Senior Bioinformatician

CareDx - Brisbane, CA (30+ days ago)3.3


CareDx, Inc., headquartered in Brisbane, California, is a global molecular diagnostics company focused on the discovery, development and commercialization of clinically differentiated, high-value diagnostic solutions for transplant patients. CareDx offers AlloMap®, a gene expression test that aids clinicians in identifying heart transplant patients with stable graft function who have a low probability of moderate to severe acute cellular rejection. CareDx is developing additional products for transplant monitoring using a variety of technologies, including AlloSure®, a proprietary next-generation sequencing–based test to detect donor-derived cell-free DNA after transplantation.

CareDx, with its presence through Olerup, also develops, manufactures, markets and sells high quality products that increase the chance of successful transplants by facilitating a better match between a donor and a recipient of stem cells and organs. Olerup SSP® is a set of HLA typing used prior to hematopoietic stem cell/bone marrow transplantation and organ transplantation. XM-ONE® is the first standardized test that quickly identifies a patient’s antigens against HLA Class I, Class II or antibodies against a donor’s endothelium. For more information, please visit: www.CareDx.com.

Senior Bioinformatician
We are seeking a highly motivated programmer / developer to work in a Bioinformatics group to assist in the construction of software and processes necessary to build bioinformatic and data workflows for clinical tests relating to human organ transplantation. These tests include but are not exclusive to next generation DNA sequencing, digital PCR, and expression analysis of selected genes of interest. Individual should have excellent working skills in multiple programming languages (Perl, bash shell, Java, Python or others), be familiar with manipulating large databases, especially SQL in Oracle databases and be comfortable with Linux environments.

Responsibilities:
Help design and produce bioinformatic data workflows including analytical processing and QC metrics
Implement statistical procedures necessary for data processing and algorithm development
Help develop new next generation sequencing tests for transplantation which may include but not limited to data-mining and bioinformatic evaluation of markers
Work with team to develop additional high data flow diagnostic tests beyond NGS
Prototype, develop, improve, maintain, and apply tools construct pipelines for the management and analysis for large amounts of complex data • Design, build, maintain and monitor current test and data flows
Produce well-written, well-documented, and well-behaved software components
Debug and problem solve production issues, as well as develop appropriate solutions
Evaluates new technologies while keeping up to date with technological developments in relevant areas
Work as part of the cross-functional team

Related Experience:
Approximately 7 plus years programming experience
Work experience with a large complex data sets
Expertise and experience with data manipulation and analysis (ETL)
Professional level code documentation and version control
Database design and implementation experience especially in Oracle
Familiarity with HL7 and EMRs (Epic preferred)

Qualifications:
Bachelor's Degree or Masters degree in Physics, Biology or Computer Science or equivalent experience
Proficiency in programming in Python Perl and Unix / Linux Shell scripting
Experience using Linux command-line tools and writing shell scripts
Experience handling large complex datasets: sequencing (NGS) data, mass-spectroscopy or other biological datasets preferred
Ability to program against REST APIs
Experience with version control tools (preferably git)
Strong team player and self-motivated
Strong quantitative abilities and problem solving skills
Strong attention to detail and process follow-through
Able to work both independently and cross-functionally
Works well in a high-performance team environment
Excellent communication skills, both verbal and written
Drafts complete, clear documentation • Delivers on time
Considers, values and incorporates when appropriate recommendations from others
Experience in biotechnology or genomics settings is a plus
Proficient UNIX/Linux with administration skills is a plus
Experience with relational databases (Oracle preferred), SQL, PL-SQL is a plus
Familiarity with cloud services and cloud management systems would be a plus
Experience with parallel computing a plus
Proficiency in JAVA or C a plus
Experience with regulated environments, i.e. SOX, HIPAA, CLIA, FDA, a plus.

Additional Information:
Benefits & Perks: We provide Medical, Dental, Vision and Life Insurance, Flexible Spending and Dependent Care, Commuter Accounts, 401(k) match, 3 weeks of vacation, 5 days sick leave, 1 personal floating holiday, 9 paid holidays, gym reimbursement, yoga onsite, ping pong, foosball, BBQ’s, social hours, and more!

CareDx, Inc. is an Equal Opportunity Employer