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Bioinformatics: One Minute and One Hour at a Time

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Bioinformatics and intro molecular biology. or. One of several 300-level biology courses ... Bioinformatics Course. Prerequisites ... – PowerPoint PPT presentation

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Title: Bioinformatics: One Minute and One Hour at a Time


1
Bioinformatics One Minute and One Hour at a
Time
  • Laurie J. Heyer
  • L.R. King Asst. Professor of Mathematics
  • Davidson College
  • laheyer_at_davidson.edu

2
What is Bioinformatics?
Computer Science
Mathematics
Bioinformatics
Biology
3
Genomics, Proteomics and Systems Biology
  • Primary audience
  • Junior bio majors
  • Prerequisites
  • Bioinformatics and intro molecular biology or
  • One of several 300-level biology courses
  • Course home page
  • http//www.bio.davidson.edu/genomics
  • Math Minutes
  • Taught by A. Malcolm Campbell (Biology)

4
Sample TopicDNA Microarrays
5
Plotting Expression Data
  • One highlighted gene is induced 16 fold
  • One highlighted gene is repressed 16 fold
  • But induction looks much more dramatic

6
Log Transformation
  • Calculate log2 of each ratio
  • Ratio of 16 becomes value of 4
  • Ratio of .0833 (1/16) becomes value of 4
  • Induction and repression look equal, but opposite
    sign

7
Hierarchical Clustering
  • Join two most similar genes
  • Join next two most similar objects (genes or
    clusters of genes)
  • Distance from one gene to a set of genes is
    minimum of all distances from the gene to the
    individual members (Single Linkage)
  • Repeat until all genes have been joined

8
Genome Consortium for Active Teaching (GCAT)
http//www.bio.davidson.edu/GCAT
9
High School Chips
See Kathy Gabrics page http//cstaff.hinsdale86.
org/kgabric/honorscalendar.html
10
Bioinformatics Course
  • Prerequisites
  • Genomics or experience with modeling and
    algorithmic thinking
  • Goals
  • To understand and apply various algorithms and
    statistical tests for analyzing DNA, RNA and
    protein sequences, and DNA microarray data. 
  • To gain practical experience with Perl, a
    programming language widely used in molecular
    biology, web design, and text processing.
  • Course home page
  • http//gcat.davidson.edu/bioinformatics/bioinf.htm
    l

11
Bioinformatics Topics
  • Determining sequences
  • Comparing sequences
  • Finding genes
  • Predicting structure
  • Comparing genomes
  • Inferring phylogenies
  • Analyzing images
  • Clustering gene expression patterns
  • Designing experiments

12
Bioinformatics Projects
13
Image Segmentation
  • Locate spot (signal) pixels
  • Measure intensity of signal and background in
    each channel
  • Compute ratio

14
Adaptive Circle Algorithm
  • Specify threshold between darkest and lightest
    pixel
  • Pixels above threshold are on, others are off
  • Combine two binary images if pixel is on in
    either image, it is on in combined image
  • Search for radius and center that maximize
    percent of on pixels

15
Adaptive Circle V2 (Dapple)
  • Compute 4-neighbor second-difference
    approximation to the Laplacian
  • Find sharply defined upper edge by convolving
    Laplacian with annular filters

From Dapple Improved Techniques for Finding
Spots on DNA Microarrays UW CSE Technical Report
UWTR-2000-08-05
16
Quality Clustering QT Clust
1. Each gene builds a supervised cluster 2.
Gene with best list, and genes in its list,
becomes next cluster 3. Remove these genes from
consideration, and repeat 4. Stop when all
genes are clustered, or largest cluster is
smaller than user specified threshold
17
Why teach Bioinformatics?
  • Critical thinking
  • Interdisciplinary
  • Integrative
  • Modeling
  • Data analysis
  • Computational science
  • Discrete math
  • Probability and statistics
  • Student research opportunities
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