BME 580.688/580.488, CS 600.688/600.488, Spring 2009
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Schedule
Date Lecturer
[Slides/Notes]		 Location Lecture Topic(s) Handout(s) Reading Hand In
Jan 26
(Mon)		 Karchin


 Shaffer 301 Lecture 1. Logistics. Course overview and objectives. What is computational biology and bioinformatics and why is it important?

Extras:
Nine short bios of leaders in the computational biology field. What makes someone a "big picture thinker"?: Jones & Pevzner, Chap. 2 pp. 52-53, Chap. 3 pp. 79-82, Chap. 4 pp. 116-118, Chap.5 pp. 139-142, Chap. 6 pp. 209-210, Chap. 7 pp. 241-243, Chap. 9 pp. 333-336, Chap. 10 pp. 380-383, Chap. 11 pp. 403-406

Intake Background Quiz
Jan 28
(Wed)		 Karchin/Carter Shaffer 301 Practical 1: Setting up your computer to do the programming assignments: Python, R, emacs, ESS         Background Survey

Jan 30
(Fri)

Carter Jenkins
122
 Tutorial session: Python programming
     
Feb 2
(Mon)		 Karchin







 Shaffer 301 Lecture 2. Introduction to probabilistic models for computational molecular biology in the 21st century (Part 1). Getting the biology right. Null models and statistical significance.

Due by midnight Feb. 9




Required:
Durbin et. al, Chap. 1, Chap 3.1,
Chap 5.6, Chap. 11.1

Extras:


  
Feb 4
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Lecture 2    
Feb 6
(Fri)		 Carter Jenkins
122
 Tutorial session: R programming      
Feb 9
(Mon)		 Karchin



 Shaffer 301 Lecture 3. Introduction to probabilistic models in computational biology. Part 2: parametric probability distributions and their alternatives


 Required:
HW1 Due by midnight. Email to fcbb2homework at gmail dot com
Feb 11
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Lecture 3

Null hypothesis design (from Lecture 3)
-  GATC enrichment in E. coli
-  GO term enrichment in a microarray experiment
-  Nucleotide conservation at enhancer site
Improving on the spectrum kernel 		       
Feb 13
(Fri)		 Carter Jenkins
122
 Programming Lab      
Feb 16
(Mon)		 Karchin Clark 110 and CSEB 220
Special time		 Special Lecture. Protein-protein interactions: what is the preferred way for proteins to interact?
Ruth Nussinov 1-2pm
Group discussion with Dr. Nussinov from 2-3pm
   Required:
One paper by Dr. Nussinov (your choice)
Come prepared with at least one question for her.		  
Feb 18
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Nussinov visit

Null hypothesis design for 3D matching (based on structural alignment) 		     
Feb 20
(Fri)		 Carter Jenkins
122
 Programming Lab      
Feb 23
(Mon)		 Karchin Shaffer 301 Lecture 4: Introduction to Maximum Likelihood in Computational Biology
Due by midnight Mar 13


 Extras:
 Prog 1 Due by midnight. Email to fcbb2homework at gmail dot com
Feb 25
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Lecture 4      
Feb 27
(Fri)		 Carter Jenkins
122
 Programming Lab      
Mar 2
(Mon)		 Karchin Shaffer 301 Lecture 5. Pairwise sequence alignment algorithms
Required:
Durbin et. al, Chap. 2
Extras:
Jones & Pevzner, Chap. 6 pp. 167-192 		 
Mar 4
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Lecture 5      
Mar 6
(Fri)		 Carter Jenkins
122
 Programming Lab      
Mar 9
(Mon)		 Karchin Shaffer 301 Lecture 6. Hidden Markov models in computational biology,
Required:
Durbin et. al, Chap. 3
Extras:
Jones & Pevzner, Chap. 11 		Proposal abstracts due by midnight. Email to karchin@jhu.edu
Mar 11
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Lecture 6      
Mar 13
(Fri)		 Carter Jenkins
122
 Programming Lab     Prog 2 Due by midnight. Email to fcbb2homework at gmail dot com
Spring
Vacation		            
Mar 23
(Mon)		 Karchin Clark 110 and CSEB 220
Special time		 Special Lecture. Combinatorial drug perturbations of cancer cells
Chris Sander 1-2pm
Group discussion with Dr. Sander from 2-3pm
Due by midnight Mar 30		    
Mar 25
(Wed)
 Karchin Shaffer 301 Practical: Exercises from Special Lecture      
Mar 27
(Fri)		 Carter Jenkins
122
 Programming Lab      
Mar 30
(Mon)		 Karchin Shaffer 301 Lecture 7. Multiple sequence alignment.
Due by midnight Apr 13


 Required:
Durbin et. al, Chaps. 5 and 6
Extras:
 HW2 Due by midnight. Email to fcbb2homework at gmail dot com
Apr 1
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Lecture 7    
Apr 3
(Fri)		 Carter Jenkins
122
 Programming Lab      
Apr 6
(Mon)		 Karchin Shaffer 301 Lecture 8. Research in the Karchin Lab: Annotating human genomic variation with computational biology

   
Apr 8
(Wed)		 Karchin Shaffer 301 Practical: TBD      
Apr 10
(Fri)		 Carter Jenkins
122
 Programming Lab      
Apr 13
(Mon)		 Carter Shaffer 301 Lecture 9. CHASM - predicting driver missense mutations in cancer
Due by midnight May 1

   HW3 Due by midnight. Email to fcbb2homework at gmail dot com
Apr 15
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Lecture 9      
Apr 17
(Fri)		 Carter Jenkins
122
 Programming Lab      
Apr 20
(Mon)		 Chen Shaffer 301 Lecture 10. Bayesian modeling in computational biology

   
Apr 22
(Wed)		 Karchin Shaffer 301 Practical: Exercises from Lecture 10      
Apr 24
(Fri)		 Carter Jenkins
122
 Programming Lab      
Apr 27
(Mon)		 Final project
presentations
 Shaffer 301 Sancar Adali
Yun Liu
     
Apr 29
(Wed)		 Final project
presentations
 Shaffer 301 Celal Alagoz
Ashok Sivokumar
    Prog 3 Due by midnight May 1. Email to fcbb2homework at gmail dot com
Reading Period            
May 8
(Fri)		 Final project presentations
 Shaffer 301 Ting Li
David Simcha
      
May 11
(Mon)		 Final project presentations
Shaffer 301 Yun-Ching Chen
Dongwon Lee
     
May 13
(Wed)		 Final project
presentations
Shaffer 301 Andy Wong
Dewey Kim