The single-cell transcriptional landscape of mammalian organogenesis von Cao, Junyue, Spielmann, Malte, Qiu, Xiaojie, Huang, Xingfan, Ibrahim, Daniel M., Hill, Andrew J., Zhang, Fan, Mundlos, Stefan, Christiansen, Lena, Steemers, Frank J., Trapnell, Cole, Shendure, Jay

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Comprehensive single-cell transcriptional profiling of a multicellular organism von Cao, Junyue, Packer, Jonathan S., Ramani, Vijay, Cusanovich, Darren A., Huynh, Chau, Daza, Riza, Qiu, Xiaojie, Lee, Choli, Furlan, Scott N., Steemers, Frank J., Adey, Andrew, Waterston, Robert H., Trapnell, Cole, Shendure, Jay

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Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing von Cusanovich, Darren A., Daza, Riza, Adey, Andrew, Pliner, Hannah A., Christiansen, Lena, Gunderson, Kevin L., Steemers, Frank J., Trapnell, Cole, Shendure, Jay

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A human cell atlas of fetal gene expression von Cao, Junyue, O'Day, Diana R, Pliner, Hannah A, Kingsley, Paul D, Deng, Mei, Daza, Riza M, Zager, Michael A, Aldinger, Kimberly A, Blecher-Gonen, Ronnie, Zhang, Fan, Spielmann, Malte, Palis, James, Doherty, Dan, Steemers, Frank J, Glass, Ian A, Trapnell, Cole, Shendure, Jay

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Joint profiling of chromatin accessibility and gene expression in thousands of single cells von Cao, Junyue, Cusanovich, Darren A, Ramani, Vijay, Aghamirzaie, Delasa, Pliner, Hannah A, Hill, Andrew J, Daza, Riza M, McFaline-Figueroa, Jose L, Packer, Jonathan S, Christiansen, Lena, Steemers, Frank J, Adey, Andrew C, Trapnell, Cole, Shendure, Jay

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Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data von Pliner, Hannah A., Packer, Jonathan S., McFaline-Figueroa, José L., Cusanovich, Darren A., Daza, Riza M., Aghamirzaie, Delasa, Srivatsan, Sanjay, Qiu, Xiaojie, Jackson, Dana, Minkina, Anna, Adey, Andrew C., Steemers, Frank J., Shendure, Jay, Trapnell, Cole

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Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility von Lareau, Caleb A., Duarte, Fabiana M., Chew, Jennifer G., Kartha, Vinay K., Burkett, Zach D., Kohlway, Andrew S., Pokholok, Dmitry, Aryee, Martin J., Steemers, Frank J., Lebofsky, Ronald, Buenrostro, Jason D.

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A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility von Cusanovich, Darren A., Hill, Andrew J., Aghamirzaie, Delasa, Daza, Riza M., Pliner, Hannah A., Berletch, Joel B., Filippova, Galina N., Huang, Xingfan, Christiansen, Lena, DeWitt, William S., Lee, Choli, Regalado, Samuel G., Read, David F., Steemers, Frank J., Disteche, Christine M., Trapnell, Cole, Shendure, Jay

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A human cell atlas of fetal chromatin accessibility von Domcke, Silvia, Hill, Andrew J, Daza, Riza M, Cao, Junyue, O'Day, Diana R, Pliner, Hannah A, Aldinger, Kimberly A, Pokholok, Dmitry, Zhang, Fan, Milbank, Jennifer H, Zager, Michael A, Glass, Ian A, Steemers, Frank J, Doherty, Dan, Trapnell, Cole, Cusanovich, Darren A, Shendure, Jay

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The cis-regulatory dynamics of embryonic development at single-cell resolution von Cusanovich, Darren A., Reddington, James P., Garfield, David A., Daza, Riza M., Aghamirzaie, Delasa, Marco-Ferreres, Raquel, Pliner, Hannah A., Christiansen, Lena, Qiu, Xiaojie, Steemers, Frank J., Trapnell, Cole, Shendure, Jay, Furlong, Eileen E. M.

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Highly scalable generation of DNA methylation profiles in single cells von Mulqueen, Ryan M, Pokholok, Dmitry, Norberg, Steven J, Torkenczy, Kristof A, Fields, Andrew J, Sun, Duanchen, Sinnamon, John R, Shendure, Jay, Trapnell, Cole, O'Roak, Brian J, Xia, Zheng, Steemers, Frank J, Adey, Andrew C

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In vitro, long-range sequence information for de novo genome assembly via transposase contiguity von Adey, Andrew, Kitzman, Jacob O, Burton, Joshua N, Daza, Riza, Kumar, Akash, Christiansen, Lena, Ronaghi, Mostafa, Amini, Sasan, Gunderson, Kevin L, Steemers, Frank J, Shendure, Jay

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Spatially mapped single-cell chromatin accessibility von Thornton, Casey A., Mulqueen, Ryan M., Torkenczy, Kristof A., Nishida, Andrew, Lowenstein, Eve G., Fields, Andrew J., Steemers, Frank J., Zhang, Wenri, McConnell, Heather L., Woltjer, Randy L., Mishra, Anusha, Wright, Kevin M., Adey, Andrew C.

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High-throughput robust single-cell DNA methylation profiling with sciMETv2 von Nichols, Ruth V., O’Connell, Brendan L., Mulqueen, Ryan M., Thomas, Jerushah, Woodfin, Ashley R., Acharya, Sonia, Mandel, Gail, Pokholok, Dmitry, Steemers, Frank J., Adey, Andrew C.

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The accessible chromatin landscape of the murine hippocampus at single-cell resolution von Sinnamon, John R, Torkenczy, Kristof A, Linhoff, Michael W, Vitak, Sarah A, Mulqueen, Ryan M, Pliner, Hannah A, Trapnell, Cole, Steemers, Frank J, Mandel, Gail, Adey, Andrew C

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Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons von Hodge, Rebecca D., Miller, Jeremy A., Novotny, Mark, Kalmbach, Brian E., Ting, Jonathan T., Bakken, Trygve E., Aevermann, Brian D., Barkan, Eliza R., Berkowitz-Cerasano, Madeline L., Cobbs, Charles, Diez-Fuertes, Francisco, Ding, Song-Lin, McCorrison, Jamison, Schork, Nicholas J., Shehata, Soraya I., Smith, Kimberly A., Sunkin, Susan M., Tran, Danny N., Venepally, Pratap, Yanny, Anna Marie, Steemers, Frank J., Phillips, John W., Bernard, Amy, Koch, Christof, Lasken, Roger S., Scheuermann, Richard H., Lein, Ed S.

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Whole genome genotyping technologies on the BeadArray™ platform von Steemers, Frank J., Gunderson, Kevin L.

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Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube von Zhang, Fan, Christiansen, Lena, Thomas, Jerushah, Pokholok, Dmitry, Jackson, Ros, Morrell, Natalie, Zhao, Yannan, Wiley, Melissa, Welch, Emily, Jaeger, Erich, Granat, Ana, Norberg, Steven J, Halpern, Aaron, C Rogert, Maria, Ronaghi, Mostafa, Shendure, Jay, Gormley, Niall, Gunderson, Kevin L, Steemers, Frank J

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High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping von Peiffer, Daniel A, Le, Jennie M, Steemers, Frank J, Chang, Weihua, Jenniges, Tony, Garcia, Francisco, Haden, Kirt, Li, Jiangzhen, Shaw, Chad A, Belmont, John, Cheung, Sau Wai, Shen, Richard M, Barker, David L, Gunderson, Kevin L

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Massively multiplex single-cell Hi-C von Ramani, Vijay, Deng, Xinxian, Qiu, Ruolan, Gunderson, Kevin L, Steemers, Frank J, Disteche, Christine M, Noble, William S, Duan, Zhijun, Shendure, Jay

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