Gregory Way, PhD, MS
Assistant Professor, Biomedical Informatics

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Graduate Schools :
  • MS, Saint Joseph's University (2014)
  • PhD, University of Pennsylvania (2018)
Undergraduate School:
  • BS, The College of New Jersey (NJ) (2011)
Department: Biomedical Informatics

Professional Titles

  • Assistant Professor

Recognition & Awards

  • 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
  • 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, 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
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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
Care Philosophy
I believe that we can improve patient lives through biomedical data science and artificial intelligence.

Public Speaking
Yes

General Information

Graduate Schools:
  • MS, Saint Joseph's University (2014)
  • PhD, University of Pennsylvania (2018)
Undergraduate Schools:
  • BS, The College of New Jersey (NJ) (2011)
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Department: Biomedical Informatics
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13001 East 17th Place
Campus Box C290
Aurora, CO 80045

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