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) building and supporting an open source compute platform and database to more effectively harness genome-scale data by enabling disease models to be evolved by contributor scientists with a shared vision to accelerate the elimination of human disease.We are leading a national effort to build an integrated data and analysis portal serving as a Bioinformatics Core facility for the NHLBI-funded Progenitor Cell Biology Consortium (PCBC). By serving as the central analytic resource for one of the largest stem cell focused efforts in the world, we expect the PCBCBioinformatics Core will become a central computational resource for the stem cell research community. The Bioinformatics Core will leverage Sage’s Synapse software platform and integrate closely with co-investigators from Harvard, Cincinnati, and Gladstone Institutes to integrate functionality developed by their groups, such as Stem Cell Commons, Galaxy, ToppGene, Cytoscape, and AltAnalyze.
We are seeking an exception candidate to lead this effort. The PCBC Bioinformatics Core will serve a central data processing and hosting capability for data generated throughout the PCBC as well as related publicly available stem cell datasets. Extracting maximum scientific value from these PCBC projects requires: 1) sophisticated computational tools and pipelines that carry out consistent and genome-knowledge-aware data processing; 2) detailed data standardization; 3) the ability to share, analyze, and compare all raw, processed, and analyzed data with the PCBC and the broader scientific community; 4) the construction or adaptation of flexible user-driven computational tools that allow further focused analyses; and 5) that the Bioinformatics Core provides help and collaborative resources to assist Consortium investigators data analyses.
Specific responsibilities include:
• Work with software engineers from Sage Bionetworks and other institutions involved in the Bioinformatics Core to develop the PCBC data and analysis portal.
• Work closely with developers from Synapse, Stem Cell Commons, Galaxy, ToppGene, Cytoscape, AltAnalyze, and related efforts to integrate analytical functionality into a centralized resource.
• Develop data processing pipelines to provide reusable, standardized software to process PCBC-generated omics data into analysis-ready formats. Data processing workflows will support all major technologies used in PCBC projects, including RNAseq, miRseq, ExomeSeq, ChIP-seq.
• Develop analytical pipelines, including integration of existing efforts, for analyzing differential gene expression and pathway signatures and functional drivers of stem cell differentiation.
• Help develop strategy for the PCBC Bioinformatics Core.
• Help with grant writing efforts for extensions and collaborative projects working with the Bioinformatics Core.
• Automate the execution and implementing new methods using scripting and statistical programming.
• Work with scientific staff to utilize data resources in research projects.
• Assist in the evaluation and implementation of data and phenotype curation tools.
Qualifications:
• Preferred candidate will hold a Ph.D. in computer science, bioinformatics, or related quantitative discipline plus at least 2 years of work experience. Strong candidates will also be considered holding Masters or Bachelors degree, with 6+ years of significant relevant work experience and strong track records of bioinformatics tool development.
• 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.
• Professional software development experience, including strong programming skills in a high level language such as Python, R, or Java. Experience with database development is a plus.
• Strong collaboration, teamwork, and communication skills.
• 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: compbio@sagebase.org.
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