Search Results - "Schapiro, Denis"

Explainable multiview framework for dissecting spatial relationships from highly multiplexed data by Tanevski, Jovan, Flores, Ricardo Omar Ramirez, Gabor, Attila, Schapiro, Denis, Saez-Rodriguez, Julio

“…The advancement of highly multiplexed spatial technologies requires scalable methods that can leverage spatial information. We present MISTy, a flexible,…”
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Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis by Arnol, Damien, Schapiro, Denis, Bodenmiller, Bernd, Saez-Rodriguez, Julio, Stegle, Oliver

“…Technological advances enable assaying multiplexed spatially resolved RNA and protein expression profiling of individual cells, thereby capturing molecular…”
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histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data by Schapiro, Denis, Jackson, Hartland W, Raghuraman, Swetha, Fischer, Jana R, Zanotelli, Vito R T, Schulz, Daniel, Giesen, Charlotte, Catena, Raúl, Varga, Zsuzsanna, Bodenmiller, Bernd

“…The histology topography cytometry analysis toolbox (histoCAT) enables quantitative analysis and exploration of highly multiplexed imaging data for better…”
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High-definition spatial transcriptomics for in situ tissue profiling by Vickovic, Sanja, Eraslan, Gökcen, Salmén, Fredrik, Klughammer, Johanna, Stenbeck, Linnea, Schapiro, Denis, Äijö, Tarmo, Bonneau, Richard, Bergenstråhle, Ludvig, Navarro, José Fernandéz, Gould, Joshua, Griffin, Gabriel K., Borg, Åke, Ronaghi, Mostafa, Frisén, Jonas, Lundeberg, Joakim, Regev, Aviv, Ståhl, Patrik L.

“…Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed…”
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Identification of an embryonic differentiation stage marked by Sox1 and FoxA2 co-expression using combined cell tracking and high dimensional protein imaging by Arekatla, Geethika, Skylaki, Stavroula, Corredor Suarez, David, Jackson, Hartland, Schapiro, Denis, Engler, Stefanie, Auler, Markus, Camargo Ortega, German, Hastreiter, Simon, Reimann, Andreas, Loeffler, Dirk, Bodenmiller, Bernd, Schroeder, Timm

“…Pluripotent mouse embryonic stem cells (ESCs) can differentiate to all germ layers and serve as an in vitro model of embryonic development. To better…”
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High-Dimensional Phenotyping Identifies Age-Emergent Cells in Human Mammary Epithelia by Pelissier Vatter, Fanny A., Schapiro, Denis, Chang, Hang, Borowsky, Alexander D., Lee, Jonathan K., Parvin, Bahram, Stampfer, Martha R., LaBarge, Mark A., Bodenmiller, Bernd, Lorens, James B.

“…Aging is associated with tissue-level changes in cellular composition that are correlated with increased susceptibility to disease. Aging human mammary tissue…”
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Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer by Rashid, Rumana, Gaglia, Giorgio, Chen, Yu-An, Lin, Jia-Ren, Du, Ziming, Maliga, Zoltan, Schapiro, Denis, Yapp, Clarence, Muhlich, Jeremy, Sokolov, Artem, Sorger, Peter, Santagata, Sandro

“…In this data descriptor, we document a dataset of multiplexed immunofluorescence images and derived single-cell measurements of immune lineage and other…”
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Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium by Vickovic, Sanja, Schapiro, Denis, Carlberg, Konstantin, Lötstedt, Britta, Larsson, Ludvig, Hildebrandt, Franziska, Korotkova, Marina, Hensvold, Aase H., Catrina, Anca I., Sorger, Peter K., Malmström, Vivianne, Regev, Aviv, Ståhl, Patrik L.

“…The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in…”
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Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry by Giesen, Charlotte, Wang, Hao A O, Schapiro, Denis, Zivanovic, Nevena, Jacobs, Andrea, Hattendorf, Bodo, Schüffler, Peter J, Grolimund, Daniel, Buhmann, Joachim M, Brandt, Simone, Varga, Zsuzsanna, Wild, Peter J, Günther, Detlef, Bodenmiller, Bernd

“…This paper reports the use of mass cytometry on adherent cells and tissue samples for highly multiplexed imaging at subcellular resolution. Mass cytometry…”
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A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry by Damond, Nicolas, Engler, Stefanie, Zanotelli, Vito R.T., Schapiro, Denis, Wasserfall, Clive H., Kusmartseva, Irina, Nick, Harry S., Thorel, Fabrizio, Herrera, Pedro L., Atkinson, Mark A., Bodenmiller, Bernd

“…Type 1 diabetes (T1D) results from the autoimmune destruction of insulin-producing β cells. A comprehensive picture of the changes during T1D development is…”
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A molecular single-cell lung atlas of lethal COVID-19 by Melms, Johannes C., Biermann, Jana, Huang, Huachao, Wang, Yiping, Nair, Ajay, Tagore, Somnath, Katsyv, Igor, Rendeiro, André F., Amin, Amit Dipak, Schapiro, Denis, Frangieh, Chris J., Luoma, Adrienne M., Filliol, Aveline, Fang, Yinshan, Ravichandran, Hiranmayi, Clausi, Mariano G., Alba, George A., Rogava, Meri, Chen, Sean W., Ho, Patricia, Montoro, Daniel T., Kornberg, Adam E., Han, Arnold S., Bakhoum, Mathieu F., Anandasabapathy, Niroshana, Suárez-Fariñas, Mayte, Bakhoum, Samuel F., Bram, Yaron, Borczuk, Alain, Guo, Xinzheng V., Lefkowitch, Jay H., Marboe, Charles, Lagana, Stephen M., Del Portillo, Armando, Tsai, Emily J., Zorn, Emmanuel, Markowitz, Glen S., Schwabe, Robert F., Schwartz, Robert E., Elemento, Olivier, Saqi, Anjali, Hibshoosh, Hanina, Que, Jianwen, Izar, Benjamin

“…Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2 infection 1 , 2 , but the host response at the lung tissue level is poorly…”
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Spatial multi-omic map of human myocardial infarction by Kuppe, Christoph, Ramirez Flores, Ricardo O., Li, Zhijian, Hayat, Sikander, Levinson, Rebecca T., Liao, Xian, Hannani, Monica T., Tanevski, Jovan, Wünnemann, Florian, Nagai, James S., Halder, Maurice, Schumacher, David, Menzel, Sylvia, Schäfer, Gideon, Hoeft, Konrad, Cheng, Mingbo, Ziegler, Susanne, Zhang, Xiaoting, Peisker, Fabian, Kaesler, Nadine, Saritas, Turgay, Xu, Yaoxian, Kassner, Astrid, Gummert, Jan, Morshuis, Michiel, Amrute, Junedh, Veltrop, Rogier J. A., Boor, Peter, Klingel, Karin, Van Laake, Linda W., Vink, Aryan, Hoogenboezem, Remco M., Bindels, Eric M. J., Schurgers, Leon, Sattler, Susanne, Schapiro, Denis, Schneider, Rebekka K., Lavine, Kory, Milting, Hendrik, Costa, Ivan G., Saez-Rodriguez, Julio, Kramann, Rafael

“…Myocardial infarction is a leading cause of death worldwide 1 . Although advances have been made in acute treatment, an incomplete understanding of remodelling…”
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In silico tissue generation and power analysis for spatial omics by Baker, Ethan A. G., Schapiro, Denis, Dumitrascu, Bianca, Vickovic, Sanja, Regev, Aviv

“…As spatially resolved multiplex profiling of RNA and proteins becomes more prominent, it is increasingly important to understand the statistical power…”
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Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry by Schulz, Daniel, Zanotelli, Vito Riccardo Tomaso, Fischer, Jana Raja, Schapiro, Denis, Engler, Stefanie, Lun, Xiao-Kang, Jackson, Hartland Warren, Bodenmiller, Bernd

“…To build comprehensive models of cellular states and interactions in normal and diseased tissue, genetic and proteomic information must be extracted with…”
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Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer by Färkkilä, Anniina, Gulhan, Doga C., Casado, Julia, Jacobson, Connor A., Nguyen, Huy, Kochupurakkal, Bose, Maliga, Zoltan, Yapp, Clarence, Chen, Yu-An, Schapiro, Denis, Zhou, Yinghui, Graham, Julie R., Dezube, Bruce J., Munster, Pamela, Santagata, Sandro, Garcia, Elizabeth, Rodig, Scott, Lako, Ana, Chowdhury, Dipanjan, Shapiro, Geoffrey I., Matulonis, Ursula A., Park, Peter J., Hautaniemi, Sampsa, Sorger, Peter K., Swisher, Elizabeth M., D’Andrea, Alan D., Konstantinopoulos, Panagiotis A.

“…Combined PARP and immune checkpoint inhibition has yielded encouraging results in ovarian cancer, but predictive biomarkers are lacking. We performed…”
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MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging by Schapiro, Denis, Sokolov, Artem, Yapp, Clarence, Chen, Yu-An, Muhlich, Jeremy L., Hess, Joshua, Creason, Allison L., Nirmal, Ajit J., Baker, Gregory J., Nariya, Maulik K., Lin, Jia-Ren, Maliga, Zoltan, Jacobson, Connor A., Hodgman, Matthew W., Ruokonen, Juha, Farhi, Samouil L., Abbondanza, Domenic, McKinley, Eliot T., Persson, Daniel, Betts, Courtney, Sivagnanam, Shamilene, Regev, Aviv, Goecks, Jeremy, Coffey, Robert J., Coussens, Lisa M., Santagata, Sandro, Sorger, Peter K.

“…Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of…”
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Evolution of delayed resistance to immunotherapy in a melanoma responder by Liu, David, Lin, Jia-Ren, Robitschek, Emily J., Kasumova, Gyulnara G., Heyde, Alex, Shi, Alvin, Kraya, Adam, Zhang, Gao, Moll, Tabea, Frederick, Dennie T., Chen, Yu-An, Wang, Shu, Schapiro, Denis, Ho, Li-Lun, Bi, Kevin, Sahu, Avinash, Mei, Shaolin, Miao, Benchun, Sharova, Tatyana, Alvarez-Breckenridge, Christopher, Stocking, Jackson H., Kim, Tommy, Fadden, Riley, Lawrence, Donald, Hoang, Mai P., Cahill, Daniel P., Malehmir, Mohsen, Nowak, Martin A., Brastianos, Priscilla K., Lian, Christine G., Ruppin, Eytan, Izar, Benjamin, Herlyn, Meenhard, Van Allen, Eliezer M., Nathanson, Katherine, Flaherty, Keith T., Sullivan, Ryan J., Kellis, Manolis, Sorger, Peter K., Boland, Genevieve M.

“…Despite initial responses 1 – 3 , most melanoma patients develop resistance 4 to immune checkpoint blockade (ICB). To understand the evolution of resistance,…”
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Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry by Lun, Xiao-Kang, Zanotelli, Vito R T, Wade, James D, Schapiro, Denis, Tognetti, Marco, Dobberstein, Nadine, Bodenmiller, Bernd

“…Mass-cytometry analysis reveals how signaling networks respond to changes in the abundance of their nodes. Signaling networks are key regulators of cellular…”
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Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment by Hodis, Eran, Torlai Triglia, Elena, Kwon, John Y H, Biancalani, Tommaso, Zakka, Labib R, Parkar, Saurabh, Hütter, Jan-Christian, Buffoni, Lorenzo, Delorey, Toni M, Phillips, Devan, Dionne, Danielle, Nguyen, Lan T, Schapiro, Denis, Maliga, Zoltan, Jacobson, Connor A, Hendel, Ayal, Rozenblatt-Rosen, Orit, Mihm, Jr, Martin C, Garraway, Levi A, Regev, Aviv

“…Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially…”
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Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions by Lerma-Martin, Celia, Badia-i-Mompel, Pau, Ramirez Flores, Ricardo O., Sekol, Patricia, Schäfer, Philipp S. L., Riedl, Christian J., Hofmann, Annika, Thäwel, Thomas, Wünnemann, Florian, Ibarra-Arellano, Miguel A., Trobisch, Tim, Eisele, Philipp, Schapiro, Denis, Haeussler, Maximilian, Hametner, Simon, Saez-Rodriguez, Julio, Schirmer, Lucas

“…Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system. Inflammation is gradually compartmentalized and restricted to specific…”
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