Student abstracts chosen for oral presentations:

• Annie Chiang, Genetics, University of Iowa, Phylogenetic profile of human disease genes
• Garrett Dancik, BCB, Iowa State, Computer simulations of Leishmania infection: a tool for understanding host susceptibility to L. amazonensis
• Marijn de Jong, Molecular Biology, New Mexico State University, Plant-fungal symbiosis and heavy metal tolerance: microarray based analysis of fungal transcription after cadmium exposure
• Matthew Moscou, BCB, Iowa State, Markermaker: an iterataive algorithm for optimization of fit between expression level polymorphisms and genetic marker datasets
• Ahmed Moustafa, Genetics, University of Iowa, Computational approach to predict Interferon Regulatory Factor 6 (IRF6) targets
• Sally Pias, Biochemistry, New Mexico State University, Modeling the structural consequences of zinc-site mutations in the cell cycle regulatory protein Mob1A
• Yves Sucaet, BCB, Iowa State, A stochastic simulation program for metabolic pathways

• Kishore Nannapaneni, Biomedical Engineering, University of Iowa, Computational identification of operon-like candidates in Drosophila melanogaster and
• Deepti Reddy, Bioinformatics Summer Institute, Iowa State, Predicting protein-protein binding sites using conservatism-of-conservatism

Second place winners in the poster competition, which included $25 prizes:

• Marijn de Jong, Molecular Biology, New Mexico State University, Plant-fungal symbiosis and heavy metal tolerance: microarray based analysis of fungal transcription after cadmium exposure and
• Ananth Kalyanaram, Electrical and Computer Engineering, Iowa State, Scaffolding genomic contigs using LTR retrotransposons

In a new competition this year, symposium participants were invited to vote for their favorite poster. The $50 People's Choice Award for best poster went to Adam DeLuca, Biomedical Engineering, University of Iowa, for UIMADS: a system for sharing and analyzing gene expression data in a collaborative environment.

Well done, everyone!

Sixth Annual Joint Bioinformatics Symposium (7/11/06 kmw)
The full schedule for the Sixth Annual Joint Bioinformatics Symposium to be held this Thursday evening and all day Friday, July 13-14, is now available online. We hope to see you there!

BCB Thesis Seminars (7/6/06 kmw)
BCB student Jianmin Wang (Computer Science Department, major professors Xiaoqiu Huang and Xun Gu) will present his PhD thesis seminar Computational studies of ESTs: assembly, SNP detection, and applications in alternative splicing at 2pm today, July 6, in 217 Atanasoff. Pete Vedell, double majoring in BCB and Math (Mathematics Department, major professors Zhijun Wu and Robert Jernigan) will present his PhD thesis seminar Boundary value approaches to molecular dynamics simulation at 1:30pm Monday, July 10, in 390 Carver Hall. Good luck to both of you!

Sixth Annual Joint Bioinformatics Symposium Update (6/30/06 kmw)
You can still register for the conference to be held July 13-14 on the ISU campus. Abstracts already submitted are being reviewed and oral presenters will be announced soon. Abstracts submitted now cannot be considered for oral presentation, but will be included in the conference booklet if submitted by July 4. First, second and third place prizes will be awarded for the best posters, and a special "People's Choice" award also will be presented. Press release

BCB Summer Institute News (7/3/06 ts)
NSF sponsors very few summer institutes nationwide in Bioinformatics and one is held here at ISU. A series of mini-short course seminars, held in conjunction with the Institute, featured several BCB faculty members. Their presentations can be viewed by clicking on their names in the calendar located at: http://www.bioinformatics.iastate.edu/BBSI/course_schedule_2006.html .

On Monday, July 10, plan to attend two public seminars held in conjunction with the Institute:

Dr. Eric Vigoda, College of Computing, Georgia Institue of Technology, will speak on: "Pitfalls of Varying Substitution Rates for Phylogenetic Reconstruction ". His talk will take place in 1352 Gilman from 12 to 1 p.m. Here is the abstract on his talk:

Different genes often have different phylogenetic histories. Even within regions having the same phylogenetic history, the mutation rates often vary.  This motivates the study of phylogenetic reconstruction in heterogeneous settings.  We study the (im)possibility of reconstructing the underlying phylogeny when data is generated from a mixture of trees (same topology, different branch lengths).  We first show the pitfalls of popular methods on mixture distributions: inconsistency of maximum likelihood and slow convergence of BMCMC algorithms.  We then determine in which evolutionary models, reconstructing the tree topology, under a mixture distribution, is (im)possible.

We show that the following duality theorem holds for most substitution models. The model has either:
   (i) Ambiguity -- two different tree topologies can produce identical mixture distributions, and hence reconstructing the correct topology is impossible; or
   (ii) Linear tests -- there exist linear tests which identify the common tree topology for character data generated by a mixture distribution. The theorem holds for models whose transition matrices can be parameterized by open sets, which includes most of the popular models, such as Tamura-Nei and Kimura's 2-parameter model. The duality theorem (which is related to linear programming duality) relies on our notion of linear tests (related to linear invariants introduced by Cavender).

Dr. Soojin Yi, School of Biology, Georgia Institue of Technology, will speak on "Heterogeneity of molecular clock revealed by comparative genomics" from 4 to 5 p.m. in 1352 Gilman. The abstract:

Molecular clock is a widely tool in phylogenetics and molecular evolution. However several issues regarding the determinants and the accuracy of molecular clock remain controversial. We utilized recently obtained large scale genomic sequence data to investigate some of these topics. I will first demonstrate that molecular clocks are heterogeneous even within a genome, due to the differences in molecular origins of different mutations. This result reconciles several previous conflicting observations on mammalian molecular clock. Next, using comparative protein sequence data, we show that the degrees of 'dispersion' of protein molecular clocks in mammals vary among different functional categories.

July Birthdays (6/30/06; edited 1-4-07kmw)
Happy Birthday to all of our July celebrants - and to the US of A!

Srinivas Aluru, BCB chair
Kara Butterworth, IGERT alumna
Haitao Cheng, BCB
David Doty, BCB and IGERT
Yong Huang, BCB
Jie Li, BCB
Wiesia Mentzen, BCB alumna
Justin Schonfeld, BCB and IGERT alumnus
USA
Xiangyun Wang, BCB alumnus
Yufeng Wang, BCB alumna
Lei Yang, BCB

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