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Bioinformatics Scientist II - Maris Lab

Philadelphia, PA, US, 19104

Location: LOC_HOME-Home/Remote Office Location 

Req ID: 145735

Shift: Days

Employment Status: Regular - Full Time 

Job Summary

The Maris Laboratory is seeking a highly motivated and experienced Bioinformatics Scientist to join a dynamic multidisciplinary team focused on developing novel CAR T cell immunotherapies for pediatric cancer patient populations with high unmet needs. The successful candidate must have demonstrable skills in coding in R and/or Python. The successful candidate will have had biology training, experience with high-performance and/or cloud-based computing environments, experience in the analysis of next-generation sequencing data related to cancer (e.g. somatic single nucleotide variants (SNVs), indels, structural variations (SVs), fusion transcripts, or copy number analyses) as well as experience with structural bioinformatics. 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. There will be occasional project and data management tasks required for various projects. Creative data visualization skills are important for this position. Strong communication, time-management, and presentation skills are essential. Knowledge of cancer biology and/or genomics is preferred. The bioinformatics scientist will work as part of local and international multidisciplinary teams funded by a St. Baldrick’s Foundation/Stand Up To Cancer and the Biden Cancer Moonshot initiatives, and will benefit from exposure to local and off-site expertise.  

 

The Preferred candidate will have a PhD degree in Bioinformatics, Computational Biology, Biophysics, Cancer Biology, or a related field. The preferred candidate will have experience coding in both R and python, experience working with next-generation sequencing data structural bioinformatics, and be able to work efficiently both independently as well as in a team setting.

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

Job Responsibilities

•    Use and/or develop standard pipelines for data processing and manipulation in advance of performing analysis in a manner that best enables the analysis plan.
•    Modify existing tools or develop new bioinformatics solutions for analytical needs specific to a collaborative research project. 
•    Promote incorporation of new bioinformatics solutions into shared pipeline and code resources.
•    Provide transparency of data processing and analysis results, including sample- and cohort-level status for all collaborations projects.
 

 

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 (40%): 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.

  • 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.

  • 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

  • Strong UNIX/LINUX expertise required.
  • Proficiency in R or similar commonly used bioinformatics language required.
  • Proficiency in various open source and commercial bioinformatics resources and software 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 preferred.
  • 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 preferred.
  • 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.

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.

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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Philadelphia, PA 19146 

 

 

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