15-36797 DBHi DATA INTEGRATION ANALYST II

Description: The Data Integration Analyst II, part of the Enterprise Informatics team in The Department of Biomedical and Health Informatics (http://dbhi.chop.edu) and The Center for Childhood Cancer Research (http://cccr.research.chop.edu) is responsible for the development and operation of integrated research tools, laboratory information systems, reporting applications, data management and analytics systems within a translational research setting for biorepository operations. This individual will 1) create new processes for the CCCR focused specifically on data, 2) utilize multiple integrated tools for day-to-day operations, 3) facilitate data requests, and 4) write ETL processes based on a multi-system and distributed approach to biorepository research in pediatric cancer. This position demands an individual with superior technical and innovative database creation, administration, and programming skills, as well as diplomatic and organizational skills associated with the successful management of resources within a matrix environment. This position also requires a large degree of experience in the modeling of highly complex data types such as those associated with genomics and proteomics. This individual will interact heavily with hospital data transformation and integration initiatives to demonstrate proof-of-concept and to promote the proper representation of translational data and activities created and utilized by the diverse researcher population.

Requirements:

  • BS/BA required, Masters preferred in Computer Science, Information Science, Informatics, Biomedical Engineering, Biological Science or a related discipline.
  • Three to eight years experience in database development, database administration, data management, or related discipline, with progressively more complex projects preferably in a biomedical science or healthcare environment.
  • Previous experience in data modeling, ETL, and applications of highly dimensional data types such as derived from genomics and observational clinical or human subjects research data required.
  • Working knowledge of SQL required.
  • Working knowledge of relational database management systems such as PostgreSQL, MySQL, Oracle required.
  • Working knowledge of one or more of the following required: Python/Django, JavaScript/HTML (as used in Single Page Applications), Java, Scala.
  • Working knowledge of biomedical or healthcare data standards such as HL7, ICD, CPT, SNOMED preferred.
  • Must exhibit excellent oral, presentation, and written communication skills.
  • Experience with source code management, continuous integration, containerization, and automated testing tools and processes is preferred.
  • Project management experience preferred.

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15-36175 BIOINFORMATICS SCIENTIST III

Description: The Bioinformatics Scientist III will apply his or her knowledge of bioinformatics algorithms and analysis platforms to consult with investigators on their projects, analyze data and align with biological systems, and to serve as a collaborative, and sometimes lead, investigator in academic output including assistance in experimental design and grant writing. We are seeking a scientist who has experience in analysis and interpretation of data types including next-generation DNA sequencing, RNA-Seq, CHiP-Seq, DNA and expression arrays, or any other high-dimensional biological data type. This individual will work in a highly skilled, team-oriented environment applying knowledge of cellular, molecular, and computational biology to create novel methods and testable scientific hypotheses. Candidates will have an excellent understanding of the strengths and limitations of commonly used data generating platforms as they apply to experimental endpoints and will readily be able to set expectations and defend results through direct communication with principal investigators and their staff. This position will be able to apply a broad range of statistical methodologies such as generalized linear models, multivariate methods, and machine learning. An expert understanding of systems biology as represented by integrated pathway analysis is expected. This individual must be a functional coder in R, Perl, Python, Java, or other scripting/statistical language. Please note that those individuals who do not possess a strong knowledge of molecular biology and systems should not apply.

Requirements:

  • MS or Ph.D. In a biological, computational or related discipline
  • Five to ten (5-10) years experience in applied bioinformatics, genomics and computational work.
  • Advanced skills utilizing and in-depth knowledge of 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.
  • Ability to write and implement complex computer programs.
  • Knowledge and proficiency in commonly used bioinformatics open source resources and software.
  • Familiarity with repositories of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases.
  • Fluency in ORACLE/SQL, Java, Perl, Python, C, and etc.
  • Proficiency in Unix or Linux operating systems.
  • Strong working knowledge or training in advanced biomedical research.
  • Ability to work efficiently on multiple projects.
  • Ability to choose the correct statistical tests for the problem and help researchers in experimental design.
  • Ability to communicate scientific and informatics concepts to a wide range of audiences.
  • Knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture.
  • Excellent interpersonal skills to interact with both research and technical staff.
  • Ability to work independently with minimal guidance while consistently exercising good judgment.
  • Ability to work in a academic team environment.

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15-35181 RIA PROGRAMMER I

Responsibilities include:

  1. Design, develop, and test software and applications.
  2. Write automated unit and functional tests of complex application logic while adhering to principles and best practices of containerization and continuous integration and deployment.
  3. Document code and generate appropriate technical and user documentation for software and applications.
  4. Manage all code, documentation, and issues in modern source control repositories.
  5. Manage small projects and subprojects within larger initiatives, identifying, tracking, and reporting on tasks and deliverables against project timelines.

Summary:

  1. Develop, test, and implement translational informatics software and application solutions under direct supervision.
  2. Create re-usable open source and proprietary software and application products.
  3. Evaluate, adopt and use multiple technologies to create innovative solutions that have a high impact on data-intensive clinical and translational research.
  4. Continuously learn about a wide variety of biomedical domains in order to translate domain requirements into high-impact technical solutions.
  5. Work independently and as part of a project team in a highly matrixed research environment, including direct interaction with clinicians and biomedical researchers.

Requirements

Required Licenses/certificates/registrations
Epic certifications preferred

Required Education and Experience
Core:

  • BS/BA required in computer science, biomedical engineering, information science, or related field. Substitute years of relevant experience for specific field.
  • Zero to five years of programming experience with progressively more complex projects.
  • Demonstrated track record of continuous learning and adoption of new languages and frameworks.

Clinical Decision Support:

  • Zero to five years of experience developing, configuring, or customizing software in a clinical environment is preferred.

Quality Assurance and Continuous Integration and Deployment:

  • Zero to five years of experience in quality assurance, continuous integration and deployment, configuration management, or other aspect of software and application validation is preferred.

Additional Technical Requirements
Core:

  1. Working knowledge of one or more of the following preferred: Python/Django, JavaScript/HTML (as used in Single Page Applications), Java, Objective C, Cache/Mumps, Scala.
  2. Working knowledge of relational and/or non-relational database application development preferred.
  3. Previous experience in data modeling is preferred.
  4. Experience in healthcare and/or biomedical, genomic data management issues is preferred.
  5. Experience with mobile application (native or web) on Android and/or iOS is preferred
  6. Must exhibit excellent oral, presentation, and written communication skills.
  7. Experience with source management, continuous integration, containerization, and automated testing tools and processes is preferred.

Clinical Decision Support:

  1. Working knowledge of Epic or other electronic health record workflows is preferred.
  2. Experience with Cache/Mumps is preferred.
  3. Experience with health data application programming interfaces such as FHIR or interchange specifications such as HL7 is preferred.

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15-35361 RIA PROGRAMMER II

The Analyst/Programmer II in the Translational Informatics Unit at the Department of Biomedical and Health Informatics (DBHi) develops and implements innovative software and applications that solve challenging problems in the collection, management, analysis and interpretation of biomedical, genomic and clinical data. The successful candidate will create and contribute to DBHi open source projects (http://github.com/chop-dbhi) as well as proprietary products such as mobile health applications and implementations of data science algorithms. We are looking for highly creative people who share our mission to advance child health and who will thrive in a continuous learning environment, acquiring and applying both new technical skills and biomedical domain knowledge. Specifically, the Analyst/Programmer II will:

  • Independently develop, test and rollout translational informatics software and application solutions.
  • Create re-usable open source and proprietary software and application products.
  • Evaluate, adopt and use multiple technologies to create innovative solutions that have a high impact on data-intensive clinical and translational research.
  • Continuously learn about a wide variety of biomedical domains in order to translate domain requirements into high-impact technical solutions.
  • Work independently and as part of a project team in a highly matrixed research environment, including direct interaction with clinicians and biomedical researchers.
  • Contribute to the development, evolution, and implementation of software development methodologies that are optimized to a biomedical research setting.
  • Design, develop, and test software and applications.
  • Write automated unit and functional tests of complex application logic while adhering to principles and best practices of containerization and continuous integration and deployment.
  • Document code and generate appropriate technical and user documentation for software and applications.
  • Manage all code, documentation, and issues in modern source control repositories.
  • Manage projects and subprojects of increasing complexity within larger initiatives, identifying, tracking, and reporting on tasks and deliverables against project timelines.

Requirements

  • BS/BA required, Masters preferred in computer science, biomedical engineering, information science, or related field. Substitute years of relevant experience for specific field.
  • Three to eight years of programming experience with progressively more complex projects.
  • Demonstrated track record of continuous learning and adoption of new languages and frameworks.
  • Working knowledge of more than one of the following preferred: Python/Django, JavaScript/HTML (as used in Single Page Applications), Java, Objective C, Cache/Mumps, Scala.
  • Working knowledge of relational and/or non-relational database application development preferred.
  • Previous experience in data modeling is preferred.
  • Experience in healthcare and/or biomedical, genomic data management issues is preferred.
  • Experience with mobile application (native or web) on Android and/or iOS is preferred.
  • Must exhibit excellent oral, presentation, and written communication skills.
  • Experience with continuous integration, containerization, and automated testing tools and processes is preferred.

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15-35927 POST DOCTORAL FELLOW

A postdoctoral fellow position is open in the Bioinformatics Group at the Department of Biomedical and Health Informatics (DBHI) at the Children’s Hospital of Philadelphia (CHOP), reporting to the Director of Bioinformatics. CHOP postdoctoral fellows receive mentored training in a rich scientific environment that includes both CHOP and University of Pennsylvania research communities.

This position offers the opportunity to work in the research laboratory of Dr. Sharon Diskin at The Children's Hospital of Philadelphia (CHOP) Research Institute, an interdisciplinary institution dedicated to conducting basic, clinical and translational research on conditions and diseases that affect children. Dr. Diskin is an Assistant Professor of Pediatrics in the Division of Oncology and a member of the Genomics and Computational Biology Graduate Group and Abramson Cancer Center at the University of Pennsylvania. Her laboratory is interdisciplinary, encompassing both dry- and wet-bench research aimed at understanding the genetic basis of childhood cancers and response to treatment.

The desired candidate must have a terminal degree (PhD) in computational biology, cancer genetics, computer science, statistics, or related field. The postdoctoral fellow will be responsible for analysis of high-dimensional next-generation genome, transcriptome, and epigenome sequencing and array-based data sets in the childhood cancer neuroblastoma. This will include, but not be limited to, data generated though a neuroblastoma genome-wide association study and the National Cancer Institute (NCI) sponsored TARGET project (https://ocg.cancer.gov/programs/target).

The postdoctoral fellow will assume responsibility for a specific, on-going research project under the direction/guidance of his or her mentor. The postdoc experience will serve to extend, refine and enhance skills necessary for professional and career development, and will enable the individual to broaden his/her scientific background by acquiring new research capabilities. It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the project and the research group. Postdocs will be expected to participate in project planning, recording and interpretation/evaluation of data, and communication of results.

Postdocs will also be expected to acquire technical, lab management, and manuscript/grant writing skills; and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to supervise junior lab members, develop new methods and protocols for research, and assist with the development of other research projects in the lab.

Requirements

  • PhD in computational biology, cancer genetics, computational science, statistics, or mathematics, engineering, genomics/genetics or related fields
  • UNIX/LINUX and high performance computing experience
  • Proficiency in R or similar commonly used statistical languages
  • Basic proficiency with Python, Perl, or other languages
  • Values research integrity and collaborative research
  • Strong research skills
  • Effective problem solving/critical thinking skills
  • Ability to work independently and with a strong work ethic
  • High level of motivation
  • Excellent communication/interpersonal skills
  • Ability to exercise discretion and judgment
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      15-36731 POST DOCTORAL FELLOW

      A postdoctoral fellow position is open in the Bioinformatics Group at the Department of Biomedical and Health Informatics (DBHI) at the Children’s Hospital of Philadelphia (CHOP), reporting to the Director of Bioinformatics. CHOP postdoctoral fellows receive mentored training in a rich scientific environment that includes both CHOP and University of Pennsylvania research communities.

      A postdoctoral fellow position is open in the Bioinformatics Group at the Department of Biomedical and Health Informatics (DBHI) at the Children’s Hospital of Philadelphia (CHOP), reporting to the Director of Bioinformatics. CHOP postdoctoral fellows receive mentored training in a rich scientific environment that includes both CHOP and University of Pennsylvania research communities.

      This position offers the opportunity to work in the research group of Dr. Elizabeth Goldmuntz at The Children's Hospital of Philadelphia (CHOP) Research Institute, an interdisciplinary institution dedicated to conducting basic, clinical and translational research on conditions and diseases that affect children. Dr. Goldmuntz is a Professor of Pediatrics in the Division of Cardiology whose research for the past 20 years has focused on the genetic basis of congenital heart disease and the relationship of genotype to clinical outcome. Her research group is interdisciplinary and highly collaborative, encompassing both dry- and wet-bench research.

      The desired candidate must have a terminal degree (PhD) in computational biology, computer science, statistics, or related field. The postdoctoral fellow will be responsible for analysis of high-dimensional next-generation genome sequencing and array-based data sets derived from large sets of children with congenital heart disease. The postdoctoral fellow will assume responsibility for a specific, on-going research project under the joint direction/guidance of Drs. Goldmuntz and Taylor, head of the Bioinformatics Group in the Department of Biomedical and Health Informatics. The postdoc experience will serve to extend, refine and enhance skills necessary for professional and career development, and will enable the individual to broaden his/her scientific background by acquiring new research capabilities. It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the project and the research group. Postdocs will be expected to participate in project planning, recording and interpretation/evaluation of data, and communication of results.

      Postdocs will also be expected to acquire technical, lab management, and manuscript/grant writing skills; and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to supervise junior lab members, develop new methods and protocols for research, and assist with the development of other research projects in the lab.

      Requirements

      • PhD in computational biology, computational science, statistics, or mathematics, engineering, genomics/genetics or related fields
      • UNIX/LINUX and high performance computing experience
      • Proficiency in R or similar commonly used statistical languages
      • Basic proficiency with Python, Perl, or other languages
      • Values research integrity and collaborative research
      • Strong research skills
      • Effective problem solving/critical thinking skills
      • Ability to work independently and with a strong work ethic
      • High level of motivation
      • Excellent communication/interpersonal skills
      • Ability to exercise discretion and judgment
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          MANDATORY REQUIREMENTS

          • Child Abuse Clearances
          • FBI Fingerprint Clearance
          • Drug Screening
          • Tobacco screening

          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 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.