GS559: Introduction to Statistical and Computational Genomics (Winter 2012)
Instructors:
Jim Thomas, jht@uw.edu
Elhanan Borenstein, elbo@uw.edu
Schedule: Tues. Thurs, 3:30-4:50, Hitchcock 220. First class Jan. 3, last class Mar. 9.
News:
» Remember: The final exam will take place in class, Thursday, March 8 (last class of the quarter). You are allowed to use any static resource (i.e., books, notes).
» Due to snow days the problem set schedule has changed - problem sets 3 and 4 will be merged (and shortened a bit) and will be available by Tues. Jan. 24 to give you extra time. The Python problems are MUCH harder so don't procrastinate.
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Lectures and Reading: |
# | Date | Lecture Topic | Programming Topic | Reading |
1 | 01/03 |
Overview of course. Introduction to sequence comparison. BLAST, alignment scoring | PDF,PP |
Introduction to Python. Interpreter, objects, types, variables, command line | PDF,PP |
[1, 2] |
2 | 01/05 |
Sequence alignment - dynamic programming | PDF,PP |
Strings | PDF,PP |
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3 | 01/10 |
Sequence alignment | PDF,PP |
Numbers, lists, tuples | PDF,PP |
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4 | 01/12 |
Sequence alignment - protein score matrices | PDF,PP |
File input-ouput, if-then-else | PDF,PP |
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5 | 01/17 |
Sequence alignment - signficance of similarity scores | PDF,PP |
For loops | PDF,PP |
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6 | 01/19 |
Signficance of similarity scores continued | PDF |
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7 | 01/24 |
Whole genome alignments, Sequence trees - introduction | PDF,PP |
While loops, More on loops, Programming efficiently | PDF,PP
PDF,PP |
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8 | 01/26 |
Sequence trees - distance trees | PDF,PP |
Dictionaries (hash maps) | PDF,PP |
[3] |
9 | 01/31 |
Parsimony | PDF,PP |
Functions | PDF,PP |
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10 | 02/02 |
Small parsimony | PDF,PP |
Functions as arguments, sorting | PDF,PP |
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11 | 02/07 |
Gene ontology and functional enrichment | PDF,PP |
More on functions, modules | PDF,PP |
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12 | 02/09 |
Gene set enrichment analysis | PDF,PP |
Recursion | PDF,PP |
[4] |
13 | 02/14 |
Gene expression: Clustring | PDF,PP |
Regular expressions | PDF,PP |
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14 | 02/16 |
Gene expression: K-mean clustring | PDF,PP |
More regular expressions | PDF,PP |
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15 | 02/21 |
Biological networks; Dijkstra algorithm | PDF,PP |
Classes and objects | PDF,PP |
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16 | 02/23 |
Degree distribution and network motifs | PDF,PP |
More on classes and objects | PDF,PP |
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17 | 02/28 |
Gene prediction | PDF |
Exceptions | PDF |
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18 | 03/02 |
Artificial neural networks | PDF,PP |
More on classes, Biopython | PDF,PP |
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19 | 03/07 |
Project | PDF,PP |
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20 | 03/09 |
Final Exam |
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References:
Electronic access to journals is generally free from on-campus computers. For off-campus access, follow the "[offcampus]" links or look at the library "proxy server" instructions.
- Noble, WS, "A quick guide to organizing computational biology projects." PLoS Comput. Biol. 5 (2009) e1000424. Pmid: 19649301 [Offcampus]
- Dudley, JT and Butte, AJ, "A quick guide for developing effective bioinformatics programming skills." PLoS Comput. Biol. 5 (2009) e1000589. Pmid: 20041221 [Offcampus]
- How dictionaries work (aka hash tables or hash maps)
- Subramanian et al., "Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles"PNAS102(43) (2005)
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Python Resources:
General
Regular Expressions
"RegExPal" (For Javascript rather than Python, but similar and quite handy. Try it!)
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Biopython
Python Books
Learning Python by Mark Lutz. O'Reilly (Very comprehensive. Much is accessible to beginners.)
Dive Into Python 3 by Mark Pilgrim. (Another online book. Based on Python 3, so some differences, and more advanced, but also free.)
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Bioinformatics Books
» Biological sequence analysis: probabilistic models of proteins and nucleic acids, R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Cambridge. (Excellent reference, classics)
» Inferring Phylogenies, Joseph Felsenstein, Sinauer, 2004. (Excellent reference on this topic.)
» Introduction to Computational Genomics: A Case Studies Approach, Cristianini, Nello & Hahn, Matthew, Cambridge, 2007.
» An Introduction to Bioinformatics Algorithms, Neil C. Jones & Pavel A. Pevzner, 2004.
» Bioinformatics: Sequence and Genome Analysis, David W. Mount, Cold Spring Harbor Laboratory Press.
» Python for Bioinformatics, Sebastian Bassi, CRC Press, 2010. (A little too advanced as a progamming book for beginners, but fine now that you're experienced.)
» Python for Bioinformatics, Jason Kinser, Jones and Bartlett, 2009. (Ditto.)
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James H. Thomas
Department of Genome Sciences
University of Washington
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Elhanan Borenstein
Departments of Genome Sciences
University of Washington
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