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GCB 531 Introduction to Genome Science

Course director: Dr. John Hogenesch

Email: hogenesc@mail.med.upenn.edu

Mondays and Wednesdays, 9-10:30 am, 1001 BRB II/III

This course serves as an introduction to the main laboratory and theoretical aspects of genomics and computational biology, and is divided into four themes: computational (statistics, computational biology, systems biology), genomes (genome science, evolution, and genetics), technology (DNA array analysis, proteomics, functional genomics), and applications. 

Preliminary Lecture Schedule:

Date

Instructor

Topic

Sept. 8

Ewens

General statistics

Sept. 10

Ewens

Statistical analysis of microarrays

Sept. 15

Hannenhalli

Computer models and comparative genomics

Sept. 17

Hannenhalli

Introduction to computer models and comparative genomics

Sept. 22

Kim

Computational analysis

Sept. 24

Kim

Systems approaches in biology

Class in 1101 BRB today only

Sept. 29

Riethman

Chromosome structure

Oct. 1

Riethman

Genome mapping and sequencing

Oct. 6

Riethman

Vertebrate genome sequencing and assembly

Oct. 8

Mid-term exam

Oct. 13

Fall break

Oct. 15

Hogenesch

DNA Microarray Technology

Oct. 20

Riethman

High-throughput Sequencing

Oct. 22

Spielman

Linkage analysis in humans / lod scores

Oct. 27

Spielman

Linkage disequilibrium and haplotype blocks

Oct. 29

Spielman

Complex genetic traits  and diseases

Nov. 3

Plotkin

Molecular evolution I

Nov. 5

Plotkin

Molecular evolution II

Nov. 10

Speicher

Proteomics I

Nov. 12

Speicher

Proteomics II

Nov. 17

Bucan

Functional genomics: forward genetic screens

Nov. 19

Hogenesch

Functional genomics: reverse genetic screens

Nov. 24

Hogenesch

Applications I: Functional genomics of circadian rhythms

Nov. 26

TBA

Applications II: Cancer genomics

Dec. 1

TBA

Applications  III: TBA: Computational Topic

Dec. 3

Review

Textbooks:  We suggest two textbooks as helpful resources for this course.  The first is "Discovering Genomics, Proteomics, and Bioinformatics", by Campbell and Heyer, structured on two principles: the first is to teach subjects in the context of an interesting question or application, and the second is deliver information on the “need to know” basis. The text is structured to build upon stories or case studies taken from the literature to drive home the various subjects we will teach this year. Within each chapter are "Discovery Questions" meant to stimulate critical thinking by the students. The text also stresses math and statistics, and has excellent online resources available: http://wps.aw.com/bc_campbell_genomics_2.  The second text is, "A Primer of Genome Science" by Muse and Gibson.  This book covers areas that are not covered by Campbell and Heyer (such as forward and reverse genetics), and may have other useful information to supplement material given in lectures.

Required readings and Homework:  As there is no required text, we suggest selected readings prior to lecturing.  Also, homework assignments make up 20% of the course grade, and should be assigned by each a lecturer after their seminars.   

Exams:  There will be both mid-term and final exams. The mid-term exam covers material in the first half of the semester and the final covers the material in the second half of the semester. The final assessment of each student takes into account both exam and homework performance.  Each exam will contribute 40%.