Bioinformatics Scientist II - DBHI

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Job description

Location:LOC_HOME-Home/Remote Office Location

Req ID:150400

Shift: Days

Employment Status:Regular - Full Time

Job Summary

The Children's Hospital of Philadelphia (CHOP) Research Institute and its Department of Biomedical and Health Informatics (DBHi) are seeking a bioinformatics scientist to help advance an enterprise-level data and informatics platform called "Arcus". The Arcus team integrates with major scientific initiatives in the Research Institute strategic plan involving high-impact research areas such as lifespan, rare diseases, novel devices and therapeutics, and precision health.

This role will work with bioinformatics scientists and software engineers to operationalize a set of pipelines used to align and annotate whole exome and genome sequencing data. This role will also collaborate with data archivists and metadata librarians to advise as a subject matter expert for genomic research data contributions into Arcus.

We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge.

Job Responsibilities (Continued)

• Develop and refine bioinformatic pipelines focused but not limited to variant calling, variants annotation and germline copy number based on GATK best practices or other industry stablished workflows.
• Development of Workflow Descriptive Language (WDL) scripts in order to deploy production ready pipelines on an escalable environment using cromwell execution engine.
• Operationalize and manage genomic pipelines, including debugging issues as they arise
• Support researchers who need assistance in developing ad-hoc pipelines by understanding their scientific goals and documenting their scientific objectives in a way that can be translated to the research application development team.
• Collaborate with Library Science team to advise on genomic data preservation, organization, and description based on industry standards

Preferred Technical Requirements

• At least three (3) years of experience working with genomic data in industry standard file types (e.g. fastq, fasta, VCF, BAM or CRAM)
• At least two (2) years of experience with development and management of genomic analysis pipelines using Cromwell/WDL or Rabix/CWL based platforms
• Experience with molecular biology or clinical genetics analysis techniques and industry common high throughput sequencing technologies.
• Familiar with the use of common clinical genomic reference databases (e,g. Gnomad, ClinVar, dbSNP)
• Expertise with command-line tools on Linux batch systems and cloud compute (GCP, AWS)
• Excellent written and verbal communication skills to interact with both clinical researchers and developers

Required Education and Experience

Required Education: Bachelor's Degree in biological or computational discipline.

Required Experience:

• At least three (3) years of experience in applied bioinformatics, genomics, and computational work.
• Experience with management and analysis of complex data types.

• Experience with genomic/proteomic data analysis methods.

Preferred Education, Experience & Cert/Lic

Preferred Education: Master's or Doctorate Degree in biological or computational discipline

Preferred Experience:

• Four (4) or more years of experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation.
• Experience with Python, Perl, or other languages.
• Experience with pipeline or workflow development frameworks.
• Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture.

All CHOP employees who work in a patient building or who provide patient care are required to receive an annual influenza vaccine unless they are granted a medical or religious exemption.

Children's Hospital of Philadelphia is committed to providing a safe and healthy environment for its patients, family members, visitors and employees. In an effort to achieve this goal, employment at Children's Hospital of Philadelphia, other than for positions with regularly scheduled hours in New Jersey, is contingent upon an attestation that the job applicant does not use tobacco products.

Children's Hospital of Philadelphia is an equal opportunity employer. We do not discriminate on the basis of race, color, gender, gender identity, sexual orientation, age, religion, national or ethnic origin, disability or protected veteran status.

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Talent Acquisition

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Philadelphia, PA 19146