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 CSE 590 CB, Winter 1999
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 Course Info  

Reading and Research in Computational Biology
Wednesdays, 3:30-5:00, Loew 113

CSE 590 CB is an informal weekly seminar in Computational Biology, open to all graduate students in the computer, biological, and mathematical sciences.

Instructors:  Karp, Ruzzo, Tompa
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to instructors if you're unsure about our expectations, registrar-wise.

 Email/Bboard Email/Bboard Log (All mail sent to the seminar e-mail list, cse590cb@cs. Last: 09/30/99 at 08AM.)
 Schedule
Date Topic Presenters (Faculty Consultant) Papers
1/06 Organizational Meeting   
1/13 DNA ComputingTrey Ideker, Vibha Sazawal, Saurabh Sinha (Ruzzo) 1, 2, 3
1/20 Phylogeny: Split Decomposition Benno Schwikowski 4, Etc.
1/27 Phylogeny: Rearrangements Mathieu Blanchette 5, 6
2/03 Regulatory Networks Jeremy Buhler, Agatha Liu, Nitin Sharma, Ka Yee Yeung (Karp, Sengupta, Tompa) 7
2/108, 9
2/17 Single Nucleotide Polymorphisms Deborah Nickerson, MBT  
2/24 Multiplex SBH Agatha Liu, Nitin Sharma, Saurabh Sinha (Karp)  
3/03 Clustering Expression Array Data Amir Ben-Dor10
3/10 Gene Finding Max Robinson, Ken Yasuhara (Ruzzo) 11, 12

 Papers
  1. @article{adleman:computation, author={Adleman, L.}, title={Molecular Computation of Solutions to Combinatorial Problems}, journal=science, volume=266, year=1994, pages={1021}}

  2. @article{lipton:sat, author={Lipton, Richard J.}, title={{DNA} Solution of Hard Computational Problems}, journal={Science}, volume=268, month="28 " # apr, year=1995, pages={542-545}}

  3. @article{agd:dnacomp, author={Amos, Martyn and Gibbons, Alan and Dunne, Paul E.}, title={Toward Feasible and Efficient {DNA} Computation}, journal={Complexity}, volume=4, number=1, year=1998, pages={20-24}}

  4. @article{BandeltD92, author = {Hans-J{\"u}rgen Bandelt and Andreas Dress}, title = {Split Decomposition: {A} New and Useful Approach to Phylogenetic Analysis of Distance Data}, journal = {Molecular Phylogenetics and Evolution}, pages = {242-252}, year = 1992, month = Sep, volume = 1, number = 3, abstract = {In order to analyze the structure inherent to a matrix of dissimilarities (such as evolutionary distances) we propose to use a new technique called split decomposition. This method accurately dissects the given dissimilarity measure as a sum of elementary "split" metrics plus a (small) residue. The split summands identify related groups which are susceptible to further interpretation when casted against the available biological information. Reanalysis of previously published ribosomal RNA data sets using split decomposition illustrate the potential of this approach.}}

  5. David Sankoff, Mathieu Blanchette, "Probability Models for Genome Rearrangement and Linear Invariants for Phylogenetic Inference", RECOMB '99, to appear.

  6. Yun-Xin Fu, "Linear Invariants under Jukes' and Cantor's One-parameter Model," J. theor. Biol. (1995) 173, 339-352.

  7. Richard M. Karp, Roland Stoughton, Ka Yee Yeung, "Algorithms for Choosing Differential Gene Expression Experiments", RECOMB '99, to appear.

  8. A. Arkin, J. Ross, "Statistical Construction of Chemical Reaction Mechanisms from Measured Time-Series", J. Phys. Chem. (1995) 99:970-979.

  9. A. Arkin, P. Shen, J. Ross, "A Test Case of Correlation Metric Construction of a Reaction Pathway from Measurements", Science (1997) 277:1275-1279.

  10. Amir Ben-Dor, Zohar Yakhini, "Clustering Gene Expression Patterns", RECOMB '99, to appear.

  11. C.B. Burge and S. Karlin, "Finding the genes in genomic DNA", Current Opinion in Structural Biology (1998) 8: 346-354.

  12. M.S. Gelfand, A.A. Mironov, and P.A. Pevzner, "Gene recognition via spliced sequence alignment", PNAS (Aug 1996), 93: 9061-9066.
 Resources CSE 590 CB, Autumn, 1998.
Lecture notes from the two offerings of CSE 590 BI (Computational Biology).


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