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 cs686_assign1.pdf |
| 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 |
http://www.meilerlab.org/uploads/courses/chem238/tutorials/pymolTutCaM2.pdf http://www.rubor.de/anlagen/PyMOL_Tutorial.pdf 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 |
BLAST tutorial: protein query Lesk p259-261 |
| Sept. 21 |
BLAST scoring BLAST Lab Open Reading Frames |
Didier Gonze on BLAST scoring BLAST tutorial: gene query Lesk p267-270 Adrian will present this paper next class gene Assignment 3 due Tuesday, Sept 28 ORF finding tool |
| Sept. 23 |
mRNAsplicing Adrian presents paper on SVM classifier |
mRNAsplicing relation of genome to proteins |
| Sept. 28 |
genetics |
Genetics mitosis Meiosis |
| Sept. 30 |
multiple sequence alignment ClustalW |
|
| 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 lab |
|
| 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 |
