CS 490B Schedule

This will be updated daily to weekly with current/upcoming readings and assignments. As with weather forecasting, predictions for further in the future are a bit vague and should be taken with a grain of salt.

Date		Instr.	Assign.	Topic / reading
Introduction
Jan.	7	All		Intro: Managing and mining biomolecular information; student biographies Primer, pp. 1-4
	9	ML		Overview of the central dogma of biological information & evolution Page & Homes, 1998, Molecular Evolution, Chap.3 handout.
	11	ML		Overview of genomics
	14	JX		Overview of statistics & mathematics for analyzing biodata
	16	JX	HW 1	Stats, cont.Note on CpG dinucleotide distributions
	18	AG		Overview of algorithms for analyzing biodata
	21			Martin Luther King Jr. Holiday
	23	AG	HW 2	Algorithms, cont.
Genomics
	25	AG		Tools for sequence alignment and database searches
	28	AG		Alignment tools, cont.
	30	JX		Databases (NCBI and others)
Feb.	1	JX		Meet in lab: (Lilly Hall G431) Databases, cont.
	4	JX	MP 1	Lecture on score matrix and HMM
	6	JX		Lecture on HMM
	8	ALL	Q 1	Quiz and helps on mini project 1, SQL
	11	CBK		Algorithms on HMM
	13	CBK		Profile HMMs
	15	JX		ClustalW demonstration
	18			"Virtual Tour of Purdue Sequencing Center: Hardware" , Dr. Philip San Miguel, Director , Purdue Genomics Initiative
	20			"Sequence Comparisons: Software at the Purdue Genomics Initiative", Dr. Rick Westerman, Bioinformatics Specialist
	22	AG		multiple sequence alighment algorithms
	25	BIOL		Midterm review
Proteomics
	27	MH		Proteins and proteomics & one-letter for aa
Mar.	1	MH		Proteins, cont.
	4	MH		protein structure & motifs
	6	MH		protein structure, cont.
	8	JX	MP2	Meet in lab: Motifs, cont.
	11			Spring break
	13			Spring break
	15			Spring break
	18	CBK		Structure alignment
	20	AG		Geometric hashing
	22	AG		Molecular modeling (mechanics & dynamics)
	25	CBK		Protein threading
	27	ALL		Quiz 2
	29	JX		Probability model of motifs
Apr.	1	JX		Gibbs sampling strategy for motif alignment
Transcriptomics
	3	ML		Construction and use of microarrays
	5	ML		Microarrays, cont.
	8	JX		Statistical analysis of microarray data: clustering methods
	10	AG		Clustering expression levels
	12	CBK	MP3	Microarray Analysis: Dimensionsality Reduction
	15	CBK		Overview: Mass Spectrometry for Proteomics
	17	AG	Q3	mini-project #3 discussion
Additional topics
	19	ML		Phylogenetic analyses: Tree construction and interpretation
	22	ML		Phylogenetic analyses: Tree interpretation and evaluation
	24	JX		Parsimony and maximum likelihood methods
	26	All		Final class, course evaluation
	29	All		FINAL EXAM: April 29 10:20am - 12:20pm LAEB 2290


	Introduction to Bioinformatics Last modified:Monday, 29-Apr-2002 15:21:11 EST