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,