Cleo Fan

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 Gonzalez

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 Gomaa

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 Basant

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 Amorim

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. During her postdoc, she took 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 as a Research Associate in the Scott lab where she is integrating data from multiomic assays generated from leishmaniasis patients in Brazil.

Olivia Pilling

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 genomic methods to study the skin-dwelling parasite, Leishmania braziliensis. In her first paper, she successful developed Selective Whole Genome Amplification (SWGA) for Leishmania species. This work constitutes a breakthrough for the leishmania research field since it allows researchers to amplify whole Leishmania genomes directly from patient material to carry out population genetic studies of this important pathogen, without the need to culture or enrich parasites. She continues to use SWGA to study the population genetics of Leishmania braziliensis across South America.

Alex Berry

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.

Elise Krespan

Elise was our lab manager and sequencing guru from 2019-2021, and she played a vital role in helping the lab survive and continue to operate during the worst of the COVID19 pandemic. She left the lab to pursue a PhD in Biology at the University of Syracuse.

Clara Malekshahi

Clara came to us straight out of her undergraduate studies at Smith College, where she worked in the laboratory of Dr. Laura Katz. After learning the ropes, Clara became an incredibly effective manager of all high-throughput sequencing projects provided as a service by the lab. Clara also spent time doing field work and made critical contributions to our metagenomics work in bats affected by White Nose Syndrome. After two years as lab manager, Clara left the lab to start her Graduate program in the CAMB/MVP program at UPenn. We’re so proud of her and can’t wait to see all that she accomplishes as a PhD student!

Daniel Beiting

For nearly 20 years I have studied host-microbial interactions, with a primary focus on leveraging genomic and bioinformatic approaches to elucidate mechanisms that regulate inflammation and host defense during infection with zoonotic microbes. During my PhD in Judy Appleton’s lab at Cornell University’s Baker Institute for Animal Health, I studied the immune response during chronic infection with the parasitic helminth, Trichinella spiralis. This work led to the identification of the cytokines IL10 and TGF-β, and eosinophils, as critical regulators of inflammation and immunity to chronic helminth infection. As as postdoc in David Roos’ lab at UPenn, my work shifted from helminth to protozoan parasites, and I began to employ genome-wide transcriptional profiling and genetic screens to identify novel players involved signaling pathways that regulate both immunity and pathogenic inflammation. The results of these studies helped shed light on important immune effector mechanisms, ranging from IL27 signaling in Tregs, to identifying novel enhancers of STAT1 signaling, to reactive oxygen species production by infected monocytes, to TLR3-dependent type I interferon production. In January of 2013, I began a faculty position in the School of Veterinary Medicine at UPenn, were I Co-founded and continue to Co-direct the Center for Host-Microbial Interactions (CHMI). My primary research mission in this role is to develop interdisciplinary ‘One-health’ projects related to microbiology and infectious diseases. In parallel with my research program, I work to engage trainees at the University level in bioinformatics training for managing and analyzing genomic datasets.

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