Bioinformatics Scientist III

Philadelphia, PA, US, 19146

​Location: LOC_ROBERTS-Roberts Ctr Pediatric Research 

Req ID: 230457

Shift: Days

Employment Status: Regular - Full Time 


Seeking Breakthrough Makers   

Children’s Hospital of Philadelphia (CHOP)—named America’s 2022 Best Large Employer by Forbes—offers countless ways to change lives. Our diverse community of more than 20,000 Breakthrough Makers will inspire you to pursue passions, develop expertise, and drive innovation.

At CHOP, your experience is valued; your voice is heard; and your contributions make a difference for patients and families. Join us as we build on our promise to advance pediatric care—and your career. 


CHOP’s Commitment to Diversity, Equity, and Inclusion 

CHOP is committed to building an inclusive culture where employees feel a sense of belonging, connection, and community within their workplace. We are a team dedicated to fostering an environment that allows for all to be their authentic selves. We are focused on attracting, cultivating, and retaining diverse talent who can help us deliver on our mission to be a world leader in the advancement of healthcare for children. 

We strongly encourage all candidates of diverse backgrounds and lived experiences to apply. 

Job Summary

A newly launched Clinical and Translational Data Science Unit (CTDSU) 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 committed to accelerating cures for children with cancer. We’re looking for creative problem solvers who can leverage software and system engineering to perform both upstream and downstream large-scale genomic analysis. You will be involved in brain tumor research and clinical trials projects characterized with multiple next-generation sequencing or microarray technologies (WGS, WXS, Targeted Panel, RNA-Seq, miRNA, methylation, proteomics, scRNA-Seq). The primary goal will be to support precision medicine and clinical decision efforts as part of our ongoing pediatric oncology trials and internal molecular tumor boards for clinical diagnostics.


The candidate will focus on the development of novel methods to implement genomics-driven therapy recommendations for rare pediatric central nervous system tumors, develop novel disease subtyping algorithms, and drive translational research projects across D3b’s diverse units (Translational Imaging, Pre-Clinical Laboratory Research, Bioinformatics). This position will secondarily focus on support for molecular and data integration efforts that drive D3b’s research projects. This position is intermediate level for a PhD-level professional and a 2nd stage position for those with substantial experience without a PhD. Activities occur with minimal supervision with substantial latitude for independent judgment. Development of bioinformatics workflows and processes, and presentation of results are expectations of the position.


The Bioinformatics Scientist will attend project meetings and interact daily with CTDSU and bioinformatics team members and individual lab members on a project-by-project basis. The Scientist will be supervised by the Director of the Clinical and Translational Data Science Unit and work within a multi-disciplinary team within CHOP and with external collaborators.

Desired Candidate Qualifications

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. Demonstrable skills in the application of machine learning models in a clinical oncology context is desired. Experience in the deployment of tools in cloud-based or distributed computing environments is a plus. Experience in the application or development of multi-modal data analysis techniques across genomic and epigenomic data is highly desired.


The successful candidate should have experience in the following areas:


  • Analysis of sequencing data related to cancer (e.g. somatic single nucleotide variants (SNVs), indels, structural variations (SVs), fusions, RNA expression data, and copy number analyses).
  • Application of high dimensional statistical or machine learning techniques to address questions in clinical or translational oncology
  • Setting up pipelines and working in high-performance and/or cloud-based computing environments towards bioinformatics data processing for large-scale projects.
  • Code organization and reproducible workflow experience using Git or Docker.


The following qualifications are also highly desirable:

  • Experience in integrative analysis of multi-modal (genomic, transcriptomic, epigenomic) cancer data in a research or therapeutic context.
  • Experience with established methods for processing genomics data should allow them to develop and benchmark analytical methods.


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 will be asked to share their GitHub/Bitbucket handle and give a project presentation.

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.
  • Lead development of additional pipeline functionality and changes by providing knowledge of both collaboration-specific requirements and bioinformatics discipline advances
  • Coding (10%): Code and generally support code and applications on behalf of collaborative project and/or team.
  • Master best practices for project-based code development, QC, and execution consist with the expectations of specific collaborations
  • Lead peer-to-peer code reviews by participating in informal and formal critical code reviews
  • Data Analysis (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
  • Lead regular peer-to-peer review of analysis plans in both informal and formal settings
  • Develop multiple specialty analytical areas that serve one or more collaborative teams
  • Lead adoption of best practices in specialty analytical or biomedical areas by the bioinformatics group and peers
  • Collaboration (30%): Lead bioinformatics portion of scientific collaborations as the primary bioinformatics resource

Required Education and Experience

Required Education: Master’s Degree

Required Experience: At least five (5) years of experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation.

Preferred Education, Experience & Cert/Lic

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


Preferred Experience:

  • Five (5) 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.

Additional Technical Requirements

  • Strong UNIX/LINUX expertise required.
  • Proficiency in R, Python, and/or perl 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.

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. 

CHOP also requires employees who work in patient care buildings to receive an annual influenza vaccine. Employees may request exemptions for valid religious and medical reasons.  Start dates may be delayed until candidates are immunized or exemption requests are reviewed.  

EEO / VEVRAA Federal Contractor        |              Tobacco Statement 


Nearest Major Market: Philadelphia

Job Segment: Cloud, Open Source, Data Analyst, Medical Lab, Linux, Technology, Data, Healthcare