BENG202/CSE282 Home page (Winter 2012)

News and announcements

• No class on Wed Jan 11, make up class Friday Jan 13 @ 4pm in CSE 4217.

Contacts:

Instructor	Contact	Office hours
Nuno Bandeira, CSE, SSPPS	bandeira@ucsd.edu	Thu 4-5pm, CSE 4210, Jan 12th -Feb 9th
Terry Gaasterland, SIO	gaasterland@ucsd.edu	Thu 4-5pm, Feb 9th - Mar 8th
Christopher DeBoever (TA)	cdeboeve@ucsd.edu	By arrangement or email
Daria Merkurjev (TA)	dmerkurj@ucsd.edu	Fri 10am-noon

Homeworks

• Homework 1, due Monday Jan 23 @ 5pm (start of class).
• Homework 2, due Wed Feb 8 @ 5pm (start of class).
• Homework 3, due Wed Feb 22 @ 5pm (start of class).
• Homework 4, (updated 3/9/2012) see pdf at link for further instructions and due dates
  • data
  • By Wed Feb 29 @ 5pm, design expression comparison strategy
  • By Mon Mar 5 @ 5pm, map reads and perform expression comparisons

Project information

Textbook and Lecture slides

January 9, 2012	Class information
January 9, 2012	Finding Regulatory Motifs in DNA Sequences
January 11, 2012	Dynamic Programming: Edit Distance
January 18, 2012	Sequence Alignment
January 23, 2012	Multiple Alignment
January 25, 2012	Divide and Conquer algorithms
January 30, 2012	Graph algorithms and DNA sequencing
February 1, 2012	Tandem Mass Spectrometry: Peptide identification via database search, de novo sequencing
February 6, 2012	Tandem Mass Spectrometry: Generating function, alignment and assembly