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Vancouver Bioinformatics User Group (VanBUG) » archive for January, 2018

 Faraz Hach

Hello everyone, our next event will feature Faraz Hach from the Vancouver Prostate Centre.

Date: February 8th
Time: 6pm
Location: BCCRC ground floor lecture theatre. 675 West 10th Avenue, Vancouver BC

Title: High Throughput Sequencing Data Compression
Abstract: Modern high-throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing, downstream analysis, and computational infrastructure. As HTS data grow in size, data management and storage are becoming major logistical obstacles for adopting HTS-platforms. One way to solve storage requirements for HTS data is compression. Currently, most HTS data is compressed through general purpose algorithms such as gzip. These algorithms are not specifically designed for compressing data generated by the HTS-platforms. Recently, a number of fast and efficient compression algorithms have been designed specifically for HTS data to address some of the issues in data management, storage and communication. In this talk, I will present solutions to deal with challenges related to storing HTS data.
Bio: Faraz Hach is a Senior Research Scientist at Vancouver Prostate Centre and an assistant professor in department of Urologic Sciences at UBC. In 2013 he received his PhD from Simon Fraser University. His current research involves developing fast and efficient combinatorial algorithms to analyze genomics data generated by Next-Generation Sequencing (NGS) technologies with special focus on structural variations and segmental duplications. He is also interested in designing data structures and algorithms for compressing large quantities of sequencing data to address the challenges related to storage of NGS data. His works have been internationally recognized with several awards and honors. Among these include the Ian Lawson Van Toch Memorial Award for outstanding student paper at the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012) and the Governor General’s Gold Medal for the best doctoral thesis award from Simon Fraser University in 2014.

Website: Dr. Faraz Hach at Vancouver Prostate Centre

Suggested Reading:
Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach: Dynamic Alignment-Free and Reference-Free Read Compression. RECOMB 2017: 50-65
Faraz Hach, Ibrahim Numanagic, S Cenk Sahinalp: DeeZ: reference-based compression by local assembly. Nat Methods. 2014 Nov;11(11):1082-4.
Faraz Hach, Ibrahim Numanagic, Can Alkan, S Cenk Sahinalp: SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinformatics 2012: 28(23): 3051-3057

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


Introductory Speaker:
Phillip A. Richmond (PhD Student, Wasserman lab, CMMT)

Title: Pathogenic noncoding variants in genetic disease
Bio: Phil Richmond is a PhD graduate student in Bioinformatics studying under Dr. Wyeth Wasserman at the BC Children’s Hospital. His research focuses on maximizing the utility of whole genome sequencing in diagnosing rare genetic diseases, with an emphasis on copy number variant calling and noncoding (cis-regulatory altering) pathogenic variants. At BC Children’s Hospital he is involved in multiple clinical efforts that are using this new technology to change how rare genetic diseases are diagnosed. He also has a passion for teaching, and is always looking for teaching assistants for his courses taught through the Compute Canada Education, Outreach and Training committee.


Webcast Link:
(This technology is brought to you by Compute Canada and WestGrid with support from PHSA Telehealth)

 January 11th Special Event

Hello VanBUG followers, happy new year!

We don’t usually have an event in January, but this year Jennifer Gardy worked with us to organize a special event with two featured speakers.

Date: Jan 11th
Time: 6pm
Location: BCCRC First Floor Lecture Theatre 675 West 10th Avenue, Vancouver BC

Hope to see you there! Speaker details below:

Speaker: Gytis Dudas
Title: Virus genomes reveal factors that spread and sustained the West African Ebola virus epidemic

Abstract: The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact.
Thanks to new technologies complete Ebola virus genomes were sequenced from over 5% of the known cases by various teams operating in the region.
The sheer amount of sequence data have enabled a large international team to reconstruct the entire epidemic from the virus’ perspective, and to reveal the factors that helped sustain Ebola virus transmission across the region.
Future infectious disease outbreaks are likely to generate similar kinds of data, and hopefully follow the blueprint set by our study.

Bio: Gytis Dudas is a Lithuanian researcher based at Fred Hutchinson Cancer Research Centre in Seattle currently working with Trevor Bedford.
Gytis trained as an evolutionary biologist at the University of Edinburgh, where he stayed to do a PhD on the evolution of diverse RNA viruses with Andrew Rambaut.
Gytis’ research focuses on understanding transmission patterns of rapidly evolving RNA pathogens, by studying viral populations through the lens of population genetics, and identifying evolutionary, ecological and physical barriers that these viruses experience.

Speaker: James Hadfield
Title: Communicating genomic epidemiology in real-time

Abstract: The role of genomics in epidemiology is expanding, with recent retrospective analyses of the ebola and zika epidemics providing relevant insights for public health and epidemic control. Nextstrain and ARTIC are efforts to uncover and disseminate these results in real-time. This involves rapid field-deployable sequencing, the open sharing of genomic data, efficient bioinformatic pipelines and innovative ways to display the results.
This talk will focus on the interactive visualization of genomic data for ongoing epidemics and the role this can play in communicating information to scientists & public health officials.

Bio: James Hadfield completed a BSc (hons) in Mathematics in his home country of New Zealand and a PhD in computational biology from Cambridge University before moving to Trevor Bedford’s lab at the Fred Hutch in Seattle. He works on developing analyses and interactive visualizations for and ARTIC.