Research
Learning from patients to understand mechanisms of resistance and unlock more effective T cell therapy designs.
Our overarching goal is to lay the foundations for a clinically informed T cell design through machine learning algorithms, eventually enabling artificial intelligence (AI) systems to nominate specific genetic edits for improved clinical outcomes in a given disease. We leverage innovation in machine learning and clinical multi-omic T cell therapy datasets to build AI systems at scale to enable broad generalization. We collaborate with physicians and scientists in the Cancer Cell Therapy Program, Cellular Immune Tolerance Program, computer
science labs, experimental T cell therapy labs, and teams beyond Stanford on the analysis of primary clinical and preclinical multi-omic datasets. This work serves as the basis for training T cell therapy AI models at scale, which in turn inform our preclinical T cell designs. We integrate insights from the literature with insights from the data and models to build and test advanced T cell designs in the lab leveraging preclinical models that recapitulate resistance mechanisms observed in patients.
Selected Publications
Stiber A, Quach B, Ogunlade B, Georgiadis A, Chang K, Li Y, Quinn P, Wang H, Ang C, Sotillo E, Mackall CL§, Good Z§, Dionne JA§. Dynamic, single-cell monitoring of CAR T cell identity and activation with Raman spectroscopy. Nature – In Revision. bioRxiv (2026). DOI: 10.64898/2026.02.22.707331.
Zhan X*, Xu WJ*, Zheng Y, Good Z§, Gevaert O§. LIST-FM: A Lightweight and Interpretable Spatial Transcriptomics foundation model. Annals of Biomedical Engineering – Under Review. arXiv (2026). DOI: 10.48550/arXiv.2601.15504.
Schaefer M, Piran Z, Walter NP, Awasthi A, Bock C, Leskovec J§, Good Z§. Molecular-informed histopathology via trimodal contrastive learning. Proceedings of the 43rd International Conference on Machine Learning – In Press.
Tsui KY*, Rodrigues KB*, Zhan X*, Chen Y, Mo KC, Mackall CL, Miklos DB, Gevaert O§, Good Z§. (2025). Patient-level prediction from single-cell data using attention-based multiple instance learning with regulatory priors. Proceedings to the 39th Conference on Neural Information Processing Systems, AI4D3: 16.
Rodrigues KB, Eggenhuizen PJ, Bacchetta R, Good Z. Regulatory T cell therapies: From patient data to biological insights. Frontiers in Immunology, 16: 1675114. PMID: 41246323.
Kadaba SE*, Eapen AK*, Tsui KCY, Pang K, Roth TL§, Good Z§. (2025). Conditional normalizing flows for the design of T cell therapies. Proceedings of the 42nd International Conference on Machine Learning, FM4LS: 43.
Good Z, Borges L, Vivanco Gonzalez N, Sahaf B, Samusik N, Tibshirani R, Nolan GP§, Bendall SC§. (2019). Proliferative tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells. Nature Biotechnology, 37(3): 259-66. PMID: 30742126.
Good Z, Glanville G, Gee MH, Davis MM, Khatri P. (2019). Computational and systems immunology: a students’ perspective. Trends in Immunology, 40(8): 665-8. PMID: 31288986.
Lab members highlighted; *co-first; §co-senior
Good Z*, Spiegel JY*, Sahaf B, Malipatlolla MB, Ehlinger ZJ, Kurra S, Desai MH, Reynolds WD, Wong Lin A, Vandris P, Wu F, Prabhu S, Hamilton MP, Tamaresis JS, Hanson PJ, Patel S, Feldman SA, Frank MJ, Baird JH, Muffly L, Claire GK, Craig J, Kong KA, Wagh D, Coller J, Bendall SC, Tibshirani RJ, Plevritis SK, Miklos DB§, Mackall CL§. (2022). Post-infusion CAR TReg cells identify patients resistant to CD19-CAR therapy. Nature Medicine, 28(9): 1860-1871. PMID: 36097223.
Good Z*, Sarno J*, Jager A, Samusik N, Aghaeepour N, Simonds EF, While L, Lacayo NJ, Fantl WJ, Fazio G, Gaipa G, Biondi A, Tibshirani R, Bendall SC, Nolan GP§, Davis KL§. (2018). Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse. Nature Medicine, 24(4): 474-83. PMID: 29505032.
Other Publications
Hamilton MP*, Phillips N*, Noordenbos T*, Boegeholz J*, Sugio T, Sworder BJ, Alig SK, Good Z, Schroers-Martin JG, Tamaresis J, Esfahani MS, Lu Y, Olsen M, Liu CL, Ehlinger Z, Desai M, Muffly L, Negrin RS, Arai S, Johnston L, Lowsky R, Meyer E, Rezvani A, Shizuru JA, Weng WK, Shiraz P, Sidana S, Bharadwaj S, Smith M, Dahiya S, Sahaf B, Frank MJ, Mackall CL, Diehn M, Kurtz DM, Miklos DM§, Alizadeh AA§. CAR19 therapy drives expansion of clonal hematopoiesis and associated cytopenias. Nature Genetics – In Press. https://pubmed.ncbi.nlm.nih.gov/41282159/
Liu Q, Chen PA, Urs E, Zhang S, Arce MM, Wang CH, Yan J, Nguyen VQ, Li Z, Seo J, Kale N, Peng F, Luo Y, Goudy L, LaFlam TN, Zhong H, Modak C, Dan E, Jung JH, Kirane A, Betof Warner A, Quach BB, Good Z, Shy BR, Shifrut E, Bapat SP, Allen GM, Eyquem J, Fuh K, Dodgson SE, Cyster JG, Marson A, Carnevale J. In vivo genome-wide CRISPR screens in human T cells to enhance T cell therapy for solid tumors. Nature – In Press. https://www.biorxiv.org/content/10.1101/2025.09.23.678127v1
Koladiya A, Good Z, Varra SR, Domizi P, Bendall SC, Davis KL. CellFuse enables multi-modal integration of single-cell and spatial proteomics data for systems-level analysis in cancer. Cancer Research (2026). DOI: 10.1158/0008-5472.CAN-25-3699 (online ahead of print).
Chen X*, Mao Z*, Kolawole EM, Persechino M, Jude KM, Ogishi M, Mo KC, McLaughlin J, Cheng D, Xiang X, Yang X, Gee C, Liu S, Yang A, Obenaus M, Wang N, Noguchi M, Stoyanova T, Lee JK, Good Z, Latorraca NR, Evavold BD, Witte ON§, Garcia KC§. Overcoming T cell tolerance to tumor self-antigens through catch-bond engineering. (2026). Science, 19;391(6791):eadx3162 (Epub). PMID: 41855322. DOI: 10.1126/science.adx3162.
Deng J, Pal A, Testa S, Xu JW, Tran LM, Graham DS, Hargil A, Subramanian A, Campbell KM, Limsuwannarot S, Chumpitaz Lavalle Á, Chin SC, Kremer S, Tariveranmoshabad M, Ewongwo A, Silvia SNR, Ogana H, Nemat-Gorgani N, Dubinett SM, Jaycox JR, Felix C, Schaue D, Nelson SD, Levine B, Motamedi K, Ghazikhanian V, Chmielowski B, Reddy V, Singh AS, Trnkova ZJ, Good Z, Quintero M, Crompton JG, Bernthal N, Eilber FC, Moding EJ, Kalbasi A. (2026). Neoadjuvant BO-112 and hypofractionated radiation therapy with or without nivolumab in soft tissue sarcoma: preclinical and phase 1 results. Cancer Discovery, Epub ahead of print. PMID: 41784328. DOI: 10.1158/2159-8290.CD-25-1132.
Chen GM§, Jain A, Gering DT, Satulovsky J, Datta S, Lai P, Karar J, Gonzalez VE, Alexander K, Chew A, Jadlowsky JK, Ruella M, Paruzzo L, Amses KR, Rech AJ, Stadtmauer EA, Frey NV, Hexner EO, Porter DL, Cohen AD, Gill SI, Garfall AL, Schuster SJ, Mo KC, Liang SI, Spasic M, Levine BL, Siegel DL, Ramírez-Fernández A, Cabanski CR, Yang E, Mackall CL, Bushman FD, Good Z, Wherry EJ, June CH, Fraietta JA§. (2026). Predictive biomarkers of response to chimeric antigen receptor (CAR) T-cell therapy for pan-haematologic cancer. Nature Biomedical Engineering, 10(4):803-814. PMID: 41803255. DOI: 10.1038/s41551-026-01633-7.
Stahl D, Gödel P, Balke-Want H, Gholamipoorfard R, Segbers P, Tetenborg L, Koker M, Dörr J, Gregor L, Bachurski D, Rose F, Simon AG, Good Z, Jakob J, Haupl, B, Nill M, Flümann R, Riet T, Lange D, Blakemore SJ, Baurmann H, Voltin CA, Potter N, Schlözer L, Freihammer M, Wagener-Ryczek L, Iuga AI, Heger JM, Ludwig H, Schleifenbaum JK, Propp J, Bröckelmann PJ, Jachimowicz RD, Knittel G, Borchmann S, Merkelbach-Bruse S, Pallasch C, Peifer M, Rybniker J, Quaas A, Nitz M, Brägelmann J, Müller W, Persigehl T, Bozek K, Theobald SJ, Büttner R, Oellerich T, Hallek M, Kobold S, Chmielewski M, Reinhardt HS, Mackall CL, Abedpour N, Borchmann P, Ullrich RT. (2025). CSF1R+ myeloid-monocytic cells drive CAR-T cell resistance in aggressive B cell lymphoma. Cancer Cell, 43(8):1476-1494.e10. PMID: 40513575. DOI: 10.1016/j.ccell.2025.05.013.
Su YJ, Kramer AM, Hamilton MP, Agarwal N, Srinagesh HK, Baird JH, Sahaf B, Kuo A, Ehlinger ZJ, Desai MH, Rietberg SP, Tunuguntla R, Patel S, Chinnasamy H, Gkitsas-Long N, Klysz DD, Brown AK, Bharadwaj S, Dahiya S, Smith M, Muffly L, Mackall CL, Good Z, Feldman SA, Miklos DB, Frank MJ. (2025). Effects of an initial anti-CD19 CAR T-cell therapy on subsequent anti-CD22 CAR T-cell manufacturing and clinical outcomes in patients with relapsed/refractory LBCL. Cancer Discovery, 15(4): 733-747. PMID: 39775812.
Hamilton MP*, Sugio T*, Noordenbos T*, Shi S, Bulterys PL, Long Liu C, Olsen MN, Good Z, Dahiya S, Frank MJ, Sahaf B, Mackall CL, Gratzinger D, Diehn M, Alizadeh AA§, Miklos DB§. (2024). Risk of second malignancies & T-cell lymphoma after chimeric antigen receptor T-cell therapy. New England Journal of Medicine, 390(22): 2047-2060. PMID: 38865660.
Yamada-Hunter SA*, Theruvath J*, Radosevich MT, McIntosh BJ, Freitas KA, Leruste A, Dhingra S, Martinez-Velez N, Mount CW, Sotillo E, Xu P, Delaidelli A, Desai MH, Sahaf B, Good Z, Labanieh L, Heitzeneder S, Banuelos A, Khan O, Marjon KD, Huang J, Wasserman SL, Spiegel JY, Sorensen PH, Monje M, Majzner RG, Weissman IL, Cochran JR, Mackall CL. (2024). Selective phagocytosis of tumor cells while sparing T cells using engineered CD47 enhances antitumor immunity. Nature, 630(8016):457-465. PMID: 38750365.
Hamilton MP, Craig E, Gentille Sanchez C, Mina A, Tamaresis J, Kirmani N, Ehlinger Z, Syal S, Good Z, Sworder B, Schroers-Martin J, Lu Y, Muffly L, Negrin R, Arai S, Lowsky R, Meyer E, Rezvani A, Shizuru J, Weng W, Shiraz P, Sidana S, Bharadwaj S, Smith M, Dahiya S, Sahaf B, Kurtz D, Mackall C, Tibshirani R, Alizadeh A, Frank M, Miklos D. (2024). CAR19 monitoring by peripheral blood immunophenotyping reveals histology-specific expansion and toxicity. Blood Advances, 8(12):3314-3326. PMID: 38498731.
Alvarez-Breckenridge C, Anderson, KG, Correia AL, Demehri S, Dinh HQ, Dixon KO, Dunn GP, Evgin L, Goc J, Good Z, Hacohen N§, Han P, Hanč P, Hickey JW, Kersten K, Liu BC, Buqué A, Mao Y, Milner JJ, Pritykin Y, Pucci F, Scharping NE, Sudmeier L, Wang Y, Wieland A, Williams MW. (2023). Lessons for the next generation of scientists from the 2nd annual Arthur and Sandra Irving Cancer Immunology Symposium. Cancer Immunology Research, 11(12): 1571-1577. PMID: 37906619.
Majzner RG*, Ramakrishna S*, Yeom KW, Patel S, Chinnasamy H, Schultz LM, Richards RM, Barsan V, Mancusi R, Geraghty AC, Good Z, Mochizuki A, Gillespie SM, Martin A, Toland S, Mahdi J, Reschke A, Chau I, Nie E, Chau AJ, Rotiroti MC, Mount CW, Baggott C, Mavroukakis S, Egeler E, Moon J, Erickson C, Green S, Kunicki M, Fujimoto M, Ehlinger Z, Reynolds W, Kurra S, Warren KE, Prabhu S, Vogel H, Rasmussen L, Cornell TT, Partap S, Fisher PG, Campen CJ, Filbin M, Grant G, Sahaf B, Davis KL, Feldman SA, Mackall CL§, Monje M§. (2022). GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas. Nature, 603(7903): 934-941. PMID: 35130560.
Zhang W, Li I, Reticker-Flynn NE, Good Z, Chang S, Samusik N, Saumyaa S, Li Y, Zhou X, Liang R, Kong CS, Le QT, Gentles AJ, Sunwoo JB, Nolan GP, Engleman EG, Plevritis SK. (2022). Identification of cell types in multiplexed in situ images by combining protein expression and spatial location using CELESTA reveals spatial biology. Nature Methods, 19(6): 759-769. PMID: 35654951.
Bucktrout SL, Banovich NE, Butterfield LH, Cimen-Bozkus C, Giles JR, Good Z, Goodman D, Jonsson V, Laraeu C, Marson A, Maurer DM, Munson PV, Stubbington M, Taylor S, Cutchin A. (2022). Advancing T cell-based cancer therapy with single cell technologies. Nature Medicine, 28(9): 1761-1764. PMID: 36127419.
Weber EW, Lynn RC, Parker KR, Lattin J, Anbunathan H, Sotillo E, Good Z, Malipatlolla M, Xu P, Vandris P, Majzner RG, Chen L-C, Wandless TJ, Chang HY, Satpathy AT, Mackall CL. (2021). Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling. Science, 2;372(6537): eaba1786. PMID: 33795428.
Simonetta F, Alam IS, Lohmeyer JK, Sahaf B, Good Z, Chen W, Xiao Z, Hirai T, Scheller L, Engels P, Vermesh O, Robinson E, Haywood T, Sathirachindra A, Baker J, Malipotlalla MB, Schultz LM, Spiegel JY, Lee JT, Miklos DB, Mackall CL, Gambhir SS, Negrin RS. (2021). Molecular imaging of chimeric antigen receptor T cells by ICOS-immunoPET. Clinical Cancer Research, 27(4): 1058-68. PMID: 33087332
Lynn RC, Weber EW, Sotillo E, Gennert D, Xu P, Good Z, Anbunathan H, Lattin J, Jones R, Tieu V, Granja J, DeBourcy C, Xu P, Majzner R, Satpathy AT, Quake SR, Chang H, Mackall CL. (2019). c-Jun overexpression in CAR T cells induces exhaustion resistance. Nature, 576(7786): 293-300. PMID: 31802004.
Fahy GM, Brooke RT, Watson JP, Good Z, Vasanawala SS, Maecker H, Leipold M, Lin DTS, Kobor MS, Horvath S. (2019). Reversal of epigenetic aging and immunosenescent trends in humans. Aging Cell, 18(6): e13028. PMID: 31496122.
Samusik N, Good Z, Spitzer MH, Davis KL, Nolan GP. (2016). Automated mapping of phenotype space with single-cell data. Nature Methods, 13(6): 493-6. PMID: 27183440.
Enquist IB, Good Z, Jubb AM, Fuh G, Wang X, Junttila MR, Jackson EL, Leong KG. (2014). Lymph node-independent liver metastasis in a model of metastatic colorectal cancer. Nature Communications, 5: 3530. PMID: 24667486.
Franci C, Zhou J, Jiang Z, Modrasan Z, Good Z, Jackson EL, Kouros-Mehr H. (2013). Biomarkers of residual disease, disseminated tumor cells, and metastases in the MTV-PyMT breast cancer model. PLoS ONE, 8(3): e58183. PMID: 23520493.
Dauphinee SM, Voelcker V, Tebaykina Z, Wong F, Karsan A. (2011). Heterotrimeric Gi/Go proteins modulate endothelial TLR signaling independent of the MyD88-dependent pathway. American Journal of Physiology - Heart and Circulatory Physiology, 301(6): H2246-53. PMID: 21949112.
Strauss DM, Lute S, Tebaykina Z, Frey DD, Ho C, Blank GS, Brorson K, Chen Q, Yang B. (2009). Understanding the mechanism of virus removal by Q sepharose fast flow chromatography during the purification of CHO-cell derived biotherapeutics. Biotechnology & Bioengineering, 104(2): 371-80. PMID: 19575414.