Summer 2018
Jump to navigation
Jump to search
Rules of Conduct
- No eating, drinking, or loud talking in the lab. Socialize in the lobby only.
- Be respectful to each other, regardless of level of study
- Be on time & responsible. Communicate in advance with the PI if late or absent
Participants
- Dr Oliver Attie, Research Associate
- Brian Sulkow, Research Associate
- Saymon Akther, CUNY Graduate Center, EEB Program
- Lily Li, CUNY Graduate Center, EEB Program
- Mei Wu, Bioinformatics Research Assistant
- Yinheng Li, Informatics Research Assistant
- Christopher Panlasigui, Hunter Biology
- Dr Lia Di, Senior Scientist
- Dr Weigang Qiu, Principal Investigator
- Summer Interns
Journal Club
- a Unix & Perl tutorial
- A short introduction to molecular phylogenetics: http://www.ncbi.nlm.nih.gov/pubmed/12801728
- A review on Borrelia genomics: https://www.ncbi.nlm.nih.gov/pubmed/24704760
Projects
Borrelia genome evolution (Led by Saymon)
- Goal 1. Estimate time of cross-Atlantic dispersal using core-genome sequences
- Goal 2. Investigate codon biases with respect to levels of gene expression
Identification of host species from ticks (Led by Lily [after first-level])
- Goal 1. Protocol optimization for PCR amplification of host DNA from ticks
- Goal 2. Protocol development: library construction for MiSeq
- 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)
- Goal 1. Association of genes/SNPs with biofilm formation and c-di-GMP levels: Manuscript preparation
- Goal 2. Association of genome diversity with metabolic diversity
Machine learning approaches to evolution (Led by Oliver & Brian)
- Goal 1. Implement Hopfield network for optimization of protein structure
- Goal 2. Neural-net models of OspC
- Goal 3. K-mer-based pipeline for genome classification
Schedule
Field dates
- June 7, 2018, Thursday, Caumsette State Park
- June 14, 2018, Thursday, Fire Island National Seashore
Weekly Schedule
- Summer kickoff (June 1, 2018, Friday): Introduction & schedules
- Week 1 (June 4-8):
- Interns: Explore the "iris" data set using R, by following the the Monte Carlo Club Week 1 (1 & 2) and Week 2
- Interns: Go through the Unix & Perl Tutorial
- 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)