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.
7 Nov. First 25' of class will be devoted to Quiz #1
30 Nov. Outside lecture + summary + Quiz #2
10 Dec. Projects due
Bass 238, Phone 203 432-6200, e-mail firstname.lastname@example.org
Handouts and readings with Mary Backer email@example.com; Bass 238, 203 432-6203.
KBT 926, Phone 203 432-6139, e-mail firstname.lastname@example.org
Bass 432A, Phone 203 432-6105, e-mail Mark.Gerstein@yale.edu
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.
|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)|
|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|
Midterm Exam(covering lectures through October 10)
|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|
Papers will be assigned throughout the course. These papers will be discussed in weekly sections led by the TAs.
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.
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.
Projects done this year and previously:Fall 2005, Spring 2005, 2003, 2002, 2001, 2000, 1999, 1998
If you're really motivated, take a look at http://bioinfo.mbb.yale.edu/jobs.