Browsing by Author "Smith, Zachary"

Now showing items 1-8 of 8

    • DNA methylation dynamics of the human preimplantation embryo 

      Smith, Zachary D.; Chan, Michelle M.; Humm, Kathryn C.; Karnik, Rahul; Mekhoubad, Shila; Regev, Aviv; Eggan, Kevin; Meissner, Alexander (2014)
      In mammals, cytosine methylation is predominantly restricted to CpG dinucleotides and stably distributed across the genome, with local, cell type-specific regulation directed by DNA binding factors1-3. This comparatively ...

    • Epigenomics and Chromatin Dynamics 

      Akopian, Veronika; Chan, Michelle; Clement, Kendell; Galonska, Christina; Gifford, Casey; Lehtola, Elizabeth; Liao, Jing; Samavarchi-Tehrani, Payman; Sindhu, Camille; Smith, Zachary D; Tsankov, Alexander; Webster, Jamie Orme; Zhang, Yingying; Ziller, Michael Johannes; Meissner, Alexander (BioMed Central, 2012)
      A report of the 'Joint Keystone Symposium on Epigenomics and Chromatin Dynamics', Keystone, Colorado, 17-22 January 2012. This year's Joint Keystone Symposium on Epigenomics and Chromatin Dynamics was one of the largest ...

    • Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling 

      Boyle, Patrick; Clement, Kendell; Gu, Hongcang; Smith, Zachary D; Ziller, Michael Johannes; Fostel, Jennifer L; Holmes, Laurie; Meldrim, Jim; Kelley, Fontina; Gnirke, Andreas; Meissner, Alexander (BioMed Central, 2012)
      Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To ...

    • Genome-Scale DNA Methylation Mapping of Clinical Samples at Single-Nucleotide Resolution 

      Gu, Hongcang; Bock, Christoph; Mikkelsen, Tarjei S; Jäger, Natalie; Smith, Zachary D; Tomazou, Eleni; Gnirke, Andreas; Lander, Eric Steven; Meissner, Alexander (Nature Publishing Group, 2010)
      Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical ...

    • Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA 

      Warren, Luigi; Manos, Philip D.; Ahfeldt, Tim; Loh, Yuin-Han; Li, Hu; Lau, Frank; Ebina, Wataru; Mandal, Pankaj Kumar; Smith, Zachary D; Meissner, Alexander; Daley, George Quentin; Brack, Andrew Stephen; Collins, James J.; Cowan, Chad A.; Schlaeger, Thorsten M.; Rossi, Derrick J (Elsevier BV, 2010)
      Clinical application of induced pluripotent stem cells (iPSCs) is limited by the low efficiency of iPSC derivation and the fact that most protocols modify the genome to effect cellular reprogramming. Moreover, safe and ...

    • Lung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted Loci 

      Zacharek, Sima J.; Fillmore, Christine M.; Lau, Allison N.; Gludish, David W.; Chou, Alan; Ho, Joshua W.K.; Zamponi, Raffaella; Gazit, Roi; Bock, Christoph; Jäger, Natalie; Smith, Zachary; Kim, Tae-min; Saunders, Arven H.; Wong, Janice; Lee, Joo-Hyeon; Roach, Rebecca R.; Rossi, Derrick; Meissner, Alexander; Gimelbrant, Alexander; Park, Peter; Kim, Carla (Elsevier BV, 2011-09-02)
      Bmi1 is required for the self-renewal of stem cells in many tissues including the lung epithelial stem cells, Bronchioalveolar Stem Cells (BASCs). Imprinted genes, which exhibit expression from only the maternally- or ...

    • Molecular Recording of Mammalian Embryogenesis 

      Chan, Michelle M; Smith, Zachary; Grosswendt, Stefanie; Kretzmer, Helene; Norman, Thomas; Adamson, Britt; Jost, Marco; Yang, Dian; Quinn, Jeffrey J; Jones, Matthew G; Khodaverdian, Alex; Yosef, Nir; Meissner, Alexander; Weissman, Jonathan S; Weissman, Jonathan (Nature Publishing Group, 2018-08-03)
      Ontogeny describes the emergence of complex multicellular organisms from single totipotent cells. In mammals, this field is particularly challenging due to the indeterminate relationship between self-renewal and differentiation, ...

    • Mouse Ooplasm Confers Context-Specific Reprogramming Capacity 

      Chan, Michelle; Smith, Zachary D; Egli, Dieter; Regev, Aviv; Meissner, Alexander (Nature Publishing Group, 2012)
      Enucleated oocytes have the remarkable ability to reprogram somatic nuclei back to totipotency. Here we investigate genome-scale DNA methylation patterns after nuclear transfer and compare them to the dynamics at fertilization. ...