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10 papers
Recent·Most cited
G. J. Baker, E. Novikov, Z. Zhao, T. Vallius, J. A. Davis, J.-R. Lin, J. L. Muhlich, E. A. Mittendorf, S. Santagata, J. L. Guerriero, P. K. Sorger
This paper introduces CyLinter, a quality control tool that removes imaging artefacts from high-plex spatial profiling data, improving single-cell analysis of archival tumor specimens.
bioRxiv · Nov 1, 2023Pathology
A. L. Creason, J. Egger, C. Watson, S. Sivagnanam, K. Chin, K. MacPherson, J.-R. Lin, Y.-A. Chen, B. E. Johnson, H. S. Feiler, D. Galipeau, N. E. Navin, E. Demir, Y. H. Chang, C. L. Corless, , J. Goecks
This study creates a multimodal tumor atlas to analyze how metastatic HR+ breast cancers adapt to CDK4/6 inhibitors, revealing mechanisms like mTORC1 activation and immune microenvironment changes.
bioRxiv · Sep 27, 2023 · PreprintCancer Biology
Z. Maliga, D. Y. Kim, A.-T. N. Bui, J.-R. Lin, A. K. Dewan, G. F. Murphy, A. J. Nirmal, C. G. Lian, P. K. Sorger, N. R. LeBoeuf
This study compares CyCIF and IHC for immune profiling in ICI-induced dAEs, finding CyCIF provides more detailed single-cell characterization of immune infiltrates.
bioRxiv · Apr 3, 2023 · PreprintImmunology
J.-R. Lin, Y.-A. Chen, D. Campton, J. Cooper, S. Coy, C. Yapp, J. Tefft, E. McCarty, K. Ligon, S. J. Rodig, S. Reese, T. George, S. Santagata, P. K. Sorger
The paper develops a multi-modal imaging platform combining H&E and high-plex immunofluorescence for colorectal cancer diagnosis, showing improved predictive models for progression-free survival.
bioRxiv · Sep 28, 2022Cancer Biology
G. Gaglia, M. Burger, C. C. Ritch, D. Rammos, Y. Dai, G. E. Crossland, S. Z. Tavana, S. Warchol, A. M. Jaeger, S. Naranjo, S. Coy, A. Johnson, R. Krueger, J.-R. Lin, H. Pfister, , S. Santagata
The paper maps lymphocyte interactions in lung adenocarcinoma using spatial analysis and machine learning, revealing dynamic lymphocyte networks that support anti-tumor immune responses.
bioRxiv · Aug 11, 2022Cancer Biology
S. Coy, S. Wang, S. A. Stopka, J.-R. Lin, R. Rashid, C. Yapp, C. C. Ritch, P. Khadka, M. Regan, J. Hwang, P. Y. Wen, P. Bandopadhayay, K. L. Ligon, N. Y. Agar, P. K. Sorger, , S. Santagata
The paper uses spatial single-cell analysis to show that CD73 and CD39 expression in glioblastoma correlates with poor clinical outcomes and immunosuppressive signaling.
bioRxiv · Jan 12, 2022Cancer Biology
J.-R. Lin, S. Wang, S. Coy, Y.-A. Chen, C. Yapp, M. A. Tyler, M. Nariya, C. N. Heiser, K. Lau, S. Santagata, P. K. Sorger
This study uses multiplexed 3D imaging and machine learning to analyze colorectal cancer morphology and immune interactions, revealing molecular gradients and cell state transitions.
bioRxiv · Mar 31, 2021Cancer Biology
R. Rashid, Y.-A. Chen, J. Hoffer, J. L. Muhlich, J.-R. Lin, R. Krueger, H. Pfister, R. Mitchell, S. Santagata, P. Sorger
The paper discusses the need for interactive guides to help interpret complex tissue atlas data and digital pathology images, using Minerva software as an example.
bioRxiv · Mar 27, 2020 · PreprintScientific Communication & Education
R. Rashid, G. Gaglia, Y.-A. Chen, J.-R. Lin, Z. Du, Z. Maliga, D. Schapiro, C. Yapp, J. Muhlich, A. Sokolov, P. Sorger, S. Santagata
The paper describes a dataset of multiplexed immunofluorescence images and single-cell immune marker data from human tonsil and lung cancer tissues, along with analysis methods and tools.
bioRxiv · Jul 17, 2019Cancer Biology
J.-R. Lin, B. Izar, S. Mei, S. Wang, P. Shah, C. Yapp, S. Santagata, P. Sorger
This paper introduces t-CyCIF, a method for highly multiplexed immunofluorescence imaging of FFPE tissues using conventional microscopes, and demonstrates its application in analyzing tumor antigens and immune markers.
bioRxiv · May 10, 2018Cancer Biology