John Earls

Senior Software Engineer

Computer Scientist, Computational Biologist, Gentleman Adventurer

John Earls is primarily interested in applying machine learning techniques to biological data. John started studying Computational Biology under Nathan Price at the University of Illinois, where he receive an MS in Bioinformatics from the Computer Science department.

John is a PhD student at University of Washington in the Computer Science and Engineering department.

Mr. Earls has an Erdos number of 4.

Specialties: Python, C/C++, Java, php, SQL, Machine Learning, Statistics, being Awesome, CUDA

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