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: Muhammad, Pavan, Roman, Benjamen, Andrew, Michelle, Hannah

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
5. Codon usage changes fitness in E.coli: Frumkin et al (2018) "Codon usage of highly expressed genes affects proteome-wide translation efficiency". PNAS

Projects

Borrelia genome evolution (Led by Saymon)

Codon biase measured by Shanon information (bits)

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

* Andrew's BioPython code to calculate CAI

#Opens the fasta file and reads contents into a string (myStr).
myFile = open("B31-cp26.txt","r")
myStr = myFile.read()
myFile.close()

#Imports codon usage module.
from Bio.SeqUtils import CodonUsage as cu

#Takes myStr and processes it into a list of sequences (FastaList).
FastaList = myStr.split(">")
FastaList = FastaList[1:]
IDList = []
EnterList = []
##Separates FastaList into a list of sequence IDs (IDList) and a list of sequences (EnterList).
for seq in FastaList:
    IDList += [seq[:6]]
    EnterList += [seq[6:]]
##Removes enter characters from each sequence in EnterList.
SeqList = []
for seq in EnterList:
    SeqStr = seq.replace("\n", "")
    SeqList += [SeqStr]

#Calculates and presents the CAI value for each sequence using functions from the module.
myObject = cu.CodonAdaptationIndex()
myObject.generate_index("B31-cp26.txt")
for SeqIndex in range(len(SeqList)):
    print (IDList[SeqIndex], '   CAI =', myObject.cai_for_gene(SeqList[SeqIndex]))

Output for cp26:
BB_B01 CAI = 0.7190039074113422
BB_B02 CAI = 0.678404951527374
BB_B03 CAI = 0.6893076488255271
BB_B04 CAI = 0.7250154635421513
BB_B05 CAI = 0.6971190458423587
BB_B06 CAI = 0.67042305582205
BB_B07 CAI = 0.6971020959083346
BB_B09 CAI = 0.6786931743972611
BB_B10 CAI = 0.7224886929887183
BB_B12 CAI = 0.6997502136447451
BB_B13 CAI = 0.7592966148479222
BB_B14 CAI = 0.6959525612884284
BB_B16 CAI = 0.6835709626613392
BB_B17 CAI = 0.6974779110749645
BB_B18 CAI = 0.7052250722958308
BB_B19 CAI = 0.7049049245887261
BB_B22 CAI = 0.6860641572293008
BB_B23 CAI = 0.6915165725213809
BB_B24 CAI = 0.7025276490965267
BB_B25 CAI = 0.7439914547011712
BB_B26 CAI = 0.7255623088410704
BB_B27 CAI = 0.7161378416520467
BB_B28 CAI = 0.7316661839512337
BB_B29 CAI = 0.6919705705489939

1. Codon bias by Shannon information: BASH pipeline
   1. Simulate 100 sequences for each CDS: cat filename.txt | while read line; do ./codon-info-sim.pl -n 100 BbB31.cutg.GCG "$line".fas > "$line"-sim.fas; done;
   2. Calculate Shannon index for each CDS (simulated & actual)./codon-info.pl BbB31.cutg.GCG foo.fas

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

• (Christopher) This script parses excel peak-area file into database & R inputs

#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Getopt::Std;

my %opts;
my $line_ct = 0;
my (@colnames, @areas, %seen_cmps, %seen_gids);

getopts('dr', \%opts);
while(<>) {
    chomp;
    $line_ct++;
    next unless $line_ct >=4;
    if ($line_ct == 4) {
        @colnames = split "\t", $_;
        for (my $i=5; $i<=$#colnames; $i++) { $seen_gids{$colnames[$i]}++ } # get uniq gids
        next;
    }
    my @data = split "\t", $_;
    $seen_cmps{$data[1]}++; # get unique compound formula
    for (my $i=5; $i<=$#data; $i++) {
        my $area = { 'compound' => $data[1], 'gid' =>$colnames[$i],  'peak_area' => $data[$i]};
        push @areas, $area;
    }
}

if ($opts{d}) { # for database output
    foreach my $cmp (sort keys %seen_cmps) {
        foreach my $gid (sort keys %seen_gids) {
            my @peaks = grep { $_->{compound} eq $cmp && $_->{gid} == $gid } @areas;
            my $peak_str = join ",", map {$_->{peak_area} || "NULL"} @peaks;
            print join "\t", ($gid, $cmp, "{" . $peak_str . "}");
            print "\n";
        }
    }
}

if ($opts{r}) { # for R output
    foreach my $cmp (sort keys %seen_cmps) {
        foreach my $gid (sort keys %seen_gids) {
            my @peaks = grep { $_->{compound} eq $cmp && $_->{gid} == $gid } @areas;
            foreach my $peak (@peaks) {
                next unless $peak->{peak_area};
                print join "\t", ($peak->{peak_area}, $gid, $cmp);          
                print "\n";
            }
        }
    }
}
exit;

Compound amount in each genome

• (Benjamen) Creates a sample simple force directed network in R using networkD3. Install packages "igraph" and "networkD3".

Simple Sample

library(igraph)
library(networkD3)
nodes <- c(rep('x1', 10), rep('x2',10), rep('x3',10), rep('x4',10))
ids <- c(1,1,1,-1,0,-1,0,0,-1,0,0,0,0,0,0,0,0,0,1,-1,0,0,0,0,0,1,-1,-1,0,0,0,0,0,1,-1,0,0,0,0,0)
df <- data.frame(nodes, ids)
df$ids
matrix(df$ids, nrow = 4, ncol = 10, byrow = T)
testmat<-matrix(df$ids, nrow = 4, ncol = 10, byrow = T)
rownames(testmat) <- c("x1", "x2", "x3", "x4")
colnames(testmat) <- c("v1", "v2", "v3", "v4", "v5", "v6", "v7", "v8", "v9", "v10")
testmat.inc <- graph_from_incidence_matrix(testmat)
testmat.edge <- as_edgelist(testmat.inc)
colnames(testmat.edge) <- c("From", "To")
testmat.df <- as.data.frame(testmat.edge)
simpleNetwork(testmat.df, opacity = .8, fontSize = 16)

• (Benjamen) Force-Directed Network Graph Visualization of the iJN746 S Matrix (Only Metabolites in Our Database)

Force-Directed Network Graph of iJN746 (Only Metabolites in Our Database)

library(igraph)
library(networkD3)

#create a preliminary edgelist from the original matrix. If using the simpleNetwork() function, this
#is the only required step.
stwo <- read.table("Stwo.tsv", header=T)
stwo.inc <- graph_from_incidence_matrix(stwo)
stwo.edge <- as_edgelist(stwo.inc)
colnames(stwo.edge) <- c("from", "to")
stwo.df <- as.data.frame(stwo.edge)

#both the "from" and "to" columns must be given a unique numerical value, as this is the only way
#forceNetwork() will run. To assign numerical values, we index each unique instance of a metabolite
#or reaction in order.

#index "from" column
unique(stwo.edge[,1])
order(unique(stwo.edge[,1]))
from.idx <- data.frame(row.names=unique(stwo.edge[,1]), row.idx=1:82)
stwo.df$from
from.idx[as.character(stwo.df$from),1]
stwo.df$from.idx <- from.idx[as.character(stwo.df$from),1]

#index "to" column
unique(stwo.edge[,2])
order(unique(stwo.edge[,2]))
to.idx <- data.frame(row.names=unique(stwo.edge[,2]), row.idx=1:188)
stwo.df$to
to.idx[as.character(stwo.df$to),1]
stwo.df$to.idx <- to.idx[as.character(stwo.df$to),1]

#add 81 to every value in "to" column and subtract 1 from every value in "from" column. This is so
#the indexing starts from 0, and every indexed variable on the "to" side continues from where "from"
#left off, which, in this case, is variable #82.
stwo.df$to.idx <- stwo.df[,4]+81
stwo.df$from.idx <- stwo.df[,3]-1

#create new data frame with just the "from" and "to" columns.
stwo.new <- data.frame(stwo.df$from.idx, stwo.df$to.idx)
colnames(stwo.new) <- c("from", "to")

#order the edgelist by the to column. The ordered "to" column is then appended to the "from" column,
#and the now disordered "from" column is appended to the "to" column, effectivley mirroring the original
#edgelist. This is done because every variable in the network must show up in the "from" column for
#the forceNetwork() function to work.
stwo.new2 <- stwo.new[order(stwo.new$to),]

#zoom in and out by rolling mouse wheel or double clicking. Click and drag to pan the model.
forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label", 
linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1, 
charge = -50, width = 1920, height = 1080)

Machine learning approaches to evolution (Led by Oliver & Brian)

OspC structural alignment, converted from S2 from Baum et al (2013)

1. Goal 1. Implement Hopfield network for optimization of protein structure
2. Goal 2. Neural-net models of OspC. Structural alignment (S2 from Baum et al 2013):

1. Goal 3. K-mer-based pipeline for genome classification

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, Muhammad, 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: 2nd field day (Fire Island National Seashore). Participants: John, Brian, Mei, Muhammad, Pavan, Benjamin, and Weigang. Got ~100 lone-star ticks and 4 deer tick nymphs
• Week 3 (June 18-22):
  • Monday: Lab meeting, 1st project reports
    • Codon Bias: Theory, Coding, and Data (Andrew, Pavan, Saymon)
    • OspC epitope identification: Serum correlation, sequence correlation, immunity-sequence correction (Muhammad, Roman, Brian)
    • Pseudomonas metabolomics: parsing intensity file; theory & parsing SMBL file (Chris & Benjamin)
  • Tuesday: working groups
  • Wed: working groups
  • Thursday: Big Data Workshop
  • Friday: working groups
• Week 4 (June 25-29):
  • Monday: Lab meeting
  • Tu-Th: work sessions
  • Friday: Joint lab meeting with MSKCC/Lab visit
• Week 5 (July 2-6):
  • Monday: Lab meeting
  • Tuesday/Wed: 4th of July Break
  • Thursday & Friday: work sessions
• Week 6 (July 9-13)
  • Monday (July 9): E-reports & Wiki posts
• Week 7 (July 16-20)
  • Monday (July 16): E-reports * Wiki posts
• Week 8 (July 23-27)
  • Monday: lab meeting resumes
  • Monte Carlo Club, Season 3 (Evolutionary Computing) starts
• Week 9 (July 30-Aug 3)
• Week 10 (Aug 6-Aug 10)
  • Final report

Lab notes for Summer HS Interns

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

Notes & Scripts

• (Weigang) Re-analysis of ospC cross-reactivity using normalization:
  • Fold change vs alleles for mouse + humans: interactive heatmap by heatmaply
  • Correlation matrix based on N=23 mouse samples (and 7 controls): interactive heatmap by heatmaply
  • Correlation matrix based on N=55 human samples (and 25 controls): interactive heatmap by heatmaply
  • Correlation matrix based on both mouse & human samples: interactive heatmap by heatmaply]

• (Weigang) A sample R script to parse Table S2 from Baum et al 2013, sera-antigen reactivity measurements

# 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")
x.cor$estimate
levels(x[,8]) # obtain ospC allele types; to be looped through in pairwise
for (i in 1:?) { for (j in ?:?) {cor.test(....)}}

• (Muhammad) Output generates data frame of correlation/p values for 23 different Osp-C allele types in pairwise

setwd("C:/R_OspC")
x <- read.table("Table-S2.txt", sep="\t", header=T)
a<-levels(x[,8])
output = data.frame(i=character(), j=character(), cor = numeric(), p = numeric());
#k <-0;
for(i in 1:22) {
  allele.i <- a[i];
  vect.i <- x[which(x[,8]==allele.i),12];
  
  for(j in (i+1):23) {
    allele.j <- a[j];
    vect.j <-x[which(x[,8]==allele.j),12];
    cor <- cor.test(vect.i,vect.j, method = "pearson");
    output <- rbind (output, data.frame(i=allele.i, j=allele.j, cor=cor$estimate, p=cor$p.value)); 
  }
}
 write.table(output, "immune-output.txt", quote = F, sep = "\t")

• (Muhammad) Creates a plot for the correlation values of the lab's data and the author's data

#read in the authors cross reactivity correlation matrix
cr<- read.csv("C:/ospc/matricesospc.csv", header=F, sep = ",")
#puts all of the values of cr into corvect
corvect<-c()
for (i in 1:(nrow(cr)-1)) {
  for (j in (i+1):ncol(cr)) {
    corvect[length(corvect)+1]<- cr[i,j]
  }
    }
#merging cross reactivity correlation data and the authors data
df<- data.frame(output, corvect)
#plots the dataframe
plot(output[,3], corvect, main="Cross Reactivity Correlation Comparison", ylab = "Author's Output", xlab="Lab Output")
#gives the liner model, relationship between our data and the authors
b<-lm(corvect~output[,3])
#places the ab line on the plot
abline(b, col=2)

Cross Reactivity Correlation Comparison

East/East Cross Reactivity Matrix

West/West Cross Reactivity Matrix

West/West Cross Reactivity Matrix