CS374: Algorithms In Biology


4/11: Topic and date assignments posted in the schedule.

3/30: Please email the following information by Sunday 4/3 (11:59pm)

  • Presentation preferences. Email staff *list* a list of five of the selected topics and five times to present, both in order of preference.
  • Whether you are taking the class for 2 or 3 units
Administrative information
  • Lectures: Tues/Thurs 1:30-2:50pm in Clark Center, room S361 (enter by going through Peet's Coffee on the third floor)
Instructor: Serafim Batzoglou (office hours: 3-4pm Tues and Thurs in Clark S266, email: ude.drofnats.sc@mifares)
Course assistants:
  • Alex Bishara (office hours: 12:30-1:30pm Tues and Thurs in Clark S260, email: ude.drofnats@arahsiba)
Contact: Please email staff *list* cs374-spr1516-staff (at) lists (dot) stanford (dot) edu to communicate with staff to set up appointments
Course content
Description: This course covers recent developments in computational algorithms applied to a large variety of problems in biology. We will discuss computational methods that are used in current research with sequencing technologies, genome assembly, functional genomics, disease association mapping, and more. The content of the course should be of interest to computer scientists and biologists alike.

The course will consist primarily of student presentations on topics in selected applications. Presentations will be prepared with the help of the instructor. Students will help form the class content 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.

Selected Topics and Papers
Assignment information
  • Meet with Serafim at least two weeks before presenting to discuss the papers and to outline the presentation. Make sure to read the papers carefully before the meeting.
  • Meet with one of the TAs at least one week before presenting to discuss your presentation outline.
  • Meet with one of the TAs at least two weekdays before presenting for feedback on a completed set of slides.
  • The presentation should be approximtely 40 minutes in length plus discussion.
  • Please send the slides in PDF format to the TAs 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.
  • Choose one paper from the assigned topic section to critique.
  • The critique should be 2 to 3 pages long (single-spaced, using a 12pt font and standard page setup). Please send in PDF
  • The assignment must be submitted to the TAs before the topic is presented in class.
  • Write summary one on a topic presented on or before 5/3. Due Tuesday, 5/3 (11:59pm).
  • Write summary two on a topic presented between after 5/3. Due Tuesday, 5/31 (11:59pm).
  • The summary should be 1 page long (single-space, using a 12pt font and standard page setup). Please send in PDF
  • You do not need to sign up for summaries; you just need to turn in each summary before its due date.
  • Write each summary on one paper related to a topic on the schedule. The summaries cannot be on one of the papers presented in class and cannot be on a topic that you are presenting or critiquing.
  • Please submit this assignment to the TAs in PDF format, with the filename formatted as lastname.topicnumber.pdf. Also, please attach a copy of the paper itself to the email.
Options for 3 units:
  • One presentation, one critique and two summaries
  • Two presentations (if enough slots available)
Options for 2 units:
  • One presentation and one critique
  • One presentation and two summaries

Attendance is required for all students in the class (only two unexcused allowed).

Honor Code: The Stanford Honor Code applies to every document you submit for this class. In particular, please be careful not to plagiarize the papers you are presenting or summarizing. Make sure that you always correctly cite your sources (for examples, when you show figures or use illustrations in your presentations). Summaries and critiques must be written using your own words, not by copying text from the respective papers. If you need to cite text verbatim from some source, always put it in quotes and mention the source. If you have any question about this, or in case of doubt, please contact the TA.

Topics (tentative list)
De novo assembly I
De novo assembly II (long reads)
De novo assembly III (molecular barcoding)
Read Alignment and Resequencing
RNA sequencing and transcript assembly/quantification
Compressive Genomics
Genome-Wide Association Studies with Mixed Models
Identity By Descent
Ancestry Inference
Single-cell RNA sequencing
Imputing Genotypes and Haplotype Phase
Functional Genomics

Week 1
  • 3/29: Course Logistics and Introduction
  • 3/31: Intro to Assembly I slides
Week 2
  • 4/5: Intro to Assembly II slides
  • 4/7: Sequencing Populations slides
  • Functional Genomics, Christine Tataru
  • Compressive Genomics, Richard Tang
  • Single-cell RNA Sequencing, Yuan Xue
  • Cancer, Mark Berger and
  • RNA sequencing and transcript assembly/quantification, Nimit Jain
  • Ancestry Inference, Kat Gregory
  • Imputing Genotypes and Haplotype Phase, Nico Chaves
  • Genome-Wide Association Studies with Mixed Models, Kai Kent
  • Read Alignment and Resequencing, Lauren Ellis
  • Metagenomics, Danielle Kain
  • Functional Genomics (p2), Dana Wyman
  • De novo Assembly II, Sheila Ramaswamy

5/10,5/12:Guest Lecture TBA

  • Ancestry Inference (p2), Sebastian Le Bras
  • Metagenomics (p2), Yuki Yoshiyasu
  • Read Alignment and Resequencing (p2), Ponan Li
  • IBD, Pavitra Rengarajan
  • Cancer (p2), Shirin Sadri
  • De novo Assembly III, Alec Tarashansky
  • Genome-Wide Association Studies with Mixed Models (p2), Kapil Kanagal
  • Imputing Genotypes and Haplotype Phase (p2), Joe Wan
  • Epidemiology, Russ Islam
  • Gene regulatory network inference, Russ Islam