LSP Bibliography

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. https://doi.org/10.1038/s41591-025-04141-4

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. Genetics. 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

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

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

Rossine, F., Sanchez, C., Eaton, D., Paulsson, J., & Baym, M. (2025). Intracellular competition shapes plasmid population dynamics. Science (New York, N.Y.), 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

Warchol, S., Guo, G., Knittel, J., Freeman, D., Bhalla, U., Muhlich, J. L., Sorger, P. K., & Pfister, H. (2025). Spatially-resolved Embedding Analysis with Linked Imaging Data. IEEE Transactions on Visualization and Computer Graphics, PP. https://doi.org/10.1109/TVCG.2025.3634794

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

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

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. bioRxiv. https://doi.org/10.1101/2025.10.21.683143

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, S0092-8674(25)01089-X. https://doi.org/10.1016/j.cell.2025.09.021

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

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

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. https://doi.org/10.1038/s41592-025-02824-x

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

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

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

Warchol, S., Guo, G., Knittel, J., Freeman, D., Bhalla, U., Muhlich, J. L., Sorger, P. K., & Pfister, H. (2025). SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data. bioRxiv. https://doi.org/10.1101/2025.07.19.665696

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

Baker, G. J., Novikov, E., Coy, S., Chen, Y.-A., Hug, C. B., Ahmed, Z., Ordóñez, S. A. C., Huang, S., Yapp, C., Sokolov, A., Pfister, H., Santagata, S., & Sorger, P. K. (2025). Morphology-Aware Profiling of Highly Multiplexed Tissue Images using Variational Autoencoders. bioRxiv. https://doi.org/10.1101/2025.06.23.661064

Vallius, T., Shi, Y., Novikov, E., Pant, S. M., Pelletier, R., Chen, Y.-A., Tefft, J. B., Johnson, A. N., Maliga, Z., Wan, G., Murphy, G., Santagata, S., Semenov, Y. R., Liu, D., Lian, C. G., & Sorger, P. K. (2025). Spatial determinants of tumor cell dedifferentiation and plasticity in primary cutaneous melanoma. bioRxiv. https://doi.org/10.1101/2025.06.21.660851

Smith, N. P., Yan, Y., Pan, Y., Williams, J. B., Manakongtreecheep, K., Pant, S. M., Zhao, J., Tian, T., Pan, T., Stingley, C., Wu, K., Zhang, J., Kley, A. L., Sorger, P. K., Villani, A.-C., & Kupper, T. S. (2025). Resident memory T cell development is gradual and shows AP-1 gene expression in mature cells. JCI Insight, 10(12), e187381. https://doi.org/10.1172/jci.insight.187381

Rand, E. A., Quinones-Olvera, N., Jean, K. D. C., Hernandez-Perez, C., Owen, S. V., & Baym, M. (2025). Phage DisCo: targeted discovery of bacteriophages by co-culture. mSystems, 10(6), e0164424. https://doi.org/10.1128/msystems.01644-24

Kader, T., Lin, J.-R., Hug, C. B., Coy, S., Chen, Y.-A., de Bruijn, I., Shih, N., Jung, E., Pelletier, R. J., Lopez Leon, M., Mingo, G., Omran, D. K., Lee, J. S., Yapp, C., Satravada, B. A., Kundra, R., Xu, Y., Chan, S., Tefft, J. B., … Santagata, S. (2025). Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma. Cancer Discovery, 15(6), 1180–1202. https://doi.org/10.1158/2159-8290.CD-24-1366

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, S0012-1606(25)00145-9. https://doi.org/10.1016/j.ydbio.2025.05.022

Price, F. D., Matyas, M. N., Gehrke, A. R., Chen, W., Wolin, E. A., Holton, K. M., Gibbs, R. M., Lee, A., Singu, P. S., Sakakeeny, J. S., Poteracki, J. M., Goune, K., Pfeiffer, I. T., Boswell, S. A., Sorger, P. K., Srivastava, M., Pfaff, K. L., Gussoni, E., Buchanan, S. M., & Rubin, L. L. (2025). Organoid culture promotes dedifferentiation of mouse myoblasts into stem cells capable of complete muscle regeneration. Nature Biotechnology, 43(6), 889–903. https://doi.org/10.1038/s41587-024-02344-7

Prabhakaran, S., Yapp, C., Baker, G. J., Beyer, J., Chang, Y. H., Creason, A. L., Krueger, R., Muhlich, J., Patterson, N. H., Sidak, K., Sudar, D., Taylor, A. J., Ternes, L., Troidl, J., Yubin, X., Sokolov, A., & Tyson, D. R. (2025). Addressing persistent challenges in digital image analysis of cancer tissue: resources developed from a hackathon. Molecular Oncology, 19(6), 1565–1581. https://doi.org/10.1002/1878-0261.13783

Mon-Wei Yu, S., Choi, J. Y., Kady, J., De Cos, M., Wong, J. S., King, E., Younis, N., Al Rahy, N., Al Chaar, S., Djebli, H., Eskandari, S., Samuel, S., Merhej, T., Sukumar, N., Lin, J.-R., Chen, J.-Y., Xu, Y., Santagata, S., Weins, A., … Azzi, J. (2025). Transplantation of human kidney organoids elicited a robust allogeneic response in a humanized mouse model. Kidney International, 107(6), 1011–1016. https://doi.org/10.1016/j.kint.2025.02.027

Oskolas, H., Nogueira, F. C. N., Domont, G. B., Yu, K.-H., Semenov, Y. R., Sorger, P., Steinfelder, E., Corps, L., Schulz, L., Wieslander, E., Fenyö, D., Kárpáti, S., Holló, P., Kemény, L. V., Döme, B., Megyesfalvi, Z., Pawłowski, K., Nishimura, T., Kwon, H., … Gil, J. (2025). Comprehensive biobanking strategy with clinical impact at the European Cancer Moonshot Lund Center. Journal of Proteomics, 316, 105442. https://doi.org/10.1016/j.jprot.2025.105442

Sadeghi, M., Kareva, I., Pogudin, G., & Sontag, E. D. (2025). Quantitative Pharmacology Methods for Bispecific T Cell Engagers. Bulletin of Mathematical Biology, 87(7), 85. https://doi.org/10.1007/s11538-025-01455-9

Sherman, S., Sandusky, Z. M., Russo, D., Zak, D., Nardone, A., Friel, D., Hermida-Prado, F., Heraud, C., Kuziel, G., Verma, A., Gaglia, G., Kabraji, S., Nguyen, Q.-D., Santagata, S., Fanning, S. W., & Jeselsohn, R. (2025). Imlunestrant a next-generation oral SERD overcomes ESR1 mutant resistance in estrogen receptor-positive breast cancer. JCI Insight, e188051. https://doi.org/10.1172/jci.insight.188051

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

MacDonald, J. A., Bradshaw, G. A., Jochems, F., Bernards, R., & Letai, A. (2025). Apoptotic priming in senescence predicts specific senolysis by quantitative analysis of mitochondrial dependencies. Cell Death and Differentiation, 32(5), 802–817. https://doi.org/10.1038/s41418-024-01431-1

Fang, R., Vallius, T., Zhang, A., Van Cura, D., Alicandri, F., Fischer, G., Draper, E., Xu, S., Pelletier, R., Wang, J., Mandinova, A., Katsyv, I., Sorger, P. K., Murphy, G. F., & Lian, C. G. (2025). PRAME Expression in Melanoma is Negatively Regulated by TET2-Mediated DNA Hydroxymethylation. Laboratory Investigation; a Journal of Technical Methods and Pathology, 105(5), 104123. https://doi.org/10.1016/j.labinv.2025.104123

Gui, F., Jiang, B., Jiang, J., He, Z., Tsujino, T., Takai, T., Arai, S., Pana, C., Köllermann, J., Bradshaw, G. A., Eisert, R., Kalocsay, M., Fassl, A., Balk, S. P., Kibel, A. S., & Jia, L. (2025). Acute BRCAness induction and AR pathway blockage through CDK12/7/9 degradation enhances PARP inhibitor sensitivity in prostate cancer. Science Advances, 11(17), eadu0847. https://doi.org/10.1126/sciadv.adu0847

Gevertz, J. L., Greene, J. M., Prosperi, S., Comandante-Lou, N., & Sontag, E. D. (2025). Understanding therapeutic tolerance through a mathematical model of drug-induced resistance. NPJ Systems Biology and Applications, 11(1), 30. https://doi.org/10.1038/s41540-025-00511-3

Ma, X. C., & Clardy, J. (2025). Spontaneous Generation of an Endogenous RORγt Agonist. Journal of the American Chemical Society, 147(14), 11688–11692. https://doi.org/10.1021/jacs.5c02724

Kelley, L. P., Hu, S.-H., Boswell, S. A., Sorger, P. K., Ringel, A. E., & Haigis, M. C. (2025). Integrated analysis of transcriptional and metabolic responses to mitochondrial stress. Cell Reports Methods, 101027. https://doi.org/10.1016/j.crmeth.2025.101027

Břinda, K., Lima, L., Pignotti, S., Quinones-Olvera, N., Salikhov, K., Chikhi, R., Kucherov, G., Iqbal, Z., & Baym, M. (2025). Efficient and robust search of microbial genomes via phylogenetic compression. Nature Methods, 22(4), 692–697. https://doi.org/10.1038/s41592-025-02625-2

de Bruijn, I., Nikolov, M., Lau, C., Clayton, A., Gibbs, D. L., Mitraka, E., Pozhidayeva, D., Lash, A., Sumer, S. O., Altreuter, J., Anton, K., DeFelice, M., Li, X., Lisman, A., Longabaugh, W. J. R., Muhlich, J., Santagata, S., Nandakumar, S., Sorger, P. K., … Eddy, J. A. (2025). Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement. Nature Methods, 22(4), 664–671. https://doi.org/10.1038/s41592-025-02643-0

Mukhija, S., Sunog, M., Magdamo, C., & Albers, M. W. (2025). Impact of Severe COVID-19 on Accelerating Dementia Onset: Clinical and Epidemiological Insights. medRxiv. https://doi.org/10.1101/2025.03.26.25324688

Jobin, B., Magdamo, C., Delphus, D., Runde, A., Reineke, S., Soto, A. A., Ergun, B., Mukhija, S., Albers, A. D., & Albers, M. W. (2025). The AROMHA brain health test is a remote olfactory assessment to screen for cognitive impairment. Scientific Reports, 15(1), 9290. https://doi.org/10.1038/s41598-025-92826-8

Lee, E. Q., Alexander, B. M., Romo, C. G., Supko, J. G., Agar, N. Y. R., Talebi, Z., Ahluwalia, M. S., Desai, A. S., Dietrich, J., Kaley, T. J., Peereboom, D. M., Gantchev, J., Baquer, G., Santagata, S., Takebe, N., Desideri, S., Fisher, J. D., Sims, M., Ye, X., … Wen, P. Y. (2025). Phase I Study of Adavosertib with Radiotherapy and Temozolomide in Newly Diagnosed Glioblastoma and Intratumoral Drug Levels in Recurrent Glioblastoma. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 31(6), 983–992. https://doi.org/10.1158/1078-0432.CCR-24-2311

Vidović, D., Shamsaei, B., Schürer, S. C., Kogan, P., Chojnacki, S., Kouril, M., Medvedovic, M., Niu, W., Azeloglu, E. U., Birtwistle, M. R., Chen, Y., Chen, T., Hansen, J., Hu, B., Iyengar, R., Jayaraman, G., Li, H., Liu, T., Sobie, E. A., … MacCoss, M. J. (2025). Comprehensive proteomics metadata and integrative web portals facilitate sharing and integration of LINCS multiomics data. Molecular & Cellular Proteomics: MCP, 100947. https://doi.org/10.1016/j.mcpro.2025.100947