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  CSE 590CAu '09:  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 026 (schematic)
Organizers:  Joe Felsenstein, Bill Noble, 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
10/05---- Organizational Meeting ----
10/12Elizabeth (Tompa)New human genesDetails
10/19Sean (Noble)ProteomicsDetails
10/26Daniel (Felsenstein, Ruzzo)Phyogenies from CoalecencesDetails
11/02Wendy Thomas, BioengineeringComputational problems in bio-nano-mechanics 
11/09Luay Nakhleh, RiceAccurate Inference of Phylogenetic Relationships from Multi-locus DataDetails
11/16Elizabeth/Xinxia (Tompa)Short-read error correctionDetails
11/23Adrienne (Ruzzo)Genomic Mapping of Next Gen Seq readsDetails
11/30Xiaoyu (Noble)Indirect ChIP artifactsDetails
12/07Benjamin (Ruzzo)Novel ncRNAsDetails

 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.  

10/05: ---- Organizational Meeting ----

10/12: New human genes -- Elizabeth (Tompa)

10/19: Proteomics -- Sean (Noble)

10/26: Phyogenies from Coalecences -- Daniel (Felsenstein, Ruzzo)

11/02: Computational problems in bio-nano-mechanics -- Wendy Thomas, Bioengineering

11/09: Accurate Inference of Phylogenetic Relationships from Multi-locus Data -- Luay Nakhleh, Rice

   Abstract:   Accurate inference of phylogenetic relationships of species, and understanding their relationships with gene trees are two central themes in molecular and evolutionary biology. Traditionally, a species tree is inferred by (1) sequencing a genomic region of interest from the group of species under study, (2) reconstructing its evolutionary history, and (3) declaring it to be the estimate of the species tree. However, recent analyses of increasingly available multi-locus data from various groups of organisms have demonstrated that different genomic regions may have evolutionary histories (called "gene trees") that may disagree with each other, as well as with that of the species. This observation has called into question the suitability of the traditional approach to species tree inference. Further, when some, or all, of these disagreements are caused by reticulate evolutionary events, such as hybridization, then the phylogenetic relationship of the species is more appropriately modeled by a phylogenetic network than a tree. As a result, a new, post-genomic paradigm has emerged, in which multiple genomic regions are analyzed simultaneously, and their evolutionary histories are reconciled in order to infer the evolutionary history of the species, which may not necessarily be treelike. In this talk, I will describe our recent work on developing mathematical criteria and algorithmic techniques for analyzing incongruence among gene trees, and inferring phylogenetic relationships among species despite such incongruence. This includes work on lineage sorting, reticulate evolution, as well as simultaneous treatment of both. Further, I will describe our recent work on population genomic analysis of bacterial data, and the implications on the evolutionary forces shaping the genomic diversity in these populations.

11/16: Short-read error correction -- Elizabeth/Xinxia (Tompa)

11/23: Genomic Mapping of Next Gen Seq reads -- Adrienne (Ruzzo)

11/30: Indirect ChIP artifacts -- Xiaoyu (Noble)

12/07: Novel ncRNAs -- Benjamin (Ruzzo)

 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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