Search Results - "Cusanovich, Darren A"

Joint profiling of chromatin accessibility and gene expression in thousands of single cells by 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

“…Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays…”
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Comprehensive single-cell transcriptional profiling of a multicellular organism by 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

“…To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei, termed sci-RNA-seq…”
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Genome-Wide Association Studies of the Human Gut Microbiota by Davenport, Emily R, Cusanovich, Darren A, Michelini, Katelyn, Barreiro, Luis B, Ober, Carole, Gilad, Yoav

“…The bacterial composition of the human fecal microbiome is influenced by many lifestyle factors, notably diet. It is less clear, however, what role host…”
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Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing by Cusanovich, Darren A., Daza, Riza, Adey, Andrew, Pliner, Hannah A., Christiansen, Lena, Gunderson, Kevin L., Steemers, Frank J., Trapnell, Cole, Shendure, Jay

“…Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the…”
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Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data by 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

“…Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an…”
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A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility by 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

“…We applied a combinatorial indexing assay, sci-ATAC-seq, to profile genome-wide chromatin accessibility in ∼100,000 single cells from 13 adult mouse tissues…”
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A human cell atlas of fetal chromatin accessibility by 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

“…The chromatin landscape underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of chromatin accessibility…”
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The cis-regulatory dynamics of embryonic development at single-cell resolution by 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.

“…An improved assay for chromatin accessibility at single-cell resolution in Drosophila melanogaster embryos enables identification of developmental-stage- and…”
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The functional consequences of variation in transcription factor binding by Cusanovich, Darren A, Pavlovic, Bryan, Pritchard, Jonathan K, Gilad, Yoav

“…One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of…”
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CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions by Gasperini, Molly, Findlay, Gregory M., McKenna, Aaron, Milbank, Jennifer H., Lee, Choli, Zhang, Melissa D., Cusanovich, Darren A., Shendure, Jay

“…The extent to which non-coding mutations contribute to Mendelian disease is a major unknown in human genetics. Relatedly, the vast majority of candidate…”
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Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures by Khan, Zia, Ford, Michael J., Cusanovich, Darren A., Mitrano, Amy, Pritchard, Jonathan K., Gilad, Yoav

“…Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across…”
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The effects of EBV transformation on gene expression levels and methylation profiles by CALTSKAN, Minal, CUSANOVICH, Darren A, OBER, Carole, GILAD, Yoav

“…Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional genomic studies…”
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txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility by Zhang, Hao, Mulqueen, Ryan M, Iannuzo, Natalie, Farrera, Dominique O, Polverino, Francesca, Galligan, James J, Ledford, Julie G, Adey, Andrew C, Cusanovich, Darren A

“…We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000…”
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Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 infection by Kang, HyunJin, Allison, Sheilah, Spangenberg, Amber, Carr, Tara, Sprissler, Ryan, Halonen, Marilyn, Cusanovich, Darren A.

“…The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing has led to issues in scaling diagnostic lab efforts and in securing basic supplies for…”
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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 by 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.

“…Type 2 diabetes (T2D) is a complex disease characterized by pancreatic islet dysfunction, insulin resistance, and disruption of blood glucose levels…”
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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 activating perturbations by 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

“…Heterogeneity in endothelial cell (EC) sub-phenotypes is becoming increasingly appreciated in atherosclerosis progression. Still, studies quantifying EC…”
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Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei by Zhang, Hao, Rice, Michael E, Alvin, Joseph W, Farrera-Gaffney, Dominique, Galligan, James J, Johnson, Michael D L, Cusanovich, Darren A

“…The "Assay for Transposase Accessible Chromatin sequencing" (ATAC-seq) is an efficient and easy to implement protocol to measure chromatin accessibility that…”
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Breast tumor stiffness instructs bone metastasis via maintenance of mechanical conditioning by 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

“…While the immediate and transitory response of breast cancer cells to pathological stiffness in their native microenvironment has been well explored, it…”
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CC16 drives VLA-2-dependent SPLUNC1 expression by 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

“…CC16 (Club Cell Secretory Protein) is a protein produced by club cells and other non-ciliated epithelial cells within the lungs. CC16 has been shown to protect…”
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Lactoylglutathione promotes inflammatory signaling in macrophages through histone lactoylation by 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.

“…Chronic, systemic inflammation is a pathophysiological manifestation of metabolic disorders. Inflammatory signaling leads to elevated glycolytic flux and a…”
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