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Draft:Nautilus Biotechnology

  • Comment: Many of the sources are press releases or research articles by people associated with the company. These are not suitable sources for establishing the notability of the company. Stuartyeates (talk) 23:22, 16 August 2025 (UTC)
  • Comment: In accordance with the Wikimedia Foundation's Terms of Use, I disclose that I have been paid by my employer for my contributions to this article. Narec51 (talk) 00:35, 16 August 2025 (UTC)
Nautilus Biotechnology
Company typePublic
Nasdaq: NAUT
IndustryBiotechnology
Founded2016; 9 years ago
FounderParag Mallick, Sujal Patel
HeadquartersSeattle, Washington
Websitenautilus.bio

Nautilus Biotechnology, Inc. is a biotechnology company developing a single-molecule proteomics platform.[1] The Nautilus™ Proteome Analysis Platform is designed to integrate machine learning and biochemistry approaches to measure substantively the entire proteome and its myriad proteoforms.[2][3]

Nautilus was founded in 2016 by Parag Mallick and Sujal Patel, who serve as the company’s Chief Scientist and CEO, respectively.[4][5] With corporate headquarters in Seattle, Washington, and research headquarters in San Carlos, California, Nautilus became a publicly traded company in 2021 through a merger with special-purpose acquisition company ARYA Life Sciences Acquisition Corp. III.[6]

History

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Co-founders Parag Mallick and Sujal Patel met when Mallick, now an Associate Professor at Stanford University, was Director of Clinical Proteomics at Cedars-Sinai and a customer of Isilon Systems, where Patel was previously founder and CEO before Isilon was acquired by EMC Corporation (now Dell EMC).[7][8][9] They established Nautilus after Mallick approached Patel with his idea for a single-molecule proteomics technology.[10]

In 2020, the company raised $76 million in a Series B financing round.[11] The round was led by Vulcan Capital and included participation from AME Cloud Ventures, Andreessen Horowitz, Madrona Venture Group, and others.[11][12]

It received $345 million in additional funding through its listing as a publicly traded company in 2021.[3][13]

In 2022, Nautilus joined the Human Proteome Organization’s Industrial Advisory Board, an international committee supporting the development of innovative proteomics technologies and standards.[14][15]

Partnerships

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In 2020, the company initiated a research collaboration with Genentech to engage a pilot study using Nautilus’ technology on a protein target selected by Genentech.[16]

The following year, Nautilus inked research collaborations with Amgen to investigate proteins and proteoforms of interest as well as with The University of Texas MD Anderson Cancer Center to measure the quantity and patterns of post-translational modifications on specific oncology protein targets of interest across pre- and post-treatment settings.[16]

In 2023, Nautilus began working with a small cohort of researchers, including scientists at the Buck Institute for Research on Aging, as part of its First Access Challenge aiming to explore some of the first research applications of its platform.[17]

Technology

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The Nautilus™ Proteome Analysis Platform is designed to provide comprehensive analysis of the proteome, including known proteins, proteoforms, and the dark proteome.[4][18] It applies a method the company calls “Iterative Mapping” to repeatedly interrogate billions of individual, intact, and uniformly distributed protein molecules deposited on massive flow cells using probes that either:[19]

  • Bind short protein sequences (~3 amino acids) shared across many proteins. The resulting single-molecule binding patterns are decoded using a machine-learning enabled algorithm to identify each single protein molecule in broadscale proteomics analyses.[2][20]
  • Bind to a specific protein and its many possible modifications. Computational analyses resolve the observed single-molecule binding patterns to identify each individual proteoform in targeted proteoform studies.[21][22]

The Proteome Analysis Platform provides a list of protein or proteoform identities and abundances. Identification at the single-molecule level enables the quantification of proteins or proteoforms in a sample by counting molecules of the same species.[3]

The technology differs from traditional approaches to protein measurement such as mass spectrometry in that it is designed to quantify high and low-abundance proteins simultaneously without sacrificing quality.[22] On traditional platforms there can be trade-offs between proteome coverage and data quality stemming from factors such as inferring full protein identities from the measurement of small pieces of proteins and interpreting signals coming from many proteins at once.[23][24] In theory, the Nautilus Platform is designed to measure billions of intact proteins at the single-molecule level and thereby provide high-resolution views of the full proteome.[25] It is also designed to distinguish protein variants known as proteoforms, which is difficult to accomplish with traditional protein analysis methods that cannot repeatedly interrogate intact, single-molecules—although much progress has been made in proteoform studies leveraging top-down proteomics.[26][27][28]

Applications

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Broadscale proteomics studies are designed to determine how protein levels and interactions change across the entire proteome in response to a perturbation or as part of a particular cellular function, and can be used to discover novel disease biomarkers, new drug targets, and to determine how drug treatment may impact entire biological systems.[29]

Targeted proteoform studies may reveal the mechanisms through which single proteins adopt various functions in health and disease.[2] In addition, identifying proteoforms or groups of proteoforms associated with a particular disease may make it possible to develop highly specific biomarkers and therapeutics for those diseases.[28] For example, Nautilus has developed an assay to measure thousands of proteoforms of the tau protein.[22][30] This protein is known to aggregate and associate with cognitive decline in Alzheimer’s disease.[31] In addition, studies show that tau becomes gradually more modified as Alzheimer’s progresses yet it is not known what specific combinations of modifications are associated with progression and whether the proteoforms they create cause disease.[32] Future targeted proteoform studies may resolve the relationship between tau and Alzheimer’s.[30]

Both broadscale proteomic studies and targeted proteoform studies could have impacts on healthcare, agriculture, and climate.[33] As an initial step toward broad applications in life sciences research, Nautilus announced plans to work with a variety of scientists as part of its First Access Challenge.[17][34]

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  • James Joly, et al. Development of a method for large-scale single-molecule analysis of tau proteoforms. bioRxiv(2025). doi:10.1101/2025.06.26.660445
  • Jarrett D. Egertson, et al. A theoretical framework for proteome-scale single-molecule protein identification using multi-affinity protein binding reagents. bioRxiv(2021). doi:10.1101/2021.10.11.463967
  • Tural Aksel, et al. High-density and scalable protein arrays for single-molecule proteomic studies. bioRxiv(2022). doi:10.1101/2022.05.02.490328

References

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  1. ^ "Nautilus Biotechnology Debuts as Publicly Traded Company, Seeks to Deliver on the Untapped Potential of the Human Proteome". GlobeNewswire (Press release). 2021-06-10. Retrieved 2025-08-11.
  2. ^ a b c Coddington, Molly (2024-12-20). "When Science and Magic Collide in Proteomics". Technology Networks. Retrieved 2025-08-11.
  3. ^ a b c Dutton, Gail (2023-11-27). "Proteomics Platform Reduces Quantification to Counting". Genetic Engineering and Biotechnology News. Retrieved 2025-08-11.
  4. ^ a b "Meet the man who combines science, technology and magic to understand proteins". Marketplace. 2024-06-18. Retrieved 2025-08-11.
  5. ^ "Biotech's Race for Drug Development". Bloomberg. 2021-07-07. Retrieved 2025-08-11.
  6. ^ Cumbers, John (2021-06-16). "New Technology Could Unlock The Secrets Of Every Protein In The Body". Forbes. Retrieved 2025-08-11.
  7. ^ "Parag Mallick". Stanford University. Retrieved 2025-08-11.
  8. ^ Press, Gil (2016-09-06). "A Very Short History Of EMC Corporation". Forbes. Retrieved 2025-08-11.
  9. ^ Hodgkinson, Mike (2024-05-28). "Startup leadership wisdom: From "hands-on humility" to trusting your gut". Big Think. Retrieved 2025-08-11.
  10. ^ Schubert, Charlotte (2021-06-10). "Sujal Patel-led Nautilus Biotechnology goes public as it tackles ambitious plan to analyze proteins". GeekWire. Retrieved 2025-08-11.
  11. ^ Idrus, Amirah Al (2020-05-21). "Nautilus emerges with $76M to become the 'Illumina of proteomics'". Fierce Biotech. Retrieved 2025-08-11.
  12. ^ "Nautilus Biotechnology Raises $76 Million in Series B Funding to Be the First to Quantify the Human Proteome". Business Wire. 2020-05-21. Retrieved 2025-08-11.
  13. ^ Pasricha, Akash (2021-08-01). "Seattle biotech startup aims for 'new paradigm' in medicine by parsing proteins". The Seattle Times. Retrieved 2025-08-11.
  14. ^ "Nautilus Biotechnology Joins Human Proteome Organization (HUPO) Industrial Advisory Board". GlobeNewswire (Press release). 2022-09-01. Retrieved 2025-08-11.
  15. ^ "2025 IAB Companies and Representatives". Human Proteome Organization (HUPO). Retrieved 2025-08-11.
  16. ^ a b Borfitz, Deborah; Gloss, Stan (2021-12-15). "Nautilus Biotechnology Taking Protein Analysis To The Single-Molecule Level". Bio-IT World. Retrieved 2025-08-11.
  17. ^ a b Bonislawski, Adam (2023-04-12). "Nautilus Biotechnology Early-Access Users Exploring Platform's Discovery Proteomics Potential". GenomeWeb. Retrieved 2025-08-11.
  18. ^ Howes, Laura (2022-01-24). "Many of our proteins remain hidden in the dark proteome". Chemical & Engineering News. Retrieved 2025-08-11.
  19. ^ "The Next Generation of Proteome Analysis". The Scientist. 2025-07-08. Retrieved 2025-08-11.
  20. ^ Egertson, Jarrett D.; DiPasquo, Dan; Killeen, Alana; Lobanov, Vadim; Patel, Sujal; Mallick, Parag (2021-10-12), A theoretical framework for proteome-scale single-molecule protein identification using multi-affinity protein binding reagents, bioRxiv, doi:10.1101/2021.10.11.463967, retrieved 2025-08-11
  21. ^ Joly, J.; Budamagunta, V.; Zhang, Z.; Nortman, B.; Jouzi, M.; et al. (2025-07-21), "Large-scale single-molecule analysis of tau proteoforms", bioRxiv : The Preprint Server for Biology, bioRxiv, doi:10.1101/2025.06.26.660445, PMC 12262352, PMID 40667364, retrieved 2025-08-11
  22. ^ a b c Bonislawski, Adam (2024-12-04). "Nautilus Proteomics Platform Could Bring New Depth to Proteoform Analyses". GenomeWeb. Retrieved 2025-08-11.
  23. ^ Alfaro, Javier Antonio; Bohländer, Peggy; Dai, Mingjie; Filius, Mike; Howard, Cecil J.; et al. (2021-06-07). "The emerging landscape of single-molecule protein sequencing technologies". Nature Methods. 18 (6): 604–617. doi:10.1038/s41592-021-01143-1. ISSN 1548-7105. PMC 8223677. PMID 34099939.
  24. ^ Mallick, Parag; Kuster, Bernhard (2010-07-09). "Proteomics: a pragmatic perspective". Nature Biotechnology. 28 (7): 695–709. doi:10.1038/nbt.1658. ISSN 1546-1696. PMID 20622844.
  25. ^ Brighton, Katie (2023-06-14). "Advancing Biomedicine With Single-Molecule Proteomics". Technology Networks. Retrieved 2025-08-11.
  26. ^ Melani, Rafael D.; Gerbasi, Vincent R.; Anderson, Lissa C.; Sikora, Jacek W.; Toby, Timothy K.; et al. (2022-01-27). "The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells". Science. 375 (6579): 411–418. Bibcode:2022Sci...375..411M. doi:10.1126/science.aaz5284. PMC 9097315. PMID 35084980.
  27. ^ Drown, Bryon S.; Jooß, Kevin; Melani, Rafael D.; Lloyd-Jones, Cameron; Camarillo, Jeannie M.; et al. (2022-04-12). "Mapping the Proteoform Landscape of Five Human Tissues". Journal of Proteome Research. 21 (5): 1299–1310. doi:10.1021/acs.jproteome.2c00034. ISSN 1535-3893. PMC 9087339. PMID 35413190.
  28. ^ a b Marx, Vivien (2023-03-10). "Proteomics sets up single-cell and single-molecule solutions". Nature Methods. Retrieved 2025-08-11.
  29. ^ Beeton-Kempen, Natasha (2024-07-05). "Proteomics: Principles, Techniques and Applications". Technology Networks. Retrieved 2025-08-11.
  30. ^ a b Sullivan, Danny (2024-06-06). "Proteomics platform sheds new light on tau's role in Alzheimer's". Longevity.Technology. Retrieved 2025-08-11.
  31. ^ Dujardin, Simon; Commins, Caitlin; Lathuiliere, Aurelien; Beerepoot, Pieter; Fernandes, Analiese R.; et al. (2020-06-22). "Tau molecular diversity contributes to clinical heterogeneity in Alzheimer's disease". Nature Medicine. 26 (8): 1256–1263. doi:10.1038/s41591-020-0938-9. ISSN 1546-170X. PMC 7603860. PMID 32572268.
  32. ^ Wesseling, Hendrik; Mair, Waltraud; Kumar, Mukesh; Schlaffner, Christoph N.; Tang, Shaojun; et al. (2020-12-10). "Tau PTM Profiles Identify Patient Heterogeneity and Stages of Alzheimer's Disease". Cell. 183 (6): 1699–1713.e13. doi:10.1016/j.cell.2020.10.029. ISSN 1097-4172. PMC 8168922. PMID 33188775.
  33. ^ Mallick, Parag (2022-04-20). "Why proteins may help solve existential crises in healthcare, food security, and climate". UN Trade and Development (UNCTAD). Retrieved 2025-08-11.
  34. ^ "Nautilus Biotechnology Announces "First Access Challenge" Winners". GlobeNewswire (Press release). 2023-03-07. Retrieved 2025-08-11.
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