MaMolBiol 2002

Content

Syllabus

Prerequisites

Bibliography

Problem Sheets

Some Links

Syllabus

1. Brief Primer in Molecular Biology: Nucleotides(A,C,G,T),Base pairs, the Double helix,DNA, 3', 5', Genes, Chromosomes, Genome, introns and exons, promotors, RNA, mRNA, tRNA, Amino acids, Proteins, Proteome, Primary, Secondary, Tertiary, QuartiaryStructures, Folding, Cell, Nucleus, Ribosomes.
   
2. Mathematical Preliminaries : (Probability, Conditional Expectation, Bayesian theorem, Entropy, Gibbs distribution, Markov Chains (Irreducibility and Ergodicity), Gibbs Sampler and PCAs, Heat Bath and Metropolis Algorithms, Simulated annealing, Genetic Algorithms, Learning algorithms, Markov Chain Monte Carlo Methods)
   
3. Comparison of molecular sequences : Global pairwise sequence alignment, Edit and Alignment distances, Alignment with gaps, Multiple sequence alignments (via Gibbs sampling).
   
4. Symmetry and Group Theory : Genome Rearrangement and Symmetric Group, [Lie (and Quantum) Groups and Genetic Code (optional)].
   
5. Probabilistic models of evolution : Phylogenetic trees, ultrametric topology, Genetic Algorithms
6. Hidden Markov Models : Baum-Welch and Viterbi Algorithms, Stochastic Grammars and HMMs, Applications of Grammars to Biological Sequences.
7. Topology of Macromolecules : Math description of knots, linking=twisting+writhing, (Knots invariants), Topological aspects of DNA replication and protein synthesis.
8. Models of Protein Folding
9. Basics of DNA Computing : P- and NP-hard problems, hamiltonian path problem, Adleman DNA based algorithm for TSP

Prerequisites

Undergraduate probability theory, algebra, anlysis, geometry and topology, logic.

Bibliography

Recommended reading on the contents of the course 

Smith, C.U.M., Molecular biology : a structural approach, / 577.23 SMI

Waterman, Michael S., Introduction to computational biology : maps, sequences, genomes /
519.24.578 WAT

Clote, Peter and Backhofen Rolf., Computational Molecular Biology, An Introduction. /
57:681.3 CLO (Central Lib)

Richard Durbin ... [et al], Biological sequence analysis : probabilistic models of proteins and nucleic acids /
577.112.5 BIO

Brzezniak, Zdzislaw and Zastawniak, Tomasz, Basic Stochastic Processes /
519.216 BRZ/

R.C. Bose and B.Manvel, Introduction to Combinatorial Theory /
519.11 BOS

Brualdi, Richard A., Introductory Combinatorics /
519.11 BRU

Some Texbooks on Line

MIT Biology Hypertextbook

Biophysics Hypertextbook

Some Advanced Reading

Problem Sheets

Get problems, hints & solns here

SOME LINKS

History of Biology, Mathematics & Physics

* Experiments in Plant Hybridization (1865) by Gregor Mendel
* A structure for Deoxyribose Nucleic Acid (1953) James Watson and Francis Crick
* Linus Pauling (1901-1994)
* Biotech Chronicles : Classic Biotech Stories , Biotech Briefs

Biochemistry Links

Some sites

Some Info

Cell : Structure and Function of Organels

Brief Primer in Molecular Biology: Nucleotides (A,C,G,T),Base pairs, the Double helix,DNA, 3', 5', Genes, Chromosomes, Genome, introns and exons, promotors, RNA, mRNA, tRNA, Amino acids, Proteins, Proteome, Primary, Secondary, Tertiary, QuartiaryStructures, Folding, Cell, Nucleus, Ribosomes.

Some Pictures

The Nucleic Acids

The Amino Acids

Some Classical Proteins

Some Applets & SoftW

* Visualizing Molecules with gOpenMol

Societies

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