CB&B752/CPSC452/CPSC752/ MB&B452/MB&B752/MCDB452/MCDB752

GENOMICS & BIOINFORMATICS

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

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

Spring 2005, 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 Monday and Wednesday, in Bass 305.

Discussion section on Tuesday and Wednesday from 5-6 in Bass 405.

Key dates:

7 Nov. First 25' of class will be devoted to Quiz #1

30 Nov. Outside lecture + summary + Quiz #2

Class will start 40' late at 1:40.

For the beginning of class people are encouraged to go to the following lecture on horizontal gene transfer:
Peter Gogarten (University of Connecticut). Horizontal gene transfer and microbial evolution: Is the ?Tree of Life? a tree? (see http://www.eeb.yale.edu/resources/calendar.htm), 12:30 to 1:30 in OML 226.

The remainder of the 30 Nov. class will be taken up with Quiz #2 (~25 minutes), a brief summary of the lectures and a discussion of the final project papers.

10 Dec. Projects due

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.

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

Teaching Fellows

Sara Nichols, SCL 20, 203 432-6288
e-mail sara.nichols@yale.edu
Xiaowei Zhu, KBT 932, 203 432-3514
e-mail xiaowei.zhu@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.

Rough Outline of Topics

Genomics Section
Aug	31	DS	Genomics: Overview. The Diversity of Life (Life at 110 C, at pH 1, or in 5M salt)
Sept	05	DS	Genomics: Overview of Proteins and Nucleic Acids
	6 or 7	Section 1:	Asai,T et al. 1999 PNAS 96, 1971-1976 and Woese, C.R. et al. 1977 PNAS 74, 5088-5090
	07	DS	Genome Sequencing, Sequence Annotation
	12	DS	Metabolomics (Sunil Kochhar, Nestle)
	13 or 14	Section 2:	Vieille and Zeikus, 1996 TIBTECH 14, 183-189 and Doolittle W.F, Science, 284, 2124-2128
	14	DS	Functional Genomics I (array technologies and uses)
	19	DS	Functional Genomics II (proteomics)
	20 or 21	Section 3:	Chin et al. 2003 Science 301, 964-967 and Iyer et al. 2001 GenomeBiology 12,RESEARCH0051
	21	DS	Impact of Genomics on Parasitology (John Roger, NIH)
	26	DS	Structural Genomics
	27 or 28	Section 4:	DeRisi J.L. et al., Science 278, 680-696 and Golub, T.R. et al. 1999 Science 286, 531-537
	28	MS	Functional Genomics III
Oct	03	MS	Functional Genomics IV
	4 or 5	Section 5:	Hughes TR et. al. Cell. 2000 Jul 7;102(1):109-26. and Kolfschoten IG, Cell. 2005 Jun 17;121(6):849-58.
	05	DS	Genomics and the Environment (Chris Greer, NSF)
	10	DS	Chemical Genomics / Phylogenomics
	12	DS	Midterm Exam (covering lectures through October 10)
Bioinformatics Section
	17	MG	Bioinformatics: Overview [Main Points]
	18 or 19	Section : 6	Luscombe et al. 2001 Methods Inf Med. 40(4):346-58. and Greenbaum et al. 2001 Genome Research 11 (9): 1463.
	19	MG	Overview Continued [Main Points]
	24	MG	Analysis of Sequences I [Main Points]
	24 or 26	Section : 7	Review Sequence Alignment
	26	MG	Analysis of Sequences II [Main Points]
	31	MG	Analysis of Sequences III [Main Points]
	31 or 2	Section : 8	Altschul et al. 1997 Nucl. Acids Res. 25 (17): 3389 and Levitt and Gerstein 1998 PNAS 95 (11): 5913.
Nov	02	MG	Demonstration of Web Resources [Main Points]
	07	MG	Analysis of Sequences IV [Main Points]
	7 or 9	Section : 9	Altschul, SF. et. al. Nature Genetics. 1994;6(2):119-29. and Eddy, SR. Bioinformatics. 1998;14(9):755-63.
	09	MG	Structures I [Main Points]
	14	MG	Structures II [Main Points]
	14 or 16	Section : 10	Nucleic Acids Res. 2005 Apr 1;33(6):1874-91.
	16	MG	Structures III [Main Points]
	28	MG	Simulation [Main Points]
	28 or 30	Section : 11	J Mol Biol. 1997 Apr 11;267(4):1026-38. and J Mol Biol. 1993 Sep 5;233(1):123-38.
	30	MG	LECTURE STARTS LATE, QUIZ, FINAL PROJECT DISCUSSION

Grades

One midterm exam (covering lectures from August 31 - October 10)

A take-home final exam/project (covering lectures from October 17th - November 30)
Grades: 40% Genomics , 40% Bioinformatics 20% discussion section.

Class Requirements

Attendance, class participation

Readings

Papers will be assigned throughout the course. These papers will be discussed in weekly sections led by the TAs.

Bioinformatics Quizzes

There will be 2 short quizzes (25 minutes) in class comprising SIMPLE questions that you should be able to answer from the lectures plus the main readings. The first quiz will cover the first part of the bioinformatics lectures. The second quiz will cover the rest of the material in the bioinformatics section.

Final Project Description

PLEASE CHOOSE *ONE* OF THE FOLLOWING TWO PAPERS to do the final paper on

You can select ONE of them for your project. The final project should be 8 pages long, (double spaced, 12 font, 1 inch margins), with the first half as a review of the paper you choose and the second half as an extension for new ideas. Please carefully cite your references (MLA) at the end of your project (not included in the 8 pages).

The review section will contain 1) a background introduction, 2) a summary of the general concepts and methods, 3) a *new* figure designed by you that helps to illustrate the basic schemes and 4) your comments on the paper including its advantages and disadvantages and other appropriate comments we've discussed in section such: as who would you refer this paper to, pitfalls, obviously wrong data, different ways to approach what the authors are discussing, things to ass to make the argument more sound, ideas that popped into your head after reading the paper, things that were not clear, similar concepts in another field you realize can be applied.

In the second half, imagine you were a post-doc who wants to design a summer project to further investigate the work in the selected paper. You will write a simple proposal describing your thoughts and methods to test them.

You are expected to read relevant background to help you formulate your review and project proposal. This can come from the references in the reviewed paper itself and, more broadly, from literature mentioned in the class. You should explain your ideas on basis of the knowledge from the class and describe them with your own words.

Please submit an electronic version (PDF) of your project onto the classes server before midnight on November 10th. Late submissions will not be accepted.

The project will make up 30% of your final grade, and we will put it on our public web site after the grading. You can see previous projects below.

Final Projects Handed In

Projects done this year and previously:Fall 2005, Spring 2005, 2003, 2002, 2001, 2000, 1999, 1998

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.

Home

MB&B Department, Bass building, Yale University, New Haven, CT 06520