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

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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.

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Stepwise-edited, human melanoma models reveal mutations’ effect on tumor and microenvironment by Hodis, Eran, Triglia, Elena Torlai, Kwon, John YH, 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, Martin C, Garraway, Levi A, Regev, Aviv

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Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells by Gerosa, Luca, Chidley, Christopher, Fröhlich, Fabian, Sanchez, Gabriela, Lim, Sang Kyun, Muhlich, Jeremy, Chen, Jia-Yun, Vallabhaneni, Sreeram, Baker, Gregory J, Schapiro, Denis, Atanasova, Mariya I, Chylek, Lily A, Shi, Tujin, Yi, Lian, Nicora, Carrie D, Claas, Allison, Ng, Thomas SC, Kohler, Rainer H, Lauffenburger, Douglas A, Weissleder, Ralph, Miller, Miles A, Qian, Wei-Jun, Wiley, H Steven, Sorger, Peter K

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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

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