Example 200-level Syllabus
BIOL 244 Genomics Fall 2009
Instructor:
Jodi Schwarz, Olmsted 313, Ext: 5266: joschwarz@vassar.edu
Lab Technician:
Barbara Holloway, baholloway@vassar.edu
Lab Intern:
Sam Woodle, sawoodle@vassar.edu
Text:
Genomes 3 by T.A. Brown. Garland Science. 2007.
Additional Readings: Primary literature and additional text chapters (all will be available as pdfs)
The Genome War by James Shreeve (purchase or borrow from me) --OR-The Making of the Fittest by Sean Carroll (purchase or borrow from me)
Meeting Times:
Office Hours:
M/W
10:30 – 11:45
Olmsted Hall 203
Th
1:30 – 5:30
SciVis OR Olmsted Hall 322
Note room locations on the syllabus!
M/W noon – 1:00, and by appointment
Summary: The past decade of biological science has experienced a revolution in which the development of “highthroughput” techniques have allowed scientists to begin thinking about biology from a genome-scale perspective. This
has had dramatic effects on how we think about biology, including questions that affect us personally, such as how we
understand human disease. In this course, we will learn what it means to think at a genome-scale and we will begin
thinking and working as Genomicists, exploring questions such as how whole genome projects are organized and run, the
structure and evolution of genomes, questions in microbial, eukaryotic, and ecological genomics, and questions in human
genomics. We will also take a field trip to Cold Spring Harbor Lab, a historical setting for genomics. By the nature of the
subject, this course will be integrative, moving across biological levels of organization from molecular to physiological to
ecological scales, and also focusing on in silico (computer-based) approaches for studying biological problems. I am really
excited to share this with you, and to help you train yourselves to become critical thinkers, genomic thinkers and
biologists. So, welcome!
Readings: There is no perfect textbook for this topic. Therefore, we will utilize one primary textbook (Genomes 3), but will
read selections from other textbooks, many research papers, several news accounts, and a novel. Links to pdfs of papers
and textbook chapters will be available on Blackboard. The Thursday Lab consists of 5 modules, and you will be able to
access the lab manuals and associated reading on Blackboard.
Class/Lecture time: The purpose of these sessions is to explore in detail the major topics in genomics, and master the
relevant foundational concepts, processes, and terminology. These sessions will consist of lectures and class discussions.
Major topics to be explored are listed in the first column of the schedule. Your mastery of these topics will be assessed
with 3 exams, many small assignments to be given throughout the semester, group discussions, and presentations.
Lab time: One of the goals of this class is to help you learn how to do genomics research, which includes both molecular
and in-silico (computational) techniques. As a result, we will be meeting in a wet-lab (OH322) for some of the lab sessions,
and in a computer lab the rest of the lab sessions (SciVis). The lab sessions together comprise 5 lab modules, each of
Example 200-level Syllabus
which will help you explore specific areas of genomics research, and also help you solidify a detailed understanding of the
larger topics in genomics.
Lab Modules:
1.
Human SNPs and Personal Genomics: exploring types of genomic variation among humans, understanding
different ways for detecting SNPS. Connections to disease and evolution.
2.
Comparative Pathogenomics of E. coli: Which genes transform non-pathogenic bacteria into pathogenic
strains? Visualization and analysis of whole genomes. Lateral gene transfer and genome evolution in prokaryotes
3.
Gene and Genome Annotation: Use of bioinformatic tools in DNA and protein research. Annotation of genes.
4.
Genomics of Aiptasia Symbiosis: Build on your expertise gained from the previous lab projects to design and
conduct a genomics experiment to examine a question on coral symbiosis, disease, or bleaching.
5.
The Human Genome Project / History of Genomics: Readings and Field trip to Cold Spring Harbor Lab
Your mastery of the SNP module, the Pathogenomics module, and the Gene Annotation module will be assessed with
short manuscript style lab reports at the end of each module. The Aiptasia Genomics Research Project will conclude with a
more extensive research paper and a group presentation. The Cold Spring Harbor Lab module will be discussion and
field-trip based, and will have a short essay-style report as the final assignment.
Note on scheduling: I have designed the syllabus according to the topics that I think are important to explore, as well as
the amount of time I expect that it will take to cover these topics adequately, but we may need to adjust the schedule
along the way. I left some “open” lecture times take up topics that we discover along the way, or to expand on topics that
we did not have a chance to fully explore. If any assignment dates are altered, we will discuss the revised due date in class.
Assignments
Points
3 exams (15pt each)
45
Lab: Human SNP assignment
5
Lab: Pathogenomics of E. coli assignment
5
Lab: Annotation of Mystery Gene assignment
5
Lab: Human Genome and CSHL assignment
5
Lab: Aiptasia Genomics Research Paper
15
Aiptasia Genomics Project presentation
5
Misc. lecture and lab assignments along the way
10
Participation (presence, enthusiasm, preparation, active discussion)
5
Academic accommodations are available for students with disabilities who are registered with the Office of
Disability and Support Services. Please schedule an appointment with me early in the semester to discuss any
accommodations for this course which have been approved by the Director of Disability and Support Services as
indicated in your DSS accommodation letter.