Charlotte Nelson
Ph.D. Biological & Medical Informatics
Domain-crossing scientist passionate about harnessing biological complexity to bridge the gap between basic science and precision medicine. Focused on building tools that empower researchers to leverage data and knowledge beyond their core discipline to gain a comprehensive, systems-level understanding of their research problems. Demonstrated independent research and leadership skills in both academic and business settings.
Experience - Industry
CEO / CSO MateBioservices
2021 - present
Mate Bioservices (Mate) was spun out of UCSF in 2021 after the Scalable Precision Medicine Open Knowledge Engine (SPOKE) project won the National Science Foundation Convergence Accelerator. Mate’s mission is to accelerate scientific breakthroughs by making interdisciplinary research possible for a single individual.
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Translated customer needs into commercial products.
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Led stakeholder discussions across the biomedical ecosystem to uncover critical customer pain points.
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Incorporated stakeholder needs into product applications, including Mate’s retail (BRIC) and commercial (SPOKE Cloud) bioinformatics platforms; worked directly with early users to continuously enhance each platform.
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Designed user interfaces and managed development teams.
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Engineered the functionality for BRIC and led a team of 5 UX designers and software developers in building the BRIC prototype and minimum viable product.
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Advised a team of 9 SPOKE bioinformaticians on the integration of new resources into the SPOKE knowledge graph and SPOKE Cloud fabric.
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Architected business model transformation.
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Identified a structural industry shift away from traditional service-based expert consultancy models towards scalable SaaS frameworks.
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Devised and led the implementation of a new business model and go-to-market strategy centered on SaaS and data sales across academic and industry settings.
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Launched commercial products and secured customer contracts.
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Independently negotiated and closed SaaS contracts with major academic institutions as well as pharmaceutical and biotech companies passing $200K ARR, including contracts with the top ten big pharma, within the first year of SPOKE Cloud launch.
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Engaged with major universities, national labs, and non-profits (UCSF, ISB, LLNL, NASA, Phenome Health, etc.).
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Developed and executed a comprehensive investor relations and public relations program.
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Represented Mate at industry events including main stage presentation at the Precision Medicine World Conference.
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Led venture capital investor pitches and reached late-stage negotiations with highly prominent VCs in Mate’s vertical despite fundraising in the most challenging environment of the last several decades.
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Managed operations. Oversaw day-to-day operations, including customer service, legal, and accounting functions.
Experience - Academia
University of California, San Francisco (UCSF)
Principal Investigators: Atul Butte & Sergio Baranzini
2015-2020
University of California, Santa Cruz (UCSC)
Principal Investigators: Harry Noller
2013-2015
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Modeled biological complexity across scales.
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Leader in the foundation and evolution of the Scalable Precision Medicine Open Knowledge Engine (SPOKE).
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Advanced the goal of unifying multi-modal data and cross-disciplinary knowledge into a single platform that enables scientists to extract novel insights spanning biological scales (Morris et al., 2023).
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Advised the development of a framework that combines explicit and implicit knowledge of SPOKE and LLM which streamlines the process of extracting insights from SPOKE while minimizing “hallucination”. Watch LabMate.
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Integrated basic science into precision medicine applications.
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Developed a graph theory method to generate biologically and clinically meaningful "patient signatures" by connecting Electronic Health Records (EHRs) to SPOKE (Nelson, et al., 2019).
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Established machine learning methods leveraging novel patient signatures for predicting multiple sclerosis up to 5 years prior to MS diagnosis and uncovered biological features linked to prodromal MS (Nelson, et al., 2022).
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Advised Karthik Soman and Alice Tang on the development of machine learning applications leveraging patient signature for Parkinson’s disease (Soman, et al., 2023) and Alzheimer’s disease (Tang, et al. 2024), alongside researchers at the UCSF Weill Institute for Neurosciences and UCSF Memory and Aging Center (MAC).
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Harmonized multi-omics data into a single analysis.
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Collaborated with NASA GeneLab to connect model organism gene expression data to SPOKE to identify phenotypes and physiological changes impacted by spaceflight. (Nelson, et al., 2021; Sanders, et al., 2023; Scott, et al., 2023).
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Conceived and constructed a multi-omics data fabric (transcriptomics, proteomics, epigenomics, metabolomics, etc.) connected to Mate Bioservices SPOKE Cloud, enabling streamlined analyses of NASA’s multi-modal data.
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Pioneered real world evidence (RWE) pilot studies.
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Alongside Atul Butte, secured UCSF’s first RWE pilot study with a major pharma company. This study was the precursor to UCSF’s Center for Real World Evidence, which generates millions of dollars in funding annually today.
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Investigated how the company’s new drug was performing in the UCSF patient population compared to the original clinical trials.
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Uncovered ribosomal structure-function relationships.
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Leveraged biological assays and x-ray crystallography to further elucidate the role of Elongation Factor G in translation (NIblett, Nelson, et al., 2020).
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Education
University of California, San Francisco (UCSF)
Degree: Biomedical and Biological Informatics PhD
Advisors: Atul Butte and Sergio Baranzini
2015-2020
University of California, Santa Cruz (UCSC)
Degree: Biochemistry and Molecular Biology B.S.
Degree: Bioinformatics B.S.
Advisor: Harry Noller
2009-2014
“Perhaps we see equations as simple because they are easily expressed in terms of mathematical notation already invented at an earlier stage of development of the science, and thus what appears to us as elegance of description really reflects the interconnectedness of Nature’s laws at different levels.”
― Dr. Murray Gell-Mann