CAMB/GCB 752 Seminar in Genomics

GCB/CAMB 752      Seminar in Genomics

Harold Riethman

Riethman@wistar.org

Thursdays 3 PM to 6 PM

BRB 252

Prerequisite: GCB 531 Intro to Genomics or equivalent or permission of instructor

Class Size limited to 16.

The class will meet once a week for a 3 hr period. Recent papers from the primary genomics literature will form the core material for the course. Each 3-hr session will feature a major topic in Genomics, with student presentations (usually two per session) centered on papers selected within the topic area. While the “presenting” student will give a 10- 15 min introduction to the paper and will show powerpoint slides of the data in the paper, all students in the class are expected to have read and to be prepared to discuss the papers presented. For example, following the introduction, non-presenting students will be called upon to explain a particular table or figure, or to discuss a point raised in the paper. Grades will be based upon the student presentations and upon class participation.

Some topics will be decided upon jointly by the students and the course organizers during the Introductory/Organizational meeting on January 11. Topics that will be covered this semester include:

Mandatory Topics selected by course organizers

Gene Expression Profiling and Cancer

Genome-wide Location Analysis, ChIP

HapMap and Association Studies

DNA re-sequencing and mutational profiling in Cancer

Comparative Genomics and Genome Annotation

Analysis of Copy Number Polymorphisms (CNPs)

Genome-wide functional analysis using RNA interference

Protein Interaction Networks

Elective Topics selected by students in class discussion

Epigenomics

Ecological Genomics/Comparative Metagenomics

Array Comparative Genomic Hybridization (array-CGH) and Cancer

Comparative Genomics and Human-Primate comparisons

Synthetic Biology

Proteomics and biomarkers

SNPs and the regulation of gene expression.

Variation in Gene Expression

Genome-wide functional screens

Other…         

The course organizers may suggest potential papers for each topic. Students can either select papers for presentation from among the course organizers’ selections, or they may choose their own papers subject to approval by the course organizers. 

Thursday Jan 11.   Introduction to course. Selection/assignment of dates and topics for individual student presentations.

 Thursday Jan 18.  

Copy Number Variation and Fosmid End Sequence Analysis of Structural Variation

Background:

Eichler EE.  Widening the spectrum of human genetic variation. Nat Genet. 2006 Jan;38(1):9-11. (background).

Jeremy Purvis:

Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, et al. (2006) Global variation in copy number in the human genome. Nature 444:444-454

Rumen Kostadinov:

Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE.  Fine-scale structural variation of the human genome. Nat Genet. 2005 Jul;37(7):727-32. Epub 2005 May 15.

Thursday Jan 25.  

Logan Everett

Genome Wide Location Analysis

Tae Hoon Kim, Leah O. Barrera, Chunxu Qu, Sara Van Calcar, Nathan D.

Trinklein, Sara J. Cooper, Rosa M. Luna, Christopher K. Glass, Michael

G. Rosenfeld, Richard M. Myers, and Bing Ren.

"Direct isolation and identification of promoters in the human genome"

Genome Research May 2005 15:830-839.

Anthony Olarerin-George

Genome-wide functional analysis using RNAi

Kent Nybakken, Steven A Vokes, Ting-Yi Lin, Andrew P McMahon &Norbert Perrimon.  A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nature Genetics 37, 1323 - 1332 (2005).

Thursday Feb 1.

Kathleen Sprouffske

DNA re-sequencing and mutational profiling in Cancer

Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The consensus coding sequences of human breast and colorectal cancers. Science. 2006 Oct 13;314(5797):268-74. Epub 2006 Sep 7.

Perry Evans     

Protein Interaction Networks

Brian P. Kelley, Roded Sharan, Richard M. Karp, Taylor Sittler, David E. Root, Brent R. Stockwell, and Trey Ideker. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. PNAS 2003 Sep 30;100(20):11394-9.

Thursday Feb 8.

Na Rae Ju

Gene Expression Profiling and Cancer

Adam Ewing

HapMap and Association Studies

Cheung VG, et al. Mapping determinants of human gene expression by

regional and genome-wide association. Nature 437:1365-1369. (27 Oct.

2005)

And also for background, I will be covering some of the HapMap paper

so people should at least take a look at it.

The Int'l. HapMap Consortium. A Haplotype Map of the Human Genome.

Nature 437:1299-1320. (27 Oct. 2005)

Thursday Feb 15.  

Richard Dunbar

Biomarkers/Association studies

Kotowski IK, Pertsemlidis A, Luke A, Cooper RS, Vega GL, Cohen JC, Hobbs HH. A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol.
Am J Hum Genet. 2006 Mar;78(3):410-22. Epub 2006 Jan 20.

Tong Zhou

Genomics/Epigenomics

Honeybee Genome Sequencing Consortium. Insights into social insects from the genome of the honeybee Apis mellifera.

Nature. 2006 Oct 26;443(7114):931-49.

Wang Y, Jorda M, Jones PL, Maleszka R, Ling X, Robertson HM, Mizzen CA, Peinado MA, Robinson GE. Functional CpG methylation system in a social insect. Science. 2006 Oct 27;314(5799):645-7.

Thursday Feb 22.  

Thursday Mar 1.       

Thursday Mar 8.      Spring Break

Thursday Mar 15.  

Thursday Mar 22.

Thursday Mar 29.  

Thursday Apr 5.     

Thursday Apr 12.   

Thursday Apr 19