Most information preliminary.

Lecturer: Dr. Matej Lexa, FI C505.
Office hours: Thu 1PM - 3PM, or other time by appointment
Spring 2007. Will meet 1hr every week (Tue 12:00-12:50, B411).

Those who sign up for this interdisciplinary course should be able to read and comprehend a scientific paper or book chapter written in English. Deeper knowledge of algorithm design and programming will allow the particular student to focus more on the biological side of the studied problems or vice versa. Students of non-biological fields should be concurrently enrolled in, or have previously passed IV107 Bioinformatics I. Alternatively they may frequent the course with the consent of the teacher.

This seminar 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. The Spring Term seminar will be titled "Genomic sequence analysis for detection of genes, promoter sequences and other elements". The course will convene for 1hr weekly. Every student that presents his material and receives at least 50% of the maximal score on the final test will pass the course.

Students will chose publications to study recent methods in genomic sequence analysis (using suggested journal articles or other material approved by the teacher). Towards the end of the course the students will pass a short test.

Official description: IV106 (IS MU)

See Czech version for assigned papers.

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)

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

RESEARCH PAPERS
(each student is required to choose one of these for class presentation)

1) T01: O.Delgrange, E.Rivals (2004). STAR: an algorithm to search for tandem approximate repeats. 
Bioinformatics 20(16),2812-2820 -RX-xerox-

2) T02: J.S.Chuang, D.Roth (2001). Gene recognition based on DAG shortest paths.Bioinformatics 17(Suppl.1),56-64 -RX-xerox-

3) T03: R.Bundschuh (2004). Computational prediction of RNA editing sites. 
Bioinformatics 20(17),3214-3220 -RX-xerox-

4) T04: S.Aerts et al. (2004). A genetic algorithm for the detection of new cis-regulatory modules 
in sets of coregulated genes. Bioinformatics 20(12), 1974-1976. -RX-xerox-

5) T05: M.C.Accardo (2004). A computational search for box C/D snoRNA genes in the Drosophila 
melanogaster genome. Bioinformatics 20(18), 3293-3301 -RX-xerox-

6) T06: S.Keles et al. (2004). Regulatory motif finding by logic regression. 
Bioinformatics 20(16),2799-2811. -RX-xerox-

7) T07: WS.Feng et al. (2004). CTRD: a fast applet for computing signed translocation distance between genomes. 
Bioinformatics 20(17),3256-3257 -RX-xerox-

8) T08: H-Q.Zhu et al. (2004). Accuracy improvement for identifying translation initiation sites 
in microbial genomes. Bioinformatics 20(18),3308-3317. -RX-xerox-

9) T09: M.G.Tadesse et al. (2004). Identification of DNA regulatory motifs usingBayesian variable selection. 
Bioinformatics 20(16),2553-2561 -RX-xerox-

10) T10: B.E.Suzek et al. (2001). A probabilistic method for identifying start codons in bacterial genomes. 
Bioinformatics 17(Suppl.1),1123-1130 -RX-xerox-

11) T11: M.Stanke, S.Waack (2003). Gene prediction with a hidden Markov model and a new intron submodel. 
Bioinformatics 19(Suppl.2),215-225 -RX-xerox-

12) T12: B-Y. Lao et al. (2004). The UniMarker (UM) method for synteny mapping of large genomes. 
Bioinformatics 20(17), 3156-3165 -RX-xerox- 

13) T13: A.Krishnan, F.Tang (2004). Exhaustive whole-genome tandem repeat search. 
Bioinformatics 20(16), 2702-2710 -RX-xerox-

14) RECOMB 2001 -RX-K384.01-
15) RECOMB 2002 -RX-K384.02-
16) RECOMB 2003 -RX-K384.03-
17) RECOMB 2004 -RX-K384.04-
18) LNCS 2149 O.Gascuel, B.M.E.Moret (Eds.) Algorithms in Bioinformatics, 2001  -K397.01-
19) LNCS XXXX R.Guigo,D.Gusfield (Eds.) Algorithms in Bioinformatics, 2002 -K397.02-
20) LNCS XXXX G.Benson, R.Page (Eds.) Algorithms in Bioinformatics, 2003 -K397.03-

Bioinformatic links