Summer 2018

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)

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 & Yinheng, 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 to evolution (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

Field dates

• June 7, 2018, Thursday, Caumsette State Park
• June 14, 2018, Thursday, Fire Island National Seashore

Lab meetings

• June 8 (Friday)
• June 15 (Friday)
• June 22 (Friday)
• June 29 (Friday)
• July 5 (Thursday)
• July 12 (Thursday, by skype)
• July 19 (Thursday, by skype)
• July 26 (Thursday, by skype)