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  CSE 590CWi '11:  Reading & Research in Comp. Bio.
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 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 037 (schematic)
Organizers:  Elhanan Borenstein, Joe Felsenstein, Hamid Bolouri, Bill Noble, Su-In Lee, Larry Ruzzo, Martin Tompa
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to the organizers if you are unsure of our expectations.
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 Date  Presenters/Participants Topic Details
01/03---- Organizational Meeting ----
01/10Erick Matsen, FHCRCNew theory and code for the analysis of microbial communitiesDetails
01/24Miles; Felsensteinvon Neuman rejection samplingDetails
01/31Brandon; BorensteinEvolvability in metabolic networksDetails
02/07Rita, Elizabeth; RuzzodsRNA in ArabidopsisDetails
02/14Benjamin; NobleConservation of nucleosome positioningDetails
02/28James, Kris; TompaCoevolution in a transcriptional networkDetails
03/07Daniel; BolouriModENCODE analysis of C. elegansDetails

 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.  

01/03: ---- Organizational Meeting ----

01/10: New theory and code for the analysis of microbial communities -- Erick Matsen, FHCRC

   Abstract:   The human microbiome is the collection of microorganisms which live inside and on us; recent studies have established the centrality of the microbiome to human health. These studies raise a number of questions: Given a collection of samples from a single body location, which samples indicate a healthy versus unhealthy phenotype? Do these samples fall into natural "types" from which one can generalize? What are the "units" of microbial communities, and what are the significant synergistic and antagonistic interactions between microbes?

High-throughput sequencing technologies have opened the door to understanding these questions via sequencing of genetic material extracted in bulk from a collection of microorganisms. Statistical methods can be used to assign these fragmentary sequences to locations on a "reference" phylogenetic tree using information about the genomes of previously identified species; each sample thus results in a cloud of points on the reference tree. One can approach the above questions by developing statistical methods for comparing such clouds. From a probabilistic perspective, an appropriate comparative tool is the classical Kantorovich-Rubinstein metric (a.k.a. "earth-mover's distance"), which we have shown is a generalization of the "UniFrac" metric popularized in 2005 by microbial ecologists. One can define related clustering and ordination techniques which operate directly on the underlying clouds of points, rather than solely on a matrix of distances derived from the clouds. I will describe this theoretical work, as well as my OCaml software implementation, in the context of our project researching the microbiome of the human vagina. This is joint work with Steve Evans (UC Berkeley), Robin Kodner (UW), Ginger Armbrust (UW), Noah Hoffman (UW), David Fredricks (FHCRC), Sujatha Srinivasan (FHCRC), and Martin Morgan (FHCRC).

See the first two papers on The third is also relevant.

01/17:   -- Holiday

01/24: von Neuman rejection sampling -- Miles; Felsenstein

01/31: Evolvability in metabolic networks -- Brandon; Borenstein

02/07: dsRNA in Arabidopsis -- Rita, Elizabeth; Ruzzo

  • Q Zheng, P Ryvkin, F Li, I Dragomir, O Valladares, J Yang, K Cao, LS Wang, BD Gregory, "Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis." PLoS Genet., 6, #9 (2010) . [offcampus]

02/14: Conservation of nucleosome positioning -- Benjamin; Noble

02/21:   -- Holiday

02/28: Coevolution in a transcriptional network -- James, Kris; Tompa

  • D Kuo, K Licon, S Bandyopadhyay, R Chuang, C Luo, J Catalana, T Ravasi, K Tan, T Ideker, "Coevolution within a transcriptional network by compensatory trans and cis mutations." Genome Res., 20, #12 (2010) 1672-8. [offcampus]

03/07: ModENCODE analysis of C. elegans -- Daniel; Bolouri

  • MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng, BI Arshinoff, T Liu, KY Yip, R Robilotto, A Rechtsteiner, K Ikegami, P Alves, A Chateigner, M Perry, M Morris, RK Auerbach, et 117 al., "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project." Science, (2010) . [offcampus]

 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, 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

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Seattle, WA  98195-2350
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