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Talk Title:
Recent advances in computer-aided drug design

Date/Time:
April 10, 2008, 6:00pm

Affiliation:
Faculty of Medicine, UBC

URL:
Artem Cherkasov

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Introductory Speaker:

Malachi Griffith

Talk Title:
ALEXA – a microarray design platform for alternative expression analysis

Affiliation:
Marra Lab, Genome Sciences Centre

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Talk Title:
Interactive Views for Navigating Ontologies and Data at the National Center for Biomedical Ontology

Date/Time:
March 13, 2007, 6:00pm

Affiliation:
Department of Computer Science, University of Victoria

URL:
Margaret-Anne Storey

Abstract:
The National Center for Biomedical Ontology is developing tools and methods for assimilating, archiving, and accessing machine processable representations of biomedical domain objects, processes, and relations. These tools will assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. The center involves the participation of scientific groups from a number of institutions including Stanford University, Lawrence Berkeley National Laboratory, the University of California at San Francisco, Mayo Clinic, and the University of Victoria. In this talk, I will present several research problems being addressed by the team at the University of Victoria. Broadly, our goal is to develop visual interfaces to assist in ontology annotation, mapping and management of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal. I will demonstrate visualization tools for browsing ontologies, mapping ontologies and browsing sets of clinical trials. As this talk reports work in progress at the National Center for Biomedical Ontology, I welcome
discussion and suggestions on the technology being developed by the center.

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Introductory Speaker:

Matthew Whiteside

Talk Title:
Improving ortholog identification

Affiliation:
Brinkman Lab, SFU

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Talk Title
Exploring ectopic expression in E.coli hybrid cells

Affiliation:
Genome Sciences Centre

URL:
Rob Holt

Abstract:
Engineered microbes are of great potential utility in biotechnology and basic research. For whole genome engineering, compatibilities of genetic material between microbes must be explored. We have developed a system for constructing large episomal elements in E.coli and have reassembled portions of the H.influenzae genome in an E.coli host, with the long term aim complete genome exchange. We have explored gene incompatibilities between E.coli, H.flu and other bacteria, and we have gathered extensive data on expression of exogenous DNA in E.coli that suggests cross-talk in gene regulation between E.coli and other organisms is extensive. These results will be discussed.

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Introductory Speaker:

Chi Kin Ho

Talk Title:
Computationally identifying novel essential genes, including non-coding RNAs, in intergenic sequences in bacterial genomes

Affiliation:
Brinkman Lab, SFU

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Talk Title:
Data Mining Methods for Learning Regulatory Modules from High-Throughput Data

Date/Time:
January 10, 2007, 6:00pm

Affiliation:
Simon Fraser University Computing Science Department

URL:
Martin Ester

Abstract:
The reconstruction of regulatory networks from high-throughput experimental data is one of the major challenges of current bioinformatics research. An important task toward this goal is the discovery of regulatory modules, consisting of a regulatory program, in particular a set of transcription factors, and a corresponding set of co-regulated genes. Genes can have different regulatory programs in different experimental conditions such as tissues and developmental stage, which implies that genes may not be co-regulated in all experimental conditions observed in comprehensive expression data sets. This has motivated the development of subspace clustering (biclustering) methods that find clusters of genes that have similar expression patterns in subsets of the set of all conditions. We present the KiWi algorithm, a novel subspace clustering algorithm that scales much better to large and high-dimensional datasets than existing algorithms. Different high-throughput d! ata such as cDNA microarrays, protein-protein interaction data and ChIP-Seq data reflect only partial information of the biological system from different points of view, and none of them can alone accurately reconstruct a regulatory network. Therefore, integrated approaches incorporating different types of experimental data are required. We propose a new approach to module discovery based on interaction network and expression data, finding dense subnetworks of genes that are co-expressed in large enough subspaces. The talk concludes with the discussion of future research directions.

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Introductory Speaker:

Olena Morozova

Affiliation:
Marra Lab, Genome Sciences Centre

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Talk Title
Rethinking Experimental Design in High-dimensional Biology

Date/Time:
December 13, 2007, 6:00pm

Affiliation:
Lewis-Sigler Institute for Integrative Genomics, Princeton University

URL:
John Storey

Presentation:
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Abstract:
In classical settings, a well-designed randomized study allows one to avoid confounding and potentially infer causality among variables of interest. High-dimensional biology brings a new set of challenges to this paradigm because thousands of highly related variables are considered simultaneously. In this talk, I will revisit the idea of well-designed randomized studies in the context of high-dimensional biology. First, I will demonstrate some problems that arise when a traditional randomized experiment is applied, and I will present a new technique called “surrogate variable analysis” for overcoming these problems. Second, I will show that a new experimental technique provides a powerful means for providing many local randomizations of “hardwired” components of the genome so that causal relationships among genes may be inferred on a large scale. I apply this technique to an experiment in yeast, showing how transcriptional regulatory networks may be inferred.

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Introductory Speaker:

Meeta Mistry

 
Talk Title:
Evaluating the Functional Similarity of Gene Pairs

Affiliation:
Pavlidis Lab, UBC

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Talk Title
Computational and Statistical Challenges in the Design of Genetic Association Studies

Date/Time:
November 8, 2007, 6:00pm

Affiliation:
Department of Computer Science, UCLA

URL:
Eleazar Eskin

Presentation:
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Abstract:
Variation in human DNA sequences account for a significant amount of genetic risk factors for common disease such as hypertension, diabetes, Alzheimer’s disease, and cancer. Identifying the human sequence variation that makes up the genetic basis of common disease will have a tremendous impact on medicine in many ways. Recent efforts to identify these genetic factors through large scale association studies which compare information on variation between a set of healthy and diseased individuals have been remarkably successful. However, despite the success of these initial studies, many challenges and open questions remain on how to design and analyze the results of association studies. In this talk, I will formulate association study design as an optimization problem where the goal is to design a study which maximizes the statistical power to detect genetic risk factors given a fixed budget. I will demonstrate how we can leverage the inherent correlation structure of variation in the human genome to design efficient association studies.

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Introductory Speaker:

Sohrab Shah

Talk Title
Detection of structural abnormalities in tumour genomes using model based approaches: application to 107 patients with follicular lymphoma.

Affiliation:
Department of Computer Science

URL:
Sohrab Shah

Presentation:
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Talk Title
Genomics Data Mining for Personalized Medicine

Date/Time:
October 11, 2007, 6:00pm

Affiliation:
Molecular Biology and Biochemistry, Simon Fraser University

URL:
Jack Chen

Abstract:
Understanding the mechanisms underlying life and causes of
most diseases demands a global view and understanding of genes in the
entire genome. The accomplishment of the Human Genome Projects and
success of many subsequent advances in genomics have made it possible to
examine the expression and function of many genes simultaneously.
However, the availability of these data sets and resources has not
provided immediate insight into the mechanisms underlying our lives, nor
has it provided cures to numerous devastating diseases. My laboratory is
interested in developing bioinformatics and genomics data mining
programs and in applying these programs in identifying novel genes,
structural variations, and regulatory mechanisms. The ultimate goal is
to understand, using combined computational and experimental approaches,
gene structure, function, and regulation in health and disease
conditions. Such understanding will eventually lead to the practice of
personalized medicine.

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Introductory Speaker:

Simon Chan

Talk Title
A Bioinformatics Meta-analysis of Differentially Expressed Genes in Colorectal Cancer

Affiliation:
Genome Sciences Centre, Jones Lab

Presentation:
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Talk Title
Large-scale mining of gene expression patterns

Date/Time:
September 13, 2007, 6:00pm

Affiliation:
Psychiatry Department, UBC

URL:
Paul Pavlidis

Presentation:
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Abstract:
In my group we focus our efforts at the intersection of bioinformatics and neuroscience. We have a special interest in expression analysis and how it can be used to improve our understanding of gene function in the nervous system. The possibilities presented by using the accumulated data in public archives are a major focus. Despite the availability of thousands of expression data sets, efforts to combine and contrast studies from different laboratories are just beginning. In my talk I will describe ongoing work in my lab to develop tools for expression data meta-analysis; describe some applications; and discuss how we are integrating RNA profiles with resources with a specific neuroscience focus. A beta version of our software system is available at http://www.bioinformatics.ubc.ca/Gemma.

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Introductory Speaker:

Asim Siddiqui

Talk Title
Personalized medicine in the ICU

Affiliation:
Sirius Genomics

URL:
Asim Siddiqui

Presentation:
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Date/Time:
April 12, 2007, 7:00pm

Affiliation:
NIH National Human Genome Research Institute

URL:
Eric Green

Description:
The first human genome sequence was published in April 2003. Since that
time, scientists from many disciplines have begun to develop
applications for predicting how medical treatments will affect individuals.

Internationally-renowned Dr. Eric Green, of the National Human Genome
Research Institute at the National Institutes of Health in Bethesda,
Maryland, will discuss his ongoing research. His work focuses on
unraveling the complexities of genome function through large-scale
comparative genomics, and seeks to understand the genetic basis for
certain human diseases. To date, his group has identified genes
associated with hereditary deafness, vascular disease, cancer, and
neurological disease.

About the speaker
Reporting directly to Dr. Francis Collins, Dr. Eric Green is the
Scientific Director of the Division of Intramural Research (DIR) at the
National Human Genome Research Institute (NHGRI). The DIR is a focal
point at the National Institutes of Health (NIH) for genome research and
maintains core facilities that serve as a resource for the entire NIH
intramural research community. In addition, Dr. Green serves as Chief of
the NHGRI Genome Technology Branch (since 1996) and Director of the NIH
Intramural Sequencing Center (since 1997).

Dr. Green received his B.S. degree in Bacteriology from the University
of Wisconsin-Madison in 1981, and his M.D. and Ph.D. degrees from
Washington University in 1987. Since the early 1990s, Dr. Green’s
research program has been at the forefront of efforts to map, sequence,
and understand eukaryotic genomes. His work includes significant,
start-to-finish involvement in the Human Genome Project.

co-sponsored with Genome BC

***Register online:
https://www.sporg.com/registration?link_type=form&form_id=77030&view_type=windowed

***Location:
Science World
1455 Quebec Street
Vancouver

***Date/Time:
Start Date: 04/12/2007
Start Time: 7pm (doors open at 6.30pm)
End Time: 8:30pm

Date/Time:
March 8, 2007, 6:00pm

Affiliation:
Swiss Institute of Bioinformatics

URL:
Amos Bairoch

Presentation:
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Meet with Amos Bairoch
You are invited to meet with Dr. Bairoch individually or as a group
(e.g. a lab visit), on Thursday, March 8 or Friday, March 9.
Individual meetings can be set up at at the UBC Bioinformatics Centre,
but it is also possible to schedule meetings for Dr. Bairoch at other
labs on the main UBC campus or off campus.

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Student Speaker:
Siddhartha Srivastava

Title:
D-GRIP: A genotype analysis system to predict genetic risk profile for an individual.

Presentation:
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