SFU Computational Biology Seminar 2009-10

2009-2010 Computational Biology Seminar

We are happy to announce the return of the Computational Biology Seminar at SFU. We plan to meet roughly once a month to discuss interesting research topics in computational biology. This seminar is sponsored by BCID (Bioinformatics for Combating Infectious Diseases), CORDS (Centre for Operations Research and Decision Sciences) and IRMACS. Unless noted the talks will be at 3:30 on Thursday in the IRMACS Theatre, ASB 10900. Please contact Cenk Sahinalp or Tamon Stephen if you would like to speak.

Date Speaker Title and Abstract

June 3 Julien Allali

PIMS and CNRS A survey of RNAs secondary structures comparison

Abstract:
RNAs are one of the fundamental elements of a cell. It is the link between DNA and proteins but most of RNAs have a molecular function in the cell: proteins synthesis, genes regulation, mRNA maturation... Theses functions strongly depend on the spatial 3D shape of the molecule. Comparing RNAs secondary structures allows to detect similarity in both structure and sequence and thus is of major importance in RNomics.

After a short introduction on RNAs, I will detail the different models proposed for the secondary structure of RNAs and the corresponding pairwise comparison algorithms based on the edit distance and alignment principles. Next, I will do a quick review of the different tools available to compare secondary structure. I will conclude by describing a preliminary benchmark to evaluate these different tools.

March 11th Ugur Sezerman

Computational Biology Laboratory

Sabanci University Using Graph Properties to Identify Functional Domains in Protein Structures

Abstract:
Understanding the structural mechanism of protein function via structural comparisons have wide range of applications such as protein fold classification, protein structure modeling and design. Three dimensional structures of proteins can be represented by graphs. The similarities between protein structures can be found using attributed sub-graph matching algorithms using graph properties such as cliquishness and connectivity while taking into account the sequence similarity and secondary structure information. The structural alignments obtained are used to discover functional structural subunits called domains and to discover overall structural similarity of two proteins. We tested our domain prediction results on the existing domain recognition benchmark set and our global structural alignment results are compared with state of the art CE alignments.

March 4th Colin Collins

Vancouver Prostate Centre Personalized Medicine and Prostate Cancer

February 4th Dan Jupiter

Scott and White Hospital Recent Developments in Assessing Gene Ontology Term Enrichments

Abstract:
Gene Ontology enrichment testing is widely used in the analysis of high throughput biological data. We have recently developed a new test, TreeHugger, to perform these types of enrichment tests. In this talk the new method will be introduced, in the context of the many other types of enrichment testing already extant. The pros and cons of the various methodologies will be examined. Background on high throughput biology and data analysis, as well as on the ontology will be provided.

January 13th

Wednesday,
6 p.m.,
B.C. Cancer Research Centre Evan Eichler

Genome Sciences,
University of Washington

Human Genome Structural Variation, Disease and Evolution

This seminar meets as part of VanBUG at the B.C. Cancer Research Centre in Vancouver. Please see the VanBUG poster for details.

November 19th Can Alkan

Genome Sciences,
University of Washington

and

Howard Hughes Medical Institute Structural Variation Discovery and Characterization of Segmental Duplications with Next-Gen Sequencing Technologies

Abstract:
The realization of new ultra-high-throughput sequencing platforms such as Roche/454, Illumina/Solexa and ABI/SOLiD now makes it feasible to detect the full spectrum of genomic variation among many individual genomes, including cancer patients and others suffering from diseases of genomic origin. Recently we have developed a set of computational methods to comprehensively detect and characterize structural variation and segmental duplications using next-gen sequencing technology. We apply our algorithms to characterize structural variation and segmental duplications to genomes sequenced by Illumina and 454 technologies. We initially examine the genomes of three humans and experimentally validate copy-number differences in the organization of these genomes, and extend the application of our methods to study the genomes of >160 individuals sequenced as part of the 1000 Genomes Project.

October 22nd Inanc Birol

Genome Sciences Centre,
BC Cancer Agency Advances In Sequencing Technologies And De Novo Assembly Techniques

Abstract:
The read lengths and quality of sequences generated by the next generation sequencing platforms showed remarkable improvement since they were commercialized. In parallel, their throughput also increased. Illumina and SOLiD platforms notably yield about 5-fold coverage for human genome sequencing experiments in a single run. This is a significant milestone, as it represents the original coverage goal of the Human Genome Project.

The Assembly By Short Sequences (ABySS) software was primarily developed for assembling large genomes using reads generated by the Illumina platform. It is extended to assemble transcriptomes and to use data generated by multiple platforms.

Last modified September 14th, 2010.

Date	Speaker	Title and Abstract
June 3	Julien Allali PIMS and CNRS	A survey of RNAs secondary structures comparison Abstract: RNAs are one of the fundamental elements of a cell. It is the link between DNA and proteins but most of RNAs have a molecular function in the cell: proteins synthesis, genes regulation, mRNA maturation... Theses functions strongly depend on the spatial 3D shape of the molecule. Comparing RNAs secondary structures allows to detect similarity in both structure and sequence and thus is of major importance in RNomics. After a short introduction on RNAs, I will detail the different models proposed for the secondary structure of RNAs and the corresponding pairwise comparison algorithms based on the edit distance and alignment principles. Next, I will do a quick review of the different tools available to compare secondary structure. I will conclude by describing a preliminary benchmark to evaluate these different tools.
March 11th	Ugur Sezerman Computational Biology Laboratory Sabanci University	Using Graph Properties to Identify Functional Domains in Protein Structures Abstract: Understanding the structural mechanism of protein function via structural comparisons have wide range of applications such as protein fold classification, protein structure modeling and design. Three dimensional structures of proteins can be represented by graphs. The similarities between protein structures can be found using attributed sub-graph matching algorithms using graph properties such as cliquishness and connectivity while taking into account the sequence similarity and secondary structure information. The structural alignments obtained are used to discover functional structural subunits called domains and to discover overall structural similarity of two proteins. We tested our domain prediction results on the existing domain recognition benchmark set and our global structural alignment results are compared with state of the art CE alignments.
March 4th	Colin Collins Vancouver Prostate Centre	Personalized Medicine and Prostate Cancer
February 4th	Dan Jupiter Scott and White Hospital	Recent Developments in Assessing Gene Ontology Term Enrichments Abstract: Gene Ontology enrichment testing is widely used in the analysis of high throughput biological data. We have recently developed a new test, TreeHugger, to perform these types of enrichment tests. In this talk the new method will be introduced, in the context of the many other types of enrichment testing already extant. The pros and cons of the various methodologies will be examined. Background on high throughput biology and data analysis, as well as on the ontology will be provided.
January 13th Wednesday, 6 p.m., B.C. Cancer Research Centre	Evan Eichler Genome Sciences, University of Washington	Human Genome Structural Variation, Disease and Evolution This seminar meets as part of VanBUG at the B.C. Cancer Research Centre in Vancouver. Please see the VanBUG poster for details.
November 19th	Can Alkan Genome Sciences, University of Washington and Howard Hughes Medical Institute	Structural Variation Discovery and Characterization of Segmental Duplications with Next-Gen Sequencing Technologies Abstract: The realization of new ultra-high-throughput sequencing platforms such as Roche/454, Illumina/Solexa and ABI/SOLiD now makes it feasible to detect the full spectrum of genomic variation among many individual genomes, including cancer patients and others suffering from diseases of genomic origin. Recently we have developed a set of computational methods to comprehensively detect and characterize structural variation and segmental duplications using next-gen sequencing technology. We apply our algorithms to characterize structural variation and segmental duplications to genomes sequenced by Illumina and 454 technologies. We initially examine the genomes of three humans and experimentally validate copy-number differences in the organization of these genomes, and extend the application of our methods to study the genomes of >160 individuals sequenced as part of the 1000 Genomes Project.
October 22nd	Inanc Birol Genome Sciences Centre, BC Cancer Agency	Advances In Sequencing Technologies And De Novo Assembly Techniques Abstract: The read lengths and quality of sequences generated by the next generation sequencing platforms showed remarkable improvement since they were commercialized. In parallel, their throughput also increased. Illumina and SOLiD platforms notably yield about 5-fold coverage for human genome sequencing experiments in a single run. This is a significant milestone, as it represents the original coverage goal of the Human Genome Project. The Assembly By Short Sequences (ABySS) software was primarily developed for assembling large genomes using reads generated by the Illumina platform. It is extended to assemble transcriptomes and to use data generated by multiple platforms.