Job:Senior Bioinformatician, pipeline development - University of Chicago
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4.6 years ago
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Design and develop high-throughput bioinformatic pipelines for the NCI Genomic Data Commons, a unified knowledge base that promotes sharing of genomic and clinical data between researchers and facilitates precision medicine in oncology.  

Job Description

As a Senior Bioinformatician, you will use strong programming skills to design and implement bioinformatics services for projects in the Center for Data Intensive Science. You will be focused on hands-on technical activities for a wide range of high-throughput genomic technologies spanning pipeline development, optimization, automation, operations, and user support. Projects range from multi-petabyte community platforms such as the NCI Genomic Data Commons, to small-scale research projects with faculty, to multifaceted international collaborations.

Responsibilities will include developing and implementing software methodologies and computational tools as needed, keeping abreast of industry trends and new technologies, and recommending potential solutions based on the latest technical developments. You will use best practices to prototype, develop, execute, test and roll out production quality solutions. You may analyze data of high complexity by applying sound statistical and commonly accepted bioinformatics methods on a collaborative team project. You will shepherd projects as the primary bioinformatics resource to ensure they are managed in a timely and efficient manner, appropriately documented, and provide follow up support services after initial project completion. You may also revise or modify procedures to solve complex problems and work at a high technical level in all phases of data management and bioinformatics support activities.

To be successful in this role, you will work toward a deep knowledge of internally developed systems, open-source programs and pipelines, and cancer genomic datasets. You will work on a team of bioinformaticians, and frequently interact with other engineers across the stack. You will also engage with the bioinformatics community at large on pipeline development and have opportunities to collaborate with internationally recognized leaders in cancer genomics and biomedical informatics. You will participate in the writing and delivery of presentations, grant proposal sections, and manuscript sections.

Education and Experience

Doctoral degree in Bioinformatics, the Biological Sciences, Computer Science, or a related field required. 

Two (2) or more years of experience in the field of bioinformatics required.
Two (2) or more years of experience programming in at least three (3) of the following languages: Python, Java, SQL, XML, Perl, and R required.
Demonstrated experience and proficiency in analysis pipeline development of high-throughput data required.
Hands-on experience with next generation sequencing technologies such as BWA, Novoalign, STAR, GATK, samtools, Picard, and other tools required.
Experience and a working understanding of algorithms, data structures, and scientific programming required.
Experience working on Linux and/or Unix systems required.

Demonstrated experience in the development, optimization, automation, and operations support of analysis pipelines for high-dimensional data including whole-genome, whole-exome, and RNA sequencing data preferred.
Experience in employing high performance computing to solve parallelizable compute problems preferred.
Experience providing bioinformatics services or other service roles preferred.
Experience with project management preferred.
Experience with genomic datasets such as TCGA, TARGET, CGCI, MMRF, and ICGC preferred.
Experience with version control, such as git, preferred.
Experience with both molecular and clinical data preferred.
Experience mentoring early career bioinformaticians preferred.

The Center for Data Intensive Science

The Center for Data Intensive Science is a research center at the University of Chicago that focuses on data science and its applications to problems in biology, medicine, health care, and the environment. We're a dedicated team of researchers and engineers drawing from different backgrounds and ideas to push the boundaries of data intensive science. We develop technology to manage, analyze and share large complex datasets and apply this technology to make discoveries in biology, medicine and health care. Our mission is to pioneer the emerging field of translational data science. Our research interests include data commons, bioinformatics, high performance analytics, virtualized infrastructure, and pipelines for large-scale data analysis. We work closely with researchers at the University of Chicago and others around the world to pursue discovery and make an impact on society.


Apply under Requisition #101933 at or contact us at for questions.


The University of Chicago is an Affirmative Action / Equal Opportunity / Disabled / Veterans Employer.


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