Syllabus: Biol 444/544

Spring 2008 (updated 2/10/2008)

Text: Discovering Genomics, Proteomics, and Bioinformatics

Campbell and Heyer; Benjamin Cummings (publisher)

Grading: 1/3 quizzes and final; 1/3 paper , 1/3 in-class participation (this will also include office hours - which are mandatory for people taking 544 and strongly suggested for 444 students. This is where you will begin to integrate genomics into how you think about biology.

Text webpage

All papers are on ERESERVES 544: http://ereserves.unm.edu

Research proposal instructions

Fred Sherman yeast reference

Here is a cool cell animation -

© MWW 2008

• January 28 - Introduction; Genetics Approaches
  • Papers- week 1
  • Read: A new approach to decoding life: Systems biology ; Ideker, T; Galitski, T; Hood, L
    ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS; 2001; v.2, p.343-372
  • Optional: Whither Genomics - Andrew Murray - theoretical view of genomics
  • Optional: Functional genomics and proteomics:charting a multidimensional map of the yeast cells
    Gary D. Bader, Adrian Heilbut, Brenda Andrews, Mike Tyers, Timothy Hughes and Charles Boone TRENDS in Cell Biology Vol.13 No.7 July 2003
  • Questions for Hood and Functional Genomics Paper
  • Notes: week 1;
  • Molec Biol online texts and yeast information
• Feb 4 - Genomics - - Chapter 2.1 in your book
  • Notes
  • Class powerpoint 1 on genome sequencing projects (also in the notes)
• Feb 11 -Genomics - Genome sequencing tools and applications
  • Whole genome shotgun sequencing from Wickipedia
  • Weber and Meyers - paper outlining plan for WGS
  • How Genbank is dealing with WGS and Metagenomic entries
  • Optional Bioinformatics for metagenomics
  • PLOS and BioMedCentral Journals
  • Nature gateway
  • Rice and Magnaportha genome papers are in eReserves
  • Class notes for this week
  • NOTES on Polony-based sequencing
  • Diego Martinez will speak on Gene Finding. I'll add some recent Science pages on challenges to gene finding.
  • Quiz 1
• Feb 18 - Comparative and Evolutionary Genomics - Chapter 3.1 and 3.2
  • notes (doc file)
  • Evolutionarily conserved elements in vertebrate,insect, worm, and yeast genomes
    Adam Siepel et al. Genome Research 15:1034-1050 (2005)
  • Gene finding (optional - for your own edification
• Feb 25 - Genomic variation - Hap Map
• Chapter 4.1 and 4.2
• Notes for today
• Variation Discovery Website - Seattle SNPs
• NCBI SNP site
• HapMap project website
• modENCODE website
• Genome Research ENCODE issue, June 2007
• Read Drosophila -elements and the Human Encode Data 2007 papers in EReserves Comparative Genomics file
• Powerpoint (past information from your book - this will be updated)
• Mar 3 - Functional Genomics (tools and approaches)
• Notes
• Two HOX transcription factor binding papers from Research folder
• Mar 10 - Microarrays - Chapter 4 -(identify research proposal papers)
• Powerpoint
• Kendra's notes
• Butte, A;; The use and analysis of microarray data NATURE REVIEWS DRUG DISCOVERY; DEC 2002; v.1, no.12, p.951-960
• Today's takehome exam
• Mar 24 - Microarrays - (identify research proposal papers) Chapter 6 in your book
• Holstege paper in EReserves - MIcroarray file
• Powerpoint for Holstege
• Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-phase cultures.Aragon AD, Rodriguez AL, Meirelles O, Roy S, Davidson GS, Tapia PH, Allen C, Joe R, Benn D, Werner-Washburne M. Mol Biol Cell. 2008 Mar;19(3):1271-80.
• Aragon ppt
• Mar 31- Microarrays - (we'll talk about approaches to good papers)
• Finish Aragon paper
• Giaever, G ; et al: Nature; JUL 25 2002; v.418, no.6896, p.387-391 ; Functional profiling of the Saccharomyces cerevisiae genome Powerpoint
• (start your research paper)
• Apr 7 -Week of meetings to discuss papers
• Apr 14 Proteomics - Chapter 6
• Powerpoint on proteomics
• Nature reviews on proteomics
• Ann Rev Genomics and Human Genetics, 2004
• S D Patterson & R H Aebersold; Proteomics: the first decade and beyond Nature Genetics 33: pp 311 - 323 (REVIEW)
• Zhu, H et al. 2003. Proteomics. Ann Rev Biochem 72:783-812 (REVIEW)
• READ: Global analysis of protein phosphorylation in yeast; Snyder, Nature 2005
  
• Apr 21 - Proteomics (papers due)
• Yeast 2-hybrid Fields and Uetz papers
• Questions these are from last years' class.
• Power point-Fields/Powerpoint Uetz
• Gavin - MS/MS yeast proteome
• Apr 28 - Systems Biology: Chapter 9
• Powerpoint
• Charles Boone & Brenda Andrews ORFeomics: correcting the wiggle in worm genes Nature Genetics, May 2003, pp 8 - 9, Reboul, J et. al.; C-elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression . NATURE GENETICS; MAY 2003; v.34, no.1, p.35-41
• Computational approaches to Genomics
• May 5 Graduate student (and some undergraduate) presentations

FINAL

 

FAQS:

Are you going to teach us everything about genomics?

Sorry, no one knows everything about genomics. The goal of this class is to understand what genomics is, the types of questions that can be asked with genomic-scale tools, begin to use available analysis tools and databases so that you can begin to use them efficiently to answer questions that are biologically important, and to begin to understand the mathematical underpinnings of genome-scale analyses.

What book do I use for this course? This is the first year I am trying a book for this course. I hope it works - we'll just have to see how it integrates with what you have had (and remember) from your earlier courses.

What work is necessary for this class? 1)There will be homework/quizzes plus a paper. 2) Each student will give an in-class presentation of a paper using Powerpoint. 3) Participation in class is manditory. 4) If you want to set up a webpage, this is a good idea.

Dr. WW, what are your goals for this class?

for students to understand the levels of genomic analysis, how they relate to molecular, genetics, and biochemical approaches, and how to apply genomics to the questions they are currently asking and to new areas of biology