FL103 | Cambridge, MA Scientist, Computational Biology

Flagship Pioneering; Cambridge (MA); On-site; USD 115,000 - 165,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering's FL103 project in Cambridge, MA seeks a highly motivated computational biologist to help build a core platform for liquid biopsy technologies. You will develop pipelines for proteomics and transcriptomics, integrate diverse datasets, and apply ML to identify disease biomarkers and assay features.

You will collaborate with biologists, engineers, and leadership to design experiments, validate hypotheses, and ensure analyses are reproducible and well documented as the company

Qualifications

• PhD in computational biology or related field with 2–4 years of industry experience.
• Experience supporting wet-lab experimental design.
• Understanding of NGS approaches and ability to collaborate with experimental biologists.
• Experience analyzing -omics data (single-cell and bulk RNA-seq, mass spec) using R or Python.
• Strong hands-on experience with mass spectrometry proteomics data including raw data processing, QC, normalization, and feature extraction.

Responsibilities

• Develop, maintain, and scale computational pipelines for proteomics, transcriptomics, and internal assay data.
• Integrate multi-modal biological datasets to identify disease-relevant molecular patterns and biomarkers.
• Apply statistical, ML, and bioinformatics methods to improve assay performance and interpretability.
• Collaborate with biologists, assay developers, and leadership to design experiments and validate hypotheses.
• Build internal tools and dashboards for scientists to explore FL103 data.
• Develop workflows connecting internal findings with external scientific evidence.

Skills

Computational biology

Bioinformatics

Machine learning

Statistics

NGS data analysis

Data visualization

Scientific programming

Education

PhD in computational biology

Tools

R

Python

NGS data processing

Mass spectrometry software

Job description

What if… you could help build a life sciences company developing breakthrough technologies to transform how disease is detected,monitored, and treated?

Liquid biopsies have opened the possibility of understanding disease through minimally invasive biospecimens rather than relying solely on tissue biopsies and other invasive procedures. Yet today’s liquid biopsy technologies still capture only a fraction of the biology needed to detect disease early,monitorprogression, and guide intervention across many high-burden conditions. As a result, many diseases are still diagnosed only after symptoms emerge or after invasive testing, limiting the opportunity to intervene when treatments may have the greatest impact.

FL103 was founded by Flagship Pioneering, an innovation enterprise dedicated to originating and developing companies that invent breakthrough technologies to transform health care, agriculture, and sustainability. Since Flagship’s founding in 2000, the firm has originated and fostered more than 100 scientific ventures, including Moderna Therapeutics, Generate Biomedicines, and Indigo Agriculture.

Position Summary

FL103isseekinga highly motivated and experiencedcomputationalbiologist to join our early-stage biotech company. The successful candidate will be a driven, experienced scientist who is enthusiastic about developingstate-of-the-arttechniques to pioneer the detection of cellular dynamics from minimally invasive biospecimens. The position willprovidea unique opportunity to play a foundational role in the development of FL103’score platform.

Responsibilities

• Develop,maintain, and scale computational pipelines for proteomics, transcriptomics, and internal proprietary assay data.
• Integrate multi-modal biological datasets toidentifydisease-relevant molecular patterns, candidate biomarkers, and assay features.
• Design and apply statistical, machine learning, and bioinformatics methods to improve assay sensitivity, specificity, reproducibility, and biological interpretability.
• Partner with biologists, assay developers, and leadership to design experiments, define success criteria, analyze results, andvalidatekey biological and computational hypotheses.
• Collaborate with software and data engineers to build internal tools, dashboards, and user interfaces that enable scientists to explore, interpret, and pressure-test FL103 data.
• Build literature- and knowledge-based contextualization workflows, including responsible use of LLMs, to connect internal findings with external scientific evidence and disease biology.
• Develop rigorous analytical frameworks for comparing candidate markers, assay conditions, biological cohorts, and disease states.
• Ensure analyses are reproducible, well-documented, and version-controlled, with clear standards for data provenance, code quality, and interpretation.
• Translate complex computational analyses into clear biological and strategic recommendations for cross-functional teams.
• Maintain deep scientific and technicalexpertiseby staying current with advances in computational biology, liquid biopsy technologies, biomarker discovery, multi-omics analysis, and disease biology.
• Communicate results clearly through presentations, written reports, technical documentation, and cross-functional discussions with the FL103 team.

Qualifications

• PhDincomputational biology, systems biology, bioinformatics, computerscienceor related fields with2-4 years of industry experience
• Experienced in standard and advanced computational support of wet-lab experimental design
• Understanding of NGS approaches anddemonstratedability to collaborate with experimental biologists to conduct quality control, design experiments, andoptimizeprotocols
• Experience analyzing -omics data (e.g., single-cell and bulk RNA-seq,mass spec) using a scientific programming language such as R or Python.
• Strong hands-on experience analyzing mass spectrometry-based proteomics data isrequired; direct experience with raw mass spec data processing, QC, normalization, and feature extraction is stronglypreferred.
• Experience withbothstatistical inferenceandmachine learning(e.grandom forests, SVMs, neural networks, transformers, etc.).
• Ability to manage multiple projects, working both independently and collaboratively within a dynamic team
• Excellent written and verbal communication skills to present results and scientific data to the internal team and/or collaborators
• Highly attentive to detail, flexible, and curious
• Enthusiastic about playing a pivotal role in building the foundation of a new biotech company

Flagship Pioneering is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, genderidentityor Veteran status.

The salary range for this role is $115,000 - $165,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL103 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits.