Informace jsou predbezne.

Prednasejici: Dr. Matej Lexa, FI C505.
Konzultacni hodiny: Ct 13:00 - 15:00, nebo dle domluvy
Jaro 2010. Bude se schazet 1 h tydne (Po 9:00-9:50, B411).

Od zajemcu o tento mezioborovy kurz se ocekava schopnost precist odborny clanek nebo kapitolu knihy v anglickem jazyce. Hlubsi znalosti konstrukce algoritmu a programovani pomohou studentum soustredit se na biologickou stranku prezentovane latky nebo naopak. U studentu nebiologickych oboru se vyzaduje paralelni navstevovani nebo predchazejici absolvovani predmetu IV107 - Bioinformatika I nebo souhlas ucitele.

Spolecnym tematem seminare pro jaro je "Analyza genu a genomovych sekvenci novou generaci sekvenacnich metod (Next-generation sequencing)". Kurz se bude konat jednou tydne po 1 hodine, kolokvium ziska kazdy student, ktery odprezentuje nastudovanou metodu a (a v pripade neucasti na nekterem ze seminaru jestli taky ziska nejmene 50% bodu na kontrolnim testu).

Studenti samostatne nastuduji a prezentuji svym kolegum konkretni metodu pro analyzu genomovych sekvenci dle vlastniho vyberu (z navrzenych clanku nebo po konzultaci). Navrhy clanku k precteni a prezentaci naleznete v ISu, v ucebnich materialech predmetu. Jeste pred zahajenim cyklu prezentaci doporucuju precist si uvodny clanek nebo clanky vysvetlujici principy a aplikace NGS.

Oficialni popis kurzu: IV106 (IS MU)

TYDEN
1) Organizace seminare

2) 29.3.2010 Pencikov PDF DRIMM-Synteny: decomposing genomes into evolutionary conserved segments

2) 5.4.2010 Krejci PDF Sahota: Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes

2) 12.4.2010 Horsky PDF Mugsy: Fast multiple alignment of closely related whole genomes

ODBORNE CLANKY
(kazdy student si vybere jeden clanek k prezentaci na seminari)

Zakladni informace: Kellum and Elgin (1998). Chromatin boundaries: punctuating the genome.
   Current Biology 8:R521-R524 PDF

1) Glazko et al. (2001). Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix.  
   Biochimica et Biophysica Acta 1517: 351-364 PDF

2) Namciu et al. (2003). Sequence organization and matrix attachment regions of the human serine protease inhibitor gene cluster at 14q32.1
   Mammalian Genome 15:162-178 PDF

3) S.Keles et al. (2004). Regulatory motif finding by logic regression. 
Bioinformatics 20(16), 2799-2811

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

5) A.dela Fuente et al. (2004). Discovery of meaningful associations in 
genomic data using partial correlation coefficients. Bioinformatics 20(18), 3565-3574

6) M.G.Tadesse et al. (2004). Identification of DNA regulatory motifs using Bayesian variable selection. 
Bioinformatics 20(16), 2553-2561

7) P.Sumazin et al. (2005). DWE: Discriminating word enumerator. Bioinformatics 21(1), 31-38

8) J.P.Massar et al. (2005). BioLingua: a programmable knowledge environment for biologists. Bioinformatics 21(2), 199-207

9) L.Chen et al. (2005). Gene name ambiguity of eukaryotic nomenclatures.
Bioinformatics 21(2), 248-256

10) A.Krishnan, F.Tang (2004). Exhaustive whole-genome tandem repeat search. 
Bioinformatics 20(16), 2702-2710 

11) D.E.Schones et al. (2005). Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics 21(3), 307-313

12) J.Healy et al. (2003). Annotating large genomes with exact word matches. Genome research 13, 2306-2315

- LNCS proceedings from Algorithms in Bioinformatics
- RECOMB proceedings

WWW adresy pro bioinformatiku