Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography von Andersson, Alma, Bergenstråhle, Joseph, Asp, Michaela, Bergenstråhle, Ludvig, Jurek, Aleksandra, Fernández Navarro, José, Lundeberg, Joakim

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Super-resolved spatial transcriptomics by deep data fusion von Bergenstråhle, Ludvig, He, Bryan, Bergenstråhle, Joseph, Abalo, Xesús, Mirzazadeh, Reza, Thrane, Kim, Ji, Andrew L., Andersson, Alma, Larsson, Ludvig, Stakenborg, Nathalie, Boeckxstaens, Guy, Khavari, Paul, Zou, James, Lundeberg, Joakim, Maaskola, Jonas

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Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues von Berglund, Emelie, Saarenpaa, Sami, Jemt, Anders, Gruselius, Joel, Larsson, Ludvig, Bergenstrahle, Ludvig, Lundeberg, Joakim, Giacomello, Stefania

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Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones von Marklund, Maja, Schultz, Niklas, Friedrich, Stefanie, Berglund, Emelie, Tarish, Firas, Tanoglidi, Anna, Liu, Yao, Bergenstråhle, Ludvig, Erickson, Andrew, Helleday, Thomas, Lamb, Alastair D., Sonnhammer, Erik, Lundeberg, Joakim

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High-definition spatial transcriptomics for in situ tissue profiling von 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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SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation von Bergenstrahle, Joseph, Bergenstrahle, Ludvig, Lundeberg, Joakim

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Spatially resolved clonal copy number alterations in benign and malignant tissue von Erickson, Andrew, He, Mengxiao, Berglund, Emelie, Marklund, Maja, Mirzazadeh, Reza, Schultz, Niklas, Kvastad, Linda, Andersson, Alma, Bergenstråhle, Ludvig, Bergenstråhle, Joseph, Larsson, Ludvig, Alonso Galicia, Leire, Shamikh, Alia, Basmaci, Elisa, Díaz De Ståhl, Teresita, Rajakumar, Timothy, Doultsinos, Dimitrios, Thrane, Kim, Ji, Andrew L., Khavari, Paul A., Tarish, Firaz, Tanoglidi, Anna, Maaskola, Jonas, Colling, Richard, Mirtti, Tuomas, Hamdy, Freddie C., Woodcock, Dan J., Helleday, Thomas, Mills, Ian G., Lamb, Alastair D., Lundeberg, Joakim

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Spatial transcriptomics von Larsson, Ludvig, Bergenstråhle, Ludvig, He, Mengxiao, Andrusivova, Zaneta, Lundeberg, Joakim

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Integrating spatial gene expression and breast tumour morphology via deep learning von He, Bryan, Bergenstråhle, Ludvig, Stenbeck, Linnea, Abid, Abubakar, Andersson, Alma, Borg, Åke, Maaskola, Jonas, Lundeberg, Joakim, Zou, James

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Spatial landmark detection and tissue registration with deep learning von Ekvall, Markus, Bergenstråhle, Ludvig, Andersson, Alma, Czarnewski, Paulo, Olegård, Johannes, Käll, Lukas, Lundeberg, Joakim

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ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets von Wong, Kim, Navarro, José Fernández, Bergenstråhle, Ludvig, Ståhl, Patrik L, Lundeberg, Joakim

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Super-resolved spatial transcriptomics by deep data fusion von Bergenstrahle, Ludvig, He, Bryan, Bergenstrahle, Joseph, Abalo, Xesus, Mirzazadeh, Reza, Thrane, Kim, Ji, Andrew L, Andersson, Alma, Larsson, Ludvig, Stakenborg, Nathalie, Boeckxstaens, Guy, Khavari, Paul, Zou, James, Lundeberg, Joakim, Maaskola, Jonas

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SnapShot: Spatial transcriptomics von Larsson, Ludvig, Bergenstråhle, Ludvig, He, Mengxiao, Andrusivova, Zaneta, Lundeberg, Joakim

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The spatial landscape of clonal somatic mutations in benign and malignant tissue von Erickson, Andrew, Berglund, Emelie, He, Mengxiao, Marklund, Maja, Mirzazadeh, Reza, Schultz, Niklas, Kvastad, Linda, Andersson, Alma, Bergenstråhle, Ludvig, Bergenstråhle, Joseph, Larsson, Ludvig, Shamikh, Alia, Basmaci, Elisa, De Stahl, Teresita Diaz, Rajakumar, Timothy, Thrane, Kim, Ji, Andrew L., Khavari, Paul A., Tarish, Firaz, Tanoglidi, Anna, Maaskola, Jonas, Colling, Richard, Mirtti, Tuomas, Hamdy, Freddie, Woodcock, Dan J., Helleday, Thomas, Mills, Ian G., Lamb, Alastair D., Lundeberg, Joakim

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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics von Luecken, Malte D., Sikkema, Lisa, Waghray, Avinash, Heimberg, Graham, Kobayashi, Yoshihiko, Vaishnav, Eeshit Dhaval, Subramanian, Ayshwarya, Smillie, Christopher, Jagadeesh, Karthik A., Duong, Elizabeth Thu, Torlai Triglia, Elena, Ansari, Meshal, Cai, Peiwen, Lin, Brian, Chen, Sijia, Shu, Jian, Haber, Adam L., Chung, Hattie, Montoro, Daniel T., Adams, Taylor, Aliee, Hananeh, Andrusivova, Zaneta, Angelidis, Ilias, Ashenberg, Orr, Bassler, Kevin, Bécavin, Christophe, Benhar, Inbal, Bergenstråhle, Joseph, Bergenstråhle, Ludvig, Braun, Emelie, Bui, Linh T., Chaffin, Mark, Chichelnitskiy, Evgeny, Chiou, Joshua, Conlon, Thomas M., Cuoco, Michael S., Cuomo, Anna S. E., Deprez, Marie, Duclos, Grant, Fischer, David S., Ghazanfar, Shila, Gillich, Astrid, Giotti, Bruno, Gould, Joshua, Guo, Minzhe, Gutierrez, Austin J., Habermann, Arun C., Harvey, Tyler, He, Peng, Hou, Xiaomeng, Hu, Yan, Jaiswal, Alok, Ji, Lu, Jiang, Peiyong, Kapellos, Theodoros S., Kuo, Christin S., Leney-Greene, Michael A., Lim, Kyungtae, Litviňuková, Monika, Ludwig, Leif S., Lukassen, Soeren, Luo, Wendy, Maatz, Henrike, Madissoon, Elo, Mamanova, Lira, Manakongtreecheep, Kasidet, Leroy, Sylvie, Mayr, Christoph H., McAdams, Alexi M., Nabhan, Ahmad N., Nyquist, Sarah K., Penland, Lolita, Poirion, Olivier B., Poli, Sergio, Qi, CanCan, Queen, Rachel, Reichart, Daniel, Rosas, Ivan, Schupp, Jonas C., Shea, Conor V., Shi, Xingyi, Sinha, Rahul, Slowikowski, Kamil, Smith, Neal P., Sountoulidis, Alex, Strunz, Maximilian, Sullivan, Travis B., Sun, Dawei, Talavera-López, Carlos, Tan, Peng, Tantivit, Jessica, Travaglini, Kyle J., Tucker, Nathan R., Vernon, Katherine A., Wadsworth, Marc H., Waldman, Julia, Wang, Xiuting, Yan, Wenjun, Zhao, William, Ziegler, Carly G. K.

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The spatial landscape of clonal somatic mutations in benign and malignant prostate epithelia von Erickson, A.M., Berglund, E., He, M., Marklund, M., Mirzazadeh, R., Schultz, N., Bergenstråhle, L., Kvastad, L., Andersson, A., Bergenstråhle, J., Larsson, L., Rajakumar, T., Thrane, K., Ji, A.L., Tarish, F., Tanoglidi, A., Maaskola, J., Colling, R., Mirtti, T., Hamdy, F.C., Woodcock, D.J., Helleday, T., Mills, I.G., Lamb, A., Lundenberg, J.

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Abstract A051: The spatial landscape of clonal somatic copy number alterations in benign and malignant prostate epithelia von Erickson, Andrew, He, Mengxiao, Berglund, Emelie, Marklund, Maja, Mirzazadeh, Reza, Schultz, Niklas, Kvastad, Linda, Andersson, Alma, Bergenstråhle, Ludvig, Bergenstråhle, Joseph, Larsson, Ludvig, Galicia, Leire Alonso, Shamikh, Alia, Basmaci, Elisa, De Ståhl, Teresita Díaz, Rajakumar, Timothy, Doultsinos, Dimitrios, Thrane, Kim, Ji, Andrew L., Khavari, Paul A., Tarish, Firaz, Tanoglidi, Anna, Maaskola, Jonas, Colling, Richard, Mirtti, Tuomas, Hamdy, Freddie C., Woodcock, Dan J., Helleday, Thomas, Mills, Ian G., Lamb, Alastair D., Lundeberg, Joakim

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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics von Muus, Christoph, Sikkema, Lisa, Heimberg, Graham, Vaishnav, Eeshit Dhaval, Fiskin, Evgenij, Torlai Triglia, Elena, Cai, Peiwen, Lin, Brian, Chen, Sijia, Shu, Jian, Adams, Taylor, Aliee, Hananeh, Ashenberg, Orr, Bécavin, Christophe, Bergenstråhle, Joseph, Bergenstråhle, Ludvig, Bolt, Liam, Bui, Linh T, Chaffin, Mark, Chichelnitskiy, Evgeny, Conlon, Thomas M, Duclos, Grant, Fine, Denise, Ghazanfar, Shila, Guo, Minzhe, Harvey, Tyler, He, Peng, Hou, Xiaomeng, Jiang, Peiyong, Larsson, Ludvig, Lim, Kyungtae, Litviňuková, Monika, Mamanova, Lira, Manakongtreecheep, Kasidet, Leroy, Sylvie, Mayr, Christoph H, McAdams, Alexi M, Qi, CanCan, Queen, Rachel, Rosas, Ivan, Shi, Xingyi, Slyper, Michal, Smith, Neal P, Strunz, Maximilian, Sullivan, Travis B, Talavera-López, Carlos, Vernon, Katherine A, Wang, Xiuting, Xu, Ke, Huyck, Heidie L, Preissl, Sebastian, Rogers, Lisa, Wang, Allen, Xu, Yan, Barbry, Pascal, Beane, Jennifer E, Brazma, Alvis, Cho, Josalyn L, Conrad, Christian, Ellinor, Patrick T, Getz, Gad, Hennon, Mark W, Hung, Deborah T, Kaminski, Naftali, Koenigshoff, Melanie, Krasnow, Mark A, Kuhnemund, Malte, Lander, Eric S, Lee, Haeock, Marquette, Charles-Hugo, Linnarsson, Sten, Liu, Gang, Lo, Yuk Ming Dennis, Marioni, John C, Mazzilli, Sarah A, Medoff, Benjamin D, Miao, Zhichao, Ordovas-Montanes, Jose, Powell, Joseph E, Quake, Stephen R, Rajagopal, Jayaraj, Tata, Purushothama Rao, Regev, Aviv, Reyfman, Paul A, Samakovlis, Christos, Sanes, Joshua R, Schiller, Herbert B, Segre, Ayellet V, Seibold, Max A, Seidman, Jon G, Shalek, Alex K, Spira, Avrum, Theis, Fabian J, Tsankov, Alexander M, Vallier, Ludovic, van den Berge, Maarten, Xavier, Ramnik J, Yildirim, Ali Önder, Zerti, Darin, Zhang, Xiaohui

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Abstract 2171: The spatial landscape of clonal somatic mutations in benign and malignant tissue von Erickson, Andrew, Berglund, Emelie, He, Mengxiao, Marklund, Maja, Mirzazadeh, Reza, Schultz, Niklas, Kvastad, Linda, Andersson, Alma, Bergenstråhle, Ludvig, Bergenstråhle, Joseph, Larsson, Ludvig, Shamikh, Alia, Basmaci, Elisa, De Ståhl, Teresita Diaz, Rajakumar, Timothy, Thrane, Kim, Ji, Andrew L., Khavari, Paul A., Tarish, Firaz, Tanoglidi, Anna, Maaskola, Jonas, Colling, Richard, Mirtti, Tuomas, Hamdy, Freddie, Woodcock, Dan J., Helleday, Thomas, Mills, Ian G., Lamb, Alastair D., Lundenberg, Joakim

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Abstract PR016: The spatial landscape of clonal somatic mutations in benign and malignant tissue von Erickson, Andrew, Berglund, Emelie, He, Mengxiao, Marklund, Maja, Mirzazadeh, Reza, Schultz, Niklas, Bergenstråhle, Ludvig, Kvastad, Linda, Andersson, Alma, Bergenstråhle, Joseph, Larsson, Ludvig, Shamikh, Alia, Basmaci, Elisa, De Ståhl, Teresita Diaz, Rajakumar, Timothy, Thrane, Kim, Ji, Andrew L., Khavari, Paul A., Tarish, Firaz, Tanoglidi, Anna, Maaskola, Jonas, Colling, Richard, Mirtti, Tuomas, Hamdy, Freddie C., Woodcock, Dan J., Helleday, Thomas, Mills, Ian G., Lamb, Alastair D., Lundeberg, Joakim

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