Search Results - "Speed, Terence"

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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DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data by Ye, Chengzhong, Speed, Terence P, Salim, Agus

“…Dropout is a common phenomenon in single-cell RNA-seq (scRNA-seq) data, and when left unaddressed it affects the validity of the statistical analyses. Despite…”
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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 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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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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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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A new normalization for Nanostring nCounter gene expression data by Molania, Ramyar, Gagnon-Bartsch, Johann A, Dobrovic, Alexander, Speed, Terence P

“…Abstract The Nanostring nCounter gene expression assay uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts…”
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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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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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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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Using control genes to correct for unwanted variation in microarray data by Gagnon-Bartsch, Johann A, Speed, Terence P

“…Microarray expression studies suffer from the problem of batch effects and other unwanted variation. Many methods have been proposed to adjust microarray data…”
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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 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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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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Comparing somatic mutation-callers: beyond Venn diagrams by Kim, Su Yeon, Speed, Terence P

“…Somatic mutation-calling based on DNA from matched tumor-normal patient samples is one of the key tasks carried by many cancer genome projects. One such…”
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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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Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis by Savas, Peter, Virassamy, Balaji, Ye, Chengzhong, Salim, Agus, Mintoff, Christopher P., Caramia, Franco, Salgado, Roberto, Byrne, David J., Teo, Zhi L., Dushyanthen, Sathana, Byrne, Ann, Wein, Lironne, Luen, Stephen J., Poliness, Catherine, Nightingale, Sophie S., Skandarajah, Anita S., Gyorki, David E., Thornton, Chantel M., Beavis, Paul A., Fox, Stephen B., Darcy, Phillip K., Speed, Terence P., Mackay, Laura K., Neeson, Paul J., Loi, Sherene

“…The quantity of tumor-infiltrating lymphocytes (TILs) in breast cancer (BC) is a robust prognostic factor for improved patient survival, particularly in…”
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A molecular threshold for effector CD8+ T cell differentiation controlled by transcription factors Blimp-1 and T-bet by Xin, Annie, Masson, Frederick, Liao, Yang, Preston, Simon, Guan, Tianxia, Gloury, Renee, Olshansky, Moshe, Lin, Jian-Xin, Li, Peng, Speed, Terence P, Smyth, Gordon K, Ernst, Matthias, Leonard, Warren J, Pellegrini, Marc, Kaech, Susan M, Nutt, Stephen L, Shi, Wei, Belz, Gabrielle T, Kallies, Axel

“…Using genetic approaches and transcriptional profiling, Kallies and colleagues reveal a common program of effector CD8 + T cell differentiation that is…”
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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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