Most information final.

Lecturer: Dr. Matej Lexa, FI C505.
Office hours: Thu 1PM - 3PM, or other time by appointment
Fall 2005. Will meet 1hr every week (Tue 11:00-11:50 B411).
Discussion forum

This seminar is an applied subject available at the Faculty of Informatics. It will lead the students into the fascinating world of molecules, genes and proteins. The Fall seminar will be titled "Protein function and structure prediction from the amino-acid sequence".

Official description: IV105 (IS MU)

The seminar will take place on Nov 15 2005 at 11 AM in B411

2-10) SEMINAR (students 20-30min/presentation)
(each student is required to choose one of these for class presentation)

T04 PDF V. Bystry
Dafas P et al. (2004). 
Using convex hulls to extract interaction interfaces from known structures. 
Bioinformatics 20(10):1486-1490

T06 PDF J. Hapala
Ferre F et al. (2005).
Functional annotation by identification of local surface similarities: a novel tool for structural genomics 
BMC Bioinformatics 6:194

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

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 (200X). 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
5) B.Rost et al. (2003). Automatic prediction of protein function. CMLS 60, 2637-2650. -RX-xerox-

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

6) Starr and Taggart (1992). Biology: The Unity and Diversity of Life. Belmont:WPC, 921p. -RX-A225-
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
49) J.-M.Claverie. (2003). Bioinformatics for dummies. Hoboken, Wiley Publishing, 452p. -RX-Z1
50) T.Jiang (2003). Current topics in computational molecular biology. Cambridge, MIT Press, 542p. RX-Z2 

ALTERNATIVE RESEARCH PAPERS

Predicting protein functions with message passing algorithms
M.Leone and A.Pagnani (2004). Bioinformatics (advance access, Sept 17) -RX-xerox

Protein beta-turn prediction using nearest-neighbor method
S.Kim (2004). Bioinformatics 20(1),40-44 -RX-xerox

MeKE: discovering the functions of gene products from biomedical literature via sentence alignment
J.-H. Chiang and H.-C.Yu (2003). Bioinformatics 19(11),1417-1422 -RX-xerox

The hydrophobic cores of proteins predicted by wavelet analysis
H.Hirakawa et al. (1999). Bioinformatics 15(2),141-148 -RX-xerox

Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins
A.Heger and L.Holm (2003). Bioinformatics 19(Suppl.1),130-137 -RX-xerox

Prediction of protein subcellular locations using fuzzy k-NN method
Y.Huang and Y.Li (2004). Bioinformatics 20(1),21-28 -RX-xerox

A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach
S.Hua and Z.Sun (2001). JMB 308,397-407 -RX-xerox

Finding nuclear localization signals
M.Cokol et al. (2000). EMBO Reports 1(5),411-415 -RX-xerox

Protein structure prediction using Rosetta
C.A.Rohl et al. (2004). Numerical Computer Methods,66-93 -RX-xerox 

36) RECOMB 2001 -RX-K384.01-
37) RECOMB 2002 -RX-K384.02-
38) RECOMB 2003 -RX-K384.03-
39) RECOMB 2004 -RX-K384.04-
40) K.M.Merz (1994). The protein folding problem and tertiary structure prediction. -RX-A37-
41) R.Nair, B.Rost 2004. Annotating protein function through lexical analysis, AI Mag., Spring 2004, 45-56. -RX-xerox-
42) R.D.King 2004. Applying Inductive logic programming to predicting gene function, AI Mag., Spring 2004, 57-68. -RX-xerox-
43a) LNCS 2149 O.Gascuel, B.M.E.Moret (Eds.) Algorithms in Bioinformatics, 2001  -K397.01-
  N.von Ohsen, R.Zimmer. Improving profile-profile alignments via log average scoring, 11-26. 
  J.Viksna,D.Gilbert. Pattern matching and pattern discovery algorithms for protein topologies. 98-111.
43b) LNCS XXXX R.Guigo,D.Gusfield (Eds.) Algorithms in Bioinformatics, 2002 -K397.02-
43c) LNCS XXXX G.Benson, R.Page (Eds.) Algorithms in Bioinformatics, 2003 -K397.03-
44) LNBI 2666 C.Guerra,S.Istrail (Eds.), Mathematical methods for protein structure analysis and design, 2003. 
  M.Kann, R.A.Goldstein. OPTIMA: A new score function for the detection of remote homologs, 99-108. 
  C.Lundegaard et al. Prediction of protein secondary structure at high accuracy using a combination of many neural networks, 117-122 -RX-xerox-
  F.Seno et al. Learning effective amino-acid interactions, 139-145. 
45) LNCS 2066 O.Gascuel, M.-F. Sagot (Eds.), Computational Biology, 2000
  N.Thierry-Mieg, L.Trilling. InterDB, a prediction-oriented protein interaction database for C.elegans., 135-146. 
46) LNCS 2388 S.-W. Lee, A.Verri (Eds.) Pattern recognition with support vector machines, 2002
  N.Mukherjee, S.Mukherjee. Predicting signal peptides with support vector machines, 1-7.

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