BCB 444X/544X

Revised Lecture Schedule – Fall 2005

 

#

 

Date

 

Topic

 

Reading

 

Instructor

 

1

Aug 22 M

Course Overview – What is bioinformatics?

Mount, Ch 1

DD

2

Aug 24 W

Alignment of pairs of sequences: Overview of methods

Mount, Ch 3

DFB

3

Aug 26 F

Alignment of pairs of sequences: Dynamic programming

Mount, Ch 3

DFB

4

Aug 29 M

Alignment of pairs of sequences: Substitution matrices and parameter choice

Mount, Ch 3

DFB

5

Aug 31 W 

Statistical analysis of alignments: Overview of statistical issues

Mount, Ch 4

DFB

6

Sep  2 F

Statistical analysis of alignments: Assessing significance

Mount, Ch 4

DFB

-

Sep  5 M

NO CLASS – University Holiday

 

 

7

Sep  7 W

Statistical analysis of alignments: Bayesian methods

Mount, Ch 4+

DFB

8

Sep  9 F

Multiple sequence alignment: Definitions, global vs. local    

Mount, Ch 5

DFB

9

Sep 12 M

Multiple sequence alignment: Profiles

Mount, Ch 5

DFB

10

Sep 14 W

Multiple sequence alignment: Hidden Markov models, position-specific scoring

Mount, Ch 5

DFB

11

Sep 16 F

Database searching: Overview of FASTA

Mount, Ch 6

DFB

12

Sep 19 M

Database searching: Overview of BLAST

Mount, Ch 6

DFB

13

Sep 21 W

Database searching: Scoring issues

Mount, Ch 6

DFB

14

Sep 23 F

MIDTERM EXAM #1         

 

MT

15

Sep 26 M

PERL                                

Mount, Ch 12

XW

16

Sep 28 W

PERL                              

Mount, Ch 12

XW

17

Sep 30 F

Phylogenetic prediction: Definitions and basic concepts, overview of methods

Mount, Ch 7+

DFB

18

Oct  3 M

Phylogenetic prediction:  Parsimony I

Mount, Ch 7+

DFB

19

Oct  5 W

Phylogenetic prediction:  Parsimony II

Mount, Ch 7+

DFB

20

Oct  7 F

Phylogenetic prediction: Distance Methods

Mount, Ch 7+

DFB

21

Oct 10 M

Phylogenetic prediction: Maximum Likelihood

Mount, Ch 7+

DFB

22

Oct 12 W

Phylogenetic prediction:

Mount, Ch 7+

DFB

23

Oct 14 F

Phylogenetic prediction:

Mount, Ch 7+

DFB

24

Oct 17 M

Genes & genomes:  Eukaryotes  vs prokaryotes

Mount, Ch 9  plus

DD

25

Oct 19 W

Gene regulation:  Promoters, enhancers

Mount, Ch 9  plus

DD

26

Oct 21 F

Gene prediction

Mount, Ch 9  plus

DD

27

Oct 24 M

Promoter prediction

Mount, Ch 9  plus

DD

28

Oct 26 W

Promoter prediction (really)

Mount, Ch 9  plus

DD

29

Oct 28 F

MIDTERM EXAM #2

 

DFB/DD/MT

30

Oct 31 M

RNA structure & function

Mount, Ch 8 plus

DD

31

Nov  2 W

Predicting RNA structure, miRNAs & targets

Mount, Ch 8 plus

DD

32

Nov  4 F

Protein structure and function

Mount, Ch 10 plus

DD

33

Nov  7 M

Protein structure classification, databases & visualization tools

Mount, Ch 10 plus

DD

34

Nov  9 W

Protein structural prediction and modeling

Mount, Ch 10 plus

DD

35

Nov 11 F

Protein-nucleic acid interactions; protein-ligand docking

TBA

DD

36

Nov 14 M

Genome analysis: Genome projects & comparative genomics

Mount, Ch 11 plus

DD

37

Nov 16 W

ENCODE, SNPs, HapMaps & Medical genomics

TBA

DD

38

Nov 18 F

Experimental methods:  microarrays, proteomics, metabolomics, chemical genomics

Mount, Ch 13 plus

DD

  -

Nov 21-25

NO CLASS – Thanksgiving Break

 

 

39

Nov 28 M

Machine learning algorithms

TBA

V Honavar

40

Nov 30 W

Microarrays & proteomics analysis; Protein function prediction

Mount, Ch 13 plus

V Honavar

41

Dec  2 F

Modeling Networks: Pathway & interaction databases;

         Genetic, regulatory & metabolic networks                            

TBA

DD

42

Dec  5 M

Student Project Presentations (2 X 20')

 

DFB/DD

43

Dec  7 W

Student Project Presentations (2 X 20')

 

DFB/DD

44

Dec  9 F

Student Project Presentations (2 X 20')

 

DFB/DD

45

Dec 15  Th

FINAL EXAM

 

 


 

BCB 444X/544X

Revised Lab Schedule

 

 

 

#

 

Date (Th)

 

Topic

 

Reading

 

Instructor

 

1

Aug 25

Sequences & databases

Mount, Ch 2

MT

2

Sep  1

Sequence alignment

Mount, Ch 3

MT

3

Sep  8

Sequence alignment

Mount, Ch 4

MT

4

Sep 15

Sequence alignment

Mount, Ch 5

MT

5

Sep 22

Database searching

Mount, Ch 6

MT

6

Sep 29

PERL

Mount, Ch 12

XW

7

Oct   6

BLAST

Mount, Ch 7+

MT

8

Oct 13

Phylogenetic prediction

Mount, Ch 7+

MT

9

Oct 20

Gene & promoter prediction

Mount, Ch 9 plus

DD

10

Oct 27

Extra Office Hours for Exam 2

 

DFB/DD

11

Nov  3

RNA structure prediction

Mount, Ch 8 plus

MT

12

Nov 10

Protein structure analysis & prediction

Mount, Ch 10 plus

MT

13

Nov 17

Comparative genomics, SNPs

Mount, Ch 11 & 13

MT

 -

Nov 24

NO LAB – Thanksgiving Break

 

 

14

Dev  1

Machine learning & “-omics” analyses

Mount, Ch 13 plus

MT

15

Dec  8

Student Project Presentations

     (4 X 20')

 

DFB/DD

 -

Dec 15

NO LAB – Finals Week