Bioinformatics Scientist III

Philadelphia, PA, US, 19104

Job Type: 

Req ID: 26449

Shift: Days

Employment Status: AF - Active - Regular - Full Time 

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 lead analytical activities in proteomics and genomics of ongoing research in histone PTMs and cell surface proteins in pediatric hematologic malignancies. The candidate will be expected to work closely with groups in the bioinformatics group in DBHI, and primary Investigators at the Children’s Hospital of Philadelphia and the Proteomics Core Facility at the University of Pennsylvania. 

The candidate should possess in-depth experience in computational genomics and proteomics, particularly in the analysis of next generation sequencing. The successful candidate should be able to independently learn and apply established analytic algorithms/pipelines to genomics and proteomics data, be able to develop innovative algorithms for the analyses of these data, and provide data management for various types of omics data. 

In addition, the candidate should have a strong interest in integrating proteomic data with transcriptome and genomic/epigenomic data. While experience with WGS, WES, RNA-Seq and ChiP-Seq data analysis is not required, the candidate should have a demonstrated ability to learn the implementation of established WGS/WES, RNA-Seq, and ChiP-Seq pipelines and an ability to interpret data from these pipelines with training with bioinformatics collaborators in DBHI. 


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
    • 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
    • Directly manage all elements of project satisfaction and performance relative to scientific project aims
    • Promote continual objective, “hard” discussions about overall health of project and relationship
    • Develop new collaborations with moderate degree of supervision
  • Academic Output (20%): Lead project-based presentations, grant sections, and manuscript sections with subsequent review by peers and mentors
    • Regularly coordinate and write bioinformatics-focused manuscripts and publications
    • Regularly coordinate and lead podium presentations and posters
    • Proactively contribute to entire bioinformatics and other sections of grant and award proposals
Job Responsibilities (Continued)

▪ Basic understanding of statistics
▪ Working experience with next generation sequencing data 
▪ UNIX/LINUX and high performance computing experience 
▪ Proficiency with R as well as Python, Perl, or other scripting languages 

Required Education and Experience

Required Education: Master’s Degree in biological or computational discipline.

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: PhD in biological or computational discipline

Additional Technical Requirements


  • Ability to, under supervision, conceive of, plan, implement, validate, and disseminate entire research projects is required.
  • Ability to assume principal investigator or similar role in academic research is preferred.
  • Strong UNIX/LINUX expertise required.
  • Proficiency in R or similar commonly used bioinformatics language required
  • Experience with Python, Perl, or other languages required.
  • Experience with pipeline or workflow development frameworks preferred.
  • Experience with management and analysis of complex data types required.
  • Proficiency in various open source and commercial bioinformatics resources and software required.
  • Experience with genomic/proteomic data analysis methods required.
  • Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture 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 required.
  • 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 required.
  • Ability to leverage unique knowledge of bioinformatics, applied biostatistics, molecular biology, and measurement platforms for effective scientific discussion with biologists and clinicians is required.
  • Ability to determine most favorable academic output as a primary research outcome is preferred.
  • Ability to objectively critique results and present as valid or questionable, taking into account all aspects of study design, technical issues, and limitations of workflows 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 or nicotine in any form and a negative nicotine screen (the latter occurs after a job offer).

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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Philadelphia, PA 19146 

Phone: 866-820-9288




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