Current best practices in single‐cell RNA‐seq analysis: a tutorial von Luecken, Malte D, Theis, Fabian J

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Benchmarking atlas-level data integration in single-cell genomics von Luecken, Malte D., Büttner, M., Chaichoompu, K., Danese, A., Interlandi, M., Mueller, M. F., Strobl, D. C., Zappia, L., Dugas, M., Colomé-Tatché, M., Theis, Fabian J.

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Mapping single-cell data to reference atlases by transfer learning von Lotfollahi, Mohammad, Naghipourfar, Mohsen, Luecken, Malte D., Khajavi, Matin, Büttner, Maren, Wagenstetter, Marco, Avsec, Žiga, Gayoso, Adam, Yosef, Nir, Interlandi, Marta, Rybakov, Sergei, Misharin, Alexander V., Theis, Fabian J.

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Primary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease von Schmidt, Sebastian, Luecken, Malte D., Trümbach, Dietrich, Hembach, Sina, Niedermeier, Kristina M., Wenck, Nicole, Pflügler, Klaus, Stautner, Constantin, Böttcher, Anika, Lickert, Heiko, Ramirez-Suastegui, Ciro, Ahmad, Ruhel, Ziller, Michael J., Fitzgerald, Julia C., Ruf, Viktoria, van de Berg, Wilma D. J., Jonker, Allert J., Gasser, Thomas, Winner, Beate, Winkler, Jürgen, Vogt Weisenhorn, Daniela M., Giesert, Florian, Theis, Fabian J., Wurst, Wolfgang

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Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage von Lutz, Konstantin, Musumeci, Andrea, Sie, Christopher, Dursun, Ezgi, Winheim, Elena, Bagnoli, Johannes, Ziegenhain, Christoph, Rausch, Lisa, Bergen, Volker, Luecken, Malte D., Oostendorp, Robert A. J., Schraml, Barbara U., Theis, Fabian J., Enard, Wolfgang, Korn, Thomas, Krug, Anne B.

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A reversible state of hypometabolism in a human cellular model of sporadic Parkinson’s disease von Schmidt, Sebastian, Stautner, Constantin, Vu, Duc Tung, Heinz, Alexander, Regensburger, Martin, Karayel, Ozge, Trümbach, Dietrich, Artati, Anna, Kaltenhäuser, Sabine, Nassef, Mohamed Zakaria, Hembach, Sina, Steinert, Letyfee, Winner, Beate, Jürgen, Winkler, Jastroch, Martin, Luecken, Malte D., Theis, Fabian J., Westmeyer, Gil Gregor, Adamski, Jerzy, Mann, Matthias, Hiller, Karsten, Giesert, Florian, Vogt Weisenhorn, Daniela M., Wurst, Wolfgang

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The scverse project provides a computational ecosystem for single-cell omics data analysis von Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe'er, Dana, Regev, Aviv, Teichmann, Sarah A, Finotello, Francesca, Wolf, F Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J

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Probe set selection for targeted spatial transcriptomics von Kuemmerle, Louis B., Luecken, Malte D., Firsova, Alexandra B., Barros de Andrade e Sousa, Lisa, Straßer, Lena, Mekki, Ilhem Isra, Campi, Francesco, Heumos, Lukas, Shulman, Maiia, Beliaeva, Valentina, Hediyeh-Zadeh, Soroor, Schaar, Anna C., Mahbubani, Krishnaa T., Sountoulidis, Alexandros, Balassa, Tamás, Kovacs, Ferenc, Horvath, Peter, Piraud, Marie, Ertürk, Ali, Samakovlis, Christos, Theis, Fabian J.

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A Roadmap for a Consensus Human Skin Cell Atlas and Single-Cell Data Standardization von Almet, Axel A, Yuan, Hao, Annusver, Karl, Ramos, Raul, Liu, Yingzi, Wiedemann, Julie, Sorkin, Dara H, Landén, Ning Xu, Sonkoly, Enikö, Haniffa, Muzlifah, Nie, Qing, Lichtenberger, Beate M, Luecken, Malte D, Andersen, Bogi, Tsoi, Lam C, Watt, Fiona M, Gudjonsson, Johann E, Plikus, Maksim V, Kasper, Maria

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Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice von Aliluev, Alexandra, Tritschler, Sophie, Sterr, Michael, Oppenländer, Lena, Hinterdobler, Julia, Greisle, Tobias, Irmler, Martin, Beckers, Johannes, Sun, Na, Walch, Axel, Stemmer, Kerstin, Kindt, Alida, Krumsiek, Jan, Tschöp, Matthias H., Luecken, Malte D., Theis, Fabian J., Lickert, Heiko, Böttcher, Anika

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Synthetic enforcement of STING signaling in cancer cells appropriates the immune microenvironment for checkpoint inhibitor therapy von Vornholz, Larsen, Isay, Sophie E, Kurgyis, Zsuzsanna, Strobl, Daniel C, Loll, Patricia, Mosa, Mohammed H, Luecken, Malte D, Sterr, Michael, Lickert, Heiko, Winter, Christof, Greten, Florian R, Farin, Henner F, Theis, Fabian J, Ruland, Jürgen

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Early life adversity shapes social subordination and cell type-specific transcriptomic patterning in the ventral hippocampus von Kos, Aron, Lopez, Juan Pablo, Bordes, Joeri, de Donno, Carlo, Dine, Julien, Brivio, Elena, Karamihalev, Stoyo, Luecken, Malte D, Almeida-Correa, Suellen, Gasperoni, Serena, Dick, Alec, Miranda, Lucas, Büttner, Maren, Stoffel, Rainer, Flachskamm, Cornelia, Theis, Fabian J, Schmidt, Mathias V, Chen, Alon

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A cellular reference atlas of the human lung

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SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis von Wendisch, Daniel, Dietrich, Oliver, Mari, Tommaso, von Stillfried, Saskia, Ibarra, Ignacio L., Mittermaier, Mirja, Mache, Christin, Chua, Robert Lorenz, Knoll, Rainer, Timm, Sara, Brumhard, Sophia, Krammer, Tobias, Zauber, Henrik, Hiller, Anna Luisa, Pascual-Reguant, Anna, Mothes, Ronja, Bülow, Roman David, Schulze, Jessica, Leipold, Alexander M., Djudjaj, Sonja, Erhard, Florian, Geffers, Robert, Pott, Fabian, Kazmierski, Julia, Radke, Josefine, Pergantis, Panagiotis, Baßler, Kevin, Conrad, Claudia, Aschenbrenner, Anna C., Sawitzki, Birgit, Landthaler, Markus, Wyler, Emanuel, Horst, David, Hippenstiel, Stefan, Hocke, Andreas, Heppner, Frank L., Uhrig, Alexander, Garcia, Carmen, Machleidt, Felix, Herold, Susanne, Elezkurtaj, Sefer, Thibeault, Charlotte, Witzenrath, Martin, Cochain, Clément, Suttorp, Norbert, Drosten, Christian, Goffinet, Christine, Kurth, Florian, Schultze, Joachim L., Radbruch, Helena, Ochs, Matthias, Eils, Roland, Müller-Redetzky, Holger, Hauser, Anja E., Luecken, Malte D., Theis, Fabian J., Conrad, Christian, Wolff, Thorsten, Boor, Peter, Selbach, Matthias, Saliba, Antoine-Emmanuel, Sander, Leif Erik

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Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2 von Lopez, Juan Pablo, Lücken, Malte D, Brivio, Elena, Karamihalev, Stoyo, Kos, Aron, De Donno, Carlo, Benjamin, Asaf, Yang, Huanqing, Dick, Alec L W, Stoffel, Rainer, Flachskamm, Cornelia, Ressle, Andrea, Roeh, Simone, Huettl, Rosa-Eva, Parl, Andrea, Eggert, Carola, Novak, Bozidar, Yan, Yu, Yeoh, Karin, Holzapfel, Maria, Hauger, Barbara, Harbich, Daniela, Schmid, Bianca, Di Giaimo, Rossella, Turck, Christoph W, Schmidt, Mathias V, Deussing, Jan M, Eder, Matthias, Dine, Julien, Theis, Fabian J, Chen, Alon

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Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis von Lang, Niklas J, Gote-Schniering, Janine, Porras-Gonzalez, Diana, Yang, Lin, De Sadeleer, Laurens J, Jentzsch, R. Christoph, Shitov, Vladimir A, Zhou, Shuhong, Ansari, Meshal, Agami, Ahmed, Mayr, Christoph H, Hooshiar Kashani, Baharak, Chen, Yuexin, Heumos, Lukas, Pestoni, Jeanine C, Molnar, Eszter Sarolta, Geeraerts, Emiel, Anquetil, Vincent, Saniere, Laurent, Woegrath, Melanie, Gerckens, Michael, Lehmann, Mareike, Yildirim, Ali Onder, Hatz, Rudolf, Kneidinger, Nikolaus, Behr, Juergen, Wuyts, Wim A, Stoleriu, Mircea-Gabriel, Luecken, Malte D, Theis, Fabian J, Burgstaller, Gerald, Schiller, Herbert B

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The scverse project provides a computational ecosystem for single-cell omics data analysis von Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe’er, Dana, Regev, Aviv, Teichmann, Sarah A., Finotello, Francesca, Wolf, F. Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J.

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Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation von Baßler, Kevin, Fujii, Wataru, Kapellos, Theodore S, Dudkin, Erika, Reusch, Nico, Horne, Ari, Reiz, Benedikt, Luecken, Malte D, Osei-Sarpong, Collins, Warnat-Herresthal, Stefanie, Bonaguro, Lorenzo, Schulte-Schrepping, Jonas, Wagner, Allon, Günther, Patrick, Pizarro, Carmen, Schreiber, Tina, Knoll, Rainer, Holsten, Lisa, Kröger, Charlotte, De Domenico, Elena, Becker, Matthias, Händler, Kristian, Wohnhaas, Christian T, Baumgartner, Florian, Köhler, Meike, Theis, Heidi, Kraut, Michael, Wadsworth, 2nd, Marc H, Hughes, Travis K, Ferreira, Humberto J, Hinkley, Emily, Kaltheuner, Ines H, Geyer, Matthias, Thiele, Christoph, Shalek, Alex K, Feißt, Andreas, Thomas, Daniel, Dickten, Henning, Beyer, Marc, Baum, Patrick, Yosef, Nir, Aschenbrenner, Anna C, Ulas, Thomas, Hasenauer, Jan, Theis, Fabian J, Skowasch, Dirk, Schultze, Joachim L

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IF and SCRINSHOT image data of probe set selection for targeted spatial transcriptomics von Kuemmerle, Louis B.

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Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage von Lutz, Konstantin, Musumeci, Andrea, Sie, Christopher, Dursun, Ezgi, Winheim, Elena, Bagnoli, Johannes, Ziegenhain, Christoph, Rausch, Lisa, Bergen, Volker, Luecken, Malte D, Oostendorp, Robert A. J, Schraml, Barbara U, Theis, Fabian J, Enard, Wolfgang, Korn, Thomas, Krug, Anne B

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