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

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. ospC epitope mapping: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067445

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. Data file:
   File:B31-cp26.txt

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

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):
  • Monday: the Unix & Perl Tutorial, Part 1
  • Tuesday: Unix Part2. Explore the "iris" data set using R, by following the the Monte Carlo Club Week 1 (1 & 2) and Week 2. Read McKay (2003), Chapters 38 & 39
  • Thursday: 1st field day (Caumsett State Park); Participants: John, Mahamad, Pavan, Andrew, Dr Sun, Weigang, with 3 members of Moses team from Suffolk County Vector Control. Got ~110 deer tick nymphs
  • Friday: meeting with MSKCC group at 11am; BBQ afterwards
• Week 2 (June 11-15):
  • Monday: Lab meeting, projects assigned
  • Tuesday: neural net tutorial (by Brian)
  • Thursday: Fieldwork on Fire Island
• Week 3 (June 18-22):
  • Monday: Lab meeting, 1st project reports
• June 29 (Friday)
• July 5 (Thursday)
• July 12 (Thursday, by skype)
• July 19 (Thursday, by skype)
• July 26 (Thursday, by skype)

Lab notes for Summer HS Interns

• NCI Cloud: Seven Bridges Cloud Platform. Create an user account
• Read documentation & tutorials: Documentation

Sample Scripts/Templates

# preliminaries: save as TSV; substitute "\r" if necessary; substitute "N/A" to "NA"; remove extra columns
setwd("Downloads/")
x <- read.table("table-s2.txt4", sep="\t", header=T)
View(x)
colnames(x)
which(x[,8]=="A")
x[which(x[,8]=="A"),12]
x[which(x[,8]=="A3"),12]
cor.test(x[which(x[,8]=="A3"),12], x[which(x[,8]=="A"),12], method = "pearson")
levels(x[,8]) # obtain ospC allele types; to be looped through in pairwise