Software Engineer

SecureBio, LLC; Cambridge (MA); On-site; USD 165,000 - 195,000; Full time

Benefits offered by this job

401(k) match

Unlimited PTO

Parental leave (min 12 weeks)

Job summary

SecureBio, LLC in Cambridge, MA seeks a software engineer to build and strengthen pipelines for a pandemic early warning system. You will design features, optimize performance, and enhance detection accuracy, shaping data models for growing sequencing data volumes.

Join a mission-driven team focused on biosecurity. The role emphasizes robust testing, thoughtful algorithm design, and collaboration with cross-functional stakeholders in a rapid, results-driven environment.

Qualifications

• 2+ years of professional software engineering experience.
• Strong fundamentals: reliable, maintainable code and solid design.
• Rigorous testing mindset and awareness of failure modes.
• Creative algorithm design.
• Experience with distributed or cloud-based data pipelines.
• Proficient programming skills in a language of your choice with a solid execution model.
• Enthusiasm for using AI tools to boost velocity.
• Clear communication and strong technical specification writing.
• Good judgment in prioritizing projects and approaches.
• Interest in biosecurity and pandemic prevention.

Responsibilities

• Design and build new pipeline features from prototype to production.
• Benchmark pipelines, identify bottlenecks, and optimize performance.
• Improve the accuracy of detection algorithms.
• Design schemas and data models for large sequencing data volumes.
• Build internal tooling to accelerate the team and pipelines.
• Stay current with AI progress and creatively apply AI to workflows.

Skills

Distributed pipelines

AI acceleration

Testing & reliability

Algorithm design

Communication

Code quality

Tools

Python

Rust

Nextflow

Terraform

AWS

Job description

• Approximate compensation: $165,000 - $195,000
  
• Visa sponsorship: not available
  
• Work location: in-person in Cambridge, MA strongly preferred

Role Overview

SecureBio is a nonprofit working to protect the world from catastrophic pandemics. As advances in biotechnology lower the barriers to engineering pathogens, our mission is to ensure humanity’s detection and alert systems are ready. As part of this mission, our Detection team is building a pathogen-agnostic pandemic early warning system: we operate the world’s largest metagenomic biosurveillance network, which performs daily sequencing of wastewater samples and nasal swabs to screen for emerging pathogens. Our computational team develops detection pipelines responsible for rapid processing of deep sequencing data in order to flag potential threats.

In pandemic early detection, speed is critical: novel pathogens spread exponentially, so every day of delay means many more people are infected by the time of detection. To meet this challenge, SecureBio Detection plans to more than double our sampling frequency and sequencing volume (currently ~50 billion read pairs per week) while reducing computational end-to-end time from ~12 hours to ~2 hours.

As our early warning system scales, we’re looking for a software engineer to help us build out and strengthen the pipelines behind it. This is a broad software engineering role: you’ll develop new pipeline capabilities, improve the performance and accuracy of our detection algorithms, build internal tooling, and shape how we model and store our data. Prior experience with biology or bioinformatics is not required.

Responsibilities

• Pipeline development: design and build new pipeline features and stages, from prototype to production.
  
• Pipeline performance: benchmark pipelines, identify bottlenecks, and implement optimizations.
  
• Pipeline accuracy: improve the sensitivity and specificity of our detection algorithms.
  
• Data modeling and databases: design schemas and data models that keep our growing volume of sequencing data queryable and maintainable.
  
• Internal tooling: build tools and abstractions that make the team faster and the pipelines easier to work with.
  
• AI acceleration: stay current with rapid AI progress and creatively use AI tools to accelerate your work.

Qualifications

Must have

• 2+ years of professional experience in software engineering or a related field
  
• Strong software engineering fundamentals: reliable, maintainable code and sound software design
  
• A rigorous approach to testing and reliability – you write well-tested code and think carefully about failure modes
  
• Creativity in algorithm design
  
• Experience with distributed or cloud-based data pipelines
  
• Strong programming skills in a language of your choice, with a robust mental model of that language’s execution
  
• Enthusiasm and ability to use AI tools to complement your skills and boost your velocity
  
• Careful listener, strong communicator, and writes excellent tech specs
  
• Judgment and taste in prioritizing projects and selecting technical approaches
  
• Excited about biosecurity and pandemic prevention

Nice to have

• Proficiency with performance patterns across the full stack, e.g.memory access patterns, networking, and algorithm asymptotic complexity
  
• Experience with workflow orchestrators like Nextflow, Flyte, Airflow, etc.
  
• Experience managing cloud resources via infrastructure as code
  
• Experience with tools and technologies we currently use, including Python, Rust, Nextflow, Terraform, or AWS
  
• Experience processing large-scale sequencing data

Logistics and benefits

This is a full-time in-person role located in our Cambridge, MA office. For exceptional candidates, there may be flexibility on remote/hybrid work and starting salary. Depending on prior experience and demonstrated skills, this role may be hired at the Software Engineer or Senior Software Engineer level.

Flexible work hours; unlimited paid time off (PTO) for all employees; and minimum 12 weeks fully-paid parental leave.

401(k)

Employer 401(k) match up to 4% of total salary.

Relocation & commuter support

Free commuter benefits up to $250/month, plus a generous relocation allowance for employees who move to the Boston area.

Referral bonus

We offer a referral bonus of up to $6,000 to individuals who refer successful candidates for this position:

To receive these bonuses, we must reasonably believe that you were responsible for referring the candidate to us (e.g.due to you introducing them to us when we didn’t previously know them, or them mentioning you on their application as the reason they heard about the position).

• If you refer a candidate that we invite to an in-person work trial, you will receive $1,200;
  
• If the candidate accepts a job offer from us, you will receive a further $4,800, for a total of $6,000.