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

Other benefits

Job summary

Flagship Pioneering's FL103 is seeking a highly motivated computational biologist to join our early-stage biotech company and help build a core platform for detecting disease from liquid biopsy data.

You will develop scalable pipelines for proteomics and transcriptomics, integrate multi-omics datasets, and translate complex analyses into actionable biological and strategic insights for cross-functional teams.

Qualifications

• PhD in computational biology or related field with 2–4 years industry experience.
• Experience with wet-lab experimental design support.
• Strong omics data analysis experience (single-cell, RNA-seq, proteomics).
• Proficiency in Python or R for scientific computing.
• Ability to collaborate with experimental biologists.

Responsibilities

• Develop, maintain, and scale computational pipelines for proteomics and transcriptomics.
• Integrate multi-modal datasets to identify biomarkers.
• Apply statistical, ML, and bioinformatics methods to improve assay performance.
• Collaborate with biologists, engineers, and leadership to design experiments.
• Build internal tools and dashboards to explore FL103 data.
• Develop contextualization workflows linking findings to literature.
• Ensure analyses are reproducible and well-documented.
• Translate analyses into actionable recommendations.
• Stay current with advances in computational biology and liquid biopsy.
• Communicate results through presentations and technical reports.

Skills

Machine learning

Statistical inference

Experimental design support

Data provenance

Communication skills

Education

PhD in computational biology

Tools

Python

R

Mass spectrometry data

NGS data analysis

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, monitor progression, 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 is seeking a highly motivated computational biologist to join our early‑stage biotech company. The successful candidate will be a driven scientist who is excited to develop and apply state‑of‑the‑art computational approaches to detect disease‑relevant cellular dynamics from minimally invasive biospecimens. This position provides a unique opportunity to play a foundational role in building FL103’s core platform and translating complex biological data into insights that can shape the future of disease detection, monitoring, and intervention.

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

FL103 is seeking a highly motivated and experienced computational biologist to join our early‑stage biotech company. The successful candidate will be a driven, experienced scientist who is enthusiastic about developing state‑of‑the‑art techniques to pioneer the detection of cellular dynamics from minimally invasive biospecimens. The position will provide a unique opportunity to play a foundational role in the development of FL103’s core platform.

Responsibilities

• Develop, maintain, and scale computational pipelines for proteomics, transcriptomics, and internal proprietary assay data.
• Integrate multi‑modal biological datasets to identify disease‑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, and validate key 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 technical expertise by 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

• PhD in computational biology, systems biology, bioinformatics, computer science or related fields with 2–4 years of industry experience.
• Experienced in standard and advanced computational support of wet‑lab experimental design.
• Understanding of NGS approaches and demonstrated ability to collaborate with experimental biologists to conduct quality control, design experiments, and optimize protocols.
• 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 is required; direct experience with raw mass spec data processing, QC, normalization, and feature extraction is strongly preferred.
• Experience with both statistical inference and machine learning (e.g., random 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.

Benefits and Compensation

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.

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