Search Results - "Neri, Fidencio"

Global reference mapping of human transcription factor footprints by Vierstra, Jeff, Lazar, John, Sandstrom, Richard, Halow, Jessica, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Dunn, Douglas, Neri, Fidencio, Haugen, Eric, Rynes, Eric, Reynolds, Alex, Nelson, Jemma, Johnson, Audra, Frerker, Mark, Buckley, Michael, Kaul, Rajinder, Meuleman, Wouter, Stamatoyannopoulos, John A.

“…Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been…”
Get full text

Index and biological spectrum of human DNase I hypersensitive sites by Meuleman, Wouter, Muratov, Alexander, Rynes, Eric, Halow, Jessica, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Dunn, Douglas, Neri, Fidencio, Teodosiadis, Athanasios, Reynolds, Alex, Haugen, Eric, Nelson, Jemma, Johnson, Audra, Frerker, Mark, Buckley, Michael, Sandstrom, Richard, Vierstra, Jeff, Kaul, Rajinder, Stamatoyannopoulos, John

“…DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA 1 – 5 and contain genetic variations associated with diseases and phenotypic traits 6…”
Get full text

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana by Sullivan, Alessandra M., Arsovski, Andrej A., Lempe, Janne, Bubb, Kerry L., Weirauch, Matthew T., Sabo, Peter J., Sandstrom, Richard, Thurman, Robert E., Neph, Shane, Reynolds, Alex P., Stergachis, Andrew B., Vernot, Benjamin, Johnson, Audra K., Haugen, Eric, Sullivan, Shawn T., Thompson, Agnieszka, Neri, Fidencio V., Weaver, Molly, Diegel, Morgan, Mnaimneh, Sanie, Yang, Ally, Hughes, Timothy R., Nemhauser, Jennifer L., Queitsch, Christine, Stamatoyannopoulos, John A.

“…Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. We mapped DNase I…”
Get full text

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA by Maurano, Matthew T., Humbert, Richard, Rynes, Eric, Thurman, Robert E., Haugen, Eric, Wang, Hao, Reynolds, Alex P., Sandstrom, Richard, Qu, Hongzhu, Brody, Jennifer, Shafer, Anthony, Neri, Fidencio, Lee, Kristen, Kutyavin, Tanya, Stehling-Sun, Sandra, Johnson, Audra K., Canfield, Theresa K., Giste, Erika, Diegel, Morgan, Bates, Daniel, Hansen, R. Scott, Neph, Shane, Sabo, Peter J., Heimfeld, Shelly, Raubitschek, Antony, Ziegler, Steven, Cotsapas, Chris, Sotoodehnia, Nona, Glass, Ian, Sunyaev, Shamil R., Kaul, Rajinder, Stamatoyannopoulos, John A.

“…Genome-wide association studies have identified many noncoding variants associated with common diseases and traits. We show that these variants are…”
Get full text

Conservation of trans-acting circuitry during mammalian regulatory evolution by Stergachis, Andrew B., Neph, Shane, Sandstrom, Richard, Haugen, Eric, Reynolds, Alex P., Zhang, Miaohua, Byron, Rachel, Canfield, Theresa, Stelhing-Sun, Sandra, Lee, Kristen, Thurman, Robert E., Vong, Shinny, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Giste, Erika, Dunn, Douglas, Vierstra, Jeff, Hansen, R. Scott, Johnson, Audra K., Sabo, Peter J., Wilken, Matthew S., Reh, Thomas A., Treuting, Piper M., Kaul, Rajinder, Groudine, Mark, Bender, M. A., Borenstein, Elhanan, Stamatoyannopoulos, John A.

“…The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence…”
Get full text

Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques by Sullivan, Alessandra M., Arsovski, Andrej A., Thompson, Agnieszka, Sandstrom, Richard, Thurman, Robert E., Neph, Shane, Johnson, Audra K., Sullivan, Shawn T., Sabo, Peter J., Neri, Fidencio V., Weaver, Molly, Diegel, Morgan, Nemhauser, Jennifer L., Stamatoyannopoulos, John A., Bubb, Kerry L., Queitsch, Christine

“…The genome is reprogrammed during development to produce diverse cell types, largely through altered expression and activity of key transcription factors. The…”
Get full text

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays by Stamatoyannopoulos, John A, Sabo, Peter J, Kuehn, Michael S, Thurman, Robert, Johnson, Brett E, Johnson, Ericka M, Cao, Hua, Yu, Man, Rosenzweig, Elizabeth, Goldy, Jeff, Haydock, Andrew, Weaver, Molly, Shafer, Anthony, Lee, Kristin, Neri, Fidencio, Humbert, Richard, Singer, Michael A, Richmond, Todd A, Dorschner, Michael O, McArthur, Michael, Hawrylycz, Michael, Green, Roland D, Navas, Patrick A, Noble, William S

“…Localized accessibility of critical DNA sequences to the regulatory machinery is a key requirement for regulation of human genes. Here we describe a…”
Get full text

Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling by Lazar, John E., Stehling-Sun, Sandra, Nandakumar, Vivek, Wang, Hao, Chee, Daniel R., Howard, Nicholas P., Acosta, Reyes, Dunn, Douglass, Diegel, Morgan, Neri, Fidencio, Castillo, Andres, Ibarrientos, Sean, Lee, Kristen, Lescano, Ninnia, Van Biber, Ben, Nelson, Jemma, Halow, Jessica, Sandstrom, Richard, Bates, Daniel, Urnov, Fyodor D., Stamatoyannopoulos, John A., Funnell, Alister P.W.

“…The human genome encodes millions of regulatory elements, of which only a small fraction are active within a given cell type. Little is known about the global…”
Get full text

A comparative encyclopedia of DNA elements in the mouse genome by Breschi, Alessandra, Vierstra, Jeff, Wu, Weisheng, Ryba, Tyrone, Sandstrom, Richard, Ma, Zhihai, Davis, Carrie, Pope, Benjamin D., Shen, Yin, Pervouchine, Dmitri D., Djebali, Sarah, Kaul, Rajinder, Kirilusha, Anthony, Marinov, Georgi K., Williams, Brian A., Trout, Diane, Antoshechkin, Igor, See, Lei-Hoon, Zaleski, Chris, Dobin, Alex, Tanzer, Andrea, Denas, Olgert, Li, Kanwei, Bender, M. A., Zhang, Miaohua, Groudine, Mark T., McCleary, David, Pham, Long, Ye, Zhen, Kuan, Samantha, Edsall, Lee, Wu, Yi-Chieh, Rasmussen, Matthew D., Bansal, Mukul S., Keller, Cheryl A., Morrissey, Christapher S., Mishra, Tejaswini, Dogan, Nergiz, Harris, Robert S., Cayting, Philip, Boyle, Alan P., Euskirchen, Ghia, Lin, Shin, Lin, Yiing, Jansen, Camden, Malladi, Venkat S., Cline, Melissa S., Learned, Katrina, Sloan, Cricket A., Rosenbloom, Kate R., Beal, Kathryn, Pignatelli, Miguel, Flicek, Paul, Lian, Jin, Kahveci, Tamer, Lee, Dongwon, Notredame, Cedric, Johnson, Audra, Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Canfield, Theresa, Wilken, Matthew S., Giste, Erika, Shafer, Anthony, Kutyavin, Tanya, Dunn, Douglas, Humbert, Richard, De Bruijn, Marella, Selleri, Licia, Rudensky, Alexander, Josefowicz, Steven, Samstein, Robert, Orkin, Stuart H., Levasseur, Dana, Chang, Kai-Hsin, Skoultchi, Arthur, Gosh, Srikanta, Disteche, Christine, Treuting, Piper, Wang, Yanli, Weiss, Mitchell J., Zhong, Sheng, Good, Peter J., Adams, Leslie B., Zhou, Xiao-Qiao, Pazin, Michael J., Feingold, Elise A., Wold, Barbara, Taylor, James, Mortazavi, Ali, Weissman, Sherman M., Stamatoyannopoulos, John A., Snyder, Michael P., Guigo, Roderic, Gingeras, Thomas R., Beer, Michael A., Ren, Bing

“…The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two…”
Get full text

The accessible chromatin landscape of the human genome by Thurman, Robert E., Rynes, Eric, Humbert, Richard, Vierstra, Jeff, Maurano, Matthew T., Haugen, Eric, Sheffield, Nathan C., Stergachis, Andrew B., Wang, Hao, Vernot, Benjamin, Garg, Kavita, John, Sam, Sandstrom, Richard, Bates, Daniel, Boatman, Lisa, Canfield, Theresa K., Diegel, Morgan, Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Giste, Erika, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tanya, Lajoie, Bryan, Lee, Bum-Kyu, Lee, Kristen, London, Darin, Lotakis, Dimitra, Neph, Shane, Neri, Fidencio, Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Safi, Alexias, Sanchez, Minerva E., Sanyal, Amartya, Shafer, Anthony, Simon, Jeremy M., Song, Lingyun, Vong, Shinny, Weaver, Molly, Yan, Yongqi, Zhang, Zhancheng, Zhang, Zhuzhu, Lenhard, Boris, Tewari, Muneesh, Dorschner, Michael O., Hansen, R. Scott, Navas, Patrick A., Stamatoyannopoulos, George, Iyer, Vishwanath R., Lieb, Jason D., Sunyaev, Shamil R., Akey, Joshua M., Sabo, Peter J., Kaul, Rajinder, Furey, Terrence S., Dekker, Job, Crawford, Gregory E., Stamatoyannopoulos, John A.

“…DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis -regulatory elements including…”
Get full text

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease by Stranger, Barbara E, Brigham, Lori E, Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F, Lonsdale, John T, McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A, Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A, Gillard, Bryan M, Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T, Jewell, Scott D, Montroy, Robert G, Rohrer, Daniel C, Valley, Dana R, Davis, David A, Mash, Deborah C, Gould, Sarah E, Guan, Ping, Koester, Susan, Little, A Roger, Martin, Casey, Moore, Helen M, Rao, Abhi, Struewing, Jeffery P, Volpi, Simona, Hansen, Kasper D, Hickey, Peter F, Rizzardi, Lindsay F, Hou, Lei, Liu, Yaping, Molinie, Benoit, Park, Yongjin, Rinaldi, Nicola, Wang, Li, Van Wittenberghe, Nicholas, Claussnitzer, Melina, Gelfand, Ellen T, Li, Qin, Linder, Sandra, Zhang, Rui, Smith, Kevin S, Tsang, Emily K, Chen, Lin S, Demanelis, Kathryn, Doherty, Jennifer A, Jasmine, Farzana, Kibriya, Muhammad G, Jiang, Lihua, Lin, Shin, Wang, Meng, Jian, Ruiqi, Li, Xiao, Chan, Joanne, Bates, Daniel, Diegel, Morgan, Halow, Jessica, Haugen, Eric, Johnson, Audra, Kaul, Rajinder, Lee, Kristen, Maurano, Matthew T, Nelson, Jemma, Neri, Fidencio J, Sandstrom, Richard, Fernando, Marian S, Linke, Caroline, Oliva, Meritxell, Skol, Andrew, Wu, Fan, Akey, Joshua M, Feinberg, Andrew P, Li, Jin Billy, Pierce, Brandon L, Stamatoyannopoulos, John A, Tang, Hua, Ardlie, Kristin G, Kellis, Manolis, Snyder, Michael P, Montgomery, Stephen B

“…Genetic variants have been associated with myriad molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and…”
Get full text

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution by Vierstra, Jeff, Rynes, Eric, Sandstrom, Richard, Zhang, Miaohua, Canfield, Theresa, Hansen, R. Scott, Stehling-Sun, Sandra, Sabo, Peter J., Byron, Rachel, Humbert, Richard, Thurman, Robert E., Johnson, Audra K., Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Giste, Erika, Haugen, Eric, Dunn, Douglas, Wilken, Matthew S., Josefowicz, Steven, Samstein, Robert, Chang, Kai-Hsin, Eichler, Evan E., De Bruijn, Marella, Reh, Thomas A., Skoultchi, Arthur, Rudensky, Alexander, Orkin, Stuart H., Papayannopoulou, Thalia, Treuting, Piper M., Selleri, Licia, Kaul, Rajinder, Groudine, Mark, Bender, M. A., Stamatoyannopoulos, John A.

“…To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I–hypersensitive sites (DHSs) in 45 mouse cell and tissue types,…”
Get full text

Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling by Lazar, John E., Stehling-Sun, Sandra, Nandakumar, Vivek, Wang, Hao, Chee, Daniel R., Howard, Nicholas P., Acosta, Reyes, Dunn, Douglass, Diegel, Morgan, Neri, Fidencio, Castillo, Andres, Ibarrientos, Sean, Lee, Kristen, Lescano, Ninnia, Van Biber, Ben, Nelson, Jemma, Halow, Jessica, Sandstrom, Richard, Bates, Daniel, Urnov, Fyodor D., Stamatoyannopoulos, John A., Funnell, Alister P.W.

Get full text