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Old 06-27-2014, 09:52 AM   #1
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Default Bioinformatics postdoc for Cannabis genome assembly - New York, NY

The van Bakel lab in the Icahn School of Medicine at Mount Sinai is looking for a Postdoctoral Fellow with a strong background in de novo genome assembly. Our lab previously assembled the draft genome and transcriptome of Cannabis sativa and the successful applicant will further build on this work. One of the earliest domesticated plants, Cannabis sativa L. (marijuana, hemp; Cannabaceae) is a multipurpose species that has been used for millennia as a source of fibre, oil- and protein-rich seeds and for its medicinal and psychoactive properties. There are few other plants that elicit so much controversy: cannabis is currently the most widely consumed illegal drug worldwide yet it is legally used for its medicinal properties in many countries. We aim to better understand how cannabis produces medicinal compounds so that its potential to treat disease and alleviate suffering can be fully exploited.

The candidate will work with the PI to perform genome and transcriptome assemblies using hybrid short/long-read next-generation sequencing data (NGS), and to identify SNPs and e-QTLs that affect cannabinoid biosynthesis. Additionally, the candidate will help develop novel algorithms and methods to improve upon existing assembly and genomic analysis pipelines using emergent technologies. We seek a highly motivated and dedicated Ph.D. in genomics or bioinformatics with excellent quantitative skills and the ability to work well in a collaborative environment. The successful applicant will have strong training in sequence assembly, genomic analysis and data mining. Specific qualifications include:

Advanced experience in several of the following areas:
  • De novo genome/transcriptome assembly (e.g. Cabog, Inchworm, Allpaths, Amos, etc.)
  • Linux/Unix operating systems
  • High-performance computer clusters and resource managers (e.g. Torque/Moab, etc.)
  • Scripting languages and shell utilities (e.g., perl/python, awk, sed, etc.)
  • Statistical packages (e.g., R, Matlab, etc.)
  • Programming languages (e.g., C/C++, Java, etc.)
  • Database and website development (e.g. MySQL/MariaDB, PostgreSQL)

Additional qualifications:
  • Ability to complete tasks efficiently and independently
  • Strong work ethic and attention to detail
  • Excellent communication and writing skills
  • Ability to work well with others

The Icahn School of Medicine at Mount Sinai is an equal opportunity/affirmative action employer. We recognize the power and importance of a diverse employee population and strongly encourage applicants with various experiences and backgrounds.

To apply, please use the posting on the Nature Jobs website:
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