Bioinformatics Scientist II

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A Brief Overview

The Genomic Diagnostic Laboratory (GDL) of the Children's Hospital of Philadelphia is seeking a highly motivated Bioinformatics Scientist II with an interest in laboratory diagnostics to join our team. This is an exciting opportunity to work collaboratively within the bioinformatics team and together with our laboratory directors, supervisors, analysts, genetic counselors, and wet bench team to develop and improve pipelines and other tools to support accurate, timely diagnostic testing that has a direct impact on establishing the diagnosis, prognosis, treatment, and management plan for our patients. The team also supports cutting edge R&D efforts including new clinical test development and clinical research. The ability to communicate in a highly matrixed environment will be key to the candidate's success. Seasoned professionals as well as new graduates are welcome to apply and will be considered for the career ladder position commensurate with their experience. This position is hybrid with weekly onsite work at our Philadelphia campus as appropriate.

The Bioinformatics Scientist II is primarily focused on developing and validating frameworks and algorithms supporting clinical diagnostic tests as a bioinformatics domain expert. The scope of the work will include the development and improvement of bioinformatics workflows and processes, bioinformatics pipeline QC and troubleshooting, as well as presentation of results for multi-omics-based tests. The position allows for a wide variety of activities described within the job responsibilities. Activities occur with a moderate degree of supervision with moderate latitude for independent judgment.

The ideal candidate will have experience in the following:

• NGS analysis pipelines and applications, including SNV, copy number variation, structure variation, and RNAseq, including filtering, annotation, and prioritization
• Machine learning and data modeling of genomic data
• Deep knowledge in Illumina short read technology:
• a) Instrumentation and the molecular biology/biochemistry
• b) Dragen workflow
• Familiarity with resources of genomic data sets, data bases, and tools, such as UCSC Genome Browser, gnomAD, HGMD, ClinVar, OMIM, ACMG, and various NCBI databases
• Strong skills in Python and related ML and mathematical libraries
• UNIX/GNU/Linux
• GitHub

What you will do

• Coding and Software Development (40%):
• CI/CD development of bioinformatics pipelines, applying best practices
• Review existing applications and code sources (both commercial and free/open source) and select the best strategy for development or adoption.
• Routine peer-to-peer code reviews
• Analysis (30%):
• Analyze high complexity genomics data
• Contribute to the development of additional pipeline functionality and changes by providing knowledge of both collaboration-specific requirements and bioinformatics discipline advances.
• Advocate for specific collaboration requirements for continual advancement of shared pipeline and code resources
• Provide collaboration-specific transparency for data processing and pre-analysis, including sample- and cohort-level status.
• Collaboration (20%)
• Contribute to the development of application portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications
• Provide efficient data management support
• Establish role within collaborative project team as primary bioinformatics resource
• Contribute to and influence project-level management by serving as bioinformatics point.
• Define and promote boundaries of support by assessing all stakeholders, including bioinformatics management, collaborator expectations, and funding levels and mechanisms.
• Regularly discuss satisfaction and expectations with collaborators; continually advocate for clear understanding of role.
• Academic Output (10%)
• Regularly contribute to bioinformatics-focused manuscripts and publications.
• Regularly contribute to podium presentations and posters.
• Contribute to bioinformatics sections of grant and award proposals.

Education Qualifications

• Bachelor's Degree - Required
• Bachelor's Degree in Bioinformatics, Data Science, Engineering or related fields - Preferred
• Master's Degree in Bioinformatics, Data Science, Engineering or related field - Preferred

Experience Qualifications

• At least three (3) years experience in applied bioinformatics, genomics, and computational work - Required
• Experience with management and analysis of complex data types - Required
• Scripting and application development in R - Preferred
• Knowledge in long read technology, such as PacBio or ONT - Preferred
• HPC job scheduler, e.g., Slurm or Airflow - Preferred
• Pipeline implementation in cloud environment such as AWS, Azure, or Google VPC - Preferred
• Bioinformatics pipeline or workflow development frameworks, e.g. WDL, CWL, SnakeMake, or NextFlow - Preferred
• Knowledge of the working mechanism of microarray, protein mass spectrometry, or other high-throughput technologies and awareness of their strengths and weaknesses - Preferred
• Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture - Preferred

Skills and Abilities

• Ability to interact with biologists and clinicians during a scientific discussion
• Accountability and attention to timelines
• Excellent organization and communication skills with an emphasis on strong presentation skills
• Ability to provide objective validation of results
• Ability to work in a team environment

To carry out its mission, CHOP is committed to supporting the health of our patients, families, workforce, and global community. As a condition of employment, professionals working onsite-at any CHOP location, for any portion of time-must be vaccinated for COVID-19. Learn more.

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SALARY RANGE:

Salary ranges are shown for full-time jobs. If you're working part-time, your pay will be adjusted accordingly.

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At CHOP, we are committed to fair and transparent pay practices. Factors such as skills and experience could result in an offer above the salary range noted in this job posting. Click here for more information regarding CHOP's Compensation and Benefits.