Summer 2019

Rules of Conduct

1. No eating, drinking, or loud talking in the lab. Socialize in the lobby only.
2. Be respectful to each other, regardless of level of study
3. Be on time & responsible. Communicate in advance with the PI if late or absent
4. No use of phone or laptop during lab meetings

Schedule

• June 19 (Wed). Summer research kickoff. Papers assigned.
• June 21 (Fri). Python Tutorial I. Jupyter notebook, string, list, conditions, loops (by Edgar)
• June 24 (Mon). Python Tutorial II. string functions, function, dictionary, modules (by Edgar)
• June 26 (Wed). Python Tutorial III. BioPython (Edgar & Muhammud)
• June 27 (Thur). Paper presentations

Participants

1. Dr Oliver Attie, Research Associate
2. Brian Sulkow, Research Associate
3. Saymon Akther, CUNY Graduate Center, EEB Program
4. Lily Li, CUNY Graduate Center, EEB Program
5. Christopher Panlasigui, Hunter Biology
6. Summer Interns: Muhammad, Radhika Mohan, Oscar Eng, Oliver Cai

Journal Club

1. A Python Tutorial (by Edgar)
2. a Unix & Perl tutorial
3. A short introduction to molecular phylogenetics: http://www.ncbi.nlm.nih.gov/pubmed/12801728
4. A review on Borrelia genomics: https://www.ncbi.nlm.nih.gov/pubmed/24704760
5. A model of immune selection: He et al (2018). https://www.nature.com/articles/s41467-018-04219-3
6. A model of flu evolution: Neher et al (2016). https://www.pnas.org/content/113/12/E1701?ijkey=72c6025e999dd043d32f6822dc06c7356d8494b2&keytype2=tf_ipsecsha

Projects

Borrelia genome evolution (Saymon)

1. genome tree & phylogeography
2. genome intragression

Antigen evolution

1. Borrelia OspC
2. Immune selection model
3. Flue