A Good Week at the Phyloinformatics Lab
What a week
The Phyloinformatics Lab had one of its best weeks yet. In seven days we gained a new Ph.D. Candidate, gave a symposium talk, hosted an industry seminar, published one paper, submitted two more, and sent new sequence data to public databases.
A new Ph.D. Candidate
Anastasiia Duchenko passed her dissertation proposal defense on September 16. She is now a Ph.D. Candidate, her proposal is approved, and she starts on the dissertation itself. Read more in our post about her defense.
A talk at the Charlotte Regional Biomedical Symposium
Omkar Marne presented our SARS-CoV-2 work at the Charlotte Regional Biomedical Symposium on September 14. He showed that the SARS-CoV-2 tree changes with alignment parameters and outgroup selection. Read more in our post about his talk.
One paper published
PLOS Computational Biology published “Eight quick tips for requesting materials from natural history collections”, by Giovanna Yumi Scorsim Omura, Denise Furr, and me. The paper teaches researchers how to borrow museum specimens and build good relationships with the collections that lend them. Read more in our post about the paper.
An industry seminar for our students
On September 15, the Bioinformatics Assembly of Students (BiAS) hosted Dr. Janice Kofsky for a conversation about careers in bioinformatics. Dr. Kofsky is a UNC Charlotte alumna and a Plant Genomics and Quantitative Genetics Data Scientist at Confluence Genetics. She talked about her own job and about the broader market for bioinformaticians, and she took questions from the students who came. Read more in our post about the seminar.
Two manuscripts submitted
On September 11, we submitted “Alignment, outgroup, and branch statistic choices shape SARS-CoV-2 phylogenomics” for peer review. Omkar Marne, Brad Bartman, and Anastasiia Duchenko wrote it with me. The study tests how annotation, outgroup sampling, alignment, and branch statistics change the SARS-CoV-2 tree. The data are already public on Zenodo.
We also submitted a large study of genome recombination in flaviviruses. This paper is a collaboration with the Brazilian National Laboratory for Scientific Computing (LNCC), and our coauthors include Kary Ocaña and Hugo de Paula Oliveira. It builds on our earlier preprint on recombination in dengue virus.
New data in public databases
Giovanna Yumi Scorsim Omura submitted every sequence from her dissertation to the NCBI databases. Her dissertation studies Triodopsis land snails, and anyone will be able to reuse those sequences.
Reyhaneh Nouri kept up with demanding bench work and also managed her own data submission to the NCBI databases. Data submission takes patience and attention to detail, and Reyhaneh showed plenty of both.
Service to the university
I serve on the UNC Charlotte Faculty Council ad hoc committee that reviews the structure of the standing committees and the governance documents behind them. The committee finished a preliminary report, and that report now goes out for comment. The point of this round is to collect opinions from everyone the committee structure affects before anything is recommended for a vote.
Thank you
Good weeks like this one do not happen by chance. Each student and collaborator did careful work, and that work also gives me the time to plan, promote, and fund the lab. Thank you all.
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Anastasiia Duchenko Is Now a Ph.D. Candidate