Computational Biology (ENS 210)

2021 Fall
Faculty of Engineering and Natural Sciences
Engineering Sciences(ENS)
3
6.00 / 6.00 ECTS (for students admitted in the 2013-14 Academic Year or following years)
Ogün Adebali -oadebali@sabanciuniv.edu,
English
Undergraduate
MATH101 IF100
Formal lecture,On-line task/distance,Laboratory
Interactive,Learner centered,Discussion based learning,Project based learning,Guided discovery
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CONTENT

1. Basic Concepts of Molecular Biology; Life, Proteins, Nucleic acids. 2. The Mechanisms of Molecular Genetics; Genes and the Genetic Code, Transcription, Translation and Protein Synthesis, junk DNA and Reading frames,Chromosomes 3. How the Genome is Studied; Maps and Sequences, Specific Techniques 4. The Human Genome Project 5. Molecular Biology Databases on the Web 6. Strings, Graphs and Algorithms 7. Sequence Alignment Algorithms; Global, Semiglobal, and Local Alignment 8. Multiple Sequence Alignment; Star alignment, Tree alignment 9. Database Search; PAM, BLOSSUM matrices, BLAST, FASTA 10. Quantitative and Probabilistic Pattern Matching 11. Protein Ligand Docking 12. Bio-ethics Also part of the "core course" pools for the BIO and CS degree program.

OBJECTIVE

To supply the students with the foundations in Computational Biology.

LEARNING OUTCOME

To have basic knowledge of molecular biology genetics and biochemistry
To learn PYTHON and at to be able write PYTHON programs for basic computational biology problems.
To gain basic knowledge of the sequence alignment, database search , clustering, and profile algorithms in computational biology.
To learn ways to model biological problems and analyticla methodsfor solving problems in biology and medicine.
To learn to design an implement an algorithm and analyze the results of their algorithm that they developed as a team.

ASSESSMENT METHODS and CRITERIA

  Percentage (%)
Final 25
Midterm 50
Other 25

RECOMENDED or REQUIRED READINGS

Readings

Python textbook:
> Martin Jones, Python for Biologists, http://pythonforbiologists.com
Supporting reading material:
> Donald Forsdyke, Evolutionary Bioinformatics, 3rd ed., Springer 2015. (Chs: 2, 4, 7, and 12.)
> Stephen D. Bentley and Julian Parkhill, Comparative Genomic Structure of Prokaryotes, Annual Reviews of Genetics, 38:771-791 (2004).
> John Lightfield, Noah R. Fram, Bert Ely, Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage, PLoS ONE, 6:e17677 (2011).
> Karen E. Nelson et al., Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima, Nature, 399: 323-329 (1999).
> Carl R. Woese and George E. Fox, Phylogenetic structure of the prokaryotic domain: The primary kingdoms, Proc. Natl. Acad. Sci. USA, 74: 5088-5090 (1977).
> Nick Lane, Power, Sex, Suicide: Mitochondria and the Meaning of Life, Oxford University Press, 2005. (Introduction, Chs. 1 and 7.)
> Nick Lane, The Vital Question: Energy, Evolution, and the Origins of Complex Life, Norton & Company, 2015. (Introduction and beginning of Ch. 4.)