Now showing items 1-6 of 6

    • Accounting for cellular heterogeneity is critical in epigenome-wide association studies 

      Jaffe, Andrew E; Irizarry, Rafael A (BioMed Central, 2014)
      Background: Epigenome-wide association studies of human disease and other quantitative traits are becoming increasingly common. A series of papers reporting age-related changes in DNA methylation profiles in peripheral ...
    • A benchmark for RNA-seq quantification pipelines 

      Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. (BioMed Central, 2016)
      Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, ...
    • Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors 

      Timp, Winston; Bravo, Hector Corrada; McDonald, Oliver G; Goggins, Michael; Umbricht, Chris; Zeiger, Martha; Feinberg, Andrew P; Irizarry, Rafael A (BioMed Central, 2014)
      Background: One of the most provocative recent observations in cancer epigenetics is the discovery of large hypomethylated blocks, including single copy genes, in colorectal cancer, that correspond in location to heterochromatic ...
    • MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens 

      Li, Wei; Xu, Han; Xiao, Tengfei; Cong, Le; Love, Michael I; Zhang, Feng; Irizarry, Rafael A; Liu, Jun S; Brown, Myles; Liu, X Shirley (BioMed Central, 2014)
      We propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK demonstrates better ...
    • Mortality in Puerto Rico after Hurricane Maria 

      Kishore, Nishant; Marqués, Domingo; Mahmud, Ayesha S; Kiang, Mathew Vinhhoa; Rodriguez, Irmary; Fuller, Arlan F.; Ebner, Peggy; Sorensen, Cecilia; Racy, Fabio De Castro Jorge; Lemery, Jay; Maas, Leslie; Leaning, Jennifer; Irizarry, Rafael A.; Balsari, Satchit Siddharth; Buckee, Caroline O'Flaherty (New England Journal of Medicine (NEJM/MMS), 2018)
      BACKGROUND Quantifying the effect of natural disasters on society is critical for recovery of public health services and infrastructure. The death toll can be difficult to assess in the aftermath of a major disaster. In ...
    • quantro: a data-driven approach to guide the choice of an appropriate normalization method 

      Hicks, Stephanie C.; Irizarry, Rafael A. (BioMed Central, 2015)
      Normalization is an essential step in the analysis of high-throughput data. Multi-sample global normalization methods, such as quantile normalization, have been successfully used to remove technical variation. However, ...