(:cell:) TR 11:00am-12:15pm at CSB 325

(:table border=0 cellpadding=0 cellspacing=0:) (:cellnr:) Instructor   (:cell:) Asa Ben-Hur
Office: 448
Office Hours: By appointment. (:cellnr:) Lecture   (:cell:) TR 11:00am-12:15pm at Engineering E206 (:tableend:)

Textbook:

Also useful:

Neil C. Jones and Pavel A. Pevzner
An introduction to bioinformatics algorithms
MIT Press, 2004

We will also use:

Textbooks:

Prerequisites:

Prerequisites:

Course Outline

Neil C. Jones and Pavel A. Pevzner
An introduction to bioinformatics algorithms
MIT Press, 2004|| Attach:bioalgs.jpg Δ||

Richard Durbin, Sean R. Eddy, Anders. Krogh and Graeme Mitchison. Biological Sequence Analysis. Cambridge UP, 1998.

Midterm: TBA

• A primer in biology; computational problems arising in biology (week 1)
• Sequence alignment for DNA and protein sequences (weeks 2 – 4)
  • Concepts: homology, sequence similarity and sequence alignment; dynamic programming algorithms
  • Pairwise alignment
  • Global and local alignment using dynamic programming
  • Heuristic alignment methods: BLAST/FASTA and the statistics of local alignments
  • Multiple sequence alignment
    • Definition, scoring, techniques
    • Aligners for proteins sequences
    • Spliced alignment
• Motif finding in DNA and proteins (week 5)
• Hidden Markov models (HMMs) (week 6 – 8)
  • The basic HMM algorithms: forward, backward, Viterbi, Baum-Welch
  • Applications: CpG islands, gene finding, profile HMMs, pair HMMs
• Genome assembly (week 9)
• Analysis of high-throughput sequencing data (week 10)
• Phylogenetic analysis (week 11 – 12)
  • Why phylogeny?
  • Neighbor joining, parsimony, and maximum likelihood methods
• Comparative genomics: gene regulation, gene finding, genome rearrangements (week 13)
• High throughput biological data: microarrays, mass spectrometry, and protein-protein interactions (week 14)
• Student project presentations and class summary (week 15)

Some background in statistics and ability to program (R and matlab are good enough)

• Prerequisites:**
  

Textbooks:

Who, Where, When

Course Description

CS200 revisits and extends the principles of programming and discrete math that are introduced in CS161 and applies them to the development, analysis and implementation of data structures and efficient software. The course is taught using the Java language and emphasizes an object oriented approach to data structures. Specific topics in data structures/algorithms include advanced sorting, queues, stacks, hashing, trees, and graphs. Complementary topics from theory include recurrence relations, trees, and graphs. The course requires larger programs and team programming.

Topics

• Linear Data Structures: Stacks and Queues
• Advanced Sorting
• Trees
• Graphs
• Hash Tables
• Computational Complexity

Grading:

Assignments will be done individually, except selected programming assignments

Quizzes will typically be given during one lecture class each week, except those weeks in which a midterm exam is being given. No makeups will be given for quizzes, but two quiz grades will be dropped.

Class participation is strongly encouraged. Students who ask or answer a question during lecture will be given a chit (maximum of one per student per class session). Three chits earned translate into 10 additional points on the next quiz.

The assignment of letter grades will be made as follows:

NOTE: We will NOT cut higher than these points (but may cut lower).

Late and Makeup Policy

Midterm and Finals: Make-up exams are only given in extraordinary circumstances (e.g., illness, death of family member). Students must consult with the instructor as soon as possible, preferably before the start of the exam. Course examination dates are listed in the syllabus; be aware of them and plan accordingly.

No make-ups will be given for missed quizzes.

Programming assignments are to be submitted electronically using the checkin program. Always check the assignment page for due dates. Late assignments submitted within 48 hours of the time required (or otherwise specified) will receive a 20% late penalty. Electronic submission is closed 48 hours after assignments are due (or as otherwise specified); students not having submitted programs receive an automatic zero on the assignment.

Written assignments are to be submitted in class. These may be handwritten, but must be legible. The instructors and TAs reserve the right to decide whether or not a paper is legible. Late assignments are accepted in class on the first MWF after the original due date, and will receive a 20% late penalty.

Assignment will be returned within 5 working days of the end of the late period.

Important Dates

First Midterm: TBA

Second Midterm: TBA

Final Exam: TBA

All midterm exams are in the same room as the lecture.

Course withdrawal date:

Professional Conduct

All students are expected to conduct themselves professionally. We assume you are familiar with the policies in the student information sheet.

Additionally, you are (beginning) computing professionals, so you should be familiar with the code of conduct for the primary professional society, the Association for Computing Machinery (ACM).

We work to maintain an environment supportive of learning in the classroom and laboratory. Towards this end, we require that you be courteous to and respectful of your fellow participants (i.e., classmates, instructors, TAs and tutors). In particular:

• Please turn off the ring on your cell phone. If you are expecting an emergency call, sit near the door and slide out discretely to take it.
• If you plan to use a laptop during class, please sit at the back of the classroom and turn off any sound from the machine. The tap-tap of the keyboard and the images showing on a screen can be distracting to those sitting around you. Also, be aware if you IM during class, that giggles, snorts or other reactions to what you are reading can be heard by the class and instructors and may be completely inappropriate with what is going on in the classroom.
• Laptops and other personal computing devices must be shut during exams and quizzes.