What is the Summer of 2024 in the Phyloinformatics Lab looking like?

What is the Summer of 2024 in the Phyloinformatics Lab looking like?

In the summer of 2024, the Phyloinformatics Lab will be full of potential. We have ten members working on projects combining phylogenetics and computational intelligence. Here is a list of their names and projects.

Our team and their projects

• Dr. Paula Prieto Oliveira (post-doctoral fellow): Paula is combining phylogenetics with AI to propose new strategies to detect viral recombination. Viruses that infect the same host cell can sometimes undergo events in which they exchange fragments of their genomes, potentially leading to new viruses that may pose an increased threat to animal or human health. Current tools cannot process datasets of a pandemic scale. Therefore, our knowledge about viral recombination in the viruses that pose the most significant health risks is limited. We are collaborating with Dr. Kary Ocaña and her team from the Brazilian National Laboratory of Scientific Computing (LNCC; part of the Brazilian Ministry of Science, Technology and Innovation) to find solutions. During the summer of 2024, we recruited three Master’s students to help us in that endeavor: Isha Jain, Tulasi Arla, and Vedika Jeswani Judyani.

• Reyhaneh Nouri (Ph.D. student): Bioinformatics applied to unveil the sects of mutable collagenous tissue in echinoderms, with possible applications in the development of new smart and dynamic biomaterials. Echinoderms like sea cucumbers, sand dollars, and sea stars can change the pliability of their collagen reversibly and at will. We hope to translate that ability into the collagen industry to facilitate or expand medical applications of collagen.

• Anastasiia Duchenko (Ph.D. student): Phylogenetics and AI applied to understand the evolution of SARS-CoV-2 and how its mutations in the virus genome could promote differential infectivity among variants and viral escape from natural immunity, current treatments, or vaccines.

• Giovanna Yumi Scorsim Omura (Ph.D. student): Giovanna’s project will apply genome skimming and AI to reconcile the evolutionary history of terrestrial snails North Carolina with their difficult morphological characteristics and the complex biogeographical history of our state. She will do that in partnership with local natural history repositories, ultimately bridging the gap between those zoology museums and cutting-edge bioinformatics that can make their resources more readily available for biomedical applications.

• Melissa Sagastume (undergrad): Melissa is collaborating with Susana Cisneros (a Senior Lecturer of Spanish and Affiliate Faculty of Latin American Studies) and I to update and improve the latinXrail.com website. That website is a result of the “More Than a Train Ride” project, a community-based education and outreach project carried out by University of North Carolina Charlotte students, sponsored by NC Campus Engagement and in collaboration with the Levine Museum of the New South. The project is used for language education at UNC Charlotte in collaboration with partners in Argentina. It highlights the contribution of the LatinX community in different areas, such as small and mid-size businesses that promote economic development, access to legal, medical, and cultural resources, as well as leadership at different levels, among others.

• Manish Kota and Amariah Robinson (undergrads): The Phyloinformatics Lab participates on CCI’s REU site (NSF #2244424) on Smart and Secure Future Computing. Manish and Amariah are helping the Phyloinformatics Lab generate pilot data for an NSF submission in collaboration with Dr. Larry Jiménez Ferbans, from the Universidad del Magdalena (Santa Marta, Colombia) and Dr. Cristian Beza-Beza, from the University of Minnesota’s Dept. of Entomology (St. Paul, MN). We are testing different AI technologies to create a taxonomy chat-bot and image identification tool to help experts classify species of bess beetles. We are also using AI to reconcile the evolutionary history of bess beetles with their microbiome. This research is part of a larger project to understand and harvest the best beetles’ power to store and produce organic matter in tropical forests, which awards them a critical role in the global carbon cycle.

BONUS: A great collaboration

This summer we are saying goodbye to Dr. Philippe Vieira Alves, who is returning to the São Paulo State University (UNESP) in Botucatu-SP, Brazil. Philippe collaborated with us for one yer, funded by the São Paulo Reserach Foundation (FAPESP, proc. no. 2023/00714-5).

Philippe has been applying genome skimming to sequenge mitochondrion genomes of dozens of proteocephalids tapeworms. Hw is also reviewing the phylogeny of proteocephalids and using AI to reconcile their evolutionary history with metadata from hosts and biogeography. His research will be presented in two separate talks at this years meeting of the American Society of Parasitologists.

The Phyloinformatics Lab hopes to keep collaborating with Philippe and appreciates his kindness and hard work.

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