The Human Cell Atlas: from vision to reality von Rozenblatt-Rosen, Orit, Stubbington, Michael J. T., Regev, Aviv, Teichmann, Sarah A.

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Single-cell transcriptomics to explore the immune system in health and disease von Stubbington, Michael J. T., Rozenblatt-Rosen, Orit, Regev, Aviv, Teichmann, Sarah A.

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T cell fate and clonality inference from single-cell transcriptomes von Stubbington, Michael J T, Lönnberg, Tapio, Proserpio, Valentina, Clare, Simon, Speak, Anneliese O, Dougan, Gordon, Teichmann, Sarah A

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Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA) von Schattgen, Stefan A., Guion, Kate, Crawford, Jeremy Chase, Souquette, Aisha, Barrio, Alvaro Martinez, Stubbington, Michael J. T., Thomas, Paul G., Bradley, Philip

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Decoding human fetal liver haematopoiesis von Popescu, Dorin-Mirel, Botting, Rachel A., Stephenson, Emily, Green, Kile, Webb, Simone, Jardine, Laura, Calderbank, Emily F., Polanski, Krzysztof, Goh, Issac, Efremova, Mirjana, Acres, Meghan, Maunder, Daniel, Vegh, Peter, Gitton, Yorick, Park, Jong-Eun, Vento-Tormo, Roser, Miao, Zhichao, Dixon, David, Rowell, Rachel, McDonald, David, Fletcher, James, Poyner, Elizabeth, Reynolds, Gary, Mather, Michael, Moldovan, Corina, Mamanova, Lira, Greig, Frankie, Young, Matthew D., Meyer, Kerstin B., Lisgo, Steven, Bacardit, Jaume, Fuller, Andrew, Millar, Ben, Innes, Barbara, Lindsay, Susan, Stubbington, Michael J. T., Kowalczyk, Monika S., Li, Bo, Ashenberg, Orr, Tabaka, Marcin, Dionne, Danielle, Tickle, Timothy L., Slyper, Michal, Rozenblatt-Rosen, Orit, Filby, Andrew, Carey, Peter, Villani, Alexandra-Chloé, Roy, Anindita, Regev, Aviv, Chédotal, Alain, Roberts, Irene, Göttgens, Berthold, Behjati, Sam, Laurenti, Elisa, Teichmann, Sarah A., Haniffa, Muzlifah

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Aging increases cell-to-cell transcriptional variability upon immune stimulation von Martinez-Jimenez, Celia Pilar, Eling, Nils, Chen, Hung-Chang, Vallejos, Catalina A., Kolodziejczyk, Aleksandra A., Connor, Frances, Stojic, Lovorka, Rayner, Timothy F., Stubbington, Michael J. T., Teichmann, Sarah A., de la Roche, Maike, Marioni, John C., Odom, Duncan T.

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Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types von Carmona, Santiago J, Teichmann, Sarah A, Ferreira, Lauren, Macaulay, Iain C, Stubbington, Michael J T, Cvejic, Ana, Gfeller, David

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Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE von Wu, Yee Ling, Stubbington, Michael J T, Daly, Maria, Teichmann, Sarah A, Rada, Cristina

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Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation von Hegazy, Ahmed N., West, Nathaniel R., Stubbington, Michael J.T., Wendt, Emily, Suijker, Kim I.M., Datsi, Angeliki, This, Sebastien, Danne, Camille, Campion, Suzanne, Duncan, Sylvia H., Owens, Benjamin M.J., Uhlig, Holm H., McMichael, Andrew, Bergthaler, Andreas, Teichmann, Sarah A., Keshav, Satish, Powrie, Fiona

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Single-cell reconstruction of the early maternal–fetal interface in humans von Vento-Tormo, Roser, Efremova, Mirjana, Botting, Rachel A., Turco, Margherita Y., Vento-Tormo, Miquel, Meyer, Kerstin B., Park, Jong-Eun, Stephenson, Emily, Polański, Krzysztof, Goncalves, Angela, Gardner, Lucy, Holmqvist, Staffan, Henriksson, Johan, Zou, Angela, Sharkey, Andrew M., Millar, Ben, Innes, Barbara, Wood, Laura, Wilbrey-Clark, Anna, Payne, Rebecca P., Ivarsson, Martin A., Lisgo, Steve, Filby, Andrew, Rowitch, David H., Bulmer, Judith N., Wright, Gavin J., Stubbington, Michael J. T., Haniffa, Muzlifah, Moffett, Ashley, Teichmann, Sarah A.

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Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination von Bolland, Daniel J., Koohy, Hashem, Wood, Andrew L., Matheson, Louise S., Krueger, Felix, Stubbington, Michael J.T., Baizan-Edge, Amanda, Chovanec, Peter, Stubbs, Bryony A., Tabbada, Kristina, Andrews, Simon R., Spivakov, Mikhail, Corcoran, Anne E.

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BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq von Lindeman, Ida, Emerton, Guy, Mamanova, Lira, Snir, Omri, Polanski, Krzysztof, Qiao, Shuo-Wang, Sollid, Ludvig M., Teichmann, Sarah A., Stubbington, Michael J. T.

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Single-cell analysis at the threshold von Chen, Xi, Love, J Christopher, Navin, Nicholas E, Pachter, Lior, Stubbington, Michael J T, Svensson, Valentine, Sweedler, Jonathan V, Teichmann, Sarah A

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The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding von Xie, Xin, Stubbington, Michael J T, Nissen, Jesper K, Andersen, Kristian G, Hebenstreit, Daniel, Teichmann, Sarah A, Betz, Alexander G

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scHLAcount: allele-specific HLA expression from single-cell gene expression data von Darby, Charlotte A, Stubbington, Michael J T, Marks, Patrick J, Martínez Barrio, Álvaro, Fiddes, Ian T

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The Human Cell Atlas: Technical approaches and challenges von Hon, Chung-Chau, Shin, Jay W, Carninci, Piero, Stubbington, Michael J T

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Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes von Mielczarek, Olga, Rogers, Carolyn H., Zhan, Yinxiu, Matheson, Louise S., Stubbington, Michael J.T., Schoenfelder, Stefan, Bolland, Daniel J., Javierre, Biola M., Wingett, Steven W., Várnai, Csilla, Segonds-Pichon, Anne, Conn, Simon J., Krueger, Felix, Andrews, Simon, Fraser, Peter, Giorgetti, Luca, Corcoran, Anne E.

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Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes von Hurtado, Jonathan, Rogers, Thomas F., Jaffe, David B., Adams, Bruce A., Bangaru, Sandhya, Garcia, Elijah, Capozzola, Tazio, Messmer, Terrence, Sharma, Pragati, Song, Ge, Beutler, Nathan, He, Wanting, Dueker, Katharina, Musharrafieh, Rami, Burbach, Sarah, Truong, Alina, Stubbington, Michael J.T., Burton, Dennis R., Andrabi, Raiees, Ward, Andrew B., McDonnell, Wyatt J., Briney, Bryan

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Single‐cell immune profiling reveals new insights into colorectal cancer von Lönnberg, Tapio, Stubbington, Michael JT

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Transcriptional profiling of human Vδ1 T cells reveals a pathogen-driven adaptive differentiation program von McMurray, Jack L., von Borstel, Anouk, Taher, Taher E., Syrimi, Eleni, Taylor, Graham S., Sharif, Maria, Rossjohn, Jamie, Remmerswaal, Ester B.M., Bemelman, Frederike J., Vieira Braga, Felipe A., Chen, Xi, Teichmann, Sarah A., Mohammed, Fiyaz, Berry, Andrea A., Lyke, Kirsten E., Williamson, Kim C., Stubbington, Michael J.T., Davey, Martin S., Willcox, Carrie R., Willcox, Benjamin E.

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