Circuitry and Dynamics of Human Transcription Factor Regulatory Networks
Neph, Shane, Stergachis, Andrew B., Reynolds, Alex, Sandstrom, Richard, Borenstein, Elhanan, Stamatoyannopoulos, John A.
Published in Cell (14.09.2012)
Published in Cell (14.09.2012)
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Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution
Mayer, Andreas, di Iulio, Julia, Maleri, Seth, Eser, Umut, Vierstra, Jeff, Reynolds, Alex, Sandstrom, Richard, Stamatoyannopoulos, John A, Churchman, L Stirling
Published in Cell (23.04.2015)
Published in Cell (23.04.2015)
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Journal Article
Human Mitochondrial Transcriptome
Mercer, Tim R, Neph, Shane, Dinger, Marcel E, Crawford, Joanna, Smith, Martin A, Shearwood, Anne-Marie J, Haugen, Eric, Bracken, Cameron P, Rackham, Oliver, Stamatoyannopoulos, John A, Filipovska, Aleksandra, Mattick, John S
Published in Cell (19.08.2011)
Published in Cell (19.08.2011)
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Journal Article
Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification
Samstein, Robert M., Arvey, Aaron, Josefowicz, Steven Z., Peng, Xiao, Reynolds, Alex, Sandstrom, Richard, Neph, Shane, Sabo, Peter, Kim, Jeong M., Liao, Will, Li, Ming O., Leslie, Christina, Stamatoyannopoulos, John A., Rudensky, Alexander Y.
Published in Cell (28.09.2012)
Published in Cell (28.09.2012)
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Journal Article
Role of DNA Methylation in Modulating Transcription Factor Occupancy
Maurano, Matthew T., Wang, Hao, John, Sam, Shafer, Anthony, Canfield, Theresa, Lee, Kristen, Stamatoyannopoulos, John A.
Published in Cell reports (Cambridge) (18.08.2015)
Published in Cell reports (Cambridge) (18.08.2015)
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Journal Article
Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes
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.
Published in Cell (15.08.2013)
Published in Cell (15.08.2013)
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Journal Article
Global reference mapping of human transcription factor footprints
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.
Published in Nature (London) (30.07.2020)
Published in Nature (London) (30.07.2020)
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Journal Article
Quantifying similarity between motifs
Gupta, Shobhit, Stamatoyannopoulos, John A, Bailey, Timothy L, Noble, William Stafford
Published in Genome biology (01.01.2007)
Published in Genome biology (01.01.2007)
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Cell-of-origin chromatin organization shapes the mutational landscape of cancer
Polak, Paz, Karlić, Rosa, Koren, Amnon, Thurman, Robert, Sandstrom, Richard, Lawrence, Michael S., Reynolds, Alex, Rynes, Eric, Vlahoviček, Kristian, Stamatoyannopoulos, John A., Sunyaev, Shamil R.
Published in Nature (London) (19.02.2015)
Published in Nature (London) (19.02.2015)
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Journal Article
Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding
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.
Published in Molecular cell (08.07.2011)
Published in Molecular cell (08.07.2011)
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Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism
Voss, Ty C., Schiltz, R. Louis, Sung, Myong-Hee, Yen, Paul M., Stamatoyannopoulos, John A., Biddie, Simon C., Johnson, Thomas A., Miranda, Tina B., John, Sam, Hager, Gordon L.
Published in Cell (19.08.2011)
Published in Cell (19.08.2011)
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Journal Article
Resolving the complexity of the human genome using single-molecule sequencing
Chaisson, Mark J. P., Huddleston, John, Dennis, Megan Y., Sudmant, Peter H., Malig, Maika, Hormozdiari, Fereydoun, Antonacci, Francesca, Surti, Urvashi, Sandstrom, Richard, Boitano, Matthew, Landolin, Jane M., Stamatoyannopoulos, John A., Hunkapiller, Michael W., Korlach, Jonas, Eichler, Evan E.
Published in Nature (London) (29.01.2015)
Published in Nature (London) (29.01.2015)
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Journal Article
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo
Maurano, Matthew T, Haugen, Eric, Sandstrom, Richard, Vierstra, Jeff, Shafer, Anthony, Kaul, Rajinder, Stamatoyannopoulos, John A
Published in Nature genetics (01.12.2015)
Published in Nature genetics (01.12.2015)
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Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
Hager, Gordon L, Stamatoyannopoulos, John A, John, Sam, Sabo, Peter J, Thurman, Robert E, Sung, Myong-Hee, Biddie, Simon C, Johnson, Thomas A
Published in Nature genetics (01.03.2011)
Published in Nature genetics (01.03.2011)
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Journal Article
BEDOPS: high-performance genomic feature operations
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
Published in Bioinformatics (15.07.2012)
Published in Bioinformatics (15.07.2012)
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Topologically associating domains are stable units of replication-timing regulation
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.
Published in Nature (London) (20.11.2014)
Published in Nature (London) (20.11.2014)
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Journal Article
Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells
Arvey, Aaron, van der Veeken, Joris, Samstein, Robert M, Feng, Yongqiang, Stamatoyannopoulos, John A, Rudensky, Alexander Y
Published in Nature immunology (01.06.2014)
Published in Nature immunology (01.06.2014)
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