Principal II Scientist, Applied Chemistry Full-time

Principal II, Applied Chemistry Scientist

At Roche you can show up as yourself, embraced for the unique qualities you bring. Our culture encourages personal expression, open dialogue, and genuine connections, where you are valued, accepted and respected for who you are, allowing you to thrive both personally and professionally. This is how we aim to prevent, stop and cure diseases and ensure everyone has access to healthcare today and for generations to come. Join Roche, where every voice matters.

The Position

At Roche, we are working to make next-generation sequencing simple and accessible enough for routine use. By accelerating clinical research, streamlining workflows, and expanding assay menus, we are broadening access to genomic data and lowering barriers to adoption. From robust sample isolation and preparation tools to novel sequencing technology and advanced bioinformatics, we are developing differentiated, highly integrated end-to-end solutions for next-generation sequencing, resulting in a sample in, result out workflow.

Our Systems Technology Group, a part of Roche Sequencing Solutions, is seeking a Principal II, Applied Chemistry Scientist to lead our applied chemistry efforts. This is a hands-on role for a multidisciplinary expert focused on solving the core chemical challenges at the heart of our next-generation platforms. You will be responsible for inventing, developing, and integrating the novel chemical processes and formulations that ensure the ultimate performance, reliability, and longevity of our systems. In this role, you will lead early-stage R&D projects and collaborate closely with materials, mechanical, consumables, and integration engineers to develop robust solutions—from inventing novel surface modification strategies to formulating reagents that solve complex challenges like non-specific binding and carryover—bridging the gap between fundamental chemistry and applied systems engineering.

Core Responsibilities:

• You will pioneer and optimize novel surface chemistries and conjugation methodologies for the attachment of coatings, polymers and biomolecules to various surfaces, ensuring high efficiency, stability, and optimal density for downstream applications.
• You will invent, screen, and validate novel chemical formulations and buffer additives to mitigate biofouling and the non-specific adsorption of sensitive molecules within complex fluidic systems.
• You will lead the development and validation of comprehensive chemical hygiene protocols for complex fluidic systems, selecting chemistries and defining procedures to eliminate molecular carryover and ensure robust, reproducible performance over the lifetime of the system.
• You will design and execute studies to determine optimal process conditions and chemical compatibility for on-instrument processes and chemical reactions.
• You will drive root cause investigations of system-level contamination issues, utilizing advanced surface and trace analysis techniques such as GC-MS, LC-MS, ToF-SIMS, XPS, and Auger spectroscopy.

Assay Development & System Performance

• You will design, develop, and execute robust analytical assays to rigorously quantify the effectiveness of chemical hygiene protocols, measure residual carryover at trace levels, and assess the long-term impact of chemical treatments on material integrity and system performance.
• You will develop novel characterization methods and assays to assess the performance of surface modifications, including the quantification of ligand density, binding capacity, and chemical stability.
• You will develop and manage end-to-end analytical workflows for trace contaminant detection, including selection of instrumentation and collaboration with external labs.
• You will utilize simulation tools and scripting to model chemical and fluidic workflows, predict system behavior, and accelerate the optimization of experimental protocols.

Workflow Implementation & System Troubleshooting

• You will conduct hands-on experiments and activities on breadboards, custom fixtures, and early-stage prototype systems, personally driving the optimization of chemical workflows on fluidic systems and related hardware.
• You will lead investigations and chemical compatibility studies across multi-site operations to ensure process reliability in fluidic systems.
• You will troubleshoot complex, system-level performance issues where the root cause may be chemical in nature and will require a deep, first-principles approach to problem-solving that spans chemistry, materials, hardware and software.

Cross-Functional Collaboration & Strategy

• You will serve as the team's primary subject matter expert on applied chemistry, partnering closely with Materials, Consumables and Fluidics Engineers to select, test, and qualify new materials for chemical compatibility and performance.
• You will collaborate with Systems, Mechanical, and Software Engineers to ensure seamless integration of chemical processes with the overall system architecture, defining requirements for fluidic control, thermal management, and automated protocol execution.
• You will analyze complex data sets, author technical reports, generate intellectual property, and present findings and strategic recommendations to the team, the organization, and senior leadership.

This is an on-site position based in Santa Clara, CA. Relocation benefits are not being offered for this role.

Who You Are (Required):

• You have a PhD in Chemistry, Chemical Engineering or a closely related discipline with at least 7 years of relevant industry experience in a product development environment; OR a Master's degree with at least 9 years of relevant industry experience; OR a Bachelor's degree with at least 11 years of relevant industry experience.
• You are a demonstrated expert in surface chemistry, bioconjugation techniques, and the chemical principles governing interactions at solid-liquid interfaces.
• You have a demonstrated track record of developing and validating chemical processes or formulations on prototypes with complex fluidic or microfluidic systems within the life sciences, sequencing or diagnostics industries.
• You have significant experience developing and implementing a wide variety of analytical assays to characterize chemical processes and quantify performance.
• You have demonstrated proficiency with data analysis and scripting languages for automating experiments and analyzing complex datasets.
• You are an expert at troubleshooting complex integrated systems, with a proven ability to identify and resolve elusive issues that span chemistry, materials, hardware, and biology.

Leadership & Interpersonal Skills

• You have demonstrated strong interpersonal and communication skills with the ability to communicate complex chemical concepts in a clear and understandable manner to both technical and non-technical stakeholders.
• You have successfully demonstrated the ability to lead technical initiatives and mentor junior scientists and engineers.

Who You Are (Preferred):

• You have direct experience with the chemistry of next-generation sequencing, solid-phase oligonucleotide synthesis and multi-step enzymatic workflows.
• You have direct experience with a range of surface characterization techniques.
• You have direct experience developing products in a regulated environment and are familiar with methodologies such as Design of Experiments (DOE) and statistical process control (SPC).
• You have a strong record of innovation, demonstrated by a portfolio of patents and/or publications in relevant fields.
• You have excellent organizational skills, with proven experience planning, prioritizing, and executing on multiple technical projects in a fast-paced, ambiguous R&D environment.
• You are an action-oriented and decisive problem-solver, thriving in a fast-paced environment where you work with a sense of urgency and optimism.
• You possess a deep scientific curiosity and an innate desire to learn, be challenged, and challenge the status quo.

The expected salary range for this position based on the primary location of Santa Clara, CA is $125,500 – $233,500. Actual pay will be determined based on experience, qualifications, geographic location, and other job-related factors permitted by law. A discretionary annual bonus may be available based on individual and Company performance.

This position also qualifies for the benefits detailed at the link provided below.