The single-cell transcriptional landscape of mammalian organogenesis
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
Published in Nature (London) (01.02.2019)
Published in Nature (London) (01.02.2019)
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Comprehensive single-cell transcriptional profiling of a multicellular organism
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
Published in Science (American Association for the Advancement of Science) (18.08.2017)
Published in Science (American Association for the Advancement of Science) (18.08.2017)
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Journal Article
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
Cusanovich, Darren A., Daza, Riza, Adey, Andrew, Pliner, Hannah A., Christiansen, Lena, Gunderson, Kevin L., Steemers, Frank J., Trapnell, Cole, Shendure, Jay
Published in Science (American Association for the Advancement of Science) (22.05.2015)
Published in Science (American Association for the Advancement of Science) (22.05.2015)
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A human cell atlas of fetal gene expression
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
Published in Science (American Association for the Advancement of Science) (13.11.2020)
Published in Science (American Association for the Advancement of Science) (13.11.2020)
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Journal Article
Joint profiling of chromatin accessibility and gene expression in thousands of single cells
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
Published in Science (American Association for the Advancement of Science) (28.09.2018)
Published in Science (American Association for the Advancement of Science) (28.09.2018)
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Journal Article
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
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
Published in Molecular cell (06.09.2018)
Published in Molecular cell (06.09.2018)
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Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility
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.
Published in Nature biotechnology (01.08.2019)
Published in Nature biotechnology (01.08.2019)
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Journal Article
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
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
Published in Cell (23.08.2018)
Published in Cell (23.08.2018)
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Journal Article
A human cell atlas of fetal chromatin accessibility
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
Published in Science (American Association for the Advancement of Science) (13.11.2020)
Published in Science (American Association for the Advancement of Science) (13.11.2020)
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Journal Article
The cis-regulatory dynamics of embryonic development at single-cell resolution
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.
Published in Nature (London) (22.03.2018)
Published in Nature (London) (22.03.2018)
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Journal Article
Highly scalable generation of DNA methylation profiles in single cells
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
Published in Nature biotechnology (01.06.2018)
Published in Nature biotechnology (01.06.2018)
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Journal Article
In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
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
Published in Genome research (01.12.2014)
Published in Genome research (01.12.2014)
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Journal Article
Spatially mapped single-cell chromatin accessibility
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.
Published in Nature communications (24.02.2021)
Published in Nature communications (24.02.2021)
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Journal Article
The accessible chromatin landscape of the murine hippocampus at single-cell resolution
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
Published in Genome research (01.05.2019)
Published in Genome research (01.05.2019)
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Journal Article
High-throughput robust single-cell DNA methylation profiling with sciMETv2
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.
Published in Nature communications (09.12.2022)
Published in Nature communications (09.12.2022)
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Journal Article
Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons
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.
Published in Nature communications (03.03.2020)
Published in Nature communications (03.03.2020)
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Journal Article
Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube
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
Published in Nature biotechnology (01.09.2017)
Published in Nature biotechnology (01.09.2017)
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Journal Article
High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
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
Published in Genome Research (01.09.2006)
Published in Genome Research (01.09.2006)
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Journal Article
Massively multiplex single-cell Hi-C
Ramani, Vijay, Deng, Xinxian, Qiu, Ruolan, Gunderson, Kevin L, Steemers, Frank J, Disteche, Christine M, Noble, William S, Duan, Zhijun, Shendure, Jay
Published in Nature methods (01.03.2017)
Published in Nature methods (01.03.2017)
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