STA/BST226
Statistical Methods for Bioinformatics
Winter 2007

Instructor: Katherine S. Pollard

Syllabus

Email
stabst226@wald.ucdavis.edu

Textbooks

Biological Sequence Analysis, 2nd Edition ("BSA")
By R. Durbin, S. Eddy, A. Krogh, G. Mitchinson





Bioinformatics and Computational Biology Solutions Using R and Bioconductor ("BCBS")
By R. Gentleman, V.J. Carey, W. Huber, R.A. Irizarry, S. Dudoit (eds)


These texts and some other helpful books are on reserve at Shields Library.

Class Meetings

DayTimeLocationTA/InstructorClass
Monday (M)3:10-4:00pmHUTCHN 93Sandy TaylorComputer Lab
Wednesday (W)3:10-4:00pmMATHSCI 1143Katie PollardLecture
Thursday (R)3:10-4:00pmPHYGEO 148Katie PollardJournal Club
Friday (F)3:10-4:00pmMATHSCI 1147Katie PollardLecture

Office Hours

DayTimeLocationTA/Instructor
Wednesday (W)4-5pmMSB 4220Katie Pollard
Thursday (R)2-3pmMSB 4220Katie Pollard
Friday (F)11am-12pmMSB 1117Sandy Taylor
Map of MSB=Mathematical Sciences Building

Reading

WeekTextbooksJournal ClubBackground ReadingHandouts/Slides
1/1-1/5BSA1,11--Molecular Biology Intro
Alignment Exercise
1/8-1/12BSA2-3Blanchette et al. 2004Rabiner 1989-
1/15-1/19BSA4Rivas & Eddy 2001 Dempster et al. 1977
EM Algorithm Tutorial 		-
1/22-1/26BSA5-Krogh et al. 1994Sequence Logos
1/29-2/2BCBS1van Zwet et al. 2005Rogic et al. 2001Zif268 Strcuture
2/5-2/9BCBS2-4Yang & Speed 2002The Chipping Forcast 1999Omics Intro
Pre-processing
2/12-2/16BCBS14-15,23van de Peppel et al. 2003The Chipping Forcast 2002Differential Expression
2/19-2/23BCBS7-9Smyth et al. 2005Dudoit et al. 2003
NAR Database Issue 2007		Multiple Testing
2/26-3/2BCBS12-13Kerr & Churchill 2001Eisen et al. 1998Annotation
3/5-3/9BCBS16-17Dai et al. 2005-Machine Learning
3/12-3/16BCBS10--Visualization

Computer Lab

DateTopicsFiles
1/8Computing Accounts
Introduction to Perl		Server Access
Handout
Example 1
Example 2
1/17Files
Regular Expressions
Subroutines		Handout
1/22Hashes
Random Numbers
Output
Libraries		Handout
2/5Introduction to R
and Bioconductor		Handout
R code
2/12Pre-processing
Gene Filtering		Handout
R code
2/26Multiple Testing
Annotation		Handout
R code
3/12ClusteringHandout
R code

Assignments

DueDescriptionFiles
2/2Homework 1Assignment
pine.fasta
chlorella.fasta
3/9Homework 2Assignment
3/14Final ProjectAssignment

Genomics Websites

Genome Databases: GENBANK EMBL TIGR
Genome Browsers: UCSC Ensembl
Tutorials: Transcription Translation DNA Microarrays 2Can Bioinformatics PSSMs Intro to BioPerl
Software: R Bioconductor Perl BioPerl Unix

Copyright

Federal and State copyrights are reserved by K.S. Pollard and The Regents of the University of California for all original material presented in this course through any medium, including lecture, print or via the internet.