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

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Normalization of RNA-seq data using factor analysis of control genes or samples von Risso, Davide, Ngai, John, Speed, Terence P, Dudoit, Sandrine

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GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly von Cameron, Daniel L, Schröder, Jan, Penington, Jocelyn Sietsma, Do, Hongdo, Molania, Ramyar, Dobrovic, Alexander, Speed, Terence P, Papenfuss, Anthony T

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RLE plots: Visualizing unwanted variation in high dimensional data von Gandolfo, Luke C, Speed, Terence P

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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... von Zhang, Yu, Mayba, Oleg, Pfeiffer, Anne, Shi, Hui, Tepperman, James M, Speed, Terence P, Quail, Peter H

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A Tetrahymena Piwi Bound to Mature tRNA 3′ Fragments Activates the Exonuclease Xrn2 for RNA Processing in the Nucleus von Couvillion, Mary T., Bounova, Gergana, Purdom, Elizabeth, Speed, Terence P., Collins, Kathleen

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The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE" von 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

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A statistical framework for analyzing deep mutational scanning data von Rubin, Alan F, Gelman, Hannah, Lucas, Nathan, Bajjalieh, Sandra M, Papenfuss, Anthony T, Speed, Terence P, Fowler, Douglas M

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Network inference using informative priors von Mukherjee, Sach, Speed, Terence P

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scClassify: sample size estimation and multiscale classification of cells using single and multiple reference von Lin, Yingxin, Cao, Yue, Kim, Hani Jieun, Salim, Agus, Speed, Terence P, Lin, David M, Yang, Pengyi, Yang, Jean Yee Hwa

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RUV-III-NB: normalization of single cell RNA-seq data von Salim, Agus, Molania, Ramyar, Wang, Jianan, De Livera, Alysha, Thijssen, Rachel, Speed, Terence P

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A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development von 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

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scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets von 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

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Identification of cancer sex-disparity in the functional integrity of p53 and its X chromosome network von Haupt, Sue, Caramia, Franco, Herschtal, Alan, Soussi, Thierry, Lozano, Guillermina, Chen, Hu, Liang, Han, Speed, Terence P., Haupt, Ygal

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Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments von 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.

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Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis von Yu, Chi-Yi, Mayba, Oleg, Lee, Joyce V, Tran, Joanna, Harris, Charlie, Speed, Terence P, Wang, Jen-Chywan

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The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective von Jacob, Laurent, Speed, Terence P

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GOstat: find statistically overrepresented Gene Ontologies within a group of genes von Beißbarth, Tim, Speed, Terence P.

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Changes in ferrous iron and glutathione promote ferroptosis and frailty in aging Caenorhabditis elegans von Jenkins, Nicole L., James, Simon A., Salim, Agus, Sumardy, Fransisca, Speed, Terence P., Conrad, Marcus, Richardson, Des R., Bush, Ashley, McColl, Gawain

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Comparing somatic mutation-callers: beyond Venn diagrams von Kim, Su Yeon, Speed, Terence P

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