LSP Bibliography

Ma, Y., Tagore, M., Hunter, M. V., Huang, T.-H., Montal, E., Weiss, J. M., Shi, Y., Vallius, T., Sorger, P. K., & White, R. M. (2026). Restraint of melanoma progression by cells in the local skin environment. eLife, 13, RP101974. https://doi.org/10.7554/eLife.101974

Gonzalez Castro, L. N., Wu, Y.-C., Lin, J.-R., Santiago-Ribeiro, M.-J., Laurenge, A., Carpentier, A., Coy, S., Lin, N. U., Mokhtari, K., Ligon, K. L., Touat, M., & Santagata, S. (2026). Clinical responses to trastuzumab deruxtecan in molecularly defined ependymoma. NPJ Precision Oncology. https://doi.org/10.1038/s41698-026-01514-x

Xu, R., Wu, G., Rice, S., Booker, M., Weekes, J., Bell, H., Gao, Y., Nirmal, A. J., Liu, H., Ciantra, Z., Luo, Q., Fortune, A., Whalen, K., Guanci, T., Wan, Y., Louissaint, A., Nordberg, J. J., Lin, J.-R., Hemann, M., … Lane, A. A. (2026). Live-cell Pick-Seq (LiP-Seq): Interrogating ultra-rare mantle cell lymphoma persistent cells after CART19 therapy. Blood Advances, 10(11), 3845–3855. https://doi.org/10.1182/bloodadvances.2025016688

Ogbonna, E. C., Talemi, S. R., Maliga, Z., Zhao, Z., Yapp, C., Pant, S. M., Lu, Y. D., Muhlich, J., Gagné, A., Martinot, A. J., Coy, S., Santagata, S., Shih, A. R., Solomon, I. H., Naidoo, T., Aldridge, B. B., Steyn, A. J. C., & Sorger, P. K. (2026). Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis [Preprint]. bioRxiv. https://doi.org/10.64898/2026.06.02.725201

Li, B., & Mitchison, T. J. (2026). Rebinding drives cellular retention of small-molecule drugs with abundant targets. Proceedings of the National Academy of Sciences of the United States of America, 123(21), e2531949123. https://doi.org/10.1073/pnas.2531949123

Rudra Gupta, T., Polley, M.-Y. C., Redd, R., Lee, E. Q., Arrillaga-Romany, I., Gilbert, M. R., Tan, Y., Touat, M., Drappatz, J., Welch, M. R., Galanis, E., Ahluwalia, M. S., Colman, H., Nabors, L. B., Hepel, J., Elinzano, H., Schiff, D., Chukwueke, U. N., Beroukhim, R., … Rahman, R. (2026). Treatment Effect Reanalysis of the Randomized Individual Screening Trial of Innovative Glioblastoma Therapy in Newly Diagnosed Glioblastoma With External Control Data. Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology, JCO2501586. https://doi.org/10.1200/JCO-25-01586

Wong, A. Y. H., Lu, Y. D., Zhao, Z., Zhou, F., Park, H., Maliga, Z., Anang, Y. N. A., Coy, S., Danuser, G., Santagata, S., Yapp, C., & Sorger, P. K. (2026). Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue [Preprint]. bioRxiv. https://doi.org/10.64898/2026.05.17.725158

Petrova, V., Mills, C. E., Hug, C., Cetinkaya-Fisgin, A., Splaine, J., Fouladzadeh, S., Hakim, S., Powell, R., Zhen, S., Chung, M., Bradshaw, G. A., Deng, T., Singec, I., Wang, Q., Kawaguchi, R., Jonnagaddala, H., Barrett, L. B., Smith, J. A., Kalocsay, M., … Woolf, C. J. (2026). A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy. Cell Reports. Medicine, 7(5), 102787. https://doi.org/10.1016/j.xcrm.2026.102787

Shi, Y., Savchenko, A., Brase, J. C., Reardon, B., Ricker, C. A., Park, J., Tarantino, G., Manos, M. P., Huang, A. Y., Van Allen, E. M., Garraway, L. A., Flaherty, K. T., & Liu, D. (2026). Genomic, Clinical, and Spatial Predictors of Durable Response to BRAF/MEK Inhibition in BRAF -Mutant Melanoma [Preprint]. bioRxiv. https://doi.org/10.64898/2026.05.09.721157

Cheng, X., Zhang, Y., Qian, C., Holdridge, E., Ananda, G., Jiang, T., Ni, J., Xie, S., Gu, H., Ji, R., Ivanova, E. V., Nucci, M. R., Wang, Z., Chen, K., Kochupurakkal, B., Freeman, G. J., Shapiro, G. I., Liu, J., Konstantinopoulos, P. A., … Zhao, J. J. (2026). Targeting FGFR signaling overcomes therapeutic resistance and immune evasion in oncogenic PIK3CA-driven serous-like endometrial cancer. Nature Communications, 17(1), 5994. https://doi.org/10.1038/s41467-026-72544-z

Guo, X., Moynihan, Z. A., Driver, J., Patel, R. V., Bhave, V. M., Maury, E. A., Knelson, E. H., Guo, H., Lin, J.-R., Coy, S. M., Wang, A., Gupta, S., Hoffman, S. E., Dunn, I. F., Dunn, G. P., Petti, A., Choi, B. D., Choudhury, A., Raleigh, D. R., … Bi, W. L. (2026). Meningioma microenvironment harbors a rich immune landscape that evolves with biological state. Neuro-Oncology, 28(5), 1193–1208. https://doi.org/10.1093/neuonc/noag022

Hess, J. M., Dzeng, R. K., Ilieş, I., Schapiro, D., Iskra, J. J., Mirgh, D., Nam, J., Seeley, E. H., Verrill, D. E., Abdelmoula, W. M., Regan, M. S., Theocharidis, G., Wu, C. L., Veves, A., Agar, N. Y. R., Sluder, A. E., Poznansky, M. C., Sîrbulescu, R. F., & Reeves, P. M. (2026). MIAAIM: Multi-omics image integration with dimensional reduction for tissue state mapping. PLoS Computational Biology, 22(5), e1014274. https://doi.org/10.1371/journal.pcbi.1014274

Cassandras, M., Sanchez, X., Hsu, L., Huang, Y., Getzler, A. J., Ganguly, D., Baldominos, P., Codinachs, I., Chuong, J., Martin, E. E., Smith, B. E., Marina, E., Spasic, M., Qin, X., Parsons, H. A., Mayer, E. L., Sarosiek, K. A., Dougan, S. K., Mittendorf, E. A., … Agudo, J. (2026). A glucocorticoid-FAS axis controls immune evasion during metastatic seeding. Nature, 653(8114), 567–575. https://doi.org/10.1038/s41586-026-10222-2

Gagné, A., & Lin, J.-R. (2026). Moving Beyond Morphology to Multiplexed Molecular Imaging as the Next Frontier in Diagnostic Pathology. The American Journal of Pathology, S0002-9440(26)00123-9. https://doi.org/10.1016/j.ajpath.2026.03.015

Tan, S. Z. K., Puig-Barbe, A., Goutte-Gattat, D., Eastwood, C., Aevermann, B., Avola, A., Balhoff, J. P., Bayindir, I. U., Belfiore, J., Caron, A. R., Fischer, D. S., George, N., Gyori, B. M., Haendel, M. A., Hoyt, C. T., Kir, H., Lubiana, T., Matentzoglu, N., Overton, J. A., … Osumi-Sutherland, D. (2026). The Cell Ontology in the age of single-cell omics. Scientific Data, 13(1), 946. https://doi.org/10.1038/s41597-026-07173-8

Kader, T., Chen, Y.-A., Hug, C. B., Lin, J.-R., Muhlich, J. L., Coy, S., Jung, E., Schwartz, L. E., Fazio, T., Chiu, C., Ryall, S. T., Drescher, C. W., Sorger, P. K., Drapkin, R., & Santagata, S. (2026). Spatial integration of protein and chromosomal states reveals early copy number changes and genotype-associated immune neighborhoods in serous ovarian cancer evolution. Cancer Discovery. https://doi.org/10.1158/2159-8290.CD-26-0171

Mills, C. E., Hug, C., Sajeevan, K. A., Clark, N., Victor, C., Chung, M., Rawat, S., D’Erasmo, H., Moraes, M. P., Aldridge, B., Albers, M. W., Chowdhury, R., Gyori, B. M., & Sorger, P. K. (2026). Polypharmacology is an enduring and nearly universal property of kinase inhibitors [Preprint]. bioRxiv. https://doi.org/10.64898/2026.03.17.711623

König, L. E., Rodriguez, S., Hug, C., Daneshvari, S., Chung, A., Appleman, M., Tsai, M., Bradshaw, G. A., Sahin, A., Song, Y., Zhou, G., Eisert, R. J., Piccioni, F., Marques, C., Powley, S., Yarmolinsky, J., Wainger, B. J., Das, S., Kalocsay, M., … Albers, M. W. (2026). TYK2 mediates neuroinflammation in Alzheimer’s disease brains with TDP-43 pathology. Nature Communications, 17(1), 3967. https://doi.org/10.1038/s41467-026-70243-3

Perez-Villatoro, F., Shabanova, A., van Wagensveld, L., Junquera, A., Niemiec, I., Hincapié-Otero, M. M., Kang, Z., Falco, M. M., Birgin, K., Wolf, S., Anttila, E., Anandagoda, G., Casado, J., Marcus, E., Gaillard, D., Kahelin, E., Chamchougia, F., Salko, M., Shah, S., … Farkkila, A. (2026). Single-cell spatial atlas of high-grade serous ovarian cancer uncovers MHC class II as a key predictor of spatial tumor ecosystems and clinical outcomes. Cancer Discovery. https://doi.org/10.1158/2159-8290.CD-25-1492

Zimmerman, M. P., Huang, A. Y., Cox, E. K., Al Abosy, R., Chong, W. L., Bastian, A. G., Vietor, K., Choutri, Y., Collier, J., Zhabotynsky, V., Wang, H., Fung, M., Weiss, S. A., Robitschek, E. J., Lin, J.-R., Vallius, T., Pant, S. M., Sorger, P. K., Hugo, W., … Miller, B. C. (2026). Harnessing Inflammatory Monocytes to Overcome Resistance to Anti-PD-1 Immunotherapy. bioRxiv. https://doi.org/10.64898/2026.02.05.704029

Brastianos, P. K., Dooley, K., Geyer, S., Gerstner, E. R., Kaufmann, T. J., Iafrate, A. J., Martinez-Lage, M., Milhem, M., Welch, M. R., Kaley, T. J., Drappatz, J., Chan, A., Kumthekar, P., Matsuoka, C. K., Strowd, R. E., Cohen, A. L., Jaeckle, K., Robell, L., Magge, R. S., … Galanis, E. (2026). Abemaciclib in meningiomas with somatic NF2 or CDK pathway alterations: the phase 2 Alliance A071401 trial. Nature Medicine, 32(2), 717–724. https://doi.org/10.1038/s41591-025-04141-4

Pimenta, E. M., Garza, A. E., Camp, S. Y., Park, J., Hoffman, S. E., Valderrábano, L., Fu, J., Bi, K., Carson, M. T., Karam, J., Titchen, B. M., Medjahed, S., Khandekar, M. J., Shannon, E., Kang, Y. J., Coy, S., Lin, J.-R., Nag, A., Thorner, A. R., … Van Allen, E. M. (2026). Epigenetic dysregulation of metabolic programs mediates liposarcoma cell plasticity. Science Translational Medicine, 18(833), eadw4689. https://doi.org/10.1126/scitranslmed.adw4689

Darnell, A. M., Chidley, C., Paradise, V., Cui, D. S., Davidsen, K., Lincoln, S. C., Abbott, K. L., Elbashir, R., Vander Heiden, C. P., Sorger, P. K., Sullivan, L. B., Davis, J. H., & Vander Heiden, M. G. (2026). Ribosome-associated quality control of aberrant protein production during amino acid limitation. bioRxiv. https://doi.org/10.64898/2026.01.14.699605

Ribas, G. T., Cunha, A. F., Avila, J. P., Giarraputo, A., Morena, L., Lima, K., Gassen, R. B., Chen, J.-Y., Lin, J.-R., Santagata, S., Avillach, C. T., Ryback, B. A., Lindner, M. S., Bercovici, S., Rosales, I. A., Kawai, T., Nakaya, H. I., Colvin, R. B., Borges, T. J., & Riella, L. V. (2026). Immune profiling in a living human recipient of a gene-edited pig kidney. Nature Medicine. https://doi.org/10.1038/s41591-025-04053-3

Weems, A. D., Islam, M. T., Borges, H., Yapp, C., Perez-Castro, L., Nogueira, P., Lin, J., Maliga, Z., Lewis, A. J., Kutter, C., Mannino, M., Vallius, T., Santagata, S., Sorger, P. K., Conacci-Sorrell, M., Dean, K. M., & Danuser, G. M. (2026). In vivo evidence for bleb-induced survival signaling in metastatic melanoma. Cancer Biology. https://doi.org/10.64898/2026.01.05.697601

Burn, T. N., Schröder, J., Gandolfo, L. C., Osman, M., Wainwright, E. N., Lam, E. Y. N., McDonald, K. M., Evans, R. B., Li, S., Rawlinson, D., Dryburgh, L., Zaid, A., Maliga, Z., Schienstock, D., Meiser, P., Lee, H. J., Lai, H., Moreira, M. L., Zareie, P., … Mackay, L. K. (2026). Antigen reactivity defines tissue-resident memory and exhausted T cells in tumors. Nature Immunology, 27(1), 98–109. https://doi.org/10.1038/s41590-025-02347-9

Warchol, S., Guo, G., Knitte, J., Freeman, D., Shalla, U., Muhlich, J. L., Sorger, P. K., & Pfister, H. (2026). SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data. IEEE Transactions on Visualization and Computer Graphics, 32(1), 484–494. https://doi.org/10.1109/TVCG.2025.3634794

Rapisuwon, S., Slingluff, C. L., Wargo, J. A., Sullivan, R. J., Izar, B., Lin, J.-R., Mauldin, I. S., Olson, W. C., Tran, C. A., Schwartzman, G. H., Gibney, G. T., Al-Refaie, W., & Atkins, M. B. (2026). Effects of Vemurafenib ± Cobimetinib on Intratumoral and Host Immunity in Patients With BRAFV600 Mutant Melanoma: Implications for Combination With Immunotherapy. Cancer Medicine, 15(1), e71526. https://doi.org/10.1002/cam4.71526

Rossine, F., Sanchez, C., Eaton, D., Paulsson, J., & Baym, M. (2025). Intracellular competition shapes plasmid population dynamics. Science, 390(6779), eadx0665. https://doi.org/10.1126/science.adx0665

Shi, Y., Maliga, Z., Vallius, T., Pant, S. M., Pelletier, R., Kobs, B., Solanky, P., He, Y., Van Allen, E., Santagata, S., Ott, P., Lian, C. G., Buchbinder, E., Liu, D., & Sorger, P. K. (2025). Mechanisms of tumor persistence in metastatic melanoma following successful immunotherapy. bioRxiv. https://doi.org/10.64898/2025.12.11.692633

Deng, X., Bradshaw, G. A., Kalocsay, M., & Mitchison, T. (2025). Tubulin regulates stability and localization of STMN2 by binding preferentially to its soluble form. The Journal of Cell Biology, 224(12), e202502192. https://doi.org/10.1083/jcb.202502192

Ludin, A., Stirtz, G. L., Tal, A., Nirmal, A. J., Pfaff, K. L., Manos, M., Besson, N., Eskndir, N., Porter, B., Jones, S. M., Faulkner, H. M., Gong, Q., Liu, S., Barrera, I., Wu, L., Pessoa Rodrigues, C., Sahu, A., Jerison, E., Alessi, J. V., … Zon, L. I. (2025). CRATER tumor niches facilitate CD8+ T cell engagement and correspond with immunotherapy success. Cell, 188(24), 6720-6736.e26. https://doi.org/10.1016/j.cell.2025.09.021

Girnius, N., Vallius, T., Chen, W., Launonen, I.-M., Palomino-Echeverria, S., Lin, J.-R., Mills, C. E., Kauppila, S., Kronqvist, P., Ellonen, A., Perala, M., Withnell, E., Chen, Y.-A., Secrier, M., Santagata, S., Sorger, P. K., & Farkkila, A. (2025). Integrative single-cell and spatial mapping of oxidative stress response uncovers GCLC+ mesenchymal tumor cell state linked with favorable outcomes in triple negative breast cancer. bioRxiv. https://doi.org/10.1101/2025.11.06.686771

Stopka, S. A., Bodineau, C., Baquer, G., Lin, J.-R., Hossain, M. A., Martinez, C. J., Regan, M. S., Ruiz, D., Fletcher, S.-M., Pourquié, O., Lutsenko, S., Payne, C. N., Agar, J. N., Mazitschek, R., McDannold, N. J., Sorger, P. K., Santagata, S., & Agar, N. Y. R. (2025). Spatial Profiling of Elements through Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging. Analytical Chemistry. https://doi.org/10.1021/acs.analchem.5c05632

Li, D., Wan, G., Wu, X., Wu, X., Chen, X., He, Y., Chen, Z., Sorger, P. K., & Zhao, C. (2025). Multi-Modal Foundation Models for Computational Pathology: A Survey. Transactions on Machine Learning Research, 2025, 5715.

Zhou, F. Y., Marin, Z., Yapp, C., Zou, Q., Nanes, B. A., Daetwyler, S., Jamieson, A. R., Islam, M. T., Jenkins, E., Gihana, G. M., Lin, J., Borges, H. M., Chang, B.-J., Weems, A., Morrison, S. J., Sorger, P. K., Fiolka, R., Dean, K. M., & Danuser, G. (2025). Universal consensus 3D segmentation of cells from 2D segmented stacks. Nature Methods, 22(11), 2386–2399. https://doi.org/10.1038/s41592-025-02887-w

Williams, J. B., Pant, S. M., Kley, A. L., Rajmalani, B. A., Yapp, C., Zhang, J., Rotrosen, E., Sales, A., Sorger, P. K., & Kupper, T. S. (2025). Regulatory T cells inhibit CD8+ TRM-like cells during the early stages of tumor immune escape [Preprint]. bioRxiv. https://doi.org/10.1101/2025.10.21.683143

Tarantino, G., Zaremba, A., Vallius, T., Woodnorth, M., Hua, Y., Pelletier, R., Lopez Leon, M., Shi, Y., Maliga, Z., Makhzami, S., Aprati, T. J., Karlas, B., Glutsch, V., Schilling, B., Hassel, J., Berking, C., Utikal, J., Meier, F., Meiss, F., … Schadendorf, D. (2025). Multiomic profiling of a unique in-transit melanoma cohort identifies melanoma differentiation as predictor of tumor progression and therapy response. bioRxiv. https://doi.org/10.1101/2025.10.01.679282

Yapp, C., Nirmal, A. J., Zhou, F., Wong, A. Y. H., Tefft, J. B., Lu, Y. D., Shang, Z., Maliga, Z., Llopis, P. M., Murphy, G. F., Lian, C. G., Danuser, G., Santagata, S., & Sorger, P. K. (2025). Highly multiplexed 3D profiling of cell states and immune niches in human tumors. Nature Methods, 22(10), 2180–2193. https://doi.org/10.1038/s41592-025-02824-x

Cortés-Ríos, J., Rodriguez-Fernandez, M., Sorger, P. K., & Fröhlich, F. (2025). Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches. PLoS Computational Biology, 21(10), e1012890. https://doi.org/10.1371/journal.pcbi.1012890

Jain, Y., Jepson, J., Chen, R., Maier, E., Herr, B. W., Puig-Barbe, A., Quardokus, E. M., Qaurooni, D., Yapp, C., Ewing, S. L., Enninful, A., Farzad, N., Bueckle, A., Easter, Q. T., Matuck, B., Zhu, C., Monte, E. M., Purkerson, J. M., Jehrio, M., … Börner, K. (2025). Exploring endothelial cell environments across organs in spatially resolved omics data. bioRxiv. https://doi.org/10.1101/2025.09.23.678129

Barkai, O., Zhang, B., Turnes, B. L., Arab, M., Yarmolinsky, D. A., Zhang, Z., Barrett, L. B., & Woolf, C. J. (2025). A machine learning tool with light-based image analysis for automatic classification of 3D pain behaviors. Cell Reports Methods, 5(9), 101145. https://doi.org/10.1016/j.crmeth.2025.101145

Kaul, A., Souque, C., Holland, M., & Baym, M. (2025). Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics. Microbial Genomics, 11(9), 001474. https://doi.org/10.1099/mgen.0.001474

Van Itallie, E., Sonnett, M., Kalocsay, M., Wühr, M., Peshkin, L., & Kirschner, M. W. (2025). Transitions in the proteome and phospho-proteome during Xenopus laevis development. Developmental Biology, 525, 155–171. https://doi.org/10.1016/j.ydbio.2025.05.022

Alessi, J. V., Lindsay, J. R., Giobbie-Hurder, A., Sharma, B., Felt, K., Kumari, P., Mazor, T., Cerami, E., Lotter, W., Altreuter, J., Weirather, J., Dryg, I., Hoebel, K., Manos, M., Adib, E., Curtis, J. D., Ricciuti, B., Di Federico, A., Ghandour, F., … Rodig, S. J. (2025). Immunoprofiling at an Institutional Scale Reveals That High Numbers of Intratumoral CD8+ and PD-1+ Cells Predict Superior Patient Survival Across Major Cancer Types Independent of Major Risk Factors. JCO Precision Oncology, 9, e2500240. https://doi.org/10.1200/PO-25-00240

Johnson, W. C., Alivisatos, A., Smith, T. C., Van, N., Soni, V., Wallach, J. B., Clark, N. A., Fitzgerald, T. A., Whiteley, J. J., Tan, S., Sokolov, A., Ando, D. M., Schnappinger, D., Rhee, K. Y., & Aldridge, B. B. (2025). Integration of multi-modal measurements identifies critical mechanisms of tuberculosis drug action. Cell Systems, 16(8), 101348. https://doi.org/10.1016/j.cels.2025.101348

Mahmoud, N., Qin, X., Bzeih, W., Khabibullin, D., Alchoueiry, M., Safi, S., Chami, J., Han, T., Salem, S., Priolo, C., Chakraborty, A. A., Sarosiek, K. A., & Henske, E. P. (2025). BCL-xL dependency in chromophobe renal cell carcinoma. Cancer Gene Therapy. https://doi.org/10.1038/s41417-025-00953-1

Das, T., Bradshaw, G. A., Hyer, J., Masek, M., Kuo, Y.-M., Bachmann-Gagescu, R., Kalocsay, M., & Nachury, M. V. (2025). BBSome-Mediated Clearance of Ubiquitinated IMPG2 Defines a Constitutive Ciliary Retrieval Pathway in Photoreceptors. bioRxiv. https://doi.org/10.1101/2025.07.29.667331

Khoury, R., Longobardi, G., Barnatan, T. T., Venkert, D., García Alvarado, A., Yona, A., Green Buzhor, M., Shahar, S., Wang, Q., Acúrcio, R. C., Guedes, R. C., Florindo, H. F., Zhao, J. J., & Satchi-Fainaro, R. (2025). Radiation-guided nanoparticles enhance the efficacy of PARP inhibitors in primary and metastatic BRCA1-deficient tumors via immunotherapy. Journal of Controlled Release: Official Journal of the Controlled Release Society, 383, 113812. https://doi.org/10.1016/j.jconrel.2025.113812

Patel, R. V., Ghosh, H. S., Meredith, D. M., Ryall, S., Claus, E. B., Beroukhim, R., Ligon, A. H., Santagata, S., & Bi, W. L. (2025). Distribution of copy number alterations and impact of chromosome arm call thresholds for meningioma. Nature Communications, 16(1), 6025. https://doi.org/10.1038/s41467-025-60734-0