Bioinformatics Scientist III

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Job description

Thermo Fisher Scientific Inc. is the world leader in serving science, with annual revenue exceeding $25 billion. Our Mission is to enable our customers to make the world healthier, cleaner and safer. Whether our customers are accelerating life sciences research, solving complex analytical challenges, improving patient diagnostics and therapies or increasing productivity in their laboratories, we are here to support them.
Location/Division Specific Information:

• Carlsbad, CA
• Biosciences Division

How will you make an impact?

• Directly interact with senior R&D leadership, software, engineers, product and project management to develop and execute project plans that support product development initiatives towards analysis of the transcriptome at the single cell level
• Deliver on executing these plans according to a planned set of milestones, deliverables and timelines.
• Clearly present ideas, designs, algorithms and results to both experts and non-experts in the field
• Create intellectual property

Scientific leadership, significant independence, and strong teamwork are absolutely required.

What will you do?

• Contribute to the new technology development within a multidisciplinary team of scientists focused on a single cell research
• Develop molecular tagging and barcoding designs to uniquely identify thousands of samples
• Design oligos and primers to implement these designs in RT, amplification, barcoding reactions with whole transcriptomes
• Analyzing and troubleshooting NGS data, hidden biases, read structures to support experimental optimization and development of advanced molecular tagging and to provide constructive feedback to the bench scientists
• Developing new and customized NGS single cell analysis tools for internal R&D use and as part of customer-facing production software
• Proactively communicating across functions, especially with cell and molecular biologists to interpret sequence results, propose additional experiments, dynamically adjust designs to support the fast-paced development work
• Contributing to the development of customer-facing software, algorithms, visualization

This role may involve any of the following:

• Assay Design: Optimizing primer designs, RT and PCR reactions, sequencing approaches
• Sequencing Support: Developing a pipeline for assay design through analysis of RNAseq data

• Bioinformatics: Development of data analysis algorithms and tools
• Data Visualization: Developing "intuitive" methods for data visualization

How will you get there?
Education/Experience:

• A graduate degree in bioinformatics, physics, statistics, biological or computer sciences is a strong preference.
• Candidates with a bachelor's degree and a relevant 7+ years of experience in industry will also be considered.
• 3+ years of experience in bioinformatics or a related field
• 2+ years of experience with next generation sequencing data analysis
• Preferred: 1+ years of experience with single cell sequencing or other single cell techniques
• Direct experience with single cell data analysis is preferred.

Knowledge, Skills, Abilities:

• A solid knowledge of next-generation sequencing analysis with a good understanding of software engineering and data analysis principles
• Experience with a custom NGS analysis and troubleshooting of NGS assay designs
• Understanding of the molecular and cellular biology associated with gene expression and sequencing
• Understanding and experience with primer design, PCR technology, and molecular barcoding methods
• Proficiency in Python, R and Shiny, Linux shell scripting. Experience with C++ and Java is a plus
• Background in statistics and experience with standard RNAseq libraries
• Direct experience with single cell transcriptomic analysis is preferred
• Strong communication skills and proficiency in scientific data presentation and visualization
• History of successful collaborative work with molecular biologists and technology development teams

Working Conditions:

• Majority of working time will be spent designing strategies for sequence acquisition and analysis of whole transcriptomes from many single cells
• Significant collaboration between cell and molecular biologists to test designs, analyze and interpret results and change design based on that feedback
• Carrying out analysis of large RNAseq data sets
• Recording activities appropriately in notebooks
• Must be capable of observing and adhering to lab safety standards and protocols
• Must be able to identify deviations from expected outcomes and participate in trouble-shooting those deviations and suggesting alternatives
• Critical to success in this position will be the individual's ability to work independently and to work as part of a high-performing team
• Must be able to work as part of a team in the laboratory (extended R&D team) and as part of a broader cross-functional team (R&D, Project Management, Product Management, Quality, Operations, Marketing, Commercial)

Our global team of more than 80,000 colleagues delivers an unrivaled combination of innovative technologies, purchasing convenience and pharmaceutical services through our industry-leading brands, including Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific, Unity Lab Services and Patheon. For more information, please visit .

Thermo Fisher Scientific is an EEO/Affirmative Action Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability or any other legally protected status.