Irving Institute for Cancer Dynamics

Displaying 1 - 46 of 46CSV
Dinh, K. N., Vázquez-García, I., Chan, A., Malhotra, R., Weiner, A., McPherson, A. W., & Tavaré, S. (2025). CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution. PLOS Computational Biology, 21(4), e1012902. https://doi.org/10.1371/journal.pcbi.1012902
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Salcedo, A., Tarabichi, M., Buchanan, A., Espiritu, S. M. G., Zhang, H., Zhu, K., Ou Yang, T.-H., Leshchiner, I., Anastassiou, D., Guan, Y., Jang, G. H., Mootor, M. F. E., Haase, K., Deshwar, A. G., Zou, W., Umar, I., Dentro, S., Wintersinger, J. A., Chiotti, K., … Boutros, P. C. (2024). Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nature Biotechnology, 43(4), 581–592. https://doi.org/10.1038/s41587-024-02250-y
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Maurer, K., Park, C. Y., Mani, S., Borji, M., Raths, F., Gouin, K. H., Penter, L., Jin, Y., Zhang, J. Y., Shin, C., Brenner, J. R., Southard, J., Krishna, S., Lu, W., Lyu, H., Abbondanza, D., Mangum, C., Olsen, L. R., Lawson, M. J., … Azizi, E. (2025). Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy. Science Immunology, 10(103). https://doi.org/10.1126/sciimmunol.adr0782
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Goldberg, A. R., Dovas, A., Torres, D., Pereira, B., Viswanathan, A., Das Sharma, S., Mela, A., Merricks, E. M., Megino-Luque, C., McInvale, J. J., Olabarria, M., Shokooh, L. A., Zhao, H. T., Chen, C., Kotidis, C., Calvaresi, P., Banu, M. A., Razavilar, A., Sudhakar, T. D., … Canoll, P. (2025). Glioma-induced alterations in excitatory neurons are reversed by mTOR inhibition. Neuron. https://doi.org/10.1016/j.neuron.2024.12.026
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Tan, M. C., Li, Z., Patel, K. K., Zhang, F., Yu, X., Wang, X., Rosen, D. G., Dawsey, S. M., Xue, L., Hur, C., Schwarz, R. A., Vohra, I., Tang, Y., Wu, M., Wang, T., Carns, J., Xu, H., Richards-Kortum, R. R., Wang, G., & Anandasabapathy, S. (2024). A High-Resolution Microendoscope Improves Esophageal Cancer Screening and Surveillance: Implications for Underserved Global Settings Based on an International Randomized Controlled Trial. Gastroenterology. https://doi.org/10.1053/j.gastro.2024.10.025
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Shafighi, S., Geras, A., Jurzysta, B., Sahaf Naeini, A., Filipiuk, I., Ra̧czkowska, A., Toosi, H., Koperski, Ł., Thrane, K., Engblom, C., Mold, J. E., Chen, X., Hartman, J., Nowis, D., Carbone, A., Lagergren, J., & Szczurek, E. (2024). Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-53374-3
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Gu, J., Iyer, A., Wesley, B., Taglialatela, A., Leuzzi, G., Hangai, S., Decker, A., Gu, R., Klickstein, N., Shuai, Y., Jankovic, K., Parker-Burns, L., Jin, Y., Zhang, J. Y., Hong, J., Niu, X., Costa, J. A., Pezet, M. G., Chou, J., … Gaublomme, J. T. (2024). Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap. Nature Biotechnology. https://doi.org/10.1038/s41587-024-02386-x
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Tschuck, J., Padmanabhan Nair, V., Galhoz, A., Zaratiegui, C., Tai, H.-M., Ciceri, G., Rothenaigner, I., Tchieu, J., Stockwell, B. R., Studer, L., Cabianca, D. S., Menden, M. P., Vincendeau, M., & Hadian, K. (2024). Suppression of ferroptosis by vitamin A or radical-trapping antioxidants is essential for neuronal development. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-51996-1
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Park, C., Mani, S., Beltran-Velez, N., Maurer, K., Huang, T., Li, S., Gohil, S., Livak, K. J., Knowles, D. A., Wu, C. J., & Azizi, E. (2024). A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. Genome Research, 34(9), 1384–1396. https://doi.org/10.1101/gr.279126.124
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Kabeer, F., Tran, H., Andronescu, M., Singh, G., Lee, H., Salehi, S., Wang, B., Biele, J., Brimhall, J., Gee, D., Cerda, V., O’Flanagan, C., Algara, T., Kono, T., Beatty, S., Zaikova, E., Lai, D., Lee, E., … Moore, R. (2024). Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers. Genome Biology, 25(1). https://doi.org/10.1186/s13059-024-03318-3
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Suryadevara, V., Hudgins, A. D., Rajesh, A., Pappalardo, A., Karpova, A., Dey, A. K., Hertzel, A., Agudelo, A., Rocha, A., Soygur, B., Schilling, B., Carver, C. M., Aguayo-Mazzucato, C., Baker, D. J., Bernlohr, D. A., Jurk, D., Mangarova, D. B., Quardokus, E. M., Enninga, E. A. L., … Neretti, N. (2024). SenNet recommendations for detecting senescent cells in different tissues. Nature Reviews Molecular Cell Biology. https://doi.org/10.1038/s41580-024-00738-8
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Ng, A. W. T., McClurg, D. P., Wesley, B., Zamani, S. A., Black, E., Miremadi, A., Giger, O., Hoopen, R. ten, Devonshire, G., Redmond, A. M., Grehan, N., Jammula, S., Blasko, A., Li, X., Aparicio, S., Tavaré, S., Edwards, P. A. W., Grehan, N., … Fitzgerald, R. C. (2024). Disentangling oncogenic amplicons in esophageal adenocarcinoma. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47619-4
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He, S., Jin, Y., Nazaret, A., Shi, L., Chen, X., Rampersaud, S., Dhillon, B. S., Valdez, I., Friend, L. E., Fan, J. L., Park, C. Y., Mintz, R. L., Lao, Y.-H., Carrera, D., Fang, K. W., Mehdi, K., Rohde, M., McFaline-Figueroa, J. L., Blei, D., … Azizi, E. (2024). Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor–immune hubs. Nature Biotechnology. https://doi.org/10.1038/s41587-024-02173-8
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González-Solares, E. A., Dariush, A., González-Fernández, C., Küpcü Yoldaş, A., Molaeinezhad, A., Al Sa’d, M., Smith, L., Whitmarsh, T., Millar, N., Chornay, N., Falciatori, I., Fatemi, A., Goodwin, D., Kuett, L., Mulvey, C. M., Páez Ribes, M., Qosaj, F., Roth, A., Vázquez-García, I., … Walton, N. A. (2023). Imaging and Molecular Annotation of Xenographs and Tumours (IMAXT): High throughput data and analysis infrastructure. Biological Imaging, 3. https://doi.org/10.1017/s2633903x23000090
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Babushku, T., Lechner, M., Ehrenberg, S., Rambold, U., Schmidt-Supprian, M., Yates, A. J., Rane, S., Zimber-Strobl, U., & Strobl, L. J. (2024). Notch2 controls developmental fate choices between germinal center and marginal zone B cells upon immunization. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-46024-1
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Fuller, J., Abramov, A., Mullin, D., Beck, J., Lemaitre, P., & Azizi, E. (2024). A Deep Learning Framework for Predicting Patient Decannulation on Extracorporeal Membrane Oxygenation Devices: Development and Model Analysis Study. JMIR Biomedical Engineering, 9, e48497. https://doi.org/10.2196/48497
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Rajbhandari, P., Neelakantan, T. V., Hosny, N., & Stockwell, B. R. (2024). Spatial pharmacology using mass spectrometry imaging. Trends in Pharmacological Sciences, 45(1), 67–80. https://doi.org/10.1016/j.tips.2023.11.003
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Mann, J., Reznik, E., Santer, M., Fongheiser, M. A., Smith, N., Hirschhorn, T., Zandkarimi, F., Soni, R. K., Dafré, A. L., Miranda-Vizuete, A., Farina, M., & Stockwell, B. R. (2024). Ferroptosis inhibition by oleic acid mitigates iron-overload-induced injury. Cell Chemical Biology, 31(2), 249-264.e7. https://doi.org/10.1016/j.chembiol.2023.10.012
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Wang, X. K., Uzuni, A., Belay, K., Harle, D. W., Gordillo, C. A., Macedo, R. J., Chakrabarti, S., Shi, L., Pressler, M., Fuller, J., Azizi, E., & Reshef, R. (2023). Characteristics of Alloreactive T-Cell Clones That Predict Early Development of Acute GvHD Following Allogeneic HCT. Blood, 142(Supplement 1), 2042–2042. https://doi.org/10.1182/blood-2023-187932
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Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Hanikel, N., Pellock, S. J., Courbet, A., Sheffler, W., Wang, J., Venkatesh, P., Sappington, I., Torres, S. V., … Baker, D. (2023). De novo design of protein structure and function with RFdiffusion. Nature, 620(7976), 1089–1100. https://doi.org/10.1038/s41586-023-06415-8
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Jayasinghe, Y. P., Banco, M. T., Lindenberger, J. J., Favrot, L., Palčeková, Z., Jackson, M., Manabe, S., & Ronning, D. R. (2023). The Mycobacterium tuberculosis mycothiol S-transferase is divalent metal-dependent for mycothiol binding and transfer. RSC Medicinal Chemistry, 14(3), 491–500. https://doi.org/10.1039/d2md00401a
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Santhanam, B., Oikonomou, P., & Tavazoie, S. (2023). Systematic assessment of prognostic molecular features across cancers. Cell Genomics, 3(3), 100262. https://doi.org/10.1016/j.xgen.2023.100262
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Wang, Y., Fan, J. L., Melms, J. C., Amin, A. D., Georgis, Y., Barrera, I., Ho, P., Tagore, S., Abril-Rodríguez, G., He, S., Jin, Y., Biermann, J., Hofree, M., Caprio, L., Berhe, S., Khan, S. A., Henick, B. S., Ribas, A., Macosko, E. Z., … Izar, B. (2023). Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens. Nature Genetics, 55(1), 19–25. https://doi.org/10.1038/s41588-022-01268-9
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Bondaruk, J., Jaksik, R., Wang, Z., Cogdell, D., Lee, S., Chen, Y., Dinh, K. N., Majewski, T., Zhang, L., Cao, S., Tian, F., Yao, H., Kuś, P., Chen, H., Weinstein, J. N., Navai, N., Dinney, C., Gao, J., Theodorescu, D., … Czerniak, B. (2022). The origin of bladder cancer from mucosal field effects. IScience, 25(7), 104551. https://doi.org/10.1016/j.isci.2022.104551
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Biermann, J., Melms, J. C., Amin, A. D., Wang, Y., Caprio, L. A., Karz, A., Tagore, S., Barrera, I., Ibarra-Arellano, M. A., Andreatta, M., Fullerton, B. T., Gretarsson, K. H., Sahu, V., Mangipudy, V. S., Nguyen, T. T. T., Nair, A., Rogava, M., Ho, P., Koch, P. D., … Izar, B. (2022). Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell, 185(14), 2591-2608.e30. https://doi.org/10.1016/j.cell.2022.06.007
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Tourigny, D. S., Zucker, M., Kim, M., Russo, P., Coleman, J., Lee, C.-H., Carlo, M. I., Chen, Y.-B., Hakimi, A. A., Kotecha, R. R., & Reznik, E. (2022). Molecular Characterization of the Tumor Microenvironment in Renal Medullary Carcinoma. Frontiers in Oncology, 12. https://doi.org/10.3389/fonc.2022.910147
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Rane, S., Hogan, T., Lee, E., Seddon, B., & Yates, A. J. (2022). Towards a unified model of naive T cell dynamics across the lifespan. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.78168
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Boehm, K. M., Aherne, E. A., Ellenson, L., Nikolovski, I., Alghamdi, M., Vázquez-García, I., Zamarin, D., Long Roche, K., Liu, Y., Patel, D., Aukerman, A., Pasha, A., Rose, D., Selenica, P., Causa Andrieu, P. I., Fong, C., Capanu, M., Reis-Filho, J. S., Vanguri, R., … Shah, S. P. (2022). Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer. Nature Cancer, 3(6), 723–733. https://doi.org/10.1038/s43018-022-00388-9
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Ng, A. W. T., Contino, G., Killcoyne, S., Devonshire, G., Hsu, R., Abbas, S., Su, J., Redmond, A. M., Weaver, J. M. J., Eldridge, M. D., Tavaré, S., Grehan, N., Nutzinger, B., Fidziukiewicz, E., Freeman, A., Smyth, E. C., O’Donovan, M., Miremadi, A., … Fitzgerald, R. C. (2022). Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Communications Biology, 5(1). https://doi.org/10.1038/s42003-022-03238-7
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Jin, J., Schorpp, K., Samaga, D., Unger, K., Hadian, K., & Stockwell, B. R. (2022). Machine Learning Classifies Ferroptosis and Apoptosis Cell Death Modalities with TfR1 Immunostaining. ACS Chemical Biology, 17(3), 654–660. https://doi.org/10.1021/acschembio.1c00953
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Liu, H., Forouhar, F., Seibt, T., Saneto, R., Wigby, K., Friedman, J., Xia, X., Shchepinov, M. S., Ramesh, S. K., Conrad, M., & Stockwell, B. R. (2021). Characterization of a patient-derived variant of GPX4 for precision therapy. Nature Chemical Biology, 18(1), 91–100. https://doi.org/10.1038/s41589-021-00915-2
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Bachireddy, P., Azizi, E., Burdziak, C., Nguyen, V. N., Ennis, C. S., Maurer, K., Park, C. Y., Choo, Z.-N., Li, S., Gohil, S. H., Ruthen, N. G., Ge, Z., Keskin, D. B., Cieri, N., Livak, K. J., Kim, H. T., Neuberg, D. S., Soiffer, R. J., Ritz, J., … Wu, C. J. (2021). Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Reports, 37(6), 109992. https://doi.org/10.1016/j.celrep.2021.109992
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