Bioinformatics Scientist III - D3b

Philadelphia, PA, US, 19146

Location: LOC_ROBERTS-Roberts Ctr Pediatric Research 

Req ID: 134035

Shift: Days

Employment Status: Regular - Full Time 

Job Summary

The Bioinformatics Unit (BIXU) within the Center for Data Driven Discovery (D3b) at The Children’s Hospital of Philadelphia (CHOP) is seeking a level III Bioinformatics Scientist to join our over 30 professional data engineers, developers, and bioinformatics scientists. The Bioinformatics Scientist will be supporting analytics for NIH-funded, nationally visible projects in partnership with the Department of Bioinformatics and Health Informatics (DBHI) and the Division of Oncology and Center for Childhood Cancer Research (CCCR) at CHOP. This position will be embedded within a highly collaborative environment and will initially be focused on task-driven data processing, data harmonization, data analytics, and R Shiny application development for a national data integration project for pediatric cancer. 

The Bioinformatics Scientist will attend project meetings and interact daily with BIXU team members and individual lab members on a project-by-project basis. The Scientist will be mentored by Dr. Jo Lynne Rokita within D3b, but will be expected to take a lead, proactive scientific role as a bioinformatics domain expert within multi-disciplinary teams made up of internal and external collaborators. Ongoing projects in which the candidate will participate include Open Pediatric Cancer analysis (https://github.com/PediatricOpenTargets/OpenPedCan-analysis) stemming from the OpenPBTA project with Alex’s Lemonade Stand Foundation (https://github.com/AlexsLemonade/OpenPBTA-analysis) and RNA splicing analysis, neoepitope identification and prioritization across pediatric tumors.

The successful candidate will have had either academic or on-the-job training on subjects related to cancer biology. They must have demonstrable productivity in bioinformatics, and at least five years of experience (inclusive of focused academic training) in bioinformatics projects utilizing bash and either Python or R programming.  

The successful candidate must have experience in the following areas: 

a) Experience setting up analysis pipelines and working in high-performance and/or cloud-based computing environments towards bioinformatics data processing for large-scale projects.
b) Code organization and reproducible workflow experience using git, docker, and R or Python notebooks.
c) Experience analyzing sequencing data related to cancer or other diseases/quantitative traits (e.g. germline or somatic single nucleotide variants (SNVs), indels, structural variations (SVs), fusions, RNA expression data, and copy number variants).

The successful candidate’s experience with established methods for processing genomics data should allow them to develop and benchmark tests of performance of analytical methods as benefits the project. 

The successful candidate should be able to work in cross-site teams on deadlines and have strong communication and listening skills. The candidate must be able to manage multiple projects and be prepared to work both independently and on collaborative efforts to complete projects within expected timelines.

The candidate should be ready to commit to full data, code, and open research transparency and reproducibility. 

The candidate will be asked to share their GitHub/Bitbucket handle and give a project presentation as part of the interview process.

This position is flexible and can be can be fully remote, hybrid, or on site.

Job Responsibilities

Pre-Analysis (10%): Actively participate in the development of application portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications. Provide efficient data management support.
o    Lead development of additional pipeline functionality and changes by providing knowledge of both collaboration-specific requirements and bioinformatics discipline advances
Coding and code review (30%): Code and generally support code and applications on behalf of collaborative project and/or team.
o    Master best practices for project-based code development, QC, and execution consist with the expectations of specific collaborations
o    Perform and manage peer-to-peer code reviews by participating in informal and formal critical code reviews through GitHub
Data Analysis and Application Development (30%): Analyze data of high complexity by applying sound statistical and commonly accepted bioinformatics methods to -omics data primarily under the direction of the collaborative project team 
o    Develop multiple “specialty” analytical areas that serve one or more collaborative teams
o    Create flexible and scalable project-based R Shiny applications 
o    Lead adoption of best practices in specialty analytical or biomedical areas by the bioinformatics group and peers
Collaboration (20%): Lead bioinformatics portion of scientific collaborations as the primary bioinformatics resource
o    As bioinformatics point, assume management role for projects of low-to-moderate complexity, including all aspects of timelines, risk identification and mitigation strategies, and communication mechanisms
o    Directly manage all elements of project satisfaction and performance relative to scientific project aims
o    Promote continual objective, “hard” discussions about overall health of project and relationship
o    Develop new collaborations with moderate degree of supervision
Academic Output (10%): Lead project-based presentations, grant sections, and manuscript sections with subsequent review by peers and mentors
o    Regularly contribute to manuscripts, conference posters, and/or platform presentations
o    Proactively contribute to bioinformatics and other sections of grant and award proposals

Required Education and Experience

•    MS/PhD in biological or computational discipline.
•    5-10 years experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation.

Preferred Education, Experience & Cert/Lic

•    Five (5) or more years of experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation.
•    Demonstrable experience in project-level data harmonization and integration, including phenotype and genotype harmonization for multi-omics datasets, for cancer data resources is a plus.
•    Experience or knowledge of technologies commonly used in biological labs, such as next generation sequencing, PCR, cloning, electrophoresis gels, and cell culture.

Additional Technical Requirements

•    Strong UNIX/LINUX expertise required. 
•    Proficiency in R and/or Python required.
•    Proficiency creating R Shiny applications required.
•    Proficiency using GitHub and Docker required.
•    Proficiency in various open source and commercial bioinformatics resources and software required. 
•    Strong knowledge of, and experience with, cancer genomics bioinformatics applications and research preferred.
•    Knowledge of the working mechanism of microarray, NGS, other high-throughput technologies and awareness of their strengths and weaknesses, as well as applicability to a specific biological problem is preferred.
•    Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is required.
•    Ability to correctly select and perform statistical tests for most types of genomic data, and to properly interpret their results in the scenario of a specific study is preferred.
•    Ability to interact with biologists and clinicians during a scientific discussion is required. 
•    Accountability and attention to timelines. 
•    Excellent organization and communication skills with an emphasis on strong presentation skills.
•    Ability to independently plan and execute analyses of moderate complexity required.
•    Ability to provide objective validation of results required.
•    Ability to work in a team environment.

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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