Bioinformatics I and II, 2008
MSCI814 and MSCI815
David Nelson course director
Guest Lecturers
Yan Cui, Microarray
George Hilliard, Proteomics
Ron Adkins, Genome assembly and annotation
Rob Williams, QTL (Quantitative Trait Locus) mapping
Julia Krushkal, Human HapMap
Larry Reiter, Homophila
Ramin Homayouni, Mining of abstract databases, Knowledge mining
Modules for MSCI814
Module 1
A First Introduction to NCBI Nelson, Jan. 10, 2008
Module 2
Superfamily Genomics/Eukaryotic Gene Assembly, duck-billed platypus Nelson, Jan. 17, 2008
Module 3
Multiple sequence alignments and sequence editors Nelson, Jan. 24, 2008 (under revision)
Module 4
Phylogenetic trees Nelson, Jan. 31, 2008)
Module 5
Proteomics I Hilliard, Feb. 7, 2008
Module 6
Proteomics II Hilliard, Feb. 14, 2008
Module 7
Microarray I Cui, Feb. 21, 2008
Module 8
Microarray II Cui, Feb. 28, 2008
Module 9, 2008
Comparative Genomics/Human and Amphioxus, evolution of P450 gene clusters between chordate species. Nelson, March 6, 2008 (under construction)
Module 9, 2006
Comparative Genomics/Human and Chimpanzee, evolution of gene clusters between closely related species, including pseudogenes Nelson, March 6, 2006
Module 10
Microarray III Cui, March 13, 2008
March 20, 2008 no class, Spring Break
Module 11
QTL Mapping Williams, March 27, 2008, date confirmed
Modules for MSCI815
Dates confirmed
Module 1
3D structure Viewers and VAST Nelson, April 3, 2008
Module 2
Phenotype prediction of SNPs Cui, April 10, 2008
Module 3
Human HapMap 2008 PowerPoint Julia Krushkal, April 17, 2008
Human HapMap 2008, Haploview exercise Julia Krushkal, April 17, 2008
Module 4
Knowledge base mining PowerPoint Homayouni, April 24, 2008
Knowledge base mining assignment Homayouni, April 24, 2008
Archived modules from 2006
Knowledge base mining I. SGO new version
Homayouni, 2006
Knowledge base mining I. PowerPoint Homayouni, 2006
Knowledge base mining I. SGO old version Homayouni
Module 5
Genome Assembly and Annotation Adkins, May 1, 2008
Genome Assembly and Annotation Adkins, May 1, 2008
Genome &Annotation file Adkins, May 1, 2008
Genbank format sequence Adkins, May 1, 2008
Fasta file sequence Adkins, May 1, 2008
Module 6
Homophila, human-fly disease gene research Larry Reiter, May 8, 2008
Extra Modules, self study, optional
Module A
Vector NTI I Edwards
Module B
Vector NTI II Edwards
Module C
Knowledge base mining II. Arrowsmith Homayouni
Module D
Genome Assembly and Annotation Edwards,