Qiu Lab Meetings

Projects & Goals

• Borrelia population genomics: Recombination & Natural Selection (Published)
• Borrelia pan-genomics (Submitted)
• Positive and negative selection in Borrelia ORFs and IGS (In submission)
• Dr Bargonetti's project (Summer 2013)
• A new pipeline using MUGSY-FastTree (Summer 2013)
• Borrelia Genome Database & Browser (Summer 2013)
• Pseudomonas population genomics (Summer 2013)
• Hypothesis Testing: Do host-interacting genes show adaptive codon usage? (Summer 2013): Project page
• Frequency distribution of ospC types in wild tick populations (Fall 2013)

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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 Readings

• Molecular phylogenetics
• Population genetics
• Genomics
• Systems Biology

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Informatics Architecture

• Operating Systems: Linux OS/Ubuntu, Mac OS
• Programming languages: BASH, Perl/BioPerl, R
• Relational Databases: PostgreSQL
• Software architecture
  • bb2: Borrelia Genome Database
  • bb2i: an Perl API for bb2
  • DNATweezer: Perl wrappers of most frequently used BioPerl modules, including Bio::Seq, Bio::SimpleAlign, and Bio::Tree [1]
  • SimBac: A Perl/Moose package for simulating bacterial genome evolution [2]
  • Borrelia Ortholog Retriever: Download ortholog alignments from 23 Borrelia spp genomes. Search by gene names and IDs.[3]
• Hardware Setup
  • NSF File Server
  • Database and Application Server
  • Web Server
  • Linux Workstations

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