back to Syllabus

week by week schedule to semester end

Date Topics Lecture Slides/Notes
Aug. 24 Introduction to Bioinformatics, Proteomics cs686_01_intro.pdf
Lesk p1-22
Aug. 26 Protein Sequence Alignment
Dynamic Programming Algorithm
Patrice Koehl's slides on sequence comparsion
Lesk p242-254, 261-267
Aug. 31 Amino Acids in Proteins cs686_03_aminoAcids.pdf
Lesk p42-52
Sept. 2 Transcription and Translation cs686_04_transcription_translation.pdf
read this paper
Sept. 7 Promoters and Transcription Factors
Research using PubMed
Paper: detecting transcription enhancers with IMEter
Lesk p441, p446-448, p452-455
Sept. 9 Ian Korf's lecture
Molecular visualization with Pymol
assignment2 due Thursday, Sept 16
sample pymol script
assignment2 due Thursday, Sept 16
Sept. 14 Heuristic sequence alignment methods
Finish lab on Pymol
This paper on flu will be presented Thurs
2 page news summary of above flu paper
Similarity Measures
Lesk p254-258
Review for next quiz
Sept. 16 paper on flu
BLAST tutorial: protein query
Lesk p259-261
Sept. 21 BLAST scoring
Open Reading Frames
Didier Gonze on BLAST scoring
BLAST tutorial: gene query
Lesk p267-270
Adrian will present this paper next class
Assignment 3 due Tuesday, Sept 28 ORF finding tool
Sept. 23 mRNAsplicing
Adrian presents paper on SVM classifier
relation of genome to proteins
Sept. 28 genetics
Sept. 30 multiple sequence alignment
Oct. 5 profiles, PsiBlast, HMMs Paper on HMMs by Sean Eddy
Crystal will present this paper next class
Oct. 7 HMM definition and forward algorithm
Crystal presents paper on SVM classifier
probability and log rules
assignment4 due Tues, Oct 14 (Options 1&2)
Oct. 14 Dr Frank McCormick's talk, pathways
Protein Secondary Structure
MAPK/ERK pathway
Patrice Koehl's slides on protein secondary structure
Oct. 19 Protein Tertiary Structure Protein Tertiary Structure
Jia will present this paper next class
Oct. 21 Energy of Protein Structures
Jia presents paper
Dr. Sean Mooney speaks next Thurs
Energy of Protein Structures
assignment5 due Tues, Nov 2
Oct. 26 Neural Networks
Oct. 28 midterm review
Dr Sean Mooney's talk at 11:45
Nov. 2 midterm  
Nov. 4 ROC curves
midterm corrections
quiz 6 is midterm corrections
Nov. 9 Pakkapon presents paper on HMM analysis of ChIP-chip data
ROC example
Zeynep presents paper on protein docking
Nov. 11 Bioinformatics Lecture Series:
Dr Bob Horton presents on biological sequence determination
Nov. 16 database design
Evan presents paper
Database lecture
Nov. 18 database implementation
Feros presents paper
assignment6 due Tues Nov 30
Nov. 23 Dr. Sean Mooney on partnership with the Buck Institute next semester
informal talk with Sean over pizza  
Nov. 25 Thanksgiving Holiday