Browsing by Author "Jaakkola, Tommi"

Now showing items 1-2 of 2

    • Discovery of non-directional and directional pioneer transcription factors by modeling DNase profile magnitude and shape 

      Sherwood, Richard I; Hashimoto, Tatsunori; O'Donnell, Charles W; Lewis, Sophia; Barkal, Amira A; van Hoff, John Peter; Karun, Vivek; Jaakkola, Tommi; Gifford, David K (2014)
      Here we describe Protein Interaction Quantitation (PIQ), a computational method that models the magnitude and shape of genome-wide DNase profiles to facilitate the identification of transcription factor (TF) binding sites. ...

    • Lineage-Based Identification of Cellular States and Expression Programs 

      Hashimoto, Tatsunori Benjamin; Jaakkola, Tommi; Sherwood, Richard Irving; Mazzoni, Esteban O.; Wichterle, Hynek; Gifford, David Kenneth (Oxford University Press, 2012)
      Summary: We present a method, LineageProgram, that uses the developmental lineage relationship of observed gene expression measurements to improve the learning of developmentally relevant cellular states and expression ...