Flagship Pioneering

Scientist, Computational Biology

Flagship Pioneering$115K — $165K *
Pharmaceuticals & Biotech
Less than 5 years of experience
Job Overview by Ladders

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 ability to collaborate with experimental biologists on quality control and protocol optimization
  • Experience analyzing -omics data using R or Python
  • Strong hands-on experience analyzing mass spectrometry-based proteomics data; direct experience with raw data processing is preferred
  • Experience with statistical inference and machine learning methods
  • Ability to manage multiple projects, both independently and collaboratively
  • Excellent written and verbal communication skills
  • Highly attentive to detail, flexible, and curious
  • Enthusiastic about building the foundation of a new biotech company

Responsibilities

  • Develop, maintain, and scale computational pipelines for proteomics and transcriptomics
  • Integrate multi-modal biological datasets to identify molecular patterns and candidate biomarkers
  • Design and apply statistical, machine learning, and bioinformatics methods to enhance assay performance
  • Collaborate with biologists and assay developers to define experiments and validate hypotheses
  • Partner with engineers to create tools and interfaces for data exploration
  • Build contextualization workflows that connect internal findings with external scientific evidence
  • Develop analytical frameworks to compare markers and disease states
  • Ensure reproducibility and documentation of analyses
  • Translate complex computational analyses into strategic recommendations
  • Communicate results through presentations and technical documentation

Benefits

  • Healthcare coverage
  • Annual incentive program
  • Retirement benefits
  • Broad range of other benefits
Full Job Description
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

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. Compensation and benefits information is based on FL103's good faith estimate as of the date of publication and may be modified in the future.

About Flagship Pioneering

Flagship Pioneering is a life sciences innovation enterprise that conceives, creates, resources, and develops first-in-category life sciences companies. The firm operates through its Flagship Labs unit, which is a dedicated innovation foundry that invents and launches transformative companies. Flagship Pioneering has created over 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents. The firm's portfolio includes companies in the fields of therapeutics, health technologies, and sustainability. Flagship Pioneering was founded in 2000 and is headquartered in Cambridge, Massachusetts.
Learn more about Flagship Pioneering
Size
500 employees
Industry

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