| title | layout |
|---|---|
Course Info |
page |
cbb752 (at) gersteinlab.org
(Please use this in preference to mailing individually the TFs or the instructors.)
| Name | Abbr | Office | |
|---|---|---|---|
| Mark Gerstein | MG | Bass 432A | contact.gerstein.info |
| Name | Abbr | Office | |
|---|---|---|---|
| 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 | |
| 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.
| Name | Abbr | Office | |
|---|---|---|---|
| Suchen Zheng | SZ | 100 College St (9/F) | suchen.zheng (at) yale.edu |
| Michelle Yu | MY | 100 College St (9/F) | michelle.yu (at) yale.edu |
| Yunzhe Jiang | YJ | 100 College St (9/F) | yunzhe.jiang (at) yale.edu |
| Donglu Bai | DB | 100 College St (9/F) | donglu.bai (at) yale.edu |
This term we will be using Piazza for class discussion. The system is highly catered to getting you help fast and efficiently from classmates and the TAs. Rather than emailing questions to the teaching staff, I encourage you to post your questions on Piazza.
Find our class page at: Link to Piazza (TBA)
The first lecture will be held on Mon. Jan 20th, 2025.
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% |
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.
Students may have questions concerning end-of-term matters. Links to further information about these regulations can be found below:
- http://catalog.yale.edu/ycps/academic-regulations/reading-period-final-examination-period/
- http://catalog.yale.edu/ycps/academic-regulations/completion-of-course-work/
- Brief presentation on how to cite correctly : http://archive.gersteinlab.org/mark/out/log/2012/06.12/cbb752b12/cbb752_cite.ppt
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
We are committed to creating a course that is inclusive in its design. If you encounter barriers, please let us know immediately so that we can determine if there is a design adjustment that can be made or if an accommodation might be needed to overcome the limitations of the design. We are always happy to consider creative solutions as long as they do not compromise the intent of the assessment or learning activity. You are also welcome to contact Student Accessibility Services to begin this conversation or to establish accommodations for this or other courses. We welcome feedback that will assist us in improving the usability and experience for all students.
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.