MBB 452a (752a12) Syllabus

MB&B 452a / 752a12, Fall 2000

GENOMICS & BIOINFORMATICS

bioinfo.mbb.yale.edu/mbb452a

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

Fall 1999, Spring 1999, Spring 1998

Timing and Location

Meeting from 1:00-2:15 PM on Mondays and Wednesday, in Bass 305.
First meeting: Bass 305, 1:00-2:15 PM, Wednesday 6 September 2000.
MB&B Department, Bass building, Yale University, New Haven, CT 06520

Instructors

Genomics Section

Dieter Söll
Bass 238, Phone 203 432-6200, e-mail dieter.soll@yale.edu
Handouts and readings with Ava Artaiz <ava.artaiz@yale.edu> Bass 238, 203 432-6203.

Michael Snyder
KBT 926, Phone 203 432-6139, e-mail michael.snyder@yale.edu

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> J W Gibbs 309C, 203 432-5566.

Teaching Fellows

Weikai Li
Bass 415, Phone 203 432-5627, e-mail wl43@pantheon.yale.edu

Vadim Alexandrov
Gibbs 370, e-mail Vadim.Alexandrov@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
Sep	06	MG	Overview of Bioinformatics [html] [pdf]
	11	DS	Genomics: Overview. The diversity of life (Life at 105°C, at pH 1 or in 5M KCl)
	13	DS	Genomics: Overview of Proteins & Nucleic Acids
	18	DS	Physical and genetic maps. Whole genome sequences
	20	DS	Whole genome sequences; annotation
	25	DS	Functional genomics I (array technologies & uses)
	27	DS	Proteomics
Oct	02	MS	Functional genomics II (gene disruptions, fusions, etc)
	04	MS	Functional genomics II contd.
	09	DS	SNPs, Human Genetic Diversity, Drug Development (Uli Thomann, Genome Therapeutics)
	11	DS	Structural genomics. Whole genome comparisons
	16	DS	Agricultural genomics (Carl Simmons, Pioneer Hi-Bred)
	18	DS	MIDTERM EXAM (covering lectures through October 06)
Bioinformatics Section (also includes updated READING LIST)
	23	MG	Sequence Alignment I (via Dynamic Programming)
	25	MG	Sequence Alignment II
	30	MG	Web resources for bioinformatics
Nov	01	MG	Multiple alignment and HMMs
	06	MG	Macromolecular Geometry I (Structural Alignment and Threading)
	08	DS	Genomics and Society
	13	MG	Bioinformatics in Society
	15	MG	Databases and Integrative Analysis I
	27	MG	Databases and Integrative Analysis II
	29	MG	Databases and Integrative Analysis III
Dec	04	MG	Macromolecular Geometry II
	06	MG	Macromolecular Geometry III

Work Required and Grading

Genomics section: One midterm exam (covering lectures from September 1
- October 06), 50% of the final grade towards 452a.
Bioinformatics section: take-home final exam/project (covering lectures from
October 18 - December 1) and homework. 50% of the final grade towards 452a.

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.

Image

The DNA-mouse image is adapted from the GCB-98 homepage. What's wrong with the adaptation?

Quick Links (that may no longer work)

Bioinformatics section, Survey, "Demographics", Projects, Intro. lecture [html] [pdf], Sequences lectures [html] [pdf], Databases lectures [html] [pdf], Structures lectures [html] [pdf], Simulation lectures [html] [pdf]