E11 Bio - Spatial ‘Omics Scientist

E11 Bio is on a mission to unlock whole-brain mammalian connectomics. We’re a collaborative and interdisciplinary team of scientists and engineers developing an innovative technology platform for scalable brain mapping. E11 Bio is a non-profit focused research organization organized under the Convergent Research umbrella and located in Alameda, California. We are pursuing ambitious neuroscience research and operating like a nimble start-up while organized as a non-profit. Read our technology roadmap for more.

Position

E11 Bio is seeking a creative and passionate spatial ‘omics scientist to co-develop next-generation technology for high-throughput connectomic imaging using molecular barcodes. As a core member of the E11 team, you’ll develop innovative methods for highly-multiplexed imaging of protein barcodes at the scale of mammalian brains. Working closely with world experts in cellular barcoding and computational connectomic reconstruction, you’ll design spatial ‘omics and barcode detection experiments, collect, analyze, and interpret multiplexed image data, and present or publish open scientific results for public benefit.

• Develop proteomics methods (e.g. based on oligo-conjugated antibodies) for highly multiplexed detection of antibodies in expansion microscopy using combinatorial imaging.
• Develop robust signal amplification methods (e.g. rolling circle amplification, hybridization chain reaction) for detection of protein-based cellular barcodes and molecular markers at proteomic scale in swellable hydrogels.
• Design probe sets and combinatorial imaging experiments (e.g., in situ sequencing, MERFISH) compatible with expansion microscopy to detect cell barcodes in brain tissue.
• Integrate and apply automatic liquid handling and automatic fluorescence imaging methods in a robust and reproducible pipeline.
• Process and analyze multiplexed image volumes, including stitching and registration across imaging cycles, and feature detection, decoding and classification.
• Work closely with experimental and computational scientists at E11 and through external partnerships to collaboratively design experiments, analyze experimental data, and interpret results.
• Maintain excellent laboratory notebook practices, prepare reports and manuscripts, and present results internally and externally, and source new techniques from the scientific community.

• PhD in biology (e.g. biophysics, bioengineering, molecular biology) or a related field in science and/or engineering, or equivalent working experience and track record.
• Scientist I: 0-3 years of experience post-PhD, or equivalent industry track record; Scientist II: 3-6 years of experience post-PhD, or equivalent industry track record.
• Experience with 3D spatial transcriptomics (e.g. in situ sequencing and/or multiplexed hybridization) and/or spatial proteomics (e.g. multiplexed DNA-barcoded antibodies).
• Extensive experience with spatial methods/protocol development, with emphasis on DNA-based readout such as HCR or RCA.
• Experience with fluorescence microscope modalities, including spinning-disc confocal microscopy.
• Experience with molecular biology laboratory techniques, e.g. cell and tissue culture, molecular cloning, quantitative PCR, immunohistochemistry, etc.

• Experience with expansion microscopy and/or hydrogel embedding for expansion microscopy.
• Experience with fluidics for multiplexing, microfluidics, and automation.
• Experience with computational image analysis methods for combinatorial imaging
• Excellent communication skills, record keeping ability, and attention to detail.
• Excellent interpersonal and collaboration skills.
• Strong record of publications in peer reviewed scientific journals.

• You are excited by applying cutting edge spatial ‘omics technology to an effort that could broadly benefit humanity.
• You are driven by mission and enjoy working among a team focused on a shared audacious goal.
• You enjoy the energy of a small team and the exploration of a wide open, uncharted space.

• An opportunity to help change the world and work with some of the most talented and collaborative experts across scientific fields.
• An opportunity to gain experience on a field-defining moonshot effort.
• Excellent medical, dental, and vision insurance through a PPO plan; parental leave.
• Generous time off + paid holidays.
• Ample healthy and energizing food including daily lunches.
• Wellness allowance for fitness and wellness activities.