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  CSE 590CSp '10:  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 042 (schematic)
Organizers:  Joe Felsenstein, 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
03/29---- Organizational Meeting ----
04/05Xiaoyu ChenGenome-wide Analyses of Protein-binding Footprints and Transcriptional Regulatory ElementsDetails
04/12Martin TompaComparing genomic multiple sequence alignments 
04/19Larry RuzzoMyoD profiling with ChIP-seqDetails
04/26Su-In Lee - CSE & Genome SciencesMachine learning approaches for understanding the genetic basis of complex traitsDetails
05/03Elhanan Borenstein - Genome SciencesSystems Biology of Microbes and Microbiomes: Reverse Ecology, Super-Metabolism, and Metagenomic Analysis. 
05/10Benjamin DiamentSequencing a familyDetails
05/17Paul FearnTowards a Common Informatics Framework for BiorepositoriesDetails
05/24The 2010 CMB Spring Symposium: CSE 590c is preempted this week so everyone may attend the Fourth Annual CMB Spring Symposium. Seven Great Talks! All Afternoon! Coffee! Details here.

 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.  

03/29: ---- Organizational Meeting ----

04/05: Genome-wide Analyses of Protein-binding Footprints and Transcriptional Regulatory Elements -- Xiaoyu Chen
Several papers, including

  • JR Hesselberth, X Chen, Z Zhang, PJ Sabo, R Sandstrom, AP Reynolds, RE Thurman, S Neph, MS Kuehn, WS Noble, S Fields, JA Stamatoyannopoulos, "Global mapping of protein-DNA interactions in vivo by digital genomic footprinting." Nat. Methods, 6, #4 (2009) 283-9. [offcampus]

04/12: Comparing genomic multiple sequence alignments -- Martin Tompa

04/19: MyoD profiling with ChIP-seq -- Larry Ruzzo

  • Y Cao, Z Yao, D Sarkar, M Lawrence, GJ Sanchez, MH Parker, KL MacQuarrie, J Davison, MT Morgan, WL Ruzzo, RC Gentleman, SJ Tapscott, "Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming." Dev. Cell, 18, #4 (2010) 662-74. [offcampus]

04/26: Machine learning approaches for understanding the genetic basis of complex traits -- Su-In Lee - CSE & Genome Sciences

   Abstract:   Humans differ in many "phenotypes" such as weight, hair color and more importantly disease susceptibility. These phenotypes are largely determined by each individual's specific genotype, stored in the 3.2 billion bases of his or her genome sequence. Deciphering the sequence by finding which sequence variations cause a certain phenotype would have a great impact. The recent advent of high-throughput genotyping methods has enabled retrieval of an individual's sequence information on a genome-wide scale. Classical approaches have focused on identifying which sequence variations are associated with a particular phenotype. However, the complexity of cellular mechanisms, through which sequence variations cause a particular phenotype, makes it difficult to directly infer such causal relationships. In this talk, I will present machine learning approaches that address these challenges by explicitly modeling the cellular mechanisms induced by sequence variations. Our approach takes as input genome-wide expression measurements and aims to generate a finer-grained hypothesis such as "sequence variations S induces cellular processes M, which lead to changes in the phenotype P." Furthermore, we have developed the "meta-prior algorithm" which can learn the regulatory potential of each sequence variation based on their intrinsic characteristics. This improvement helps to identify a true causal sequence variation among a number of polymorphisms in the same chromosomal region. Our approaches have led to novel insights on sequence variations, and some of the hypotheses have been validated through biological experiments.

05/03: Systems Biology of Microbes and Microbiomes: Reverse Ecology, Super-Metabolism, and Metagenomic Analysis. -- Elhanan Borenstein - Genome Sciences

05/10: Sequencing a family -- Benjamin Diament

  • JC Roach, G Glusman, AF Smit, CD Huff, R Hubley, PT Shannon, L Rowen, KP Pant, N Goodman, M Bamshad, J Shendure, R Drmanac, LB Jorde, L Hood, DJ Galas, "Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing." Science, (2010) . [offcampus]

05/17: Towards a Common Informatics Framework for Biorepositories -- Paul Fearn

   Abstract:   Many biomedical research laboratories, departments and organizations struggle to manage data in biospecimen repositories that supply basic and translational research. Biorepository information systems have been developed from a variety of perspectives, and are often difficult to integrate or network within and across organizations due to lack of structural and semantic alignment with standards.

Biospecimen science is the study of the collection, processing and handling factors that affect the quality and characteristics of samples, including the their effects on the results and reproducibility of biological and biomedical investigations. To account and control for variation in samples, biorepository systems need to incorporate both workflow support and provenance information.

By leveraging existing and emerging best practices, data models, data exchange formats and vocabularies, informatics can facilitate and advance the quality and reproducibility of research. This paper reviews and synthesizes requirements and standards for biorepositories and biospecimen science, and proposes a common framework.


05/24:   -- The 2010 CMB Spring Symposium: CSE 590c is preempted this week so everyone may attend the Fourth Annual CMB Spring Symposium. Seven Great Talks! All Afternoon! Coffee! Details here.

05/31:   -- 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.
S-Star Bioinformatics Online Course Schedule, a collection of video primers
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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