Job Description

Encodia is developing a new generation of protein analysis tools based on single-molecule protein sequencing. Our goal is to make protein analysis easy and ubiquitous by using a novel technology that encodes peptide sequence information in DNA. The DNA can be read by a DNA sequencer, providing a path to breakthrough proteomics research at a scale that is not practical or cost-effective using current technologies.

Encodia is seeking a Bioinformatics Scientist with deep experience in 1) developing high-performance and efficient algorithms and scientific software for users and/or 2) creating robust and flexible data analysis pipelines

Additionally, experience analyzing complex biological data and communicating results and conclusions to diverse scientific audiences is required. Strong coding skills and problem-solving ability are essential.

Location:

Onsite

Your Responsibilities:

Algorithms and software emphasis:

• Designing, implementing, documenting, and maintaining algorithms and tools for analyzing novel proteomics data.
• Maintaining disciplined coding and data management practices including source control, code review, automated testing, and deployment
• Collaborating across departments to identify and address analytical needs

Pipeline emphasis:

• Developing and managing production NGS analysis pipelines that run on a Linux cluster
• Writing novel bioinformatics algorithms to analyze large-scale data
• Establishing disciplined coding and data management practices including source control, code review, automated testing and deployment, databases

Both:

• Using probabilistic, statistical, and machine learning methods in the development of algorithms to decode proteomic signals
• Collaborating across departments to identify and address analytical needs
• Assay Development
• Engaging with molecular biologists in their language
• Debugging experimental results
• Understanding quality control metrics
• Developing new metrics and visualizations to aid in understanding experimental results

What you bring to this role:

• PhD in Computer Science, Bioinformatics, Computational Biology, or a related field with 8-10 years experience
• Expertise with high throughput ‘omics data analysis
• Self-motivated with the ability to work with and support multiple groups across the organization
• Experience with command-line Linux environments
• Knowledge of git or other version control systems.
• Expert in NGS data processing and data analysis
• Expert Python programmer for analytics and visualization

Algorithms and software emphasis:

• Deep knowledge of bioinformatics algorithms related to alignment and quantification
• Experience building scientific software that is used by other bioinformaticians and/or biologists
• Programming experience in Python as well as higher performance languages/toolkits (e.g. C++/Rust/Julia/CUDA)

Pipelines:

• Experience with pipeline workflow systems (e.g., Snakemake, Nextflow)
• Experience analyzing large-scale data with statistical methods

Highly Desirable (optional):

• Experience working in a startup environment
• Quantitative proteomics experience (e.g. mass spectrometry)
• Machine learning, especially as applied to biological data
• Experience with assay development, from concept through to product

Encodia Benefits:

Encodia is an Equal Opportunity Employer. We offer a competitive and comprehensive employee benefits package including medical, dental, vision, LTD & life insurance, a wellness reimbursement plan, flexible paid time off (PTO), paid parental leave and a stock plan.

Compensation:

$157,000 - $243,500

While compensation decisions are dependent on the facts and circumstances of each case, it is not typical for an individual to be hired at or near the top of the range for their role.

We do not discriminate in recruitment, hiring, training, promotion or other employment practices for reasons of race, color, religion, gender, national origin, age, sexual orientation, gender identity or expression, marital or veteran status, disability, or any other legally protected status. We are committed to building diverse teams, and we strive to create an inclusive workplace that cultivates bold innovation through collaboration and empowers our people to unleash their full potential.

Don't meet every single requirement?

At Encodia, we are dedicated to building a diverse and inclusive workplace, so if you are excited about this opportunity but you don't check all the boxes in the job description, we encourage you to apply anyway.

You may be just the person we are looking for.

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