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Mount Sinai Hospital - Department of Gastroenterology
Toronto (City), Ontario (CA)
Up to $70,000 + benefits
Closing date
May 12, 2023

Description of duties: Under the guidance of Dr. Croitoru the candidate is expected to draft and present research plans and projects, carry out individual experiments, analyze and present data, prepare manuscripts for publication and present data at national and international meetings. The Postdoctoral Research Fellow will be assessing how pre disease microbiota promote or induce inflammation and eventually lead to Crohn’s disease onset. The candidate must be a team play as the candidate will collaborate and work as part of Dr. Croitoru’s team notably with immunologists and other data scientists. We are looking for a highly motivated scientist with a track record of creativity in developing experimental strategies and a knowledge base in microbiome analysis. A PhD in Microbiology, Molecular Biology, bioinformatic or a related field, is required. The fellow will have the opportunity to work with established investigators in a large international study with access to a very large biosample repository as part of the GEM project. The candidate will be responsible to work with unique sample collected before the onset of the disease. Notably the candidates will be responsible for the analysis of sequences generated as part of the GEM project which include 4,000 samples with 16s rRNA data on the V4 region, and will include 2,000 samples with deep shotgun sequencing data (with a minimum of 30 Million reads per samples).

Required qualifications: A PhD in Microbiology, Immunology, Molecular biology, Biotechnology, Life sciences, Pathology, Cellular Biology or a related field, is required

  • Must be a team player, versatile, flexible, and self-motivated with strong communication/organizational skills and attention to details
  • Knowledge of Molecular biology technique (PCR, qPCR, library preparation for sequencing)
  • Evidence of scientific accomplishment via peer-reviewed publications
  • Mastery of spoken and written scientific English
  • skills and attention to detail
  • Microbiology technique (culturing, isolation, anaerobic chamber) would be an asset
  • Deep knowledge of Bioinformatic (16S sequencing, QIIME 2, PICRUSt2, DADA2)
  • Deep knowledge of Bioinformatic tool for analysis of deep shotgun sequencing HUMAnN version 3 or higher, bowtie2, Metagenome Assembled Genome analysis
  • Familiar with microbial database for taxonomic analysis, but also targeted functional analysis such antibiotic resistance, proteolytic enzyme etc.
  • Experience using super-computer.
  • Experience in coding in python or related software
  • Knowledge in statistics related to Microbiome (Lefse, vegan R package etc.)

Application instructions
All individuals interested in this position must submit CV, a Cover letter, and references contact information to and by the closing date. The position will remain open until filled


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