Bioinformatics Scientist II - DBHi

Philadelphia, PA, US, 19104

​Location: LOC_HOME-Home/Remote Office Location 

Req ID: 223217

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

The bioinformatics group in the Department of Biomedical and Health Informatics (DBHI) at The Children’s Hospital of Philadelphia (CHOP) is seeking a Bioinformatics Scientist to join our team of Bioinformatics Scientists supporting ongoing basic and translational research within the Division of Oncology and Center for Childhood Cancer Research (CCCR). The candidate will be embedded in the CCCR, a highly collaborative environment, and will primarily be focused on supporting scientific teams and projects as a bioinformatics domain expert. The candidate will attend selected lab meetings and interact daily with principal investigators and individual lab members on a project-by-project basis. Additionally, the candidate will work with a principal investigator overseeing the bioinformatics group in the CCCR and our extended bioinformatics group in DBHI to stay current on emerging technologies and algorithms. 


The successful candidate will preferably have a PhD degree in Bioinformatics, Computational Biology, or a related field, and must have demonstrable skills in coding in R and/or Python, though both are preferred. The successful candidate will have had biology training, experience with high-performance and/or cloud-based computing environments, experience in the analysis of sequencing data related to cancer (e.g. somatic single nucleotide variants (SNVs) in indels, structural variations (SVs), fusion transcripts, or copy number analyses) as well as experience in other types of bioinformatics analyses, particularly those involving next-generation sequencing. The successful candidate will have experience with established algorithms/pipelines processing genomics data, and the ability to learn and apply new methods. They will also be able to conceive and develop innovative solutions for a variety of computational challenges of these data. There will be occasional project and data management tasks required for various types of -omics data projects.  Creative data visualization skills are important for this position.


Strong communication, time-management, and presentation skills are essential.  Knowledge of cancer biology and/or genomics is preferred.

Job Responsibilities

Pre-Analysis (20%): 

  • Use and/or develop standard pipelines for data processing and manipulation in advance of performing analysis in a manner that best enables the analysis plan.
  • Modify existing tools or develop new bioinformatics solutions for analytical needs specific to a collaborative research project.
  • Promote incorporation of new bioinformatics solutions into shared pipeline and code resources.
  • Provide transparency of data processing and analysis results, including sample- and cohort-level status for all collaborations projects.

Coding (20%): 

  • Within the context of the collaboration or project, develop and apply best practices to code development.
  • Establish requirements with the project team.
  • Review existing applications and code sources (both commercial and open source) and selection of best strategy for development or adoption.
  • Advocate for chosen strategy to project team by showing value of approach.
  • Develop best practices for project-based code development, QC, and execution consist with the expectations of specific collaborations.
  • Regularly seek peer-to-peer code reviews by participating in informal and formal critical code reviews.

Data Analysis (40%): 

  • 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.
  • Develop robust analysis plans independently with regular peer-to-peer review in both informal and formal settings.
  • Incorporate more advanced applications and methods into analysis.
  • Develop at least one “specialty” analytical or biomedical area that serves the collaborative team.

Job Responsibilities (Continued)

Collaboration (10%):

  • 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.
  • Develop new collaborations.

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.

Required Education and Experience

Required Education: Bachelor’s Degree                                                                    

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.

Preferred Education, Experience & Cert/Lic

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


Preferred Experience:

  • Four (4) or more years of experience in applied bioinformatics, genomics, and computational work. 
  • 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 or similar commonly used bioinformatics language required.
  • Proficiency in various open source and commercial bioinformatics resources and software required.
  • Knowledge of the working mechanism of microarray, NGS, mass spectrometry, or 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.  

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