Ann completed her Ph.D. and postdoc in the laboratory of Danielle Bassett at UPenn, where she used network theory to address questions in cognitive neuroscience. Ann’s role on the team is to advance our data analysis and visualization methods for our microbiomeDB project, and she works closely with the larger VEuPathDB team that is our partner in this effort.
Qianxuan is completing his first of three rotations in the lab and is a member of the Microbiology, Virology and Parasitology (MVP) Graduate group. Qianxuan’s project is 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Qianxuan has worked virtually to annotate a recently completed genome of C. hiranonis, while exploring published and unpublished shotgun metagenomic datasets to better understand this organism.
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 is new to the lab and is interested in learning more about laboratory approaches to studying host-microbe interactions
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.
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.
Wojtek joined the lab in November of 2019 as our first bona fide programmer. 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 partner in this effort. Wojtek has loaded large enteric disease datasets in microbiomeDB, developed private user workspaces that allow users to directly upload and analyze their own data, and he is currently developing new tools for handling large volumes of shotgun metagenomic data from the public domain.
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 recent work identified key biomarkers that predict patient outcomes even before the first treatment has begun. Currently, she is working to integrate data from multiple tissues and assays generated from patients in Brazil, in an effort improve our understanding of disease development.
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 recently work used pigs to understand the impact of pregnancy and pregnancy history (parity) on the microbiome and offspring colonization. In addition, Alex has played a key role in supporting and developing our transcriptomics course, and is currently writing up a manuscript that outlines a model for how this class could be broadly utilized for teaching transcriptomics to parasitology and immunology researchers in the US as well as in in lower- and middle-income countries.
Elise completed a dual Master’s degree in Biology and Design at Drexel University, and is interested in interdisciplinary science that incorporates elements of design. She joined us in July 2019 and is the primary person working with collaborators to plan, develop and manage high-throughput sequencing projects, ranging from transcriptome studies, single-cell seq, 16S rRNA profiling and shotgun metagenomics.