IT 471 -
Topics in Bioinformatics
Instructors
Manish K Gupta
| Room 2209 FB 2
| mankg [at] daiict.ac.in | Phone: 91-79-30150549
|
Teaching Assitant
Overview
This course covers basic machine learning techniques that
are used in molecular biology. We will also see how we can apply them
in solving the mysteries of the living systems.
Tentative Course Content
Overview of Molecular Biology, Refresher of
Probability-Statistics and Optimization, Hidden Markov Model (HMM),
Stochastic Context-Free Grammar (SCFG), Least Square Regression,
Neural Network, Support Vector Machine (SVM), Applications of these
techniques such as in finding non-coding RNAs, RNA folding,
RNA secondary structure classification, Protein folding and misfolding,
Gene Regulatory Networks (GRN)
Text Book
There is no specific text book but the following books will be helpful. Specially the book by Pevzner. We will provide many additional material such as videos, handouts etc during the course. You do not have to purchase any book.
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Pierre Baldi and Soren Brunak, Bioinformatics: The Machine Learning Approach,
The MIT press, 2001
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Bernhard Scholkopf, Koji Tsuda and Jean-Philippe Vert, Kernel Methods in Computational Biology, The MIT press, 2004
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Pavel A. Pevzner, Computational Molecular Biology, An Algorithmic Approach,
The MIT press, 2001
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Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics
Algorithms, Indian reprint by Ane Books, 2005
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Nello Cristianini and Matthew W. Hahn, Introduction to Computational
Genomics: A Case Studies Approach, 2007, Cambridge University Press
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David Mount, Bioinformatics: Sequence and Genome Analysis, CSHL Press, 2004
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Dan Gusfield, Algorithms on Strings, Trees and Sequences, CUP, 1997
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Helen C. Causton, John Quackenbush and Alvis Brazma, Microarray Gene
Expression Data Analysis:A Beginner's Guide, Blackwell Publishing, 2003
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Scott Markel and Darryl Leon, Sequence Analysis in a Nutshell: A Guide to
Common Tools and Databases, O'Reilly, 2003
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R. Durbin, S. Eddy, A. Krogh and G. Mitchison, Biological Sequence Analysis,
1998, CUP
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Philip E. Bourne and Helge Weissig, Structural Bioinformatics, John Wiley
& Sons, 2003
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Michal Gerhard, Biochemical Pathways: An Atlas of Biochemistry and Molecular
Biology, Wiley-Spektrum, 1998
Suggested Online Material:
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Ron Shamir, Algorithms in Molecular Biology, Course Archive,
http://www.cs.tau.ac.il/~rshamir/algmb.html
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T. A. Brown, Genome (online book)
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=genomes.TOC&depth=2
Additional Material:
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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books (NCBI online book
shelf)
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http://www.web-books.com/MoBio/ (Molecular Biology Web Book)
Mark Distribution (Tentative)
Assignments - 20%
Exams -50%
Projects -30 %
Lectures
Group-D, Tue (11:00), Wed (9:30), Fri (11:00), CEP 106
Tutorials
None
Labs
None