---
title: 'Associate Director, Molecular Cloning Technologies at Flagship Pioneering, Inc.'
canonical: 'https://feeny.ai/job/associate-director-molecular-cloning-technologies-flagship-pioneering-inc-zqacad2aqsd9'
type: 'job'
last_seen: '2026-09-11'
---

# Associate Director, Molecular Cloning Technologies at Flagship Pioneering, Inc.

- **Company:** Flagship Pioneering, Inc.
- **Location:** Cambridge, MA
- **Posted:** 2026-06-29
- **Last confirmed live:** 2026-09-11
- **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8606888002?gh_jid=8606888002

## Job description

## COMPANY DESCRIPTION

Founded through Flagship Pioneering’s venture creation engine, Terrana Biosciences is a cutting-edge agricultural biotechnology company developing innovative RNA-based products to address global agricultural challenges. We are committed to advancing sustainable farming solutions through precision technologies that ensure environmental safety and regulatory compliance.

## THE ROLE

Terrana Biosciences is building a new generation of RNA-based technologies to transform agriculture. We are seeking an innovative and strategic Associate Director, Molecular Cloning Technologies to lead the vision, development, and scaling of cloning and construct generation capabilities across the company.

As a scientific leader, you will define and drive cloning strategies that accelerate discovery, platform development, and product advancement. You will serve as the technical authority for molecular cloning technologies, develop novel high-throughput workflows, and identify emerging approaches that strengthen Terrana's RNA technology platform. This role requires a highly creative scientist who thrives at the intersection of technology innovation, scientific leadership, and operational excellence.

## KEY RESPONSIBILITIES

- Define and execute the long-term cloning strategy supporting Terrana's research and platform development efforts.
- Own the cloning function and construct generation operations at Terrana, ensuring reliable, scalable, and cost-effective delivery of high-quality constructs supporting company pipeline activities.
- Conceive, develop, and implement novel cloning technologies, workflows, and automation solutions to enable rapid construct generation and testing.
- Drive continuous improvements in construct generation throughput, turnaround time, automation, quality, and unit economics while expanding organizational capacity.
- Lead innovation in high-throughput DNA assembly, plasmid engineering, vector development, and viral engineering technologies.
- Evaluate emerging technologies and establish new capabilities that improve speed, scale, quality, and efficiency.
- Partner closely with Molecular Biology, Delivery, Discovery, Sequencing, and Bioinformatics teams to enable key research objectives and accelerate innovation.
- Mentor scientists and contribute to the development of technical talent and scientific culture across the organization.
- Drive external collaborations and represent Terrana's cloning capabilities with scientific partners and collaborators.
- Communicate scientific strategy, findings, and recommendations to senior leadership.

## PROFESSIONAL EXPERIENCE & QUALIFICATIONS

- Ph.D. in Molecular Biology, Synthetic Biology, Biotechnology, Biochemistry, Plant Biology, or a related field and 10+ years of relevant industry and/or postdoctoral experience with a demonstrated record of scientific leadership and innovation.
- Demonstrated ability to balance scientific leadership with hands-on laboratory execution in a fast-paced, resource-constrained environment.
- Deep expertise in molecular cloning, DNA assembly technologies, vector engineering, and construct design.
- Proven track record of developing and implementing novel technologies or platform capabilities.
- Experience leading complex, cross-functional scientific initiatives from concept to execution.
- Experience developing, implementing, and scaling high-throughput cloning workflows, laboratory automation solutions, and production operations.
- Strong communication, influence, and problem-solving skills.
- Demonstrated creativity, scientific rigor, and an entrepreneurial mindset.

## Preferred Qualifications

- Expertise in viral vector biology, host-virus interactions, plant virology, or RNA virus engineering.
- Experience in agricultural biotechnology, plant biology, microbial engineering, or RNA-based technologies.
- Familiarity with automated liquid handling platforms and laboratory information management systems (LIMS).
- Working knowledge of sequencing-based construct verification and associated data analysis workflows.

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](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.flagshippioneering.com%2F&data=05%7C02%7Cemccurdy%40flagshippioneering.com%7C8e54295c994c4d440a7b08ddc94a4a72%7Cd00b8682fc8b4548b82dda0524788e9b%7C0%7C0%7C638888043086011906%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=gknIK%2BmYfQpsSi0%2FyQmhzNBo4DurYfmbUQpruIKf6Mc%3D&reserved=0).

At Flagship, we accept impossible missions to enable bigger leaps. Our [core values](https://www.flagshippioneering.com/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 $161,000 - $203,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Terrana Biosciences, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Terrana Biosciences, Inc.'s good faith estimate as of the date of publication and may be modified in the future.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.

## About Flagship Pioneering, Inc.

## Company Overview
- **One-liner**: Flagship Pioneering is a life sciences venture creation firm that conceives, creates, and capitalizes breakthrough bioplatform companies in biotechnology, health, and sustainability.
- **Entity Type**: Private (Venture Creation Firm)
- **Headquarters**: Cambridge, Massachusetts, United States
- **Founded**: 2000
- **Founders**: Noubar Afeyan (Co-Founder & CEO)

## Core Business
- **Primary industry/industries**: Biotechnology Research, Life Sciences Venture Creation, Company Incubation
- **Target customers**: B2B / B2G – partners with academic institutions, pharma companies, and investors; also acts as an employer for scientists, entrepreneurs, and corporate builders
- **Mission or purpose statement**: “To harness the 21st century's most powerful technological forces for good to deliver a better future for all.”

## Products & Services
Flagship does not sell products directly; its offerings are the companies it creates and the innovation platform it operates.
- **Innovation Platform**: A systematic, institutionalized process to identify “unreasonable” scientific questions, test them rigorously, and spin out independent companies that develop therapeutics, diagnostics, agricultural technologies, and more.
- **Portfolio Companies**: Over 120 companies founded, including Moderna, Generate:Biomedicines, Inari Agriculture, Tessera Therapeutics, Lila Sciences, and others. Each is a separate enterprise with its own products (e.g., mRNA vaccines, gene-editing tools, AI-driven drug discovery).

## Market Standing
- **Valuation/Market Cap**: Not publicly disclosed (privately held)
- **Key Metric**: Annual revenue of approximately $800 million (2025/2026 estimate) and 620 employees (+9.7% YoY growth)
- **Notable Investors/Partners**: Flagship is itself an investor and partner; key collaborations include AWS (to accelerate drug discovery), Harvard Medical School, Broad Institute, and multiple top-tier biopharma companies. Portfolio company Moderna is a publicly traded giant.
- **Growth Signals**: 78 active job postings (+50% quarterly), recent formation of Terion (digital agriculture infrastructure) and Serif Biomedicines (modified DNA platform), and expanded presence in Europe and Asia.

## Competitive Advantages
- **Unique Model**: Combines scientific exploration, company creation, and capital investment under one roof – “a way that is largely without precedent”
- **Deep Talent Pool**: Exceptional network of scientist-entrepreneurs and company builders; top hires from MIT, Harvard, Biogen, Novartis, and Pfizer
- **Track Record**: Over two decades of founding transformational companies (e.g., Moderna’s COVID‑19 vaccine), demonstrating repeatable innovation
- **Process-Driven**: Systematic methodology for turning “what‑if” questions into patentable bioplatforms, reducing risk compared to ad‑hoc startup creation

## Strategic Focus
- **Current priorities**: Expanding AI/machine learning integration across drug discovery and life sciences (highlighted by AWS collaboration); entering preemptive health and medicine; advancing sustainable agriculture and climate solutions; growing international operations (UK, Singapore, Canada, Switzerland, Japan)
- **Direction for growth**: Launching new platform companies at a steady cadence (e.g., Terion, Serif in 2026); deepening expertise in computational protein design, modified DNA, and gene editing

## Why Work Here
- **Culture**: “Brave and bold organization of creative-thinkers with insurgent mindsets” – emphasis on fearlessness, mentorship, and teamwork across science and business
- **Work Environment**: Headquarters in Cambridge, MA with 5 US offices; roles span research, strategy, finance, and operations; hybrid/remote flexibility varies by role
- **Notable Perks**: Opportunity to work on world-changing science (e.g., COVID‑19 vaccine, gene editing) alongside top scientists and company builders; strong compensation (salary range example: Sr. Associate ~$68K, ML Engineer ~$122K; overall comp rating 3.7/5)
- **Engineering/Science Culture**: Heavy investment in R&D (15% of workforce in research), cutting-edge tools (Cryo‑EM, AI/ML), and a process that encourages bold leaps

## Sources
1. [flagshippioneering.com](https://www.flagshippioneering.com/)
2. [flagshippioneering.com/about](https://www.flagshippioneering.com/about)
3. [flagshippioneering.com/join](https://www.flagshippioneering.com/join)
4. [flagshippioneering.com/join/roles](https://www.flagshippioneering.com/join/roles)
5. [linkedin.com/company/flagship-pioneering](https://www.linkedin.com/company/flagship-pioneering)

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