Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography by 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 by 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 by Berglund, Emelie, Saarenpää, Sami, Jemt, Anders, Gruselius, Joel, Larsson, Ludvig, Bergenstråhle, Ludvig, Lundeberg, Joakim, Giacomello, Stefania

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Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones by 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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SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation by Bergenstråhle, Joseph, Bergenstråhle, Ludvig, Lundeberg, Joakim

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Spatially resolved clonal copy number alterations in benign and malignant tissue by 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 by Larsson, Ludvig, Bergenstråhle, Ludvig, He, Mengxiao, Andrusivova, Zaneta, Lundeberg, Joakim

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

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SnapShot: Spatial transcriptomics by 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 by 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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The spatial landscape of clonal somatic mutations in benign and malignant prostate epithelia by 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 by 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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Abstract 2171: The spatial landscape of clonal somatic mutations in benign and malignant tissue by 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 by 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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Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlig... by Muus, Christoph, Luecken, Malte D, Eraslan, Gokcen, Heimberg, Graham, Sikkema, Lisa, Kobayashi, Yoshihiko, Eeshit Dhaval Vaishnav, Subramanian, Ayshwarya, Smillie, Christopher, Duong, Elizabeth Thu, Fiskin, Evgenij, Triglia, Elena Torlai, Becavin, Christophe, Ansari, Meshal, Cai, Peiwen, Lin, Brian, Buchanan, Justin, Chen, Sijia, Shu, Jian, Haber, Adam L, Chung, Hattie, Montoro, Daniel T, Adams, Taylor, Hananeh Aliee, Allon, Samuel J, Andrusivova, Zaneta, Angelidis, Ilias, Orr Ashenberg, Bassler, Kevin, Benhar, Inbal, Bergenstrahle, Joseph, Bergenstrahle, Ludvig, Bolt, Liam, Braun, Emelie, Chaffin, Mark, Chichelnitskiy, Evgeny, Chiou, Joshua, Conlon, Thomas M, Cuoco, Michael S, Deprez, Marie, Fischer, David S, Gillich, Astrid, Gould, Joshua, Guo, Minzhe, Gutierrez, Austin J, Habermann, Arun C, Tyler, Harvey, He, Peng, Hou, Xiaomeng, Jaiswal, Alok, Jiang, Peiyong, Kapellos, Theodoros, Kuo, Christin S, Larsson, Ludvig, Leney-Greene, Michael A, Lim, Kyungtae, Litvinukova, Monika, Lu, Ji, Ludwig, Leif S, Luo, Wendy, Maatz, Henrike, Lira Mamanova, Manakongtreecheep, Kasidet, Charles-Hugo Marquette, Mbano, Ian, Mcadams, Alexi M, Metzger, Ross J, Nabhan, Ahmad N, Nyquist, Sarah K, Ordovas-Montanes, Jose, Penland, Lolita, Poirion, Olivier B, Poli, Segio, Cancan Qi, Reichart, Daniel, Rosas, Ivan, Schupp, Jonas, Sinha, Rahul, Sit, Rene V, Slowikowski, Kamil, Slyper, Michal, Smith, Neal, Sountoulidis, Alex, Strunz, Maximilian, Talavera-Lopez, Carlos, Tan, Peng, Tantivit, Jessica, Travaglini, Kyle J, Tucker, Nathan R, Vernon, Katherine, Wadsworth, Marc H, Waldman, Julia, Wang, Xiuting, Yan, Wenjun, Ali Onder Yildirim, Zhao, William, Ziegler, Carly G K, Regev, Aviv, The Nhlbi Lungmap Consortium, The Human Cell Atlas Lung Biological Network

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Learning Stationary Markov Processes with Contrastive Adjustment by Bergenstråhle, Ludvig, Lagergren, Jens, Lundeberg, Joakim

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Seamless integration of image and molecular analysis for spatial transcriptomics workflows by Bergenstråhle, Joseph, Larsson, Ludvig, Lundeberg, Joakim

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Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity by Berglund, Emelie, Maaskola, Jonas, Schultz, Niklas, Friedrich, Stefanie, Marklund, Maja, Bergenstråhle, Joseph, Tarish, Firas, Tanoglidi, Anna, Vickovic, Sanja, Larsson, Ludvig, Salmén, Fredrik, Ogris, Christoph, Wallenborg, Karolina, Lagergren, Jens, Ståhl, Patrik, Sonnhammer, Erik, Helleday, Thomas, Lundeberg, Joakim

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Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma by Ji, Andrew L., Rubin, Adam J., Thrane, Kim, Jiang, Sizun, Reynolds, David L., Meyers, Robin M., Guo, Margaret G., George, Benson M., Mollbrink, Annelie, Bergenstråhle, Joseph, Larsson, Ludvig, Bai, Yunhao, Zhu, Bokai, Bhaduri, Aparna, Meyers, Jordan M., Rovira-Clavé, Xavier, Hollmig, S. Tyler, Aasi, Sumaira Z., Nolan, Garry P., Lundeberg, Joakim, Khavari, Paul A.

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Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma by Ji, Andrew L., Rubin, Adam J., Thrane, Kim, Jiang, Sizun, Reynolds, David L., Meyers, Robin M., Guo, Margaret G., George, Benson M., Mollbrink, Annelie, Bergenstråhle, Joseph, Larsson, Ludvig, Bai, Yunhao, Zhu, Bokai, Bhaduri, Aparna, Meyers, Jordan M., Rovira-Clavé, Xavier, Hollmig, S. Tyler, Aasi, Sumaira Z., Nolan, Garry P., Lundeberg, Joakim, Khavari, Paul A.

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