Summer 2021: Difference between revisions

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** Participant: Saymon, Brian, Lia, Weigang
** Participant: Saymon, Brian, Lia, Weigang
** Outcome: ~130 nymph ticks
** Outcome: ~130 nymph ticks
* June 22, 2021 (Tuesday).
** Niemah & Jackie will work on collecting transcriptome data into Excel sheets
** Lily presented latest trees on HIV compartmentalization
** Roman will work on env gene embedding using Facebook pretrained ESM model


==Project 1. Borrelia genomics==
==Project 1. Borrelia genomics==

Revision as of 18:24, 22 June 2021

Group meeting/trip schedule

Quabbin Reservoir & Beaver Lake, MA
  • June 3, 2021 (Thursday). Summer research kickoff
  • June 8, 2021 (Tuesday). 11-2
    • Algorithm development (Brian)
    • NLP models of protein structure (Eamen, Roman, Edgar)
    • Bb transcriptomics (Niemah & Jackie)
    • HIV compartmentalization (Lily)
  • June 10, 2021 (Thursday). No meeting. Field day
    • Location: Hackscher State Park, Long Island
    • Participants: Desiree, Lily, Lia, John, Weigang
    • Outcome: ~60 nymph ticks
  • June 15, 2021 (Tuesday). 11-2. Lab meeting
  • June 17, 2021 (Thursday). No meeting. Field day
    • Location: Quabbin Reservoir, MA
    • Participant: Saymon, Brian, Lia, Weigang
    • Outcome: ~130 nymph ticks
  • June 22, 2021 (Tuesday).
    • Niemah & Jackie will work on collecting transcriptome data into Excel sheets
    • Lily presented latest trees on HIV compartmentalization
    • Roman will work on env gene embedding using Facebook pretrained ESM model

Project 1. Borrelia genomics

Transcriptome-table.png

Project 2. Design algorithms for vaccines

  • Participants: Dr Saad Mneimneih (CS Department), Brian
  • Questions & Goals:
    • Generalized algorithms for antigen with arbitrary tree shape
      • Data set 1. Neutral evolution (with exponentially distributed branch lengths). Binary strings (L=100 bits) evolved from a coalescent tree of 20 leaves. Simulated with rcoal(20); rTraitDisc; simSeq(). code from previous work
      • Data set 2. Two major clades. HA sequences from fluB
      • Data set 3. Four major clades. Dengue
      • Data set 4. Star-shaped tree, driven by recombination. OspC
      • Data set 5. Multiple major clades. vls cassette in Lyme species
    • 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

by Lily
  • 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
  • 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 adaptive selection
    • Homoplasy index as a measure of compartmentalization? Randomization to obtain p-values of HI.
    • Evolutionary rates & signature (BEAST)
    • Tests of natural selection (PAML site models, branch-site models & MK analysis)
    • Phylogenetic analysis: tree per individual; supertree; haplotype networks (per individual)
    • Simulated compartmentalization

Project 4. Natural Language models of proteins

  • Participants: Eamen, Roman, and Edgar
  • Questions & Goals
  1. Learn, implement, and compare the existing tools
  2. Fine-tuning for OspC, to be integrated with the centroid algorithm
  3. 2nd-generation centroid design: k-means algorithm (with applications to vls, Dengue, flu B)