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Dhirubhai Ambani Institute of Information and Communication Technology

Course Description
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Gupta Lab
Instructor's Page

DA-IICT Moodle

IT 470 - Foundations of Computational and Systems Biology

Manish K Gupta Room 2209 Faculty Block 2 mankg [at] daiict.ac.in Phone: 91-79-30150549

Teaching Assitant


Did you ever wonder what is the recipe for making us who we are, with 3.5 billion letters of A, C, G and T? What is the difference between mouse and Humans at molecular level? What happens when a virus attacks us? How are all forms of life related? I think many of you have several such questions at some stage of your life and still don't know the answer. You will be surprised to know that now with a degree in Information and Communication Technology (ICT) you can be really close to finding answers to many such questions with interdisciplinary approach of using mathematics, computer science, statistics, molecular biology, physics, electrical engineering, communication etc. Many aspects of molecular biology can be viewed as information processing and so molecular biology and computer science are very close to each other. It is for this reason one can say that the 21st century is for molecular biology.

This course covers basic techniques mainly algorithmic in nature to answer many questions in molecular biology. We will go through this journey with many case studies

Tentative Course Content

1. Introduction
2. Sequencing and Microarray
3. Genome assembly
4. Tools and Databases
5. Computational gene hunting (gene predication -HMM)
6. Alignment of bio-molecular sequences (Local, Global, DP, Blast, multiple)
7. Genomic regulation
8. Protein folding
9. Genetic variation
10.RNA world
11. Systems Biology (gene, protein and membrane machine)
                       --Human and Pathogens
                   --Cancer genomics (Tumor complexity)
                   --Gene regulatory networks
12. Codon optimization
13. Algorithmic Drug designs  

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.

  1. Pavel A. Pevzner, Computational Molecular Biology, An Algorithmic Approach, The MIT press, 2001
  2. Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, Indian reprint by Ane Books, 2005
  3. Nello Cristianini and Matthew W. Hahn, Introduction to Computational Genomics: A Case Studies Approach, 2007, Cambridge University Press
  4. David Mount, Bioinformatics: Sequence and Genome Analysis, CSHL Press, 2004
  5. Dan Gusfield, Algorithms on Strings, Trees and Sequences, CUP, 1997
  6. Helen C. Causton, John Quackenbush and Alvis Brazma, Microarray Gene Expression Data Analysis:A Beginner's Guide, Blackwell Publishing, 2003
  7. Scott Markel and Darryl Leon, Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, O'Reilly, 2003
  8. R. Durbin, S. Eddy, A. Krogh and G. Mitchison, Biological Sequence Analysis, 1998, CUP
  9. Philip E. Bourne and Helge Weissig, Structural Bioinformatics, John Wiley & Sons, 2003
  10. Hiroaki Kitano, Foundations of Systems Biology, The MIT Press, 2001
  11. Uri Alon and Alon Alon, An Introduction to Systems Biology:Design Principles of Biological Circuits, Taylor & Francis, July 2006
  12. Peter Parham, The Immune System, Garland Science, 2004
  13. Darren J Wilkinson, Stochastic Modelling for Systems Biology, Chapman & Hall/CRC, April 2006
  14. Bernhard O. Palsson, Systems Biology, Cambridge University Press, January 2006
  15. Michal Gerhard, Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, Wiley-Spektrum, 1998
  16. Dominik Wodarz and Natalia Komarova, Computational Biology of Cancer, World Scientific, Jan 2005
  17. Eric H. Davidson, The Regulatory Genome: Gene Regulatory Networks in Development and Evoluation, Academic Press, 2006

Suggested Online Material:

  1. Luca Cardelli, Artificial Biochemistry Course, Microsoft Research, May 2006 (see http://lucacardelli.name/ArtificialBiochemistry.htm )
  2. Ron Shamir, Algorithms in Molecular Biology, Course Archive, http://www.cs.tau.ac.il/~rshamir/algmb.html
  3. 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:

  1. http://www.nature.com/focus/systemsbiologyuserguide/index.html   (Nature's Sys Bio focus)
  2. http://en.wikipedia.org/wiki/Systems_biology    (Sys Bio wiki)
  3. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books (NCBI online book shelf)
  4. http://www.web-books.com/MoBio/ (Molecular Biology Web Book)
Mark Distribution

Assignments - 10%
Mid Term -20%
Scribes -10%
Projects -20 %
Final- 40%


Group-D, Tue (11:00), Wed (9:30), Fri (11:00), CEP 108