Computational Scientist - Single-Cell Algorithms

Parallel Squared Technology Institute (PTI) is a non-profit research institute aiming to catalyze a leap in protein analysis technology and use it to explore new biological frontiers. PTI supports open research and educational opportunities supporting rapid career development for scientists, engineers, and mathematicians.

Why? Protein dysfunctions directly cause many diseases, such as Alzheimer’s disease. Yet, proteins remain understudied because of technological hurdles.

How? To resolve these limitations, PTI will develop mass tags enabling a new framework for multiplexed protein analysis by mass spectrometry towards achieving 100-fold increase in throughput. Scientists at and collaborating with the institute will use these gains to directly investigate disease mechanisms and resolve problems that have proven intractable for decades. Our proof of principle technology and strategies are outlined at: parallelsq.org.

New career opportunities

Members of PTI will be supported with industry-level resources to lead research projects and disseminate their discoveries and innovations to the broader biomedical community through frequent publications, presentations, and submissions to public data portals.  

Summary of Position

We are looking for an individual contributor with previous experience in ‘omics data interpretation,  who will lead the design and development of new computational analysis pipelines. This position will involve analyses of mass spectrometry proteomics data in order to infer biological mechanisms at play in either the Alzheimer’s Disease or Immuno-Proteome Aging projects at PTI. The successful candidate will work in a highly interdisciplinary team environment with other scientists. In order to be seriously considered for this position, we require a cover letter as part of the candidate’s application.

• Develop and adapt pre-processing algorithms for mitigation of data collection artifacts
• Work with biological project leads to define hypotheses and apply appropriate statistical framework
• Design and develop optimized analysis pipelines for large ‘omics datasets
• Perform deep and detailed analyses for data-intensive experiments with team members and communicate interpretable results
• Hands-on development of interactive tools for data interpretation of high throughput proteomics datasets for other team members using RShiny, Python, D3, or other tools
• Curate large-scale datasets for internal and external usage
• Mentor scientists and research associates
• Prepare internal reports and manuscripts as well as present results at internal or external scientific meetings as appropriate
• Demonstrate a commitment to diversity, inclusion, and cultural awareness through actions, interactions, and communications with others
• Other duties as assigned

• Advanced degree in Statistics, Mathematics, Bioengineering, Computer Science, or other computational science. 
• Demonstrable professional or PhD experience working with professional biologists on single cell ‘omics questions
• Strong understanding of generalized linear models and nonparametric regression, hypothesis testing, optimization, dimension reduction techniques, and machine learning algorithms
• Advanced proficiency in R and/or Python
• Demonstrable experience with data set alignment, batch correction, cell type assignment, differential abundance testing, and gene ontology mapping
• Experience handling terabyte-scale biological data
• Demonstrable experience with model validation: cross validation, bootstrapping, posterior predictive, or simulation-based model checking

• Experience with proteomics spectral library prediction
• Must have single cell 'omics experience OR experience working with mass spectrometry data

• An opportunity to change the world and work with some of the smartest and the most talented experts from different fields.
• Excellent medical, dental, and vision insurance with many $0 premium options for you and your family with several national and regional providers. Most employees have more than 20 plan options to choose from.
• Company-paid group life, AD&D, long- and short-term disability insurance
• 15 days PTO + 10 sick days per year
• 18 company holidays + your birthday off
• $5,000 per year educational reimbursement
• Up to 16 weeks paid parental leave

We aim to help fill a structural gap in today's R&D system. We enable fundamental research that requires unusual levels of scale and coordination yet is not rapidly monetizable by industry. We’re bringing together top talent from academia, industry, and startups to build a new model for innovative R&D. As an incubator within the Schmidt Futures Network, we identify high-impact scientific or technical research and development opportunities, ultimately defining and launching these projects as Focused Research Organizations.

We are an Equal Employment Opportunity employer that proudly pursues and hires a diverse workforce. We do not make hiring or employment decisions on the basis of race, color, religion or religious belief, ethnic or national origin, nationality, sex, gender, gender-identity, sexual orientation, disability, age, military or veteran status, or any other characteristic protected by applicable local, state, or federal law or company policy. We strive for a healthy and safe workplace and strictly prohibit harassment of any kind.