--- title: 'Research Associate, Transcriptomics (Contract) at Flagship Pioneering, Inc.' canonical: 'https://feeny.ai/job/research-associate-transcriptomics-contract-flagship-pioneering-inc-cambridge-pmwatvndjc3x' type: 'job' last_seen: '2026-09-25' --- # Research Associate, Transcriptomics (Contract) at Flagship Pioneering, Inc. - **Company:** Flagship Pioneering, Inc. - **Location:** Cambridge, MA - **Posted:** 2026-09-21 - **Last confirmed live:** 2026-09-25 - **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8815277002?gh_jid=8815277002 ## Job description ## About Empress Empress is pioneering mechanistic intelligence for drug discovery — helping R&D teams understand what their molecules are doing, what is driving activity, what liabilities may emerge, and which candidates are best positioned to advance. By integrating multi-omics, chemoproteomics, proteomics, transcriptomics, computational inference, knowledge graphs, and CRISPR-based functional validation, Empress turns biological complexity into clearer development decisions. Our platform gives discovery teams access to capabilities that would otherwise require years, specialized infrastructure, and rare cross-functional expertise to build internally. Empress is a privately held biotech conceived by Flagship Pioneering, which brings the courage, long-term vision, and resources needed to realize unreasonable results. ## The Role We're looking for a Research Associate II to join the Genomics team and own day-to-day operations of our automated high-throughput bulk RNA sequencing platform. The bulk-Tx platform is a core component of Empress's Integromyx platform, generating the transcriptomic data that drives mechanistic insights across our drug discovery programs. This is a hands-on role with end-to-end responsibility for someone who wants to build deep technical expertise in NGS and functional genomics. Primary Responsibilities Bulk Transcriptomics Platform - Operate and maintain the automated high-throughput bulk RNA-seq platform end-to-end - Perform RNA extraction from diverse sample types following established protocols - Execute RNA quality control assessments and library preparation for NGS, including QC steps - Set up and support sequencing runs on a next-generation sequencing instrument - Design and execute RT-qPCR experiments - Maintain accurate records of experimental workflows, sample metadata, and QC metrics in the ELN/LIMS Cell Culture & Sample Preparation - Maintain mammalian cell cultures and perform cell treatments to generate samples for the bulk-Tx platform - Coordinate timely sample handoff from cell culture to downstream RNA processing Motivated candidates will have opportunities to cross-train in complementary areas such as molecular cloning within a production-scale platform, including DNA assembly, transformation, colony picking, and plasmid verification. ## Qualifications Required - Bachelor’s (and 2-4 years of relevant academic/industry experience) or Master’s degree (and 0-2 years) in biology, Molecular Biology, Biochemistry, Genetics, or a related field - Hands-on experience with mammalian cell culture - Strong organizational skills, attention to detail, and commitment to data integrity ## Preferred - Prior experience with RNA extraction and QC (e.g., NanoDrop, Bioanalyzer) - Familiarity with NGS library preparation workflows or sequencing platforms (e.g., Illumina) - Experience with RT-qPCR or basic molecular cloning - Experience in a high-throughput or production-style lab environment - Proficiency with ELN or LIMS systems Flagship Pioneering and our ecosystem companies are 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. 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. 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. The pay range for this role is $35 - $45 per hour and the contractor will be employed by a third-party staffing company. Certain employee benefits may be available to the contractor through the staffing company after meeting minimum criteria. Compensation and benefits information is based on Empress Tx'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. 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