Statement of Purpose

Technical Proficiencies

Programming Examples

Vegan Restaurants

Computational Proficiencies

Cloud Computing

  • Amazon Web Services on demand computational resources
    • Elastic Compute Cloud (EC2) - virtual servers
      • Amazon Machine Image (AMI) creation and maintenance
    • Simple Storage Service (S3) - data storage
    • Elastic Block Storage (EBS) - flexible storage

Computer Programming

  • Software design, development and documentation
    • Object oriented: Java, C++ and Python
    • Scripted: shell (BASH/CSH/SH), PHP and Python
  • Web based application development and implementation
    • Django and PHP
  • Network routing and protocols
    • Cisco Certified Network Administrator (CCNA) until 2006
  • Database development and implementation
    • Relational SQL based databases
  • Large-scale data management and analysis
  • Run-time profiling
  • Optimization of code

Microarray Analysis

  • Pre-processing and quality control
    • Background Subtraction/Normalization
    • Batch effect removal
    • Clustering and outlier removal
  • Differential expression analysis
  • Regression based analysis with covariates
  • Pathway enrichment analysis
    • DAVID/Ease
    • Ingenuity Pathway Analysis
  • Weighted gene co-expression networking (WGCNA)
  • Modeling and causality testing
  • cMonkey gene regulatory network inference
  • Inferring regulatory factors from gene co-expression / gene co-regulation

Genetic Analysis

  • Quality control
    • Hardy-Weinberg equilibrium (HWE)
    • Mendelian error checking
  • Linkage analysis
    • Non-parametric
    • Parametric
    • Two-point
    • Multi-point
    • Software used:
      • Simwalk
      • MENDEL
      • SOLAR
  • Association testing
    • TDT based
    • Regression based
    • Haplotype based
    • R (kinship package)
    • Software used:
      • PLINK
      • MENDEL
      • FBAT
      • SOLAR
      • QTDT
      • R (kinship, haplo)
  • Integration with gene expression data
  • Analysis scripting
  • Modeling

Illustration and Graphical Representation

  • Figure design
  • Poster design
  • Textbook chapter figure design
  • Tracing
  • Web graphic design
  • Software used:
    • Raster:
      • Adobe Photoshop
      • GIMP
    • Vector:
      • Adobe Illustrator
      • Inkscape
    • General plotting:
      • R
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