Now showing items 1-10 of 10

    • Cas9 Functionally Opens Chromatin 

      Barkal, Amira A.; Srinivasan, Sharanya; Hashimoto, Tatsunori; Gifford, David K.; Sherwood, Richard I. (Public Library of Science, 2016)
      Using a nuclease-dead Cas9 mutant, we show that Cas9 reproducibly induces chromatin accessibility at previously inaccessible genomic loci. Cas9 chromatin opening is sufficient to enable adjacent binding and transcriptional ...
    • 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. ...
    • Functional evaluation of ES cell-derived endodermal populations reveals differences between Nodal and Activin A-guided differentiation 

      Chen, Alice E.; Borowiak, Malgorzata; Sherwood, Richard Irving; Kweudjeu, Anastasie; Melton, Douglas A. (The Company of Biologists, 2013)
      Embryonic stem (ES) cells hold great promise with respect to their potential to be differentiated into desired cell types. Of interest are organs derived from the definitive endoderm, such as the pancreas and liver, and ...
    • Generation of Multipotent Lung and Airway Progenitors from Mouse ESCs and Patient-Specific Cystic Fibrosis iPSCs 

      Mou, Hongmei; Zhao, Rui; Sherwood, Richard Irving; Ahfeldt, Tim; Lapey, Allen; Wain, John Charles; Sicilian, Leonard; Izvolsky, Konstantin; Lau, Frank; Musunuru, Kiran; Cowan, Chad A.; Rajagopal, Jayaraj (Elsevier BV, 2012)
      Deriving lung progenitors from patient-specific pluripotent cells is a key step in producing differentiated lung epithelium for disease modeling and transplantation. By mimicking the signaling events that occur during mouse ...
    • Genetic Targeting of the Endoderm with Claudin-6CreER 

      Anderson, William J.; Zhou, Qiao; Alcalde, Victor; Kaneko, Osamu F; Blank, Leah J; Sherwood, Richard Irving; Guseh, James Sawalla; Rajagopal, Jayaraj; Melton, Douglas A. (Wiley-Blackwell, 2008)
      A full description of the ontogeny of the β cell would guide efforts to generate β cells from embryonic stem cells (ESCs). The first step requires an understanding of definitive endoderm: the genes and signals responsible ...
    • An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding 

      Mahony, Shaun; Edwards, Matthew D.; Mazzoni, Esteban O.; Sherwood, Richard I.; Kakumanu, Akshay; Morrison, Carolyn A.; Wichterle, Hynek; Gifford, David K. (Public Library of Science, 2014)
      Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning ...
    • 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 ...
    • MicroRNAs Are Indispensable for Reprogramming Mouse Embryonic Fibroblasts into Induced Stem Cell-Like Cells 

      Kim, Byeong-Moo; Thier, Marc-Christian; Oh, Sangnam; Sherwood, Richard Irving; Kanellopoulou, Chryssa; Edenhofer, Frank; Choi, Michael Yoon-Suk (Public Library of Science, 2012)
      MicroRNAs play a pivotal role in cellular maintenance, proliferation, and differentiation. They have also been implicated to play a key role in disease pathogenesis, and more recently, cellular reprogramming. Certain ...
    • Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal 

      Niakan, K. K.; Ji, H.; Maehr, R.; Vokes, S. A.; Rodolfa, K. T.; Sherwood, Richard Irving; Yamaki, M.; Dimos, J. T.; Chen, A. E.; Melton, Douglas A.; McMahon, Andrew P.; Eggan, Kevin Carl (Cold Spring Harbor Laboratory Press, 2010)
      In embryonic stem (ES) cells, a well-characterized transcriptional network promotes pluripotency and represses gene expression required for differentiation. In comparison, the transcriptional networks that promote ...
    • Wnt signaling specifies and patterns intestinal endoderm 

      Sherwood, Richard I.; Maehr, Rene; Mazzoni, Esteban O.; Melton, Douglas A. (Elsevier BV, 2011)
      Wnt signaling has been implicated in many developmental processes, but its role in early endoderm development is not well understood. Wnt signaling is active in posterior endoderm as early as E7.5. Genetic and chemical ...