Research Associate, Transcriptomics (Contract)

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 View email address on click.appcast.io. 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 View email address on click.appcast.io.