MBB 452b (752b) Syllabus

MB&B 452b / 752b, Spring 2005

GENOMICS & BIOINFORMATICS

http://www.gersteinlab.org/courses/452/

Previous Year's Course Pages (all links still work)

Fall 2003, Fall 2002, Fall 2001, Fall 2000, Fall 1999, Spring 1999, Spring 1998

Timing and Location

Meeting from 1:00-2:15 PM on Mondays and Wednesday, in Bass 305.

Instructors

Genomics Section

Dieter Söll
Bass 238, Phone 203 432-6200, e-mail dieter.soll@yale.edu
Handouts and readings with Mary Backer <mary.backer@yale.edu> Bass 238, 203 432-6203.

Bioinformatics Section

Mark Gerstein
Bass 432A, Phone 203 432-6105, e-mail Mark.Gerstein@yale.edu
Handouts and readings with Joann Delvecchio <joann.delvecchio@yale.edu> Bass 432, 203 432-8189.

Teaching Fellows

Tom Royce, Bass 426, 203 432-8972
e-mail thomas.royce@yale.edu
Fang Fang Yin, TAC S-610, 203 785-3247
e-mail fangfang.yin@yale.edu

Brief Description

Genomics describes the determination of the nucleotide sequence as well as many further analyses used to discover functional and structural gene information on all the genes of an organism. Topics include the methods and results of analysis on a genome-wide scale as well as a discussion of the implications of this research. Bioinformatics describes the computational analysis of gene sequences and protein structures on a large scale. Topics include sequence alignment, biological database design, geometric analysis of protein structure, and macromolecular simulation. [Blue Book Entry]

Rough Outline of Topics

Genomics Section
Jan	10	DS	Genomics: Overview. The Diversity of Life (Life at 110 C, at pH 1, or in 5M salt)
	12	DS	Genomics: Overview of Proteins and Nucleic Acids
	17		Martin Luther King Day (no class)
	19	DS	Genome Sequencing, Sequence Annotation
	24	DS	Genomics I (array technologies and uses)
	26	DS	Functional Genomics II (proteomics)
	31	DS	Functional Genomics III (Mike Smith)
Feb	02	DS	Genomics/Pharma (Klaus Melchers, Altana Pharma)
	07	DS	Functional Genomics IV (Mike Smith)
	09	DS	Structural Genomics
	14	DS	Chemical Genomics / Phylogenomics
	16	DS	Pharmacogenomics (Madan Kumar, Genaissance)
	21	MG	Midterm Exam (covering lectures through February 16)
	23	MG	Bioinfomatics: Overview
	28	MG	Analysis of Sequences I
Mar	02	MG	Analysis of Sequences II
	21	MG	Analysis of Sequences III
	23	DS	Metabolomics (Sunil Kochhar, Néstle)
	28	MG	Analysis of Sequences IV
	30	MG	Structures
Apr	04	MG	Demonstration of Web Resources
	06	MG	Surveys I
	11	MG	Surveys II: Whole Genome Comparisons
	13	MG	Datamining
	18	MG	Simulation
	20	MG	Summary: Industrial Perspectives

Work Required and Grading

Examination: One midterm exam (covering lectures from January 10 - February 16)
Project: a take-home final exam/project (covering lectures from February 23 - April 20)
Quizzes: Two very short quizes during bioinformatics section (covering lectures from February 23 - April 20)
Literature Discussion Section One session of 60 minutes per week. Student Presentations of recent research papers relevant to the topics of the course.
Led by TAs: Tom Royce, Fang Fang Yin
Grades 40% Genomics Midterm + 32% Bioinformatics Project + 2 * 4% Bioinformatics Quizzes + 20% Discussion Section

Prerequisites

The course is keyed towards advanced MB&B undergraduates and graduate students wishing to learn about types of large-scale quantitative analyses that whole-genome sequencing will make possible. It would also be suitable for students from other fields such as computer science or physics wanting to learn about an important new biological application for computation.
Students should have :
1. A basic knowledge of biochemistry and molecular biology.
2. A knowledge of basic quantitative concepts, such as single variable calculus, some probability and statistics, and basic programming skills.
These can be fulfilled by the following prerequisites statement: "Prerequisites: MB&B 200 and Mathematics 115 or permission of the instructor."

Research Jobs in Bioinformatics

If you're really motivated, take a look at http://bioinfo.mbb.yale.edu/jobs.

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