LSP Bibliography

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

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

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

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, e0164424. https://doi.org/10.1128/msystems.01644-24

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

Jobin, B., Zigrand, C., Frasnelli, J., Boller, B., & Albers, M. W. (2025). Lower Odor Identification in Subjective Cognitive Decline: A Meta-analysis. MedRxiv: The Preprint Server for Health Sciences, 2025.04.15.25325887. https://doi.org/10.1101/2025.04.15.25325887

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

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

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

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

Zhou, F. Y., Marin, Z., Yapp, C., Zou, Q., Nanes, B. A., Daetwyler, S., Jamieson, A., 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. P., Dean, K. M., & Danuser, G. (2025). Universal consensus 3D segmentation of cells from 2D segmented stacks [Preprint]. bioRxiv. https://doi.org/10.1101/2024.05.03.592249

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

Deng, X., Bradshaw, G., Kalocsay, M., & Mitchison, T. (2025). Tubulin Regulates the Stability and Localization of STMN2 by Binding Preferentially to Its Soluble Form [Preprint]. bioRxiv. https://doi.org/10.1101/2025.02.27.640326

He, X., Wang, Q., Cheng, X., Wang, W., Li, Y., Nan, Y., Wu, J., Xiu, B., Jiang, T., Bergholz, J. S., Gu, H., Chen, F., Fan, G., Sun, L., Xie, S., Zou, J., Lin, S., Wei, Y., Lee, J., … Zhao, J. J. (2025). Lysine vitcylation is a vitamin C-derived protein modification that enhances STAT1-mediated immune response. Cell, S0092-8674(25)00145-X. https://doi.org/10.1016/j.cell.2025.01.043

Cortés-Ríos, J., Rodriguez-Fernandez, M., Sorger, P. K., & Fröhlich, F. (2025). Dynamic Modeling of Cell Cycle Arrest Through Integrated Single-Cell and Mathematical Modelling Approaches [Preprint]. bioRxiv. https://doi.org/10.1101/2025.02.20.639240

Mears, K. S., Rossine, F. W., Quinones-Olvera, N., Souque, C., & Baym, M. (2025). RNA-guided nucleases enable a gene drive of insertion sequences in plasmids [Preprint]. https://doi.org/10.1101/2025.02.20.638934

Rossine, F., Sanchez, C., Eaton, D., Paulsson, J., & Baym, M. (2025). Intracellular competition shapes plasmid population dynamics [Preprint]. bioRxiv. https://doi.org/10.1101/2025.02.19.639193

Rendo, V., Lee, E. Q., Bossi, C., Khuu, N., Rudek, M. A., Pal, S., Azazmeh, N., Rashid, R., Lin, J.-R., Cusick, M., Reynolds, A. R. N., Fassinou, A. C. R., Ayoub, G., Malinowski, S., Lapinskas, E., Pisano, W., Jeang, J., Stopka, S. A., Regan, M. S., … Beroukhim, R. (2025). A window-of-opportunity trial reveals mechanisms of response and resistance to navtemadlin in patients with recurrent glioblastoma. Science Translational Medicine, 17(786), eadn6274. https://doi.org/10.1126/scitranslmed.adn6274

Sun, Y., Maggs, L., Panda, A., Wright, S. J., Cicerchia, A. M., Jenney, A., Perricone, M. D., Mills, C. E., Cattaneo, G., Ventin, M., Chen, F., Rasmussen, M. Q., Miranda, A., Revach, O.-Y., Fang, J., Fu, A., Bowling, P. J., Sharova, T., Lawless, A., … Jenkins, R. W. (2025). TBK1 Targeting Is Identified as a Therapeutic Strategy to Enhance CAR T-Cell Efficacy Using Patient-Derived Organotypic Tumor Spheroids. Cancer Immunology Research, 13(2), 210–228. https://doi.org/10.1158/2326-6066.CIR-23-1011

Spellberg, B., Gilbert, D. N., Baym, M., Bearman, G., Boyles, T., Casadevall, A., Forrest, G. N., Freling, S., Ghanem, B., Hamilton, F., Luna, B., Moore, J., Musher, D. M., Nielsen, T. B., Nori, P., Phillips, M. C., Pirofski, L.-A., Shorr, A. F., Tong, S. Y. C., … McDonald, E. G. (2025). Sustainable solutions to the continuous threat of antimicrobial resistance. Health Affairs Scholar, 3(2), qxaf012. https://doi.org/10.1093/haschl/qxaf012

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 radiation therapy 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. https://doi.org/10.1158/1078-0432.CCR-24-2311

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. bioRxiv. https://doi.org/10.1101/2025.01.16.633422

Stojanovic, L., Abbotts, R., Tripathi, K., Coon, C. M., Rajendran, S., Abbasi Farid, E., Hostetter, G., Guarnieri, J. W., Wallace, D. C., Liu, S., Wan, J., Calendo, G., Marker, R., Gohari, Z., Inayatullah, M. M. A., Tiwari, V. K., Kader, T., Santagata, S., Drapkin, R., … Rassool, F. V. (2025). ZNFX1 functions as a master regulator of epigenetically induced pathogen mimicry and inflammasome signaling in cancer. Cancer Research. https://doi.org/10.1158/0008-5472.CAN-24-1286

Morth, E., Sidak, K., Maliga, Z., Moller, T., Gehlenborg, N., Sorger, P., Pfister, H., Beyer, J., & Kruger, R. (2025). Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data. IEEE Transactions on Visualization and Computer Graphics, 31(1), 569–579. https://doi.org/10.1109/TVCG.2024.3456406

Oka, T., Hasegawa, T., Lee, T., Oliver-Garcia, V. S., Mortaja, M., Azin, M., Horiba, S., Smith, S. S., Khattab, S., Trerice, K. E., Chen, S. T., Semenov, Y. R., & Demehri, S. (2025). Langerhans Cells Directly Interact with Resident T Cells in the Human Epidermis. JID Innovations: Skin Science from Molecules to Population Health, 5(1), 100324. https://doi.org/10.1016/j.xjidi.2024.100324

Mollaoglu, G., Tepper, A., Falcomatà, C., Potak, H. T., Pia, L., Amabile, A., Mateus-Tique, J., Rabinovich, N., Park, M. D., LaMarche, N. M., Brody, R., Browning, L., Lin, J.-R., Zamarin, D., Sorger, P. K., Santagata, S., Merad, M., Baccarini, A., & Brown, B. D. (2024). Ovarian cancer-derived IL-4 promotes immunotherapy resistance. Cell, 187(26), 7492-7510.e22. https://doi.org/10.1016/j.cell.2024.10.006

Girnius, N., Henstridge, A. Z., Marks, B., Yu, J. K., Gray, G. K., Sander, C., Zervantonakis, I. K., & Luna, A. (2024). Cilengitide sensitivity is predicted by overall integrin expression in breast cancer. Breast Cancer Research: BCR, 26(1), 187. https://doi.org/10.1186/s13058-024-01942-2

Letai, A., & de The, H. (2024). Conventional chemotherapy: millions of cures, unresolved therapeutic index. Nature Reviews. Cancer. https://doi.org/10.1038/s41568-024-00778-4

Yu, W.-W., Barrett, J. N. P., Tong, J., Lin, M.-J., Marohn, M., Devlin, J. C., Herrera, A., Remark, J., Levine, J., Liu, P.-K., Fang, V., Zellmer, A. M., Oldridge, D. A., Wherry, E. J., Lin, J.-R., Chen, J.-Y., Sorger, P., Santagata, S., Krueger, J. G., … Lu, C. P. (2024). Skin immune-mesenchymal interplay within tertiary lymphoid structures promotes autoimmunepathogenesis in hidradenitis suppurativa. Immunity, 57(12), 2827-2842.e5. https://doi.org/10.1016/j.immuni.2024.11.010

Launonen, I.-M., Niemiec, I., Hincapié-Otero, M., Erkan, E. P., Junquera, A., Afenteva, D., Falco, M. M., Liang, Z., Salko, M., Chamchougia, F., Szabo, A., Perez-Villatoro, F., Li, Y., Micoli, G., Nagaraj, A., Haltia, U.-M., Kahelin, E., Oikkonen, J., Hynninen, J., … Färkkilä, A. (2024). Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer. Cancer Cell, 42(12), 2045-2063.e10. https://doi.org/10.1016/j.ccell.2024.11.005

Loi, P., Schade, A. E., Rodriguez, C. L., Krishnan, A., Perurena, N., Nguyen, V. T. M., Xu, Y., Watanabe, M., Davis, R. A., Gardner, A., Pilla, N. F., Mattioli, K., Popow, O., Gunduz, N., Lannagan, T. R. M., Fitzgerald, S., Sicinska, E. T., Lin, J.-R., Tan, W., … Cichowski, K. (2024). Epigenetic and Oncogenic Inhibitors Cooperatively Drive Differentiation and Kill KRAS-Mutant Colorectal Cancers. Cancer Discovery, 14(12), 2430–2449. https://doi.org/10.1158/2159-8290.CD-23-0866

Tobochnik, S., Regan, M. S., Dorotan, M. K. C., Reich, D., Lapinskas, E., Hossain, M. A., Stopka, S., Meredith, D. M., Santagata, S., Murphy, M. M., Arnaout, O., Bi, W. L., Chiocca, E. A., Golby, A. J., Mooney, M. A., Smith, T. R., Ligon, K. L., Wen, P. Y., Agar, N. Y. R., & Lee, J. W. (2024). Pilot Trial of Perampanel on Peritumoral Hyperexcitability in Newly Diagnosed High-grade Glioma. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 30(23), 5365–5373. https://doi.org/10.1158/1078-0432.CCR-24-1849

Baker, G. J., Novikov, E., Zhao, Z., Vallius, T., Davis, J. A., Lin, J.-R., Muhlich, J. L., Mittendorf, E. A., Santagata, S., Guerriero, J. L., & Sorger, P. K. (2024). Quality control for single-cell analysis of high-plex tissue profiles using CyLinter. Nature Methods, 21(12), 2248–2259. https://doi.org/10.1038/s41592-024-02328-0

Shimada, K., Michaud, D. E., Cui, Y. X., Zheng, K., Goldberg, J., Ju, Z., Schnitt, S. J., Pastorello, R., Kania, L. D., Hoffer, J., Muhlich, J. L., Hyun, N., Krueger, R., Gottlieb, A., Nelson, A., Wanderley, C. W., Antonellis, G., McAllister, S. S., Tolaney, S. M., … Guerriero, J. L. (2024). An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer [Preprint]. bioRxiv. https://doi.org/10.1101/2024.11.23.619172

Rand, E. A., Owen, S. V., Quinones-Olvera, N., Jean, K. D. C., Hernandez-Perez, C., & Baym, M. (2024). Phage DisCo: targeted discovery of bacteriophages by co-culture [Preprint]. bioRxiv. https://doi.org/10.1101/2024.11.22.624878

Vaelli, P., Fujita, A., Jo, S., Zhang, H.-X. B., Osorno, T., Ma, X., & Bean, B. P. (2024). State-Dependent Inhibition of Nav1.8 Sodium Channels by VX-150 and VX-548. Molecular Pharmacology, 106(6), 298–308. https://doi.org/10.1124/molpharm.124.000944

Souque, C., González Ojeda, I., & Baym, M. (2024). From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance. Annual Review of Microbiology, 78(1), 361–382. https://doi.org/10.1146/annurev-micro-041522-102707