Search Results - "Yigit, Erbay"

The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1 by Grünberg, Sebastian, Doyle, Lindsey A, Wolf, Eric J, Dai, Nan, Corrêa, Jr, Ivan R, Yigit, Erbay, Stoddard, Barry L

“…The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification…”
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A method for selectively enriching microbial DNA from contaminating vertebrate host DNA by Feehery, George R, Yigit, Erbay, Oyola, Samuel O, Langhorst, Bradley W, Schmidt, Victor T, Stewart, Fiona J, Dimalanta, Eileen T, Amaral-Zettler, Linda A, Davis, Theodore, Quail, Michael A, Pradhan, Sriharsa

“…DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component…”
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Expression of Human ACE2 N-terminal Domain, Part of the Receptor for SARS-CoV-2, in Fusion With Maltose-Binding Protein, E. coli Ribonuclease I and Human RNase A by Xu, Shuang-yong, Fomenkov, Alexey, Chen, Tien-Hao, Yigit, Erbay

“…Graphical Abstract Cartoon illustration part of this work (Human ACE2 N-terminal domain tethered to RNase A and RNA degradation by the fusion enzyme). The…”
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An RIG-I-Like RNA helicase mediates antiviral RNAi downstream of viral siRNA biogenesis in Caenorhabditis elegans by Lu, Rui, Yigit, Erbay, Li, Wan-Xiang, Ding, Shou-Wei

“…Dicer ribonucleases of plants and invertebrate animals including Caenorhabditis elegans recognize and process a viral RNA trigger into virus-derived small…”
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Genome and Metagenome Sequencing: Using the Human Methyl-Binding Domain to Partition Genomic DNA Derived from Plant Tissues by Yigit, Erbay, Hernandez, David I, Trujillo, Joshua T, Dimalanta, Eileen, Bailey, C. Donovan

“…Premise of the study: Variation in the distribution of methylated CpG (methyl-CpG) in genomic DNA (gDNA) across the tree of life is biologically interesting…”
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A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome by Ettwiller, Laurence, Buswell, John, Yigit, Erbay, Schildkraut, Ira

“…The initiating nucleotide found at the 5' end of primary transcripts has a distinctive triphosphorylated end that distinguishes these transcripts from all…”
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Comparative analysis of strand-specific RNA sequencing approaches by Munafo, Daniela, Liu, Ping, Sumner, Christine, Yigit, Erbay, Merrill, Landon, Apone, Lynne, Langhorst, Brad, Stewart, Fiona, Dimalanta, Eileen T, Davis, Theodore

“…Doc number: P30…”
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A fast solution to NGS library preparation with low nanogram DNA input by Liu, Pingfang, Lohman, Gregory JS, Cantor, Eric, Langhorst, Bradley W, Yigit, Erbay, Apone, Lynne M, Munafo, Daniela B, Sumner, Christine, Stewart, Fiona J, Evans, Thomas C, Nichols, Nicole M, Dimalanta, Eileen T, Davis, Theodore B

“…Doc number: P26…”
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The amino terminus of the coat protein of Turnip crinkle virus is the AVR factor recognized by resistant arabidopsis by YAJUAN ZHAO, DELGROSSO, L, YIGIT, E, D'MARIS AMICK DEMPSEY, KLESSIG, D. F, WOBBE, K. K

“…We have isolated three naturally occurring strains of Turnip crinkle virus (TCV) that break resistance in Di-17 Arabidopsis. Two mutations in the N terminus of…”
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Human RNase 4 improves mRNA sequence characterization by LC–MS/MS by Wolf, Eric J, Grünberg, Sebastian, Dai, Nan, Chen, Tien-Hao, Roy, Bijoyita, Yigit, Erbay, Corrêa, Ivan R

“…Abstract With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of…”
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E. coli RNase I exhibits a strong Ca2+-dependent inherent double-stranded RNase activity by Grünberg, Sebastian, Coxam, Baptiste, Chen, Tien-Hao, Dai, Nan, Saleh, Lana, Corrêa, Ivan R, Nichols, Nicole M, Yigit, Erbay

“…Abstract Since its initial characterization, Escherichia coli RNase I has been described as a single-strand specific RNA endonuclease that cleaves its…”
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Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme by Vaisvila, Romualdas, Johnson, Sean R, Yan, Bo, Dai, Nan, Bourkia, Billal M, Chen, Minyong, Corrêa, Jr, Ivan R, Yigit, Erbay, Sun, Zhiyi

“…Deaminases have important uses in modification detection and genome editing. However, the range of applications is limited by the small number of characterized…”
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Analysis of the C. elegans Argonaute Family Reveals that Distinct Argonautes Act Sequentially during RNAi by Yigit, Erbay, Batista, Pedro J., Bei, Yanxia, Pang, Ka Ming, Chen, Chun-Chieh G., Tolia, Niraj H., Joshua-Tor, Leemor, Mitani, Shohei, Simard, Martin J., Mello, Craig C.

“…Argonaute (AGO) proteins interact with small RNAs to mediate gene silencing. C. elegans contains 27 AGO genes, raising the question of what roles these genes…”
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The dsRNA Binding Protein RDE-4 Interacts with RDE-1, DCR-1, and a DExH-Box Helicase to Direct RNAi in C. elegans by Tabara, Hiroaki, Yigit, Erbay, Siomi, Haruhiko, Mello, Craig C.

“…Double-stranded (ds) RNA induces potent gene silencing, termed RNA interference (RNAi). At an early step in RNAi, an RNaseIII-related enzyme, Dicer (DCR-1),…”
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Enhanced expression and purification of nucleotide-specific ribonucleases MC1 and Cusativin by Grünberg, Sebastian, Wolf, Eric J., Jin, Jingming, Ganatra, Mehul B., Becker, Kelly, Ruse, Cristian, Taron, Christopher H., Corrêa, Ivan R., Yigit, Erbay

“…Combinations of ribonucleases (RNases) are commonly used to digest RNA into oligoribonucleotide fragments prior to liquid chromatography-mass spectrometry…”
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The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1 by Sebastian Grünberg, Lindsey A. Doyle, Eric J. Wolf, Nan Dai, Ivan R. Corrêa, Erbay Yigit, Barry L. Stoddard

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Abstract 820: Enzymatic Methyl-Seq: methylome analysis of challenging DNA samples by Williams, Louise, Ponnaluri, V K Chaithanya, Sexton, Brittany S., Saleh, Lana, Marks, Katherine, Samaranayake, Mala, Ettwiller, Laurence, Guan, Shengxi, Church, Heidi E., Dai, Nan, Tamanaha, Esta, Yigit, Erbay, Langhorst, Bradley, Sun, Zhiyi, Evans, Thomas C., Vaisvila, Romualdas, Dimalanta, Eileen, Davis, Theodore B.

“…Abstract DNA isolated from blood draws (cell-free DNA (cfDNA)) or from archival material like formalin fixed paraffin embedded (FFPE) tissues have advanced the…”
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High-resolution nucleosome mapping of targeted regions using BAC-based enrichment by Yigit, Erbay, Zhang, Quanwei, Xi, Liqun, Grilley, Dan, Widom, Jonathan, Wang, Ji-Ping, Rao, Anjana, Pipkin, Matthew E

“…We report a target enrichment method to map nucleosomes of large genomes at unprecedented coverage and resolution by deeply sequencing locus-specific…”
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Abstract 5406: Low-input transcript profiling with enhanced sensitivity using a highly efficient, low-bias and strand-specific RNA-Seq library preparation method by Krishnan, Keerthana, Yigit, Erbay, Karaca, Mehmet, Rodriguez, Deyra, Langhorst, Bradley, Shtatland, Timur, Munafo, Daniela, Liu, Pingfang, Apone, Lynne, Panchapakesa, Vaishnavi, Duggan, Karen, Sumner, Christine, Rozzi, Christine, Stewart, Fiona, Mazzola, Laurie, Bybee, Joanna, Rivizzigno, Danielle, Dimalanta, Eileen T., Davis, Theodore B.

“…Abstract RNA-seq has become the most popular method for transcriptome analysis and is widely used to study gene expression, detect mutations, fusion…”
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High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster by Freaney, Jonathan E, Zhang, Quanwei, Yigit, Erbay, Kim, Rebecca, Widom, Jonathan, Wang, Ji-Ping, Horvath, Curt M

“…Genome-wide investigations have dramatically increased our understanding of nucleosome positioning and the role of chromatin in gene regulation, yet some…”
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