Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments von Bullard, James H, Purdom, Elizabeth, Hansen, Kasper D, Dudoit, Sandrine

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Functional normalization of 450k methylation array data improves replication in large cancer studies von Fortin, Jean-Philippe, Labbe, Aurélie, Lemire, Mathieu, Zanke, Brent W, Hudson, Thomas J, Fertig, Elana J, Greenwood, Celia Mt, Hansen, Kasper D

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Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data von Fortin, Jean-Philippe, Hansen, Kasper D

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Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays von Aryee, Martin J., Jaffe, Andrew E., Corrada-Bravo, Hector, Ladd-Acosta, Christine, Feinberg, Andrew P., Hansen, Kasper D., Irizarry, Rafael A.

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Biases in Illumina transcriptome sequencing caused by random hexamer priming von Hansen, Kasper D, Brenner, Steven E, Dudoit, Sandrine

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Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver von Li, Xin, Liu, Yun, Salz, Tal, Hansen, Kasper D, Feinberg, Andrew

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Addressing the mean-correlation relationship in co-expression analysis von Wang, Yi, Hicks, Stephanie C, Hansen, Kasper D

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recount3: summaries and queries for large-scale RNA-seq expression and splicing von Wilks, Christopher, Zheng, Shijie C., Chen, Feng Yong, Charles, Rone, Solomon, Brad, Ling, Jonathan P., Imada, Eddie Luidy, Zhang, David, Joseph, Lance, Leek, Jeffrey T., Jaffe, Andrew E., Nellore, Abhinav, Collado-Torres, Leonardo, Hansen, Kasper D., Langmead, Ben

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A mammalian methylation array for profiling methylation levels at conserved sequences von Arneson, Adriana, Haghani, Amin, Thompson, Michael J., Pellegrini, Matteo, Kwon, Soo Bin, Vu, Ha, Maciejewski, Emily, Yao, Mingjia, Li, Caesar Z., Lu, Ake T., Morselli, Marco, Rubbi, Liudmilla, Barnes, Bret, Hansen, Kasper D., Zhou, Wanding, Breeze, Charles E., Ernst, Jason, Horvath, Steve

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BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions von Hansen, Kasper D, Langmead, Benjamin, Irizarry, Rafael A

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nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes von Weber, Lukas M., Saha, Arkajyoti, Datta, Abhirup, Hansen, Kasper D., Hicks, Stephanie C.

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Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates von Zheng, Shijie C, Stein-O'Brien, Genevieve, Boukas, Leandros, Goff, Loyal A, Hansen, Kasper D

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Bacterial infection remodels the DNA methylation landscape of human dendritic cells von Pacis, Alain, Tailleux, Ludovic, Morin, Alexander M, Lambourne, John, MacIsaac, Julia L, Yotova, Vania, Dumaine, Anne, Danckaert, Anne, Luca, Francesca, Grenier, Jean-Christophe, Hansen, Kasper D, Gicquel, Brigitte, Yu, Miao, Pai, Athma, He, Chuan, Tung, Jenny, Pastinen, Tomi, Kobor, Michael S, Pique-Regi, Roger, Gilad, Yoav, Barreiro, Luis B

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Common DNA sequence variation influences 3-dimensional conformation of the human genome von Gorkin, David U, Qiu, Yunjiang, Hu, Ming, Fletez-Brant, Kipper, Liu, Tristin, Schmitt, Anthony D, Noor, Amina, Chiou, Joshua, Gaulton, Kyle J, Sebat, Jonathan, Li, Yun, Hansen, Kasper D, Ren, Bing

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Social environment is associated with gene regulatory variation in the rhesus macaque immune system von Tung, Jenny, Barreiro, Luis B, Johnson, Zachary P, Hansen, Kasper D, Michopoulos, Vasiliki, Toufexis, Donna, Michelini, Katelyn, Wilson, Mark E, Gilad, Yoav

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Universal prediction of cell-cycle position using transfer learning von Zheng, Shijie C, Stein-O'Brien, Genevieve, Augustin, Jonathan J, Slosberg, Jared, Carosso, Giovanni A, Winer, Briana, Shin, Gloria, Bjornsson, Hans T, Goff, Loyal A, Hansen, Kasper D

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A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome von Benjamin, Joel S., Pilarowski, Genay O., Carosso, Giovanni A., Zhang, Li, Huso, David. L., Goff, Loyal A., Vernon, Hilary J., Hansen, Kasper D., Bjornsson, Hans T.

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Growth deficiency in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1 von Gao, Christine W, Lin, WanYing, Riddle, Ryan C, Chopra, Sheetal, Kim, Jiyoung, Boukas, Leandros, Hansen, Kasper D, Björnsson, Hans T, Fahrner, Jill A

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Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin von Vandiver, Amy R, Irizarry, Rafael A, Hansen, Kasper D, Garza, Luis A, Runarsson, Arni, Li, Xin, Chien, Anna L, Wang, Timothy S, Leung, Sherry G, Kang, Sewon, Feinberg, Andrew P

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Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits von Rizzardi, Lindsay F., Hickey, Peter F., Idrizi, Adrian, Tryggvadottir, Rakel, Callahan, Colin M., Stephens, Kimberly E., Taverna, Sean D., Zhang, Hao, Ramazanoglu, Sinan, Hansen, Kasper D., Feinberg, Andrew P.

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