| DAY |
DATE |
CHAPTER |
TOPIC |
LECTURER |
| Tues |
Jan 9 |
0.1 |
Orientation
Vingron's Editorial, Bioinformatics 17, 389 [2001]
Berthou and Alcaraz, BMC Biolgoy: "...statistical practice is generally poor, even in the most renowned scientific journals ..." [2004]
|
Volker Brendel |
| Thur |
Jan 11 |
1.1 |
Sequence analysis with scores
(Karlin & Altschul (1990) PNAS 87: 2264
Karlin & Brendel (1992) Science 257: 39)
|
Volker Brendel |
| Tues |
Jan 16 |
1.2 |
Amino acid substitution scoring matrices
(Henikoff & Henikoff (1992) PNAS 89: 10915)
|
Volker Brendel |
| Thur |
Jan 18 |
1.3 |
Amino acid substitution scoring matrices: PAM model
Homework project #1
| Volker Brendel |
| Tues |
Jan 23 |
2.1 |
Motifs: reguluar expressions, weight matrices, and profiles
Stormo (2000) Bioinformatics 16: 16
Henikoff & Henikoff (1994)J. Mol. Biol. 243: 574
|
Xiaoqiu Huang |
| Thur |
Jan 25 |
2.2 |
Profile alignments; PSI-BLAST
Altschul et al. (1997) Nucl. Acids Res. 17: 3389
|
Xiaoqiu Huang |
| Tues |
Jan 30 |
2.3 |
New directions in sequence alignment
Huang & Brutlag (2007) Nucl. Acids Res. 35: advance publication
|
Xiaoqiu Huang |
| Thur |
Feb 1 |
2.4 |
Identifcation of motifs I: EM-algorithm
|
Volker Brendel |
| Tues |
Feb 6 |
2.5 |
Identifcation of motifs II: Gibbs sampling and other approaches
Homework project #2
|
Volker Brendel |
| Thur |
Feb 8 |
3.1 |
Sequence models I (permutations; Markov models; pattern occurrence probabilities)
|
Volker Brendel |
| Tues |
Feb 13 |
3.2 |
Sequence models II (advanced Markov models)
Patchiness and correlations in DNA sequences
|
Volker Brendel |
| Thur |
Feb 15 |
4.1 |
Hidden Markov models - Theory I (Rabiner's Tutorial)
|
Volker Brendel |
| Tues |
Feb 20 |
4.2 |
Hidden Markov models - Theory II
|
Volker Brendel |
| Thur |
Feb 22 |
4.3 |
Applications I: Prokaryotic genome annotation
GENMARK: Parallel gene recognition for both DNA strands
GeneMark.hmm
GeneMarkS
|
Xiaoqiu Huang |
| Tues |
Feb 27 |
4.4 |
Applications I: Eukaryotic protein-coding gene identification
Prediction of complete gene structures in human genomic DNA
HW#2 due!
|
Xiaoqiu Huang |
| Thur |
Mar 1 |
4.5 |
Applications II: Other topics of eukaryotic genome annotation
Computational analysis of RNAs
Homework assignment #3
|
Xiaoqiu Huang |
| Tues |
Mar 6 |
5.1 |
Splice site prediction models
PMB36-573.pdf
NAR24-4709.pdf
NAR26-4748.pdf
|
Volker Brendel |
| Thur |
Mar 8 |
5.2 |
Gene identification by transcript mappting and comparative genomics: spliced alignment
Bioinformatics16-203.pdf
Bioinformatics20-1157.pdf
|
Volker Brendel |
| Tues |
Mar 13 |
|
SPRING BREAK |
|
| Thur |
Mar 15 |
|
SPRING BREAK |
|
| Tues |
Mar 20 |
6.1 |
Molecular Phylogeny I (basics)
HW#3 due!
|
Volker Brendel |
| Thur |
Mar 22 |
6.2 |
Molecular Phylogeny II (parsimony and distance matrix methods) |
Volker Brendel |
| Tues |
Mar 27 |
6.3 |
Molecular Phylogeny III (synonymous and nonsynonymouse substitutions I) |
Xiaoqiu Huang |
| Thur |
Mar 29 |
6.4 |
Molecular Phylogeny III (synonymous and nonsynonymouse substitutions II)
Goldman & Yang (1994) Mol. Biol. Evol. 11: 725
|
Xiaoqiu Huang |
| Tues |
Apr 3 |
7.1 |
Tools and resources for comparative plant genomics, with applications to the analysis of alternative pre-mRNA splicing
Wang & Brendel (2006) PNAS 103: 7175
Homework assignment #4
|
Volker Brendel |
| Thur |
Apr 5 |
7.2 |
Applications of Ka/Ks measures to genome analysis (exon finding, duplicated genes)
GenomeResearch12-198.pdf
|
Xiaoqiu Huang |
| Tues |
Apr 10 |
8.1 |
Recent methods for eukaryotic genome annotation
Sparks & Brendel (2005) Bioinformatics 21 Suppl. 3: iii20
Bioinformatics17-S140.pdf
|
Volker Brendel |
| Thur |
Apr 12 |
8.2 |
Working groups: Designing a comprehensive genome annotation work flow I
|
Volker Brendel |
| Tues |
Apr 17 |
8.3 |
Working groups: Designing a comprehensive genome annotation work flow II
GenomeBiology7-S9.pdf
BioDAS
|
Volker Brendel |
| Thur |
Apr 19 |
8.4 |
Databases for Practical Bioinformatics: MySQL, xGDB, UCSC Genome Browser, and Ensembl
|
Matthew Wilkerson |
| Tues |
Apr 24 |
|
Review I: Genome Annotation - Practice at PlantGDB
|
Matthew Wilkerson and Jon Duvick |
| Thur |
Apr 26 |
|
Review II: Genome Informatics
|
Xiaoqiu Huang and Matthew Wilkerson |
| Tues |
May 1 |
|
Orals I
|
Volker Brendel and Xiaoqiu Huang |
| Thur |
May 3 |
|
Orals II
|
Volker Brendel and Xiaoqiu Huang |