Course Schedule - BIOS 599 - Bioinformatics for Biologists - Spring 2004

DATE	TOPIC	Sub-Topics	Instr.
Jan 13	Welcome, sylabus	Intro to Bioinformatics	Mike
Jan 15	Data & databases	Types, formats, storage, retrieval - Supplement	Mike

Jan 20	Bioinformatics tools	Bioinformatics: small tools, complex tools, one goal	Mike
Jan 22	Unix	The standard OS for science	Mitch

Jan 27	Perl	A computer language for sequence analysis	Mitch
Jan 29	More Perl (& homework assigned)	Making a Perl script	Mitch

Feb 03	BioPERL	Modules & shortcuts for Perl applications	Mitch
Feb 05	EMBOSS & iNquiry	Using bioinformatics applications	Mike

Feb 10	Alignments	Pairwise sequence alignments: scoring matrices - Slide Show, Matrix Usage	Mike
Feb 12	Alignments	Pairwise sequence alignments: dynamic programming for global and local alignments, intro to BLAST - Slide Show	Mike

Feb 17	Tool: BLAST	BLAST: Using, interpretting, specialized features, similar tools - Slide Show	Mike
Feb 19	Tool: BLAST	Advanced BLAST: PSI-Blast, PHI-Blast - Slide Show	Mike

Feb 24	Homework Presentations
Feb 26	Homework presentations		Mike

Mar 02	Multiple Sequence Alignments	ClustalW, HMM's - Slide Show	Mike
Mar 04	Perl for parsing data	Data format structure, finding and parsing data	Mitch

Mar 09	class cancelled
Mar 11	Multiple Sequence Alignments	Advanced MSA: issues, applications	Mike

Mar 16	SPRING BREAK
Mar 18	SPRING BREAK

Mar 23	Gene Prediction	Theory & application - Slide Show	Mike
Mar 25	Gene Prediction - Mike's Slide Show	Tool presentation: gene finding tools - Eric's Slide Show	Mike, James Lee

Mar 30	Genome analysis - Mike's Slide Show	Tool presentation: Sequence alignments - multiple, consensus - Lyla's Slide Show	Mike, Lyla Lipscomb
Apr 01	Genome analysis - Mike's Slide Show	Tool presentation: Sequence alignments - dot plots, global, local - Pahresah's Slide Show	Mike, Pahresah Roomiany

Apr 06	Genome analysis - Mike's Slide Show	Tool presentation: Nucleotide sequence composition, codon usage, translation, mutation, profiles, 2d structure	Mike, Erin Olson
Apr 08	Genome analysis - Mike's Slide Show	Tool presentation: Nucleotide sequence transcription, restriction, primers, repeats, motifs, cpg islands Tejas' Slide Show	Mike, Tejaswita Karve

Apr 13	Protein analysis & proteomics - Mike's Slide Show	Tool presentation: Protein sequence composition, profiles, mutation, MOTIFS	Mike, Zhen Li
Apr 15	Protein analysis & proteomics - Mike's Slide Show	Tool presentation: Protein sequence 2d structure, 3d structure	Mike, Amy Runck

Apr 20	Protein analysis & proteomics	Tool presentation: Profile HMM for protein searches	Mike, Deborah Johnson
Apr 22	Gene Expression Analysis	Tool presentation: Gene Expression Analysis	Mike, Quinn Shurtliff

Apr 27	Phylogenetics	Tool presentation: Likelihood, parsimony approaches	Mike, Kayce Bell
Apr 29	Phylogenetics	Tool presentation: Distance approaches	Mike, Kurino Ashizawa

May 02	Phylogenetics	Tool presentation: MrBayes	Mike, Eric Waltari
May 04	TBA