Special Topics in Math Biology
Computational Genomics:
G63.2856.002/G22.3033.006
Of related interest: 1997 CMU School of Computer Science
Distinguished Lecture:
Alchemy of Genomics
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Description:
The genome contained within a human cell is very large and complex.
It holds all of the genetic information necessary for its creation and
function encoded with a total of six feet of DNA. The goals of the
Human Genome Initiative (HGI), as framed by the National Institutes of
Health and the Department of Energy, are to generate a complete map,
containing well-defined markers, and to sequence the entire human
genome within the next seven, or less years. The sequencing aspects
of this project will have to deal with approximately 3 billion base
pairs. A large number of genes (70,000-100,000) will be identified
and characterized in terms of biochemical, developmental, and clinical
criteria. Additionally, the development of approaches to globally,
and quantitatively, characterize message (RNA transcripts, which
direct synthesis of specific proteins) will also play a major role in
virtually every aspect of biological, pharmaceutical and clinical
research.
The science of computational genomics and bio-informatics have been
created out of this massive sea of sequence data and the need to
establish functionality of genes largely based on similarities
discerned at the level of the DNA code; bypassing the need for
extensive biochemical characterization.
This emerging subfield relies on some classical and many novel
mathematical, statistical and algorithmic ideas that are essential to
accomplish this task. This course deals with mainly these mathematical
and computational approaches. The course is self contained, developing
the biological, statistical, probabilistic and algorithmic tools and
techniques along the way.
- Lecturer:
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Professor B. Mishra
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Introduction & History.
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Some Molecular Biology: DNA, Transfer RNA and Protein
sequence.
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Biochemistry.
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Restriction Maps.
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DDP (Double Digestion Problem): Complexity and Algorithms.
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Cloning and Clone Libraries.
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Physical Genome Maps (Oceans, Islands and Anchors):
Lander-Waterman statistics.
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Sequence Assembly.
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Alignment of Two and Multiple Sequences.
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Lander-Waterman Statistics and Applications to Sequence
Alignment.
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RNA Secondary Structure.
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Optical Mapping and Map-Based Sequence Assembly.
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Research Problems.
Office Hours: TBA
Office Phone: 212.998.3464
Email Address: mishra@nyu.edu
- Day and Time:
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Tuesdays, 5:00-6:50pm EST
- Place:
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Room 101, WWH, 251 Mercer Street.
- Credits for Course:
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3
- Prerequisites:
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Mathematical Maturity, Combinatorics, Statistics and
Algorithms Design
- Required Text(s):
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Statistical Genomics: Linkage, Mapping and QTL
Analysis.
By Ben Hui Liu, CRC Press, ISBN 0-8493-3166-8.
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Introduction to Computational Molecular Biology.
By Setubal & Meidanis, PWS Publishing Company, ISBN 0-534-95262-3.
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Introduction to Computational Biology: Maps, Sequences
and Genomes.
By Michael Waterman, Chapman and Hall, ISBN 0-412-99391-0
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Analysis of Human Genetic Linkage,
By Jurg Ott, The Johns Hopkins University Press, ISBN
0-8018-4257-3.
- Recommended Text(s):
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Principles of Genome Analysis.
By S.B. Primrose, Blackwell Science, ISBN 0-86542-946-4.
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The Human Genome Project: Deciphering the Blueprint of
Heredity.
Edited by N.G. Cooper, University Science Books, ISBN
935702-29-6.
- Midterm Date:
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No Midterm.
- Final Date:
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Class Project.
- Homework(s):
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Class Presentation.
Bud Mishra
November 1 1998