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Seeking Breakthrough Makers

Children's Hospital of Philadelphia (CHOP) offers countless ways to change lives. Our diverse community of more than 20,000 Breakthrough Makers will inspire you to pursue passions, develop expertise, and drive innovation.

At CHOP, your experience is valued; your voice is heard; and your contributions make a difference for patients and families. Join us as we build on our promise to advance pediatric care-and your career.

CHOP's Commitment to Diversity, Equity, and Inclusion

CHOP is committed to building an inclusive culture where employees feel a sense of belonging, connection, and community within their workplace. We are a team dedicated to fostering an environment that allows for all to be their authentic selves. We are focused on attracting, cultivating, and retaining diverse talent who can help us deliver on our mission to be a world leader in the advancement of healthcare for children.

We strongly encourage all candidates of diverse backgrounds and lived experiences to apply.


A Brief Overview

The bioinformatics group in the Department of Biomedical and Health Informatics (DBHI) at Children's Hospital of Philadelphia (CHOP) is seeking a Bioinformatics Scientist to join our team to support ongoing basic and translational research within the Center for Childhood Cancer Research (CCCR) and the Department of Anesthesiology and Critical Care Medicine. The candidate will be embedded in the laboratories of Dr. Caroline Diorio and Dr. Robert B. Lindell and will support scientific projects focused on immune dysregulation disorders related to infection, or due to cancers or cancer therapies. Major areas of focus will be CAR-T and cytokine release syndrome/immune effector cell associated neurotoxicity syndrome, and the immunologic phenotypes of sepsis. The candidate will attend lab meetings and interact daily with principal investigators and individual lab members. Additionally, the candidate will work with a principal investigator overseeing the bioinformatics group in the CCCR and our extended bioinformatics group in DBHI to stay current on emerging technologies and algorithms.

The successful candidate will preferably have a MS degree in Bioinformatics, Computational Biology, or a related field, and must have demonstrable skills in coding in R and/or Python, though both are preferred. The successful candidate will have had biology training, experience with high-performance and/or cloud-based computing environments and will be expected to analyze data generated from proximity extension assays (i.e. Olink), bulk RNA sequencing, and multiparameter flow cytometry. Additionally, the successful candidate is expected to have experience with single cell RNA sequencing somatic single nucleotide variants (SNVs), indels, structural variations (SVs), fusion transcripts, or copy number analyses as well as experience in other types of bioinformatics analyses, particularly those involving next-generation sequencing. The successful candidate will have experience with established algorithms/pipelines processing genomics data, and the ability to learn and apply new methods. They will also be able to conceive and develop innovative solutions for a variety of computational challenges of these data and develop creative data visualizations. Strong communication, time-management, and presentation skills are essential. Knowledge of cancer biology and/or genomics is preferred.

The Bioinformatics Scientist I position is an entry level position for a non-PhD level professional. The focus of the position is development, maintenance, and evolution of the tools that support management and analysis of genomic, proteomic, and other complex molecular data types. This includes the support of internal bioinformatics software, implementation and modifications of existing algorithms, and execution of routine tasks of limited complexity within the general area of bioinformatics analysis. The position allows for a wide variety of activities described within the job responsibilities and encompasses positions within both research and clinical environments. All activities occur with a moderate to high degree of supervision and the individual will rely on a high degree of peer-to-peer mentorship. The Bioinformatics Scientist I is primarily focused on the support of higher level bioinformatics personnel but may have minor direct interaction with collaborators and designees to resolve primarily technical issues and solutions.

What you will do

• Pre-Analysis (40%): Contributes to the maintenance and development of bioinformatics tool portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications. Provides efficient data management support.
• Works with bioinformatics group members to develop functioning pipelines upstream of customized analysis workflows.
• Maintains pipelines by staying current with evolving algorithms and standards and incorporating into pipeline.
• Executes robust development testing for commonly used applications such as data processing pipelines.
• Optimizes performance of applications by working with scientific computing and information systems groups to optimize hardware/software parameters.
• Defines and prioritizes requirements for pipeline development over time to incorporate new technologies and platforms via functional communication with bioinformatics group members and bioinformatics end users.
• Identifies appropriate open-source and commercial products that serve needs of pipeline and/or customized analyses of end users.
• Implements and maintains commercial and open-source software for common bioinformatics and genomics data analysis.
• Implements, updates and maintains locally stored data resources required for various analysis tasks.
• Provides ad hoc support and one-on-one and group-based training on key bioinformatics software, features, and workflows.
• Provides efficient data management support including file transfers, data formatting and manipulation, and basic integration of data from a variety of experimental and reference resources.
• Develops and maintains working relationship with data providers such as sequencing cores within CHOP and infrastructure groups such as information systems.
• Continually keeps abreast of evolving data generation platform fundamentals, file-specific information representation, and strategic application of code base to optimize value of data.
• Maintains working knowledge of available commercial and openly accessible knowledge bases as they apply to bioinformatics analysis.
• Coding (30%): Codes and generally supports both ad hoc, single task applications and larger pipeline applications that may combine multiple 3rd party and internally developed applications for genomics/proteomics/other complex data types and projects.
• Implements, maintains, and regularly contributes to formal and bioinformatics group-centralized code management system.
• Adopts appropriate forking and other strategies for robust code development. Apply to general bioinformatics group code base.
• Adopts best practices for code development consistent with larger bioinformatics group. This includes choice of language based on the type of solution being developed, the likely life cycle and downstream usage of the resulting application, and integration with other systems.
• Ensures that all routinely used tools (e.g. those included in shared analysis pipelines) are versioned and managed through a source control system.
• Ensures that configuration files that provide parameters to algorithms and analysis software are versioned and managed through a source control system.
• Develops and implements automated data-driven testing processes that test reproducibility of results between versions of pipeline software.
• Develops and implements automated deployment processes that build and configure systems from source control repositories, eliminating the need to manually modify configuration files.
• Regularly documents code, troubleshoot, and provide training when necessary.
• Data Analysis (10%): Analyzes data of high complexity by applying sound statistical and commonly accepted bioinformatics methods to -omics data under supervision from mentors and peers.
• Develops robust analysis plans under supervision.
• Incorporates QA/QC in analysis workflows.
• Delivers analytical endpoints such as feature identification, annotation, characterization, prioritization, etc.
• Reports results using, primarily, spreadsheets and, secondarily, abstracted materials such as slides and visuals.
• Collaboration (10%): Works with both bioinformatics group members and end users/clients to understand specific needs in bioinformatics and end user-specific domains.
• Attends group and team meetings and contributes primarily factual information regarding processes and approach.
• Defers to mentors and peers in establishing relationships, but works within boundaries to accomplish analytical goals.
• Academic Output (10%): Contributes to presentations, grants, and manuscripts under supervision by mentors and peers.

Education Qualifications

• Bachelor's Degree Required
• Master's Degree biological or computational discipline Preferred

Experience Qualifications

• At least one (1) year in applied bioinformatics, computational, and genomics/proteomics experience.

Preferred Experience

• Four (4) or more years of experience in applied bioinformatics, genomics, and computational work.
• Knowledge of cancer biology and/or genomics.

Skills and Abilities

• Strong UNIX/LINUX expertise required.
• Experience with R strongly preferred.
• Experience with Python, Perl, or other languages preferred.
• Experience with pipeline or workflow development frameworks preferred.
• Experience with data management preferred.
• Familiarity with open source and commercial bioinformatics resources and software preferred.
• Experience with genomic data analysis 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.
• Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases is preferred.
• Accountability and attention to timelines.
• Excellent organization and communication skills with an emphasis on strong presentation skills.
• Ability to work in a team environment.

To carry out its mission, CHOP is committed to supporting the health of our patients, families, workforce, and global community. As a condition of employment, CHOP employees who work in patient care buildings or who have patient facing responsibilities must be fully vaccinated against COVID-19 and receive an annual influenza vaccine.

Employees may request exemptions for valid religious and medical reasons. Start dates may be delayed until candidates are immunized or exemption requests are reviewed.

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