02/24/2016 | Problem set 4 is out! It is due on 3/8 at the beginning of the lecture. |

02/10/2016 | Problem set 3 is out! It is due on 2/23 at the beginning of the lecture. |

01/26/2016 | Problem set 2 is out! It is due on 2/9 at the beginning of the lecture. |

01/12/2016 | Problem set 1 is out! It is due on 1/26 at the beginning of the lecture. I encourage you to start forming teams quickly and to start working on the homework ASAP. |

01/7/2016 | Students are encouraged to start forming homework groups. Let us know if you need some help. First assignment is coming up on January 12th! |

01/7/2016 | The Winter 2016 website for CS262 is up! Please sign up for Piazza here. |

*strongly recommended*:

CS161: Design and Analysis of Algorithms, or equivalent familiarity with algorithmic and data structure concepts.

Durbin, Eddy, Krogh, Mitchison: Biological Sequence Analysis

Makinen, Belazzougui, Cunial, Tomescu: Genome-Scale Algorithm Design

**Homework**. Course will be graded based on the homeworks, NO FINAL. The course will have four challenging problem sets of equal size and grading weight. These must be handed in at the beginning of class on the due date, which will usually be two weeks after they are handed out. Recognizing that students may face unusual circumstances and require some flexibility in the course of the quarter, each student will have a total of**three free**late days (weekends are NOT counted) to use as s/he sees fit. Once these late days are exhausted, any homework turned in late will be penalized at the rate of**20%**per late day (or fraction thereof). Under no circumstances will a homework be accepted more than three days after its due date.Late homeworks should be turned in to a member of the course staff, or, if none are available, placed under the door of S266 Clark Center. You must write the time and date of submission on the assignment. It is an honor code violation to write down the wrong time. Students with biological and computational backgrounds are encouraged to work together.

**Scribing**. Optionally, a student can scribe one lecture. Lecture notes will be due one week after the lecture date, and the grade on the lecture notes will substitute the two lowest-scoring problems in the homeworks. To ensure even coverage of the lectures, please sign up to scribe beforehand with one of the course staff.

Students may discuss and work on problems in groups of at most three people but must write up their own solutions. A student can be part of at most one group. If a student works individually, then the worst problem per problem set will be dropped. When writing up the solutions, students should write the names of people with whom they discussed the assignment. Also, when writing up the solutions students should not use written notes from group work.

Students are expected not to look at the solutions from previous years. Copying or intentionally refering to solutions from previous years will be considered an honor code violation.

**Lecture:**Tuesday and Thursday 1:30pm - 2:50pm in Y2E2 111

**Serafim Batzoglou**

Office: Clark S266

Office hours: By Appointment

Phone: (650) 723-3334

Email: ude.drofnats@mifares (written backwards to avoid spam)

**Ali Sharafat**

Office hours: Monday 10:00am - noon

Location: Shriram 052

Email: sharafat@stanford

**Bo Wang**

Office hours: Tuesday 3:00pm - 4:30pm

Location: Shriram 054

Email: wangbo.yunze@gmail

**Jason (Junjie) Zhu**

Office hours: Tuesday 3:00pm - 4:30pm

Location: Shriram 054

Office hours: Thursday 3:00pm - 3:30pm

Location: Clark S256

Email: jjzhu@stanford

All email correspondence should be sent to the course staff mailing list,

**cs262-win1516-staff@lists.stanford.edu**. Alternatively, you can communicate your questions in person after lecture or during office hours.