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 

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 highly motivated, proactive, and detail-oriented Sr. Engineer II, Mechanical/Dispersion Systems to lead the design and development of aerosol dispersal systems. This role will be responsible for owning the mechanical design and performance of systems that control the release and distribution of particulate materials in real-world trials.

The ideal candidate combines strong fundamentals in fluid/particle dynamics with hands-on experience building and iterating physical systems. The individual will work cross-functionally with scientists, engineers, and external partners to translate novel materials into robust hardware. Success in this role requires comfort operating in a fast-paced, experimental environment and the ability to independently drive complex engineering efforts from concept through deployment.

KEY RESPONSIBILITIES

• Lead the design and development of dispersion systems, owning mechanical performance from concept through prototyping and validation.
• Design and optimize particle and fluid handling systems, including mechanisms for controlled release, flow regulation, and dispersal behavior.
• Develop hardware intended for integration with mobile and diverse platforms, accounting for size, weight, power, and environmental constraints.
• Rapidly prototype and iterate on designs using hands-on build methods (e.g. 3D printing, machining) with a strong emphasis on learning and designing through experimentation.
• Design and execute bench-scale tests to evaluate system performance, including flow rates, particle distribution, and repeatability.
• Work with external manufacturers and machine shops to fabricate components, refine designs for manufacturability, and scale builds.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Bachelor’s degree in mechanical, aerospace or related engineering discipline with 8+ years of relevant industry experience, or Master’s degree with 6+ years of experience, or PhD with 3+ years of experience.
• Strong foundation in fluid dynamics and particle behavior with experience designing systems involving spray or particulate dispersion.
• Demonstrated ability to own end-to-end mechanical design from concept -> prototype -> testing -> iteration.
• Proficiency in 3D CAD tools (SolidWorks, Fusion, OnShape).
• Must be available for onsite employment in North Denver/Boulder Metro, Colorado.
• Initiative and ability to manage multiple, competing priorities, to think strategically and execute methodically.
• Strong organizational and project management skills, with the ability to independently drive initiatives in a fast-paced environment.
• Excellent communication and documentation skills, with the ability to clearly articulate design decisions and tradeoffs.

LOCATION:  Boulder, CO

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 $120,000 - $164,500. 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.

COMPANY DESCRIPTION

Flagship Pioneering is a platform 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

This role will be a foundational hire supporting our formulation and product development efforts, with a primary focus on the development, screening, and optimization of dried powder formulations. The individual will play a critical hands-on role in executing formulation strategies using techniques such as lyophilization and spray drying, while contributing experimental rigor, physical insight, and data-driven decision-making to early-stage platform development.

The Senior Research Associate will work closely with process development partners to produce robust, stable, and scalable powders. In addition to executing experiments, this role will contribute to experimental design, data interpretation, and the establishment of best practices for formulation screening, characterization, and documentation in a fast-moving, early-stage environment.

KEY RESPONSIBILITIES

• Design, execute, and optimize dried powder formulations using lyophilization and spray drying, with a focus on stability, reproducibility, and performance across multiple formulation variables;
• Execute formulation screening efforts using statistically grounded experimental designs (e.g., DoEs), including selection of factors, responses, and experimental conditions, and translate results into actionable next steps;
• Evaluate the impact of excipients, processing conditions, and storage environments on material stability, integrity, and functionality, including under accelerated or stress conditions;
• Characterize dried powder products using appropriate analytical and physical methods (e.g., particle size and morphology, thermal analysis, moisture content, bulk properties) to inform formulation and process decisions;
• Support process development and scale-awareness by documenting critical parameters, identifying sources of variability, and generating data relevant to future scale-up, tech transfer, or external partnerships;
• Maintain clear, rigorous experimental documentation and generate high-quality summaries, figures, and datasets suitable for internal decision-making, patent disclosures, and external communication;
• Contribute to the establishment of long-term formulation workflows, best practices, and standards that support platform development in a small, highly collaborative team.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Bachelor’s degree (with 5-7 years of relevant research experience) or Master’s degree (with 3-5 years of relevant research experience) in chemistry, chemical engineering, pharmaceutical sciences, materials science, biotechnology, or a related discipline.
• Demonstrated experience with drying-based formulation techniques, including lyophilization and/or spray drying, and an understanding of how process parameters influence solid-state properties;
• Strong grounding in physical chemistry or materials science principles relevant to dried systems, including glass transition behavior, crystallinity, moisture interactions, and excipient effects;
• Experience designing and executing statistically informed experiments (e.g., DoEs), with the ability to interpret interaction effects and use data to guide experimental iteration;
• Familiarity with analytical and characterization techniques for powders and solid-state materials (e.g., DSC, TGA, particle sizing, microscopy, bulk property measurements), and the ability to select fit-for-purpose methods;
• Familiarity with downstream processing operations (e.g., tangential flow filtration and other purification workflows);
• Proven ability to work independently in a dynamic, early-stage research environment, balancing hands-on execution with thoughtful experimental planning and cross-functional communication;
• Strong scientific documentation and communication skills, with experience generating reproducible records and decision-enabling datasets;
• Embodies resilience and scientific rigor in pursuing complex technical questions by iteratively testing hypotheses and refining parameters through uncertainty to converge on robust, optimized solutions.
• Demonstrated curiosity, adaptability, and comfort working across disciplines, with an interest in translating early scientific concepts into robust, scalable technologies.

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 $81,000 - $107,250. 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.

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.