IBIOS/BMMB 551: Genomics

Fall semester

10-10am-11:00am, Monday, Wednesday and Friday

UP: 108 Wartik Lab, HMC: Lecture Room D

Instructors and support

Position	Name	Title	Office	E-mail	Phone
Course coordinator	Loida Escote-Carlson	Asst Prof Biochem & Mol Biol	201 Life Sciences Building, UP	lje6@psu.edu	814 863 5751
Contact at HMC	Kathleen Marie Simon	Adminsitrative Asst II	H170 Office Of Graduate Education, HMC	ksimon@psu.edu kzs2@psu.edu	717 531 6608
Course supervisor, Instructor	Ross Hardison	T. Ming Chu Prof Biochem & Mol Biol	304 Wartik Laboratory, UP	rch8@psu.edu	814 863 0113
Instructor	Stephan Schuster	Assoc Prof Biochem & Mol Biol	314 Wartik Laboratory, UP	scs19@psu.edu	814 863 9278
Instructor	Hiroshi Akashi	Assoc Prof Biology	208 Mueller Lab, UP	aqa1@psu.edu akashi@psu.edu	814 865 5013
Instructor	Cooduvalli Shashikant	Assoc Prof Mol & Developmtl Biol	323 Ag Sci & Ind Bldg, UP	css13@psu.edu cshashikant@psu.edu	814 863 0658
Instructor	Keith C Cheng	Prof Path., Biochem, & Pharm., Coll. of Medicine	H059 Gittlen Cancer Res. I, HMC	kcc2@psu.edu kcheng@psu.edu	717 531 5635
Instructor	Laura Carrel	Asst Prof Biochem & Mol Biol, Coll. of Medicine	H171 Biochem & Mol Biology, HMC	lcarrel@psu.edu luc3@psu.edu	717 531 5419
Instructor	Kenneth Monrad Weiss	Evan Pugh Prof Anthropology & Genetics	523 Carpenter Bldg., UP	kenweiss@psu.edu kmw4@psu.edu	814 865 0989

UP = University Park

HMC = Hershey Medical Center

Required text

Readings assigned and provided via ANGEL site

Suggested text

Introduction to Bioinformatics, by Arthur Lesk

Course Description

This graduate course in Genomics deals with the structure and function of genomes including the use of some of the web-based tools and resources for studies and research in genomics. The course is taught by a team of faculty members active in genomics research from both University Park and Hershey (College of Medicine) campuses.

Course Objectives

The overall objective is to learn current information about the structure and function of genomes, to develop facility in the many web-based tools and resources for further studies and research in genomics, and to appreciate the power and limitations of current resources and knowledge. The material will be covered in several related sections.

1.1 Introduction (Schuster)

Students should learn what genomes are and major steps in determining genome sequences.

1.2. Microbial genome annotation and comparisons (Schuster)

Students will learn about the landscape and functional annotations of genomes using microbial genomes as examples. Comparisons of the genomes to better understand common and distinctive functions will be emphasized. New high-throughput technologies will be discussed.

2. Sequence comparison and tools for analysis (Hardison, Nekrutenko)

Students should learn the basic types of alignment strategies along with their features and limitations. They will be introduced to a suite of computational tools on Galaxy. Completing the assignment will give students experience with the multiple alignment programs and other analysis tools.

3. Evolutionary genomics (Akashi)

Students will learn how the application of evolutionary theory to sequence alignments gives insights into functions by providing signatures of negative or positive selection. Completing the assignment will give practical experience and introduce students to the complications of turnover of regulatory elements.

4. Genome structure of mammals (Hardison)

Readings and class presentations will teach students about the landscape and function of mammalian genomes. Multiple strategies for gene prediction will be explored. The genome landscape will surveyed for microbes and vertebrates. The power and limitations of interspecies alignments will be emphasized. In the assignments, students will use web-based resources to explore general and specific features of genomes, and for functional inference.

5. Functional genomics I: Mouse genetics and transgenetics (Shashikant)

Students will learn current techniques of mutagenesis and transgenic analysis in mice, including large-scale mutagenesis. The assignment gives the students the opportunity to integrate this information on a topic of interest.

6. Functional genomics II: Zebrafish and human genetics (Cheng)

Students will learn the power and potential of forward and reverse genetics for studies in developmental biology and in pathobiology, including cancer. Students will be expected to understand the rationale behind both forward and reverse genetic experiments, be able to design genetic screens and morpholino knock-down experiments, and understand the reason behind the use of the zebrafish as a "hub" model system for a new field: Systems morphogenetics. Students will also learn about the power and potential of the human polymorphism and haplotype data in the HapMap and related projects, with specific examples from skin pigmentation.

7. Epigenetics (Carrel)

Students will learn the importance of modifications to the genome, including DNA methylation and chromatin alterations, in determining the expression of genes, with special emphasis on the function of sex chromosomes.

8. Transcriptome analysis (Hardison)

Students will learn about conventional large-scale analysis of gene expression patterns using different kinds of microarrays and SAGE analysis. They will learn the rationale and features of applying the approaches of multivariant analysis to these large data sets.

9. Human evolutionary genomics and complex traits (Weiss)

Students will learn the impact of population structure and evolution on human genetics, and the opportunities and complications they bring to the mapping and analysis of complex traits. Some basic principles by which genes produce biological traits will be presented and illustrated by the development of the vertebrate dentition. Finally, this section explores the role that evolutionary theory plays as we face challenges to the nature and development of knowledge in genetics and genomics.

Course Requirements

Students are expected to attend and participate in class (questions, answers and discussion), read the assigned material, and complete reports on the assigned work. The instructor for each part of the course will assign problems or projects that give the student the opportunity to explore further the concepts, experimental work, analytical approaches and results that are being discussed in class. The assignments will frequently involve the use of web-based servers that are commonly used in genomics research. Other assignments require the student to assimilate and analyze material in the readings. Each student must write a report independently on their results from each assignment, and submit it through the ANGEL system. Grades on these reports will be the major determinant of the students’ grades; the other factor is participation in class. No examinations will be given; the written reports provide ample opportunity to evaluate student learning and development.

Course Prerequisites

A knowledge of basic genetics and molecular biology.

Grading Policy

Grades on reports from assignments: 75%

Class participation 25%

Total 100%

Attendance Policy

Class participation is essential to success in this class. With the six different instructors covering nine different topics, all with assigned readings and projects, it is difficult to imagine doing this without coming to class. Class time is an excellent time to get clarification and help on the assignments. It is also a good idea to let Dr. Hardison or Dr. Escote-Carlson know if you will miss classes, e.g. to go to a conference or other good reason.

Academic Integrity

All Penn State policies regarding ethics and honorable behavior apply to this course (see links below for policy statements).

Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational requirement of this institution. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students. For any material or ideas obtained from other sources, such as the text or things you see on the web, in the library, etc., a source reference must be given. Direct quotes from any source must be identified as such. All written reports must be your own.

To elaborate on that last point, you will be writing several (about nine) reports on projects and assignments during the course. It is permitted, even encouraged, for you to do the assigned work with fellow students and discuss and compare the results. This is a good way to learn from each other. However, once you have done the assigned work and it is time to write the report, DO IT YOURSELF. Do not ask to see another student’s report, but rather take this opportunity to communicate to the instructor what YOU learned, and IN YOUR OWN WORDS. Many students are tempted to just cut an paste text from an article they read as an answer in the report. This is technically permitted, but if you do so, you MUST cite the source of that text in the report. However, it is not a good idea. Forcing yourself to say it in your own words is the way to really learn and deeped your understanding.

Any instances of academic dishonesty will be pursued under the University and Eberly College of Science regulations concerning academic integrity. Penalties for academic dishonesty range from an official warning to an assignment of "F" by the course instructors or "XF" by Judicial Affairs as the final grade for the student.

Refer to the following URLs for further details on the academic integrity policies of the Eberly College of Science and the University:

http://www.science.psu.edu/academic/Integrity/Policy.htm

http://www.psu.edu/ufs/policies/

Examination Policy

The written reports are the main source used to evaluate student learning, development and performance. No additional examinations will be given.