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

T

SCIE 141

4. cont.

4.6 Clustering Algorithms

HANDOUT 8 - Clustering Algorithm (UPGMA)

 

HANDOUT 9 - Clustering Algorithm (Neighbor-Joining)

3/27

Th

SCIE 74

4. cont.

Problem set 5 due

 

Computer Lab: CLUSTAL & BLAST

4/1

T

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

Th

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

T

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

Th

SCIE 74

6. cont.

Computer Lab: Information Theoretic Analysis of Sequences

4/15

T

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

Th

SCIE 74

7. cont.

Computer Lab: Sequence Assembly

4/22

T

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

Th

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

T

SCIE 74

8. cont.

Computer Lab: Microarray Clustering Analysis

5/1

Th

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

T

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)]

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