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Bioinformatics Specialist, Sage Bionetworks, Seattle, WA

Bioinformatics Specialist, Sage Bionetworks, Seattle, WA

Sage Bionetworks is a world-leading nonprofit biomedical research organization dedicated to: (1) developing predictive models of disease-related phenotypes through integrative analysis of large- scale genomic data sets; (2) and to connect scientists using our open source compute platform and database to enable active sharing of research to more effectively harness genome-scale data by enabling disease models to be evolved by contributor scientists.

We are seeking a candidate for our data science group to lead the interaction with several external research consortia and to develop bioinformatics processing pipelines in collaboration with scientists and external bioinformaticians. These automated data processing and QC pipelines will be designed to process data derived from most commonly used genomics technologies – but especially RNA-seq and whole genome sequencing. All data is processed and shared through Synapse (www.synapse.org), our software platform, allowing data to be queried, versioned, access controlled, and linked downstream analytical pipelines through provenance records. The effort to support research consortia is central to our efforts to enable collaborative development of disease models by investigators worldwide.

Specific responsibilities include:

• Work within a team of biologists, statisticians and software engineers to compile and format large, high-dimensional data sets for downstream analysis. Detect, model and normalize batch and experimental artifacts in data.

• Support scientists involved in multiple projects both within Sage Bionetworks and external collaborators in developing data processing pipelines, and coordinate these efforts to develop reusable pipelines that synergize into a coherent overall effort.

• Work closely with software development team and communicate requirements and features of Synapse.

• Stay abreast of new biological experimental protocols as experimental technology changes.

• Automate the execution and implementation of new analysis methods using scripting and statistical programming.

• Assist in the evaluation and implementation of data and phenotype curation tools.

Qualifications:

• Candidate will either (1) hold a Masters or Bachelors degree, with 4+ years of significant relevant work experience (2) hold a Ph.D. in computer science, bioinformatics, or related quantitative discipline plus at least 2 years of work experience;

• Experience working with high dimensional genomic data, such as sequencing data, gene expression, genotype, CNV, sequence and/or data from other high throughput biological technologies. Experience working with clinical data is desired. Will have basic expertise in the informatics methods used to analyze these types of data.

• Software development experience, including strong programming skills in a high level language especially Python and/or R. Experience with Linux shell scripting required.

• Strong collaboration, teamwork, and communication skills. Past experience supporting multi- institutional research collaborations or projects desired.

• Desire to work in a core services group supporting a variety of internal and external research projects.

• A desire to change the world and contribute to the elimination of human disease.

Sage Bionetworks, www.sagebase.org, is a medical research organization building advanced predictive models of disease. Sage offers a comprehensive benefits package, including relocation benefits to bring the right talent to the team.
To apply for this position, please contact: datascience@sagebase.org
 
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