Search Results - "O'Malley, Ronan"

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape by O’Malley, Ronan C., Huang, Shao-shan Carol, Song, Liang, Lewsey, Mathew G., Bartlett, Anna, Nery, Joseph R., Galli, Mary, Gallavotti, Andrea, Ecker, Joseph R.

“…The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific…”
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Mapping genome-wide transcription-factor binding sites using DAP-seq by Bartlett, Anna, O'Malley, Ronan C, Huang, Shao-shan Carol, Galli, Mary, Nery, Joseph R, Gallavotti, Andrea, Ecker, Joseph R

“…This protocol describes DAP-seq, a transcription-factor binding site discovery assay that can be used to produce cistrome and epicistrome maps for any…”
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High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types by Shulse, Christine N., Cole, Benjamin J., Ciobanu, Doina, Lin, Junyan, Yoshinaga, Yuko, Gouran, Mona, Turco, Gina M., Zhu, Yiwen, O’Malley, Ronan C., Brady, Siobhan M., Dickel, Diane E.

“…Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but…”
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Persistence and plasticity in bacterial gene regulation by Baumgart, Leo A., Lee, Ji Eun, Salamov, Asaf, Dilworth, David J., Na, Hyunsoo, Mingay, Matthew, Blow, Matthew J., Zhang, Yu, Yoshinaga, Yuko, Daum, Chris G., O’Malley, Ronan C.

“…Organisms orchestrate cellular functions through transcription factor (TF) interactions with their target genes, although these regulatory relationships are…”
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Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii by Weng, Xiaoyu, Song, Haili, Sreedasyam, Avinash, Haque, Taslima, Zhang, Li, Chen, Cindy, Yoshinaga, Yuko, Williams, Melissa, O’Malley, Ronan C, Grimwood, Jane, Schmutz, Jeremy, Juenger, Thomas E

“…Abstract The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass…”
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Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis by Lister, Ryan, O'Malley, Ronan C., Tonti-Filippini, Julian, Gregory, Brian D., Berry, Charles C., Millar, A. Harvey, Ecker, Joseph R.

“…Deciphering the multiple layers of epigenetic regulation that control transcription is critical to understanding how plants develop and respond to their…”
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Phased diploid genome assembly with single-molecule real-time sequencing by Chin, Chen-Shan, Peluso, Paul, Sedlazeck, Fritz J, Nattestad, Maria, Concepcion, Gregory T, Clum, Alicia, Dunn, Christopher, O'Malley, Ronan, Figueroa-Balderas, Rosa, Morales-Cruz, Abraham, Cramer, Grant R, Delledonne, Massimo, Luo, Chongyuan, Ecker, Joseph R, Cantu, Dario, Rank, David R, Schatz, Michael C

“…The open-source FALCON and FALCON-Unzip software utilize long-read sequencing data to generate contiguous, accurate and phased diploid assemblies, even from…”
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IgG4 Disease-Related Ataxia by Hadjivassiliou, Marios, Blackburn, Daniel, O’Malley, Ronan, Hoggard, Nigel

“…We describe a male patient presenting with cerebellar ataxia and behavioural frontotemporal dementia in whom imaging showed cerebellar atrophy. He had…”
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Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells by Lister, Ryan, Pelizzola, Mattia, Kida, Yasuyuki S., Hawkins, R. David, Nery, Joseph R., Hon, Gary, Antosiewicz-Bourget, Jessica, O’Malley, Ronan, Castanon, Rosa, Klugman, Sarit, Downes, Michael, Yu, Ruth, Stewart, Ron, Ren, Bing, Thomson, James A., Evans, Ronald M., Ecker, Joseph R.

“…Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development. Somatic cell reprogramming…”
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A Qualitative Meta-Analysis Exploring Client-Reported Outcomes of Couple Therapy by O'Malley, Ronan, Glenny, Rebecca, Poppleton, Simone, Timulak, Ladislav

“…The quantitative reviews of the outcome research on couple therapy show that this type of therapy can produce positive outcomes for couples and improve…”
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The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus by Wu, Vincent W., Thieme, Nils, Huberman, Lori B., Dietschmann, Axel, Kowbel, David J., Lee, Juna, Calhoun, Sara, Singan, Vasanth R., Lipzen, Anna, Xiong, Yi, Monti, Remo, Blow, Matthew J., O’Malley, Ronan C., Grigoriev, Igor V., Benz, J. Philipp, Glass, N. Louise

“…Filamentous fungi, such as Neurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading…”
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Voltage-dependent gating of SV channel TPC1 confers vacuole excitability by Jaślan, Dawid, Dreyer, Ingo, Lu, Jinping, O’Malley, Ronan, Dindas, Julian, Marten, Irene, Hedrich, Rainer

“…In contrast to the plasma membrane, the vacuole membrane has not yet been associated with electrical excitation of plants. Here, we show that mesophyll…”
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The Arabidopsis Auxin Receptor F-Box Proteins AFB4 and AFB5 Are Required for Response to the Synthetic Auxin Picloram by Prigge, Michael J, Greenham, Kathleen, Zhang, Yi, Santner, Aaron, Castillejo, Cristina, Mutka, Andrew M, O'Malley, Ronan C, Ecker, Joseph R, Kunkel, Barbara N, Estelle, Mark

“…The plant hormone auxin is perceived by a family of F-box proteins called the TIR1/AFBs. Phylogenetic studies reveal that these proteins fall into four clades…”
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CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping by Wanamaker, Shelly A, Garza, Renee M, MacWilliams, Andrew, Nery, Joseph R, Bartlett, Anna, Castanon, Rosa, Goubil, Adeline, Feeney, Joseph, O'Malley, Ronan, Huang, Shao-shan C, Zhang, Zhuzhu Z, Galli, Mary, Ecker, Joseph R

“…CrY2H-seq, a Cre recombinase reporter-mediated yeast two-hybrid method coupled with next-generation sequencing, enables ultra-high-throughput screening of…”
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PO236 A rare encounter with a common condition: encephalopathy in a tourist by O’Malley, Ronan, Majid, Arshad

“…A 24 year old lady with a background of an arteriovenous malformation treated with the Gamma Knife. She had travelled extensively throughout South East Asia…”
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Rear-Lamp Vehicle Detection and Tracking in Low-Exposure Color Video for Night Conditions by O'Malley, Ronan, Jones, Edward, Glavin, Martin

“…Automated detection of vehicles in front is an integral component of many advanced driver-assistance systems (ADAS), such as collision mitigation, automatic…”
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Genome Sequencing by Yoshinaga, Yuko, Daum, Christopher, He, Guifen, O'Malley, Ronan

“…Strategies for sequencing fungal genomes on next-generation sequencing (NGS) platforms depend on the characteristics of the genome of the targeted species,…”
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DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus by Huberman, Lori B., Wu, Vincent W., Kowbel, David J., Lee, Juna, Daum, Chris, Grigoriev, Igor V., O’Malley, Ronan C., Glass, N. Louise

“…Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of…”
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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis by Potok, Magdalena E, Zhong, Zhenhui, Picard, Colette L, Liu, Qikun, Do, Truman, Jacobsen, Cassidy E, Sakr, Ocean, Naranbaatar, Bilguudei, Thilakaratne, Ruwan, Khnkoyan, Zhanna, Purl, Megan, Cheng, Harrison, Vervaet, Helena, Feng, Suhua, Rayatpisheh, Shima, Wohlschlegel, James A, O'Malley, Ronan C, Ecker, Joseph R, Jacobsen, Steven E

“…ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Reduction of…”
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The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle by Strenkert, Daniela, Yildirim, Asli, Yan, Juying, Yoshinaga, Yuko, Pellegrini, Matteo, O'Malley, Ronan C., Merchant, Sabeeha S., Umen, James G.

“…SUMMARY Chromatin modifications are epigenetic regulatory features with major roles in various cellular events, yet they remain understudied in algae. We…”
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