen, without the need to culture or enrich parasites.
Alex completed his PhD in biology at UPenn, working in Dustin Brisson’s lab where he studied the population genetics of Trypanosoma cruzi in Peru. He was a postdoc with us from 2018-2020, during which time he instrumental in our studies of the microbiome in large animal models. He was the first to show that natural parasite infections are a dominant factor in shaping microbiome structure in humans and animals (preprint here), and his most recent work used pigs to understand the impact of pregnancy and pregnancy history (parity) on the microbiome and offspring colonization (see here). In addition, Alex played a key role in supporting and developing our transcriptomics course, and was one of the lead authors on this perspectives piece that lays out our approach for teaching bioinformatics to bench biologists and how our curriculum was adapted to improve virtual content during the COVID19 pandemic.