Summer 2018

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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

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. Mei Wu, Bioinformatics Research Assistant
  6. Yinheng Li, Informatics Research Assistant
  7. Christopher Panlasigui, Hunter Biology
  8. Dr Lia Di, Senior Scientist
  9. Dr Weigang Qiu, Principal Investigator
  10. Summer Interns

Readings & Journal Club

  1. A short introduction to molecular phylogenetics: http://www.ncbi.nlm.nih.gov/pubmed/12801728
  2. The latest tree of life: http://www.nature.com/articles/nmicrobiol201648
  3. Microbiome Initiative: http://mbio.asm.org/content/7/3/e00714-16.full?sid=a47e19d3-10c1-408d-9d56-2cecaa73d585

Projects

Borrelia genome evolution (led by Saymon Akther; Other Team)

  1. Goal 1. Estimate time of cross-Atlantic dispersal using core-genome sequences
  2. Goal 2. Investigate codon biases with respect to levels of gene expression

Identification of host species from ticks (led by Lily [after first-level])

  1. Goal 1. Protocol optimization for PCR amplification of host DNA from ticks
  2. Goal 2. Protocol development: library construction for MiSeq
  3. Goal 3. Development of bioinformatics protocols and sequence database

Pseudomonas Genome-wide Association Studies (GWAS) (Led by Mai Wu & Yinheng Li, in collaboration with Dr Xavier of MSKCC)

  1. Goal 1. Association of genes/SNPs with biofilm formation and c-di-GMP levels: Manuscript preparation
  2. Goal 2. Association of genome diversity with metabolic diversity

Machine learning approaches (Led by Oliver & Brian)

  1. Goal 1. Implement Hopfield network for optimization of protein structure
  2. Goal 2. Neural-net models of OspC
  3. Goal 3. K-mer-based pipeline for genome classification

Weekly Schedule

Friday, May 31, 2018. Kickoff

  • Summer planning
  • Lab system tutorial

July 13 - July 17, 2018. Project conclusion

July 17 - August 20, 2016. PI vacation

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