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Schedule
Introduction to BioInformatics
Fall 2005

This schedule may be modified both in advance (to reflect anticipated changes in material and schedule) and in retrospect (to reflect what was actually covered each week).  Dates of midterms may change.

Links to lecture notes and lab handouts will be made active each week

Announcement!!

.

AmiGo link for Q6 has been added into HW7

Moday's lecture will be hold in Moore 100A at 2 pm. 11/14/05

A clustering software tutoiral will be hold in my office hr. tomorrow 11/9/05.

Miler Lee's email address <miler at mail.med.upenn.edu>

Students who attend the lab session may want an eniac account to store results when they are working at lab. Get it at www.seas.upenn.edu/accounts

	Date	Subject (click for lecture notes)	HW Due	Readings
1	Wed 9/7	Introduction		Pevzner Chapter 1
2	Fri 9/9	NO CLASS
3	Mon 9/12	Sequence alignment and algorithms		Pevzner 2.1-2.7, 4
4	Wed 9/14	Dynamic Programming	HW1 due 9/23	Pevzner 6.1-6.5Pevzner 2.7-2.9
5	Fri 9/16	Discussion:circadian rhythms		paper1: Satchidananda Panda et al, Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock paper2: Lisa D. Wilsbacher, Ashvin M. Sangoram, Marina P. Antoch, and Joseph S. Takahashi ,The Mouse Clock Locus: Sequence and Comparative Analysis of 204 Kb from Mouse Chromosome 5 paper 3: Jean-Christophe, Leloup Albert Goldbeter , A Model for Circadian Rhythms in Drosophila Incorporating the Formation of a Complex between the PER and TIM Proteins
6	Mon 9/19	Local and global alignments, PAM and BLOSUM, gaps		Pevzner 6.6-6.9
7	Wed 9/21	BLAST & its variants
8	Fri 9/23	Lab: alignment	Hw2 due 9/30
9	Mon 9/26	BLAST- statistics		Pevzner 12.2 handout
10	Wed 9/28	Motifs, PWMs, EM & Gibbs	Hw2a due 9/30	Pevzner 4.4-4.6
11	Fri 9/30	Discussion: homology of the CLOCK gene		W.J Kent et al. Exploring relationships and mining data with the UCSC Gene Sorter
12	Mon 10/3	Promoter prediction	HW3 due 10/7
13	Wed 10/5	Comparative methods/multiple alignment	HW3 solution
14	Fri 10/7	Discussion: How well does motif finding work?		Panda et al.
15	Mon 10/10	Review/ motif finding
	Wed 10/12	Midterm I	2004 midterm	2005 midterm
	Fri 10/14	NO CLASS	2004 midterm sol	2005 midterm sol
	Mon 10/17	FALL BREAK
16	Wed 10/19	Comparative methods/multiple alignment		Pevzner  6.10
17	Fri 10/21	Gene Finding	Homework4	Pevzner 6.11-6.13
18	Mon 10/24	Regression, neural nets, SVMs
19	Wed 10/26	Comparative Genomics	Homework5 Data for regression	Reading1:   Bejerano G , Ultraconserved elements in the human genome. Reading2: Xiaohui Xie, Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
20	Fri 10/28	Gene Prediction:HMMs	Homework6	Pevzner 11 Readings: chicken genome
21	Mon 10/31	Discussion: how well does gene prediction work?		Reading 1: HMM_superfamilies Reading 2: Gene Prediction
22	Wed 11/2	Gene expression: methods & application		Reading: Cancer gene expression
23	Fri 11/4	Discussion of Final projects
24	Mon 11/7	Clustering (k-means, hierarchical, PCA)	Final project descriptions	Pevzner 10.1-10.3
25	Wed 11/9	More clustering
26	Fri 11/11	Interpretation of clusters (GO, etc.)	HW7 data HW7 Probe2Entrz
27	Mon 11/14	clusters: laboratory
28	Wed 11/16	Microarray applications		paper1: Golub et al., Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring paper2: Michael B. Eisen et al. Cluster analysis and display of genome-wide expression patterns supplemental: Dirix et al. Genomics and circulating tumor cells: promising tools for choosing and monitoring adjuvant therapy in patients with early breast cancer?
29	Fri 11/18	gene regulatory networks
30	Mon 11/21	protein structure		Pevzner  8.11-8.15
31	Wed 11/23	Discussion of final projects
	Fri 11/25	Thanksgiving Break (No Class)
32	Mon 11/28	proteomics		Mass spectrometry-based proteomics
33	Wed 11/30	RNA structure
34	Fri 12/2	structure -discussion		Readings Mapping of conserved RNA secondary structure
35	Mon 12/5	Review
	Wed 12/7	Metabolic Network	2004  Midterm2
	Fri 12/9	Midterm2 Final Project Due 12/16	2004 Midterm2 solution