image University of Washington Computer Science & Engineering
  CSE 590CSp '12:  Reading & Research in Comp. Bio.
  CSE Home   About Us    Search    Contact Info 

 Course Info    CSE 590C is a weekly seminar on Readings and Research in Computational Biology, open to all graduate students in computational, biological, and mathematical sciences.
When/Where:  Mondays, 3:30 - 4:50, EEB 031 (schematic)
Organizers:  Elhanan Borenstein, Joe Felsenstein, Larry Ruzzo, Martin Tompa
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to the organizers if you are unsure of our expectations.
 Email
cse590cb@cs.washington.edu Course-related announcements and discussions
  Manage Your Subscription List Archives
compbio-seminars@cs.washington.edu Biology seminar announcements from all around campus
  Manage Your Subscription List Archives
compbio-group@cs.washington.edu Computational biology discussions, conference/job postings, etc.,
  Manage Your Subscription List Archives
 Schedule
 Date  Presenters/Participants Topic Details
03/26---- Organizational Meeting ----
04/02Daniel JonesAccurate isoform quantification with RNA-Seq 
04/09Max LibbrechtUbiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elementsDetails
04/16John EarlsOGNAC: Oh God, Not Another Classifier -- A generative model for supervised learning of discriminatively perturbed biological networks from transcriptomics. 
04/23Huei-Hun Elizabeth TsengUsing RNA secondary structure to improve phylogenetic tree estimation 
04/30Tomer Hertz, FHCRCSequence similarity through the prism of the adaptive immune system 
05/07Christopher MilesImprovements in Protein Structure Prediction for CASP 10 
05/14Erick Matsen, FHCRCSometimes something fun happens when you are trying to do something practical: two optimization problems on trees. 
05/21The Sixth CMB Spring Symposium
05/28Holiday

 Papers, etc.

  Note on Electronic Access to Journals

Links to full papers below are often to journals that require a paid subscription. The UW Library is generally a paid subscriber, and you can freely access these articles if you do so from an on-campus computer. For off-campus access, follow the "[offcampus]" links below or look at the library "proxy server" instructions. You will be prompted for your UW net ID and password once per session.  


03/26: ---- Organizational Meeting ----

04/02: Accurate isoform quantification with RNA-Seq -- Daniel Jones

04/09: Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements -- Max Libbrecht
Joint work with Anshul Kundaje*, Sofia Kyriazopoulou-Panagiotopoulou*, Max Libbrecht*, Cheryl L. Smith, Debasish Raha, Steven M. Johnson, Michael P. Snyder, Serafim Batzoglou and Arend Sidow

04/16: OGNAC: Oh God, Not Another Classifier -- A generative model for supervised learning of discriminatively perturbed biological networks from transcriptomics. -- John Earls

04/23: Using RNA secondary structure to improve phylogenetic tree estimation -- Huei-Hun Elizabeth Tseng

04/30: Sequence similarity through the prism of the adaptive immune system -- Tomer Hertz, FHCRC

05/07: Improvements in Protein Structure Prediction for CASP 10 -- Christopher Miles

05/14: Sometimes something fun happens when you are trying to do something practical: two optimization problems on trees. -- Erick Matsen, FHCRC

05/21:   -- The Sixth CMB Spring Symposium

See link for details. The subsumes CSE 590C this week.

05/28:   -- Holiday

 Other  Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Applied Math Department Mathematical Biology Journal Club
Biostatistics Seminars
Microbiology Department Seminars

 Resources Molecular Biology for Computer Scientists, a primer by Lawrence Hunter (46 pages)
A Quick Introduction to Elements of Biology, a primer by Alvis Brazma et al.
A very comprehensive FAQ at bioinformatics.org, including annotated references to online tutorials and lectures.
CSE 527: Computational Biology
CSE 590TV/CSEP 590A: Computational Biology (Professional Masters Program)
Genome 540/541: Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis

CSE's Computational Molecular Biology research group
Interdisciplinary Ph.D. program in Computational Molecular Biology


CSE logo Computer Science & Engineering
University of Washington
Box 352350
Seattle, WA  98195-2350
(206) 543-1695 voice, (206) 543-2969 FAX