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

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

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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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Spatiotemporal structure of cell fate decisions in murine neural crest von Soldatov, Ruslan, Kaucka, Marketa, Kastriti, Maria Eleni, Petersen, Julian, Chontorotzea, Tatiana, Englmaier, Lukas, Akkuratova, Natalia, Yang, Yunshi, Häring, Martin, Dyachuk, Viacheslav, Bock, Christoph, Farlik, Matthias, Piacentino, Michael L., Boismoreau, Franck, Hilscher, Markus M., Yokota, Chika, Qian, Xiaoyan, Nilsson, Mats, Bronner, Marianne E., Croci, Laura, Hsiao, Wen-Yu, Guertin, David A., Brunet, Jean-Francois, Consalez, Gian Giacomo, Ernfors, Patrik, Fried, Kaj, Kharchenko, Peter V., Adameyko, Igor

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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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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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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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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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Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators von Silberstein, Lev, Goncalves, Kevin A., Kharchenko, Peter V., Turcotte, Raphael, Kfoury, Youmna, Mercier, Francois, Baryawno, Ninib, Severe, Nicolas, Bachand, Jacqueline, Spencer, Joel A., Papazian, Ani, Lee, Dongjun, Chitteti, Brahmananda Reddy, Srour, Edward F., Hoggatt, Jonathan, Tate, Tiffany, Lo Celso, Cristina, Ono, Noriaki, Nutt, Stephen, Heino, Jyrki, Sipilä, Kalle, Shioda, Toshihiro, Osawa, Masatake, Lin, Charles P., Hu, Guo-fu, Scadden, David T.

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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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Publisher Correction: The triumphs and limitations of computational methods for scRNA-seq von 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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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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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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Design and analysis of ChIP-seq experiments for DNA-binding proteins von Kharchenko, Peter V, Tolstorukov, Michael Y, Park, Peter J

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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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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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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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