Summer 2019

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Revision as of 16:20, 27 June 2019 by imported>Weigang (→‎Projects)
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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

conda install numpy
conda install pandas
conda install matplotlib
conda install jupyter
  • 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)
    • Tutorial
  • 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 Unix & Perl tutorial
  2. A short introduction to molecular phylogenetics: http://www.ncbi.nlm.nih.gov/pubmed/12801728
  3. A review on Borrelia genomics: https://www.ncbi.nlm.nih.gov/pubmed/24704760
  4. A model of immune selection: He et al (2018). https://www.nature.com/articles/s41467-018-04219-3
  5. A model of flu evolution: Neher et al (2016). https://www.pnas.org/content/113/12/E1701?ijkey=72c6025e999dd043d32f6822dc06c7356d8494b2&keytype2=tf_ipsecsha
  6. Reading on Dengue virus
    1. Bäck & Lundkvist 2013
    2. Overview (from Scitable)

Projects

Project Description/Goal Participants Leader Header text
Lyme genomics phylogeography & genome intragression Saymon, Chris Saymon Example
Lyme ecology & population genetics host identification; SIR model; coalescence Lily Lily Example
Borrelia peptide library Compile ORFs from genome database & send to Mt Sinai team Chris, Saymon Chris Example
Origin of genetic code manuscript revision Oliver & Brian Oliver Example
Pseudomonas metabolomics Shiny Web portal development Chris, Edgar Chris Example
Dengue antigenic variations Parse Dengue sequences Oliver Cai, Muhammad, Che Muhammad Example
OspC design Optimization by GA Edgar, Lia Weigang Example
OspC antigenecity model Develop model with mice data by Invanova et al Nevila, Brian Brian Example
OspC per-site model CW50, site=i} Radhika, Muhammad, Brian Brian Example