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The 2007 DBW was featured on NPR by WUNC's Rose Hoban. Click here to listen to the report.

2013 Bioinformatics Workshop Content

Web based tools are used in each of the workshop modules to help interrogate biological data. The aims of each of the modules is outlined below.

De novo Analysis of Sequence

  • View manually annotated genes in the Vega browser.
  • Sequence similarity searching using Blastn and PSI-blast to identify similar proteins.
  • De novo analysis of cDNAs, including ORF finder to highlight putative protein products of a cDNA, blastp link from within this to investigate the potential protein products, Spidey to align cDNA to genomic DNA.
  • Clustalw to align similar sequences, view in Jalview and use GeneDoc to produce a graphics file.
  • InterPro to investigate protein domain structures.

Browsing the Human Genome

  • Appreciate ability to now work with the whole genome
  • Introduce primary human genome browsers
  • Discuss how genome annotations are displayed and relevant information is made accessible
  • Demonstrate some general features and applications of genome browsers.
  • Introduction to the applications of the UCSC genome browser
  • Introduction to the applications of the Ensembl
  • Explore ability to view your own annotations in the browser
  • Provide examples to facilitate becoming more comfortable using browser resources.

Comparative Genomics

  • Review the sequence available from different organisms
  • Identify putative homologous genes and generate a phylogenetic tree
  • Compare genome sequences from different organisms and identify conserved sequences
  • Analyze conserved sequences for potential regulatory function

Exploring Gene and Protein Function and Disease

  • Identify information available to determine the possible function of a gene product
  • Highlight various inter-linked information resources that are available for this purpose
  • Identify published information on the gene
  • Identify known Mendelian inherited disorder(s) associated with the gene
  • Summarize predicted function from several linked databases
  • Identify domains found within the protein
  • Protein databases and analysis
  • View structural information if available.

Sequence Variation

  • Introduction to SNPs
  • Introduction to various SNP resources on the web, including Ensembl, dbSNP and JSNP
  • Integration of information from various databases to identify SNPs in target gene or chromosomal regions
  • Export SNP information from databases
  • Introduction to genotypes and haplotypes, including the HapMap database
  • Introduction to genotyping low, medium and high throughput genotyping platforms and information about study design and QC

Major Bioinformatic Resources

  • Introduction to GenBank
  • Introduction to the Gene expression Omnibus (GEO)
  • Introduction to the Short Read Archive (SRA)
  • Introduction to the Database of Genotypes and Phenotypes (dbGAP)

Next Generation Sequencing

  • An exploration of next generation sequencing platforms including:
    • Platform description
    • De novo sequence generation
    • Sequence QC metrics and assembly
    • Sequence Assembly via Galaxy
  • RNA-Seq Analysis

DNA/RNA Microarrays

  • Review common array-based technologies to measure DNA and RNA
  • Review common approaches to analysis
  • Identify a region of chromosomal gain using Array CGH data
  • Determine Genes with differential expression in region of chromosomal gain

The Human Epigenome

  • Defining the field of epigenomics
  • Exploring DNA methylation and histone modifications
  • Methods of how to interrogate the methylome
  • The use of next-generation sequencing approaches in epigenomic profiling
  • Description of how to target the methylation status of genes
  • Worked examples of methylation analyses

Proteomics

  • Basics of protein chemistry
  • Basics of mass spectrometry for characterization of peptides and proteins
  • Common LC/MS/MS methods for protein identification
  • Software tools for interpreting qualitative LC/MS/MS data
  • Methods for differential expression proteomics
  • Software tools for interpreting differential expression proteomics data
  • Tools for placing differentially expressed proteins into signaling/regulatory pathways

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