Cell2location maps fine-grained cell types in spatial transcriptomics
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
Published in Nature biotechnology (01.05.2022)
Published in Nature biotechnology (01.05.2022)
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Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE
Missarova, Alsu, Dann, Emma, Rosen, Leah, Satija, Rahul, Marioni, John
Published in Genome Biology (18.07.2024)
Published in Genome Biology (18.07.2024)
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Mapping the developing human immune system across organs
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
Published in Science (American Association for the Advancement of Science) (03.06.2022)
Published in Science (American Association for the Advancement of Science) (03.06.2022)
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Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer
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
Published in The Journal of clinical investigation (01.04.2020)
Published in The Journal of clinical investigation (01.04.2020)
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Differential abundance testing on single-cell data using k-nearest neighbor graphs
Dann, Emma, Henderson, Neil C., Teichmann, Sarah A., Morgan, Michael D., Marioni, John C.
Published in Nature biotechnology (01.02.2022)
Published in Nature biotechnology (01.02.2022)
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Puccia, Brittany, Puccia, Brittany, Magni, Katherine, Worrell, Jane, Dann, Emma
Published in Oncology nursing forum (01.03.2023)
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Published in Oncology nursing forum (01.03.2023)
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Best practices for single-cell analysis across modalities
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.
Published in Nature reviews. Genetics (01.08.2023)
Published in Nature reviews. Genetics (01.08.2023)
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Cells of the human intestinal tract mapped across space and time
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.
Published in Nature (London) (09.09.2021)
Published in Nature (London) (09.09.2021)
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A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
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.
Published in Cell (08.12.2022)
Published in Cell (08.12.2022)
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Precise identification of cell states altered in disease using healthy single-cell references
Dann, Emma, Cujba, Ana-Maria, Oliver, Amanda J., Meyer, Kerstin B., Teichmann, Sarah A., Marioni, John C.
Published in Nature genetics (01.11.2023)
Published in Nature genetics (01.11.2023)
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Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins
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.
Published in Nature biotechnology (01.01.2024)
Published in Nature biotechnology (01.01.2024)
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Blood and immune development in human fetal bone marrow and Down syndrome
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
Published in Nature (London) (14.10.2021)
Published in Nature (London) (14.10.2021)
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Llewellyn, Elizabeth, Magni, Katherine, Kosiba, Anna, Dann, Emma, Nixon, Janet, Jabaley, Terri
Published in Oncology nursing forum (01.03.2022)
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Published in Oncology nursing forum (01.03.2022)
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Gene-level alignment of single-cell trajectories
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
Published in Nature methods (19.09.2024)
Published in Nature methods (19.09.2024)
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Yolk sac cell atlas reveals multiorgan functions during human early development
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
Published in Science (American Association for the Advancement of Science) (18.08.2023)
Published in Science (American Association for the Advancement of Science) (18.08.2023)
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Journal Article
Circulating tumor DNA (ctDNA) to detect neuroendocrine prostate cancer genomic and DNA methylation changes
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
Published in Journal of clinical oncology (20.02.2020)
Published in Journal of clinical oncology (20.02.2020)
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Journal Article
Yolk sac cell atlas reveals multiorgan functions during human early development
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
Published in Science (American Association for the Advancement of Science) (18.08.2023)
Published in Science (American Association for the Advancement of Science) (18.08.2023)
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Early human lung immune cell development and its role in epithelial cell fate
Barnes, Josephine L, Yoshida, Masahiro, He, Peng, Worlock, Kaylee B, Lindeboom, Rik G H, Suo, Chenqu, Pett, J Patrick, Wilbrey-Clark, Anna, Dann, Emma, Mamanova, Lira, Richardson, Laura, Polanski, Krzysztof, Pennycuick, Adam, Allen-Hyttinen, Jessica, Herczeg, Iván T, Arzili, Romina, Hynds, Robert E, Teixeira, Vitor H, Haniffa, Muzlifah, Lim, Kyungtae, Sun, Dawei, Rawlins, Emma L, Oliver, Amanda J, Lyons, Paul A, Marioni, John C, Ruhrberg, Christiana, Tuong, Zewen Kelvin, Clatworthy, Menna R, Reading, James L, Janes, Sam M, Teichmann, Sarah A, Meyer, Kerstin B, Nikolić, Marko Z
Published in Science immunology (15.12.2023)
Published in Science immunology (15.12.2023)
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Sensitive cluster-free differential expression testing
Missarova, Alsu, Dann, Emma, Rosen, Leah, Satija, Rahul, Marioni, John
Published in bioRxiv (10.03.2023)
Published in bioRxiv (10.03.2023)
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