Download Seminar Poster

Presentation
Download Presentation

Download Movie

Talk Title:
What Really Happens When We Take a Drug?

Date/Time:
Thursday, April 12th, 2011, 6:00 pm

Affiliation:
Professor, Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego
Associate Director, RCSB Protein Data Bank and Adjunct Professor, Burnham Institute

URL:
Philip E. Bourne
The Bourne Lab

Abstract:
This is a question which, after generic clinical trials, is still very much answered by observing patient outcomes. Methods from bioinformatics and systems biology are making some inroads into answering this question more systematically through integration of a variety of data sources and important algorithmic developments. I will dig in to some of our work in this area, but if you cant wait refer to Xie et al. (2012) Annual Review of Pharmacology and Toxicology 52: 361-379. I’ll also describe the importance of open science to this collective effort.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 4:30-5:30pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings
Ten Simple Rules

——————————

Introductory Speaker:
Andrew McPherson, PhD candidate, Sahinalp lab, SFU and Huntsman lab, UBC

Title: Predicting the complex origins of chimeric transcripts using nFuse

Download Seminar Poster

Presentation
Download Presentation

Download Movie

Talk Title:
Integrated modeling of metabolic and regulatory networks

Date/Time:
Thursday, March 8th, 2011, 6:00 pm

Affiliation:
Associate Professor, Institute for Systems Biology, Seattle, WA

URL:
Nathan Price

Abstract:
To harness the power of genomics, it is essential to link genotype to phenotype through the construction of quantitative systems models. I will discuss approaches for the creation of such quantitative models that can simulate a variety of cellular functions. I will focus particularly on automated methods for integrating metabolic and regulatory networks such as our newly developed approach, Probabilistic Regulation of Metabolism (PROM) (Chandrasekaran and Price, PNAS, 2010). PROM is notable in that it represents the successful integration of a top-down reconstructed, statistically inferred regulatory network with a bottom-up reconstructed, biochemically detailed metabolic network, bridging two important classes of systems biology models that are rarely combined quantitatively. Additionally, I will discuss our new strategy to curate the inference of regulatory interactions from high throughput data using metabolic networks—providing multiple layers of biological context to the problem of regulation. Finally, I will describe our approach to building tissue and cell type specific metabolic models, which we have now done for 131 different cell types and tissues in the human body.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 4:30-5:30pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings
Modeling of genome-scale metabolic and regulatory networks

——————————

Introductory Speaker:
Evan Morien, MSc candidate, Pavlidis lab, CHiBi, UBC

Title: Genomic Expression Patterns in WIld Pacific Salmon

Download Seminar Poster

Presentation:
Download Presentation

Talk Title:
Microbial Genomics, Pangenomics, and Metagenomics in Disease and in Health

Date/Time:
Thursday, February 9th, 2011, 6:00 pm

Affiliation:
Bioinformatician, BCCDC Public Health Microbiology & Reference Laboratory

Abstract:
As DNA sequencing technologies continue to improve, sequencing of microbial genomes can now be done routinely. We have gone from a group of researchers spending years to generated and study one bacterial genome to an individual researcher comparing tens or hundreds of similar genomes at a time with the help of bioinformatic applications. Pangenomic analysis allows us to decipher how a bacterium evolves and how certain small mutations could have a large impact on disease outcome. In recent years, we have also started to sequence the genetic material directly isolated from a microbial community (microbiota) in order to bypass culturing. The International Human Microbiome Consortium and associated efforts are trying to decipher the interactions between our bodies and our microbiotas. The metagenomics approach allows researchers to study an entire microbial community in relation to health and diseases but new challenges arise on how to assign taxonomic and functional information to incomplete and sometimes novel sequences. With the increased scale of sequencing, new bioinformatics and statistical tools are needed to facilitate data process and interpretation. In this talk, I’ll discuss the progress and challenges of microbial genomic analysis with examples drawn from my own research and from literature. Through this talk, I wish to demonstrate that microbial genomics has benefit greatly from the technological improvements over the years and there is a bright future in applying microbial genomics to improve human health.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 4:30-5:30pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC

——————————

Introductory Speaker:
Warren Cheung, PhD candidate, Wasserman lab, CMMT

Title: Biomedical Topic Profiles from Bibliographical Literature Evidence

Download Seminar Poster

Talk Title:
Simulating and Predicting the MicroTargetome

Date/Time:
Thursday, December 8th, 2011, 6:00 pm

Affiliation:
Institut de Recherche en Immunologie et en Cancérologie and Département d’Informatique et de Recherche Opérationnelle, Université de Montréal

URL:
François Major

Abstract:
Protein output determines cell types and states. In animals, microRNAs (miRNAs) are key actors in controlling protein output. Mature miRNAs are about 22-nucleotide long. They are loaded in RNA-induced silencing complexes (RISCs), which bind to miRNA complementary sites in messenger RNAs (mRNAs) to repress their translation. Besides, recent studies indicate that various non-coding RNAs control protein output by competitive attraction of miRNAs. I will present an algorithm to predict the microTargetome, i.e. the RISC/mRNA matching, which considers all competing endogenous RNAs (ceRNAs). The model uses a free-energy of hybridization, and an algorithm that mimics miRNA competition and cooperation. Using this algorithm, we simulated the overexpression of single miRNAs in a specific cell line, and derived a series of biological consequences related to such a protein expression control system. MiRNA, ceRNA, and mRNA levels vary in different cell types and states, including cancer cells. Understanding and predicting microTargetome changes could thus bring insights into the role of RNA in cell differentiation, as well as in cancer development and progression.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 4:30-5:30pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings
MC-Fold and MC-Sym pipeline
Designing artificial RNAs
E2F/mir-20a autoregulatory feedback loop

——————————

Introductory Speaker:
Fong Chun Chan, MSc candidate, Gascoyne Lab, BC Cancer Research Centre

Title:
Detection of Differentially Expressed Alternative Transcripts using Conventional Microarrays

Download Seminar Poster

Presentation:
Download Presentation
Download Movie

Talk Title:
The ruin of gene network analysis by multifunctionality

Date/Time:
Thursday, November 17th, 2011, 6:00 pm

Affiliation:
Associate Professor, Department of Psychiatry, University of British Columbia and Member of the Brain Research Centre

URL:
Paul Pavlidis

Abstract:
A major goal of biology is to identify the functional relationships and interactions among genes and apply this knowledge to make predictive models. In bioinformatics, it is now routine to use various types of gene network and gene function information to interpret
high-throughput experiments. Examples include “GO enrichment”, network-motivated clustering or gene function prediction methods (e.g. “guilt by association”) and candidate gene prioritization methods. I will describe how a phenomenon we call “gene multifunctionality” distorts such analyses. Genes having high multifunctionality are the source of serious biases or artifacts that can distract attention from more interesting signals, cause
misleading results in algorithm evaluations, and generally make meaningfully applying known information on gene function extremely difficult. I will argue that this problem is ignored at our peril, and suggest some possible remedies and strategies for making progress.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion
of both science and career paths. This takes place 4:30-5:30pm in either
the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings
The impact of multifunctional genes on “guilt by association” analysis

——————————

Introductory Speaker:
Rebecca Worsley Hunt, PhD candidate, Wasserman Lab at Centre for Molecular Medicine and Therapeutics (CMMT)

Title:
Genome nucleotide composition and sequence length affect over-representation predictions of transcription factor binding sites in ChIP-based experiments

Download Seminar Poster

Download Presentation

Talk Title:
Haploid Assembly of Diploid Genomes

Date/Time:
Thursday, October 13, 2011, 6:00 pm

Affiliation:
Bioinformatics Group Leader, Genome Sciences Centre, BC Cancer Agency and Adjunct Professor, School of Computing Science, Simon Fraser University

URL:
Inanc Birol

Abstract:
Most assembly algorithms in use have an implicit assumption that a sequenced nucleic acid has a haploid-like structure, or at worst that the sequence representing a genomic location is present with a high similarity in the read data. This assumption holds nicely in the case of model organisms, which are usually inbred to reduce haplotypic
diversity, and is even not challenged significantly in the case of human samples because of an evolutionarily recent population bottleneck our species experienced. However, when an organism of interest has a diploid genome with a pronounced distance between haplotypes, or when an environmental sample is investigated that represents a collection of similar species, the assumption fails.

Furthermore, read lengths of popular high throughput sequencing technologies, and even the spatial associations brought by paired end reads are often not enough to completely de-phase the assembled sequences. In this talk, I will discuss the particular challenges one faces during de novo assembly of such datasets, and describe how we
approach to their solution within the ABySS framework.

ABySS is a short read assembly tool, particularly developed to address large scale assembly problems. I will introduce how it handles distance information to extend and scaffold contigs, and how it represents haplotypic information in its output. I will demonstrate its performance on the assembly of the mountain pine beetle genome.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion
of both science and career paths. This takes place 4:30-5:30pm in either
the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings
ABySS
Assemblathon 1

——————————

Introductory Speaker:
Olena Morozova, PhD candidate, Marra Lab, Genome Sciences Centre, BC Cancer Agency

Title:
A wide spectrum of somatic mutation in high-risk neuroblastoma

Presentation:
Download Presentation

Download Seminar Poster

Presentation:
Download Presentation
Talk Title:
Reconstructing Ancient Genome Architechtures

Date/Time:
Thursday, September 8, 2011, 6:00 pm

Affiliation:
Associate Professor of Mathematics, Simon Fraser University

URL:
Cedric Chauve

Abstract:
Paleogenomics aims at reconstructing the genomes of extinct species, whose DNA can not be sequenced due to molecular decay. Hence the only possible approach is the study of current genomes (i.e. descendants of these extinct species) to detect conserved features that might indicate ancestral genomic characters and then to assemble these characters into ancestral genomes. In this talk I will describe recent (successfull?) efforts to reconstruct the architecture of ancient vertebrate genomes, from placental mammalians to amniotes.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion
of both science and career paths. This takes place 5:00-5:45pm in either
the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings
Reconstructing ancestral genomes
Framework for reconstruction and application to mammalian genomes

——————————

Introductory Speaker:
Christian Frech, PhD candidate, Chen Lab, Simon Fraser University

Title:
Genome comparison of human and non-human malaria parasites reveals species-specific genes potentially linked to human disease

Download Seminar Poster

Make sure that your question gets answered by submitting by email to
dev@vanbug.org.

Panelists:
Benjamin Good, PhD, Postdoctoral Fellow, Genomics Institute of the Novartis Research Foundation
Inanc Birol, PhD, Bioinformatics Group Leader, Michael Smith Genome Sciences Centre, BC Cancer Agency & Adjunct Professor, School of Computing Science, Simon Fraser University
Anthony Fejes, MSc, Co-founder, Zymeworks and PhD candidate, Michael Smith Genome Sciences Centre, BC Cancer Agency
Phil Hieter, PhD, Professor of Medical Genetics, Michael Smith Laboratories, University of British Columbia

Bring your questions to the VanBUG Bioinformatics Careers Panel
Thursday, April 14, 6-7pm. Panelists include a recent Bioinformatics
Training Program graduate currently doing a post-doc at the Genomics
Institute of the Novartis Research Foundation, an entrepreneur who
co-founded Zymeworks, a computational biotech company, a sage academic
who has participated in many UBC hiring committees, and a bioinformatics
group leader from the largest bioinformatics employer in BC.

A 1-hour moderated panel discussion will be followed by networking over
pizza and refreshments.

Download Seminar Poster

Talk Title:
Transcription factor - DNA interactions: cis regulatory codes in the genome

Date/Time:
Thursday, March 17, 2011, 6:00 pm

Affiliation:
Associate Professor of Medicine and Pathology, Harvard Medical School

URL:
Martha Bulyk

Abstract:
The interactions between sequence-specific transcription factors (TFs) and their DNA binding sites are an integral part of the gene regulatory networks within cells. My group developed highly parallel in vitro microarray technology, termed protein binding microarrays (PBMs), for the characterization of the sequence specificities of DNA-protein interactions at high resolution. Using universal PBMs, we have determined the DNA binding specificities of >500 TFs from a wide range of species. These data have permitted us to identify novel TFs and their DNA binding site motifs, predict the target genes and condition-specific regulatory roles of TFs, predict tissue-specific transcriptional enhancers, investigate functional divergence of paralogous TFs within a TF family, investigate the molecular determinants of TF-DNA ‘recognition’ specificity, and distinguish direct versus indirect TF-DNA interactions in vivo. Further analyses of TFs and cis regulatory elements are likely to reveal features of cis regulatory codes important for driving appropriate gene expression patterns.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion
of both science and career paths. This takes place 4:30-5:30pm in either
the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.

——————————

Introductory Speaker:
Yvonne Li, PhD Candidate, Jones Lab, Genome Sciences Centre, BCCRC

Title:
A large-scale computational approach to finding new uses for existing drugs

Download Seminar Poster

Presentation:
Download Presentation
Download Movie *Note: There is a problem with the sound for the second half of the talk.

Talk Title:
Human genomics with large sample size and full genome sequences

Date/Time:
Thursday, March 10, 2011, 6:00 pm

Affiliation:
Professor of Population Genetics, Department of Molecular Biology and Genetics, Cornell University

URL:
Andrew G. Clark

Abstract:
The 1000 Genomes Project has completed its pilot phases including (1) low-coverage whole-genome sequencing of 179 individuals, (2) high-coverage sequencing of two mother–father–child trios; and (3) exon-targeted sequencing of 697 individuals from seven populations. These data present an unprecedented level of detail about the allele frequency spectrum and local haplotype structure of ~15 million SNPs, 1 M indels, and 20,000 structural variants across the human genome. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes. Data from the two trios produced an estimate of 1028 germline mutations per genome per generation. These data also present an opportunity to test for past signatures of natural selection and demographic effects. In a separate study we examined sequence variation in just two genes from the ARIC cohort study of 13,715 people. This analysis resulted in nearly 4x the expected count of singleton variants which were subsequently confirmed. These data are consistent with a very recent explosive population growth model that matches the historical and archeological record. The data are also consistent with the observation that each new full human genome that is sequenced typically finds upwards of 100,000 novel SNPs that are not yet in any database.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion
of both science and career paths. This takes place 4:30-5:30pm in either
the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings:
Human genome variation
Deep resequencing

——————————

Introductory Speaker:
Rodrigo Goya, PhD Candidate, Marra Lab, Genome Science Centre, BCCA & Meyer Lab, Centre for High-Throughput Biology (CHiBi), UBC

Title:
Characterizing alternative expression profiles in cancer samples using RNA-Seq