Gregory Way, PhD, MS

Professional Titles

• Assistant Professor

Recognitions

• Team Science Award, American Association for Cancer Research (2020)

Research Interests

I am interested in advancing the capabilities of biomedical data science, deep learning, and software to improve clinical decision-making and drug discovery. We are pursuing these goals through two complementary approaches: 1) Developing cell morphology as a high-dimensional indicator of cell state through the re-analysis of large microscopy imaging datasets, and 2) Discovering disease vulnerabilities through high-throughput measurements of CRISPR and drug perturbations on biologically relevant cell models.

Publications

• Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley SD, Gosline SJC, L? Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, Fertig EJ. A field guide to cultivating computational biology. PLoS Biol. 2021 Oct;19(10):e3001419. PubMed PMID: 34618807
• Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM. Sharing biological data: why, when, and how. FEBS Lett. 2021 Apr;595(7):847-863. PubMed PMID: 33843054
• Way GP, Kost-Alimova M, Shibue T, Harrington WF, Gill S, Piccioni F, Becker T, Shafqat-Abbasi H, Hahn WC, Carpenter AE, Vazquez F, Singh S. Predicting cell health phenotypes using image-based morphology profiling. Mol Biol Cell. 2021 Apr 19;32(9):995-1005. PubMed PMID: 33534641
• Cousminer DL, Wagley Y, Pippin JA, Elhakeem A, Way GP, Pahl MC, McCormack SE, Chesi A, Mitchell JA, Kindler JM, Baird D, Hartley A, Howe L, Kalkwarf HJ, Lappe JM, Lu S, Leonard ME, Johnson ME, Hakonarson H, Gilsanz V, Shepherd JA, Oberfield SE, Greene CS, Kelly A, Lawlor DA, Voight BF, Wells AD, Zemel BS, Hankenson KD, Grant SFA. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual. Genome Biol. 2021 Jan 4;22(1):1. PubMed PMID: 33397451
• Way GP, Zietz M, Rubinetti V, Himmelstein DS, Greene CS. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations. Genome Biol. 2020 May 11;21(1):109. PubMed PMID: 32393369
• Upton K, Modi A, Patel K, Kendsersky NM, Conkrite KL, Sussman RT, Way GP, Adams RN, Sacks GI, Fortina P, Diskin SJ, Maris JM, Rokita JL. Epigenomic profiling of neuroblastoma cell lines. Sci Data. 2020 Apr 14;7(1):116. PubMed PMID: 32286315
• Lin YT, Way GP, Barwick BG, Mariano MC, Marcoulis M, Ferguson ID, Driessen C, Boise LH, Greene CS, Wiita AP. Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma. Blood Adv. 2019 Nov 12;3(21):3214-3227. PubMed PMID: 31698452
• Martinez-Lage M, Lynch TM, Bi Y, Cocito C, Way GP, Pal S, Haller J, Yan RE, Ziober A, Nguyen A, Kandpal M, O'Rourke DM, Greenfield JP, Greene CS, Davuluri RV, Dahmane N. Immune landscapes associated with different glioblastoma molecular subtypes. Acta Neuropathol Commun. 2019 Nov 29;7(1):203. PubMed PMID: 31815646
• Rokita JL, Rathi KS, Cardenas MF, Upton KA, Jayaseelan J, Cross KL, Pfeil J, Egolf LE, Way GP, Farrel A, Kendsersky NM, Patel K, Gaonkar KS, Modi A, Berko ER, Lopez G, Vaksman Z, Mayoh C, Nance J, McCoy K, Haber M, Evans K, McCalmont H, Bendak K, Böhm JW, Marshall GM, Tyrrell V, Kalletla K, Braun FK, Qi L, Du Y, Zhang H, Lindsay HB, Zhao S, Shu J, Baxter P, Morton C, Kurmashev D, Zheng S, Chen Y, Bowen J, Bryan AC, Leraas KM, Coppens SE, Doddapaneni H, Momin Z, Zhang W, Sacks GI, Hart LS, Krytska K, Mosse YP, Gatto GJ, Sanchez Y, Greene CS, Diskin SJ, Vaske OM, Haussler D, Gastier-Foster JM, Kolb EA, Gorlick R, Li XN, Reynolds CP, Kurmasheva RT, Houghton PJ, Smith MA, Lock RB, Raman P, Wheeler DA, Maris JM. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Rep. 2019 Nov 5;29(6):1675-1689.e9. PubMed PMID: 31693904
• Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):172-180.e3. PubMed PMID: 29617658
• Way GP, Greene CS. Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. Pac Symp Biocomput. 2018;23:80-91. PubMed PMID: 29218871
• Way GP, Greene CS. Bayesian deep learning for single-cell analysis. Nat Methods. 2018 Dec;15(12):1009-1010. PubMed PMID: 30504887
• Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS. Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 2018 Apr;15(141). PubMed PMID: 29618526
• Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ Jr, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):239-254.e6. PubMed PMID: 29617664
• Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 Apr 5;173(2):321-337.e10. PubMed PMID: 29625050
• Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS. PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. BioData Min. 2018;11:14. PubMed PMID: 29988723
• Harrington LX, Way GP, Doherty JA, Greene CS. Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. Pac Symp Biocomput. 2018;23:157-167. PubMed PMID: 29218878
• Way GP, Allaway RJ, Bouley SJ, Fadul CE, Sanchez Y, Greene CS. A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. BMC Genomics. 2017 Feb 6;18(1):127. PubMed PMID: 28166733
• Way GP, Youngstrom DW, Hankenson KD, Greene CS, Grant SF. Implicating candidate genes at GWAS signals by leveraging topologically associating domains. Eur J Hum Genet. 2017 Nov;25(11):1286-1289. PubMed PMID: 28792001
• Titus AJ, Way GP, Johnson KC, Christensen BC. Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes. Sci Rep. 2017 Sep 14;7(1):11594. PubMed PMID: 28912426
• Doherty JA, Peres LC, Wang C, Way GP, Greene CS, Schildkraut JM. Challenges and Opportunities in Studying the Epidemiology of Ovarian Cancer Subtypes. Curr Epidemiol Rep. 2017 Sep;4(3):211-220. PubMed PMID: 29226065
• Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny GE, Goode EL, Greene CS, Doherty JA. Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. G3 (Bethesda). 2016 Dec 7;6(12):4097-4103. PubMed PMID: 27729437
• Way GP, Southwell M, McRobert SP. Boldness, Aggression, and Shoaling Assays for Zebrafish Behavioral Syndromes. J Vis Exp. 2016 Aug 29;(114). PubMed PMID: 27684060
• Moss S, Tittaferrante S, Way GP, Fuller A, Sullivan N, Ruhl N, McRobert SP. Interactions between aggression, boldness and shoaling within a brood of convict cichlids (Amatitlania nigrofasciatus). Behav Processes. 2015 Dec;121:63-9. PubMed PMID: 26497098
• Way GP, Ruhl N, Snekser JL, Kiesel AL, McRobert SP. A comparison of methodologies to test aggression in zebrafish. Zebrafish. 2015 Apr;12(2):144-51. PubMed PMID: 25621988
• Way GP, Kiesel AL, Ruhl N, Snekser JL, McRobert SP. Sex differences in a shoaling-boldness behavioral syndrome, but no link with aggression. Behav Processes. 2015 Apr;113:7-12. PubMed PMID: 25562194
• Chow Y., Singh, S., Carpenter, A.E., Way, G.P. (2021) Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. bioRxiv: https://doi.org/10.1101/2021.09.02.458673
• Way, G.P.*, Natoli, T.*, Adeboye, A.*, Litichevskiy, L., Yang, A.X., Lu, X., Caicedo, J., Cimini, B.C., Karhohs, K., Logan, D.J., Rohban, M., Kost-Alimova, M., Hartland, K., Bornholdt, M., Chandrasekaran, N., Haghighi, M., Singh, S., Subramanian, A., Carpenter A.E., (2021) Morphology and gene expression profiling provide complementary information for mapping cell state. bioRxiv: https://doi.org/10.1101/2021.10.21.465335
• Way GP, Natoli T, Adeboye A, Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban MH, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, Haghighi M, Weisbart E, Singh S, Subramanian A, Carpenter AE. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Syst. 2022 Nov 16;13(11):911-923.e9. PubMed PMID: 36395727
• Chow YL, Singh S, Carpenter AE, Way GP. Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. PLoS Comput Biol. 2022 Feb;18(2):e1009888. PubMed PMID: 35213530
• Way GP, Spitzer H, Burnham P, Raj A, Theis F, Singh S, Carpenter AE. Image-based profiling: a powerful and challenging new data type. Pac Symp Biocomput. 2022;27:407-411. PubMed PMID: 34890168
• Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley SD, Gosline SJC, L? Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, Fertig EJ. A field guide to cultivating computational biology. PLoS Biol. 2021 Oct;19(10):e3001419. PubMed PMID: 34618807
• Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM. Sharing biological data: why, when, and how. FEBS Lett. 2021 Apr;595(7):847-863. PubMed PMID: 33843054
• Way GP, Kost-Alimova M, Shibue T, Harrington WF, Gill S, Piccioni F, Becker T, Shafqat-Abbasi H, Hahn WC, Carpenter AE, Vazquez F, Singh S. Predicting cell health phenotypes using image-based morphology profiling. Mol Biol Cell. 2021 Apr 19;32(9):995-1005. PubMed PMID: 33534641
• Cousminer DL, Wagley Y, Pippin JA, Elhakeem A, Way GP, Pahl MC, McCormack SE, Chesi A, Mitchell JA, Kindler JM, Baird D, Hartley A, Howe L, Kalkwarf HJ, Lappe JM, Lu S, Leonard ME, Johnson ME, Hakonarson H, Gilsanz V, Shepherd JA, Oberfield SE, Greene CS, Kelly A, Lawlor DA, Voight BF, Wells AD, Zemel BS, Hankenson KD, Grant SFA. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual. Genome Biol. 2021 Jan 4;22(1):1. PubMed PMID: 33397451
• Kelley ME, Berman AY, Stirling DR, Cimini BA, Han Y, Singh S, Carpenter AE, Kapoor TM, Way GP. High-content microscopy reveals a morphological signature of bortezomib resistance. Elife. 2023 Sep 27;12. PubMed PMID: 37753907
• Way GP, Sailem H, Shave S, Kasprowicz R, Carragher NO. Evolution and impact of high content imaging. SLAS Discov. 2023 Sep 3. [Epub ahead of print] PubMed PMID: 37666456
• Laber S, Strobel S, Mercader JM, Dashti H, Dos Santos FRC, Kubitz P, Jackson M, Ainbinder A, Honecker J, Agrawal S, Garborcauskas G, Stirling DR, Leong A, Figueroa K, Sinnott-Armstrong N, Kost-Alimova M, Deodato G, Harney A, Way GP, Saadat A, Harken S, Reibe-Pal S, Ebert H, Zhang Y, Calabuig-Navarro V, McGonagle E, Stefek A, Dupuis J, Cimini BA, Hauner H, Udler MS, Carpenter AE, Florez JC, Lindgren C, Jacobs SBR, Claussnitzer M. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. Cell Genom. 2023 Jul 12;3(7):100346. PubMed PMID: 37492099
• Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, Rathi KS, Zhu Y, Egolf LE, Farrow BK, Miller DP, Yang Y, Koganti T, Noureen N, Koptyra MP, Duong N, Santi M, Kim J, Robins S, Storm PB, Mack SC, Lilly JV, Xie HM, Jain P, Raman P, Rood BR, Lulla RR, Nazarian J, Kraya AA, Vaksman Z, Heath AP, Kline C, Scolaro L, Viaene AN, Huang X, Way GP, Foltz SM, Zhang B, Poetsch AR, Mueller S, Ennis BM, Prados M, Diskin SJ, Zheng S, Guo Y, Kannan S, Waanders AJ, Margol AS, Kim MC, Hanson D, Van Kuren N, Wong J, Kaufman RS, Coleman N, Blackden C, Cole KA, Mason JL, Madsen PJ, Koschmann CJ, Stewart DR, Wafula E, Brown MA, Resnick AC, Greene CS, Rokita JL, Taroni JN. OpenPBTA: The Open Pediatric Brain Tumor Atlas. Cell Genom. 2023 Jul 12;3(7):100340. PubMed PMID: 37492101
• Serrano, E., Chandrasekaran, S. N., Bunten, D., Brewer, K. I., Tomkinson, J., Kern, R., Bornholdt, M., Fleming, S., Pei, R., Arevalo, J., Tsang, H., Rubinetti, V., Tromans-Coia, C., Becker, T., Weisbart, E., Bunne, C., Kalinin, A. A., Senft, R., Taylor, S. J., … Way, G. P. (2023). Reproducible image-based profiling with Pycytominer.
• Davidson NR, Barnard ME, Hippen AA, Campbell A, Johnson C, Way GP, Dalley BK, Berchuck A, Salas LA, Peres LC, Marks JR, Schildkraut JM, Greene CS, Doherty JA. Molecular subtypes of high grade serous ovarian cancer across racial groups and gene expression platforms. bioRxiv. 2023 Dec 2. PubMed PMID: 37961178
• Carragher, N. O., Wardwell-Swanson, J., & Way, G. P. (2023). High-content imaging 2023: A joint special collection with the society for biomolecular imaging. In SLAS Discovery (Vol. 28, Issue 7, pp. 289–291). Elsevier BV. https://doi.org/10.1016/j.slasd.2023.10.001
• Ramezani M, Bauman J, Singh A, Weisbart E, Yong J, Lozada M, Way GP, Kavari SL, Diaz C, Haghighi M, Batista TM, Pérez-Schindler J, Claussnitzer M, Singh S, Cimini BA, Blainey PC, Carpenter AE, Jan CH, Neal JT. A genome-wide atlas of human cell morphology. bioRxiv. 2023 Aug 7. PubMed PMID: 37609130
• Tegtmeyer, M., Arora, J., Asgari, S., Cimini, B. A., Peirent, E., Liyanage, D., Way, G., Weisbart, E., Nathan, A., Amariuta, T., Eggan, K., Haghighi, M., McCarroll, S. A., Carpenter, A. E., Singh, S., Nehme, R., & Raychaudhuri, S. (2023). High-dimensional phenotyping to define the genetic basis of cellular morphology. BioRxiv. https://doi.org/10.1101/2023.01.09.522731

Professional Memberships

• Infixion Biosciences, Scientific Advisory Board
• Broad Institute of Harvard and MIT, Visiting Scientist
• CytoData Soceity, Board Member
• Cancer Systems Biology Consortium, Member
• The Society of Biomolecular Imaging and Informatics, Board of Directors

Practice Locations

UCHealth Anschutz Outpatient Pavilion - Anschutz Medical Campus
1635 Aurora Ct
Aurora, CO 80045
720-848-0000

Center Affiliations

• Center for Health Artificial Intelligence
• University of Colorado Cancer Center