E11 Bio - Scientist/Senior Scientist, Molecular Engineering & Sample Optimization

About the role

Position: Scientist, Molecular Engineering and Sample Optimization

E11 Bio is a non-profit research organization dedicated to achieving whole brain connectomics for humans and other mammals. Our interdisciplinary team of scientists and engineers functions as a convergent research group, operating with the agility of a start-up while pursuing a deep neuroscience mission. Based in Alameda, California, we are developing a novel technology platform to map the mammalian brain at scale. This role is central to our efforts, bridging molecular engineering, advanced imaging, and computational analysis to define and produce the biological substrates necessary for our mapping pipeline.

Role and Responsibilities

The Scientist, Molecular Engineering and Sample Optimization is responsible for establishing and maintaining the rigorous material standards that enable high-fidelity whole-brain mapping. This position requires a hands-on individual who works directly at the laboratory bench and analysis station to design, implement, and refine the sample preparation pipeline. You will serve as the primary interface between physical sample integrity and molecular readout capability, ensuring that tissue is optimized for downstream analysis.

A core function of this role is the definition of quantitative benchmarks for tissue quality. You will establish objective criteria that determine whether a biological sample meets the strict standards required for our mapping workflows. This involves translating broad morphological goals into specific, measurable protocols that can be consistently applied by the imaging and biology teams. Your work will directly define what constitutes high-quality input material for our entire system.

You will lead the engineering of reagent panels that serve two critical molecular functions. The first focus is on developing and optimizing reagents for comprehensive synapse identification, ensuring that the complex connectivity between neurons can be accurately resolved. The second focus involves engineering reagents for barcode epitopes, which are essential for the specific molecular tagging and spatial indexing required within our platform. This requires a deep understanding of biochemical interactions and an ability to balance reactivity, specificity, and stability.

Collaboration is integral to this position. You will work closely with molecular biology specialists to refine fixation, permeabilization, and labeling steps. This partnership ensures that protein structures necessary for identification are preserved and accessible for labeling. You will also coordinate extensively with the imaging team to implement protocols that maintain the structural integrity necessary for high-resolution morphological assessment. Finally, you will partner with computational groups to ensure that the physical sample preparation aligns with the requirements of subsequent data analysis, creating a seamless pipeline from tissue to insight.

The successful candidate will oversee the continuous improvement of sample preparation protocols. This involves iterative testing and refinement to balance comprehensive molecular coverage with practical considerations such as reagent stability, processing time, and equipment compatibility. The goal is to consistently deliver optimized samples that maximize the quality of both morphological data and protein readouts. This optimized material flow is critical for achieving the milestone of scalable, whole-brain connectomics mapping.

Qualifications

The ideal candidate possesses a strong foundation in the practical methods required for molecular biology applications on nervous tissue. This includes direct, hands-on experience with tissue handling, sectioning, and processing techniques that preserve antigenicity and ultrastructure. A demonstrated ability to operate microscopy systems is essential for evaluating tissue morphology and assessing the quality of histological preparations.

You must have a proven track record in quantitative data analysis as it applies to biological samples. This skill is used to evaluate imaging results, measure morphological parameters, and use data to drive iterative improvements in sample preparation. Your analytical approach will transform subjective observations into actionable engineering parameters for the pipeline.

Specific, required experience includes working with technologies related to barcode epitope reagents and comprehensive synapse labeling strategies. You must be proficient in applying these molecular tools to complex mammalian tissue. This background is necessary to successfully optimize the protocols that generate the specific signals required for our mapping technology.

Location and Compensation

This role is based in Alameda, California. It is offered as a full-time position. The compensation package for this role is 180,000 USD per year.