PL Network


Scientific Programmer



Software Engineering
Watertown, MA, USA
Posted on Saturday, June 1, 2024
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 a research associate who has previously developed algorithms to analyze high throughput data. This position will involve the investigation and development of algorithms that are robust in interpreting the many various features of mass spectrometry proteomics data. The successful candidate will work in a 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 implement robust algorithms for deeper interpretation of high throughput proteomics datasets, which will include both bulk and single-cell samples
  • Write clear and reproducible code that includes validation, testing and version control
  • Provide high-quality documentation and annotated code that ensures your work is reproducible and understandable by other team members
  • Collaborate with other scientists to demultiplex proteomics data that use our ever-evolving novel barcoding chemistries
  • 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


  • Bachelor or Master’s degree(s) in Statistics, Mathematics, Computational Biology, Bioinformatics, Computer Science or related field
  • Experience in building computational algorithms. Experience with mass spectrometry proteomics data analysis
  • Proficiency in good practices for reproducible research using tools such as git, Jupyter notebooks, etc
  • Strong quantitative and analytical skills, with a proclivity for reasoning from first principles
  • Highly motivated and organized researcher with strong analytical and coding skills

Preferred Qualifications:

  • Experience with high throughput data analysis

We offer:

  • An opportunity to change the world and work with some of the smartest and the most talented experts from different fields
  • Tuition reimbursement
  • Excellent medical, dental, and vision insurance through a PPO plan; parental leave; wellness allowance
  • Generous time off + paid holidays