Tag: breden

Job Posting: SFU iReceptor Research Project Data Curator

October 26, 2016

ireceptor
iReceptor is a distributed data management system and scientific gateway for mining “Next Generation” sequence data from immune responses.

An exciting opportunity to work with state-of-the-art, big-data research in immunogenetics is currently available with the iReceptor team at Simon Fraser University. This opportunity is available for current or past students of health-science or biomedical research programs. An understanding of immunology is preferred and would be a positive for applicants.

The job entails (i) performing literature searches and reading scientific literature on the sequencing of B-cell/antibody- and T-cell-receptor repertoires, (ii) documenting metadata characterizing the acquisition and processing of samples for each study, and (iii) stating the research goals of each paper. Additionally, the data curator will run annotation tools to process publicly available sequence datasets and curate these in an iReceptor database of immune receptor repertoires. The data curator will be provided assistance in learning what is needed to complete these tasks. S/he will work with senior scientists with expertise in evolutionary genetics and immunology, and with a bioinformatics graduate student.

This is a great opportunity to learn basic bioinformatic skills and to work with state-of-the-art bioinformatics as applied to immunogenetics. This field is rapidly expanding with applications in cancer immunotherapy and treatment of autoimmune and infectious diseases.

Minimal requirements

  • Skill in reading and understanding the biomedical literature
  • Course work in and a broad knowledge of molecular biology and immunology
  • Basic computational proficiency and some experience working with large data sets.

Preferred

  • BSc in biology, molecular biology, life sciences or computer science
  • Experience with bioinformatics tools
  • Experience in working with biological data
  • Comfortable working with command-line tools

Send resume and short description of how your experience could contribute to this effort to:

Felix Breden
Department of Biological Sciences
Simon Fraser University
Burnaby, Canada V5A 1S6
Email: breden@sfu.ca

Ben Sandkam wins Quirks and Quarks Award!

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Ben (and Felix) hard at work in the field.

Congratulations to Ben Sandkam of the Breden Lab, whose PhD thesis “Beauty in the Eyes of the Beholders: Colour Vision and Mate Choice in the Family Poeciliidae,” has earned the Quirks and Quarks Graduate Award for Best PhD Thesis!

Ben studied sexual selection in guppies, and his thesis work was characterized by its integrative approach to the problem.  His work ranged from field studies in Guyana and Trinidad, to behavioural ecology, to molecular biology (sequencing and cloning opsin genes from guppy retinas to investigate gene expression).  He published a new Hybrid Sensory Expansion hypothesis in the journal Evolution, and his research on opsin expression was published inMolecular Ecology (he published a total of 9 papers from his thesis work).  Ben is currently pursuing post-doctoral research at the University of Maryland.

Here’s how Ben summarizes his work:

“For my PhD, I developed an integrated programme to discover the genetic effects of mate preferences, a powerful force shaping animal evolution and diversity. My work revealed that guppy colour vision co-varies with mate-preferences across natural populations (Sandkam et al 2015a), showing that mate preference can shape sensory genes and ability. I also revealed that colour vision differs more across populations than across species (Sandkam et al 2015b), a startling result given that colour vision was assumed to be fixed within species. My results are key to explaining how mate preferences evolve and diverge across populations, and led me to develop the Hybrid Sensory Expansion (HSE), which posits that hybrid offspring exhibit a wider range of tuning than their parental species (Sandkam et al. 2013).

I also discovered that the genomic architecture of long-wave sensitive loci results in high rates of double-recombination, which reduces the ability to discriminate red and orange colours, potentially deleterious for animals that select mates based on these colours. I showed double-recombination is significantly reduced in species with mate preferences based on red and orange colour, the first evidence that sexual selection can affect recombination rate (Sandkam et al- In review).

 

Article from the Department of Biological Sciences at Simon Fraser University

https://www.sfu.ca/biology/kudos-news/kudos/2016-sandkam-qqaward.html