Job:Bioinformatics Scientist II (Philadelphia, USA)
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7.1 years ago
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The Immunogenetics Clinical Laboratory is part of the Children's Hospital of Philadelphia Division of Genomics Diagnostics and the Department of Pathology & Laboratory Medicine. The Immunogenetics Clinical Laboratory serves the Solid Organ and Stem Cell Transplant Programs at the Children's Hospital of Philadelphia, and additionally, provides transplant support and testing for its outreach partners.

The Immunogenetics Clinical Lab focuses on the role of Histocompatibility (HLA) molecules and of the Major Histocompatibility Complex (MHC) in autoimmunity and transplantation. We are interested in the detailed characterization of the MHC by high throughput DNA sequencing technologies and the identification of polymorphisms important for many HLA-associated diseases and rejection processes in transplantation. The Bioinformatics Scientist will work in a team environment and interact with experts in immunogenetics, bioinformatics, and IT to perform, support, and develop cutting edge clinical diagnostics at CHOP. The responsibilities of the Bioinformatics Scientist include the following.

  1. Apply sequence analysis methods, clustering algorithms, and functional & statistical analysis methods to conduct data mining and in-depth data analysis of genomic data in patients.
  2. Provide bioinformatics support to the Immunogenetics Clinical Lab in the areas of data integration, data management, data visualization, and bioinformatics training.
  3. Consult with lab members on experimental design, process optimization & standardization, perform project requirement analysis, and provide pertinent user support.
  4. Identify software, hardware, and other informatics solutions and implement those tools as prioritized by the Director of the Lab.
  5. Develop pipelines, applications, algorithms, software tools, and database resources as needed to support the clinical pre-analytical, analytical, and post-analytical testing process.
  6. Design, program, test, modify, enhance, maintain, and support applications.
  7. Enable integration and construction of scientific databases and applications in a growing clinical genomics environment.
  8. Leverage existing public and commercial bioinformatics resources and tools.
  9. Assess computer hardware and software requirements for scientific computing.
  10. Coordinate bioinformatics projects and activities with other internal and external partners.
  11. Participate in grant-level collaborations on research projects, and assist with preparing manuscripts and presentations
  12. Assist with organizing and hosting bioinformatics workshops, tutorials, and seminars.

Job Responsibilities:

  1. Perform data analysis for various projects in Immunogenetics Laboratory. Identifies, ports/develops, maintains, and makes accessible all bioinformatics software for Immunogenetics Laboratory as needed. (30%)

    • Primary data analyst for genomics data in the Immunogenetics Laboratory. Includes monitoring and assessment of the data quality, data modeling, and statistical analysis.
    • Design, implement, and execute bioinformatics analysis strategies for various bioinformatics analysis tasks as requested by the Immunogenetics Laboratory.
    • Actively collaborate and communicate with Immunogenetics team and Bioinformatics Core throughout project life-cycles and for pipeline development.
    • Present and deliver analysis results to end-users.
    • Installs, maintains and updates existing software and all related programs. Determines effective porting, implementation, and maintenance plan for optimized use.
    • Continually updates and maintains locally stored datasets required for software, such as IMGT/HLA database.
    • Programs in C, C++, java, perl, or other languages as needed and appropriate.
    • Writes documentation of software implementation, maintenance, and customization according to standard programming protocols.
    • Writes protocols and documentation for tests in compliance with College of American Pathologists (CAP) and American Society for Histocompatibility and Immunogenetics (ASHI) regulatory standards.
    • Help with data presentation for manuscripts and grant proposals.
    • Actively collaborate and communicate with researchers throughout project life-cycles
  2. Works with the Immunogenetics Laboratory to help determine bioinformatic needs. Analyzes user requirements, determines user software, hardware, and data management needs. Based on feedback, implements bioinformatics solutions. Provides training to lab members. (25%)

    • Helps to identify and assess demands, requirements, and effective software solutions for the laboratory.
    • Thoroughly researches market and custom options for fulfilling demand, including functionality, ease-of-use, compatibility, and integration with existing systems, interface, and value. Communicates and establishes relationships with software vendors.
    • Install, implement, maintain, and update commercial and open-source bioinformatics software for common bioinformatics and genomics data analysis.
    • Implement, update and maintain locally stored data resources required for various analysis tasks.
    • Make required software and software/data accessible to end-users.
    • Develop and implement policies, procedures, training materials and design specifications, as needed.
    • Familiarizes end-users with access to and usage of data analysis and data maintenance software, including initial training of software, either through direct interactions or by arranging 3rd party expertise.
    • Develops any customized applications or scripts with friendly graphic or form-based user interfaces, full database access functions and other specific features as required by individual studies. Correctly chooses most efficient programming language(s).
    • Assumes responsibility for troubleshooting, error resolution, and user support. Determines causes of problems as well as resolutions.
    • Provides software and hardware documentation and creates multiple forums for end-user self-assistance in simple problems (FAQs, user groups, help website).
    • Periodically determines the need for and facilitates end-user training sessions.
    • Recognizes areas of improvement in software implementation, usage, and performance; implements improvements as appropriate and suitable for the Immunogenetics laboratory to implement.
    • Assess the bioinformatics interest and learning needs of the laboratory members
    • Train end-users on effective usage of various bioinformatics tools and resources.
    • Develop and distribute training materials for important bioinformatics applications
  3. Establishes direct, efficient, fast, and convenient data flows from data-generating parties to data analysis. (20%)

    • Works closely with the Bioinformatics Core, other data generation core facilities, to create a data pipeline.
    • Establishes methods to allow end-users to seamlessly transfer data from one data realm to another, and to access both data and data analysis tools from their desktop environments if possible. Creates user and group workspaces, websites, ftp repositories, and other solutions to ensure efficiency.
    • Works closely with IS Technical Services to establish and maintain data pipeline.
    • Works with Penn and other shared collaborative groups to establish methods for fast, efficient, and secure cross-institutional data sharing solutions.
  4. Develop bioinformatics application as needed. Standardize workflows (20%)

    • Develop bioinformatics algorithms to meet new data analysis needs or custom requirements.
    • Develop or implement enhancements to existing tools and applications.
    • Write scripts for processing large amount of genomic data.
    • Program in R and/or SAS, C/C++, Perl, SQL, PHP, Java, and HTML required.
    • Train end-users on effective usage of these tools and resources
    • Define and standardize different parts of the data analysis workflow.
    • Define and standardize result delivery mechanisms, formats, and protocols
    • Contribute to bioinformatics process optimization and standardization of Bioinformatics Core processes and services
  5. Helps to manage and maintain computer systems for the Immunogenetics Lab. (5%)

    • Works closely with IS Technical Services to assure proper installation, including upgrades, of new computer systems hardware and software (operating systems, database management systems, network, compilers and all others) for the computing systems acquired by the Immunogenetics Lab.
    • Evaluates system-wide hardware and software requirements. Evaluates vendors; recommends modifications and expansions. Makes recommendations each year for the purchase of new computer system, hardware or software to meet the requirements of the Immunogenetics Lab.
    • Provides annual evaluation of and recommendations for system-wide computer productivity.
    • Works closely with IS Technical Services to manage and maintain the computing systems acquired by the Immunogenetics Lab. Manages user accounts, authorization, system security, backup and recovery, batch and print queue set-up, system resources accounting, and establishment of network and other system administration tasks. Monitors and adjusts system performance.
    • Sets up or assists in the design and maintenance of systems networking for the computing systems acquired by the Immunogenetics Laboratory, in conjunction with Information Systems.
    • Implement, update and maintain locally stored data resources required for various analysis tasks.


  • Master's or PhD degree in Bioinformatics, Computational Biology or closely related fields.
  • Four to five (4-5) years of experience in applied bioinformatics, genomics, and computational work, which can include experience gained from PhD dissertation work.
  • HLA and/or Immunogenetics experience preferred.
  • Demonstrated skills utilizing bioinformatics algorithms, tools and resources, e.g. sequence retrieval, alignment and clustering techniques, expression profiling and protein related analysis, using major databases and data standards in the field.
  • Expertise in nucleic databases both in flat file and relational forms.
  • Experience with Next-Generation Sequencing (NGS) technologies and NGS data analysis preferred.
  • Fluency in ORACLE/SQL, JAVA, PERL, C++, Python, HTML, XML, PHP, R, Matlab, or other languages.
  • Strong working knowledge or training in advanced biomedical research.
  • Proficiency in UNIX, LINUX, Mac OS X, and Windows operating systems.
  • Familiarity with PC/MAC hardware and software.
  • Ability to independently set up and maintain multiple computer systems including cluster/server/workstation/PC/MAC.
  • Excellent interpersonal skills to interact with both clinical lab technical staff and research staff.
  • Ability to work independently with minimal guidance while consistently exercising good judgment.
  • Ability to learn new technologies quickly.
  • Ability to work efficiently on multiple projects.
  • Ability to write and implement complex computer programs.

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.

The 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 The 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).

The 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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