454 results on '"Stamatoyannopoulos, John A"'
Search Results
2. Genome-Wide Association Study Points to Novel Locus for Gilles de la Tourette Syndrome
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Barr, Cathy L., Batterson, James R., Berlin, Cheston, Budman, Cathy L., Coppola, Giovanni, Cox, Nancy J., Darrow, Sabrina, Dion, Yves, Freimer, Nelson B., Grados, Marco A., Greenberg, Erica, Hirschtritt, Matthew E., Huang, Alden Y., Illmann, Cornelia, King, Robert A., Kurlan, Roger, Leckman, James F., Lyon, Gholson J., Malaty, Irene A., McMahon, William M., Neale, Benjamin M., Okun, Michael S., Osiecki, Lisa, Robertson, Mary M., Rouleau, Guy A., Sandor, Paul, Singer, Harvey S., Smit, Jan H., Sul, Jae Hoon, Androutsos, Christos, Basha, Entela, Farkas, Luca, Fichna, Jakub, Janik, Piotr, Kapisyzi, Mira, Karagiannidis, Iordanis, Koumoula, Anastasia, Nagy, Peter, Puchala, Joanna, Szejko, Natalia, Szymanska, Urszula, Tsironi, Vaia, Apter, Alan, Ball, Juliane, Bodmer, Benjamin, Bognar, Emese, Buse, Judith, Vela, Marta Correa, Fremer, Carolin, Garcia-Delgar, Blanca, Gulisano, Mariangela, Hagen, Annelieke, Hagstrøm, Julie, Madruga-Garrido, Marcos, Pellico, Alessandra, Ruhrman, Daphna, Schnell, Jaana, Silvestri, Paola Rosaria, Skov, Liselotte, Steinberg, Tamar, Gloor, Friederike Tagwerker, Turner, Victoria L., Weidinger, Elif, Alexander, John, Aranyi, Tamas, Buisman, Wim R., Buitelaar, Jan K., Driessen, Nicole, Drineas, Petros, Fan, Siyan, Forde, Natalie J., Gerasch, Sarah, van den Heuvel, Odile A., Jespersgaard, Cathrine, Kanaan, Ahmad S., Möller, Harald E., Nawaz, Muhammad S., Nespoli, Ester, Pagliaroli, Luca, Poelmans, Geert, Pouwels, Petra J.W., Rizzo, Francesca, Veltman, Dick J., van der Werf, Ysbrand D., Widomska, Joanna, Zilhäo, Nuno R., Brown, Lawrence W., Cheon, Keun-Ah, Coffey, Barbara J., Fernandez, Thomas V., Gilbert, Donald L., Hong, Hyun Ju, Ibanez-Gomez, Laura, Kim, Eun-Joo, Kim, Young Key, Kim, Young-Shin, Koh, Yun-Joo, Kook, Sodahm, Kuperman, Samuel, Leventhal, Bennett L., Maras, Athanasios, Murphy, Tara L., Shin, Eun-Young, Song, Dong-Ho, Song, Jungeun, State, Matthew W., Visscher, Frank, Wang, Sheng, Zinner, Samuel H., Tsetsos, Fotis, Topaloudi, Apostolia, Jain, Pritesh, Yang, Zhiyu, Yu, Dongmei, Kolovos, Petros, Tumer, Zeynep, Rizzo, Renata, Hartmann, Andreas, Depienne, Christel, Worbe, Yulia, Müller-Vahl, Kirsten R., Cath, Danielle C., Boomsma, Dorret I., Wolanczyk, Tomasz, Zekanowski, Cezary, Barta, Csaba, Nemoda, Zsofia, Tarnok, Zsanett, Padmanabhuni, Shanmukha S., Buxbaum, Joseph D., Grice, Dorothy, Glennon, Jeffrey, Stefansson, Hreinn, Hengerer, Bastian, Yannaki, Evangelia, Stamatoyannopoulos, John A., Benaroya-Milshtein, Noa, Cardona, Francesco, Hedderly, Tammy, Heyman, Isobel, Huyser, Chaim, Mir, Pablo, Morer, Astrid, Mueller, Norbert, Munchau, Alexander, Plessen, Kerstin J., Porcelli, Cesare, Roessner, Veit, Walitza, Susanne, Schrag, Anette, Martino, Davide, Tischfield, Jay A., Heiman, Gary A., Willsey, A. Jeremy, Dietrich, Andrea, Davis, Lea K., Crowley, James J., Mathews, Carol A., Scharf, Jeremiah M., Georgitsi, Marianthi, Hoekstra, Pieter J., and Paschou, Peristera
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- 2024
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3. Can polygenic risk scores help explain disease prevalence differences around the world? A worldwide investigation
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Jain, Pritesh R., Burch, Myson, Martinez, Melanie, Mir, Pablo, Fichna, Jakub P., Zekanowski, Cezary, Rizzo, Renata, Tümer, Zeynep, Barta, Csaba, Yannaki, Evangelia, Stamatoyannopoulos, John, Drineas, Petros, and Paschou, Peristera
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- 2023
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4. Differences in nanoscale organization of regulatory active and inactive human chromatin
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Brandstetter, Katharina, Zülske, Tilo, Ragoczy, Tobias, Hörl, David, Guirao-Ortiz, Miguel, Steinek, Clemens, Barnes, Toby, Stumberger, Gabriela, Schwach, Jonathan, Haugen, Eric, Rynes, Eric, Korber, Philipp, Stamatoyannopoulos, John A., Leonhardt, Heinrich, Wedemann, Gero, and Harz, Hartmann
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- 2022
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5. Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations
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Breeze, Charles E., Haugen, Eric, Reynolds, Alex, Teschendorff, Andrew, van Dongen, Jenny, Lan, Qing, Rothman, Nathaniel, Bourque, Guillaume, Dunham, Ian, Beck, Stephan, Stamatoyannopoulos, John, Franceschini, Nora, and Berndt, Sonja I.
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- 2022
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6. Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease
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Anand, Shankara, Gabriel, Stacey, Getz, Gad A., Graubert, Aaron, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Li, Xiao, MacArthur, Daniel G., Meier, Samuel R., Nedzel, Jared L., Nguyen, Duyen T., Segrè, Ayellet V., Todres, Ellen, Balliu, Brunilda, Bonazzola, Rodrigo, Brown, Andrew, Conrad, Donald F., Cotter, Daniel J., Cox, Nancy, Das, Sayantan, Dermitzakis, Emmanouil T., Einson, Jonah, Engelhardt, Barbara E., Eskin, Eleazar, Flynn, Elise D., Fresard, Laure, Gamazon, Eric R., Garrido-Martín, Diego, Gay, Nicole R., Guigó, Roderic, Hamel, Andrew R., He, Yuan, Hoffman, Paul J., Hormozdiari, Farhad, Hou, Lei, Jo, Brian, Kasela, Silva, Kashin, Seva, Kellis, Manolis, Kwong, Alan, Li, Xin, Liang, Yanyu, Mangul, Serghei, Mohammadi, Pejman, Muñoz-Aguirre, Manuel, Nobel, Andrew B., Oliva, Meritxell, Park, Yongjin, Parsana, Princy, Reverter, Ferran, Rouhana, John M., Sabatti, Chiara, Saha, Ashis, Stephens, Matthew, Stranger, Barbara E., Teran, Nicole A., Viñuela, Ana, Wang, Gao, Wright, Fred, Wucher, Valentin, Zou, Yuxin, Ferreira, Pedro G., Li, Gen, Melé, Marta, Yeger-Lotem, Esti, Bradbury, Debra, Krubit, Tanya, McLean, Jeffrey A., Qi, Liqun, Robinson, Karna, Roche, Nancy V., Smith, Anna M., Tabor, David E., Undale, Anita, Bridge, Jason, Brigham, Lori E., Foster, Barbara A., Gillard, Bryan M., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Karasik, Ellen, Kopen, Gene, Leinweber, William F., McDonald, Alisa, Moser, Michael T., Myer, Kevin, Ramsey, Kimberley D., Roe, Brian, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Jewell, Scott D., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Barcus, Mary E., Branton, Philip A., Sobin, Leslie, Barker, Laura K., Gardiner, Heather M., Mosavel, Maghboeba, Siminoff, Laura A., Flicek, Paul, Haeussler, Maximilian, Juettemann, Thomas, Kent, W. James, Lee, Christopher M., Powell, Conner C., Rosenbloom, Kate R., Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Abell, Nathan S., Akey, Joshua, Chen, Lin, Demanelis, Kathryn, Doherty, Jennifer A., Feinberg, Andrew P., Hansen, Kasper D., Hickey, Peter F., Jasmine, Farzana, Jiang, Lihua, Kaul, Rajinder, Kibriya, Muhammad G., Li, Jin Billy, Li, Qin, Lin, Shin, Linder, Sandra E., Pierce, Brandon L., Rizzardi, Lindsay F., Skol, Andrew D., Smith, Kevin S., Snyder, Michael, Stamatoyannopoulos, John, Tang, Hua, Wang, Meng, Carithers, Latarsha J., Guan, Ping, Koester, Susan E., Little, A. Roger, Moore, Helen M., Nierras, Concepcion R., Rao, Abhi K., Vaught, Jimmie B., Volpi, Simona, de Goede, Olivia M., Nachun, Daniel C., Ferraro, Nicole M., Gloudemans, Michael J., Rao, Abhiram S., Smail, Craig, Eulalio, Tiffany Y., Aguet, François, Ng, Bernard, Xu, Jishu, Barbeira, Alvaro N., Castel, Stephane E., Kim-Hellmuth, Sarah, Park, YoSon, Scott, Alexandra J., Strober, Benjamin J., Brown, Christopher D., Wen, Xiaoquan, Hall, Ira M., Battle, Alexis, Lappalainen, Tuuli, Im, Hae Kyung, Ardlie, Kristin G., Mostafavi, Sara, Quertermous, Thomas, Kirkegaard, Karla, and Montgomery, Stephen B.
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- 2021
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7. Inaccessible LCG Promoters Act as Safeguards to Restrict T Cell Development to Appropriate Notch Signaling Environments
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Furuyama, Suzanne, Wu, Qian “Vicky”, Varnum-Finney, Barbara, Sandstrom, Richard, Meuleman, Wouter, Stamatoyannopoulos, John A., and Bernstein, Irwin D.
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- 2021
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8. A Quantitative Proteome Map of the Human Body
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Aguet, François, Anand, Shankara, Ardlie, Kristin G., Gabriel, Stacey, Getz, Gad, Graubert, Aaron, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, MacArthur, Daniel G., Meier, Samuel R., Nedzel, Jared L., Nguyen, Duyen Y., Segrè, Ayellet V., Todres, Ellen, Balliu, Brunilda, Barbeira, Alvaro N., Battle, Alexis, Bonazzola, Rodrigo, Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Conrad, Don, Cotter, Daniel J., Cox, Nancy, Das, Sayantan, de Goede, Olivia M., Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Eulalio, Tiffany Y., Ferraro, Nicole M., Flynn, Elise, Fresard, Laure, Gamazon, Eric R., Garrido-Martín, Diego, Gay, Nicole R., Guigó, Roderic, Hamel, Andrew R., He, Yuan, Hoffman, Paul J., Hormozdiari, Farhad, Hou, Lei, Im, Hae Kyung, Jo, Brian, Kasela, Silva, Kellis, Manolis, Kim-Hellmuth, Sarah, Kwong, Alan, Lappalainen, Tuuli, Li, Xin, Liang, Yanyu, Mangul, Serghei, Mohammadi, Pejman, Montgomery, Stephen B., Muñoz-Aguirre, Manuel, Nachun, Daniel C., Nobel, Andrew B., Oliva, Meritxell, Park, YoSon, Park, Yongjin, Parsana, Princy, Reverter, Ferran, Rouhana, John M., Sabatti, Chiara, Saha, Ashis, Skol, Andrew D., Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Teran, Nicole A., Viñuela, Ana, Wang, Gao, Wen, Xiaoquan, Wright, Fred, Wucher, Valentin, Zou, Yuxin, Ferreira, Pedro G., Li, Gen, Melé, Marta, Yeger-Lotem, Esti, Barcus, Mary E., Bradbury, Debra, Krubit, Tanya, McLean, Jeffrey A., Qi, Liqun, Robinson, Karna, Roche, Nancy V., Smith, Anna M., Sobin, Leslie, Tabor, David E., Undale, Anita, Bridge, Jason, Brigham, Lori E., Foster, Barbara A., Gillard, Bryan M., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Karasik, Ellen, Kopen, Gene, Leinweber, William F., McDonald, Alisa, Moser, Michael T., Myer, Kevin, Ramsey, Kimberley D., Roe, Brian, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Jewell, Scott D., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Branton, Philip A., Barker, Laura K., Gardiner, Heather M., Mosavel, Maghboeba, Siminoff, Laura A., Flicek, Paul, Haeussler, Maximilian, Juettemann, Thomas, Kent, W. James, Lee, Christopher M., Powell, Conner C., Rosenbloom, Kate R., Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Abell, Nathan S., Akey, Joshua, Chen, Lin, Demanelis, Kathryn, Doherty, Jennifer A., Feinberg, Andrew P., Hansen, Kasper D., Hickey, Peter F., Jasmine, Farzana, Kaul, Rajinder, Kibriya, Muhammad G., Li, Jin Billy, Li, Qin, Linder, Sandra E., Pierce, Brandon L., Rizzardi, Lindsay F., Smith, Kevin S., Stamatoyannopoulos, John, Tang, Hua, Carithers, Latarsha J., Guan, Ping, Koester, Susan E., Little, A. Roger, Moore, Helen M., Nierras, Concepcion R., Rao, Abhi K., Vaught, Jimmie B., Volpi, Simona, Jiang, Lihua, Wang, Meng, Lin, Shin, Jian, Ruiqi, Li, Xiao, Chan, Joanne, Dong, Guanlan, Fang, Huaying, Robinson, Aaron E., and Snyder, Michael P.
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- 2020
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9. Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling
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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., and Funnell, Alister P.W.
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- 2020
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10. Index and biological spectrum of human DNase I hypersensitive sites
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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, and Stamatoyannopoulos, John
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- 2020
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11. Perspectives on ENCODE
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Snyder, Michael P., Gingeras, Thomas R., Moore, Jill E., Weng, Zhiping, Gerstein, Mark B., Ren, Bing, Hardison, Ross C., Stamatoyannopoulos, John A., Graveley, Brenton R., Feingold, Elise A., Pazin, Michael J., Pagan, Michael, Gilchrist, Daniel A., Hitz, Benjamin C., Cherry, J. Michael, Bernstein, Bradley E., Mendenhall, Eric M., Zerbino, Daniel R., Frankish, Adam, Flicek, Paul, and Myers, Richard M.
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- 2020
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12. Expanded encyclopaedias of DNA elements in the human and mouse genomes
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Moore, Jill E., Purcaro, Michael J., Pratt, Henry E., Epstein, Charles B., Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A., Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L., Freese, Peter, Gorkin, David U., Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A., Mortazavi, Ali, Keller, Cheryl A., Zhang, Xiao-Ou, Elhajjajy, Shaimae I., Huey, Jack, Dickel, Diane E., Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B., Zhang, Jialing, Victorsen, Alec, White, Kevin P., Visel, Axel, Yeo, Gene W., Burge, Christopher B., Lécuyer, Eric, Gilbert, David M., Dekker, Job, Rinn, John, Mendenhall, Eric M., Ecker, Joseph R., Kellis, Manolis, Klein, Robert J., Noble, William S., Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J., Cherry, J. Michael, Myers, Richard M., Ren, Bing, Graveley, Brenton R., Gerstein, Mark B., Pennacchio, Len A., Snyder, Michael P., Bernstein, Bradley E., Wold, Barbara, Hardison, Ross C., Gingeras, Thomas R., Stamatoyannopoulos, John A., and Weng, Zhiping
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- 2020
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13. Global reference mapping of human transcription factor footprints
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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, and Stamatoyannopoulos, John A.
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- 2020
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14. Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation
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Georgolopoulos, Grigorios, Psatha, Nikoletta, Iwata, Mineo, Nishida, Andrew, Som, Tannishtha, Yiangou, Minas, Stamatoyannopoulos, John A., and Vierstra, Jeff
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- 2021
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15. Tissue context determines the penetrance of regulatory DNA variation
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Halow, Jessica M., Byron, Rachel, Hogan, Megan S., Ordoñez, Raquel, Groudine, Mark, Bender, M. A., Stamatoyannopoulos, John A., and Maurano, Matthew T.
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- 2021
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16. Author Correction: Perspectives on ENCODE
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Snyder, Michael P., Gingeras, Thomas R., Moore, Jill E., Weng, Zhiping, Gerstein, Mark B., Ren, Bing, Hardison, Ross C., Stamatoyannopoulos, John A., Graveley, Brenton R., Feingold, Elise A., Pazin, Michael J., Pagan, Michael, Gilchrist, Daniel A., Hitz, Benjamin C., Cherry, J. Michael, Bernstein, Bradley E., Mendenhall, Eric M., Zerbino, Daniel R., Frankish, Adam, Flicek, Paul, and Myers, Richard M.
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- 2022
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17. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
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Moore, Jill E., Purcaro, Michael J., Pratt, Henry E., Epstein, Charles B., Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A., Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L., Freese, Peter, Gorkin, David U., Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A., Mortazavi, Ali, Keller, Cheryl A., Zhang, Xiao-Ou, Elhajjajy, Shaimae I., Huey, Jack, Dickel, Diane E., Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B., Zhang, Jialing, Victorsen, Alec, White, Kevin P., Visel, Axel, Yeo, Gene W., Burge, Christopher B., Lécuyer, Eric, Gilbert, David M., Dekker, Job, Rinn, John, Mendenhall, Eric M., Ecker, Joseph R., Kellis, Manolis, Klein, Robert J., Noble, William S., Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J., Cherry, J. Michael, Myers, Richard M., Ren, Bing, Graveley, Brenton R., Gerstein, Mark B., Pennacchio, Len A., Snyder, Michael P., Bernstein, Bradley E., Wold, Barbara, Hardison, Ross C., Gingeras, Thomas R., Stamatoyannopoulos, John A., and Weng, Zhiping
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- 2022
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18. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
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Li, Xiao-Yong, Thomas, Sean, Sabo, Peter J, Eisen, Michael B, Stamatoyannopoulos, John A, and Biggin, Mark D
- Abstract
Abstract Background In Drosophila embryos, many biochemically and functionally unrelated transcription factors bind quantitatively to highly overlapping sets of genomic regions, with much of the lowest levels of binding being incidental, non-functional interactions on DNA. The primary biochemical mechanisms that drive these genome-wide occupancy patterns have yet to be established. Results Here we use data resulting from the DNaseI digestion of isolated embryo nuclei to provide a biophysical measure of the degree to which proteins can access different regions of the genome. We show that the in vivo binding patterns of 21 developmental regulators are quantitatively correlated with DNA accessibility in chromatin. Furthermore, we find that levels of factor occupancy in vivo correlate much more with the degree of chromatin accessibility than with occupancy predicted from in vitro affinity measurements using purified protein and naked DNA. Within accessible regions, however, the intrinsic affinity of the factor for DNA does play a role in determining net occupancy, with even weak affinity recognition sites contributing. Finally, we show that programmed changes in chromatin accessibility between different developmental stages correlate with quantitative alterations in factor binding. Conclusions Based on these and other results, we propose a general mechanism to explain the widespread, overlapping DNA binding by animal transcription factors. In this view, transcription factors are expressed at sufficiently high concentrations in cells such that they can occupy their recognition sequences in highly accessible chromatin without the aid of physical cooperative interactions with other proteins, leading to highly overlapping, graded binding of unrelated factors.
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- 2011
19. Discovery of Functional Noncoding Elements by Digital Analysis of Chromatin Structure
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Sabo, Peter J., Hawrylycz, Michael, Wallace, James C., Humbert, Richard, Yu, Man, Shafer, Anthony, Kawamoto, Janelle, Hall, Robert, Mack, Joshua, Dorschner, Michael O., McArthur, Michael, Stamatoyannopoulos, John A., and Gartler, Stanley M.
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- 2004
20. Genome-Wide Identification of DNasel Hypersensitive Sites Using Active Chromatin Sequence Libraries
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Sabo, Peter J., Humbert, Richard, Hawrylycz, Michael, Wallace, James C., Dorschner, Michael O., McArthur, Michael, Stamatoyannopoulos, John A., and Davie, Earl W.
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- 2004
21. Positively selected enhancer elements endow osteosarcoma cells with metastatic competence
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Morrow, James J, Bayles, Ian, Funnell, Alister P W, Miller, Tyler E, Saiakhova, Alina, Lizardo, Michael M, Bartels, Cynthia F, Kapteijn, Maaike Y, Hung, Stevephen, Mendoza, Arnulfo, Dhillon, Gursimran, Chee, Daniel R, Myers, Jay T, Allen, Frederick, Gambarotti, Marco, Righi, Alberto, DiFeo, Analisa, Rubin, Brian P, Huang, Alex Y, Meltzer, Paul S, Helman, Lee J, Picci, Piero, Versteeg, Henri H, Stamatoyannopoulos, John A, Khanna, Chand, and Scacheri, Peter C
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Osteosarcoma -- Development and progression -- Genetic aspects -- Research ,Cancer metastasis -- Development and progression -- Genetic aspects -- Research ,Biological sciences ,Health - Abstract
Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in enhancer activity between primary and metastatic human tumors and between near isogenic pairs of highly lung metastatic and nonmetastatic osteosarcoma cell lines. We term these regions metastatic variant enhancer loci (Met-VELs). Met-VELs drive coordinated waves of gene expression during metastatic colonization of the lung. Met-VELs cluster nonrandomly in the genome, indicating that activity of these enhancers and expression of their associated gene targets are positively selected. As evidence of this causal association, osteosarcoma lung metastasis is inhibited by global interruptions of Met-VEL-associated gene expression via pharmacologic BET inhibition, by knockdown of AP-1 transcription factors that occupy Met-VELs, and by knockdown or functional inhibition of individual genes activated by Met-VELs, such as that encoding coagulation factor III/tissue factor (F3). We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung. These findings indicate that Met-VELs and the genes they regulate play a functional role in metastasis and may be suitable targets for antimetastatic therapies., Author(s): James J Morrow [1, 2]; Ian Bayles [2]; Alister P W Funnell [3]; Tyler E Miller [1]; Alina Saiakhova [2]; Michael M Lizardo [4]; Cynthia F Bartels [2]; Maaike [...]
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- 2018
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22. Integrative detection and analysis of structural variation in cancer genomes
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Dixon, Jesse R., Xu, Jie, Dileep, Vishnu, Zhan, Ye, Song, Fan, Le, Victoria T., Yardımcı, Galip Gürkan, Chakraborty, Abhijit, Bann, Darrin V., Wang, Yanli, Clark, Royden, Zhang, Lijun, Yang, Hongbo, Liu, Tingting, Iyyanki, Sriranga, An, Lin, Pool, Christopher, Sasaki, Takayo, Rivera-Mulia, Juan Carlos, Ozadam, Hakan, Lajoie, Bryan R., Kaul, Rajinder, Buckley, Michael, Lee, Kristen, Diegel, Morgan, Pezic, Dubravka, Ernst, Christina, Hadjur, Suzana, Odom, Duncan T., Stamatoyannopoulos, John A., Broach, James R., Hardison, Ross C., Ay, Ferhat, Noble, William Stafford, Dekker, Job, Gilbert, David M., and Yue, Feng
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- 2018
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23. Genetic association of long-chain acyl-CoA synthetase 1 variants with fasting glucose, diabetes, and subclinical atherosclerosis
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Manichaikul, Ani, Wang, Xin-Qun, Zhao, Wei, Wojczynski, Mary K., Siebenthall, Kyle, Stamatoyannopoulos, John A., Saleheen, Danish, Borecki, Ingrid B., Reilly, Muredach P., Rich, Stephen S., and Bornfeldt, Karin E.
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- 2016
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24. Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA
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Turner, Tychele N., Hormozdiari, Fereydoun, Duyzend, Michael H., McClymont, Sarah A., Hook, Paul W., Iossifov, Ivan, Raja, Archana, Baker, Carl, Hoekzema, Kendra, Stessman, Holly A., Zody, Michael C., Nelson, Bradley J., Huddleston, John, Sandstrom, Richard, Smith, Joshua D., Hanna, David, Swanson, James M., Faustman, Elaine M., Bamshad, Michael J., Stamatoyannopoulos, John, Nickerson, Deborah A., McCallion, Andrew S., Darnell, Robert, and Eichler, Evan E.
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- 2016
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25. DNase I hypersensitivity mapping, genomic footprinting, and transcription factor networks in plants
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Sullivan, Alessandra M., Bubb, Kerry L., Sandstrom, Richard, Stamatoyannopoulos, John A., and Queitsch, Christine
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- 2015
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26. Role of DNA Methylation in Modulating Transcription Factor Occupancy
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Maurano, Matthew T., Wang, Hao, John, Sam, Shafer, Anthony, Canfield, Theresa, Lee, Kristen, and Stamatoyannopoulos, John A.
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- 2015
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27. Taking Stock of Regulatory Variation
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Maurano, Matthew T. and Stamatoyannopoulos, John A.
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- 2015
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28. Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution
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Mayer, Andreas, di Iulio, Julia, Maleri, Seth, Eser, Umut, Vierstra, Jeff, Reynolds, Alex, Sandstrom, Richard, Stamatoyannopoulos, John A., and Churchman, L. Stirling
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- 2015
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29. The impact of rare variation on gene expression across tissues
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Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Conrad, Donald F., Cox, Nancy J., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Sul, Jae Hoon, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Billy Li, Jin, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, 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., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, and Zhu, Jingchun
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Disease susceptibility -- Genetic aspects ,Genetic variation -- Observations ,Gene expression -- Observations ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Xin Li [1]; Yungil Kim [2]; Emily K. Tsang [1, 3]; Joe R. Davis [1, 4]; Farhan N. Damani [2]; Colby Chiang [5]; Gaelen T. Hess [4]; Zachary Zappala [...]
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- 2017
- Full Text
- View/download PDF
30. Dynamic landscape and regulation of RNA editing in mammals
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Tan, Meng How, Li, Qin, Shanmugam, Raghuvaran, Piskol, Robert, Kohler, Jennefer, Young, Amy N., Liu, Kaiwen Ivy, Zhang, Rui, Ramaswami, Gokul, Ariyoshi, Kentaro, Gupte, Ankita, Keegan, Liam P., George, Cyril X., Ramu, Avinash, Huang, Ni, Pollina, Elizabeth A., Leeman, Dena S., Rustighi, Alessandra, Goh, Y. P. Sharon, Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, 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., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Chawla, Ajay, Del Sal, Giannino, Peltz, Gary, Brunet, Anne, Samuel, Charles E., OConnell, Mary A., Walkley, Carl R., and Nishikura, Kazuko
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Genetic research ,Mammals -- Genetic aspects ,RNA processing -- Research ,Genetic regulation ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Meng How Tan (corresponding author) [1, 2, 3]; Qin Li [1]; Raghuvaran Shanmugam [2, 3]; Robert Piskol [1]; Jennefer Kohler [1]; Amy N. Young [1]; Kaiwen Ivy Liu [3]; [...]
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- 2017
- Full Text
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31. Landscape of X chromosome inactivation across human tissues
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Tukiainen, Taru, Villani, Alexandra-Chlo, Yen, Angela, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, Franois, Byrnes, Andrea, Ardlie, Kristin G., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, 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., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Regev, Aviv, and Hacohen, Nir
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Chromosomes -- Physiological aspects ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Taru Tukiainen (corresponding author) [1, 2]; Alexandra-Chlo Villani [2, 3]; Angela Yen [2, 4]; Manuel A. Rivas [1, 2, 5]; Jamie L. Marshall [1, 2]; Rahul Satija [2, 6, [...]
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- 2017
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32. Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
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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., III, Weaver, Molly, Diegel, Morgan, Mnaimneh, Sanie, Yang, Ally, Hughes, Timothy R., Nemhauser, Jennifer L., Queitsch, Christine, and Stamatoyannopoulos, John A.
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- 2014
- Full Text
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33. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
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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., and Stamatoyannopoulos, John A.
- Published
- 2014
34. Maritime route of colonization of Europe
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Paschou, Peristera, Drineas, Petros, Yannaki, Evangelia, Razou, Anna, Kanaki, Katerina, Tsetsos, Fotis, Padmanabhuni, Shanmukha Sampath, Michalodimitrakis, Manolis, Renda, Maria C., Pavlovic, Sonja, Anagnostopoulos, Achilles, Stamatoyannopoulos, John A., Kidd, Kenneth K., and Stamatoyannopoulos, George
- Published
- 2014
35. Defining functional DNA elements in the human genome
- Author
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Kellis, Manolis, Wold, Barbara, Snyderd, Michael P., Bernstein, Bradley E., Kundaje, Anshul, Marinov, Georgi K., Ward, Lucas D., Birney, Ewan, Crawford, Gregory E., Dekker, Job, Dunham, Ian, Elnitski, Laura L., Farnham, Peggy J., Feingold, Elise A., Gerstein, Mark, Giddings, Morgan C., Gilbert, David M., Gingeras, Thomas R., Green, Eric D., Guigo, Roderic, Hubbard, Tim, Kent, Jim, Lieb, Jason D., Myerst, Richard M., Pazin, Michael J., Ren, Bing, Stamatoyannopoulos, John A., Weng, Zhiping, White, Kevin P., and Hardison, Ross C.
- Published
- 2014
36. Collaborative Regulation of Development but Independent Control of Metabolism by Two Epidermis-specific Transcription Factors in Caenorhabditis elegans
- Author
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Shao, Jiaofang, He, Kan, Wang, Hao, Ho, Wing Sze, Ren, Xiaoliang, An, Xiaomeng, Wong, Ming Kin, Yan, Bin, Xie, Dongying, Stamatoyannopoulos, John, and Zhao, Zhongying
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- 2013
- Full Text
- View/download PDF
37. Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progeny
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Chang, Kai-Hsin, Huang, Andy, Han, Hemei, Jiang, Yi, Fang, Xiangdong, Song, Chao-Zhong, Padilla, Steve, Wang, Hao, Qu, Hongzhu, Stamatoyannopoulos, John, Li, Qiliang, and Papayannopoulou, Thalia
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- 2013
- Full Text
- View/download PDF
38. Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes
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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., and Stamatoyannopoulos, John A.
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- 2013
- Full Text
- View/download PDF
39. Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
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Stergachis, Andrew B., Haugen, Eric, Shafer, Anthony, Fu, Wenqing, LeProust, M., Akey, Joshua M., and Stamatoyannopoulos, John A.
- Published
- 2013
- Full Text
- View/download PDF
40. An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level
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Bauer, Daniel E., Kamran, Sophia C., Lessard, Samuel, Xu, Jian, Fujiwara, Yuko, Lin, Carrie, Shao, Zhen, Canver, Matthew C., Smith, Elenoe C., Pinello, Luca, Sabo, Peter J., Vierstra, Jeff, Voit, Richard A., Yuan, Guo-Cheng, Porteus, Matthew H., Stamatoyannopoulos, John A., Lettre, Guillaume, and Orkin, Stuart H.
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- 2013
- Full Text
- View/download PDF
41. Probing DNA shape and methylation state on a genomic scale with DNase I
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Lazarovici, Allan, Zhou, Tianyin, Shafer, Anthony, Machado, Ana Carolina Dantas, Riley, Todd R., Sandstrom, Richard, Sabo, Peter J., Lu, Yan, Rohs, Remo, Stamatoyannopoulos, John A., and Bussemaker, Harmen J.
- Published
- 2013
42. Genetic effects on gene expression across human tissues
- Author
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Aguet, François, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segrè, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frésard, Laure, Gamazon, Eric R., Garrido-Martín, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Im, Hae Kyung, Jo, Brian, Kang, Eun Yong, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muñoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, Roger A., 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., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, James W., Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Brown, Andrew A., Nguyen, Duyen Y., Sullivan, Timothy J., Addington, Anjene, Koester, Susan, Lockhart, Nicole C., Roe, Bryan, Valley, Dana, Gewirtz, Ariel D. H., He, Amy Z., Quon, Gerald, Ripke, Stephan, Shimko, Tyler C., Teran, Nicole A., Zhang, Hailei, Bustamante, Carlos D., and Guigó, Roderic
- Published
- 2017
- Full Text
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43. Cell-of-origin chromatin organization shapes the mutational landscape of cancer
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Polak, Paz, Karlic, Rosa, Koren, Amnon, Thurman, Robert, Sandstrom, Richard, Lawrence, Michael S., Reynolds, Alex, Rynes, Eric, Vlahovicek, Kristian, Stamatoyannopoulos, John A., and Sunyaev, Shamil R.
- Subjects
Gene mutations -- Research ,Chromatin -- Health aspects ,Genetic research ,Cancer -- Genetic aspects ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Cancer is a disease potentiated by mutations in somatic cells. Cancer mutations are not distributed uniformly along the human genome. Instead, different human genomic regions vary by up to fivefold in the local density of cancer somatic mutations (1), posing a fundamental problem for statistical methods used in cancer genomics. Epigenomic organization has been proposed as a major determinant of the cancer mutational landscape (1-5). However, both somatic mutagenesis and epigenomic features are highly cell-type-specific (6,7). We investigated the distribution of mutations in multiple independent samples of diverse cancer types and compared them to cell-type-specific epigenomic features. Here we show that chromatin accessibility and modification, together with replication timing, explain up to 86% of the variance in mutation rates along cancer genomes. The best predictors of local somatic mutation density are epigenomic features derived from the most likely cell type of origin of the corresponding malignancy. Moreover, we find that cell-of-origin chromatin features are much stronger determinants of cancer mutation profiles than chromatin features of matched cancer cell lines. Furthermore, we show that the cell type of origin of a cancer can be accurately determined based on the distribution of mutations along its genome. Thus, the DNA sequence of a cancer genome encompasses a wealth of information about the identity and epigenomic features of its cell of origin., Recent studies have begun to address the underlying causes of cancer mutational heterogeneity by comparing mutation rate variation to the distribution of sequence features, gene expression and epigenetic marks along [...]
- Published
- 2015
44. Resolving the complexity of the human genome using single-molecule sequencing
- Author
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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, and Eichler, Evan E.
- Subjects
Nucleotide sequencing -- Usage -- Methods ,DNA sequencing -- Usage -- Methods ,Human genome -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
The human genome is arguably the most complete mammalian reference assembly (1-3), yet more than 160 euchromatic gaps remain (4-6) and aspects of its structural variation remain poorly understood ten [...]
- Published
- 2015
45. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila
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Fisher, William W., Li, Jingyi Jessica, Hammonds, Ann S., Brown, James B., Pfeiffer, Barret D., Weiszmann, Richard, MacArthur, Stewart, Thomas, Sean, Stamatoyannopoulos, John A., Eisen, Michael B., Bickel, Peter J., Biggin, Mark D., and Celniker, Susan E.
- Published
- 2012
46. Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis
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Xu, Jian, Shao, Zhen, Glass, Kimberly, Bauer, Daniel E., Pinello, Luca, Van Handel, Ben, Hou, Serena, Stamatoyannopoulos, John A., Mikkola, Hanna K.A., Yuan, Guo-Cheng, and Orkin, Stuart H.
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- 2012
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47. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
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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, and Stamatoyannopoulos, John A.
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- 2012
- Full Text
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48. A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development
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Paige, Sharon L., Thomas, Sean, Stoick-Cooper, Cristi L., Wang, Hao, Maves, Lisa, Sandstrom, Richard, Pabon, Lil, Reinecke, Hans, Pratt, Gabriel, Keller, Gordon, Moon, Randall T., Stamatoyannopoulos, John, and Murry, Charles E.
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- 2012
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49. Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification
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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., and Rudensky, Alexander Y.
- Published
- 2012
- Full Text
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50. Circuitry and Dynamics of Human Transcription Factor Regulatory Networks
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Neph, Shane, Stergachis, Andrew B., Reynolds, Alex, Sandstrom, Richard, Borenstein, Elhanan, and Stamatoyannopoulos, John A.
- Published
- 2012
- Full Text
- View/download PDF
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