Summer 2021: Difference between revisions
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** Stevenson & Seshu (2018). [https://pubmed.ncbi.nlm.nih.gov/29064060/ Regulation of Gene and Protein Expression in the Lyme Disease Spirochete ] | ** Stevenson & Seshu (2018). [https://pubmed.ncbi.nlm.nih.gov/29064060/ Regulation of Gene and Protein Expression in the Lyme Disease Spirochete ] | ||
==Project 2. HIV compartmentalized evolution== | ==Project 2. Design algorithms for vaccines | ||
* Participants | |||
* 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 | |||
** [https://www.biorxiv.org/content/10.1101/2020.12.16.423180v1 Akther et al (2021). Maximum antigen divergence in Lyme bacterial population] | |||
==Project 3. HIV compartmentalized evolution== | |||
* Participants | * Participants | ||
** Lily | ** Lily | ||
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** Evolutionary rates & signature (BEAST) | ** Evolutionary rates & signature (BEAST) | ||
==Project | ==Project 4. Natural Language models of proteins== | ||
* Participants | * Participants | ||
* Questions & Goals | * Questions & Goals | ||
Revision as of 02:38, 3 June 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
==Project 2. Design algorithms for vaccines
- Participants
- 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
Project 3. HIV compartmentalized evolution
- 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)
Project 4. Natural Language models of proteins
- Participants
- Questions & Goals
- 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)