The Course Is Organized Into Three Segments Both Topically and in the Focus of In-Class

All,

Welcome to GCB534, Experimental Genome Science! We have organized the course to leverage two recent developments in higher education, online learning and active learning. We have developeda hybrid between the traditional lecture/discussion model and the reverse classroom model ( where some lectures are assigned as homework and given online. On days withrecorded lecture (most are 30 to 40 min.), thesewill be available in advance on Canvas ( We expect that you will have watched theselectures prior to class time. For most classes, you will also be assigned a paper to read, also on Canvas, and you should be prepared to discuss this paper in class.The first lecture (“The human genome project” for Wed Sept 4) is already posted, along with links to the readings. In addition a background lecture on

The course is organized into three segments both topically and in the focus of in-class activities. The first section of the course covers the human genome and large-scale genetics approaches and the in-class discussions and homework focus on reviewing the primary literature. The middle section of the course covers functional genomics methodology, and in class discussions and homework assignments focus on developing new questions and approaches from a foundation of existing work. The final section covers applications and advanced topics in genomics, and you will prepare a short grant proposal based on the NIH template.At the end of the class we will break the class into two “study sections” where you will review each other’s proposals.

Class time has been organized into two parts: lecture/review, and paper discussion/content creation. The first 15 min. of each class (or 30-40 minutes on in-class lecture days) will be lecture review. This is your opportunity to ask any questions you may have. After discussion, there may be a short quiz, which will either be self or peer graded. After this, we will break up into groups of different sizes on different daysfor the assigned paper discussion or in-class activity. The format here is flexible, and these discussions will take many different forms. This is your opportunity to develop your literature reading, synthesis, creativity, and presentation skills. This discussion time will take approximately 30-40 min. The course instructors will evaluate these assignments and give you feedback to help develop these important professional skills.

There will also be 2 exams and a final project. In addition, you will do two short (~8 minute) in-class presentations based on papers you select yourself and will turn in one written paper review. Your final grade will be a combination of your classroom participation (1/4) and your exams (1/4), your grades on presentations and written assignments (1/4) and the final project (1/4).

We teach this class because we enjoy thinking about the latest advances across the field of Genomics and we hope to share this enthusiasm with you during the course. Welcome!

Sincerely,

Casey Brown, Harold Riethmanand John Murray

Key assignments and dates:

9/14/2015: Paper selection due. Papers must be approved by the faculty. You will likely work with the material in this paper throughout the semester as you develop their independent proposal, so choose a paper that is in an area that is significant and of interest to you.

9/21 or 23/2015: Journal ClubPowerPoint presentations

PowerPoint or pdfpresentations due the day before you will present (either 9/20 or 9/22)

Written reviews due 9/30

You will select a paper that uses experimental genomics techniques (note that a purely computational paper is not appropriate here; must involve some experiments). You will prepare both a 1 page written review of the paper as well as a short (8 minutes with 2 minutes for questions) PowerPoint “journal club”focusing on ONE major result from the paper.

10/5/2015: Exam 1 (based on lectures through 10/5)

10/12/2015: Prepare “Next steps” outline due for workshop (workshop discussion occurs in class on 10/12)

11/1 or 3/2015: “Next steps/Aims” presentation due (presentations on 11/2 and 11/4, powerpoint due day before)

You will come up with 2-3 independent but related questions raised by EITHER the paper you selected for the first presentations OR a new paper (can be related to but must be distinct from your own planned research project). You will briefly outline (< 1 page) possible experimental approaches using genomics methods to answer these questions. After work-shopping these ideas in class on 10/12, you will update and prepare a presentation (~12 minutes with 2 minutes for questions) on 11/2 or 11/4.

11/9/2015: Draft Aims due

You will further refine your ideas from the Next Steps presentation feedback to present a formal Specific Aims page in the NIH format. You will read some of your classmates’ Aims and give each other feedback during class on 11/18 to help in writing your Final Proposal.

11/16/2015: Exam 2(based on lectures from 10/12 through 11/11)

11/30/2015: Final Proposal due

You will write a short (1 page Specific Aims PLUS 1 page Significance and Innovation PLUS 2 pages Approach) proposal in the NIH format.

12/6/2014: Reviews and scores due

12/7/2015 and Finals period: Study Section

The class will be split into two “Study Sections” and each half of the class will read the proposals from the other half, scoring them on Significance, Innovation, Approach and Overall Impact using the NIH scoring system. In class, we will discuss the proposals and each member will score each proposal to generate a final ranking.

Draft schedule of topics:

Date / Topic
8/31/15 / DNA sequencing, basics of chromosome structure and function
9/2/15 / The human genome project
9/9/15 / Principles of genetics
9/14/15 / Introduction to next-gen sequencing methods
9/16/15 / Large-scale genomics projects
9/21/15 / Forward genetic screens
9/23/15 / Reverse genetic screens
9/28/15 / Clinical genetics and sequencing
9/30/15 / Genome Engineering
10/5/15 / In vivo/model organism genomics
10/7/15 / Exam 1
10/12/15 / RNA expression analysis
10/14/15 / ncRNA structure and function
10/19/15 / Epigenomics
10/21/15 / Genome Structure and Organization
10/26/15 / Transcriptional regulation
10/28/15 / eQTL analysis
11/2/15 / Cancer genomics
11/4/15 / Single molecule genomics
11/9/15 / Introduction to proteomics
11/11/15 / Advanced proteomics
11/16/15 / Exam 2
11/18/15 / Systems biology approaches
11/23/15 / Integrative genomics
11/30/15 / Single cell genomics
12/2/15 / Microbiome
12/7/15 / Study Section