From GersteinInfo

Revision as of 20:38, 17 September 2011

CBB 752

Course Information

Course Description

Bioinformatics encompasses the analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. It represents a major practical application for modern techniques in data mining and simulation. Specific topics to be covered include sequence alignment, large-scale processing, next-generation sequencing data, comparative genomics, phylogenetics, biological database design, geometric analysis of protein structure, molecular-dynamics simulation, biological networks, normalization of microarray data, mining of functional genomics data sets, and machine learning approaches for data integration.

Concise undergraduate course description

Techniques in data mining and simulation applied to bioinformatics, the computational analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. Sequence alignment, comparative genomics and phylogenetics, biological databases, geometric analysis of protein structure, molecular-dynamics simulation, biological networks, microarray normalization, and machine-learning approaches to data integration.

See entry from undergraduate catalog: http://students.yale.edu/oci/resultDetail.jsp?course=21914&term=201201 , viz:

MB&B 452 01 (21914) /MCDB452/MB&B752/CB&B752/MCDB752/CPSC752
Bioinformatics: Practical Application of Simulation and Data Mining 
Mark Gerstein
MW 1.00-2.15 BASS 305
Spring 2012 
No regular final examination
Areas Sc
Prerequisites: MB&B 301b and MATH 115a or b, or permission of instructor.
MCDB 120a or 200b is a prerequisite for courses numbered MCDB 202 and above.

Quizzes and Final Project

There will be approximately four short quizzes during the semester and a take-home final project. For CBB and CS sections, the final project will be a programming assignment. For MB&B, the final project will be a paper. Further details will be announced at a later date.

Literature discussion section

One session of 60 minutes per week, time to be arranged. Student presentations of recent research papers relevant to the topics of the course. Led by Lucas Lochovsky (Bass, Rm 437; 432-5405; lucas.lochovsky(at)yale.edu) and Jane Leng (Bass, Rm 437; 432-5405; jing.leng(at)yale.edu).

Programming Projects/Problem Sets

Students taking this course listed under Computational Biology and Bioinformatics or Computer Science will be required to complete several short programming assignments. Further details will be discussed in the literature discussion section and during class.

Grade Categories

CBB and CPSC Sections:

Quizzes - 33% Final Project - 33% Discussion Section - 8.25% Programming Assignments - 24.75%

MBB and MCDB Sections:

Quizzes - 33% Final Project - 33% Discussion Section - 16.5% Problem Sets - 16.5%

Differences Between Class Sections

In general, the graduate level CS/CBB course is significantly different than MBB/MCDB (graduate and undergraduate) in several ways. Although the lectures are the same for each section, the graduate level CPSC/CBB course has additional programming assignments in addition to the work being completed by the MBB students. homework for the MBB section centers on the completion of several problem sets without a programming component. The CPSC/CBB section forgoes these problem sets and instead requires that students implement several of the algorithms discussed in class. Also, the final project for CPSC/CBB MUST be a programming assignment rather than the final paper equired for the MBB section. Due to the distinct course requirements, category weightings for final grades are also different.

Timing & location

Class: Meeting from 1:00-2:15 pm on Monday and Wednesday, in 305 BASS. (First meeting will be on 9 Jan.)

Discussion section: TBA

Instructors

Instructor-in-Charge

Mark Gerstein, 432A BASS, Phone 203 432-6105, e-mail mark.gerstein(at)yale.edu

Instructors

Corey O'Hern, Mason Laboratory e-mail corey.ohern(at)yale.edu, Office Hours: M 2:15-3:15 PM

Others to be listed

Teaching Fellows

Lucas Lochovsky, Bass Rm 437, (203) 432-5405

Jane Leng, Bass Rm 437, (203) 432-5405