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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Journal Article
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
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.
Published in Science (American Association for the Advancement of Science) (07.09.2012)
Published in Science (American Association for the Advancement of Science) (07.09.2012)
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Journal Article
An expansive human regulatory lexicon encoded in transcription factor footprints
NEPH, Shane, VIERSTRA, Jeff, MAURANO, Matthew T, HUMBERT, Richard, RYNES, Eric, HAO WANG, VONG, Shinny, LEE, Kristen, BATES, Daniel, DIEGEL, Morgan, ROACH, Vaughn, DUNN, Douglas, STERGACHIS, Andrew B, NERI, Jun, SCHAFER, Anthony, HANSEN, R. Scott, KUTYAVIN, Tanya, GISTE, Erika, WEAVER, Molly, CANFIELD, Theresa, SABO, Peter, MIAOHUA ZHANG, BALASUNDARAM, Gayathri, REYNOLDS, Alex P, BYRON, Rachel, MACCOSS, Michael J, AKEY, Joshua M, BENDER, M. A, GROUDINE, Mark, KAUL, Rajinder, STAMATOYANNOPOULOS, John A, HAUGEN, Eric, VERNOT, Benjamin, THURMAN, Robert E, JOHN, Sam, SANDSTROM, Richard, JOHNSON, Audra K
Published in Nature (London) (06.09.2012)
Published in Nature (London) (06.09.2012)
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Journal Article
Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
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.
Published in Cell reports (Cambridge) (25.09.2014)
Published in Cell reports (Cambridge) (25.09.2014)
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Journal Article
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
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
Published in Nature methods (01.04.2009)
Published in Nature methods (01.04.2009)
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Journal Article
Conservation of trans-acting circuitry during mammalian regulatory evolution
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
Published in Nature (London) (20.11.2014)
Published in Nature (London) (20.11.2014)
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Journal Article
Genome-scale mapping of DNase I hypersensitivity
John, Sam, Sabo, Peter J, Canfield, Theresa K, Lee, Kristen, Vong, Shinny, Weaver, Molly, Wang, Hao, Vierstra, Jeff, Reynolds, Alex P, Thurman, Robert E, Stamatoyannopoulos, John A
Published in Current protocols in molecular biology (Print) (01.07.2013)
Published in Current protocols in molecular biology (Print) (01.07.2013)
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Journal Article
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
Breeze, Charles E, Reynolds, Alex P, van Dongen, Jenny, Dunham, Ian, Lazar, John, Neph, Shane, Vierstra, Jeff, Bourque, Guillaume, Teschendorff, Andrew E, Stamatoyannopoulos, John A, Beck, Stephan
Published in Bioinformatics (01.11.2019)
Published in Bioinformatics (01.11.2019)
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Journal Article
Operating on Genomic Ranges Using BEDOPS
Neph, Shane, Reynolds, Alex P, Kuehn, M Scott, Stamatoyannopoulos, John A
Published in Methods in molecular biology (Clifton, N.J.) (2016)
Published in Methods in molecular biology (Clifton, N.J.) (2016)
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Journal Article
The accessible chromatin landscape of the human genome
THURMAN, Robert E, RYNES, Eric, GARG, Kavita, JOHN, Sam, SANDSTROM, Richard, BATES, Daniel, BOATMAN, Lisa, CANFIELD, Theresa K, DIEGEL, Morgan, DUNN, Douglas, EBERSOL, Abigail K, FRUM, Tristan, HUMBERT, Richard, GISTE, Erika, JOHNSON, Audra K, JOHNSON, Ericka M, KUTYAVIN, Tanya, LAJOIE, Bryan, LEE, Bum-Kyu, LEE, Kristen, LONDON, Darin, LOTAKIS, Dimitra, NEPH, Shane, VIERSTRA, Jeff, NERI, Fidencio, NGUYEN, Eric D, HONGZHU QU, REYNOLDS, Alex P, ROACH, Vaughn, SAFI, Alexias, SANCHEZ, Minerva E, SANYAL, Amartya, SHAFER, Anthony, SIMON, Jeremy M, MAURANO, Matthew T, LINGYUN SONG, VONG, Shinny, WEAVER, Molly, YONGQI YAN, ZHANCHENG ZHANG, ZHUZHU ZHANG, LENHARD, Boris, TEWARI, Muneesh, DORSCHNER, Michael O, HANSEN, R. Scott, HAUGEN, Eric, 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, SHEFFIELD, Nathan C, STERGACHIS, Andrew B, HAO WANG, VERNOT, Benjamin
Published in Nature (London) (06.09.2012)
Published in Nature (London) (06.09.2012)
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Journal Article
An expansive human regulatory lexicon encoded in transcription factor footprints
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, Vong, Shinny, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Roach, Vaughn, Dunn, Douglas, Neri, Jun, Schafer, Anthony, Scott Hansen, R, 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
Published in Nature (London) (06.09.2012)
Published in Nature (London) (06.09.2012)
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Journal Article