Search Results - "Schroth, Gary P"

Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins by Wang, Eric T., Cody, Neal A.L., Jog, Sonali, Biancolella, Michela, Wang, Thomas T., Treacy, Daniel J., Luo, Shujun, Schroth, Gary P., Housman, David E., Reddy, Sita, Lécuyer, Eric, Burge, Christopher B.

“…The muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in myotonic dystrophy (DM), in which…”
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From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing by Marinov, Georgi K, Williams, Brian A, McCue, Ken, Schroth, Gary P, Gertz, Jason, Myers, Richard M, Wold, Barbara J

“…Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and…”
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High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain by Gregg, Christopher, Zhang, Jiangwen, Weissbourd, Brandon, Luo, Shujun, Schroth, Gary P, Haig, David, Dulac, Catherine

“…Genomic imprinting results in preferential expression of the paternal or maternal allele of certain genes. We have performed a genome-wide characterization of…”
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Cohesin-mediated interactions organize chromosomal domain architecture by Sofueva, Sevil, Yaffe, Eitan, Chan, Wen-Ching, Georgopoulou, Dimitra, Vietri Rudan, Matteo, Mira-Bontenbal, Hegias, Pollard, Steven M, Schroth, Gary P, Tanay, Amos, Hadjur, Suzana

“…To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other…”
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Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells by Ramsköld, Daniel, Luo, Shujun, Wang, Yu-Chieh, Li, Robin, Deng, Qiaolin, Faridani, Omid R, Daniels, Gregory A, Khrebtukova, Irina, Loring, Jeanne F, Laurent, Louise C, Schroth, Gary P, Sandberg, Rickard

“…RNA-Seq of single cells has been limited by biases in transcript coverage and unknown technical variability. Ramsköld et al . describe a protocol to…”
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Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming by Kim, Daniel H., Marinov, Georgi K., Pepke, Shirley, Singer, Zakary S., He, Peng, Williams, Brian, Schroth, Gary P., Elowitz, Michael B., Wold, Barbara J.

“…Cellular reprogramming highlights the epigenetic plasticity of the somatic cell state. Long noncoding RNAs (lncRNAs) have emerging roles in epigenetic…”
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Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) by Lucks, Julius B, Mortimer, Stefanie A, Trapnell, Cole, Luo, Shujun, Aviran, Sharon, Schroth, Gary P, Pachter, Lior, Doudna, Jennifer A, Arkin, Adam P

“…New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential…”
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Alternative isoform regulation in human tissue transcriptomes by Burge, Christopher B, Wang, Eric T, Sandberg, Rickard, Luo, Shujun, Khrebtukova, Irina, Zhang, Lu, Mayr, Christine, Kingsmore, Stephen F, Schroth, Gary P

“…Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related,…”
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Mammalian microRNAs: experimental evaluation of novel and previously annotated genes by Chiang, H Rosaria, Schoenfeld, Lori W, Ruby, J Graham, Auyeung, Vincent C, Spies, Noah, Baek, Daehyun, Johnston, Wendy K, Russ, Carsten, Luo, Shujun, Babiarz, Joshua E, Blelloch, Robert, Schroth, Gary P, Nusbaum, Chad, Bartel, David P

“…MicroRNAs (miRNAs) are small regulatory RNAs that derive from distinctive hairpin transcripts. To learn more about the miRNAs of mammals, we sequenced 60…”
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Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq by Lott, Susan E, Villalta, Jacqueline E, Schroth, Gary P, Luo, Shujun, Tonkin, Leath A, Eisen, Michael B

“…When Drosophila melanogaster embryos initiate zygotic transcription around mitotic cycle 10, the dose-sensitive expression of specialized genes on the X…”
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Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing by O'Flaherty, Brigid M, Li, Yan, Tao, Ying, Paden, Clinton R, Queen, Krista, Zhang, Jing, Dinwiddie, Darrell L, Gross, Stephen M, Schroth, Gary P, Tong, Suxiang

“…Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious…”
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Carrier testing for severe childhood recessive diseases by next-generation sequencing by Bell, Callum J, Dinwiddie, Darrell L, Miller, Neil A, Hateley, Shannon L, Ganusova, Elena E, Mudge, Joann, Langley, Ray J, Zhang, Lu, Lee, Clarence C, Schilkey, Faye D, Sheth, Vrunda, Woodward, Jimmy E, Peckham, Heather E, Schroth, Gary P, Kim, Ryan W, Kingsmore, Stephen F

“…Of 7028 disorders with suspected Mendelian inheritance, 1139 are recessive and have an established molecular basis. Although individually uncommon, Mendelian…”
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Meraculous: de novo genome assembly with short paired-end reads by Chapman, Jarrod A, Ho, Isaac, Sunkara, Sirisha, Luo, Shujun, Schroth, Gary P, Rokhsar, Daniel S

“…We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp…”
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Comprehensive analysis of RNA-protein interactions by high-throughput sequencing–RNA affinity profiling by Tome, Jacob M, Ozer, Abdullah, Pagano, John M, Gheba, Dan, Schroth, Gary P, Lis, John T

“…The high-throughput sequencing–RNA affinity profiling (HiTS-RAP) assay enables large-scale profiling of protein interactions with RNA libraries using a simple…”
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Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument by Burge, Christopher B, Nutiu, Razvan, Friedman, Robin C, Luo, Shujun, Khrebtukova, Irina, Silva, David, Li, Robin, Zhang, Lu, Schroth, Gary P

“…Several methods for characterizing DNA-protein interactions are available, but none have demonstrated both high throughput and quantitative measurement of…”
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Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia by Akalin, Altuna, Garrett-Bakelman, Francine E, Kormaksson, Matthias, Busuttil, Jennifer, Zhang, Lu, Khrebtukova, Irina, Milne, Thomas A, Huang, Yongsheng, Biswas, Debabrata, Hess, Jay L, Allis, C David, Roeder, Robert G, Valk, Peter J M, Löwenberg, Bob, Delwel, Ruud, Fernandez, Hugo F, Paietta, Elisabeth, Tallman, Martin S, Schroth, Gary P, Mason, Christopher E, Melnick, Ari, Figueroa, Maria E

“…We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA…”
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PRG-1 and 21U-RNAs Interact to Form the piRNA Complex Required for Fertility in C. elegans by Batista, Pedro J., Ruby, J. Graham, Claycomb, Julie M., Chiang, Rosaria, Fahlgren, Noah, Kasschau, Kristin D., Chaves, Daniel A., Gu, Weifeng, Vasale, Jessica J., Duan, Shenghua, Conte, Darryl, Luo, Shujun, Schroth, Gary P., Carrington, James C., Bartel, David P., Mello, Craig C.

“…In metazoans, Piwi-related Argonaute proteins have been linked to germline maintenance, and to a class of germline-enriched small RNAs termed piRNAs. Here we…”
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Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver by Brunner, Alayne L, Johnson, David S, Kim, Si Wan, Valouev, Anton, Reddy, Timothy E, Neff, Norma F, Anton, Elizabeth, Medina, Catherine, Nguyen, Loan, Chiao, Eric, Oyolu, Chuba B, Schroth, Gary P, Absher, Devin M, Baker, Julie C, Myers, Richard M

“…To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions…”
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Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes by Tan, Asako, Murugapiran, Senthil, Mikalauskas, Alaya, Koble, Jeff, Kennedy, Drew, Hyde, Fred, Ruotti, Victor, Law, Emily, Jensen, Jordan, Schroth, Gary P, Macklaim, Jean M, Kuersten, Scott, LeFrançois, Brice, Gohl, Daryl M

“…Abstract The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and…”
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Modeling and automation of sequencing-based characterization of RNA structure by Aviran, Sharon, Trapnell, Cole, Lucks, Julius B., Mortimer, Stefanie A., Luo, Shujun, Schroth, Gary P., Doudna, Jennifer A., Arkin, Adam P., Pachter, Lior

“…Sequence census methods reduce molecular measurements such as transcript abundance and protein-nucleic acid interactions to counting problems via DNA…”
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