Senior Scientist – Molecular Design & Synthesis

What if the work you did every day could impact the lives of people you know? Or all of humanity? At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life-changing discoveries that are transforming human health through the early detection and diagnosis of diseases and new treatment options for patients. Working at Illumina means being part of something bigger than yourself. Every person, in every role, has the opportunity to make a difference. Surrounded by extraordinary people, inspiring leaders, and world changing projects, you will do more and become more than you ever thought possible. Position Summary We are seeking a highly motivated Senior Scientist, Molecular Design & Synthesis to drive the design, synthesis, and optimization of novel molecular architectures that enable next-generation sequencing technologies. This role combines hands-on molecular synthesis with computational molecular design and cheminformatics. The successful candidate will contribute across the full Design-Make-Test-Learn (DMTL) cycle, applying computational and data-driven approaches to generate innovative molecular designs and leveraging experimental chemistry to synthesize, characterize, and validate those concepts. The ideal candidate thrives at the intersection of chemistry and computation, translating molecular hypotheses into experimentally testable constructs while generating insights that guide future design strategies. Experience applying cheminformatics, molecular modeling, machine learning, or related computational approaches to accelerate molecular design and synthetic chemistry programs is strongly preferred. Key Responsibilities Molecular Design & Cheminformatics (40-50%) • Design and optimize novel molecular constructs using structure-property-function relationships and mechanistic insights. • Apply cheminformatics, molecular modeling, computational chemistry, and data-driven approaches to guide molecular design and prioritization. • Build, curate, and analyze molecular datasets to identify trends, establish design principles, and generate testable hypotheses. • Analyze experimental results and develop predictive models that correlate molecular features with performance. • Evaluate molecular properties including conformation, solubility, charge distribution, hydrophobicity, linker behavior, and other factors that influence molecular function. • Utilize computational tools such as RDKit, Python, molecular visualization software, and property prediction workflows to accelerate design cycles. • Assess and implement emerging artificial intelligence and machine learning approaches to enhance molecular design and optimization. • Assess synthetic feasibility and develop design strategies that balance molecular performance, manufacturability, scalability, and experimental throughput. Molecular Synthesis & Characterization (40-50%) • Design and execute synthetic routes for peptides, oligonucleotides, linkers, conjugates, and other novel molecular constructs. • Perform and optimize syntheses using techniques that may include: Solid-phase peptide synthesis (SPPS) Oligonucleotide phosphoramidite synthesis Click chemistry Bioconjugation chemistry Synthetic organic chemistry methodologies • Troubleshoot synthetic challenges and develop innovative solutions to improve yield, purity, scalability, and robustness. • Characterize molecules using analytical techniques including LC-MS, analytical and preparative HPLC, spectroscopy, and other relevant methods. • Maintain accurate experimental documentation and effectively communicate scientific findings through technical reports, presentations, and cross-functional discussions. Project Leadership & Innovation (10-20%) • Drive Design-Make-Test-Learn workflows across molecular development programs. • Collaborate effectively with cross-functional teams spanning chemistry, biology, engineering, sequencing technology, bioinformatics, and data science. • Generate innovative concepts and contribute to intellectual property development, including invention disclosures and patent applications. • Provide technical leadership and mentorship to junior scientists and project team members. • Present scientific findings, recommendations, and strategic insights to project teams and leadership. • Identify technical risks and develop mitigation strategies within areas of responsibility and at critical cross-functional interfaces. • Influence project direction through scientific expertise, critical thinking, and effective stakeholder engagement. Listed responsibilities are intended to describe the general nature and level of work performed and are not intended to be an exhaustive list of all responsibilities associated with the position. Responsibilities may evolve based on business and project needs. Success in the Role The successful candidate will: • Generate innovative molecular designs informed by computational and experimental insights. • Efficiently develop, synthesize, and characterize novel molecular constructs that advance next-generation sequencing technologies. • Establish predictive design principles that improve molecular performance and accelerate development cycles. • Reduce experimental screening burden through rational, data-driven design approaches. • Generate valuable intellectual property and contribute to technology differentiation. • Serve as a key scientific bridge between computational design and experimental chemistry capabilities. • Drive scientific innovation while enabling informed decision-making across multidisciplinary project teams. Position Requirements • Demonstrated expertise in molecular design, synthetic chemistry, and molecular characterization. • Proven track record of independently driving complex scientific projects from concept through execution. • Experience integrating computational and experimental approaches t…