John Earls, PhD

Senior Software Engineer

Hood-Price Lab

John Earls

John Earls holds a PhD in Computer Science at the University of Washington-Seattle. He is currently developing methods and systems to enable large-scale integrative analysis of personal Dense, Dynamic Data clouds to maximize wellness and predict disease in its earliest stages.

  • PhD, Computer Science, University of Washington
  • MS Bioinformatics, University of Illinois
  • MS Computer Science, University of Washington

Machine Learning, pD3 clouds, Software Engineering, Systems Architecture

Magis, Andrew T., John C. Earls, Youn-Hee Ko, James A. Eddy, and Nathan D. Price. 2011. “Graphics Processing Unit Implementations of Relative Expression Analysis Algorithms Enable Dramatic Computational Speedup.” Bioinformatics (Oxford, England) 27 (6): 872–73. https://doi.org/10.1093/bioinformatics/btr033. Cite
Earls, John C., James A. Eddy, Cory C. Funk, Younhee Ko, Andrew T. Magis, and Nathan D. Price. 2013. “AUREA: An Open-Source Software System for Accurate and User-Friendly Identification of Relative Expression Molecular Signatures.” BMC Bioinformatics 14. https://doi.org/10.1186/1471-2105-14-78. Cite
Ko, Younhee, Seth A. Ament, James A. Eddy, Juan Caballero, John C. Earls, Leroy Hood, and Nathan D. Price. 2013. “Cell Type-Specific Genes Show Striking and Distinct Patterns of Spatial Expression in the Mouse Brain.” Proceedings of the National Academy of Sciences of the United States of America 110 (8): 3095–3100. https://doi.org/10.1073/pnas.1222897110. Cite
Price, Nathan D., Andrew T. Magis, John C. Earls, Gustavo Glusman, Roie Levy, Christopher Lausted, Daniel T. McDonald, et al. 2017. “A Wellness Study of 108 Individuals Using Personal, Dense, Dynamic Data Clouds.” Nature Biotechnology. https://doi.org/10.1038/nbt.3870. Cite
Ghosh, Dhimankrishna, Cory C. Funk, Juan Caballero, Nameeta Shah, Katherine Rouleau, John C. Earls, Liliana Soroceanu, et al. 2017. “A Cell-Surface Membrane Protein Signature for Glioblastoma.” Cell Systems 4 (5): 516-529.e7. https://doi.org/10.1016/j.cels.2017.03.004. Cite
Ament, Seth A., Jocelynn R. Pearl, Andrea Grindeland, Jason St Claire, John C. Earls, Marina Kovalenko, Tammy Gillis, et al. 2017. “High Resolution Time-Course Mapping of Early Transcriptomic, Molecular and Cellular Phenotypes in Huntington’s Disease CAG Knock-in Mice across Multiple Genetic Backgrounds.” Human Molecular Genetics 26 (5): 913–22. https://doi.org/10.1093/hmg/ddx006. Cite
Magis, Andrew T., John C. Earls, Gustavo Glusman, Gilbert S. Omenn, Jennifer C. Lovejoy, Nathan D. Price, and Leroy Hood. 2018. “Reply to ‘Precision Medicine in the Clouds.’” Nature Biotechnology 36 (8): 680–82. https://doi.org/10.1038/nbt.4211. Cite
Wilmanski, Tomasz, Noa Rappaport, John C. Earls, Andrew T. Magis, Ohad Manor, Jennifer Lovejoy, Gilbert S. Omenn, Leroy Hood, Sean M. Gibbons, and Nathan D. Price. 2019. “Blood Metabolome Predicts Gut Microbiome α-Diversity in Humans.” Nature Biotechnology. https://doi.org/10.1038/s41587-019-0233-9. Cite
Earls, John C., Noa Rappaport, Laura Heath, Tomasz Wilmanski, Andrew T. Magis, Nicholas J. Schork, Gilbert S. Omenn, Jennifer Lovejoy, Leroy Hood, and Nathan D. Price. 2019. “Multi-Omic Biological Age Estimation and Its Correlation With Wellness and Disease Phenotypes: A Longitudinal Study of 3,558 Individuals.” The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences 74 (Supplement_1): S52–60. https://doi.org/10.1093/gerona/glz220. Cite
Su, Yapeng, Daniel Chen, Dan Yuan, Christopher Lausted, Jongchan Choi, Chengzhen L. Dai, Valentin Voillet, et al. 2020. “Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19.” Cell, S0092867420314446. https://doi.org/10.1016/j.cell.2020.10.037. Cite Download
Piening, Brian D., Jennifer Lovejoy, and John C. Earls. 2020. “Ageotypes: Distinct Biomolecular Trajectories in Human Aging.” Trends in Pharmacological Sciences 41 (5): 299–301. https://doi.org/10.1016/j.tips.2020.02.003. Cite
Wainberg, Michael, Andrew T. Magis, John C. Earls, Jennifer C. Lovejoy, Nasa Sinnott-Armstrong, Gilbert S. Omenn, Leroy Hood, and Nathan D. Price. 2020. “Multiomic Blood Correlates of Genetic Risk Identify Presymptomatic Disease Alterations.” Proceedings of the National Academy of Sciences of the United States of America 117 (35): 21813–20. https://doi.org/10.1073/pnas.2001429117. Cite
Levy, Roie, Andrew T. Magis, John C. Earls, Ohad Manor, Tomasz Wilmanski, Jennifer Lovejoy, Sean M. Gibbons, Gilbert S. Omenn, Leroy Hood, and Nathan D. Price. 2020. “Longitudinal Analysis Reveals Transition Barriers between Dominant Ecological States in the Gut Microbiome.” Proceedings of the National Academy of Sciences of the United States of America 117 (24): 13839–45. https://doi.org/10.1073/pnas.1922498117. Cite Download
Baloni, Priyanka, Wikum Dinalankara, John C. Earls, Theo A. Knijnenburg, Donald Geman, Luigi Marchionni, and Nathan D. Price. 2021. “Identifying Personalized Metabolic Signatures in Breast Cancer.” Metabolites 11 (1): 20. https://doi.org/10.3390/metabo11010020. Cite Download
Wilmanski, Tomasz, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C. Earls, et al. 2021. “Gut Microbiome Pattern Reflects Healthy Ageing and Predicts Survival in Humans.” Nature Metabolism 3 (2): 274–86. https://doi.org/10.1038/s42255-021-00348-0. Cite
Wilmanski, Tomasz, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C. Earls, et al. 2021. “Author Correction: Gut Microbiome Pattern Reflects Healthy Ageing and Predicts Survival in Humans.” Nature Metabolism 3 (4): 586. https://doi.org/10.1038/s42255-021-00377-9. Cite Download