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About the Elli Papaemmanuil Lab

Our lab is a collective of clinical, computational, molecular and mathematical research investigators with an interest to study the role of acquired mutations in cancer development and how these determine clinical phenotype and response to therapy. Our mission is to execute research that informs and moves clinical practices in oncology forward. We have strong expertise in genome profiling analysis consistent track record on the development of high-throughput laboratory and analytical pipelines (bioinformatics and statistical) and integrate large and complex genomic datasets. We have formed a strong network of research and clinical collaborations, to pursue innovative studies in cancer research.

We are looking for a dedicated and motivated Bioinformatics Software Engineer to join our growing team. Our laboratory designs large scale and innovative genomic studies to understand cancer biology and inform cancer patient care. To support our studies, we have built Isabl , a platform for scalable bioinformatics operations designed with a patient-centric data bank connected through an API, a command line interface, and web-based data visualization solutions. We follow principles from Agile development and engineering to build innovative software solutions that allow us to optimize, scale and innovate cancer genomics research output.

What you'll do:

• As a member of the software engineering team the applicant will be developing new solutions for our bioinformatics operations.
• Support the design, development and implementation of data processing workflows for cancer genomic data and related metadata.
• Leading the benchmarking of analytical tools, as well as the design, deployment and maintenance of efficient software solutions to automate data analyses.
• Will be working closely with computational members in the group to support innovative research and develop prototype software solutions for research and clinical applications.

Who you are:

• Masters graduate in Computer Engineering, Computer Science or Biomedical Engineer OR at least 2 years of experience in a relevant role.
• Proficient skills in Python, or some other scripting languages (JavaScript, Bash, Perl, C++ ).
• Good working knowledge of Linux (or similar operating systems), and desired knowledge with HPC or cloud computing environments (e.g. LSF, SLURM, AWS BATCH)
• Experience with SQL (Postgres) and/or noSQL (MongoDB, DynamoDB) databases.
• Familiarity with software packaging and package distribution standards (Pypi, Docker)
• Strong interest in development of documentation for the deployment and operation of software.
• Experience with NGS datasets is desirable.
• Ability to work independently and as a team depending on tasks.
• Strong written and verbal communication skills.

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Competitive compensation packages | Sick Time |Generous Vacation+ 12 holidays to recharge & refuel| Internal Career Mobility & Performance Consulting | Medical, Dental, Vision, FSA & Dependent Care|403b Retirement Savings Plan Match|Tuition Reimbursement |Parental Leave & Adoption Assistance |Commuter Spending Account |Fitness Discounts &Wellness Program | Resource Networks| Life Insurance & Disability | Remote Flexibility

We believe in communication, openness, and thinking beyond your 8-hour day @ MSK. Its important to us that you have a sense of impact, community, and work/life balance to be and feel your best.

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