BIOL/COMP 265/350/550 Bioinformatics and Functional Genomics

BIOL/COMP 265/350/550 Bioinformatics and Functional Genomics

D. Krizanc/M. Weir

Second half of course

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Date

TOPIC

READINGS/ASSIGNMENTS

3/25

SCIE 141

4. cont.

4.6 Clustering Algorithms

HANDOUT 8 - Clustering Algorithm (UPGMA)

HANDOUT 9 - Clustering Algorithm (Neighbor-Joining)

3/27

SCIE 74

4. cont.

Problem set 5 due

Computer Lab: CLUSTAL & BLAST

4/1

SCIE 141

5. RNA Secondary Structures

5.1 Introduction (base-pairing at a distance, special representations)

HANDOUT 13 - RNA Secondary Structure

Tompa, M., Lecture Notes (REF) [chapter 16 - introduction to RNA secondary structures] Lecture Slides

[Bkgd: Durbin et al. Biological Sequence Analysis (CUP, 1998) Chap 10 (Sci Lib Reserve)]

4/3

SCIE 74

5.2 Structure prediction (folding algorithms based on energy minimization, conservation of base-pairing based on mutual information)

HANDOUT 14 - RNA Folding Algorithm (Nussinov)

Powerpoint Demonstration

Computer Lab: RNA folding - mFOLD, RNAdraw

4/8

SCIE 141

6. Information Theory (information, individual information, consensus sequences, genomic datasets – splice sites, translation initiation, relational databases, SQL)

[Bkgd: Schneider Information Theory Primer ]

HANDOUT 6 - Entropy and Information

Stephens RM, Schneider TD (1992) Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J Mol Biol. 1992 Dec 20;228:1124-1136 (Sci Lib Reserve)

Weir, M.P. Rice, M.D. (2004) Ordered Partitioning Reveals Extended Splice Site Consensus Information. Genome Research 14:67-78. REF

Lecture slides

CSH: Restriction enzymes, introns

Kimball: RNA processing

4/10

SCIE 74

6. cont.

Computer Lab: Information Theoretic Analysis of Sequences

4/15

SCIE 141

7. Genome Projects

HANDOUT 15 - Sequence Assembly

CSH: Sequencing

CSH: Shotgun/ordered sequencing approaches

[Venter, J.C. et al. (2001) The Sequence of the Human Genome, Science 291:1304-1351. (REF)]

4/17

SCIE 74

7. cont.

Computer Lab: Sequence Assembly

4/22

SCIE 141

8. Gene Networks, Microarray Analysis, Clustering

Alberts et al. - Introduction to gene regulation (text and summary figures)

Alberts et al. - Introduction to gene expression (text and summary figures)

[Buhler, J., Anatomy of a Comparative Gene Expression Study (REF - discussion of microarray technology)]

Lecture slides (DOWNLOAD)

[Kauffman, S.A. (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22:437-467.] (Sci Lib Reserve)

4/24

SCIE 74

8. cont.

Web site (Wagner) - Microarray animation

DATASETS - IGS DATABASE

HANDOUT 16 - Microarrays

HANDOUT 17 - Clustering Algorithm (K-means)

HANDOUT 18 - Clustering Examples (K-means)

Lecture slides (DOWNLOAD)

4/29

SCIE 74

8. cont.

Computer Lab: Microarray Clustering Analysis

5/1

SCIE 141

9. Computational Statistics

(Score distributions,

Bootstrapping,

Maximum likelihood,

Robustness)

Lecture slides (DOWNLOAD)

[Weir, M., Eaton, M. and Rice, M. (2006) Challenging the spliceosome machine. Genome Biol. 7(1):R3 (REF)]

[Tusher, V.G., Tibshirani, R., Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98: 5116-5121 (REF)]

5/6

SCIE 141

10. Review, Future Directions

Lecture slides (DOWNLOAD) mv1, mv2

[Heyer, L.J., Kruglyak, S., Yooseph, S. (1999) Exploring expression data: Identification and analysis of Coexpressed genes, Genome Res 9 1106-1115 (REF)]