Scientist III Bioinformatics

Job Description:

The Enterprise Genomics Solutions Group (EGS), Thermo Fisher Scientific, is a leading global Genomics Medicine Enterprise Services provider, providing numerous customized population-scale infrastructure and scientific projects globally. The operational portions of our projects involve large-scale genetics studies to catalog normal and disease variation in entire populations. Studies utilize state-of-the-art laboratory facilities deployed by EGS, which integrates and leverages the Life Technologies broad product portfolio of Life Science tools, including the Ion Torrent semi-conductor sequencing technology.

We are seeking a highly motivated individual who wants to make an impact on human disease, and become an integral part of an enthusiastic and dedicated team of Bioinformaticians and Software Engineers, working towards solving genetic disease utilizing Next Generation Sequencing in collaboration with geneticists and medical research collaborators.

This job is an exciting opportunity to be part of the scientific design, validation, and data analysis of gene-panel and genome-scale re-sequencing projects aimed at clinical research and clinical applications. The right candidate will participate in large population-wide studies of genetic disease using gene-panels and whole genome re-sequencing, utilizing their knowledge of existing algorithms, statistical techniques, and a variety available open source and commercial software. This position requires an understanding of complex scientific problems in order to implement novel algorithms and solutions when needed.

ACCOUNTABILITIES:
•Bioinformatics design, implement, and support for gene-panel, exome, and whole genome sequencing software pipelines, algorithms, data QC, and analyses.
•Understand principles of hypothesis testing derived from fields such as biostatistics, statistical genetics, and/or computational biology.
•Be familiar and able to run tests involving the collection, summarization, and analysis of data from various experiments, and follow with the interpretation of results, and inferences
•Be able to summarize the information in reports that are easy to be understood and that reflect in a clear and relevant manner the problem at hand and the next steps to follow, and that are to also easy to be interpreted and reviewed by bioinformaticians, statisticians, molecular biologists, and stakeholders at large.
•Develop, improve, validate, and extend methods for the analysis of next-generation sequencing data.
•Develop novel methods, and extend, adapt and improve existing methods.
•Optimize algorithms in the context of workflows, and identify and utilize appropriate data sets, metrics, and validation methods to improve applications.
•Bring a clinical context to the design and implementation of algorithms and software.
•Deliver working solutions in a specific time period for a defined software release.
•Contribute to and follow requirements, document design and specifications, and follow standards.
•Support bioinformatics analysis of mapping, variant-detection, annotation and interpretation of variants.
•Develop new tools to aid in the analysis of sequencing and variant quality metrics, annotation and interpretation.v •Assess and integrate existing and new tools and data sources within the bioinformatics pipeline.
•Build and maintain knowledge-based for the discovery of novel variation and association with disease.
•Collaborate with software developers, bioinformaticians, and project scientists to ensure project scientific deliverables are met within the pipeline.
•Collaborate with sequencing teams and clinical researchers to qualify bioinformatics pipeline performance.
•Provide rapid and responsive bioinformatics support to population study projects for gene panels and genome re-sequencing. •Develop analysis approaches in support of clinical applications on the Ion Torrent NGS platforms.
•Work effectively with other scientists, engineers, and experimentalists to implement novel or adapt existing approaches to optimize genetic interpretation in downstream applications for the Ion platforms.

ESSENTIAL CHARACTERISTICS
•Excellent written and verbal communications skills.
•Highly motivated and able to work with minimal supervision in a collaborative, team-oriented environment.
•Desire to continuously learn new things across disciplines of genetics, biology, software engineering, bioinformatics and statistical analysis.
•Great at taking initiative and finding out what needs to be improved.
•Constructive behavior and feedback to team members and a positive energy while tackling demanding undertakings.
•Flexible and adaptable to changes, new tasks, and various customer approaches.
•Comfortable to work in an environment that evolves quickly, that necessitates continuous assimilation of information, and that moves at a fast pace.
•Considers new pieces of information an opportunity to grow.

QUALIFICATIONS
Education/Certifications:
•MS/PhD in Bioinformatics Software Engineering, Computer Science, Computational Genetics, or related field of study plus two years of experience in the position offered or two years of Software engineering, computational biology, or related analytical experience.

EXPERIENCE, KNOWLEDGE AND SKILLS:
•Must have experience in: bioinformatics; next generation sequencing; building model in complex arenas; rapid prototyping; ability to contribute to an existing code base; Java and C/C++ on a UNIX platform; algorithm development, computational biology or statistical genetics with application to next generation sequencing; software engineering skills; data analysis skills; understanding of biology and technology; developing methods in one of the following areas: variant detection (SNP's and Indels), structural variation, RNA-Seq, Chip-Seq, cancer genomics, pathway analysis, phenotype prediction based on genetic variation, pharmacogenetics, or annotation
•Be familiar with R, S-PLUS, SAS, or other statistical tools for analyzing data
•Abilities in data manipulation and analysis using tools such as Python/Perl and R/Matlab in a Linux environment.
•Some experience with handling of very large (terabyte-sized) datasets
•Familiarity with various public genomic databases, statistical software tools and packages, bioinformatics algorithms, particularly in the analysis of NGS data;
•Strong communication skills and ability to collaborate effectively with other bioinformatics scientists, software developers and experimentalists.
•Experience with developing and optimizing tools and workflows for mapping, variant detection, annotation, and interpretation for next-generation sequencing data.
•Expertise in scripting languages (Python, Perl), mathematics software (R, Matlab, Mathematica).

Minimum Qualifications (must have)
Education/Certifications:
•MS/PhD in Bioinformatics Software Engineering, Computer Science, Computational Genetics, or related field of study plus two years of experience in the position offered or two years of Software engineering, computational biology, or related analytical experience.

EXPERIENCE, KNOWLEDGE AND SKILLS:
•Must have experience in: bioinformatics; next generation sequencing; building model in complex arenas; rapid prototyping; ability to contribute to an existing code base; Java and C/C++ on a UNIX platform; algorithm development, computational biology or statistical genetics with application to next generation sequencing; software engineering skills; data analysis skills; understanding of biology and technology; developing methods in one of the following areas: variant detection (SNP's and Indels), structural variation, RNA-Seq, Chip-Seq, cancer genomics, pathway analysis, phenotype prediction based on genetic variation, pharmacogenetics, or annotation
•Be familiar with R, S-PLUS, SAS, or other statistical tools for analyzing data
•Abilities in data manipulation and analysis using tools such as Python/Perl and R/Matlab in a Linux environment.
•Some experience with handling of very large (terabyte-sized) datasets
•Familiarity with various public genomic databases, statistical software tools and packages, bioinformatics algorithms, particularly in the analysis of NGS data;
•Strong communication skills and ability to collaborate effectively with other bioinformatics scientists, software developers and experimentalists.
•Experience with developing and optimizing tools and workflows for mapping, variant detection, annotation, and interpretation for next-generation sequencing data.
•Expertise in scripting languages (Python, Perl), mathematics software (R, Matlab, Mathematica).
*LI-JK1
Preferred Qualifications (nice to have)
n/a
EOE


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