The course will consist primarily of student presentations on topics in the syllabus. Presentations will be prepared with the help of the instructor. Students will help form the syllabus by choosing the topics they would like to present.
This course offers a great opportunity to explore cutting edge research work all across the field of computational biology, to critically read and discuss recent research work, and to practice presentation skills.
Office: Clark Center S266
Office hours: TBD
Meeting before your presentation: By appointment.
Phone: (650) 723-3334
Email: ude.drofnats@mifares (written backwards to avoid spam)
- Students taking the class for three units can choose to do either of the following:
- One presentation, one critique and two summaries
- Two presentations (if enough slots available)
- Students taking the class for two units can choose to do either of the following:
- One presentation and one critique
- One presentation and two summaries
- The attendance requirement applies to all students in the class.
Presentation. The main course requirement is to select a topic and give a presentation based on two papers on the topic. In general, students should pick a topic in the list given below, but if a topic that is of particular interest to you is not on the list, feel free to suggest it to the instructor and TA. The instructor and TA will meet with each student to help with the preparation, and ensure that the resulting presentation will be interesting and accessible to students in the class who are not experts in the given topic. Most of the topics have a strong algorithmic flavor, but some topics are more geared towards biology. Please send the slides in PDF to the TA on the day of your presentation. If you would like to present from PowerPoint, please send the slides in .ppt or .pptx format as well.
Critique. For this requirement, you should write a short critique of one of the papers that will be presented in lecture. The critique has to be written and submitted before the topic is presented in class. You will be assigned one class for the critique. You should choose one of the papers that will be presented during that class, read and understand the paper, and then write a critique. The critique should be 2 to 3 pages long (using a 12pt font and standard page setup). The critique must be submitted before class by emailing a PDF file to the TA. The critique should not just be a summary of the paper, but rather demonstrate critical thinking about the content of the paper. Points that can be discussed in the critique include the methodology used in the paper, the quality of the results and their validation, possible shortcomings, alternative approaches to solving the problem, ideas for the extension of the presented approach, and comparisons between the paper and other work in the area. You are encouraged to discuss ideas for your critique with the TA. Keep in mind that your critique constitutes an original text; verbatim copying from any sources is not allowed.
Summary. For this requirement, you need to select two lectures: one of class dates between 10/04 and 11/1, and one of class dates between 11/3 and 12/8. These two summaries will be due 11/5 and 12/9, respectively, before midnight. For each summary, you have to find one paper in addition to the ones presented; the paper must be related to the topic and relatively recent (published after 2007, with exceptions given for particularly interesting and relevant papers from earlier in this millenium). Then, you must write a single-page summary, with 1/3 of the page summarizing what the paper presents and 2/3 of the page discussing how it relates to the papers presented in class. Refer to the sample entry for examples of how the summary should look like in terms of format and structure. The summaries should be submitted by emailing a PDF file to the TA. You do not need to sign up for summaries. If you are not sure if a paper is suitable for a summary, or need other advice, feel free to contact the TA. Keep in mind that your summaries constitute an original text; verbatim copying from any sources (including the paper you are summarizing) is not allowed.
Attendance. As this is a seminar-style class, attendance is mandatory, and each student can miss up to two classes without affecting his/her grade. You are required to attend the full class period. We will circulate an attendance sheet during each class. If you came late or have to leave early, please mention so on the attendance sheet. It is a Honor Code violation to sign the attendance sheet on behalf of somebody else, or to ask somebody else to sign the attendance sheet if one is not attending the class, or to indicate that you attended the whole class if you missed a part of the class.
All preliminary topic choices will be posted by Tuesday, September 27. After 9/27, but no later than Friday, 9/30, you should send email@example.com:
- A list of five topics, in order of preference.
- A list of five presentation dates, in order of preference.
- A list of five dates for the critique (if applicable).
- Mention if you are taking the class for two or for three units, and which requirements you want to complete.
De novo assembly
Short read alignment
Alternative splicing and RNA isoforms
Sequencing extinct human ancestors
DNA sequence compression
MicroRNA Folding prediction algorithms
|Population genomics and evolution|
Identifying population structure and evolution
Signs of different types of selection
Comparative genomics and evolution
Evolution in dogs
Identity-by-descent inference and mapping
|Comparing multiple genomes|
Multiple genome alignment
Identifying biological interactions
Detecting significant network structures
Reconstructing signaling with bayesian inference
Deciphering cell differentiation
Game theory for social behavior and dynamics
Genome-wide association studies:methods and applications
Privacy in genome-wide association studies
Clinical risk from common variants and environmental factors
Identifying disease genes
Missing heritability in genome-wide association studies
Imputing missing data and haplotype phase
Dysregulated subnetworks in cancer
Finding cancer driver mutations
Tumor normal algorithms
Interpreting evidence for cis-regulation
Cell tracking using imaging
Self-assembly of DNA
|Serafim Batzoglou||No critique|
|4||10/6||Identifying biological interactions|
|5||10/11||Game theory for social behavior and dynamics|
|Laney Kuenzel||Abhinay Nagpal|
|6||10/13||DNA Sequence Compression|
|Michael Chung||Simon Ye|
|7||10/18||Reconstructing signaling with bayesian inference|
|Juthika Dabholkar||Michael Chung|
|8||10/20||Genome-wide association studies and heritability|
|9||10/25||MicroRNA Folding prediction algorithms|
|George Michopoulos||Juan-Carlos Foust|
|10||10/27||Short read alignment|
|Jaehyun Park||Rifat Joyee|
|12||11/3||Privacy in genome-wide association studies|
|Yongwhan Lim||Bob Arrigo|
|13||11/8||High-throughput population genetics|
|Juan-Carlos Foust||Kevin Dalton|
|15||11/15||Alternative splicing and RNA isoforms|
|Jesse Rodriguez||Serene Kosaraju|
|16||11/17||Detecting significant network structures|
|Serene Kosaraju||Jaehyun Park|
|17||11/22||No class (Thanksgiving Break)|
|18||11/24||No class (Thanksgiving Break)|
|19||11/29||Evolution in dogs|
|Abhinay Nagpal||Juthika Dabholkar|
|20||12/1||Finding cancer driver mutations|
|Rifat Joyee||Laney Kuenzel|
|21||12/6||Methods for detecting recent positive selection and what they can tell us about disease|
|Erik Corona (Guest Lecturer)|
|22||12/8||De Novo Assembly|
|Alex Morgan||George Michopoulos|
|Comparative Genomics and Evolution|
|Max Libbrecht||1 2 3 4 5||Daniel Newburger|