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Bioinformatics Scientist II

Date: Mar 11, 2017

Location: Philadelphia, PA, US, 19104

Company: CHOP

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Job Description

Req ID: 6709

Shift: Days

Employment Status: AF - Active - Regular - Full Time 

Job Summary

We are seeking a research scientist to lead the computational proteomics and bioinformatics analyses of ongoing research in histone PTMs and cell surface proteins in pediatric hematologic malignancies. The candidate will be expected to work closely with 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 proteomics, particularly in the analysis of histone PTMs and cell surface proteins, be able to independently apply established analytic algorithms/pipelines to these data, be able to develop innovative algorithms for the analyses of these data, and provide data management for proteomic data. In addition, the candidate should have a strong interest in integrating proteomic data with transcriptome and genomic/epigenomic data. While experience with RNA-Seq and ChiP-Seq data analysis is not required, the candidate should have a demonstrated ability to learn the implementation of established RNA-Seq and ChiP-Seq pipelines and an ability to interpret data from these pipelines with training with bioinformatics collaborators in the Department of Biomedical and Health Informatics at CHOP.

Job Responsibilities

Pre-Analysis (20%): 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 (20%): 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 (20%): 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 (20%): 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

Required Education and Experience

  • BS/MS/PhD in biological or computational discipline.
  • 3-7 years’ experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation.
  • Strong UNIX/LINUX expertise required.
  • Proficiency in R or similar commonly used bioinformatics language required.
  • Experience with management and analysis of complex data types required.
  • Proficiency in various open source and commercial bioinformatics resources and software required.
  • Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is required.


Preferred Education, Experience & Cert/Lic

  • Experience with Python, Perl, or other languages preferred.
  • Experience with pipeline or workflow development frameworks preferred.
  • Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture preferred.
  • 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.
  • 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.

Additional Technical Requirements

  • 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. 


Nearest Major Market: Philadelphia

Job Segment: Hematology, Informatics, Linux, Unix, Healthcare, Technology, Research

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