The triumphs and limitations of computational methods for scRNA-seq von Kharchenko, Peter V.

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Bayesian approach to single-cell differential expression analysis von Kharchenko, Peter V, Silberstein, Lev, Scadden, David T

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Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing von Usoskin, Dmitry, Furlan, Alessandro, Islam, Saiful, Abdo, Hind, Lönnerberg, Peter, Lou, Daohua, Hjerling-Leffler, Jens, Haeggström, Jesper, Kharchenko, Olga, Kharchenko, Peter V, Linnarsson, Sten, Ernfors, Patrik

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Cell segmentation in imaging-based spatial transcriptomics von Petukhov, Viktor, Xu, Rosalind J., Soldatov, Ruslan A., Cadinu, Paolo, Khodosevich, Konstantin, Moffitt, Jeffrey R., Kharchenko, Peter V.

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RNA velocity—current challenges and future perspectives von Bergen, Volker, Soldatov, Ruslan A, Kharchenko, Peter V, Theis, Fabian J

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Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain von Kupari, Jussi, Usoskin, Dmitry, Parisien, Marc, Lou, Daohua, Hu, Yizhou, Fatt, Michael, Lönnerberg, Peter, Spångberg, Mats, Eriksson, Bengt, Barkas, Nikolaos, Kharchenko, Peter V., Loré, Karin, Khoury, Samar, Diatchenko, Luda, Ernfors, Patrik

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Cell type ontologies of the Human Cell Atlas von Osumi-Sutherland, David, Xu, Chuan, Keays, Maria, Levine, Adam P., Kharchenko, Peter V., Regev, Aviv, Lein, Ed, Teichmann, Sarah A.

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Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain von Lake, Blue B, Chen, Song, Sos, Brandon C, Fan, Jean, Kaeser, Gwendolyn E, Yung, Yun C, Duong, Thu E, Gao, Derek, Chun, Jerold, Kharchenko, Peter V, Zhang, Kun

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Publisher Correction: The triumphs and limitations of computational methods for scRNA-seq von Kharchenko, Peter V.

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Design and analysis of ChIP-seq experiments for DNA-binding proteins von Kharchenko, Peter V, Park, Peter J, Tolstorukov, Michael Y

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Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis von Pfisterer, Ulrich, Petukhov, Viktor, Demharter, Samuel, Meichsner, Johanna, Thompson, Jonatan J., Batiuk, Mykhailo Y., Asenjo-Martinez, Andrea, Vasistha, Navneet A., Thakur, Ashish, Mikkelsen, Jens, Adorjan, Istvan, Pinborg, Lars H., Pers, Tune H., von Engelhardt, Jakob, Kharchenko, Peter V., Khodosevich, Konstantin

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Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth von Krivanek, Jan, Soldatov, Ruslan A., Kastriti, Maria Eleni, Chontorotzea, Tatiana, Herdina, Anna Nele, Petersen, Julian, Szarowska, Bara, Landova, Marie, Matejova, Veronika Kovar, Holla, Lydie Izakovicova, Kuchler, Ulrike, Zdrilic, Ivana Vidovic, Vijaykumar, Anushree, Balic, Anamaria, Marangoni, Pauline, Klein, Ophir D., Neves, Vitor C. M., Yianni, Val, Sharpe, Paul T., Harkany, Tibor, Metscher, Brian D., Bajénoff, Marc, Mina, Mina, Fried, Kaj, Kharchenko, Peter V., Adameyko, Igor

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Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia von Landau, Dan A., Clement, Kendell, Ziller, Michael J., Boyle, Patrick, Fan, Jean, Gu, Hongcang, Stevenson, Kristen, Sougnez, Carrie, Wang, Lili, Li, Shuqiang, Kotliar, Dylan, Zhang, Wandi, Ghandi, Mahmoud, Garraway, Levi, Fernandes, Stacey M., Livak, Kenneth J., Gabriel, Stacey, Gnirke, Andreas, Lander, Eric S., Brown, Jennifer R., Neuberg, Donna, Kharchenko, Peter V., Hacohen, Nir, Getz, Gad, Meissner, Alexander, Wu, Catherine J.

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dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments von Petukhov, Viktor, Guo, Jimin, Baryawno, Ninib, Severe, Nicolas, Scadden, David T, Samsonova, Maria G, Kharchenko, Peter V

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Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment von Kfoury, Youmna, Baryawno, Ninib, Severe, Nicolas, Mei, Shenglin, Gustafsson, Karin, Hirz, Taghreed, Brouse, Thomas, Scadden, Elizabeth W., Igolkina, Anna A., Kokkaliaris, Konstantinos, Choi, Bryan D., Barkas, Nikolas, Randolph, Mark A., Shin, John H., Saylor, Philip J., Scadden, David T., Sykes, David B., Kharchenko, Peter V.

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Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla von Furlan, Alessandro, Dyachuk, Vyacheslav, Kastriti, Maria Eleni, Calvo-Enrique, Laura, Abdo, Hind, Hadjab, Saida, Chontorotzea, Tatiana, Akkuratova, Natalia, Usoskin, Dmitry, Kamenev, Dmitry, Petersen, Julian, Sunadome, Kazunori, Memic, Fatima, Marklund, Ulrika, Fried, Kaj, Topilko, Piotr, Lallemend, Francois, Kharchenko, Peter V., Ernfors, Patrik, Adameyko, Igor

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Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data von Fan, Jean, Lee, Hae-Ock, Lee, Soohyun, Ryu, Da-Eun, Lee, Semin, Xue, Catherine, Kim, Seok Jin, Kim, Kihyun, Barkas, Nikolaos, Park, Peter J, Park, Woong-Yang, Kharchenko, Peter V

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Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis von Fan, Jean, Salathia, Neeraj, Liu, Rui, Kaeser, Gwendolyn E, Yung, Yun C, Herman, Joseph L, Kaper, Fiona, Fan, Jian-Bing, Zhang, Kun, Chun, Jerold, Kharchenko, Peter V

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A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA von Lake, Blue B., Codeluppi, Simone, Yung, Yun C., Gao, Derek, Chun, Jerold, Kharchenko, Peter V., Linnarsson, Sten, Zhang, Kun

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Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia von Wang, Lili, Brooks, Angela N., Fan, Jean, Wan, Youzhong, Gambe, Rutendo, Li, Shuqiang, Hergert, Sarah, Yin, Shanye, Freeman, Samuel S., Levin, Joshua Z., Fan, Lin, Seiler, Michael, Buonamici, Silvia, Smith, Peter G., Chau, Kevin F., Cibulskis, Carrie L., Zhang, Wandi, Rassenti, Laura Z., Ghia, Emanuela M., Kipps, Thomas J., Fernandes, Stacey, Bloch, Donald B., Kotliar, Dylan, Landau, Dan A., Shukla, Sachet A., Aster, Jon C., Reed, Robin, DeLuca, David S., Brown, Jennifer R., Neuberg, Donna, Getz, Gad, Livak, Kenneth J., Meyerson, Matthew M., Kharchenko, Peter V., Wu, Catherine J.

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