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Aaron Coyner, PhD
Computational Biologist
I create both simple and complex models to solve healthcare-related problems in a powerful, yet interpretable, way.
Education
20212016
PhD, Bioinformatics and Computational Biomedicine
Oregon Health & Science University Portland, OR- Dissertation: Machine Learning for Disease Detection and Prediction in Retinopathy of Prematurity
20142012
BS, Chemistry
Pacific Lutheran University Tacoma, WA- Thesis: Characterization of a Novel Long-chain Polymer Electrolyte
20122010
AS, Biology/Chemistry
Pierce Community College Lakewood, WAExperience
Current2021
Senior Computational Biologist
Oregon Health & Science University Portland, OR20212018
Teaching Assistant
Oregon Health & Science University Portland, OR- BMI 669: Data Analytics
- BMI 507: Ready4R
- CS 659: Machine Learning
- MATH 630: Probability & Statistical Inference for Scientists and Engineers
- BSTA 525: Introduction to Biostatistics
20212016
NLM Predoctoral Fellow, Division of Bioinformatics and Computational Biomedicine
Oregon Health & Science University Portland, OR- Chiang Lab
2019
Mentored Teaching
Oregon Health & Science University Portland, OR- BMI 665: Bioinformatics Programming and Scripting
- BMI 669: Data Analytics
20162014
Research Assistant II
Oregon Health & Science University Portland, OR- Penessi Lab
20122011
Research Assistant I
Pacific Lutheran University Tacoma, WA- Waldow Lab
Patents
Current2018
Systems, Devices, and Methods for Identifying Plus Disease Using Deep Convolutional Neural Networks
Oregon Health & Science University Portland, OR- Chiang MF, Campbell JP, Ostmo S, Chan RVP, Kalpathy-Cramer J, Brown JM, Erdogmus D, Ioannidis S, Coyner AS
Peer-Reviewed Publications
[Aggressive Posterior Retinopathy of Prematurity: Clinical and Quantitative Imaging Features in a Large North American
Cohort](https://pubmed.ncbi.nlm.nih.gov/32197913/) Ophthalmology2020
- Bellsmith KN, Brown J, Kim SJ, Goldstein IH, Coyner AS, Ostmo S, Gupta K, Chan RVP, Kalpathy-Cramer J, Chiang MF, Campbell JP
2020
Introduction to Machine Learning, Neural Networks, and Deep Learning
Translational Vision Science and Technology- Choi RY*, Coyner AS*, Kalpathy-Cramer J, Chiang MF, Campbell JP
2019
Automated Fundus Image Quality Assessmentin Retinopathy of Prematurity Using Deep Convolutional Neural Networks
Ophthalmology Retina- Coyner AS, Swan R, Campbell JP, Ostmo S, Brown JM, Kalpathy-Cramer J, Kim SJ, Jonas KE, Chan RVP, Chiang MF
- MOST DOWNLOADED PEDIATRIC OPHTHALMOLOGY ARTICLE OF 2020
2019
Demystifying the Jargon: The Bridge between Ophthalmology and Artificial Intelligence
Ophthalmology Retina- Coyner AS, Campbell JP, Chiang MF
2018
Deep Learning for Image Quality Assessment of Fundus Images in Retinopathy of Prematurity
AMIA Annual Symposium Proceedings- Coyner AS, Swan R, Brown JM, Kalpathy-Cramer J, Kim SJ, Campbell JP, Jonas KE, Ostmo S, Chan RVP, Chiang MF
2018
Scleral Pits in Choroideremia: Implications for Retinal Gene Therapy
Retina- Al-Qahtani AA, Ba-Ali S, Alabduljalil T, Coyner AS, Patel RC, Weleber RG, Girach A, Christensen SK, Larsen M, Pennesi ME, Yang P
2018
The Role of ERK1/2 Activation in Sarpogrelate-Mediated Neuroprotection
Investigative Ophthalmology & Visual Science- Ku CA, Ryals RC, Jiang D, Coyner AS, Weller KK, Sinha W, Robb BM, Yang P, Pennesi ME
2017
Long-term Characterization of Retinal Degeneration in Royal College of Surgeons Rats Using Spectral-Domain Optical Coherence Tomography
Investigative Ophthalmology & Visual Science- Ryals RC, Andrews MD, Datta S, Coyner AS, Fischer CM, Wen Y, Pennesi ME, McGill TJ
2016
Retinal Neuroprotective Effects of Flibanserin, an FDA-Approved Dual Serotonin Receptor Agonist-Antagonist
PLoS One- Coyner AS, Ryals RC, Ku CA, Fischer CM, Patel RC, Datta S, Yang P, Wen Y, Hen R, Pennesi ME
2015
Sarpogrelate, a 5-HT2A Receptor Antagonist, Protects the Retina From Light-Induced Retinopathy
Investigative Ophthalmology & Visual Science- Tullis BE, Ryals RC, Coyner AS, Gale MJ, Nicholson A, Ku CA, Regis D, Sinha W, Datta S, Wen Y, Yang P, Pennesi ME
Conference Presentations
2018
Deep Learning for Image Quality Assessment of Fundus Images in Retinopathy of Prematurity
American Medical Informatics Association San Francisco, CA- Coyner AS, Swan R, Brown JM, Kalpathy-Cramer J, Kim SJ, Campbell JP, Jonas KE, Ostmo S, Chan RVP, Chiang MF
2018
Deep Learning for Image Quality Assessment of Fundus Images in Retinopathy of Prematurity
Association for Research in Vision and Ophthalmology Honolulu, HI- Coyner AS, Swan R, Brown JM, Kalpathy-Cramer J, Kim SJ, Campbell JP, Jonas KE, Ostmo S, Chan RVP, Chiang MF
2017
Automated Image Quality Assessment for Fundus Images in Retinopathy of Prematurity
American Medical Informatics Association Washington, DC- Coyner AS, Swan R, Brown JM, Kalpathy-Cramer J, Kim SJ, Campbell JP, Jonas KE, Ostmo S, Chan RVP, Chiang MF
2017
Automated Image Quality Assessment for Fundus Images in Retinopathy of Prematurity
Association for Research in Vision and Ophthalmology Baltimore, MD- Coyner AS, Swan R, Brown JM, Kalpathy-Cramer J, Kim SJ, Campbell JP, Jonas KE, Ostmo S, Chan RVP, Chiang MF
2016
Flibanserin, a FDA approved dual serotonin receptor agonist-antagonist, provides retinal neuroprotection from light induced damage
Association for Research in Vision and Ophthalmology Denver, CO- Coyner AS, Ryals RC, Ku CA, Datta S, Pennesi ME
Code Repositories
Current2020
ready-for-r-labs
Oregon Health & Science University Portland, OR- Notebooks for Ready4R
- Collaboration with Ted Laderas
Current2019
irop-iqa
Oregon Health & Science University Portland, OR- Automated fundus image quality assessment tool for use in retinopathy of prematurity
- Maintainer
Current2019
ml-interpretability
Oregon Health & Science University Portland, OR- Black box interpretability in R for Data Analytics
- Maintainer
Current2019
dissertate-ohsu
Oregon Health & Science University Portland, OR- Materials for writing a dissertation at Oregon Health & Science University in R Markdown
- Forked from Tyson Barrett
2018
machine-learning
- Personal code repository for machine learning methods implemented in Python.
- Maintainer
20182017
sleep-data-aligner
Oregon Health & Science University Portland, OR- File-combining software for Harvard sleep-quality research group.
- Course collaboration with Connor Smith and Sean Babcock
Relevant Coursework
2018
BMI 602: Fundamentals of Digital Image and Video Processing
Oregon Health & Science University Portland, OR2018
BMI 602: Neural Networks for Machine Learning
Oregon Health & Science University Portland, OR2018
BMI 635: Management and Processing of Large-Scale Data
Oregon Health & Science University Portland, OR2018
BMI 667: Network Science and Biology
Oregon Health & Science University Portland, OR2017
BMI 651: Statistical Methods
Oregon Health & Science University Portland, OR2017
BMI 669: Data Analytics
Biomedical Informatics, Oregon Health & Science University Portland, OR2017
CS 659: Machine Learning
Biomedical Informatics, Oregon Health & Science University Portland, OR2017
MATH 630: Probability and Statistical Inference for Scientists and Engineers
Biomedical Informatics, Oregon Health & Science University Portland, OR2016
BMI 650: Algorithms
Oregon Health & Science University Portland, ORVolunteer Experience
20172014
Casey Outreach Van
Ophthalmic Assistant Portland, OR2013
VIDA Volunteer Services
Dental Assistant Costa Rica; Nicaragua20122011