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10.1101/gr.199778.115 http://scihub22266oqcxt.onion/10.1101/gr.199778.115 C5052050!5052050!27456004     free     free     free Deprecated: Implicit conversion from float 225.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 225.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Genome+Res 2016 ; 26 (10): 1430-40 Nephropedia Template TP {{tp|p=27456004|t=2016. A synergistic DNA logic predicts genome-wide chromatin accessibility |pdf=|usr=}}{{27456004}} gab.com Text A synergistic DNA logic predicts genome-wide chromatin accessibility JO: Genome Res http://www.kidney.de/pget.php?&tw=1&pmid=27456004 #FOAvip Enhancers and promoters commonly occur in accessible chromatin characterized by depleted nucleosome contact; however, it is unclear how chromatin accessibility is governed. We show that log-additive cis-acting DNA sequence features can predict chromatin accessibility at high spatial resolution. We develop a new type of high-dimensional machine learning model, the Synergistic Chromatin Model (SCM), which when trained with DNase-seq data for a cell type is capable of predicting expected read counts of genome-wide chromatin accessibility at every base from DNA sequence alone, with the highest accuracy at hypersensitive sites shared across cell types. We confirm that a SCM accurately predicts chromatin accessibility for thousands of synthetic DNA sequences using a novel CRISPR-based method of highly efficient site-specific DNA library integration. SCMs are directly interpretable and reveal that a logic based on local, nonspecific synergistic effects, largely among pioneer TFs, is sufficient to predict a large fraction of cellular chromatin accessibility in a wide variety of cell types. Twit Text FOAVip A synergistic DNA logic predicts genome-wide chromatin accessibility ????Genome Res http://www.kidney.de/pget.php?&tw=1&pmid=27456004 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=27456004 #FOAvip English Wikipedia <ref>{{Cite pmid|27456004}}</ref> A synergistic DNA logic predicts genome-wide chromatin accessibility #MMPMID27456004 Hashimoto T; Sherwood RI; Kang DD; Rajagopal N; Barkal AA; Zeng H; Emons BJ; Srinivasan S; Jaakkola T; Gifford DK Genome Res 2016[Oct]; 26 (10): 1430-40 PMID27456004show ga Enhancers and promoters commonly occur in accessible chromatin characterized by depleted nucleosome contact; however, it is unclear how chromatin accessibility is governed. We show that log-additive cis-acting DNA sequence features can predict chromatin accessibility at high spatial resolution. We develop a new type of high-dimensional machine learning model, the Synergistic Chromatin Model (SCM), which when trained with DNase-seq data for a cell type is capable of predicting expected read counts of genome-wide chromatin accessibility at every base from DNA sequence alone, with the highest accuracy at hypersensitive sites shared across cell types. We confirm that a SCM accurately predicts chromatin accessibility for thousands of synthetic DNA sequences using a novel CRISPR-based method of highly efficient site-specific DNA library integration. SCMs are directly interpretable and reveal that a logic based on local, nonspecific synergistic effects, largely among pioneer TFs, is sufficient to predict a large fraction of cellular chromatin accessibility in a wide variety of cell types. äA synergistic DNA logic predicts genome-wide chromatin accessibility (epmc).pdf DeepDyve Pubget Overpricing