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Research assistant in bioinformatics

Posted November 27, 2020

The McGill Group for Suicide Studies is a multidisciplinary team of researchers using complementary approaches to understand what makes people at risk for depression and suicide. We are looking to hire a research assistant who will be called to work alongside students on projects dealing with the functional genomics of major depressive disorder and suicide.

We study various aspects of the function genome by generating whole genome/transcriptome datasets which include but are not limited to; RNA-seq DNA and RNA methylation, using conversion-based sequencing (bisulfite or APOBEC) or ChIP-seq approaches. As part of their work, the research assistant will be expected to process next-generation sequencing (NGS) data, from raw reads to final output, using the appropriate bioinformatic tools and pipelines on high-performance computer clusters.

Description of tasks

Analyzing NGS methylation datasets from start to finish, carrying quality control checks on the sequenced libraries, identifying and removing sequencing biases, aligning reads to the genome, extracting relevant methylation metrics (signal, percentage, position, context, motif, etc.), and conducting downstream statistical analyses.

Furthermore, they will need to synthesize the results and clearly communicate and transfer the data to other lab members. Analyses are often conducted in the context of students’ projects; it is of the upmost importance that students understand what has been done to the data and what to be mindful of when continuing the work.

The research assistant is expected to manage the data they generate and its backup. Keeping a detailed log of how analyses were carried out in order to facilitate transparency and reproducibility of the results. They are also expected to manage their own time according to the various deadlines of the projects they are working on.

Required qualifications

MSc in Bioinformatics (or relevant field) OR BSc in Bioinformatics (or relevant field) with at least 9 months of research experience (internship or otherwise)

Required skills

  • Good understanding of biochemistry is necessary.
  • Previous experience in epigenetics is an asset.
  • Fluency in either French or English, as well as being at least conversational in the other is required.
  • Good communication and people skills.
  • Good time management and organisational skills.
  • Creative problem-solving.

Required abilities

  • General computer abilities:
  • Experienced user of UNIX and working on Linux environments through command line. (At least 5 years experience)
  • Proficiency in Bash and at least one of the following scripting languages (Perl, Python, Ruby).
  • Knowledge of R and bioconductor is preferred. Knowledge of other programming languages is a plus
  • Good understanding of statistics is preferred.
  • Experience working with large datasets is required
  • Experience with the Compute Canada high-performance clusters is an asset.
  • Bioinformatic abilities:
  • Experience with analyzing NGS data is required
  • Familiarity with sequencing reads cleaning and trimming tools.
  • Experience with sequence aligners is required (specifically bowtie2 and STAR).
  • Experience with bismark is an advantage.
  • Experience working with ChIP-seq data would be ideal
  • Relevant tools and software: MACS2, ExomePeaks, HOMER
  • Familiarity with the large -OMICs databases (ei. NCBI, ENSEMBL, UCSC)
  • Knowledge of machine learning is welcome but not necessary

Location of work

Douglas Research Centre – Frank B. Common Pavilion

Will be required to travel for work?

No

Date of posting

November 24, 2020

Name of immediate supervisor

Corina Nagy

Work schedule

Full-Time, 37.5 hrs/week, 1-year contract, maternity replacement with the possibility for contract extension.

Salary

$16-$25/hr

Instructions for submitting application

Please send a one-page cover letter describing your fit with the position and your CV directly to corina.nagy@mcgill.ca


Participants wanted

Nothing at this time.