Bioinformatics Scientist II

Philadelphia, PA, US, 19104

Job Type: 

COLKET - Colket Translational Research Req ID: 28261

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%): 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.

  • Use standard pipelines for data processing and manipulation in advance of performing analysis in a manner that best enables the analysis plan.
  • 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.


Coding (10%): Code and generally support code and applications on behalf of collaborative project and/or team.

  • 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 (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.

  • 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.


Collaboration (30%): 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.
  • Develop new collaborations with high degree of supervision.


Academic Output (20%): Develop presentations, grant sections, and manuscript sections with subsequent review by peers and mentors.

  • Regularly contribute to bioinformatics-focused manuscripts and publications.
  • Regularly contribute to podium presentations and posters.
  • Contribute to bioinformatics 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: Bachelor’s Degree in biological or computational discipline.                                                                         


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.
  • Experience with genomic/proteomic data analysis methods.
Preferred Education, Experience & Cert/Lic

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


Preferred Experience:

  • Four (4) 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

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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