Qiu Lab Meetings

School Year 2015

Aug 28, 2015

• Journal Club: an recent paper claiming wide-spread gene loss & pseudogenization in bacterial pathogens. [1]. Presenter: Roy

Sept 4, 2015

• Journal Club: a nice review of bacterial population genetics (E.coli model), from protein polymorphisms to whole-genome variations. [2]. Presenter: Amanda

Sept 11, 2015

• Journal Club: an in-depth analysis of Staphylococcus aureus genomes. http://mbe.oxfordjournals.org/content/29/2/797.long. Presenter: John

==Sept 18, 2015

• Journal Club: latest statistics in detecting population admixture and genome intragression (d3, f4, h4, ChromosomePainter).

[3]. Presenter: Saymon

Summer 2014

Projects & Goals

Name	Goal/Description	Team
Pseudomonas	Gene gain/loss SNP analysis	Example
Borrelia intergenics	Clean up start-codon positions	Example
SNP pipeline	Example	Example
Gain/Loss pipeline	Example	Example

• Frequency distribution of ospC types in wild tick populations (Fall 2013) Project page
• Mutual information

Summer 2013

Projects & Goals

• Borrelia population genomics: Recombination & Natural Selection (Published)
• Borrelia pan-genomics (Submitted as of 5/25/2013)
• Positive and negative selection in Borrelia ORFs and IGS (Submitted as of 6/15/2013)
• Dr Bargonetti's project (Summer 2013)
• A population genomics pipeline using MUGSY-FastTree (Summer 2013): Project page
• Borrelia Genome Database & Browser (Summer 2013) Version 2 screen shot
• Pseudomonas population genomics (Summer 2013) Project page
• Hypothesis Testing: Do host-interacting genes show adaptive codon usage? (Summer 2013): Project page
• Phylogenomics browsing with JavaScript/JQuery, Ajax, and jsPhylosvg
• Frequency distribution of ospC types in wild tick populations (Fall 2013) Project page

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Lab meeting: June 13, 2013

• Weigang: IGS paper submission should be done by Thursday.
• Che/Slav: Workshop update (Meeting at 3:30pm?)
• Che: SILAC project (Meeting at 4pm?)
• Zhenmao: Tick processing & paired-end Illumina sequencing
• Pedro: Updates on "ncbi-orf" table
• Girish: phyloSVG extension; QuBi video
• Saymon and Deidre: consensus start-codons
• Reeyes and Raymond: Pseudomonas DB; fleN alignment and phylogeny
• Valentyna: BLASTn results (4:30pm?)

Lab meeting: May 23, 2013

• May 24, Friday: End of School Year Party in the Park (we leave from Hunter @ 1:30pm)
• Recommended reading of the week: Detecting Neanderthal genes using the D' homoplasy statistic
• Weigang: IGS paper submission
• Che: Thesis update/SILAC project/Summer teaching
• Zhenmao: Manuscript update: Material & Methods; Results (Tables and Figures)
• Pedro: Catlyst web framework
• Girish: cp26 phylogenomic analysis
• Saymon and Deidre: consensus start-codons

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Lab meeting: May 16, 2013

• Weigang: IGS paper submitted yet?
• Che: Thesis update. Chapter 3. Evolution of ospA/ospB gene family
• Pedro/Zhenmao: Can we wrap up the BLAST identification of ospC types?
• Girish: Fetch cp26 sequences from DB; Run MUGSY & FastTree
• Saymon/Deidre: Identification of consensus start-codon positions
• Pedro/Girish: orth_get/orth_igs website development. Catalyst. Implement graphics (genome map & phylogeny) query interface
• Raymond: start the Pseudomonas summer project

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Foundational papers for working in Qiu Lab

• A recent review by Qiu lab: Evolutionary genomics of Lyme bacteria
• Phylogeography of Borrelia burgdorferi sensu lato. A review by Margos et al. 2011
• A short tutorial on molecular phylogenetics: Phylogeny for the faint of heart: a tutorial
• The Ka/Ks test of natural selection: The Ka/Ks ratio: diagnosing the form of sequence evolution

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Informatics Architecture

• Operating Systems: Linux OS/Ubuntu, Mac OS
• Programming languages: BASH, Perl/BioPerl, R
• Relational Databases: PostgreSQL
• Software architecture
  • bb3: Borrelia Genome Database. To access: psql -h borreliabase.org -U lab bb3
  • Pseudomonas Genome Database. To access: psql -h ortholog -U lab paerug
  • DNATweezer: Perl wrappers of most frequently used BioPerl modules, including Bio::Seq, Bio::SimpleAlign, and Bio::Tree [4]
  • SimBac: A Perl/Moose package for simulating bacterial genome evolution [5]
  • BorreliaBase

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Perl Challenges

Problem	Input	Output
DNA transcription	A DNA sequence, in 5'-3' direction (e.g., aaatttaaaagacaaaaagactgctctaagtcttgaaaatttggttttcaaagatgat)	An RNA sequence, in 5'-3' direction
Genetic code	None	64 codons, one per line (using loops)
Count amino acids	A protein sequence	Frequency counts of individual amino acids
Count codons	A protein-coding DNA sequence	Frequency counts of individual codons
Random sequence 1	None	Generate a random DNA sequence (e.g., 1000 bases) with equal base frequencies
Random sequence 2	None	Generate a random DNA sequence with biased base frequencies, e.g., 10% G, 10% C, 40% T, and 40% A.
Graphics I	a categorical dataset, e.g., Biology	a bar graph & a pie char, using GD::Simple or Postscript::Simple