Bioinformatics Intern/Co-Op

Bioinformatics Intern/Co-Op

Position Overview

This position will work primarily with scientists using high-throughput “omics” data for projects in cancer and neurology. The intern will be mentored by staff bioinformaticians at Sage, with opportunities to participate in projects with other Sage computational biologists as well as with our collaborators.

Benefits of interning at Sage include opportunities to work with a variety of datasets and scientific projects, learn professional software engineering skills in the context of bioinformatics problems, and to further Sage’s mission of promoting open science.

Specific Responsibilities Include

• Process and load diverse omics datasets using the Synapse platform and cloud computing.
• Prototype and test new services for omics data using the Synapse platform, including visualization, documentation, computation, etc.
• Develop R Shiny applications for accesing data.
• Develop and implement standard data quality, formatting and annotation processes.
• Support DREAM challenges sponsored by Synapse.

Basic Qualifications

• Enrollment in an accredited degree program working towards a degree in bioinformatics or a closely-related discipline with at least one term to finish after the completion of the internship.
• Ability to commit to a 6-month, full-time position.
• Programming skills in R or Python.
• Experience with computing in a Unix/Linux environment.

Additional Skills/Preferences

• Graduate students are strongly preferred; exceptional junior- or senior-level undergraduates may be considered.
• Strong verbal, written, and organizational skills.
• Coursework in molecular biology, algorithms, and statistics.

About Sage Bionetworks

Sage Bionetworks is a Seattle, WA based non-profit organization dedicated to advancing biomedical research through the implementation of reproducible, open science. Using cutting edge machine-learning methodologies, in collaboration with scientists around the world, we build predictive models of disease-related phenotypes through integrative analysis of large-scale genomic and imaging data sets. To enhance collaborative efforts, we provide a collaborative compute platform (www.synapse.org) for sharing research insights in a transparent, reproducible fashion.

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Current Positions

Computational Oncology

The Computational Biology group focuses on developing integrative probabilistic models for prediction of disease phenotypes and validating of hypotheses generated by novel methodologies. Currently opportunities include: positions in Oncology focused on conducting original research in analyzing large-scale high dimensional genomics data to develop predictive models of cancer phenotypes. Positions in collaboration with the recently merged Sage/DREAM effort, focused on designing and implementing crowd-sourced collaborative challenges around cancer phenotype prediction problems. Positions in stem cell bioinformatics with a focus on development of the data and analysis bioinformatics portal for the Progenitor Cell Biology Consortium, as well as research projects on modeling molecular mechanisms underlying stem cell differentiation.

Digital Health

Sage Bionetworks’ digital health program is designed to improve disease characterization through the use of sensor-based technologies and bi-directional feedback to improve health monitoring and provide quantitative metrics to assess disease impact on health and on quality of life. We maximize the insights gained from these efforts by providing them through Synapse, a collaborative compute platform. Our mHealth team includes expertise in software engineering (both iOS and Android), clinical study design and development, data governance and data analysis. We are actively involved in projects across a range of disease areas and within the Precision Medicine Initiative.

Neurodegenerative Research

An overarching goal of the Neurodegenerative Research (NDR) group is to improve understanding of the molecular mechanisms of neurodegeneration via computational analyses of high-dimensional genomic data-sets. Our group leads analyses of such data in consortia focused on Alzheimer’s Disease (AD) and related neurodegenerative disorders, including AMP-AD and MODEL-AD. We also work across disciplines to develop technologies that make these analyses available to a wide audience of researchers. Most notably, we recently celebrated the launch of Agora, an interactive, web-based explorer that provides access to research and analyses of nascent AD drug targets produced in conjunction with the NIH-led Accelerating Medicines Partnership.

Systems Biology

The Systems Biology research group at Sage Bionetworks is working to understand the underlying mechanisms causal to common disease. We use large-scale genomic analysis to identify disease subclasses, generate diagnostic and prognostic biomarkers, and to identify pathophysiology causal to disease in collaboration with academic and industry partners. Our current portfolio is focused on neurobiology, spanning both neurodegenerative and neuropsychiatric disorders, and includes projects in other disease areas including immunology, metabolic disease and craniofacial deformation.

Technology Platforms & Services

We’re working on the tools and platforms required to gather, share and use biomedical data in novel ways. These are targeted both at the research community, as well as organizations and individuals who are involved in providing data and being involved in the research process. They range from the technology platforms Synapse and BRIDGE, through novel methods of addressing governance issues around the distribution of human data such as E-Consent, to the ability to run Challenges to solve data-driven questions through our partnership with DREAM.