Department of Bioinformatics and Computational Biology

Education:GSBS Bioinformatics Course

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Introduction to Bioinformatics

GS ???, Fall 2012

Schedule:?. We will meet in the GSBS Conference Room (?) on ? and ?.


Deadline for submitting the proposal

July. 1, 2012


To train GSBS students (from general biomedical background) to do bioinformatics

Course coordinators

Nicholas Navin, Ken Chen, Arvind Rao


Format: this will be a 2 hour class per week with 5-10 minute break in the middle. The first hour is a lecture that covers a specific topic and the second is a hand-on computer lab.

Location: BSRB classroom.

Prerequisites: No. Students are encouraged to bring laptops that have UNIX. Most students in GSBS have Macbook from their program. In addition, GSBS offered 12 Macbook Pro laptops specifically for class use. Students are expected to have some programming experience.

Number of students: >3, ~20?

Proposed topics

  • Unix and Programming (Perl)
    • File Management
    • Parser (regular expression)
    • Data structure (variables, array, hash)
    • Functions
    • Modules
  • Probability and Basic Statistics
    • Distributions
    • Statistical Significance
  • Genomics / Cancer Genomics
    • Next-Generation Sequencing DNA/RNA
      • Platforms technologies
      • Base calling
    • Sequence Alignment
      • Pairwise Sequence Alignment
      • Probabilistic Sequence Alignment
    • Coverage and copy number
      • Coverage theory
      • Experimental design and quality control
      • Copy number analysis from count data
      • Purtiy/Aneuploidy
    • Sequence Assembly
      • Algorithms: Overlap-extend, de Bruijn graphics
    • Detecting and Annotating Variants
      • SNP/SV calling statistics
      • Functional Annotation
  • Multivariate statistics (clustering, mds, pca)
  • Phylogenetics
  • Microarray Analysis / RNA-Seq
    • Platforms and Normalization
    • Transcriptome assembly, alternative splicing, and gene fusion
    • Expression analysis from count data
  • Pathway/Network Analysis
    • Enrichment
    • Topology
  • Data Visualization (R)
    • Visualize genomics data (IGV)
    • Navigating the Human Genome (UCSC)
  • Biological Databases (TCGA, Genbank)
  • Epigenomics and Chip-Seq(?)
  • Proteomics (?)

Proposed textbook

[1] Bioinformatics and Functional Genomics