Search Results - "Thurman, Robert E."

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes by Stergachis, Andrew B., Neph, Shane, Reynolds, Alex, Humbert, Richard, Miller, Brady, Paige, Sharon L., Vernot, Benjamin, Cheng, Jeffrey B., Thurman, Robert E., Sandstrom, Richard, Haugen, Eric, Heimfeld, Shelly, Murry, Charles E., Akey, Joshua M., Stamatoyannopoulos, John A.

“…Cellular-state information between generations of developing cells may be propagated via regulatory regions. We report consistent patterns of gain and loss of…”
Get full text

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding by Biddie, Simon C., John, Sam, Sabo, Pete J., Thurman, Robert E., Johnson, Thomas A., Schiltz, R. Louis, Miranda, Tina B., Sung, Myong-Hee, Trump, Saskia, Lightman, Stafford L., Vinson, Charles, Stamatoyannopoulos, John A., Hager, Gordon L.

“…Ligand-dependent transcription by the nuclear receptor glucocorticoid receptor (GR) is mediated by interactions with coregulators. The role of these…”
Get full text

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns by Hager, Gordon L, Stamatoyannopoulos, John A, John, Sam, Sabo, Peter J, Thurman, Robert E, Sung, Myong-Hee, Biddie, Simon C, Johnson, Thomas A

“…Development, differentiation and response to environmental stimuli are characterized by sequential changes in cellular state initiated by the de novo binding…”
Get full text

BEDOPS: high-performance genomic feature operations by NEPH, Shane, KUEHN, M. Scott, SANDSTROM, Richard, HUMBERT, Richard, STAMATOYANNOPOULOS, John A, REYNOLDS, Alex P, HAUGEN, Eric, THURMAN, Robert E, JOHNSON, Audra K, RYNES, Eric, MAURANO, Matthew T, VIERSTRA, Jeff, THOMAS, Sean

“…The large and growing number of genome-wide datasets highlights the need for high-performance feature analysis and data comparison methods, in addition to…”
Get full text

Topologically associating domains are stable units of replication-timing regulation by Pope, Benjamin D., Ryba, Tyrone, Dileep, Vishnu, Yue, Feng, Wu, Weisheng, Denas, Olgert, Vera, Daniel L., Wang, Yanli, Hansen, R. Scott, Canfield, Theresa K., Thurman, Robert E., Cheng, Yong, Gülsoy, Günhan, Dennis, Jonathan H., Snyder, Michael P., Stamatoyannopoulos, John A., Taylor, James, Hardison, Ross C., Kahveci, Tamer, Ren, Bing, Gilbert, David M.

“…A study of DNA replication timing in mouse and human cells reveals that replication domains (domains of the genome which replicate at the same time) share a…”
Get full text

Widespread plasticity in CTCF occupancy linked to DNA methylation by Wang, Hao, Maurano, Matthew T, Qu, Hongzhu, Varley, Katherine E, Gertz, Jason, Pauli, Florencia, Lee, Kristen, Canfield, Theresa, Weaver, Molly, Sandstrom, Richard, Thurman, Robert E, Kaul, Rajinder, Myers, Richard M, Stamatoyannopoulos, John A

“…CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin…”
Get full text

An expansive human regulatory lexicon encoded in transcription factor footprints by Neph, Shane, Vierstra, Jeff, Stergachis, Andrew B., Reynolds, Alex P., Haugen, Eric, Vernot, Benjamin, Thurman, Robert E., John, Sam, Sandstrom, Richard, Johnson, Audra K., Maurano, Matthew T., Humbert, Richard, Rynes, Eric, Wang, Hao, Vong, Shinny, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Roach, Vaughn, Dunn, Douglas, Neri, Jun, Schafer, Anthony, Hansen, R. Scott, Kutyavin, Tanya, Giste, Erika, Weaver, Molly, Canfield, Theresa, Sabo, Peter, Zhang, Miaohua, Balasundaram, Gayathri, Byron, Rachel, MacCoss, Michael J., Akey, Joshua M., Bender, M. A., Groudine, Mark, Kaul, Rajinder, Stamatoyannopoulos, John A.

“…Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic…”
Get full text

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing by Hansen, R. Scott, Thomas, Sean, Sandstrom, Richard, Canfield, Theresa K, Thurman, Robert E, Weaver, Molly, Dorschner, Michael O, Gartler, Stanley M, Stamatoyannopoulos, John A

“…Faithful transmission of genetic material to daughter cells involves a characteristic temporal order of DNA replication, which may play a significant role in…”
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

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting by Stamatoyannopoulos, John A, Hesselberth, Jay R, Chen, Xiaoyu, Zhang, Zhihong, Sabo, Peter J, Sandstrom, Richard, Reynolds, Alex P, Thurman, Robert E, Neph, Shane, Kuehn, Michael S, Noble, William S, Fields, Stanley

“…Dense mapping of DNase I cleavage sites across the whole yeast genome by next-generation sequencing reveals a global view of the binding of regulatory proteins…”
Get full text

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster by Karpen, Gary H, Park, Peter J, Kharchenko, Peter V, Alekseyenko, Artyom A, Schwartz, Yuri B, Minoda, Aki, Riddle, Nicole C, Ernst, Jason, Sabo, Peter J, Larschan, Erica, Gorchakov, Andrey A, Gu, Tingting, Linder-Basso, Daniela, Plachetka, Annette, Shanower, Gregory, Tolstorukov, Michael Y, Luquette, Lovelace J, Xi, Ruibin, Jung, Youngsook L, Park, Richard W, Bishop, Eric P, Canfield, Theresa P, Sandstrom, Richard, Thurman, Robert E, MacAlpine, David M, Stamatoyannopoulos, John A, Kellis, Manolis, Elgin, Sarah C. R, Kuroda, Mitzi I, Pirrotta, Vincenzo

“…Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and…”
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

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair by Polak, Paz, Lawrence, Michael S, Haugen, Eric, Stoletzki, Nina, Stojanov, Petar, Thurman, Robert E, Garraway, Levi A, Mirkin, Sergei, Getz, Gad, Stamatoyannopoulos, John A, Sunyaev, Shamil R

“…Polak et al . analyze somatic mutations and chromatin accessibility data to gain insight into mutational processes in cancer genomes. Carcinogenesis and…”
Get full text

Nucleosome positioning signals in genomic DNA by Peckham, Heather E, Thurman, Robert E, Fu, Yutao, Stamatoyannopoulos, John A, Noble, William Stafford, Struhl, Kevin, Weng, Zhiping

“…Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used…”
Get full text

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements by Hakim, Ofir, Sung, Myong-Hee, Voss, Ty C, Splinter, Erik, John, Sam, Sabo, Peter J, Thurman, Robert E, Stamatoyannopoulos, John A, de Laat, Wouter, Hager, Gordon L

“…The spatial organization of genes in the interphase nucleus plays an important role in establishment and regulation of gene expression. Contradicting results…”
Get full text

Nonfucosylation of an anti-TIGIT antibody enhances FcγR engagement, driving innate immune activation and antitumor activity by Smith, Alyson J, Thurman, Robert E, Zeng, Weiping, Grogan, Bryan, Lucas, Sasha, Gutierrez, Guadalupe, Heiser, Ryan A, Wo, Serena W, Blackmarr, Amber, Peterson, Scott, Gardai, Shyra J

“…TIGIT is an immune checkpoint receptor expressed on activated and memory T cells, immunosuppressive T regulatory cells, and natural killer (NK) cells. TIGIT…”
Get full text

Predicting human nucleosome occupancy from primary sequence by Gupta, Shobhit, Dennis, Jonathan, Thurman, Robert E, Kingston, Robert, Stamatoyannopoulos, John A, Noble, William Stafford

“…Nucleosomes are the fundamental repeating unit of chromatin and comprise the structural building blocks of the living eukaryotic genome. Micrococcal nuclease…”
Get full text

Identification of higher-order functional domains in the human ENCODE regions by Thurman, Robert E, Day, Nathan, Noble, William S, Stamatoyannopoulos, John A

“…It has long been posited that human and other large genomes are organized into higher-order (i.e., greater than gene-sized) functional domains. We hypothesized…”
Get full text

Unsupervised segmentation of continuous genomic data by Day, Nathan, Hemmaplardh, Andrew, Thurman, Robert E., Stamatoyannopoulos, John A., Noble, William S.

“…The advent of high-density, high-volume genomic data has created the need for tools to summarize large datasets at multiple scales. HMMSeg is a command-line…”
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