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BACKGROUND

Columbia University's Department of Systems Biology is seeking a highly motivated genomics and computer science expert to join the Rabadan lab. The incumbent will take part in a cutting-edge project on untangling the molecular biology of cancer. The overarching approach is to generate and analyze deep whole exome and whole genome from both public and private data sets and develop visualization tools for these data. The incumbent will also develop and maintain a software pipeline for the analyses of genomic sequencing data. The job would require the candidate's active participation in the design and implementation of these pipelines as well as interaction with collaborators in applying the pipeline towards achieving the goals of specific sequencing projects. The person will work in a highly multidisciplinary and supportive environment and will work directly with members of the lab in meeting assigned objectives under the supervision of the Principal Investigator.

The incumbent will also oversee the research staff technician position within the Rabadan Lab, who will be coordinating research computational efforts, as well as oversee genomic data coordination for various working groups within the Program for Mathematical Genomics (PMG) group. The position will report to the Principal Investigator of the Rabadan Lab.

RESPONSIBILITIES

Design and implement bioinformatics pipelines, as well as maintain and operate existing in-house pipelines and tools, including generating and analyzing deep whole exome and whole genome from both public and private data sets and develop visualization tool for these data.
Manage and administer cloud computing infrastructure, including the migration of files and workflows from the local computing cluster to Amazon Web Services, managing user accounts and permissions, and cost management.
Supervise data analyst staff duties and conduct quality assurance on project processes, activities and tasks from data analyst staff; Review the genomic data coordination for various working groups within the Program for Mathematical Genomics (PMG) group.
Maintain lab generated software.
Provide support and training on data pipelines, protocols and database tools for all team member projects.
Coordinate and assist with implementation and improvement of data management and data processing protocols.
Assist and advise principal investigators and lab research team members with data management needs.
Perform related duties & responsibilities as assigned/requested.

MINIMUM QUALIFICATIONS

Bachelor's degree in Computer Science, Engineering, Physics or related field, or equivalent in education and experience; plus four years of related experience.
Experience with Linux, Python, scripting, and/or cluster computing (primarily with the Oracle Grid Engine (SGE).

PREFERENCES

Master's degree preferred.
Some supervisory experience preferred.
Excellent programming and communication skills.
Proactive in making suggestions for better system design and documentation and be actively involved to ensure the project achieves its goals.
Skills on web design and graphical design.
Experience in Docker, Adobe Creative Suite (photoshop and illustrator, for designing scientific figures), and scientific writing.
Experience with Amazon web services (EC2, S3, Glacier, IAM, Batch, AWS Organizations, etc.).
Prior experience with existing sequencing technologies and their application as a tool for understanding the genetics of cancer.
Experience with Bioinformatics Software tools, such as BLAST, BWA, Samtools, Bowtie, Trinity, as well as how to access data cohorts.
Experience with Version control software (git).
Experience with back-end web development, primarily in Django (with some forays into Flask and database stuff, like Postgres, as well).
Experience with front-end web development, primarily in Javascript, HTML, and CSS (with some forays into Javascript frameworks like Vue and Angular).

TERMS

Job Type: Officer of Administration
Regular/Temporary: Regular
Hours Per Week: 35

LOCATION

New York, NY (on-site).

COMPENSATION

Salary Range: $76,000 - $85,000
Generous PTO and sick leave

The salary of the finalist selected for this role will be set based on a variety of factors, including but not limited to departmental budgets, qualifications, experience, education, licenses, specialty, and training. The above hiring range represents the University's good faith and reasonable estimate of the range of possible compensation at the time of posting.

HOW TO APPLY

Visit to apply: http://opportunities.columbia.edu/cw/en-us/job/536637?lApplicationSubSourceID=.

DEADLINE

One position open until filled.

POLICY

Equal Opportunity Employer / Disability / Veteran

Columbia University is committed to the hiring of qualified local residents.

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