Search Results - "Ryvkin, Paul"

Massively parallel digital transcriptional profiling of single cells by Zheng, Grace X. Y., Terry, Jessica M., Belgrader, Phillip, Ryvkin, Paul, Bent, Zachary W., Wilson, Ryan, Ziraldo, Solongo B., Wheeler, Tobias D., McDermott, Geoff P., Zhu, Junjie, Gregory, Mark T., Shuga, Joe, Montesclaros, Luz, Underwood, Jason G., Masquelier, Donald A., Nishimura, Stefanie Y., Schnall-Levin, Michael, Wyatt, Paul W., Hindson, Christopher M., Bharadwaj, Rajiv, Wong, Alexander, Ness, Kevin D., Beppu, Lan W., Deeg, H. Joachim, McFarland, Christopher, Loeb, Keith R., Valente, William J., Ericson, Nolan G., Stevens, Emily A., Radich, Jerald P., Mikkelsen, Tarjei S., Hindson, Benjamin J., Bielas, Jason H.

“…Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that…”
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HAMR: high-throughput annotation of modified ribonucleotides by Ryvkin, Paul, Leung, Yuk Yee, Silverman, Ian M, Childress, Micah, Valladares, Otto, Dragomir, Isabelle, Gregory, Brian D, Wang, Li-San

“…RNA is often altered post-transcriptionally by the covalent modification of particular nucleotides; these modifications are known to modulate the structure and…”
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Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis by Zheng, Qi, Ryvkin, Paul, Li, Fan, Dragomir, Isabelle, Valladares, Otto, Yang, Jamie, Cao, Kajia, Wang, Li-San, Gregory, Brian D

“…The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA…”
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Global Analysis of RNA Secondary Structure in Two Metazoans by Li, Fan, Zheng, Qi, Ryvkin, Paul, Dragomir, Isabelle, Desai, Yaanik, Aiyer, Subhadra, Valladares, Otto, Yang, Jamie, Bambina, Shelly, Sabin, Leah R., Murray, John I., Lamitina, Todd, Raj, Arjun, Cherry, Sara, Wang, Li-San, Gregory, Brian D.

“…The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in…”
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Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin by Amlie-Wolf, Alexandre, Ryvkin, Paul, Tong, Rui, Dragomir, Isabelle, Suh, EunRan, Xu, Yan, Van Deerlin, Vivianna M, Gregory, Brian D, Kwong, Linda K, Trojanowski, John Q, Lee, Virginia M-Y, Wang, Li-San, Lee, Edward B

“…TAR DNA-binding protein 43 (TDP-43) is normally a nuclear RNA-binding protein that exhibits a range of functions including regulation of alternative splicing,…”
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Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs by Ryvkin, Paul, Leung, Yuk Yee, Ungar, Lyle H., Gregory, Brian D., Wang, Li-San

“…•CoRAL is a method for classifying small non-coding RNAs using small RNA-seq data.•CoRAL uses features associated with small RNA biogenesis such as fragment…”
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Analysis of nonlinear gene expression progression reveals extensive pathway and age-specific transitions in aging human brains by Cao, Kajia, Ryvkin, Paul, Hwang, Yih-Chii, Johnson, F Brad, Wang, Li-San

“…Several recent gene expression studies identified hundreds of genes that are correlated with age in brain and other tissues in human. However, these studies…”
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Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential by Johnson, Jay E, Cao, Kajia, Ryvkin, Paul, Wang, Li-San, Johnson, F Brad

“…The human Werner and Bloom syndromes (WS and BS) are caused by deficiencies in the WRN and BLM RecQ helicases, respectively. WRN, BLM and their Saccharomyces…”
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Microarray-based cell-free DNA analysis improves noninvasive prenatal testing by Juneau, Kara, Bogard, Patrick E, Huang, Stephanie, Mohseni, Morassa, Wang, Eric T, Ryvkin, Paul, Kingsley, Christopher, Struble, Craig A, Oliphant, Arnold, Zahn, Jacob M

“…To develop a microarray-based method for noninvasive prenatal testing (NIPT) and compare it with next-generation sequencing. Maternal plasma from 878 pregnant…”
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Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence by Platt, Jesse M, Ryvkin, Paul, Wanat, Jennifer J, Donahue, Greg, Ricketts, M Dan, Barrett, Steven P, Waters, Hannah J, Song, Shufei, Chavez, Alejandro, Abdallah, Khaled Omar, Master, Stephen R, Wang, Li-San, Johnson, F Brad

“…Cellular senescence is accompanied by dramatic changes in chromatin structure and gene expression. Using Saccharomyces cerevisiae mutants lacking telomerase…”
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Abstract 1013: Analyzing infiltrating B cell populations in the tumor microenvironment using single cell transcriptomics by Taylor, Sarah E., Boutet, Stephane, Giangarrá, Valeria, Zheng, Grace X., Barrio, Alvaro M., Montesclaros, Luz, Lee, Josephine, Marrs, Samuel, Wu, Kevin J., Ryvkin, Paul, Mikkelsen, Tarjei, Church, Deanna M.

“…Abstract Understanding the complex interactions between malignant, stromal and infiltrating lymphocyte cell types within the tumor microenvironment is a…”
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CoRAL: predicting non-coding RNAs from small RNA-sequencing data by Leung, Yuk Yee, Ryvkin, Paul, Ungar, Lyle H, Gregory, Brian D, Wang, Li-San

“…The surprising observation that virtually the entire human genome is transcribed means we know little about the function of many emerging classes of RNAs,…”
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Computational detection and analysis of sequences with duplex-derived interstrand G-quadruplex forming potential by Cao, Kajia, Ryvkin, Paul, Brad Johnson, F.

“…► We present a new method for detection of DNA sequences with G-quadruplex forming potential, called ddiQFP. ► ddiQFP predicts G-quadruplexes formed from…”
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Abstract 150: Single cell mRNA quantification from 1000s of cells in healthy and malignant tumor samples using a high-throughput droplet-based system by Zheng, Grace X.y., Mikkelsen, Tarjei, Terry, Jessica, Belgrader, Phillip, Ryvkin, Paul, Wilson, Ryan, Wheeler, Tobias D., Bent, Zachary, McDermott, Geoff, Ziraldo, Solongo, Wong, Alexander, Schnall-Levin, Michael, Hindson, Ben

“…Abstract Advances in single cell RNA quantification techniques have enabled comprehensive study of subpopulations of cells within a heterogeneous population…”
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SAVoR: a server for sequencing annotation and visualization of RNA structures by Li, Fan, Ryvkin, Paul, Childress, Daniel M, Valladares, Otto, Gregory, Brian D, Wang, Li-San

“…RNA secondary structure is required for the proper regulation of the cellular transcriptome. This is because the functionality, processing, localization and…”
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Duplication mechanism and disruptions in flanking regions determine the fate of Mammalian gene duplicates by Jun, Jin, Ryvkin, Paul, Hemphill, Edward, Nelson, Craig

“…Here we identify duplicated genes in five mammalian genomes and classify these duplicates based on the mechanisms by which they were generated…”
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Methods in and applications of the sequencing of short non-coding RNAs by Ryvkin, Paul

“…Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in…”
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P3–064: Characterizing the Alzheimer's disease prefrontal cortex transcriptome by multiple RNA‐sequencing by Ryvkin, Paul, Leung, Yuk Yee, Dragomir, Isabelle, Schuck, Theresa, Schellenberg, Gerard, Arnold, Steven, Chen‐Plotkin, Alice, Van Deerlin, Vivianna, Lee, Virginia, Trojanowski, John, Gregory, Brian, Wang, Li‐San

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Characterizing the Alzheimer's disease prefrontal cortex transcriptome by multiple RNA-sequencing by Ryvkin, Paul, Leung, Yuk Yee, Dragomir, Isabelle, Schuck, Theresa, Schellenberg, Gerard, Arnold, Steven, Chen-Plotkin, Alice, Van Deerlin, Vivianna, Lee, Virginia, Trojanowski, John, Gregory, Brian, Wang, Li-San

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Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis: e1001141 by Zheng, Qi, Ryvkin, Paul, Li, Fan, Dragomir, Isabelle, Valladares, Otto, Yang, Jamie, Cao, Kajia, Wang, Li-San, Gregory, Brian D

“…The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA…”
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