Position: Postdoctoral Fellow
Site: MaRS Centre, Toronto
Department: Simpson Lab, Computational Biology
Reports To: Dr. Jared Simpson
Salary: Commensurate with level of experience
Hours: 35 hours/week
Status: Full-time, Contract (4 years)
The Simpson lab at OICR develops algorithms and software for processing genome sequencing data. We are looking for a postdoc to join us to work on tools for epigenetic profiling from nanopore-based sequencing data. This position will build upon our recent work on the detection of 5-methylcytosine directly from the signal measurements made by the Oxford Nanopore MinION sequencer:
The successful applicant will help extend the functionality of our methylation detection software (github.com/jts/nanopolish) to detect additional cytosine modifications (like 5-hydroxymethylcytosine), detect adenine modifications and/or detect differentially methylated regions in cancer. This is a collaborative project with Winston Timp’s lab at Johns Hopkins University and funded by the National Institutes of Health for a period of four years. The ideal applicant has prior experience building computational methods for biological data but strong computational candidates with other relevant experience will be considered.
• Develop methods to detect modified bases from the signals emitted by nanopore sequencers;
• Design and implement probabilistic models of nanopore data;
• Optimize software to ensure high performance and minimize compute time;
• Build methods to test the accuracy of the inference software;
• Collaborate with internal and external users of the developed software.
• Ph.D. or equivalent experience in computer science, mathematics, bioinformatics or a related discipline.
• Experience in machine learning, statistics or probabilistic modeling;
• Proficient in a compiled language (C or C++) and at least one scripting language;
• Experience working within a Linux environment;
• Familiar with best practices in software development like the use of version control systems, testing and coding standards;
• Experience with genomics or high-throughput sequencing is helpful, but not required.
OICR is an innovative cancer research institute located in the MaRS Centre in the Discovery District in downtown Toronto. OICR is addressing significant challenges in cancer research with multi-disciplinary, multi-institutional teams. New discoveries to prevent, detect and treat cancer will be moved from the bench to practical applications in patients. The OICR team is growing quickly. We are innovative, dedicated professionals who bring expertise to each of our roles. We are looking for individuals interested in being part of a culture of excellence that will result in Ontario being recognized internationally as a leading jurisdiction for cancer research.
Launched in December 2005, OICR is an independent institute funded by the Government of Ontario through the Ministry of Research, Innovation and Science.
For more information about OICR, please visit the website at www.oicr.on.ca.
CLOSING DATE: Until filled
OICR is an inclusive employer dedicated to building a diverse workforce. We encourage applications from all qualified candidates and will accommodate applicants’ needs throughout all stages of the recruitment and selection process. Please advise the Recruiter to ensure your accessibility needs are accommodated throughout this process. Information received relating to accommodation will be addressed confidentially.
The Ontario Institute for Cancer Research thanks all applicants. However, only those under consideration will be contacted.
Resume Format: If you elect to apply, you will need a text or HTML version of your resume so that you can cut and paste it into the application box provided. Before you submit the completed application, you will be asked to attach one or two files to your application. Please attach your resume as a .doc file or email it to Jared Simpson as a PDF.