Math 290 Homepage, Fall 2002.
Hidden Markov models in comparative genomics
Email: lpachter@math.berkeley.edu
Phone: (510) 642-2028.
Meeting time: Wedensday 3-4:30pm in 939 Evans.
Course control number: 55212
The goal of the seminar will be to review papers about the applications of hidden Markov models in computational biology, and more specifically cocmparative genomics.
Links to papers:
August 28th: A tutorial on hidden Markov models and selected applications in speech recognition by L. Rabiner. This is a seminal paper on the basic HMM algorithms and their application (Lior Pachter).
September 11: Prediction of Complete Gene Structures in Human Genomic DNA by Chris Burge. Single organism gene finding (Lior Pachter).
September 18: GPHMMs: comparative gene finding and alignment (Simon Cawley).
September 25: Gibbs sampling: applications to alignment (Ingileif Hallgrimsdottir).
October 2: Joint seminar: Lior Pachter and Bernd Sturmfels on "Algebraic statistics and biology". Room change: 3106 Etcheverry
October 9: Graphical Models (Jon Macauliffe)
October 16: (Sourav Chatterji) Splice site detection.
October 23: A computational algebra approach to the modeling of biochemical networks (Reinhard Laubenbacher).
October 30: (Colin Dewey) Tree-HMMs.
November 6: (Katie Schwarz) MEME
November 13:(Nicolas Bray) MAVID: multiple alignment of genomic sequences
November 20: (Kushal Chakrabarti) Structural EM algorithm
November 27: Thanksgiving break
December 4: (Tae Sung Kim) cancelled
There will be no seminar on Wednesday Sept. 4