Summer 2021

Project 1. Borrelia genomics

• Participants
• Questions & Goals:
  • Upgrade database, genome pipeline, and website
  • Evolution of
• Reading list

Project 2. HIV compartmentalized evolution

• Participants
• Reading list
  • HIV compartmentalized evolution: Evering et al (2014)

Project 3. Natural Language models of proteins

• Participants
• Questions & Goals

1. Learn, implement, and compare the existing tools
2. Fine-tuning for OspC, to be integrated with the centroid algorithm

• Reading list
  • Strodthoff et al (2020). Bioinformatics. UDSMProt: universal deep sequence models for protein classification. Source code on Github
  • Rives et al (2021). PNAS. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. Github repository