Bioinformatics Scientist II

LOC_COLKET-Colket Translational Research Req ID: 77685

Shift: Days

Employment Status: Regular - Full Time 

Job Summary

The Bioinformatics Group in the Department of Biomedical and Health Informatics (DBHI) at The Children’s Hospital of Philadelphia (CHOP) is seeking a Bioinformatics Scientist to join our team of bioinformatics scientists supporting ongoing basic and translational research within the Division of Oncology and Center for Childhood Cancer Research (CCCR). The candidate will be embedded in the CCCR, a highly collaborative environment, and will primarily be focused on supporting scientific teams and projects as a bioinformatics domain expert. The candidate will attend selected lab meetings and interact daily with principal investigators and individual lab members on a project-by-project basis. Dr. Sharon Diskin be will overseeing the bioinformatics group in the CCCR. The successful candidate will work with Dr. Diskin and their direct supervisor, as well as our extended bioinformatics group in DBHI,  to stay current on emerging technologies and algorithms. 

 

The successful candidate 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, experience in the analysis of sequencing data related to cancer (e.g. somatic single nucleotide variants (SNVs) in 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. There will be occasional project and data management tasks required for various types of -omics data 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.
 

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.
•    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.
 

Job Responsibilities (Continued)

Collaboration (10%):
-    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 (10%): 
-    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)

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

Ability to, under supervision, conceive of, plan, implement, validate, and disseminate entire research projects is required.
Ability to assume principal investigator or similar role in academic research is preferred.
Strong UNIX/LINUX expertise required.
Proficiency in R or similar commonly used bioinformatics language required
Experience with Python, Perl, or other languages required.
Experience with pipeline or workflow development frameworks preferred.
Experience with management and analysis of complex data types required.
Proficiency in various open source and commercial bioinformatics resources and software required.
Experience with genomic/proteomic data analysis methods required.
Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture 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 required.
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 required.
Ability to leverage unique knowledge of bioinformatics, applied biostatistics, molecular biology, and measurement platforms for effective scientific discussion with biologists and clinicians is required.
Ability to determine most favorable academic output as a primary research outcome is preferred.
Ability to objectively critique results and present as valid or questionable, taking into account all aspects of study design, technical issues, and limitations of workflows is required.
Accountability and attention to timelines required.
Excellent organization and communication skills, including strong presentation skills required.
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 required.
 

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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CHOP Careers Contact 

Talent Acquisition

2716 South Street, 6th Floor

Philadelphia, PA 19146 

 

 

Posted
11/04/2020
Salary Range
$77,000.00 - 153,000.00
per Year
Salary range estimated by
Location
Philadelphia, PA 19104, US