Search Results - "DAZA, Riza"

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin by Snyder, Matthew W., Kircher, Martin, Hill, Andrew J., Daza, Riza M., Shendure, Jay

“…Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA (cfDNA), isolated from circulating blood plasma, we generated maps of…”
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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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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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A human cell atlas of fetal gene expression by 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

“…The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and…”
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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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Precise genomic deletions using paired prime editing by Choi, Junhong, Chen, Wei, Suiter, Chase C., Lee, Choli, Chardon, Florence M., Yang, Wei, Leith, Anh, Daza, Riza M., Martin, Beth, Shendure, Jay

“…Current methods to delete genomic sequences are based on clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 and pairs of single-guide RNAs…”
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Pluripotent stem cell-derived model of the post-implantation human embryo by Weatherbee, Bailey A. T., Gantner, Carlos W., Iwamoto-Stohl, Lisa K., Daza, Riza M., Hamazaki, Nobuhiko, Shendure, Jay, Zernicka-Goetz, Magdalena

“…The human embryo undergoes morphogenetic transformations following implantation into the uterus, but our knowledge of this crucial stage is limited by the…”
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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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Accurate classification of BRCA1 variants with saturation genome editing by Findlay, Gregory M., Daza, Riza M., Martin, Beth, Zhang, Melissa D., Leith, Anh P., Gasperini, Molly, Janizek, Joseph D., Huang, Xingfan, Starita, Lea M., Shendure, Jay

“…Variants of uncertain significance fundamentally limit the clinical utility of genetic information. The challenge they pose is epitomized by BRCA1 , a tumour…”
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Massively multiplex chemical transcriptomics at single-cell resolution by Srivatsan, Sanjay R, McFaline-Figueroa, José L, Ramani, Vijay, Saunders, Lauren, Cao, Junyue, Packer, Jonathan, Pliner, Hannah A, Jackson, Dana L, Daza, Riza M, Christiansen, Lena, Zhang, Fan, Steemers, Frank, Shendure, Jay, Trapnell, Cole

“…High-throughput chemical screens typically use coarse assays such as cell survival, limiting what can be learned about mechanisms of action, off-target…”
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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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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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A time-resolved, multi-symbol molecular recorder via sequential genome editing by Choi, Junhong, Chen, Wei, Minkina, Anna, Chardon, Florence M., Suiter, Chase C., Regalado, Samuel G., Domcke, Silvia, Hamazaki, Nobuhiko, Lee, Choli, Martin, Beth, Daza, Riza M., Shendure, Jay

“…DNA is naturally well suited to serve as a digital medium for in vivo molecular recording. However, contemporary DNA-based memory devices are constrained in…”
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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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Fragment Length of Circulating Tumor DNA by Underhill, Hunter R, Kitzman, Jacob O, Hellwig, Sabine, Welker, Noah C, Daza, Riza, Baker, Daniel N, Gligorich, Keith M, Rostomily, Robert C, Bronner, Mary P, Shendure, Jay

“…Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor…”
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Predicting cellular responses to complex perturbations in high‐throughput screens by Lotfollahi, Mohammad, Klimovskaia Susmelj, Anna, De Donno, Carlo, Hetzel, Leon, Ji, Yuge, Ibarra, Ignacio L, Srivatsan, Sanjay R, Naghipourfar, Mohsen, Daza, Riza M, Martin, Beth, Shendure, Jay, McFaline‐Figueroa, Jose L, Boyeau, Pierre, Wolf, F Alexander, Yakubova, Nafissa, Günnemann, Stephan, Trapnell, Cole, Lopez‐Paz, David, Theis, Fabian J

“…Recent advances in multiplexed single‐cell transcriptomics experiments facilitate the high‐throughput study of drug and genetic perturbations. However, an…”
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Copy-Number Variation and False Positive Prenatal Aneuploidy Screening Results by Snyder, Matthew W, Simmons, LaVone E, Kitzman, Jacob O, Coe, Bradley P, Henson, Jessica M, Daza, Riza M, Eichler, Evan E, Shendure, Jay, Gammill, Hilary S

“…False positive results for trisomy 18 from DNA-based noninvasive prenatal screening were caused, in two of the four patients who were evaluated, by maternal…”
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High-quality draft assemblies of mammalian genomes from massively parallel sequence data by Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J, Burton, Joshua N, Walker, Bruce J, Sharpe, Ted, Hall, Giles, Shea, Terrance P, Sykes, Sean, Berlin, Aaron M, Aird, Daniel, Costello, Maura, Daza, Riza, Williams, Louise, Nicol, Robert, Gnirke, Andreas, Nusbaum, Chad, Lander, Eric S, Jaffe, David B

“…Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (approximately…”
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The continuum of Drosophila embryonic development at single-cell resolution by Calderon, Diego, Blecher-Gonen, Ronnie, Huang, Xingfan, Secchia, Stefano, Kentro, James, Daza, Riza M, Martin, Beth, Dulja, Alessandro, Schaub, Christoph, Trapnell, Cole, Larschan, Erica, O'Connor-Giles, Kate M, Furlong, Eileen E M, Shendure, Jay

“…is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost 1 million and gene expression in…”
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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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