Now showing items 1-8 of 8

    • A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression 

      Guintivano, Jerry; Aryee, Martin J.; Kaminsky, Zachary A. (Landes Bioscience, 2013)
      Brain cellular heterogeneity may bias cell type specific DNA methylation patterns, influencing findings in psychiatric epigenetic studies. We performed fluorescence activated cell sorting (FACS) of neuronal nuclei and ...
    • Coverage recommendations for methylation analysis by whole genome bisulfite sequencing 

      Ziller, Michael J.; Hansen, Kasper D.; Meissner, Alexander; Aryee, Martin J. (2014)
      Whole genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling but the associated high sequencing costs continue to limit its widespread application. We utilized several high coverage reference data ...
    • Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing 

      Tsai, Shengdar Q.; Wyvekens, Nicolas; Khayter, Cyd; Foden, Jennifer A.; Thapar, Vishal; Reyon, Deepak; Goodwin, Mathew J.; Aryee, Martin J.; Joung, J. Keith (2014)
      Monomeric CRISPR-Cas9 nucleases are widely used for targeted genome editing but can induce unwanted off-target mutations with high frequencies. Here we describe dimeric RNA-guided FokI Nucleases (RFNs) that recognize ...
    • Engineered CRISPR-Cas9 nucleases with altered PAM specificities 

      Kleinstiver, Benjamin P.; Prew, Michelle S.; Tsai, Shengdar Q.; Topkar, Ved; Nguyen, Nhu T.; Zheng, Zongli; Gonzales, Andrew P.W.; Li, Zhuyun; Peterson, Randall T.; Yeh, Jing-Ruey Joanna; Aryee, Martin J.; Joung, J. Keith (2015)
      Although CRISPR-Cas9 nucleases are widely used for genome editing1, 2, the range of sequences that Cas9 can recognize is constrained by the need for a specific protospacer adjacent motif (PAM)3–6. As a result, it can often ...
    • Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells 

      Kleinstiver, Benjamin P.; Tsai, Shengdar Q.; Prew, Michelle S.; Nguyen, Nhu T.; Welch, Moira M.; Lopez, Jose M.; McCaw, Zachary R.; Aryee, Martin J.; Joung, J. Keith (2016)
      The activities and genome-wide specificities of CRISPR-Cas Cpf1 nucleases1 are not well defined. We show that two Cpf1 nucleases from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, ...
    • GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases 

      Tsai, Shengdar Q.; Zheng, Zongli; Nguyen, Nhu T.; Liebers, Matthew; Topkar, Ved V.; Thapar, Vishal; Wyvekens, Nicolas; Khayter, Cyd; Iafrate, A. John; Le, Long P.; Aryee, Martin J.; Joung, J. Keith (2014)
      CRISPR RNA-guided nucleases (RGNs) are widely used genome-editing reagents, but methods to delineate their genome-wide off-target cleavage activities have been lacking. Here we describe an approach for global detection of ...
    • High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis 

      Gomez-Cabrero, David; Almgren, Malin; Sjöholm, Louise K.; Hensvold, Aase H.; Ringh, Mikael V.; Tryggvadottir, Rakel; Kere, Juha; Scheynius, Annika; Acevedo, Nathalie; Reinius, Lovisa; Taub, Margaret A.; Montano, Carolina; Aryee, Martin J.; Feinberg, Jason I.; Feinberg, Andrew P.; Tegnér, Jesper; Klareskog, Lars; Catrina, Anca I.; Ekström, Tomas J. (BioMed Central, 2016)
      Background: Twin studies are powerful models to elucidate epigenetic modifications resulting from gene–environment interactions. Yet, commonly a limited number of clinical twin samples are available, leading to an underpowered ...
    • Identification of direction in gene networks from expression and methylation 

      Simcha, David M; Younes, Laurent; Aryee, Martin J; Geman, Donald (BioMed Central, 2013)
      Background: Reverse-engineering gene regulatory networks from expression data is difficult, especially without temporal measurements or interventional experiments. In particular, the causal direction of an edge is generally ...