Search Results - "Speed, Terence P."

Summarizing and correcting the GC content bias in high-throughput sequencing by Benjamini, Yuval, Speed, Terence P

“…GC content bias describes the dependence between fragment count (read coverage) and GC content found in Illumina sequencing data. This bias can dominate the…”
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Normalization of RNA-seq data using factor analysis of control genes or samples by Risso, Davide, Ngai, John, Speed, Terence P, Dudoit, Sandrine

“…Remove unwanted variation (RUV) is a new statistical method for RNA-seq data normalization that uses control genes or samples to improve differential…”
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GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly by Cameron, Daniel L, Schröder, Jan, Penington, Jocelyn Sietsma, Do, Hongdo, Molania, Ramyar, Dobrovic, Alexander, Speed, Terence P, Papenfuss, Anthony T

“…The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly…”
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RLE plots: Visualizing unwanted variation in high dimensional data by Gandolfo, Luke C, Speed, Terence P

“…Unwanted variation can be highly problematic and so its detection is often crucial. Relative log expression (RLE) plots are a powerful tool for visualizing…”
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A statistical framework for analyzing deep mutational scanning data by Rubin, Alan F, Gelman, Hannah, Lucas, Nathan, Bajjalieh, Sandra M, Papenfuss, Anthony T, Speed, Terence P, Fowler, Douglas M

“…Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational…”
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Network inference using informative priors by Mukherjee, Sach, Speed, Terence P

“…Recent years have seen much interest in the study of systems characterized by multiple interacting components. A class of statistical models called graphical…”
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A Tetrahymena Piwi Bound to Mature tRNA 3′ Fragments Activates the Exonuclease Xrn2 for RNA Processing in the Nucleus by Couvillion, Mary T., Bounova, Gergana, Purdom, Elizabeth, Speed, Terence P., Collins, Kathleen

“…Emerging evidence suggests that Argonaute (Ago)/Piwi proteins have diverse functions in the nucleus and cytoplasm, but the molecular mechanisms employed in the…”
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scClassify: sample size estimation and multiscale classification of cells using single and multiple reference by Lin, Yingxin, Cao, Yue, Kim, Hani Jieun, Salim, Agus, Speed, Terence P, Lin, David M, Yang, Pengyi, Yang, Jean Yee Hwa

“…Automated cell type identification is a key computational challenge in single‐cell RNA‐sequencing (scRNA‐seq) data. To capitalise on the large collection of…”
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A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis by Zhang, Yu, Mayba, Oleg, Pfeiffer, Anne, Shi, Hui, Tepperman, James M, Speed, Terence P, Quail, Peter H

“…Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting…”
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RUV-III-NB: normalization of single cell RNA-seq data by Salim, Agus, Molania, Ramyar, Wang, Jianan, De Livera, Alysha, Thijssen, Rachel, Speed, Terence P

“…Abstract Normalization of single cell RNA-seq data remains a challenging task. The performance of different methods can vary greatly between datasets when…”
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A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development by Modzelewski, Andrew J., Shao, Wanqing, Chen, Jingqi, Lee, Angus, Qi, Xin, Noon, Mackenzie, Tjokro, Kristy, Sales, Gabriele, Biton, Anne, Anand, Aparna, Speed, Terence P., Xuan, Zhenyu, Wang, Ting, Risso, Davide, He, Lin

“…Retrotransposons mediate gene regulation in important developmental and pathological processes. Here, we characterized the transient retrotransposon induction…”
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scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets by Lin, Yingxin, Ghazanfar, Shila, Wang, Kevin Y. X., Gagnon-Bartsch, Johann A., Lo, Kitty K., Su, Xianbin, Han, Ze-Guang, Ormerod, John T., Speed, Terence P., Yang, Pengyi, Yang, Jean Yee Hwa

“…Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq) data promises further biological insights that cannot be uncovered with…”
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The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE" by Savas, Peter, Teo, Zhi Ling, Lefevre, Christophe, Flensburg, Christoffer, Caramia, Franco, Alsop, Kathryn, Mansour, Mariam, Francis, Prudence A, Thorne, Heather A, Silva, Maria Joao, Kanu, Nnennaya, Dietzen, Michelle, Rowan, Andrew, Kschischo, Maik, Fox, Stephen, Bowtell, David D, Dawson, Sarah-Jane, Speed, Terence P, Swanton, Charles, Loi, Sherene

“…Understanding the cancer genome is seen as a key step in improving outcomes for cancer patients. Genomic assays are emerging as a possible avenue to…”
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Changes in ferrous iron and glutathione promote ferroptosis and frailty in aging Caenorhabditis elegans by Jenkins, Nicole L, James, Simon A, Salim, Agus, Sumardy, Fransisca, Speed, Terence P, Conrad, Marcus, Richardson, Des R, Bush, Ashley I, McColl, Gawain

“…All eukaryotes require iron. Replication, detoxification, and a cancer-protective form of regulated cell death termed , all depend on iron metabolism. Ferrous…”
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GOstat: find statistically overrepresented Gene Ontologies within a group of genes by Beißbarth, Tim, Speed, Terence P.

“…Modern experimental techniques, as for example DNA microarrays, as a result usually produce a long list of genes, which are potentially interesting in the…”
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Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments by Feng, Yuzhou, Yang, Tianpei, Zhu, John, Li, Mabel, Doyle, Maria, Ozcoban, Volkan, Bass, Greg T., Pizzolla, Angela, Cain, Lachlan, Weng, Sirui, Pasam, Anupama, Kocovski, Nikolce, Huang, Yu-Kuan, Keam, Simon P., Speed, Terence P., Neeson, Paul J., Pearson, Richard B., Sandhu, Shahneen, Goode, David L., Trigos, Anna S.

“…Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and…”
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Identification of cancer sex-disparity in the functional integrity of p53 and its X chromosome network by Haupt, Sue, Caramia, Franco, Herschtal, Alan, Soussi, Thierry, Lozano, Guillermina, Chen, Hu, Liang, Han, Speed, Terence P., Haupt, Ygal

“…The disproportionately high prevalence of male cancer is poorly understood. We tested for sex-disparity in the functional integrity of the major tumor…”
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The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective by Jacob, Laurent, Speed, Terence P

“…In a recent publication, Sood et al. (Genome Biol 16:185, 2015) presented a set of 150 probe sets that could be used in the diagnosis of Alzheimer's disease…”
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Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis by Yu, Chi-Yi, Mayba, Oleg, Lee, Joyce V, Tran, Joanna, Harris, Charlie, Speed, Terence P, Wang, Jen-Chywan

“…Glucocorticoids play important roles in the regulation of distinct aspects of adipocyte biology. Excess glucocorticoids in adipocytes are associated with…”
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Normalizing and Integrating Metabolomics Data by De Livera, Alysha M, Dias, Daniel A, De Souza, David, Rupasinghe, Thusitha, Pyke, James, Tull, Dedreia, Roessner, Ute, McConville, Malcolm, Speed, Terence P

“…Metabolomics research often requires the use of multiple analytical platforms, batches of samples, and laboratories, any of which can introduce a component of…”
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