[R-jobs] Bioinformatics Job

Mike Kellen m|ke@ke||en @end|ng |rom @@geb@@e@org
Mon Apr 1 17:24:04 CEST 2013

*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) 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.

Central to our mission of advancing open science is our publicly available
genomics Commons, which currently contains over 17,000 curated,
standardized, and analysis-ready datasets.

We are seeking an exceptional candidate to lead the development of the
processing pipelines to seed the Commons and support scientific projects
using this data in research. 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 our Synapse software platform,
allowing data to be queried, versioned, access controlled, and linked to
downstream analytical pipelines through provenance records. The effort to
build the Commons 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 within Sage
Bionetworks in developing data processing pipelines, and coordinate these
efforts to develop reusable pipelines that synergize into a coherent
overall effort to develop the Commons.

���     Work closely with software development team and communicate
requirements and features of Synapse to help create maximum value of the

���     Help develop strategy, including how to best differentiate from
existing efforts, and how best to integrate functionality of these efforts.

���     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.

���     Work with scientific staff to utilize data resources in research

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


���     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.

���     Experience managing  large data volumes, as in a core facility or
other high throughput lab.

���     Software development experience, including strong programming skills
in a high level language especially R and/or Python. Experience with Linux
shell scripting required.  Experience with database development and/or
cloud hosted IT infrastructure (especially AWS) is a plus.

���     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.

���     Ability to drive projects to completion in a rapidly changing,
start-up environment.

���     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.  Compensation level is flexible, depending on
level of experience and expertise.

To apply for this position, please contact: sw.jobs using sagebase.org.

Michael Kellen, Ph.D.
Director, Technology Platform and Services
Sage Bionetworks

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