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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Genome-Wide Association Studies of the Human Gut Microbiota von Davenport, Emily R, Cusanovich, Darren A, Michelini, Katelyn, Barreiro, Luis B, Ober, Carole, Gilad, Yoav

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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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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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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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The functional consequences of variation in transcription factor binding von Cusanovich, Darren A, Pavlovic, Bryan, Pritchard, Jonathan K, Gilad, Yoav

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CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions von Gasperini, Molly, Findlay, Gregory M., McKenna, Aaron, Milbank, Jennifer H., Lee, Choli, Zhang, Melissa D., Cusanovich, Darren A., Shendure, Jay

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Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures von Khan, Zia, Ford, Michael J., Cusanovich, Darren A., Mitrano, Amy, Pritchard, Jonathan K., Gilad, Yoav

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The effects of EBV transformation on gene expression levels and methylation profiles von CALTSKAN, Minal, CUSANOVICH, Darren A, OBER, Carole, GILAD, Yoav

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txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility von Zhang, Hao, Mulqueen, Ryan M, Iannuzo, Natalie, Farrera, Dominique O, Polverino, Francesca, Galligan, James J, Ledford, Julie G, Adey, Andrew C, Cusanovich, Darren A

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Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 infection von Kang, HyunJin, Allison, Sheilah, Spangenberg, Amber, Carr, Tara, Sprissler, Ryan, Halonen, Marilyn, Cusanovich, Darren A.

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Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures von Rai, Vivek, Quang, Daniel X., Erdos, Michael R., Cusanovich, Darren A., Daza, Riza M., Narisu, Narisu, Zou, Luli S., Didion, John P., Guan, Yuanfang, Shendure, Jay, Parker, Stephen C.J., Collins, Francis S.

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Single-cell 'omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activati... von Adelus, Maria L, Ding, Jiacheng, Tran, Binh T, Conklin, Austin C, Golebiewski, Anna K, Stolze, Lindsey K, Whalen, Michael B, Cusanovich, Darren A, Romanoski, Casey E

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Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei von Zhang, Hao, Rice, Michael E, Alvin, Joseph W, Farrera-Gaffney, Dominique, Galligan, James J, Johnson, Michael D L, Cusanovich, Darren A

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Breast tumor stiffness instructs bone metastasis via maintenance of mechanical conditioning von Watson, Adam W., Grant, Adam D., Parker, Sara S., Hill, Samantha, Whalen, Michael B., Chakrabarti, Jayati, Harman, Michael W., Roman, Mackenzie R., Forte, Brittany L., Gowan, Cody C., Castro-Portuguez, Raúl, Stolze, Lindsey K., Franck, Christian, Cusanovich, Darren A., Zavros, Yana, Padi, Megha, Romanoski, Casey E., Mouneimne, Ghassan

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CC16 drives VLA-2-dependent SPLUNC1 expression von Iannuzo, Natalie, Welfley, Holly, Li, Nicholas C, Johnson, Michael D L, Rojas-Quintero, Joselyn, Polverino, Francesca, Guerra, Stefano, Li, Xingnan, Cusanovich, Darren A, Langlais, Paul R, Ledford, Julie G

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Lactoylglutathione promotes inflammatory signaling in macrophages through histone lactoylation von Trujillo, Marissa N., Jennings, Erin Q., Hoffman, Emely A., Zhang, Hao, Phoebe, Aiden M., Mastin, Grace E., Kitamura, Naoya, Reisz, Julie A., Megill, Emily, Kantner, Daniel, Marcinkiewicz, Mariola M., Twardy, Shannon M., Lebario, Felicidad, Chapman, Eli, McCullough, Rebecca L., D'Alessandro, Angelo, Snyder, Nathaniel W., Cusanovich, Darren A., Galligan, James J.

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