Research Assistant I - van Opijnen and Rakoff-Nahoum labs

About the Role

The van Opijnen and Rakoff-Nahoum labs are seeking a Research Assistant for a minimum commitment of 2 years. This position is ideal for recent graduates (postbacs) planning to apply to graduate or medical school in the near future.

The role involves molecular biology techniques, including DNA/RNA extraction and purification, library preparation, and next-generation sequencing for bacterial genomics, metagenomics, bacterial and host RNASeq, metatranscriptomics, and single-cell RNASeq.

About the Labs

Rakoff-Nahoum Lab: The lab aims to achieve a comprehensive understanding of the host-associated microbiota across multiple levels of biological organization—from genes to molecules to organisms to ecosystems—while determining cause and effect. Approaches include:

• Classic bacterial genetics of gut anaerobes (e.g., cultivation, random and directed mutagenesis of Bacteroidetes, Firmicutes, Actinobacteria)
• In vitro and in vivo experimental systems to study bacterial adaptation to the environment (e.g., TnSeq)
• Mouse gnotobiotics and computational approaches to microbiome ecology
• High-throughput pipelines for cultivation, genetic, chemical, and phenotypic analysis of microbiota interactions

van Opijnen Lab: Focuses on developing experimental and computational tools to capture how pathogens respond to and interact with their environment (e.g., host or drugs). Key considerations include:

• Capturing comprehensive organismal responses (e.g., entire transcriptomes under specific conditions)
• High-throughput tool development to measure responses across time and hundreds of conditions
• Machine learning/AI-mediated analysis of large datasets to uncover non-obvious patterns and design novel treatment strategies

Examples of tools developed by the lab include:

• Tn-Seq and Hii-TnSeq: Genome-wide mapping of bacterial responses to environmental stresses and host immune factors, identifying genetic determinants of drug sensitivity and immune evasion
• Droplet Tn-Seq: Microfluidic approach for analyzing thousands of single bacterial cells simultaneously, enabling insights into cell-to-cell communication and antibiotic interactions
• CRISPRi-TnSeq and dualCRISPRI: CRISPR interference combined with Tn-Seq to create detailed genetic interaction networks, expanding understanding of genome-wide bacterial architecture

Responsibilities

• Perform routine laboratory experiments and procedures using standard equipment, recording and verifying results for accuracy
• Assist in troubleshooting procedures when experimental results are unexpected or specimen quality is poor
• Execute lab techniques, including but not limited to:
  • DNA/RNA extraction and purification
  • Library preparation for sequencing
  • Next-generation sequencing for bacterial genomics, metagenomics, RNASeq, metatranscriptomics, and single-cell RNASeq
• Maintain detailed records of results and methodologies in a lab log
• Maintain equipment, lab areas, and supplies in a clean and professional manner
• Sterilize and clean glassware, and prepare media and reagents using appropriate procedures
• Inventory supplies, alert supervisors to needs, and mix standard reagents
• Process orders for lab supplies

Requirements

• A Bachelor’s degree is required

Benefits

Base pay is one part of a comprehensive benefits package that includes:

• Flexible schedules
• Affordable health, vision, and dental insurance
• Child care and student loan subsidies
• Generous time off
• 403(b) Retirement Savings plan and Pension
• Tuition and certain License/Certification Reimbursement
• Cell phone plan discounts
• Discounted rates on T-passes

Pay

The posted pay range reflects Boston Children’s reasonable and good-faith expectation at the time of posting. The final base pay offer depends on skills, experience, education, certifications, and other job-related factors.