Research Papers

  • Liu Z, Xu H, Woicik A, Shapiro LG, Blazes M, Wu Y, Steffen V, Cukras C, Lee CS, Zhang M, Lee AY, Wang S, OCTCube-M: A 3D multimodal optical coherence tomography foundation model for retinal and systemic diseases with cross-cohort and cross-device validation., Nature Biomedical Engineering, Mar 2026
  • Wu Y, Lee CS, Lee AY, Van Gelder RN, Improving Residency Matching through Computational Optimization, JAMA Open Network, Apr 2025, https://pubmed.ncbi.nlm.nih.gov/40549382/
  • Rajesh AE, Olvera-Barrios A, Warwick AN, Wu Y, Stuart KV, Biradar MI, Ung CY, Khawaja AP, Luben R, Foster PJ, Cleland CR, Makupa WU, Denniston AK, Burton MJ, Bastawrous A, Keane PA, Chia MA, Turner AW, Lee CS, Tufail A, Lee AY, Egan C. Machine learning derived retinal pigment score from ophthalmic imaging shows ethnicity is not biology. Nature Communications. Jan 2025. https://www.nature.com/articles/s41467-024-55198-7
  • Jackson VE*, Wu Y*, Bonelli R*, Owen J, Farashi S, Kihara Y, Gantner ML, Egan C, Williams K, Ansell B, Tufail A, Lee AY, Bahlo M, Multi-omic spatial effects on high-resolution AI-derived retinal thickness}, Nature Communications, Jan 2025, * Joint first authors, https://www.nature.com/articles/s41467-024-55635-7
  • Spaide T, Rajesh AE, Gim N, Blazes M, Lee CS, Macivannan N, Lee G, Lewis W, Salehi A, de Sisternes L, Herrera G, Shen M, Gregori G, Rosenfeld PJ, Pramil V, Waheed N, Wu Y, Zhang Q, Lee AY, Estimating uncertainty of geographic atrophy segmentations with Bayesian deep learning, Ophthalmology Science, Jul 2024, https://pubmed.ncbi.nlm.nih.gov/39380882/
  • Gholami S, Scheppke L, Kshirsagar M, Wu Y, Dodhia R, Bonelli R, Leung I, Sallo FB, Muldrew A, Jamison C, Peto T, Ferres JL, Weeks WB, Friedlander M, Lee AY, Enhanced Macular Telangiectasia Type 2 Detection: Leveraging Self-Supervised Learning and Ensemble Models, Ophthalmology Science, Jan 2025, https://www.sciencedirect.com/science/article/pii/S2666914525000089
  • Verma A, Tzaridis S, Blazes M, Friedlander M, Lee AY, and Wu Y, Developing a 10-layer retinal segmentation for MacTel using Semi-Supervised Learning, TVST, Oct 2024, https://pubmed.ncbi.nlm.nih.gov/39499591/
  • Kruper J, Richie-Halford A, Benson N, Caffarra S, Owen J, Wu Y, Lee AY, Lee CS, Yeatman J, Egan C, UK Biobank Eye and Vision Consortium UK Biobank Eye and Vision Consortium, Convolutional neural network-based classification of glaucoma using optic radiation tissue properties, Nature Communications Medicine, Apr 2024, https://www.nature.com/articles/s43856-024-00496-w
  • Gholami S, Scheppke L, Kshirsagar M, Wu Y, Dodhia R, Bonelli R, Leung I, Sallo FB, Muldrew A, Jamison C, Peto T, Ferres JL, Weeks WB, Friedlander M, Lee AY, Self-Supervised Learning for Improved Optical Coherence Tomography Detection of Macular Telangiectasia Type 2, JAMA Ophthalmology, Mar 2024, https://jamanetwork.com/journals/jamaophthalmology/fullarticle/2814750
  • Olvera-Barrios A, Rudnicka AR, Anderson J, Bolter L, Chambers R, Warwick AN, Welikala R, Fajtl J, Barman S, Remgnino P, Wu Y, Lee AYL, Chew EY, Ferris FL, Hingorani A, Sofat A, Egan CA, Tufail A, Owen CG, Two-year recall for people with no diabetic retinopathy: a multi-ethnic population-based retrospective cohort study using real-world data to quantify the effect, British Journal of Ophthalmology, Oct 2023, https://pubmed.ncbi.nlm.nih.gov/37875374/
  • Olvera-Barrios A, Owen CG, Anderson J, Warwick A, Chambers R, Bolter L, Wu Y, Welikala R, Fajtl J, Barman S, Remagnino P, Chew EY, Ferris FL, Hingorani AD, Sofat R, Lee AY, Egan CA, Tufail A, Rudnicka AR, Ethnic disparities in progression rates for sight-threatening diabetic retinopathy in diabetic eye screening: a population-based retrospective cohort study, BMJ, Volume 11, Issue 6, 2023, https://pubmed.ncbi.nlm.nih.gov/37949472/
  • Wu Y, Egan C, Olvera-Barrios A, Scheppke L, Peto T, Charbel Issa P, Heeren T, Leung I, Rajesh A, Tufail A, Lee CS, Chew E, Friedlander M, Lee AY, Developing a continuous severity scale for MacTel type 2 using Deep Learning and implications or disease grading, Ophthalmology, Sep 2023, https://pubmed.ncbi.nlm.nih.gov/37739233/
  • Kruper J, Benson NC, Caffarra S, Owen J, Wu Y, Lee AY, Lee CS, Yeatman J, Rokem A, Optic radiations representing different eccentricities age differently, Human Brain Mapping, Feb 2023, https://pmc.ncbi.nlm.nih.gov/articles/PMC10171550/
  • Wu Y, Egan C, Olvera-Barrios A, Scheppke L, Peto T, Charbel Issa P, Heeren T, Leung I, Rajesh A, Tufail A, Lee CS, Chew E, Friedlander M, Lee AY, Training deep learning models to work on multiple devices by unsupervised cross domain learning with no additional annotations, Ophthalmology, Sep 2023, https://pubmed.ncbi.nlm.nih.gov/36154868/
  • Olvera-Barrios A, Kihara Y, Wu Y, Warwick AN, Muller PL, Williams KM, Rudnicka AR, Owen CG, Lee AY, Egan C, Foveal Curvature and Its Associations in UK Biobank Participants, Investigative ophthalmology & visual science, Aug 2022, https://pubmed.ncbi.nlm.nih.gov/35900728/
  • VandenBosch LS, Luu K, Timms AE, Challam S, Wu Y, Lee AY, Cherry TJ, Machine Learning Prediction of Non-Coding Variant Impact in Human Retinal Cis Regulatory Element, TVST, Apr 2022, https://pubmed.ncbi.nlm.nih.gov/35435921/
  • Wu Y, Taravati P, Yanagihara RT, Francis CE, Blazes MS, Lee CS, Lee AY, Van Gelder RN,, Inefficiencies in Residency Matching Associated with Gale-Shapley Algorithms, Journal of Academic Ophthalmology, Jun 2021, https://pmc.ncbi.nlm.nih.gov/articles/PMC9927996/

2020

2019

  • Ting DSW, Pasquale LR, Peng L, Campbell JP, Lee AY, Raman R, Tan GSW, Schmetterer L, Keane PA, Wong TY. Artificial intelligence and deep learning in ophthalmology. Br J Ophthalmol. 2019 Feb;103(2):167-175. doi: 10.1136/bjophthalmol-2018-313173. Epub 2018 Oct 25. Review. PubMed PMID: 30361278; PubMed Central PMCID: PMC6362807.

2018

  • Lee A, Taylor P, Kalpathy-Cramer J, Tufail A. Reply. Ophthalmology. 2018 Dec;125(12):e86. doi: 10.1016/j.ophtha.2018.06.036. Epub 2018 Oct 19. PubMed PMID: 30343936.

2017

  • Lee JH, Agarwal A, Mahendradas P, Lee CS, Gupta V, Pavesio CE, Agrawal R. Viral posterior uveitis. Surv Ophthalmol. 2017 Jul - Aug;62(4):404-445. doi: 10.1016/j.survophthal.2016.12.008. Epub 2016 Dec 22. Review. PubMed PMID: 28012878; PubMed Central PMCID: PMC5654632.

2016

  • Lee CS, Agrawal R, Pavesio C. Ocular Tuberculosis--A Clinical Conundrum. Ocul Immunol Inflamm. 2016;24(2):237-42. doi: 10.3109/09273948.2014.985387. Epub 2015 Jun 25. PubMed PMID: 26110355; PubMed Central PMCID: PMC4760910.

2015

2014

  • Lin P, Bach M, Asquith M, Lee AY, Akileswaran L, Stauffer P, Davin S, Pan Y, Cambronne ED, Dorris M, Debelius JW, Lauber CL, Ackermann G, Baeza YV, Gill T, Knight R, Colbert RA, Taurog JD, Van Gelder RN, Rosenbaum JT. HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats. PLoS One. 2014;9(8):e105684. doi: 10.1371/journal.pone.0105684. eCollection 2014. PubMed PMID: 25140823; PubMed Central PMCID: PMC4139385.

2012

  • Sobrin L, Ripke S, Yu Y, Fagerness J, Bhangale TR, Tan PL, Souied EH, Buitendijk GH, Merriam JE, Richardson AJ, Raychaudhuri S, Reynolds R, Chin KA, Lee AY, Leveziel N, Zack DJ, Campochiaro P, Smith RT, Barile GR, Hogg RE, Chakravarthy U, Behrens TW, Uitterlinden AG, van Duijn CM, Vingerling JR, Brantley MA Jr, Baird PN, Klaver CC, Allikmets R, Katsanis N, Graham RR, Ioannidis JP, Daly MJ, Seddon JM. Heritability and genome-wide association study to assess genetic differences between advanced age-related macular degeneration subtypes. Ophthalmology. 2012 Sep;119(9):1874-85. doi: 10.1016/j.ophtha.2012.03.014. Epub 2012 Jun 15. PubMed PMID: 22705344; PubMed Central PMCID: PMC3899891.

2011

  • Yu Y, Bhangale TR, Fagerness J, Ripke S, Thorleifsson G, Tan PL, Souied EH, Richardson AJ, Merriam JE, Buitendijk GH, Reynolds R, Raychaudhuri S, Chin KA, Sobrin L, Evangelou E, Lee PH, Lee AY, Leveziel N, Zack DJ, Campochiaro B, Campochiaro P, Smith RT, Barile GR, Guymer RH, Hogg R, Chakravarthy U, Robman LD, Gustafsson O, Sigurdsson H, Ortmann W, Behrens TW, Stefansson K, Uitterlinden AG, van Duijn CM, Vingerling JR, Klaver CC, Allikmets R, Brantley MA Jr, Baird PN, Katsanis N, Thorsteinsdottir U, Ioannidis JP, Daly MJ, Graham RR, Seddon JM. Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration. Hum Mol Genet. 2011 Sep 15;20(18):3699-709. doi: 10.1093/hmg/ddr270. Epub 2011 Jun 10. PubMed PMID: 21665990; PubMed Central PMCID: PMC3159552.
  • Muthappan V, Lee AY, Lamprecht TL, Akileswaran L, Dintzis SM, Lee CS, Magrini V, Mardis ER, Shendure J, Van Gelder RN. Biome representational in silico karyotyping. Genome Res. 2011 Apr;21(4):626-33. doi: 10.1101/gr.115758.110. Epub 2011 Feb 10. PubMed PMID: 21324882; PubMed Central PMCID: PMC3065710.

2010

2009

2008

2007