Most information final.

Lecturer: Dr. Matej Lexa, FI B308.
Office hours: Thu 1PM - 3PM, or other time by appointment
Spring 2005. Will meet 2hrs every week (Tue 8:00-9:50, A107).
Discussion forum

This is an entry course into the area of bioinformatics for students of non-biological disciplines, there are no prerequisites.

This course is a new applied subject available at the Faculty of Informatics. It will lead the students into the fascinating world of molecules, genes and proteins. Currently, bioinformatics is going through a period of unusual growth. Abilities to think and act as a bioinformatician (to work with large biological datasets using modern computer science methods) are needed in many areas of science and applied disciplines, especially biology, medicine and chemistry. The first part of the course will be dedicated to basics of biology necessary for someone who has not studied biology to enter the field of bioinformatics. In the second part, important biological problems that can be best tackled by computers will be studied. Lectures will be given once a week (2hrs). Written examination will be given at the end of the semester.

Official description: IV107 (IS MU)

1. The history and subject of bioinformatics LECTURE 
2. Basics of molecular biology - Organization of living matter - DNA structure and function - 
   Protein structure and function - Evolution of genes and proteins LECTURE  
3. Bioinformatic data - Data sources - Common data types LECTURE TERMS 
4. Public sequence data and their access EMBL-EBI NCBI LIST 
5. DNA sequence analysis LECTURE
6. Protein sequence analysis LECTURE 
7. Structural and functional data LECTURE 
8. Similarity searches and scoring 
9. Other types of data and their analysis LECTURE
10. Expression data ARTICLE LECTURE
11. Protein digests and mass spectra LECTURE 
12. Literature data analysis

RX - reserved for students of Bioinformatics
DO - reserved for students of Prof. Dokulil
xerox - a copy of the original text is available at the library
B306 - catalog number in the FI Library
WEB - WWW resource, follow the link

TEXTBOOK
(on reserve in the FI library, another copy available from the lecturer for reading/copying, can be purchased on the Internet)
D.E.Krane and M.L.Raymer (2003). Fundamental Concepts of Bioinformatics. Benjamin Cummings, London, 320p (ISBN 0-8053-4633-3)
OBSAH

REQUIRED READING
(you should read these as soon as possible)


1) R.Dawkins (1998). Sobecky gen. Praha:Mlada Fronta, 319p. -DO-B306- (Ch.1,2,3,11)
2) S.Pinker (1999). Words and Rules. Weidelberg and Nicolson:London, 348p. (pages 4-9) -RX-xerox-
3) J.Glasgow, I.Jurisica, B.Rost (2004). AI and Bioinformatics. AI Magazine, Spring, 7-8. -RX-xerox-
4) J.Barker and J.Thornton (2004). Software engineering challenges in bioinformatics. Proceedings of ICSE 2004 PDF
6) Starr and Taggart (1992). Biology: The Unity and Diversity of Life. Belmont:WPC, 921p. -RX-A225-
49) J.-M.Claverie. (2003). Bioinformatics for dummies. Hoboken, Wiley Publishing, 452p. -RX-Z1

LECTURE AND BACKGROUND MATERIALS
(these are here for your convenience if you would like to review the lecture subjects and/or know more)


5) B.Rost et al. (2003). Automatic prediction of protein function. CMLS 60, 2637-2650. -RX-xerox-
7) L.Hunter 2004. Life and its molecules. A brief introduction. AI Magazine Spring 2004, 9-22. -RX-xerox-
8) Chapter 5 - Chemistry and physiology of the cell. -RX-xerox-
9) A set of schemata and electron microscope micrographs illustrating the cellular structures of plants. -RX-xerox- 
10) Z.Storchova (200X). Molekuly na povel I. Jak muzeme molekuly DNA strihat a zase spojovat. Vesmir 77(5). -RX-xerox-
11) Z.Storchova (200X). Molekuly na povel II. I jedina molekula DNA se hleda mnohem lepe nez jehla v kupce sena. Vesmir 77(6). -RX-xerox-
12) Z.Storchova (200X). Molekuly na povel III. Jak to udelat, aby molekula byla dobre viditelna. Vesmir 77(7). -RX-xerox-
13) Z.Storchova (200X). Molekuly na povel IV. Z mala mnoho neni totez jako z komara velbloud. Vesmir 77(9). -RX-xerox-
14) Z.Storchova (200X). Molekuly na povel V. Cteni (genomu) na dobrou noc. Vesmir 77(10). -RX-xerox-
15) W.W.Gibbs (2004). Synthetic life. Scientific American, May, 49-55. -RX-xerox-
16) S.J.Freland, L.D.Hurst (2004). Evolution encoded. Scientific American, April, 56-63. -RX-xerox-
17) G.Stix (2004). Making proteins without DNA. Scientific American, April, 20-21. -RX-xerox-
18) C.Choi (2004). Making and unmaking memories. Scientific American, March, 16-16. -RX-xerox-
19) T.Valeo (2004). Downsized target: A tiny protein called ADDL could be the key to Alzheimer's. Scientific American, May, 14-15. -RX-xerox
20) J.Shrager (2003). The fiction of function. Bioinformatics 19(15),1934-1936 -RX-xerox
21) S.Buckingham (2004). Data's future shock. Nature 428,774-777 -RX-xerox
22) S.Buckingham (2003). Programmed for success. Nature 425,209-214 -RX-xerox
23) M.Chicurel (2002). Bioinformatics: bringing it all together. Nature 419, 751-757 -RX-xerox
24) M.Bloom (2001). Biology in silico: the bioinformatics revolution. The Am. Biol. Teacher 63(6),397-403 -RX-xerox
25) P.Baldi and G.Pollastri (2002). A machine learning strategy for protein analysis. IEEE Intelligent Systems Mar/Apr, 28-35 -RX-xerox
26) Yoshida et al. (2001). Chaperonin turned insect toxin. Nature 411,44-44 -RX-xerox
27) E.Pennisi (2003). Gene counters struggle to get the right answer. Science 301,1040-1041 -RX-xerox
28) H.Pearson (2003). Geneticists play the numbers game in vain. Nature 423,576-576 -RX-xerox
29) C.A.Ouzounis and A.Valencia (2003). Early bioinformatics: the birth of a discipline - a personal view. Bioinformatics 19(17),2176-2190 -RX-xerox
30) S.Oliver (2000). Guilt-by-association goes global. Nature 403,601-603 -RX-xerox
31) A.J.Mungall (2003). The DNA sequence and analysis of human chromosome 6. Nature 425,805-812 -RX-xerox
32) E.Mjolsness and D.DeCoste (2001). Machine learning for science: state of the art and future prospects. Science 293,2051-2055 -RX-xerox
33) L.L.Looger et al. (2003). Computational design of receptor and sensor proteins with novel functions. Nature 423,185-190 -RX-xerox
34) S.Karlin et al. (2001). Annotation of the Drosophila genome. Nature 411,259-260 -RX-xerox
35) F.E.Cohen and J.W.Kelly (2003). Therapeutic approaches to protein-misfolding diseases. Nature 426,905-909 -RX-xerox
47) J.D.Watson (1968). The Double Helix. New American Library, New York, 143p. -RX-xerox
48) H.Kolb (2003). How the retina works. American Scientist Jan-Feb -RX-xerox
50) T.Jiang (2003). Current topics in computational molecular biology. Cambridge, MIT Press, 542p. RX-Z2 

Bioinformatic links