Single-cell RNA-seq denoising using a deep count autoencoder von Eraslan, Gökcen, Simon, Lukas M., Mircea, Maria, Mueller, Nikola S., Theis, Fabian J.

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A cellular census of human lungs identifies novel cell states in health and in asthma von Vieira Braga, Felipe A., Kar, Gozde, Berg, Marijn, Carpaij, Orestes A., Polanski, Krzysztof, Simon, Lukas M., Brouwer, Sharon, Gomes, Tomás, Hesse, Laura, Jiang, Jian, Fasouli, Eirini S., Efremova, Mirjana, Vento-Tormo, Roser, Talavera-López, Carlos, Jonker, Marnix R., Affleck, Karen, Palit, Subarna, Strzelecka, Paulina M., Firth, Helen V., Mahbubani, Krishnaa T., Cvejic, Ana, Meyer, Kerstin B., Saeb-Parsy, Kourosh, Luinge, Marjan, Brandsma, Corry-Anke, Timens, Wim, Angelidis, Ilias, Strunz, Maximilian, Koppelman, Gerard H., van Oosterhout, Antoon J., Schiller, Herbert B., Theis, Fabian J., van den Berge, Maarten, Nawijn, Martijn C., Teichmann, Sarah A.

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An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics von Angelidis, Ilias, Simon, Lukas M., Fernandez, Isis E., Strunz, Maximilian, Mayr, Christoph H., Greiffo, Flavia R., Tsitsiridis, George, Ansari, Meshal, Graf, Elisabeth, Strom, Tim-Matthias, Nagendran, Monica, Desai, Tushar, Eickelberg, Oliver, Mann, Matthias, Theis, Fabian J., Schiller, Herbert B.

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Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis von Strunz, Maximilian, Simon, Lukas M., Ansari, Meshal, Kathiriya, Jaymin J., Angelidis, Ilias, Mayr, Christoph H., Tsidiridis, George, Lange, Marius, Mattner, Laura F., Yee, Min, Ogar, Paulina, Sengupta, Arunima, Kukhtevich, Igor, Schneider, Robert, Zhao, Zhongming, Voss, Carola, Stoeger, Tobias, Neumann, Jens H. L., Hilgendorff, Anne, Behr, Jürgen, O’Reilly, Michael, Lehmann, Mareike, Burgstaller, Gerald, Königshoff, Melanie, Chapman, Harold A., Theis, Fabian J., Schiller, Herbert B.

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The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease von Schiller, Herbert B, Montoro, Daniel T, Simon, Lukas M, Rawlins, Emma L, Meyer, Kerstin B, Strunz, Maximilian, Vieira Braga, Felipe A, Timens, Wim, Koppelman, Gerard H, Budinger, G R Scott, Burgess, Janette K, Waghray, Avinash, van den Berge, Maarten, Theis, Fabian J, Regev, Aviv, Kaminski, Naftali, Rajagopal, Jayaraj, Teichmann, Sarah A, Misharin, Alexander V, Nawijn, Martijn C

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EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells von Neelakantan, Deepika, Zhou, Hengbo, Oliphant, Michael U. J., Zhang, Xiaomei, Simon, Lukas M., Henke, David M., Shaw, Chad A., Wu, Meng-Fen, Hilsenbeck, Susan G., White, Lisa D., Lewis, Michael T., Ford, Heide L.

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The spliceosome is a therapeutic vulnerability in MYC-driven cancer von Hsu, Tiffany Y.-T., Simon, Lukas M., Neill, Nicholas J., Marcotte, Richard, Sayad, Azin, Bland, Christopher S., Echeverria, Gloria V., Sun, Tingting, Kurley, Sarah J., Tyagi, Siddhartha, Karlin, Kristen L., Dominguez-Vidaña, Rocio, Hartman, Jessica D., Renwick, Alexander, Scorsone, Kathleen, Bernardi, Ronald J., Skinner, Samuel O., Jain, Antrix, Orellana, Mayra, Lagisetti, Chandraiah, Golding, Ido, Jung, Sung Y., Neilson, Joel R., Zhang, Xiang H.-F., Cooper, Thomas A., Webb, Thomas R., Neel, Benjamin G., Shaw, Chad A., Westbrook, Thomas F.

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A paradox of transcriptional and functional innate interferon responses of human intestinal enteroids to enteric virus infection von Saxena, Kapil, Simon, Lukas M., Zeng, Xi-Lei, Blutt, Sarah E., Crawford, Sue E., Sastri, Narayan P., Karandikar, Umesh C., Ajami, Nadim J., Zachos, Nicholas C., Kovbasnjuk, Olga, Donowitz, Mark, Conner, Margaret E., Shaw, Chad A., Estes, Mary K.

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Racial differences in human platelet PAR4 reactivity reflect expression of PCTP and miR-376c von Edelstein, Leonard C, Simon, Lukas M, Montoya, Raúl Teruel, Holinstat, Michael, Chen, Edward S, Bergeron, Angela, Kong, Xianguo, Nagalla, Srikanth, Mohandas, Narla, Cohen, David E, Dong, Jing-fei, Shaw, Chad, Bray, Paul F

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Single-cell multiomics decodes regulatory programs for mouse secondary palate development von Yan, Fangfang, Suzuki, Akiko, Iwaya, Chihiro, Pei, Guangsheng, Chen, Xian, Yoshioka, Hiroki, Yu, Meifang, Simon, Lukas M., Iwata, Junichi, Zhao, Zhongming

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Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers von Mayr, Christoph H, Simon, Lukas M, Leuschner, Gabriela, Ansari, Meshal, Schniering, Janine, Geyer, Philipp E, Angelidis, Ilias, Strunz, Maximilian, Singh, Pawandeep, Kneidinger, Nikolaus, Reichenberger, Frank, Silbernagel, Edith, Böhm, Stephan, Adler, Heiko, Lindner, Michael, Maurer, Britta, Hilgendorff, Anne, Prasse, Antje, Behr, Jürgen, Mann, Matthias, Eickelberg, Oliver, Theis, Fabian J, Schiller, Herbert B

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Common variants in the human platelet PAR4 thrombin receptor alter platelet function and differ by race von Edelstein, Leonard C., Simon, Lukas M., Lindsay, Cory R., Kong, Xianguo, Teruel-Montoya, Raúl, Tourdot, Benjamin E., Chen, Edward S., Ma, Lin, Coughlin, Shaun, Nieman, Marvin, Holinstat, Michael, Shaw, Chad A., Bray, Paul F.

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MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data von Wang, Mingqiang, Deng, Wankun, Samuels, David C, Zhao, Zhongming, Simon, Lukas M

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CELF1 is a central node in post-transcriptional regulatory programmes underlying EMT von Chaudhury, Arindam, Cheema, Shebna, Fachini, Joseph M., Kongchan, Natee, Lu, Guojun, Simon, Lukas M., Wang, Tao, Mao, Sufeng, Rosen, Daniel G., Ittmann, Michael M., Hilsenbeck, Susan G., Shaw, Chad A., Neilson, Joel R.

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Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2 von Simon, Lukas M., Chen, Edward S., Edelstein, Leonard C., Kong, Xianguo, Bhatlekar, Seema, Rigoutsos, Isidore, Bray, Paul F., Shaw, Chad A.

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DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development von Dai, Yulin, Itai, Toshiyuki, Pei, Guangsheng, Yan, Fangfang, Chu, Yan, Jiang, Xiaoqian, Weinberg, Seth M., Mukhopadhyay, Nandita, Marazita, Mary L., Simon, Lukas M., Jia, Peilin, Zhao, Zhongming

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Microbial fingerprints reveal interaction between museum objects, curators, and visitors von Simon, Lukas M., Flocco, Cecilia, Burkart, Franziska, Methner, Anika, Henke, David, Rauer, Luise, Müller, Christian L., Vogel, Johannes, Quaisser, Christiane, Overmann, Jörg, Simon, Stefan

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Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts von Itai, Toshiyuki, Yan, Fangfang, Liu, Andi, Dai, Yulin, Iwaya, Chihiro, Curtis, Sarah W., Leslie, Elizabeth J., Simon, Lukas M., Jia, Peilin, Chen, Xiangning, Iwata, Junichi, Zhao, Zhongming

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The HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma von Yan, Fangfang, Jiang, Vivian, Jordan, Alexa, Che, Yuxuan, Liu, Yang, Cai, Qingsong, Xue, Yu, Li, Yijing, McIntosh, Joseph, Chen, Zhihong, Vargas, Jovanny, Nie, Lei, Yao, Yixin, Lee, Heng-Huan, Wang, Wei, Bigcal, JohnNelson R, Badillo, Maria, Meena, Jitendra, Flowers, Christopher, Zhou, Jia, Zhao, Zhongming, Simon, Lukas M, Wang, Michael

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Publisher Correction: EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells von Neelakantan, Deepika, Zhou, Hengbo, Oliphant, Michael U. J., Zhang, Xiaomei, Simon, Lukas M., Henke, David M., Shaw, Chad A., Wu, Meng-Fen, Hilsenbeck, Susan G., White, Lisa D., Lewis, Michael T., Ford, Heide L.

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