Senior Bioinformatics Scientist, Immunology/Oncology

POSITION SUMMARY:

We are seeking a bioinformatician with significant oncology or immunology experience to join a multidisciplinary team developing leading-edge genomics analysis tools to understand the immune system's response to cancer. This highly motivated, detail-oriented individual would join a clinical genomics analysis group and will be responsible for developing and applying bioinformatics methods to immuno-oncology clinical datasets, creating descriptive summary statistics and data visualizations, and technical reports.

PRIMARY RESPONSIBILITIES:

• Develop or enhance computational tools to predict antigenic somatic variants with assistance from a multidisciplinary team.

• In collaboration with immunologists, develop approaches to gain better understanding of T-cell receptor binding to MHC-peptide complexes.

• Use internal and external genomics data sources to understand how somatic and germline variation impacts the immune system’s response to cancer

• Run and enhance established DNA sequencing pipelines and workflows for NGS analysis in a clinical setting

• Prototype, develop, document, deploy, and support novel clinical DNA and RNA sequencing analysis approaches NGS analysis

• Benchmark new tools for sequencing data analysis and propose improvements

• Develop QC metrics, gold standard datasets and tools for systematically testing and evaluating the accuracy of newly developed assays and methods

• Collaborate with technical teams in specifying requirements for tools to enhance workflow efficiency, turnaround times and robustness

• Participate in internal research projects and external research collaborations

• Assist in preparing text and figures for manuscripts and external presentations

• Summarize results in written or oral reports for computational biologists, molecular biologists, clinicians, and internal researchers

 

QUALIFICATIONS:

• PhD degree in bioinformatics, biology (genetics/oncology/immunology), computational biology, statistics, or related field; or MS degree with 3+ years of post-graduation experience in bioinformatics, biology(genetics/oncology/immunology), computational biology, statistics, or related field.

 

KNOWLEDGE, SKILLS AND ABILITIES:

• Proven experience applying statistical learning methods to build biologically informative classifiers from sequences and other data types.

• Experience analyzing genomic sequencing data from Illumina platforms

• Experience analyzing high-throughput RNA-seq data is a plus

• 3+ years demonstrated exposure using standard genomics/bioinformatics tools (e.g. VEP, GATK, BWA, Picard, MuTect, Bowtie, Samtools, BCFtools, etc)

• Great understanding of human molecular genetics and oncology

• Familiarity with using and scripting in UNIX shell (e.g. Bash)

• Strong programming skills in common bioinformatics scripting languages (e.g. Python, R)

• Ability to collaborate and communicate with other scientists, researchers and clinicians

• Comfort with frequent, incremental code testing (e.g. unit testing) and deployment

• Demonstrated project management skills and ability to produce readable, reproducible and documented code (e.g. Jupyter, R markdown, etc)

• Experience with version control and source code management systems (e.g., Git)

• Strong team-oriented work ethic with open, honest, and considerate communication skills

• Cloud deployment exposure (e.g. AWS, Google Cloud, Azure) is a plus

• Design and implement bioinformatics pipelines and workflows in Docker containerized environments is a plus

• Experience writing SQL queries for data retrieval is required

• Exposure to cancer genomics somatic variant calling is a plus

• Experience working with large external data sources such as TCGA, COSMIC, 1000 Genomes, ENCODE, or GTEx data is a plus

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OUR OPPORTUNITY

Natera™ is a global leader in cell-free DNA (cfDNA) testing, dedicated to oncology, women’s health, and organ health. Our aim is to make personalized genetic testing and diagnostics part of the standard of care to protect health and enable earlier and more targeted interventions that lead to longer, healthier lives.

The Natera team consists of highly dedicated statisticians, geneticists, doctors, laboratory scientists, business professionals, software engineers and many other professionals from world-class institutions, who