Lineage tracing meets single-cell omics: opportunities and challenges von Wagner, Daniel E., Klein, Allon M.

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SPRING: a kinetic interface for visualizing high dimensional single-cell expression data von Weinreb, Caleb, Wolock, Samuel, Klein, Allon M

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Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells von Klein, Allon M., Mazutis, Linas, Akartuna, Ilke, Tallapragada, Naren, Veres, Adrian, Li, Victor, Peshkin, Leonid, Weitz, David A., Kirschner, Marc W.

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Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data von Wolock, Samuel L., Lopez, Romain, Klein, Allon M.

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Lineage tracing on transcriptional landscapes links state to fate during differentiation von Weinreb, Caleb, Rodriguez-Fraticelli, Alejo, Camargo, Fernando D., Klein, Allon M.

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The emergence of transcriptional identity in somatosensory neurons von Sharma, Nikhil, Flaherty, Kali, Lezgiyeva, Karina, Wagner, Daniel E., Klein, Allon M., Ginty, David D.

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Tumor-infiltrating dendritic cell states are conserved across solid human cancers von Gerhard, Genevieve M., Bill, Ruben, Messemaker, Marius, Klein, Allon M., Pittet, Mikael J.

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A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte von Plasschaert, Lindsey W., Žilionis, Rapolas, Choo-Wing, Rayman, Savova, Virginia, Knehr, Judith, Roma, Guglielmo, Klein, Allon M., Jaffe, Aron B.

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Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo von Wagner, Daniel E, Weinreb, Caleb, Collins, Zach M, Briggs, James A, Megason, Sean G, Klein, Allon M

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Fundamental limits on dynamic inference from single-cell snapshots von Weinreb, Caleb, Wolock, Samuel, Tusi, Betsabeh K., Socolovsky, Merav, Klein, Allon M.

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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain von Raj, Bushra, Wagner, Daniel E, McKenna, Aaron, Pandey, Shristi, Klein, Allon M, Shendure, Jay, Gagnon, James A, Schier, Alexander F

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The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution von Briggs, James A, Weinreb, Caleb, Wagner, Daniel E, Megason, Sean, Peshkin, Leonid, Kirschner, Marc W, Klein, Allon M

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Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species von Zilionis, Rapolas, Engblom, Camilla, Pfirschke, Christina, Savova, Virginia, Zemmour, David, Saatcioglu, Hatice D., Krishnan, Indira, Maroni, Giorgia, Meyerovitz, Claire V., Kerwin, Clara M., Choi, Sun, Richards, William G., De Rienzo, Assunta, Tenen, Daniel G., Bueno, Raphael, Levantini, Elena, Pittet, Mikael J., Klein, Allon M.

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Universal patterns of stem cell fate in cycling adult tissues von Klein, Allon M, Simons, Benjamin D

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A comprehensive single cell transcriptional landscape of human hematopoietic progenitors von Pellin, Danilo, Loperfido, Mariana, Baricordi, Cristina, Wolock, Samuel L., Montepeloso, Annita, Weinberg, Olga K., Biffi, Alessandra, Klein, Allon M., Biasco, Luca

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Population snapshots predict early haematopoietic and erythroid hierarchies von Tusi, Betsabeh Khoramian, Wolock, Samuel L., Weinreb, Caleb, Hwang, Yung, Hidalgo, Daniel, Zilionis, Rapolas, Waisman, Ari, Huh, Jun R., Klein, Allon M., Socolovsky, Merav

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Clonal analysis of lineage fate in native haematopoiesis von Rodriguez-Fraticelli, Alejo E., Wolock, Samuel L., Weinreb, Caleb S., Panero, Riccardo, Patel, Sachin H., Jankovic, Maja, Sun, Jianlong, Calogero, Raffaele A., Klein, Allon M., Camargo, Fernando D.

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A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure von Baron, Maayan, Veres, Adrian, Wolock, Samuel L., Faust, Aubrey L., Gaujoux, Renaud, Vetere, Amedeo, Ryu, Jennifer Hyoje, Wagner, Bridget K., Shen-Orr, Shai S., Klein, Allon M., Melton, Douglas A., Yanai, Itai

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Homeostatic Epidermal Stem Cell Self-Renewal Is Driven by Local Differentiation von Mesa, Kailin R., Kawaguchi, Kyogo, Cockburn, Katie, Gonzalez, David, Boucher, Jonathan, Xin, Tianchi, Klein, Allon M., Greco, Valentina

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On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development von Peshkin, Leonid, Wühr, Martin, Pearl, Esther, Haas, Wilhelm, Freeman, Robert M., Gerhart, John C., Klein, Allon M., Horb, Marko, Gygi, Steven P., Kirschner, Marc W.

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