Search Results - "O'Geen, Henriette"

How specific is CRISPR/Cas9 really? by O’Geen, Henriette, Yu, Abigail S, Segal, David J

“…•Concerns about CRISPR specificity led to new methods for detection and avoidance.•Some studies reported many off-target events, while others observed…”
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Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing by O’Geen, Henriette, Tomkova, Marketa, Combs, Jacquelyn A, Tilley, Emma K, Segal, David J

“…Abstract Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a…”
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Using ChIP-seq technology to generate high-resolution profiles of histone modifications by O'Geen, Henriette, Echipare, Lorigail, Farnham, Peggy J

“…The dynamic modification of DNA and histones plays a key role in transcriptional regulation through -altering the packaging of DNA and modifying the nucleosome…”
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Aberrant promoter methylation contributes to LRIG1 silencing in basal/triple-negative breast cancer by Umeh-Garcia, Maxine, O’Geen, Henriette, Simion, Catalina, Gephart, Melanie Hayden, Segal, David J., Sweeney, Colleen A.

“…Background LRIG1, the founding member of the LRIG (leucine-rich repeat and immunoglobulin-like domain) family of transmembrane proteins, is a negative…”
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Architecture of the human regulatory network derived from ENCODE data by Gerstein, Mark B., Kundaje, Anshul, Hariharan, Manoj, Landt, Stephen G., Yan, Koon-Kiu, Cheng, Chao, Mu, Xinmeng Jasmine, Khurana, Ekta, Rozowsky, Joel, Alexander, Roger, Min, Renqiang, Alves, Pedro, Abyzov, Alexej, Addleman, Nick, Bhardwaj, Nitin, Boyle, Alan P., Cayting, Philip, Charos, Alexandra, Chen, David Z., Cheng, Yong, Clarke, Declan, Eastman, Catharine, Euskirchen, Ghia, Frietze, Seth, Fu, Yao, Gertz, Jason, Grubert, Fabian, Harmanci, Arif, Jain, Preti, Kasowski, Maya, Lacroute, Phil, Leng, Jing, Lian, Jin, Monahan, Hannah, O’Geen, Henriette, Ouyang, Zhengqing, Partridge, E. Christopher, Patacsil, Dorrelyn, Pauli, Florencia, Raha, Debasish, Ramirez, Lucia, Reddy, Timothy E., Reed, Brian, Shi, Minyi, Slifer, Teri, Wang, Jing, Wu, Linfeng, Yang, Xinqiong, Yip, Kevin Y., Zilberman-Schapira, Gili, Batzoglou, Serafim, Sidow, Arend, Farnham, Peggy J., Myers, Richard M., Weissman, Sherman M., Snyder, Michael

“…Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory…”
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De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms by Peng, Yanhui, Lai, Zhao, Lane, Thomas, Nageswara-Rao, Madhugiri, Okada, Miki, Jasieniuk, Marie, O'Geen, Henriette, Kim, Ryan W., Sammons, R. Douglas, Rieseberg, Loren H., Stewart, Neal

“…Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one…”
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Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm by Zhang, Bo, Zhou, Yan, Lin, Nan, Lowdon, Rebecca F, Hong, Chibo, Nagarajan, Raman P, Cheng, Jeffrey B, Li, Daofeng, Stevens, Michael, Lee, Hyung Joo, Xing, Xiaoyun, Zhou, Jia, Sundaram, Vasavi, Elliott, Ginell, Gu, Junchen, Shi, Taoping, Gascard, Philippe, Sigaroudinia, Mahvash, Tlsty, Thea D, Kadlecek, Theresa, Weiss, Arthur, O'Geen, Henriette, Farnham, Peggy J, Maire, Cécile L, Ligon, Keith L, Madden, Pamela A F, Tam, Angela, Moore, Richard, Hirst, Martin, Marra, Marco A, Zhang, Baoxue, Costello, Joseph F, Wang, Ting

“…DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and…”
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Discovering Hematopoietic Mechanisms through Genome-wide Analysis of GATA Factor Chromatin Occupancy by Fujiwara, Tohru, O'Geen, Henriette, Keles, Sunduz, Blahnik, Kimberly, Linnemann, Amelia K., Kang, Yoon-A., Choi, Kyunghee, Farnham, Peggy J., Bresnick, Emery H.

“…GATA factors interact with simple DNA motifs (WGATAR) to regulate critical processes, including hematopoiesis, but very few WGATAR motifs are occupied in…”
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DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape by Xie, Mingchao, Hong, Chibo, Zhang, Bo, Lowdon, Rebecca F, Xing, Xiaoyun, Li, Daofeng, Zhou, Xin, Lee, Hyung Joo, Maire, Cecile L, Ligon, Keith L, Gascard, Philippe, Sigaroudinia, Mahvash, Tlsty, Thea D, Kadlecek, Theresa, Weiss, Arthur, O'Geen, Henriette, Farnham, Peggy J, Madden, Pamela A F, Mungall, Andrew J, Tam, Angela, Kamoh, Baljit, Cho, Stephanie, Moore, Richard, Hirst, Martin, Marra, Marco A, Costello, Joseph F, Wang, Ting

“…Ting Wang, Joseph Costello and colleagues report DNA methylation profiles of 11 human tissue types and show that DNA hypomethylation within specific…”
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Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance by Coggins, Nicole B., Stultz, Jacob, O’Geen, Henriette, Carvajal-Carmona, Luis G., Segal, David J.

“…With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing,…”
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Transcriptional reprogramming restores UBE3A brain-wide and rescues behavioral phenotypes in an Angelman syndrome mouse model by O’Geen, Henriette, Beitnere, Ulrika, Garcia, Miranda S., Adhikari, Anna, Cameron, David L., Fenton, Timothy A., Copping, Nycole A., Deng, Peter, Lock, Samantha, Halmai, Julian A.N.M., Villegas, Isaac J., Liu, Jiajian, Wang, Danhui, Fink, Kyle D., Silverman, Jill L., Segal, David J.

“…Angelman syndrome (AS) is a neurogenetic disorder caused by the loss of ubiquitin ligase E3A (UBE3A) gene expression in the brain. The UBE3A gene is paternally…”
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Suz12 binds to silenced regions of the genome in a cell-type-specific manner by Squazzo, Sharon L, O'Geen, Henriette, Komashko, Vitalina M, Krig, Sheryl R, Jin, Victor X, Jang, Sung-wook, Margueron, Raphael, Reinberg, Danny, Green, Roland, Farnham, Peggy J

“…Suz12 is a component of the Polycomb group complexes 2, 3, and 4 (PRC 2/3/4). These complexes are critical for proper embryonic development, but very few…”
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Artificial escape from XCI by DNA methylation editing of the CDKL5 gene by Halmai, Julian A N M, Deng, Peter, Gonzalez, Casiana E, Coggins, Nicole B, Cameron, David, Carter, Jasmine L, Buchanan, Fiona K B, Waldo, Jennifer J, Lock, Samantha R, Anderson, Johnathon D, O’Geen, Henriette, Segal, David J, Nolta, Jan, Fink, Kyle D

“…Abstract A significant number of X-linked genes escape from X chromosome inactivation and are associated with a distinct epigenetic signature. One epigenetic…”
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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications by Costello, Joseph F, Harris, R Alan, Wang, Ting, Coarfa, Cristian, Nagarajan, Raman P, Hong, Chibo, Downey, Sara L, Johnson, Brett E, Fouse, Shaun D, Delaney, Allen, Zhao, Yongjun, Olshen, Adam, Ballinger, Tracy, Zhou, Xin, Forsberg, Kevin J, Gu, Junchen, Echipare, Lorigail, O'Geen, Henriette, Lister, Ryan, Pelizzola, Mattia, Xi, Yuanxin, Epstein, Charles B, Bernstein, Bradley E, Hawkins, R David, Ren, Bing, Chung, Wen-Yu, Gu, Hongcang, Bock, Christoph, Gnirke, Andreas, Zhang, Michael Q, Haussler, David, Ecker, Joseph R, Li, Wei, Farnham, Peggy J, Waterland, Robert A, Meissner, Alexander, Marra, Marco A, Hirst, Martin, Milosavljevic, Aleksandar

“…Methods for profiling DNA methylation differ in the physical principles used to detect modified cytosines. Harris et al . compare the performances of four…”
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Epigenetic and transcriptional determinants of the human breast by Gascard, Philippe, Bilenky, Misha, Sigaroudinia, Mahvash, Zhao, Jianxin, Li, Luolan, Carles, Annaick, Delaney, Allen, Tam, Angela, Kamoh, Baljit, Cho, Stephanie, Griffith, Malachi, Chu, Andy, Robertson, Gordon, Cheung, Dorothy, Li, Irene, Heravi-Moussavi, Alireza, Moksa, Michelle, Mingay, Matthew, Hussainkhel, Angela, Davis, Brad, Nagarajan, Raman P., Hong, Chibo, Echipare, Lorigail, O’Geen, Henriette, Hangauer, Matthew J., Cheng, Jeffrey B., Neel, Dana, Hu, Donglei, McManus, Michael T., Moore, Richard, Mungall, Andrew, Ma, Yussanne, Plettner, Patrick, Ziv, Elad, Wang, Ting, Farnham, Peggy J., Jones, Steven J.M., Marra, Marco A., Tlsty, Thea D., Costello, Joseph F., Hirst, Martin

“…While significant effort has been dedicated to the characterization of epigenetic changes associated with prenatal differentiation, relatively little is known…”
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Author Correction: Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance by Coggins, Nicole B., Stultz, Jacob, O’Geen, Henriette, Carvajal-Carmona, Luis G., Segal, David J.

“…A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper…”
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Autophagy Driven by a Master Regulator of Hematopoiesis by Kang, Yoon-A, Sanalkumar, Rajendran, O'Geen, Henriette, Linnemann, Amelia K., Chang, Chan-Jung, Bouhassira, Eric E., Farnham, Peggy J., Keles, Sunduz, Bresnick, Emery H.

“…Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data by Blahnik, Kimberly R, Dou, Lei, O'Geen, Henriette, McPhillips, Timothy, Xu, Xiaoqin, Cao, Alina R, Iyengar, Sushma, Nicolet, Charles M, Ludäscher, Bertram, Korf, Ian, Farnham, Peggy J

“…Next-generation sequencing is revolutionizing the identification of transcription factor binding sites throughout the human genome. However, the bioinformatics…”
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Purified Protein Delivery to Activate an Epigenetically Silenced Allele in Mouse Brain by Pyles, Benjamin, Bailus, Barbara J, O'Geen, Henriette, Segal, David J

“…The ability to activate or repress specific genes in the brain could have a tremendous impact for understanding and treating neurological disorders. Artificial…”
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ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes by Frietze, Seth, O'Geen, Henriette, Blahnik, Kimberly R, Jin, Victor X, Farnham, Peggy J

“…Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type…”
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