ECE 697S: Topics in Computational Biology

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ECE 697S Topics in Computational Biology

• Spring 2006
• Ramgopal Mettu

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Turing Machine (1936)
Church-Turing Thesis Universal Model of
Computation

Alan Turing (1912-1954)
Avery, Chargaff, Franklin, Pauling, Watson,
Crick, Wilkins et al.
X-ray structure of ribosome Yusupov et al. 2001
Rual et al. 2005
Post-Genomic Era
Collins/Venter, 2003
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Turing Machine (1936)
Church-Turing Thesis Universal Model of
Computation

Alan Turing (1912-1954)
Avery, Chargaff, Franklin, Pauling, Watson,
Crick, Wilkins et al.
One Day?
X-ray structure of ribosome Yusupov et al. 2001
Rual et al. 2005
Post-Genomic Era
Collins/Venter, 2003
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Gene Sequences
Venter et al 2001
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10,000 unique structures in 10 years
Human Genome Project
Genome sequencing is only the first step!
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What is Computation?
?
n
You are facing a high wall that stretches
infinitely in both directions. There is a door in
the wall, but you don't know how far away or in
which direction. Can you escape? If so, how
quickly? Ian Parberry, Problems on Algorithms
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What is Computation?
?
n
Can find exit in 4n-1 paces using a geometric
walk.
You are facing a high wall that stretches
infinitely in both directions. There is a door in
the wall, but you don't know how far away or in
which direction. Can you escape? If so, how
quickly? Ian Parberry, Problems on Algorithms
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What is Computation?

• Given a well-defined problem and input, how
  quickly (in the worst-case) can one produce a
  solution to the desired accuracy?
• Is there a tradeoff between resource requirements
  and accuracy?

Tractable vs. Intractable
polynomial-time n, n2,n3,
BAD
GOOD
set of all Turing-computable problems
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Computational Biology

• Data Collection/Analysis/Modeling
• Develop problem formulations that are realistic,
  and are tractable.
• Leverage 50 years of computational techniques
• Combinatorial Optimization
• Statistics
• Geometry

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This Course

• DNA/Gene sequences
• Sequence Assembly
• Gene Finding and Microarray Analysis
• Protein Structure Prediction/Determination
• Molecular Dynamics, Homology Modeling
• Protein Structure Prediction, and Protein Design
• X-ray crystallography
• Nuclear Magnetic Spectroscopy
• Protein-Ligand/Protein-Protein Binding, Docking
• Signaling and Interaction Networks
• Phylogenetics and Protein Evolution

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Administrivia
?

• Time MWF 125-215 MW 125-240
• Office Knowles 211D
• Office Hours By appointment
• Course webpage www.ecs.umass.edu/mettu/ece697s

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Class Format

• Presentations
• rotating schedule, 2-3 papers/1-2 class periods
• focus on computational techniques, practicality
• start March 6, approve topic with me
• Projects
• approve topic, meet with me before April 1
• survey new problems, open problems,
  improvements to state-of-the-art

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Coming Up

• Introductory Material
• Basic Genetics
• Computation?
• DNA sequence alignment and assembly
• Sequence Alignment via Dynamic Programming
• Graph-Theoretic Sequence Assembly Algorithms
• Guest Speaker Prof. David Kulp from CS (Gene
  Finding and Microarray Analysis)