Jobs at Flagship Pioneering

Senior Scientist will lead protein library design, construction, display, selection, sorting, and genotype-to-phenotype analysis for a biotech drug-discovery platform. Responsibilities include deep mutational scanning, FACS workflow development, library quality assessment, protein characterization, experimental data interpretation, documentation, and collaboration with computational and screening teams. The role also sets technical direction, builds the protein-engineering function, and helps shape scientific strategy as an early startup hire.

Lead strategy and operations for two Origination teams to drive biotech company creation. Set priorities, track KPIs, manage cross-functional execution, allocate resources, enable collaboration with Flagship functions, and implement program management best practices and tools. Support portfolio leadership, prepare strategic briefings, guide hiring/onboarding, develop playbooks for ideation and launch, surface risks and mitigations, and foster team culture to accelerate value creation across early- to mid-stage life sciences companies.

Lead molecular simulation efforts for an AI-enabled drug discovery platform. Characterize ligand-target interactions, assess binding pockets, validate generated designs, develop free-energy and affinity prediction workflows, and model beyond-Rule-of-5 properties. Build automated, reproducible simulation pipelines across GPU, HPC, and cloud infrastructure, translate simulation results into machine-learning signals, and collaborate with medicinal chemistry, pharmacology, structural biology, and assay teams.

Participate in a full-time summer fellowship focused on generating scientific and technology concepts, refining venture hypotheses, and exploring ideas with breakthrough company potential. Fellows collaborate across disciplines, apply AI tools alongside scientific expertise, develop creative and rigorous solutions, network with Flagship leaders, and learn the company-building process. The role is intended for early-career scientists, technologists, engineers, and physicians with advanced scientific training.

Develop and stress-test novel biotechnology venture hypotheses, create scientific and business blueprints, and help launch new companies. Responsibilities include researching emerging biology and technology frontiers, planning experiments and products, recruiting scientific partners, establishing intellectual property, building early scientific teams, and translating complex insights into actionable venture strategies.

Develop and scale lipid nanoparticle formulations for modified DNA and mRNA delivery. Responsibilities include optimizing mixing, encapsulation efficiency, reproducibility, formulation performance, and manufacturability; designing experiments; analyzing data; supporting characterization, technology transfer, and scale-up; and collaborating with internal and external manufacturing and research teams.

Manages the day-to-day workplace environment, including facilities upkeep, supplies, visitors, building access, vendors, office events, catering, onboarding and offboarding logistics, and executive scheduling support. Coordinates with HR, IT, Finance, and Operations while maintaining office communications and resolving workplace issues. The role requires strong organization, interpersonal skills, vendor management experience, budget and invoice familiarity, discretion, and a hands-on approach.

Lead product strategy and execution for Iris Chat, an AI-powered psychological fitness product. Own product vision, customer journeys, activation, retention, conversion, subscription value, experimentation, and AI quality. Manage product, design, engineering, and AI research teams; hire and develop leaders; balance research and delivery; and establish standards for evaluation, privacy, safety, reliability, and user trust. Partner with leadership to build a focused roadmap and durable consumer business.

Develop evolutionary algorithms for autonomous scientific discovery, enabling populations of models, hypotheses, programs, and representations to evolve through iterative search, selection, evaluation, and recombination. Build Bayesian and probabilistic methods for candidate ranking, uncertainty estimation, diversity preservation, and quality measurement. Establish benchmarks, integrate algorithms into autonomous-science pipelines, publish research, guide technical direction, and mentor colleagues as a senior individual contributor.

Leads research operations across biotechnology discovery programs, managing scientific information, data rooms, IP workflows, board materials, timelines, vendors, and cross-functional communications. Ensures data integrity, operational compliance, accurate leadership reporting, and process improvement while coordinating with scientific, legal, corporate development, and external partners.

Own and operate the organization’s bioinformatics platform, develop reusable production pipelines, and enable portfolio companies to deploy workflows independently. Manage genomic data consortium relationships, data access agreements, compliance reporting, and dataset onboarding. Partner with engineering, data science, research, and laboratory teams to establish reproducible standards, integrate omics data platforms, advise on computational infrastructure, and provide technical leadership across genomics, transcriptomics, and multi-omics initiatives.

Performs tissue processing, histology, plate-based reporter assays, and in vitro cell biology experiments supporting genetic medicine development. Reviews immunohistochemistry and immunofluorescence data, develops and optimizes assays, manages histology vendors and CROs, and documents results in electronic laboratory records. The role requires independent laboratory execution, troubleshooting, data analysis, and cross-functional collaboration.

Develop and optimize DNA-encoded small molecule screening platforms, including library design, synthesis, quality control, affinity selections, sequencing, hit deconvolution, and validation. The role establishes workflows, analyzes experimental data, coordinates CROs, and helps set scientific direction for an early-stage biotechnology company.

Conduct analytical method development, optimization, qualification, and testing for nucleic acid therapeutics and LNP delivery vehicles. Maintain efficient sample-testing and data-delivery systems, troubleshoot assays and instruments, analyze and communicate results, document work in Benchling, write SOPs and protocols, train team members, manage materials, and support laboratory operations.

Leads corporate strategy, portfolio planning, business development, partnering, investor engagement, financial modeling, and executive or Board communications for a clinical-stage biotechnology company. Evaluates licensing and collaboration opportunities, supports diligence and transactions, develops financing narratives, and translates scientific, clinical, competitive, and financial information into strategic recommendations and coordinated execution.

Lead full‑stack development of customer‑facing features, own product lifecycle from design to release, build scalable AI‑enabled back‑end systems on AWS, improve CI/CD and testing, collaborate with product, design, and ML researchers, and ensure security and privacy best practices.

Leads product safety and wellbeing strategy for AI-powered experiences. Owns safety roadmaps, guardrails, evaluation frameworks, benchmarks, metrics, monitoring, launch-readiness criteria, and human or automated evaluation programs. Assesses failure modes and emerging risks, including self-harm and crisis scenarios, and translates expert and user findings into product guidance. Partners with engineering, machine learning, product, design, and data science teams to improve risk detection, response generation, escalation, and user experience.

Develop and deploy LLM-powered ML applications for psychological wellbeing. Collaborate with psychologists to translate insights into computational systems, advance RLHF and agentic AI methods, build scalable data and training pipelines, integrate ML systems into real-world products, and communicate results to multidisciplinary teams.

Operate and maintain an automated high-throughput bulk RNA-seq platform, including RNA extraction, quality control, NGS library preparation, sequencing support, and RT-qPCR. Maintain mammalian cell cultures, coordinate sample handoffs, and document workflows, metadata, and QC metrics in ELN/LIMS systems. The role may also support molecular cloning activities in a production-scale laboratory.

Conduct and optimize cellular screening assays, characterize biologics, develop molecular biology and gene-editing workflows, and support therapeutic product generation. Responsibilities include cell culture, transfection, plasmid and vector construction, assay automation, NGS sample handling, data analysis, and management of CRO and CMO partners. The role requires close collaboration across experimental and computational teams in a biotechnology drug discovery environment.