Summer 2021

Project 1. Borrelia genomics

Participants
Questions & Goals:
- Upgrade database, genome pipeline, and website (Lia)
- Phylogeography & evolutionary maintenance of divided genome (Saymon)
- vls evolution (with simulation) & development of immunoflorescence microsopy methods(Lily)
Reading list
- Schward et al (2021). Multipartite Genome of Lyme Disease Borrelia: Structure, Variation and Prophages
- Stevenson & Seshu (2018). Regulation of Gene and Protein Expression in the Lyme Disease Spirochete

Participants:
- Dr Saad Mneimneih (CS Department)
- Brian
Questions & Goals:
- Generalized algorithms for antigen with arbitrary tree shape
- Combination algorithms
- Naive Bayes models to integrate immunogenicity data
- Natural language models to improve structural stability (see Project 4 below)
Reading list
- Di et al (2021). Maximum antigen divergence in Lyme bacterial population

Participants
- Lily
Questions and goals
- Do HIV evolve cell type tropisms within the host? Specifically, the Neural(N)-tropism vs T-cell(T)-tropism?
- Build a classifier of N-tropism HIV subtypes
- A presentation for an HIV conference in October
Reading list
- HIV compartmentalized evolution: Evering et al (2014)
Data sets
- ~500 sequences of env genes from 15 patients
- 2nd time point single-cell genome sequences for some of the patients
- Experimentally verified N-tropism subtypes
Approach
- Evolutionary mechanisms: mutation, recombination, and test of adaptive selection
- Evolutionary rates & signature (BEAST)

Learn, implement, and compare the existing tools
Fine-tuning for OspC, to be integrated with the centroid algorithm
2nd-generation centroid design: k-means algorithm (with applications to vls, Dengue, flu B)