COMPANY DESCRIPTION

Flagship Pioneering is a bioplatform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies.   

What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet.   

Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. 

THE ROLE

We are seeking a Senior Machine Learning Scientist, Climate and Hydrology to lead the scientific direction and machine learning development for hydrology-aware climate modeling within our broader environmental modeling platform.

This role sits at the intersection of hydrology, weather and climate science, and large-scale machine learning. The Sr. Scientist will help shape how hydrologic process understanding, climate data, and modern ML methods are brought together in next-generation prediction systems, with emphasis on scientifically grounded model development and evaluation.

The individual in this role will work across science, ML, engineering, and data teams to define research priorities, guide model training and benchmarking, build reproducible workflows, and translate scientific insight into scalable model development. This is a cross-functional role requiring strong technical depth, structured scientific thinking, and the ability to move between foundational research and applied execution.

KEY RESPONSIBILITIES

• Lead scientific and technical efforts at the intersection of hydrology, climate science, and machine learning.
• Help define research priorities, modeling directions, and evaluation strategies for next-generation climate and environmental prediction systems.
• Contribute to the development and improvement of ML-based modeling approaches informed by physical and Earth system science.
• Work with large-scale climate, weather, hydrology, and remote sensing datasets to support model development and scientific analysis.
• Build and oversee reproducible workflows for data processing, model training, benchmarking, and validation.
• Collaborate closely with research, engineering, and data teams to translate scientific goals into scalable technical execution.
• Guide assessment of model performance, uncertainty, and scientific robustness across a range of environmental conditions and applications.
• Communicate findings through internal reviews, external collaborations, publications, and technical presentations.
• Help shape the broader scientific roadmap and contribute to team growth and cross-functional leadership.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• PhD in machine learning, computational science, Earth science, atmospheric science, hydrology, AI, computer science, or a related quantitative discipline.
• 5+ years of postdoctoral, industry, or applied research experience in climate ML, weather ML, hydrologic modeling, Earth system modeling, or a closely related field.
• Demonstrated experience with ML-accelerated weather, climate, or hydrology models, with a strong publication track record in the area.
• Experience working with large climate datasets, including reanalysis products, remote sensing datasets, observational datasets, and model output.
• Experience with the computational infrastructure required to manage, preprocess, and train on large-scale climate datasets, preferably in the AWS ecosystem.
• Strong programming skills in Python and experience with modern ML frameworks such as PyTorch
• Background in scientific ML, spatiotemporal modeling, data assimilation, hybrid physics-ML methods, or related approaches is strongly preferred.
• Ability to design rigorous evaluation frameworks, performance metrics, and benchmarking approaches for environmental prediction systems.
• Strong technical writing and communication skills, including reports, presentations, and peer-reviewed publications.
• Demonstrated ability to work independently in fast-paced, ambiguous environments while collaborating effectively across disciplines.
• Experience leading cross-functional scientific efforts, mentoring researchers, or helping define research roadmaps is preferred.

LOCATION: Cambridge, MA or Boulder, CO (some travel to Cambridge, MA based headquarters if working from Colorado)

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

#LI-TL1

The salary ranges for this role are $127,000 - $205,900 (Colorado) and $168,000 - $231,000 (Massachusetts). Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protoco's good faith estimate as of the date of publication and may be modified in the future.

Company description

Serif Biomedicine is a privately held, early-stage biotechnology company developing a novel approach to gene therapy that can address currently untreatable diseases. It was founded by Flagship Pioneering, an innovation enterprise that conceives, creates, resources, and grows first-in-category life sciences companies.

Flagship Pioneering has created over 100 groundbreaking companies over the past twenty years, all of which are pioneering novel and proprietary biological, industrial, and engineering approaches to solve major needs in human health and sustainability. These companies include Moderna (MRNA), Syros Pharmaceuticals (SYRS), Seres Therapeutics (NASDAQ:MCRB), Generate Biomedicines, Tessera Tx, Evelo Biosciences (EVLO), and Indigo Agriculture.

The role

We are seeking a highly experienced Lipid Nanoparticle (LNP) Formulation Senior Scientist to lead the design, execution, and interpretation of advanced Design of Experiments (DOE) strategies to drive innovation in next-generation LNP formulations. This role will play a central role in shaping formulation and delivery strategies for nucleic acid therapeutics within a dynamic and collaborative research environment.

The successful candidate will not only develop, optimize, and characterize LNP systems, but also lead the design and establishment of a high-throughput LNP screening platform spanning in vitro systems and small and large animal models. This includes defining experimental frameworks, selecting and implementing appropriate assays, and building scalable workflows to accelerate candidate evaluation and selection.

As a senior scientific contributor, this individual will be expected to operate with a high degree of independence, influence cross-functional program direction, and identify innovative solutions to advance platform capabilities. The role also includes mentoring junior scientists and contributing to the broader scientific strategy through internal leadership and external scientific engagement.

Key responsibilities

• Drive the development, optimization, and implementation of a high-throughput LNP screening platform across small and large animal models, including experimental design, assay selection, and data analysis pipelines.
• Independently define scientific strategies and experimental roadmaps aligned with program goals.
• Serve as a scientific lead for one or more programs, influencing cross-functional decisions across biology, formulation, and translational teams.
• Identify technical gaps and proactively propose innovative solutions to improve platform capabilities and throughput.
• Mentor junior scientists and contribute to building a strong, collaborative scientific culture.
• Communicate findings clearly to internal stakeholders and external partners; contribute to publications, patents, and regulatory documentation.
• Stay at the forefront of LNP delivery technologies and emerging screening methodologies, integrating new approaches where appropriate.

Professional experience and qualifications

• PhD or MS in Chemistry, Pharmaceutical Sciences, Chemical Engineering, Materials Science, or a related field and 5+ years of industry experience 
• Proven track record of independently leading research projects and delivering impactful results.
• Demonstrated experience in nanoparticle/LNP design, screening, and in vivo evaluation, preferably including large animal models.
• Experience in developing or scaling high-throughput screening platforms is strongly preferred.
• Strong understanding of experimental design, statistics, and data interpretation.
• Evidence of scientific leadership (e.g., mentoring, leading collaborations, publications, patents).
• Excellent communication and cross-functional collaboration skills.
• Strong hands-on experience with LNP formulations, including formulation development and optimization

What We Offer

• Opportunity to work at the forefront of LNP formulation innovation
• Collaborative, science-driven culture with high impact research
• Competitive compensation and benefits package

ABOUT FLAGSHIP PIONEERING

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE Change the World list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company annual list of the World Most Innovative Companies. Learn more about Flagship https://url.us.m.mimecastprotect.com/s/xLXBCqxk3LTk9pwcZf3CEkjif?domain=flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL87 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL87's good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE 

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

We are seeking a Principal Scientist (Embedded ML/Computational) to lead multiple AI/ML or computational projects across early stage ventures, as a part of Flagship’s company origination process. You will define and deliver pragmatic AI strategies, oversee method and platform development (e.g., systems design, drug design, molecular modeling, systems biology, protein design, LLM/agentic workflows), and ensure rigor in model development, benchmarking, scaling, and reporting. You will manage cross functional contributors as applicable, influence company direction, and represent PI to venture teams and external partners. The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to mass spec or docking pipelines the next and then spin up LLM based agents that automate scientific workflows. 

KEY RESPONSIBILITIES

• Program Leadership: Lead development, implementation, control, and reporting of several AI/ML or computational projects within assigned ventures in line with broader strategic plans of PI and Flagship, budgets, and timelines. 
• Technical Ownership: Take a specialized technical role on project teams to oversee method development, pipeline development, and LLM based agent/workflow design; drive benchmarking, scaling, and implementation into production grade systems. 
• Best Practices: promote operational excellence in AI projects by educating cross-functional collaborators. 
• Team Leadership: Manage and/or coordinate internal and external scientists/engineers and crossfunctional project teams as applicable; mentor early hires; support recruiting and interview. 
• Planning & Resourcing: Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options. 
• Landscape & Strategy: Independently scout emerging literature and the AI/ML landscape; synthesize concepts to propose new development strategies and identify opportunities for PI and venture portfolios. 
• Representation & Community: Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings. 
• Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. 

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings; industry AI/ML experience preferred. 
• Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fastpaced, entrepreneurial, and technical environments. 
• Clear evidence of sustained independent thought and creativity driving high impact, cross disciplinary AI/ML projects. 
• Successful track record of leadership and contribution to decision making on progression of AI/ML models within projects or programs. 
• Depth across multiple core tools and concepts, including Python; modern ML frameworks (PyTorch or JAX/TensorFlow); version control; databases; deep learning architectures; and relevant informatics software. 
• Consistent record of outstanding performance reflected in publications, patents, or high impact internal reports where applicable 

Preferred Qualifications 

• Breadth across domains such as protein modeling/design, proteomics/mass spec, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation. 
• MLOps expertise: data contracts and lineage (e.g., DVC/LakeFS), experiment tracking (MLflow/W&B), secure AWS infrastructure (S3, Batch/ECS/EKS, SageMaker), Docker, IaC (Terraform/CDK), and CI/CD (GitHub Actions). 
• Generative modeling (diffusion/flow/VAEs) for sequences, graphs, or 3D structures; docking rescoring (e.g., gnina, DiffDock) and pose quality metrics. 
• Workflow orchestration (Airflow/Prefect/Argo), data warehouses (Redshift/Snowflake), vector search (FAISS/pgvector), and lightweight internal tools (FastAPI, Streamlit/Gradio). 
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups. 

WHY PIONEERING INTELLIGENCE

• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures. 
• Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship endtoend systems that scientists rely on daily. 
• Compound impact: Convert one off wins into shared libraries and templates adopted across the PI portfolio. 
• Work with founders: Partner closely with venture leadership and PI platform engineers; influence strategy through hands on delivery. 
• Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams. 

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

#LI-MB1

The salary range for this role is $208,000 - $286,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence’s good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE 

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

We are seeking a Principal Scientist (Embedded ML/Computational) to lead multiple AI/ML or computational projects across early stage ventures, as a part of Flagship’s company origination process. You will define and deliver pragmatic AI strategies, oversee method and platform development (e.g., systems design, drug design, molecular modeling, systems biology, protein design, LLM/agentic workflows), and ensure rigor in model development, benchmarking, scaling, and reporting. You will manage cross functional contributors as applicable, influence company direction, and represent PI to venture teams and external partners. The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to mass spec or docking pipelines the next and then spin up LLM based agents that automate scientific workflows. 

KEY RESPONSIBILITIES

• Program Leadership: Lead development, implementation, control, and reporting of several AI/ML or computational projects within assigned ventures in line with broader strategic plans of PI and Flagship, budgets, and timelines. 
• Technical Ownership: Take a specialized technical role on project teams to oversee method development, pipeline development, and LLM based agent/workflow design; drive benchmarking, scaling, and implementation into production grade systems. 
• Best Practices: promote operational excellence in AI projects by educating cross-functional collaborators. 
• Team Leadership: Manage and/or coordinate internal and external scientists/engineers and crossfunctional project teams as applicable; mentor early hires; support recruiting and interview. 
• Planning & Resourcing: Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options. 
• Landscape & Strategy: Independently scout emerging literature and the AI/ML landscape; synthesize concepts to propose new development strategies and identify opportunities for PI and venture portfolios. 
• Representation & Community: Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings. 
• Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. 

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings; industry AI/ML experience preferred. 
• Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fastpaced, entrepreneurial, and technical environments. 
• Clear evidence of sustained independent thought and creativity driving high impact, cross disciplinary AI/ML projects. 
• Successful track record of leadership and contribution to decision making on progression of AI/ML models within projects or programs. 
• Depth across multiple core tools and concepts, including Python; modern ML frameworks (PyTorch or JAX/TensorFlow); version control; databases; deep learning architectures; and relevant informatics software. 
• Consistent record of outstanding performance reflected in publications, patents, or high impact internal reports where applicable 

Preferred Qualifications 

• Breadth across domains such as protein modeling/design, proteomics/mass spec, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation. 
• MLOps expertise: data contracts and lineage (e.g., DVC/LakeFS), experiment tracking (MLflow/W&B), secure AWS infrastructure (S3, Batch/ECS/EKS, SageMaker), Docker, IaC (Terraform/CDK), and CI/CD (GitHub Actions). 
• Generative modeling (diffusion/flow/VAEs) for sequences, graphs, or 3D structures; docking rescoring (e.g., gnina, DiffDock) and pose quality metrics. 
• Workflow orchestration (Airflow/Prefect/Argo), data warehouses (Redshift/Snowflake), vector search (FAISS/pgvector), and lightweight internal tools (FastAPI, Streamlit/Gradio). 
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups. 

WHY PIONEERING INTELLIGENCE

• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures. 
• Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship endtoend systems that scientists rely on daily. 
• Compound impact: Convert one off wins into shared libraries and templates adopted across the PI portfolio. 
• Work with founders: Partner closely with venture leadership and PI platform engineers; influence strategy through hands on delivery. 
• Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams. 

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

#LI-MB1

The salary range for this role is $208,000 - $286,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence’s good faith estimate as of the date of publication and may be modified in the future.

Position Summary

We are seeking a Scientist to join a dynamic team applying computational and data-driven approaches to design novel antigens and evaluate vaccine responses. At Apriori Bio, we have built our biology-enabled AI/ML platform Octavia™ to map viral fitness landscapes, predict immune escape trajectories, and design vaccines to elicit an optimal protective response to future challenges. The successful candidate will contribute to the development and application of computational methods—including structural modeling, machine learning, and statistical inference— that build on Octavia™ insights to support the company’s vaccine design efforts. Experience working with protein engineering and immunological datasets is valuable, as is interest or training in high-throughput functional genomics, virology, or vaccinology.

The Scientist will work closely with both computational and experimental colleagues to interpret results, generate hypotheses, and support antigen design. This role is ideal for scientists eager for a unique opportunity to learn and innovate within an interdisciplinary, fast-paced startup environment.

Key Responsibilities

• Use high-dimensional datasets (e.g., mutational scanning, NGS-based phenotypic screens) and computational approaches—including structural modeling, sequence analysis, and machine learning—to support antigen and immunogen engineering
• Apply and refine computational models that integrate screening data with structural and sequence-based features to guide biomolecule engineering
• Generate hypotheses and design analyses that inform evaluation of novel immunization strategies (in partnership with experimental teams)
• Identify, evaluate, and curate external datasets relevant to vaccine design and antigen optimization
• Develop reproducible computational tools and pipelines for data-driven product design that can be integrated into broader platform workflows
• Collaborate with engineers, computational scientists, and experimentalists to execute project goals and ensure smooth integration of computational findings
• Work with immunology and characterization teams to interpret vaccine immunogenicity using next-generation immune monitoring and antibody profiling tools
• Clearly communicate results and insights to colleagues across scientific and cross-functional teams
• Tackle difficult scientific problems with creativity and resilience while iterating quickly as new data emerges
• Take ownership of complex, open-ended scientific questions, driving analyses forward through ambiguity while balancing speed, rigor, and collaborative problem-solving

Basic Qualifications

• Ph.D. in bioengineering, immunology, computational biology, or a related field (or equivalent research experience)
• Experience applying data-driven protein engineering methods to predict and affect protein function, including structural and sequence-based machine-learning approaches
• Experience or training in antigen design leveraging vaccine immune response readouts
• Solid statistical and quantitative foundation, with the ability to translate complex biological datasets into actionable insights
• Strong scientific programming skills (Python preferred) and familiarity with best practices in reproducible scientific computing
• Experience working with high-throughput biological data or NGS-based assays, including modeling and statistical analysis
• Experience using version control and collaborative coding workflows

Preferred Qualifications

• Experience in vaccine design
• Experience with deep learning approaches
• Exposure to antibody characterization, immune profiling, or immune repertoire analyses
• Experience with NGS data pipelines, from processing to interpretation
• Familiarity with cloud or distributed computing environments
• Familiarity with storage, analysis and transformation of large tabular datasets and relational databases
• Laboratory experience in molecular biology, biochemistry, or immunology (a plus, not required)

About Flagship

Flagship Pioneering is a biotechnology company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com. 

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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. Apriori Bio, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Apriori Bio, Inc.'s good faith estimate as of the date of publication and may be modified in the future.

What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

Company Description

Expedition Medicines is a privately held, early-stage biotechnology company pioneering the emerging field of Protein Editing. At Expedition Medicines we create small molecules that edit protein structure and function to unlock presently undruggable targets and a broad array of therapeutic modalities. Our platform integrates novel small molecule chemistry and chemoproteomic discovery technologies with Machine Learning (ML) to enable generative design. Expedition Medicines is backed by Flagship Pioneering, bringing their courage, vision, and resources to guide Expedition Medicines from platform validation to patient impact. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us! 

About the role:

The role of Senior/Principal Scientist, Structural Biologist will focus upon determination of protein-ligand complex structures by X-ray crystallography and cryo-EM.  The scientist in this position will be responsible for delivering structures and collaborating with project teams to enable structure-based drug design and elucidate the mechanism-of-action of small molecules. 

Candidate responsibilities:

• Design and execute structural biology strategy for one or more projects
• Oversee construct design, expression and purification of proteins for structure determination
• Develop and execute protocols to obtain high quality crystals for X-ray structures
• Develop and execute protocols for grid optimization, data collection, and data analysis for structure determination using cryo-EM
• Obtain and refine structures of protein-ligand complexes, communicate the results and collaborate with project teams to drive hit-to-lead and lead optimization
• Manage CROs for effective delivery of protein expression and structural biology services
• Expand our capabilities and serve as a trusted expert in structural biology

Qualifications:

• PhD/MS degree in structural biology, biochemistry, molecular biology, or a related field with at least 3 years of drug discovery experience in an industry setting
• In-depth knowledge and hands-on experience in X-ray crystallography and cryo-EM, including crystal optimization, grid preparation, data collection, data processing, structure refinement, and interpretation of protein structures
• Experience managing CROs for protein production and structural biology
• Excellent collaboration, communication, and organizational skills
• Strong desire to learn and implement new methods in protein biochemistry, biophysics, and structural biology
• Experience with biophysical methods (SPR, DSF, MST) or mass spectrometry (intact MS, peptide mapping, proteomics) is a plus

ABOUT FLAGSHIP PIONEERING

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $126,000 - $214,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Expedition Medicines currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Expedition Medicines's good faith estimate as of the date of publication and may be modified in the future.

Company description

Serif Biomedicines is a privately held, early-stage biotechnology company developing a novel approach to gene therapy that can address currently untreatable diseases. It was founded by Flagship Pioneering, an innovation enterprise that conceives, creates, resources, and grows first-in-category life sciences companies.

Flagship Pioneering has created over 100 groundbreaking companies over the past twenty years, all of which are pioneering novel and proprietary biological, industrial, and engineering approaches to solve major needs in human health and sustainability. These companies include Moderna (MRNA), Syros Pharmaceuticals (SYRS), Seres Therapeutics (NASDAQ:MCRB), Generate Biomedicines, Tessera Tx, Evelo Biosciences (EVLO), and Indigo Agriculture.

The role

We are seeking a motivated Associate Scientist to support the development, preparation, and characterization of Lipid Nanoparticle (LNP) formulations. This role is highly hands-on and focused on formulating, screening, and analyzing LNPs to support discovery and development programs. The ideal candidate works well in a fast-paced, team-oriented environment and is eager to deepen their expertise in formulation science.

Key responsibilities

• Prepare and formulate LNPs using established protocols and evolving methods
• Execute formulation experiments to support optimization and screening efforts
• Perform LNP characterization and analytics, including particle size, PDI, encapsulation efficiency, and stability testing
• Accurately document experimental procedures, results, and observations in laboratory records
• Analyze and summarize experimental data and communicate findings to project teams
• Collaborate closely with scientists across formulation, analytics, and biology functions
• Support routine laboratory operations, including reagent preparation, equipment upkeep, and inventory management

Professional experience and qualifications

• BS or MS in Chemistry, Biochemistry, Pharmaceutical Sciences, Chemical Engineering, or a related field and 8+ years of industry experience
• Hands-on experience with LNP formulations or lipid-based delivery systems
• Familiarity with LNP analytical techniques (e.g., DLS, encapsulation assays, basic stability studies)
• Strong attention to detail and ability to follow experimental protocols
• Ability to work effectively as part of a team in a fast-paced environment
• Good written and verbal communication skills

What We Offer

• Opportunity to work at the forefront of LNP formulation innovation
• Collaborative, science-driven culture with high impact research
• Competitive compensation and benefits package

LOCATION: Cambridge, MA

ABOUT FLAGSHIP PIONEERING

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE Change the World list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company annual list of the World Most Innovative Companies. Learn more about Flagship https://url.us.m.mimecastprotect.com/s/xLXBCqxk3LTk9pwcZf3CEkjif?domain=flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $96,000 - $126,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Serif Biomedicines currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Serif Biomedicine's good faith estimate as of the date of publication and may be modified in the future.

COMPANY DESCRIPTION

Flagship Pioneering is a bioplatform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies.   

What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet.   

Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. 

THE ROLE

We are seeking a Senior Scientist to lead the design, characterization, and performance optimization of aerosolizable particle systems. This role will be responsible for developing a foundational understanding of how engineered particles behave during generation, dispersion, and transport in air, and translating that understanding into robust, scalable material and system designs.

The Senior Scientist will operate at the interface of materials science, aerosol physics, and experimental engineering — owning the development of aerosol testing capabilities, guiding experimental strategy, and linking particle design to airborne performance. This individual will play a critical role in shaping early technical direction, establishing core methodologies, and driving progress from concept through validation.

This is a highly cross-functional role, working closely with formulation, process development, and hardware teams to ensure tight integration between particle design, production methods, and real-world deployment constraints.

KEY RESPONSIBILITIES

• Lead the design and optimization of particle systems for aerosolization, with ownership over key parameters including size distribution, morphology, density, and dispersibility;
• Develop and scale experimental capabilities for aerosol generation and testing, including selection, design, and validation of dispersal systems and measurement tools;
• Define and execute experimental strategies to understand relationships between particle properties, environmental conditions, and airborne behavior;
• Characterize aerosol performance using appropriate instrumentation (e.g., particle sizers, optical counters, flow diagnostics), and translate findings into design rules and system improvements;
• Develop and apply computational approaches to model aerosol physics and particle dispersal, integrating atmospheric transport and dispersion models or Lagrangian particle simulations with experimental data to inform particle and system design;
• Collaborate cross-functionally with formulation and process development teams to align particle production methods with aerosol performance requirements;
• Establish best practices, workflows, and technical standards for aerosol experimentation, including calibration, reproducibility, and data quality;
• Interpret complex datasets and communicate insights clearly to guide technical and strategic decision-making;
• Contribute to system-level thinking around particle generation, dispersion, and scale-up, incorporating constraints from real-world operating environments;
• Mentor junior scientists and contribute to building a strong experimental and technical culture within the team.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• PhD in aerosol science, chemical engineering, mechanical engineering, physics, materials science, or a related discipline, with 5+ years of relevant industry or applied research experience (or Master’s/Bachelor’s with significant additional experience);
• Deep expertise in aerosol science, including particle generation, transport, and measurement, with a strong understanding of how particle properties influence airborne behavior;
• Hands-on experience with aerosol instrumentation (e.g., SMPS, APS, optical particle counters) and the ability to design and interpret complex experiments;
• Strong foundation in transport phenomena, fluid dynamics, and particle physics as applied to airborne systems;
• Experience working with particulate materials, including connecting physical properties (size, shape, density, surface characteristics) to performance outcomes;
• Experience with modeling aerosol transport and dispersion using Lagrangian particle dispersion models, computational fluid dynamics (CFD) simulations, or related numerical approaches is a strong plus;
• Demonstrated ability to design experimental systems and build or adapt setups for aerosol generation and testing;
• Proven ability to lead technical projects in fast-paced, early-stage environments, balancing hands-on work with strategic thinking;
• Strong communication and documentation skills, with the ability to synthesize complex technical findings into clear, decision-relevant insights;
• Demonstrated curiosity, adaptability, and comfort working across disciplines to translate early-stage scientific ideas into functional systems.

LOCATION:  Cambridge, MA

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

#LI-TL1

The salary range for this role is $126,000 - $159,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protocos's good faith estimate as of the date of publication and may be modified in the future.

Build Models Where None Exist Yet.

At Flagship Pioneering, we create companies from first principles. Within Flagship Labs, small founding teams define new technical theses, test them rapidly, and build ventures around breakthrough ideas.

We are forming a machine learning team inside a newly launched venture, Flagship Labs 120. Our work focuses on extracting latent structure from information-rich measurements of complex physical systems—often requiring mechanism-informed modeling, thoughtful inductive bias design, and principled approaches to inverse problems.

This is a zero-to-one role focused on modeling innovation rather than routine optimization. You’ll design, prototype, test, and refine new approaches that help define the technical foundation of a platform from day one.

What You’ll Do

• Develop and iterate on ML models for complex measurement data, from representation design through validation
• Design objectives and architectures that respect known constraints, symmetries, or latent structure in the data
• Explore and compare modeling strategies, balancing strong baselines with more experimental approaches when appropriate
• Investigate model behavior and failure modes to improve robustness and interpretability
• Collaborate closely with experimental and technical teammates to align modeling with data generation
• Contribute to shaping the long-term ML strategy and technical direction of a new venture

Who You Are

You may come from physics, applied mathematics, engineering, computer science, or another quantitative field.  You have hands-on experience developing machine learning models—ideally in deep learning, representation learning, probabilistic modeling, or related areas. You are comfortable implementing and modifying models, training them end-to-end, and working directly with real data.

You likely:

• Think algorithmically and reason from underlying structure
• Are comfortable adapting or extending model architectures when needed
• Have built and debugged meaningful ML systems or research prototypes
• Enjoy operating in dynamic, early-stage environments
• Read papers, build prototypes to test ideas, and translate concepts into working systems

What matters most is your ability to reason across data, models, and the systems they represent.

Technical Background

Required

• Strong hands-on experience building and training modern ML models
• Fluency in Python and at least one major ML framework (e.g., PyTorch or equivalent)
• Experience working with real-world or experimentally generated data
• Ability to design, run, and interpret ML experiments
• Comfort working in practical development environments (e.g., cloud infrastructure, experiment tracking, reproducible workflows)

Helpful

• Experience with inverse problems, latent-variable inference, or structured generative modeling (e.g., diffusion or flow-based methods)
• Familiarity with geometric or symmetry-aware architectures
• Experience incorporating physical or structural constraints into learning systems
• Experience working with time-series or high-dimensional signal data
• Exposure to biology, chemistry, physics, or related sciences

ABOUT FLAGSHIP PIONEERING

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $130,000 - $230,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL120 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL120's good faith estimate as of the date of publication and may be modified in the future.

The Company

Flagship Labs 110 Inc. (FL110) is a privately held, early-stage technology company developing a fully integrated, end-to-end platform to enable next generation proteomics. Our platform integrates groundbreaking innovations in bioengineering, machine learning, and custom microelectronics to offer a level of precision and insight never before achieved.

FL110 is backed by Flagship Pioneering, which brings the courage, long-term vision, and resources needed to realize unreasonable results. We are uniquely cross-functional and collaborative. Our teams thrive in unstructured and creative environments. Therefore, we seek individuals with an inclusive mindset and a diversity of thought.

If this sounds like an environment you’d love to work in, even if you only have some of the experience listed below, please apply.

The Role:

FL110 is seeking a creative and talented (Senior) Scientist, Nanopore to join our team. Leveling is flexible based on experience. This role will focus on developing nanopore sensing technologies and will join a team creating a nanopore based protein reading system.

You will be part of a dynamic, cross-functional team, working closely with chemists, bioinformaticians, software developers, and hardware engineers. The ideal candidate has a strong background in nanopore technology, specifically with protein translocation, as well as either experience in biotech industry or a record of scientific achievement.

Key Responsibilities

• Conduct advanced research in nanopore technology to drive technological advancements and deliver impactful results
• Develop and implement innovative research strategies and methodologies
• Collaborate with cross-functional teams to align research activities with company objectives
• Manage resources and timelines effectively
• Foster a culture of innovation and scientific excellence within the team
• Collaborate with internal and external stakeholders, including academic institutions, industry partners, and regulatory bodies
• Present research findings at scientific conferences and contribute to patent applications
• Communicate complex scientific concepts and project updates to diverse audiences, including non-scientific stakeholders

Basic Qualifications

• Ph.D. in Physics, Molecular Biology, or related field
• Demonstrated experience in nanopore experimentation and protein translocation
• Experience with python-based data analysis and R
• Proven track record of scientific achievements demonstrated through publications, patents, and successful project completions
• Strong leadership and project management skills
• Excellent problem-solving abilities, analytical skills, and attention to detail
• Strong communication skills, both written and verbal, with the ability to convey complex scientific information to diverse audiences
• Ability to work independently and collaboratively in a fast-paced, dynamic environment

Nice-to-Haves

• Demonstrated expertise in protein biochemistry including protein expression and purification

Who Will Love This Job

• A rigorous individual with a curious mind and a love of learning who enjoys working in a fast-paced environment with a driven and collaborative team

About Flagship Pioneering

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

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.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $100,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL110 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL110's good faith estimate as of the date of publication and may be modified in the future.

Company Description: 

In today’s healthcare system, disease diagnosis often relies on invasive procedures, such as biopsies, which enable direct interrogation of cellular and tissue health at the suspected source of disease. Due to their invasiveness, cost, and general inconvenience to the patient, biopsies are often conducted after onset of symptomatic disease presenting one of the largest barriers to delivering interventions early in disease progression when they are likely to be most impactful. Flagship Labs 103, Inc. is a privately held early-stage company that is building advanced technological and computational platforms to pioneer the detection of cellular dynamics from minimally invasive biospecimens that can be leveraged to connect individuals to the most effective interventions to prevent onset and progression of disease

Job Description:

We are seeking an experienced and motivated Senior Scientist to join and lead our conjugation efforts to drive FL103’s programs forward. Ideal candidates will be self-motivated, independent, and committed to the generation of high-quality data within a fast-paced and innovative research team. The Conjugation Biochemist will support ongoing bioconjugation projects in several research and development areas.

Essential Responsibilities:

• Design, synthesis, purification and analysis of oligonucleotide-conjugates on antibodies and other modalities. Develop and optimize conjugation protocols using established and novel chemistries and technologies as part of an assay development platform.
• Collaborate closely with the assay development team to guide and optimize conjugates to support FL103’s programs.
• Work as part of a cross-functional team to manage and maintain progress against multiple project timelines, deliver routine updates, and communicate progress to the team.
• Establish and maintain excellent working relationships with critical collaborative partners throughout the company to advance discovery research activities to pre-clinical development.
• Contribute to the preparation of research reports and presentations for internal project teams, leadership team, and external audiences.
• Maintain updated and well-organized lab notebooks and batch records.

Required Qualifications:

• Ph.D. in Biochemistry, Chemistry, or related scientific discipline
• 5+ years of bioconjugation-related industrial experience, preferably in designing, preparing, and validating oligonucleotide conjugates.
• Understanding project timelines and deliverables and plans/coordinate project work accordingly with departmental, functional, and external stakeholders.
• Strong problem-solving skills and a proactive attitude towards exploring new approaches.
• Demonstrates strong written and verbal communication skills, with the ability to clearly present complex scientific data to cross‑functional and senior leadership teams.
• Hands-on expertise with current and cutting-edge bioconjugation techniques for antibodies, proteins, peptides, and other biomolecules.
• Demonstrated hands‑on experience in analytical characterization of conjugates with a strong analytical mindset.  Proficiency in purification techniques such as RP-HPLC, FPLC, SEC, and IEX.
• Able to work independently or in cross-functional team settings with minimal supervision.
• Adaptable and flexible, able to navigate shifting priorities and handle day‑to‑day challenges with professionalism and confidence in fast‑moving environments.
• Self‑motivated with strong interpersonal, organizational, and communication skills, and able to take a hands‑on approach in a dynamic, fast‑paced, and collaborative environment.

About Flagship Pioneering

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com

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.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $126,000 - $181,500. 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 PIONEERING INTELLIGENCE 

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

We are seeking a Principal Scientist (Embedded ML/Computational) to lead multiple AI/ML or computational projects across early stage ventures, as a part of Flagship’s company origination process. You will define and deliver pragmatic AI strategies, oversee method and platform development (e.g., systems design, drug design, molecular modeling, systems biology, protein design, LLM/agentic workflows), and ensure rigor in model development, benchmarking, scaling, and reporting. You will manage cross functional contributors as applicable, influence company direction, and represent PI to venture teams and external partners. The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to mass spec or docking pipelines the next and then spin up LLM based agents that automate scientific workflows. 

KEY RESPONSIBILITIES

• Program Leadership: Lead development, implementation, control, and reporting of several AI/ML or computational projects within assigned ventures in line with broader strategic plans of PI and Flagship, budgets, and timelines. 
• Technical Ownership: Take a specialized technical role on project teams to oversee method development, pipeline development, and LLM based agent/workflow design; drive benchmarking, scaling, and implementation into production grade systems. 
• Best Practices: promote operational excellence in AI projects by educating cross-functional collaborators. 
• Team Leadership: Manage and/or coordinate internal and external scientists/engineers and crossfunctional project teams as applicable; mentor early hires; support recruiting and interview. 
• Planning & Resourcing: Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options. 
• Landscape & Strategy: Independently scout emerging literature and the AI/ML landscape; synthesize concepts to propose new development strategies and identify opportunities for PI and venture portfolios. 
• Representation & Community: Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings. 
• Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. 

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings; industry AI/ML experience preferred. 
• Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fastpaced, entrepreneurial, and technical environments. 
• Clear evidence of sustained independent thought and creativity driving high impact, cross disciplinary AI/ML projects. 
• Successful track record of leadership and contribution to decision making on progression of AI/ML models within projects or programs. 
• Depth across multiple core tools and concepts, including Python; modern ML frameworks (PyTorch or JAX/TensorFlow); version control; databases; deep learning architectures; and relevant informatics software. 
• Consistent record of outstanding performance reflected in publications, patents, or high impact internal reports where applicable 

Preferred Qualifications 

• Breadth across domains such as protein modeling/design, proteomics/mass spec, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation. 
• MLOps expertise: data contracts and lineage (e.g., DVC/LakeFS), experiment tracking (MLflow/W&B), secure AWS infrastructure (S3, Batch/ECS/EKS, SageMaker), Docker, IaC (Terraform/CDK), and CI/CD (GitHub Actions). 
• Generative modeling (diffusion/flow/VAEs) for sequences, graphs, or 3D structures; docking rescoring (e.g., gnina, DiffDock) and pose quality metrics. 
• Workflow orchestration (Airflow/Prefect/Argo), data warehouses (Redshift/Snowflake), vector search (FAISS/pgvector), and lightweight internal tools (FastAPI, Streamlit/Gradio). 
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups. 

WHY PIONEERING INTELLIGENCE

• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures. 
• Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship endtoend systems that scientists rely on daily. 
• Compound impact: Convert one off wins into shared libraries and templates adopted across the PI portfolio. 
• Work with founders: Partner closely with venture leadership and PI platform engineers; influence strategy through hands on delivery. 
• Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams. 

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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The salary range for this role is $208,000 - $286,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence’s good faith estimate as of the date of publication and may be modified in the future.