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Vancouver Bioinformatics Users Group

VanBUG (Vancouver Bioinformatics Users Group) is an association of researchers, other professionals and students in the B.C. Lower Mainland who have an interest in the field of bioinformatics.

VanBUG meets on the second Thursday of every month from September through April. Research presentations by bioinformatics leaders, students and industry representatives are followed by networking over pizza and refreshments

Meetings are held in the Gordon and Leslie Diamond Family Theatre, BC Cancer Research Centre, 675 West 10th Avenue at 6:00 pm and are free and open to all.

As a service to the community, other bioinformatics events are posted to the Calendar
Visit our sister groups for bioinformatics events in Montreal (MonBUG) and now Toronto (TorBUG)!

next speakers:


Nick Loman

Talk Title:
“Genomes from metagenomes: new technologies and algorithms”

Date/Time:
Thursday, February 12, 2015. 6:00pm

Affiliation:
University of Birmingham, Inst. of Microbiology for Microbiology and Infection

URL: Nick Loman

Bio:
Dr. Loman is an Independent Research Fellow in the Institute for Microbiology and Infection at the University of Birmingham. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. He has so far used high-throughput sequencing to investigate outbreaks of important bacterial pathogens. He was involved in the crowd-sourced analysis of genomics data from the Shiga-toxin producing E. coli O104:H4 outbreak in Germany. He helped to spark a flurry of crowd-sourced analysis by putting the initial genome assembly on his blog for anyone to access. A more general aim in his group is to develop bioinformatics tools to aid the interpretation of genome and metagenome-scale data in routine clinical practice.

Abstract:
The ability to reliably reconstruct whole genomes of bacterial strains from mixed samples would enable diagnostic microbiology and environmental applications. I will present CONCOCT, an algorithm and bioinformatics package which uses both composition and read abundance from multiple samples to help assign metagenomics contigs into genome bins. I will show how CONCOCT can used to reconstruct pathogen genomes from a large E. coli outbreak and its use when comparing microbiomes. Short read de novo assembly techniques are limited in their ability to resolve closely related strains and to deal with low coverage genomes. I will discuss how the technique of phylogenetic placement can be used to analyse mixed microbial samples with low coverage, and discuss how new technologies such as Oxford Nanopore, Moleculo and metagenomics Hi-C may continue to transform this field.

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

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Introductory Speaker:
Mike Peabody (PhD Student, Dr. Fiona Brinkman’s Lab, SFU)

Title:
“Improving Water Quality Through Novel Genetic Tests Identified Using Metagenomics”






To view previous VanBUG posters and presentations, please see Archives

sponsored by:

CIHR Bioinformatics Training Program
      PIMS

Canadian Bioinformatics Workshops

Genome BC

Proof Centre
BCCDC

past sponsors:

MITACS
 

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