Cell2location maps fine-grained cell types in spatial transcriptomics von Kleshchevnikov, Vitalii, Shmatko, Artem, Dann, Emma, Aivazidis, Alexander, King, Hamish W., Li, Tong, Elmentaite, Rasa, Lomakin, Artem, Kedlian, Veronika, Gayoso, Adam, Jain, Mika Sarkin, Park, Jun Sung, Ramona, Lauma, Tuck, Elizabeth, Arutyunyan, Anna, Vento-Tormo, Roser, Gerstung, Moritz, James, Louisa, Stegle, Oliver, Bayraktar, Omer Ali

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Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE von Missarova, Alsu, Dann, Emma, Rosen, Leah, Satija, Rahul, Marioni, John

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Mapping the developing human immune system across organs von Suo, Chenqu, Dann, Emma, Goh, Issac, Jardine, Laura, Kleshchevnikov, Vitalii, Park, Jong-Eun, Botting, Rachel A, Stephenson, Emily, Engelbert, Justin, Tuong, Zewen Kelvin, Polanski, Krzysztof, Yayon, Nadav, Xu, Chuan, Suchanek, Ondrej, Elmentaite, Rasa, Domínguez Conde, Cecilia, He, Peng, Pritchard, Sophie, Miah, Mohi, Moldovan, Corina, Steemers, Alexander S, Mazin, Pavel, Prete, Martin, Horsfall, Dave, Marioni, John C, Clatworthy, Menna R, Haniffa, Muzlifah, Teichmann, Sarah A

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Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer von Beltran, Himisha, Romanel, Alessandro, Conteduca, Vincenza, Casiraghi, Nicola, Sigouros, Michael, Franceschini, Gian Marco, Orlando, Francesco, Fedrizzi, Tarcisio, Ku, Sheng-Yu, Dann, Emma, Alonso, Alicia, Mosquera, Juan Miguel, Sboner, Andrea, Xiang, Jenny, Elemento, Olivier, Nanus, David M., Tagawa, Scott T., Benelli, Matteo, Demichelis, Francesca

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Differential abundance testing on single-cell data using k-nearest neighbor graphs von Dann, Emma, Henderson, Neil C., Teichmann, Sarah A., Morgan, Michael D., Marioni, John C.

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Best practices for single-cell analysis across modalities von Heumos, Lukas, Schaar, Anna C., Lance, Christopher, Litinetskaya, Anastasia, Drost, Felix, Zappia, Luke, Lücken, Malte D., Strobl, Daniel C., Henao, Juan, Curion, Fabiola, Schiller, Herbert B., Theis, Fabian J.

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Discovering variation from cell atlases: comparative methods for single-cell genomics von Dann, Emma

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multiDGD: A versatile deep generative model for multi-omics data von Schuster, Viktoria, Dann, Emma, Krogh, Anders, Teichmann, Sarah A.

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A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates von He, Peng, Lim, Kyungtae, Sun, Dawei, Pett, Jan Patrick, Jeng, Quitz, Polanski, Krzysztof, Dong, Ziqi, Bolt, Liam, Richardson, Laura, Mamanova, Lira, Dabrowska, Monika, Wilbrey-Clark, Anna, Madissoon, Elo, Tuong, Zewen Kelvin, Dann, Emma, Suo, Chenqu, Goh, Isaac, Yoshida, Masahiro, Nikolić, Marko Z., Janes, Sam M., He, Xiaoling, Barker, Roger A., Teichmann, Sarah A., Marioni, John C., Meyer, Kerstin B., Rawlins, Emma L.

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Cells of the human intestinal tract mapped across space and time von Elmentaite, Rasa, Kumasaka, Natsuhiko, Roberts, Kenny, Fleming, Aaron, Dann, Emma, King, Hamish W., Kleshchevnikov, Vitalii, Dabrowska, Monika, Pritchard, Sophie, Bolt, Liam, Vieira, Sara F., Mamanova, Lira, Huang, Ni, Perrone, Francesca, Goh Kai’En, Issac, Lisgo, Steven N., Katan, Matilda, Leonard, Steven, Oliver, Thomas R. W., Hook, C. Elizabeth, Nayak, Komal, Campos, Lia S., Domínguez Conde, Cecilia, Stephenson, Emily, Engelbert, Justin, Botting, Rachel A., Polanski, Krzysztof, van Dongen, Stijn, Patel, Minal, Morgan, Michael D., Marioni, John C., Bayraktar, Omer Ali, Meyer, Kerstin B., He, Xiaoling, Barker, Roger A., Uhlig, Holm H., Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Zilbauer, Matthias, Clatworthy, Menna R., Haniffa, Muzlifah, James, Kylie R., Teichmann, Sarah A.

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Precise identification of cell states altered in disease using healthy single-cell references von Dann, Emma, Cujba, Ana-Maria, Oliver, Amanda J., Meyer, Kerstin B., Teichmann, Sarah A., Marioni, John C.

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Blood and immune development in human fetal bone marrow and Down syndrome von Jardine, Laura, Webb, Simone, Goh, Issac, Quiroga Londoño, Mariana, Reynolds, Gary, Mather, Michael, Olabi, Bayanne, Stephenson, Emily, Botting, Rachel A., Horsfall, Dave, Engelbert, Justin, Maunder, Daniel, Mende, Nicole, Murnane, Caitlin, Dann, Emma, McGrath, Jim, King, Hamish, Kucinski, Iwo, Queen, Rachel, Carey, Christopher D., Shrubsole, Caroline, Poyner, Elizabeth, Acres, Meghan, Jones, Claire, Ness, Thomas, Coulthard, Rowen, Elliott, Natalina, O’Byrne, Sorcha, Haltalli, Myriam L. R., Lawrence, John E., Lisgo, Steven, Balogh, Petra, Meyer, Kerstin B., Prigmore, Elena, Ambridge, Kirsty, Jain, Mika Sarkin, Efremova, Mirjana, Pickard, Keir, Creasey, Thomas, Bacardit, Jaume, Henderson, Deborah, Coxhead, Jonathan, Filby, Andrew, Hussain, Rafiqul, Dixon, David, McDonald, David, Popescu, Dorin-Mirel, Kowalczyk, Monika S., Li, Bo, Ashenberg, Orr, Tabaka, Marcin, Dionne, Danielle, Tickle, Timothy L., Slyper, Michal, Rozenblatt-Rosen, Orit, Regev, Aviv, Behjati, Sam, Laurenti, Elisa, Wilson, Nicola K., Roy, Anindita, Göttgens, Berthold, Roberts, Irene, Teichmann, Sarah A., Haniffa, Muzlifah

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Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins von Suo, Chenqu, Polanski, Krzysztof, Dann, Emma, Lindeboom, Rik G. H., Vilarrasa-Blasi, Roser, Vento-Tormo, Roser, Haniffa, Muzlifah, Meyer, Kerstin B., Dratva, Lisa M., Tuong, Zewen Kelvin, Clatworthy, Menna R., Teichmann, Sarah A.

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Gene-level alignment of single-cell trajectories von Sumanaweera, Dinithi, Suo, Chenqu, Cujba, Ana-Maria, Muraro, Daniele, Dann, Emma, Polanski, Krzysztof, Steemers, Alexander S, Lee, Woochan, Oliver, Amanda J, Park, Jong-Eun, Meyer, Kerstin B, Dumitrascu, Bianca, Teichmann, Sarah A

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Yolk sac cell atlas reveals multiorgan functions during human early development von Goh, Issac, Botting, Rachel A, Rose, Antony, Webb, Simone, Engelbert, Justin, Gitton, Yorick, Stephenson, Emily, Quiroga Londoño, Mariana, Mather, Michael, Mende, Nicole, Imaz-Rosshandler, Ivan, Yang, Lu, Horsfall, Dave, Basurto-Lozada, Daniela, Chipampe, Nana-Jane, Rook, Victoria, Lee, Jimmy Tsz Hang, Ton, Mai-Linh, Keitley, Daniel, Mazin, Pavel, Vijayabaskar, M S, Hannah, Rebecca, Gambardella, Laure, Green, Kile, Ballereau, Stephane, Inoue, Megumi, Tuck, Elizabeth, Lorenzi, Valentina, Kwakwa, Kwasi, Alsinet, Clara, Olabi, Bayanne, Miah, Mohi, Admane, Chloe, Popescu, Dorin-Mirel, Acres, Meghan, Dixon, David, Ness, Thomas, Coulthard, Rowen, Lisgo, Steven, Henderson, Deborah J, Dann, Emma, Suo, Chenqu, Kinston, Sarah J, Park, Jong-Eun, Polanski, Krzysztof, Marioni, John, van Dongen, Stijn, Meyer, Kerstin B, de Bruijn, Marella, Palis, James, Behjati, Sam, Laurenti, Elisa, Wilson, Nicola K, Vento-Tormo, Roser, Chédotal, Alain, Bayraktar, Omer, Roberts, Irene, Jardine, Laura, Göttgens, Berthold, Teichmann, Sarah A, Haniffa, Muzlifah

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Single-cell integration reveals metaplasia in inflammatory gut diseases von Oliver, Amanda J., Huang, Ni, Bartolome-Casado, Raquel, Li, Ruoyan, Koplev, Simon, Nilsen, Hogne R., Moy, Madelyn, Cakir, Batuhan, Polanski, Krzysztof, Gudiño, Victoria, Melón-Ardanaz, Elisa, Sumanaweera, Dinithi, Dimitrov, Daniel, Milchsack, Lisa Marie, FitzPatrick, Michael E. B., Provine, Nicholas M., Boccacino, Jacqueline M., Dann, Emma, Predeus, Alexander V., To, Ken, Prete, Martin, Chapman, Jonathan A., Masi, Andrea C., Stephenson, Emily, Engelbert, Justin, Lobentanzer, Sebastian, Perera, Shani, Richardson, Laura, Kapuge, Rakeshlal, Wilbrey-Clark, Anna, Semprich, Claudia I., Ellams, Sophie, Tudor, Catherine, Joseph, Philomeena, Garrido-Trigo, Alba, Corraliza, Ana M., Oliver, Thomas R. W., Hook, C. Elizabeth, James, Kylie R., Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Zilbauer, Matthias, Saez-Rodriguez, Julio, Høivik, Marte Lie, Bækkevold, Espen S., Stewart, Christopher J., Berrington, Janet E., Meyer, Kerstin B., Klenerman, Paul, Salas, Azucena, Haniffa, Muzlifah, Jahnsen, Frode L., Elmentaite, Rasa, Teichmann, Sarah A.

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A spatial human thymus cell atlas mapped to a continuous tissue axis von Yayon, Nadav, Kedlian, Veronika R., Boehme, Lena, Suo, Chenqu, Wachter, Brianna T., Beuschel, Rebecca T., Amsalem, Oren, Polanski, Krzysztof, Koplev, Simon, Tuck, Elizabeth, Dann, Emma, Van Hulle, Jolien, Perera, Shani, Putteman, Tom, Predeus, Alexander V., Dabrowska, Monika, Richardson, Laura, Tudor, Catherine, Kreins, Alexandra Y., Engelbert, Justin, Stephenson, Emily, Kleshchevnikov, Vitalii, De Rita, Fabrizio, Crossland, David, Bosticardo, Marita, Pala, Francesca, Prigmore, Elena, Chipampe, Nana-Jane, Prete, Martin, Fei, Lijiang, To, Ken, Barker, Roger A., He, Xiaoling, Van Nieuwerburgh, Filip, Bayraktar, Omer Ali, Patel, Minal, Davies, E Graham, Haniffa, Muzlifah A., Uhlmann, Virginie, Notarangelo, Luigi D., Germain, Ronald N., Radtke, Andrea J., Marioni, John C., Taghon, Tom, Teichmann, Sarah A.

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Circulating tumor DNA (ctDNA) to detect neuroendocrine prostate cancer genomic and DNA methylation changes von Beltran, Himisha, Romanel, Alessandro, Conteduca, Vincenza, Casiraghi, Nicola, Sigouros, Michael, Franceschini, Gian Marco, Fedrizzi, Tarcisio, Ku, sheng-Yu, Alonso, Alicia, Mosquera, Juan Miguel, Dann, Emma, Sboner, Andrea, Xiang, Jenny, Elemento, Olivier, Nanus, David M., Tagawa, Scott T., Benelli, Matteo, Demichelis, Francesca

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Yolk sac cell atlas reveals multiorgan functions during human early development von Goh, Issac, Botting, Rachel, Rose, Antony, Webb, Simone, Engelbert, Justin, Gitton, Yorick, Stephenson, Emily, Quiroga Londoño, Mariana, Mather, Michael, Mende, Nicole, Imaz-Rosshandler, Ivan, Yang, Lu, Horsfall, Dave, Basurto-Lozada, Daniela, Chipampe, Nana-Jane, Rook, Victoria, Lee, Jimmy Tsz Hang, Ton, Mai-Linh, Keitley, Daniel, Mazin, Pavel, Vijayabaskar, M., Hannah, Rebecca, Gambardella, Laure, Green, Kile, Ballereau, Stephane, Inoue, Megumi, Tuck, Elizabeth, Lorenzi, Valentina, Kwakwa, Kwasi, Alsinet, Clara, Olabi, Bayanne, Miah, Mohi, Admane, Chloe, Popescu, Dorin-Mirel, Acres, Meghan, Dixon, David, Ness, Thomas, Coulthard, Rowen, Lisgo, Steven, Henderson, Deborah, Dann, Emma, Suo, Chenqu, Kinston, Sarah, Park, Jong-Eun, Polanski, Krzysztof, Marioni, John, van Dongen, Stijn, Meyer, Kerstin, de Bruijn, Marella, Palis, James, Behjati, Sam, Laurenti, Elisa, Wilson, Nicola, Vento-Tormo, Roser, Chédotal, Alain, Bayraktar, Omer, Roberts, Irene, Jardine, Laura, Göttgens, Berthold, Teichmann, Sarah, Haniffa, Muzlifah

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scRNA GPLVM data von Dann, Emma

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