CS 234, Winter 2010: Computational Methods for the Analysis of Biomolecular Data
A staggering wealth of data has being ammassed by genome sequencing projects and other efforts to determine the structures and functions of biological systems. This advanced graduate course will focus on a selection of computational problems aimed at automatically analyze, cluster and classify biomolecular data.
Class Meeting
12:40 p.m. - 02:00 p.m. Engineering II room 139
Office hours
By appointment, please email me
Preliminary list of topics
overview on probability and statistics intro to molecular and computational biology analysis of 1D sequence data (DNA, RNA, proteins) combinatorial algorithms and statistical methods for pattern discovery and sequence alignment sequence alignment and hidden Markov models (HMM) analysis of 2D data (gene expression data and graphs) clustering algorithms classification algorithms subspace clustering/bi-clustering genetic networks, co-expression networks, metabolic networks, protein-protein interaction graphs
Prerequisites
CS141 (Algorithms) or CS218 (Design and Analysis of Algorithms) or equivalent knowledge. Some programming experience is expected. Students should have some notions of probability and statistics. No biology background is assumed.
Course Format
The course will include lectures by the instructor, guest lectures, and possibly discussion sessions on special problems. Students are expected to study the material covered in class. In addition to selected chapters from some of the books listed below, there may be handouts of research papers. There will be three/four assignments, mostly of theoretical nature -- although some may require programming. The actual format of the course will ultimately depend on the number and the background of the students enrolled.
Relation to Other Courses
This course is intended to complement "CS238: Algorithms in Computational Molecular Biology", and "CS235: Data Mining Concepts".
References (books)
Richard Durbin, A. Krogh, G. Mitchison, and S. Eddy, Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1999. Dan Gusfield, Algorithms on Strings, Trees and Sequences - Computer Science and Computational Biology, Cambridge University Press, 1997. Pierre Baldi, Soren Brunak, Bioinformatics: the machine learning approach, MIT press, 1998. Joao Setubal and Joao Carlos Meidanis Introduction to Computational Molecular Biology, PWS Publishing Co., 1997. Jason Wang, Bruce A. Shapiro, and Dennis Shasha, Pattern Discovery in Biomolecular Data Tools, Techniques, and Applications, Oxford University Press, 1999. David Mount, Bioinformatics: Sequence and Genome Analysis Cold Spring Harbor Laboratory Press, 2002 Dan E. Krane, Michael L. Raymer, Fundamental Concepts of Bioinformatics, Benjamin Cummings 2002 Warren J. Ewens, Gregory R. Grant, Statistical Methods in Bioinformatics: An Introduction, Springer, 2001 An Introduction to Bioinformatics Algorithms, Neil C. Jones and Pavel Pevzner, the MIT Press, 2004.
References (papers)
Anders Krogh, "An introduction to hidden Markov models for biological sequences" [PDF format] Brona Brejova, Chrysanne DiMarco, Tomas Vinar, Sandra Romero Hidalgo, Gina Holguin, Cheryl Patten. "Finding Patterns in Biological Sequences". Unpublished TR. University of Waterloo, 2000 [PDF format] Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi, Xuyan Xu, "Efficient Detection of Unusual Words", Journal of Computational Biology, vol.7, no.1/2, pp.71-94, 2000 [PDF format] Gesine Reinert, Sophie Schbath, Michael S. Waterman, "Probabilistic and Statistical Properties of Words: An Overview", Journal of Computational Biology, vol.7, no.1/2, 2000 [PDF format] Todd Mood, "The Expectation-Maximization Algorithm", IEEE Signal Processing Magazine, Nov 1996 [PDF Format] Jeff A. Bilmes, "A Gentle Tutorial of the EM Algorithm and its Applications to Parameter Estimation for Gaussian Mixture and HMM", UC Berkley, TR-97-021 [PDF Format] C. E. Lawrence, S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald, J. C. Wootton, "Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment", Science 262, 1993 [PDF Format] Jun S. Liu, Andrew F. Neuwald, Charles E. Lawrence, "Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies", Journal of the American Statistical Association, 90(432), 1995 [PDF Format]
Slides
Slides [PDF Format 2slides/page] (Course Overview) Slides [PDF Format 2slides/page] (Intro to Mol Biology) [updated Jan 26] Slides [PDF Format 2slides/page] (Sequence Analysis) Slides [PDF Format 2slides/page] (Indexing and Searching) Slides [PDF Format 2slides/page] (Bio Networks) Slides [PDF Format 2slides/page] (Microarrays)
Resources
The inner life of a Cell DNA Molecular animation A bioinformatics glossary What's a Genome (on-line book) DNA interactive Primer on Molecular Genetics PMP Resources
Projects
Project ideas and rules Doruk Sart's CS234 webpage Nkenge S. Wheatland's CS234 webpage Alex Edgcomb's CS234 webpage Jianbo Chen's CS234 webpage Busra Celikkaya's CS234 webpage Curtis Yu's CS234 webpage Dan Grissom's CS234 webpage Mohammad Farhan Habib's CS234 webpage Jesin Zakaria's CS234 webpage Sanjay Kulhari's CS234 webpage Md. Mahbub Hasan's CS234 webpage Ali Mirzabeigi's CS234 webpage Zhixing Jin's CS234 webpage Jarod Wen's CS234 webpage David Keith's CS234 webpage Xin Liu's CS234 webpage Thanawin (Art) Rakthanmanon's CS234 webpage Hanlung Lin's CS234 webpage Burair Al-Saihati's CS234 webpage Anton Polishko's CS234 webpage Denise Duma's CS234 webpage Aleksandr Levchuk's CS234 webpage Mehran Kafai's CS234 webpage Olga Tanaseichuk's CS234 webpage Katia Mkrtchyan's CS234 webpage Amirali's CS234 webpage Xiaoqing Jin's CS234 webpage Claire Huang's CS234 webpage
Homework
Homework 1 (posted Jan 12, due Jan 26) Homework 2 (posted Jan 28, due Feb 11) Homework 2 solution (by Y. Wu) Homework 3 (posted Feb 16, due Mar 2)
Midterm
Midterm 2009 (posted Feb 16)
Final report
Final report ideas and rules
Calendar of Lectures
Jan 5: Intro, Molecular Biology Jan 7: Molecular Biology Jan 12: Molecular Biology [hw1 posted] Jan 15: Molecular Biology Jan 19: Guest Lecture (Elena Harris) Jan 21: Molecular Biology Jan 26: Statistical Analysis of Sequences [hw1 due] Jan 28: Statistical Analysis of Sequences [hw2 posted] Feb 2: Statistical Analysis of Sequences Feb 4: Statistical Analysis of Sequences Feb 9: Statistical Analysis of Sequences Feb 11: Indexing for sequences[hw2 due] Feb 16: Indexing for sequences [hw3 posted] Feb 18: Indexing for sequences Feb 23: Indexing for sequences Feb 25: MIDTERM (in class, closed books, closed notes) Mar 2: Microarrays [hw3 due] Mar 4: Microarrays Mar 9: Networks Mar 11: Networks
Project Demo (20 minutes, in my office, please bring your laptop)
Mon, Mar 15
10:00 amirali
10:20 Alex
10:40 Han-lung Lin
11:00 Jian Wen
11:20 Busra Celikkaya
11:40 Burair Al-Saihati
Tue, Mar 16
10:00 Thanawin Rakthanmanon
10:20 Yu-Ting Huang
10:40 Ali Mirzabeigi
11:00 Mehran Kafai
11:20 Doruk Sart
11:40 Dan Grissom
Wed, Mar 17
10:00 Xin Liu
10:20 Olga Tanaseichuk
10:40 David Keith
11:00 Curtis Yu
11:20 Nkenge Wheatland
11:40 Sanjay Kulhari
Thu, Mar 18
10:00 Jesin Zakaria
10:20 Hasan
10:40 xiaoqing jin
11:00 Katya
11:20 Jianbo
11:40 Mohammad Farhan Habib