Contact Info

For general correspondence and questions, please contact us at:

cbb752 (at) gersteinlab.org

Instructor-in-Charge

Name Abbr Office Email
Mark Gerstein MG Bass 432A contact.gerstein.info

Guest Instructors

Name Abbr Office Email
Corey O’Hern CO Mason Laboratory corey.ohern (at) yale.edu
Jesse Rinehart JR West Campus jesse.rinehart (at) yale.edu
Matthew Simon MDS West Campus matthew.simon (at) yale.edu
Kei Cheung KC 300 George St kei.cheung (at) yale.edu
Martin Renqiang Min RM   renqiang (at) gmail.com
Dov Greenbaum DG   dov.greenbaum (at) gmail.com
Carl Zimmer CZ 266 Whitney Ave carl.zimmer (at) yale.edu

Consultation is available UPON REQUEST or according to times stipulated by the individual instructors. Prof. Gerstein’s office office hours will usually be right after some the classes.

Teaching Fellows (TF)

Name Abbr Office Email
Eric Ni EN Bass 437 eric.ni (at) yale.edu
Tianxiao Li TXL Bass 437 tianxiao.li (at) yale.edu

General Course Policy

First Meeting

The first lecture will be held on Wed. Jun 19th, 2022.

Grading Policy

We expect that this year the weighting scheme will be to a first approximation:

Category % of Total Grade
Quiz 1 15%
Quiz 2 15%
Discussion Section 20%
Homeworks 20%
Final Project 30%

Recording Policy

We will follow the default FAS policy on recording where the instructor’s lectures will be recorded, and student contributions in seminars and sections will not be recorded.

Relevant Yale College Regulations

Students may have questions concerning end-of-term matters. Links to further information about these regulations can be found below:

Useful Background Books & Websites

If you want to get more background for the course, here are some resources. All of the following textbooks you can access online through Yale’s e-library. Many of them cover the same material, but these should cover the core background that you need:

Essentials of Molecular Biology by Malathi V

important: chapters 1-5, 7, 11

recommended: everything else

Biochemistry: Essential Concepts by Hardin, Charles

chapters 1-6

For the class you can choose to do assignments in either R or python. Here are some resources for both:

The Python Tutorial - Official guide and documentation for Python3.

Learn Python with Google Colab - An interactive guide to python. Useful if you are familiar with basic programming, but not python language.

Learning Python: Powerful Object-Oriented Programming (5th edition) by Mark Lutz

The R book (2nd edition) by Michael J. Crawley

R for Data Science by Hadley Wickam

Plagiarism

Below is a message from the Dean of Yale College about citing your references and sources of information and plagiarism:

” You need to cite all sources used for papers, including drafts of papers, and repeat the reference each time you use the source in your written work. You need to place quotation marks around any cited or cut-and-pasted materials, IN ADDITION TO footnoting or otherwise marking the source. If you do not quote directly – that is, if you paraphrase – you still need to mark your source each time you use borrowed material. Otherwise you have plagiarized. It is also advisable that you list all sources consulted for the draft or paper in the closing materials, such as a bibliography or roster of sources consulted. You may not submit the same paper, or substantially the same paper, in more than one course. If topics for two courses coincide, you need written permission from both instructors before either combining work on two papers or revising an earlier paper for submission to a new course. It is the policy of Yale College that all cases of academic dishonesty be reported to the chair of the Executive Committee…. “

” Academic integrity is a core institutional value at Yale. It means, among other things, truth in presentation, diligence and precision in citing works and ideas we have used, and acknowledging our collaborations with others. In view of our commitment to maintaining the highest standards of academic integrity, the Graduate School Code of Conduct specifically prohibits the following forms of behavior: cheating on examinations, problem sets and all other forms of assessment; falsification and/or fabrication of data; plagiarism, that is, the failure in a dissertation, essay or other written exercise to acknowledge ideas, research, or language taken from others; and multiple submission of the same work without obtaining explicit written permission from both instructors before the material is submitted. Students found guilty of violations of academic integrity are subject to one or more of the following penalties: written reprimand, probation, suspension (noted on a student’s transcript) or dismissal (noted on a student’s transcript). “

Also, it might be of interest to people, to look at this recent article regarding academic dishonesty.