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Systems Biology Syllabus and Schedule

BIOL-GA 1128 - 001 New York University | Fall 2015
Th 3:30PM - 6:30PM Global Center (GCSL), 238 Thompson St., Rm. 284
Thursday, September 3, 2015 until Thursday, December 17, 2015

Prerequisites: Biocore I or by permission by instructor. No programming skills are required.

Christine Vogel Department of Biology
Email: Office: 403
Office hours: TBD Email Dr. Vogel for an appointment

Course goals and objectives:

Students will

Knowledge / Comprehension

1. Define the field of systems biology and its sub-fields

2. Identify large-scale methods used in systems biology research and their basic results
3. List limitations of current systems biology methods and needs for future development
4. Discuss examples of the latest research publications that mark the frontier of the field of
systems biology
5. Summarize lecture topics in the form of chapters for the e-SysBio book project

Application / Analysis

6. Interpret supplementary data from research publications

7. Criticize examples of recent research publications with respect to appropriateness of the
methods and interpretation of the results
8. Compare different systems biology approaches in their advantages and disadvantages
9. Compare recent research publications in their contributions to the field

Synthesis / Evaluation

10. Design mini-proposals that suggest next experiments to further elucidate the current knowledge
11. Evaluate each others mini-proposals

Course organization:
Class goal. As there is currently no textbook available which covers comprehensively what I
consider Systems Biology, our major goal is to start writing our own evolving textbook with the
lecture contents and a discussion of most relevant publications! This e-book will serve as a guide for
exam preparation and to train future generations of systems biologists. The book will evolve over the
next years.

General. The course comprises 13 lecture/discussion sessions, one midterm, one final exam, and
project work. Each session will start with a review of the class content from the week before, then
discussion of the class projects. The class projects include discussion of scientific publications, re-
analysis of systems biology datasets, and discussion of mini-proposals that use methods in the class

to enter new research areas. After a short break, we will have a lecture on the next topic. The lecture
will be given by the instructors and guest lecturers. There is no textbook as most topics are rapidly
evolving and we teach at the frontiers of current knowledge! The lectures will provide the background
to the projects and paper readings for the following week. This course will cover both methods and
results in the general field of systems biology. Note that while we do mention computational/
statistical/ mathematical methods, we place the emphasis on results and their impact on biology.
This class does neither require nor teach programming, as this is covered by plenty of other classes.

Expectations. Students are expected to attend classes unexcused absence will be noted.
Students are also expected to participate actively in ALL parts of the review/discussion and lecture
with questions and contributions from their own experience/reading. As a rule of thumb, this
participation should involve about one or two questions per discussion / lecture session per student.
All students are expected to review last weeks lecture material for questions and open issues. All
students are expected to hand in assignments/project work on time unless discussed otherwise.
Students who contribute to the evolving e-Book in a constructive and interactive way (outside the
assigned session) will receive bonus points. Over the entire term, each student is expected to
participate in one or two review session teams and one or two paper discussion teams (depending
on the total number of students signed up for the class).

Class attendance and participation 20%
Assignments, project work, and presentation 30%
Midterm 20%
Final exam 25%
Bonus (up to 5%)

Each class (180min) will consist of three parts that help students to acquire knowledge, review it
(from last week) and apply it (project work).

Lectures (~90min) - ACQUIRE KNOWLEDGE. Lectures will cover the topics listed below, subject to
minor modifications. Lectures will discuss the background to each topic, the scientific questions
involved, quantitative experimental approaches, and computational analysis techniques. The lectures
will also discuss major scientific and technological breakthroughs and remaining obstacles and

Towards a Systems Biology Wiki-Book (~45min) REVIEWING KNOWLEDGE. A team of two to

three students will review last weeks lecture and prepare a Wiki page on the respective topic, based
on the lecture content. The Wiki page will be reviewed and extended by all class participants. Each
page and topic discussion will be extended over the years, but this year, we will create a first draft.
Students are encouraged to work in a team to write this page, and to interact with the lecturer and
other classmates.

Project work (~45min) APPLICATION OF KNOWLEDGE. This time will be dedicated to applying
the knowledge gained in the lectures in various ways. We will discuss current papers relevant to the
lecture material, we will attempt to reanalyze supplementary data from publications, and work
towards new ideas in systems biology (mini-proposals). The goal of this lecture part is to help
students to truly understand the concepts and methods taught in the lectures, and to manifest this
knowledge through working with it.

Participation in discussion and lectures. Since there is no textbook, active participation in the
lectures, projects, and discussion is key to understanding the material. Interesting questions asked
by students count as much as comments on relevant papers that you may have read outside the
assignments. This course is taught at graduate level: you are responsible for your learning. If you do

not understand something, it is your obligation to ask about it. Each student is expected to read the
material assigned every week and participate in the discussions.

Midterm and final exam. Each exam will consist of brief questions (approximately 2 per session)
that cover the lecture and/or project work. Our goal is to have the e-book help with exam
preparations. The instructor will provide a set of training questions beforehand and a subset of these
will be on the exam. If you miss an exam, you must provide a documented medical excuse. If you
have a conflict with the exam date, you need to inform the lecturer as early as possible, AT LEAST
two weeks prior to the exam.

Tentative topics.

Project work - 3.30pm-4.45pm Lecture 5pm-6.30pm

3-Sep 1
Network Biology
10-Sep 2
Networks Genomics
17-Sep 3
Genomics Transcriptomics
24-Sep 4
Transcriptomics Translatomics
1-Oct 5
Translatomics Protein-Protein Interactions
8-Oct *** ***Midterm***
15-Oct 6
Protein-Protein Interactions Proteomics
22-Oct 7
Proteomics Phenomics
29-Oct 8
Phenomics Degradomics
5-Nov 9
Degradomics Metabolomics
12- 1
Nov 0 Metabolomics Systems Genetics
19- 1
Nov 1 Systems Genetics Dynamical Networks
Nov *** Thanksgiving
3-Dec 2 Dynamical Networks GWAS
10-Dec 3 GWAS Chromatinomics (Guest lecture)
17-Dec *** ***Final Exam***