Computational Biologist I

Job Posting Number: 15652

Research – Laboratory
New York, NY
September 12, 2017
Company Overview:

At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence and improving outcomes.

For the 27th year, MSK has been named a top hospital for cancer by U.S. News & World Report. We are proud to be on Becker’s Healthcare list as one of the 150 Great Places to Work in Healthcare in 2016, as well as Glassdoor’s annual Employees’ Choice Awards 2017. We’re treating cancer, one patient at a time. Join us and make a difference every day.

Job Details:

At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence and improving outcomes. For the 26th year, MSK has been named a top hospital for cancer by U.S. News & World Report. We’re treating cancer, one patient at a time. Join us and make a difference every day.

The Dana Tsui Laboratory currently has an opportunity for a Bioinformatics Technician or Computational Biologist to take part in state-of-the-art cancer research and work as an integral part of a dynamic cancer research team studying important translational questions.

Job Description:

The successful candidate will participate in projects to: (1) develop analysis pipeline for next-generation sequencing (NGS) assays to profile circulating tumor DNA (ctDNA) from body fluids and (2) evaluate its utility in different solid cancer types across adult and pediatric cancers (3) study the biological characteristics of circulating tumor DNA in body fluids.

For (1), the types of assays we develop include targeted DNA sequencing, exome sequencing, whole genome sequencing, or DNA methylation, depending on tumor types and the genomic coverage/detection sensitivity required for different clinical questions. Prior experience on analysis of NGS assays is necessary, preferably on data generated from FFPE or body fluids (plasma, urine, saliva, cerebrospinal fluid CSF) in pregnancy or pathological conditions (not limited to cancer). Basic understanding of the sequencing library preparation workflow (different molecular strategies, such as capture, targeted etc) is preferable.

For (2 and 3), we work with clinical trial teams and research groups specialized in a variety of solid tumors across MSKCC to address different questions (examples here – we collect longitudinal samples and aim to compare ctDNA dynamics with clinical responses to evaluate its utility in guiding treatment decision. Experience on data analysis related to calling variants (point mutations / indel / structural rearrangement / copy number changes) or bisulfite DNA methylation (any of the above) will be necessary. Basic understanding of cancer genomics will be preferable.

The development of analysis pipeline will be a jointed effort with the computational team(s) of the Innovation Laboratory of the Center for Molecular Oncology and the Diagnostic Molecular Pathology Laboratory. Clinical evaluation will be done in close collaboration with individual research groups and clinical trials teams. The ideal candidate will be a team-player with excellent communication and interpersonal skills.

Specific tasks:

  • Provide bioinformatics support in the development of next-generation sequencing applications to characterize the spectrum and clinical significance of genetic mutations in cell-free nucleic acids.
  • Improve and utilize existing software and database systems to track experimental parameters, catalyze technology development, and analyze next-generation sequence data.
  • Work with experimental and computational biologists, clinical and translational research collaborators, and scientists across MSKCC.
  • Analyze data sets to discover and annotate cancer-causing genetic mutations in body fluids.
  • Evaluate performance of novel technology platforms and assays.
  • Analyze biomedical data and address scientific problems with bioinformatics techniques and tools and train researchers in the use of computational and bioinformatics tools
  • Track specimen information, experimental and analysis parameters, performance metrics, and genomic results in databases
  • Maintain detailed records of all analyses, experience with version controls is preferable
  • Present results and progress updates at lab meetings and make presentations to experimental and scientific collaborators
  • Attend seminars, lectures, and training courses to learn new computational biology skills to remain up to date with the cancer genomics field and learn new programming languages or techniques as necessary.

Qualifications:

  • Bachelor’s degree or a Master’s degree with 0-2 years of experience.
  • Experience with programming in a high level language such as R, python, perl or matlab is a must.
  • An understanding of common statistical tests and ability to present results of data analysis is required.
  • Research experience and some familiarity with computational biology is preferred.

Experience with one or some of the following would be helpful: fluency with UNIX, next generation (Next-gen) sequencing data analysis using, GATK, BWA, Picard, and Bio-conductor.

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MSK is an equal opportunity and affirmative action employer committed to diversity and inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply and will receive consideration without regard to race, color, gender, gender identity or expression, sexual orientation, national origin, age, religion, creed, disability, veteran status or any other factor which cannot lawfully be used as a basis for an employment decision.

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