Search Results - "Afzal, Veena"

ChIP-seq accurately predicts tissue-specific activity of enhancers by Visel, Axel, Blow, Matthew J., Li, Zirong, Zhang, Tao, Akiyama, Jennifer A., Holt, Amy, Plajzer-Frick, Ingrid, Shoukry, Malak, Wright, Crystal, Chen, Feng, Afzal, Veena, Ren, Bing, Rubin, Edward M., Pennacchio, Len A.

“…A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of…”
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Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation by Preissl, Sebastian, Fang, Rongxin, Huang, Hui, Zhao, Yuan, Raviram, Ramya, Gorkin, David U., Zhang, Yanxiao, Sos, Brandon C., Afzal, Veena, Dickel, Diane E., Kuan, Samantha, Visel, Axel, Pennacchio, Len A., Zhang, Kun, Ren, Bing

“…Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in…”
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Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice by Cohen, Jonathan C, May, Dalit, Afzal, Veena, Gong, Elaine, Pennacchio, Len A, Zhu, Yiwen, Rubin, Edward M, Attanasio, Catia, Blow, Matthew J, Visel, Axel

“…Sequence polymorphisms in a 58-kilobase (kb) interval on chromosome 9p21 confer a markedly increased risk of coronary artery disease (CAD), the leading cause…”
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The changing mouse embryo transcriptome at whole tissue and single-cell resolution by He, Peng, Williams, Brian A., Trout, Diane, Marinov, Georgi K., Amrhein, Henry, Berghella, Libera, Goh, Say-Tar, Plajzer-Frick, Ingrid, Afzal, Veena, Pennacchio, Len A., Dickel, Diane E., Visel, Axel, Ren, Bing, Hardison, Ross C., Zhang, Yu, Wold, Barbara J.

“…During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system 1 . Here we…”
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Progressive Loss of Function in a Limb Enhancer during Snake Evolution by Kvon, Evgeny Z., Kamneva, Olga K., Melo, Uirá S., Barozzi, Iros, Osterwalder, Marco, Mannion, Brandon J., Tissières, Virginie, Pickle, Catherine S., Plajzer-Frick, Ingrid, Lee, Elizabeth A., Kato, Momoe, Garvin, Tyler H., Akiyama, Jennifer A., Afzal, Veena, Lopez-Rios, Javier, Rubin, Edward M., Dickel, Diane E., Pennacchio, Len A., Visel, Axel

“…The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major…”
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Germline Chd8 haploinsufficiency alters brain development in mouse by Gompers, Andrea L, Su-Feher, Linda, Ellegood, Jacob, Copping, Nycole A, Riyadh, M Asrafuzzaman, Stradleigh, Tyler W, Pride, Michael C, Schaffler, Melanie D, Wade, A Ayanna, Catta-Preta, Rinaldo, Zdilar, Iva, Louis, Shreya, Kaushik, Gaurav, Mannion, Brandon J, Plajzer-Frick, Ingrid, Afzal, Veena, Visel, Axel, Pennacchio, Len A, Dickel, Diane E, Lerch, Jason P, Crawley, Jacqueline N, Zarbalis, Konstantinos S, Silverman, Jill L, Nord, Alex S

“…Strong genetic evidence points to a significant role for heterozygous mutations to general chromatin remodeling factors, such as CHD8, in autism. Gompers et al…”
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Ultraconserved Enhancers Are Required for Normal Development by Dickel, Diane E., Ypsilanti, Athena R., Pla, Ramón, Zhu, Yiwen, Barozzi, Iros, Mannion, Brandon J., Khin, Yupar S., Fukuda-Yuzawa, Yoko, Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth A., Harrington, Anne N., Pham, Quan T., Garvin, Tyler H., Kato, Momoe, Osterwalder, Marco, Akiyama, Jennifer A., Afzal, Veena, Rubenstein, John L.R., Pennacchio, Len A., Visel, Axel

“…Non-coding “ultraconserved” regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as…”
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Supervised enhancer prediction with epigenetic pattern recognition and targeted validation by Sethi, Anurag, Gu, Mengting, Gumusgoz, Emrah, Chan, Landon, Yan, Koon-Kiu, Rozowsky, Joel, Barozzi, Iros, Afzal, Veena, Akiyama, Jennifer A., Plajzer-Frick, Ingrid, Yan, Chengfei, Novak, Catherine S., Kato, Momoe, Garvin, Tyler H., Pham, Quan, Harrington, Anne, Mannion, Brandon J., Lee, Elizabeth A., Fukuda-Yuzawa, Yoko, Visel, Axel, Dickel, Diane E., Yip, Kevin Y., Sutton, Richard, Pennacchio, Len A., Gerstein, Mark

“…Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays…”
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Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers by Attanasio, Catia, Nord, Alex S., Zhu, Yiwen, Blow, Matthew J., Li, Zirong, Liberton, Denise K., Morrison, Harris, Plajzer-Frick, Ingrid, Holt, Amy, Hosseini, Roya, Phouanenavong, Sengthavy, Akiyama, Jennifer A., Shoukry, Malak, Afzal, Veena, Rubin, Edward M., FitzPatrick, David R., Ren, Bing, Hallgrímsson, Benedikt, Pennacchio, Len A., Visel, Axel

“…The shape of the human face and skull is largely genetically determined. However, the genomic basis of craniofacial morphology is incompletely understood and…”
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ChIP-Seq identification of weakly conserved heart enhancers by Visel, Axel, Pennacchio, Len A, Blow, Matthew J, McCulley, David J, Li, Zirong, Zhang, Tao, Akiyama, Jennifer A, Holt, Amy, Plajzer-Frick, Ingrid, Shoukry, Malak, Wright, Crystal, Chen, Feng, Afzal, Veena, Bristow, James, Ren, Bing, Black, Brian L, Rubin, Edward M

“…Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been…”
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Large-scale discovery of enhancers from human heart tissue by May, Dalit, Blow, Matthew J, Kaplan, Tommy, McCulley, David J, Jensen, Brian C, Akiyama, Jennifer A, Holt, Amy, Plajzer-Frick, Ingrid, Shoukry, Malak, Wright, Crystal, Afzal, Veena, Simpson, Paul C, Rubin, Edward M, Black, Brian L, Bristow, James, Pennacchio, Len A, Visel, Axel

“…Len Pennacchio, Axel Visel and colleagues use an epigenomic approach to identify a large number of candidate enhancers from human heart tissue. This work will…”
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A High-Resolution Enhancer Atlas of the Developing Telencephalon by Visel, Axel, Taher, Leila, Girgis, Hani, May, Dalit, Golonzhka, Olga, Hoch, Renee V., McKinsey, Gabriel L., Pattabiraman, Kartik, Silberberg, Shanni N., Blow, Matthew J., Hansen, David V., Nord, Alex S., Akiyama, Jennifer A., Holt, Amy, Hosseini, Roya, Phouanenavong, Sengthavy, Plajzer-Frick, Ingrid, Shoukry, Malak, Afzal, Veena, Kaplan, Tommy, Kriegstein, Arnold R., Rubin, Edward M., Ovcharenko, Ivan, Pennacchio, Len A., Rubenstein, John L.R.

“…The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. Though many of the genes required for its development have been…”
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Tissue-specific RNA expression marks distant-acting developmental enhancers by Wu, Han, Nord, Alex S, Akiyama, Jennifer A, Shoukry, Malak, Afzal, Veena, Rubin, Edward M, Pennacchio, Len A, Visel, Axel

“…Short non-coding transcripts can be transcribed from distant-acting transcriptional enhancer loci, but the prevalence of such enhancer RNAs (eRNAs) within the…”
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Ultraconservation identifies a small subset of extremely constrained developmental enhancers by Pennacchio, Len A, Visel, Axel, Prabhakar, Shyam, Akiyama, Jennifer A, Shoukry, Malak, Lewis, Keith D, Holt, Amy, Plajzer-Frick, Ingrid, Afzal, Veena, Rubin, Edward M

“…Extended perfect human-rodent sequence identity of at least 200 base pairs (ultraconservation) is potentially indicative of evolutionary or functional…”
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Genome-wide compendium and functional assessment of in vivo heart enhancers by Dickel, Diane E., Barozzi, Iros, Zhu, Yiwen, Fukuda-Yuzawa, Yoko, Osterwalder, Marco, Mannion, Brandon J., May, Dalit, Spurrell, Cailyn H., Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth, Garvin, Tyler H., Kato, Momoe, Akiyama, Jennifer A., Afzal, Veena, Lee, Ah Young, Gorkin, David U., Ren, Bing, Rubin, Edward M., Visel, Axel, Pennacchio, Len A.

“…Whole-genome sequencing is identifying growing numbers of non-coding variants in human disease studies, but the lack of accurate functional annotations…”
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Human-Specific Gain of Function in a Developmental Enhancer by Prabhakar, Shyam, Visel, Axel, Akiyama, Jennifer A, Shoukry, Malak, Lewis, Keith D, Holt, Amy, Plajzer-Frick, Ingrid, Morrison, Harris, FitzPatrick, David R, Afzal, Veena, Pennacchio, Len A, Rubin, Edward M, Noonan, James P

“…Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental…”
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Deletion of ultraconserved elements yields viable mice by Ahituv, Nadav, Zhu, Yiwen, Visel, Axel, Holt, Amy, Afzal, Veena, Pennacchio, Len A, Rubin, Edward M

“…Ultraconserved elements have been suggested to retain extended perfect sequence identity between the human, mouse, and rat genomes due to essential functional…”
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Dynamic enhancer landscapes in human craniofacial development by Rajderkar, Sudha Sunil, Paraiso, Kitt, Amaral, Maria Luisa, Kosicki, Michael, Cook, Laura E., Darbellay, Fabrice, Spurrell, Cailyn H., Osterwalder, Marco, Zhu, Yiwen, Wu, Han, Afzal, Sarah Yasmeen, Blow, Matthew J., Kelman, Guy, Barozzi, Iros, Fukuda-Yuzawa, Yoko, Akiyama, Jennifer A., Afzal, Veena, Tran, Stella, Plajzer-Frick, Ingrid, Novak, Catherine S., Kato, Momoe, Hunter, Riana D., von Maydell, Kianna, Wang, Allen, Lin, Lin, Preissl, Sebastian, Lisgo, Steven, Ren, Bing, Dickel, Diane E., Pennacchio, Len A., Visel, Axel

“…The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the…”
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Function-based identification of mammalian enhancers using site-specific integration by Dickel, Diane E, Zhu, Yiwen, Nord, Alex S, Wylie, John N, Akiyama, Jennifer A, Afzal, Veena, Plajzer-Frick, Ingrid, Kirkpatrick, Aileen, Göttgens, Berthold, Bruneau, Benoit G, Visel, Axel, Pennacchio, Len A

“…Putative enhancer elements of a genomic region of interest are cloned in front of a reporter gene, integrated in a single site in mouse embryonic stem cells,…”
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Close sequence comparisons are sufficient to identify human cis-regulatory elements by Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M, Couronne, Olivier, Pennacchio, Len A

“…Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is…”
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