Bioinformatics Scientist I

Bioinformatics Scientist I

The Children's Hospital of Philadelphia (CHOP)

Philadelphia, PA, United States

Job Summary

A bioinformatician position is open within the Center for Spatial and Functional Genomics at the Children’s Hospital of Philadelphia’s. The candidate will join a strong team involved in spanning both dry and wet lab approaches in order to elucidate the genetic basis of complex traits, principally, in pediatrics. These studies will build on the seminal work that has emerged from genome wide studies conducted at CHOP and at other peer institutions. The successful candidate will be a quick learner and possess excellent communication and organizational skills (including detailed recordkeeping), programming skills, ability to follow established Standard Operating Procedures (SOP) scrupulously, ability to provide constructive feedback, and an analytical aptitude accompanied by curiosity and enthusiasm to learn the biological context of our projects. After a brief initial training period, this individual is expected to perform analyses with minimal guidance, extreme attention to detail, discretion and good judgment. It is expected that this individual will assist the Directors (Drs. Struan F.A. Grant and Andrew D. Wells), and work with our existing bioinformatics team, in analyzing high-throughput datasets generated within the center affiliated laboratories or from the public domain, such as ATAC-Seq, capture Hi-C, Chip-Seq, RNA-Seq, microarray and GWAS. Proficiency with Unix/Linux and at least one of Perl or Python, as well as working knowledge of R are required. Experience with High Performance Computing (HPC) clusters (in particular SGE) and familiarity with version control are highly desirable. Ability to comprehend technical manuals, to become familiar with the necessary biological background and to write clear and precise code documentation is required, as well as ability to critically read relevant scientific articles.

Job Responsibilities

File and data management (5%)
•    Organize files on the server according to the SOP established by our group
•    Contribute to refining existing SOP and defining new ones
•    Systematically compress or clean-up as appropriate to optimize storage usage
•    Accurately record task progress and result file information in our LIMS
Software and pipeline testing (20%)
•    Test software and pipelines, whether developed in house or externally
•    Help debug and troubleshoot software and pipelines as needed
Coding (25%)
•    Write scripts to properly prepare analyses input files as required
•    Write scripts to reformat outputs according to specific requests
•    Write scripts to extract summary results and statistics from analysis outputs
•    Apply best practices to code development and documentation
•    Contribute to our github code repository
Data analysis (40%)
•    Become familiar with the needed biological context
•    Analyze high throughput sequencing or microarray functional genomics data according to protocols established in our group
•    Write clear and detailed technical reports on the analyses done
•    Prepare presentations, complete with visualizations, to explain the results
•    Prepare sessions for browsers such as UCSC Genome and Washington Epigenome browsers
•    Keep up to date with relevant algorithm and software developments
•    Contribute to refine existing analysis protocols and develop new ones
Collaboration (10%)
•    Present results at center affiliated meetings
•    Mine result sets and genetic data sets to extract information relevant to specific requests from our group or collaborators
•    Contribute to manuscripts and grants as needed

Required Education and Experience


Required Education: Bachelor’s Degree in biological or computational discipline.

Preferred Education, Experience & Cert/Lic

Preferred Education: Master’s Degree of PhD in biological or computational discipline.


Preferred Experience: Previous experience in applied bioinformatics, computational, and genomics/proteomics areas.

Additional Technical Requirements

•    Proficiency with UNIX/LINUX required
•    Proficiency with at least one of Perl or Python, including data format conversions and debugging skills, required
•    Working knowledge of R required
•    Ability to quickly learn new programming skills
•    Familiarity with HPC clusters, in particular SGE desirable
•    Familiarity with version control desirable
•    Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, Bioconductor, ENCODE, and NCBI databases desirable
•    Familiarity with statistics desirable
•    Accountability, and attention to detail and timelines required
•    Ability to critically read scientific articles and technical manuals required
•    Ability to write clear and comprehensive code documentation required
•    Ability to interact with biologists and clinicians during a scientific discussion required
•    Ability to communicate and clearly present results as well as write detailed technical reports 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 or nicotine in any form and a negative nicotine screen (the latter occurs after a job offer).

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.

VEVRAA Federal Contractor/Seeking priority referrals for protected veterans.  Please contact our hiring official with any referrals or questions.

CHOP Careers Contact 

Talent Acquisition

2716 South Street, 6th Floor

Philadelphia, PA 19146 

Phone: 866-820-9288

Please apply via recruiter’s website.