The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites von West, Jason A., Davis, Christopher P., Sunwoo, Hongjae, Simon, Matthew D., Sadreyev, Ruslan I., Wang, Peggy I., Tolstorukov, Michael Y., Kingston, Robert E.

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Design and analysis of ChIP-seq experiments for DNA-binding proteins von Kharchenko, Peter V, Park, Peter J, Tolstorukov, Michael Y

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Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate von Chakraborty, Abhishek A, Laukka, Tuomas, Myllykoski, Matti, Ringel, Alison E, Booker, Matthew A, Tolstorukov, Michael Y, Meng, Yuzhong Jeff, Meier, Samuel R, Jennings, Rebecca B, Creech, Amanda L, Herbert, Zachary T, McBrayer, Samuel K, Olenchock, Benjamin A, Jaffe, Jacob D, Haigis, Marcia C, Beroukhim, Rameen, Signoretti, Sabina, Koivunen, Peppi, Kaelin, Jr, William G

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Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction von Mueller, Britta, Mieczkowski, Jakub, Kundu, Sharmistha, Wang, Peggy, Sadreyev, Ruslan, Tolstorukov, Michael Y, Kingston, Robert E

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SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation von Wang, Xiaofeng, Lee, Ryan S, Alver, Burak H, Haswell, Jeffrey R, Wang, Su, Mieczkowski, Jakub, Drier, Yotam, Gillespie, Shawn M, Archer, Tenley C, Wu, Jennifer N, Tzvetkov, Evgeni P, Troisi, Emma C, Pomeroy, Scott L, Biegel, Jaclyn A, Tolstorukov, Michael Y, Bernstein, Bradley E, Park, Peter J, Roberts, Charles W M

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MNase titration reveals differences between nucleosome occupancy and chromatin accessibility von Mieczkowski, Jakub, Cook, April, Bowman, Sarah K., Mueller, Britta, Alver, Burak H., Kundu, Sharmistha, Deaton, Aimee M., Urban, Jennifer A., Larschan, Erica, Park, Peter J., Kingston, Robert E., Tolstorukov, Michael Y.

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The KDM5A/RBP2 histone demethylase represses NOTCH signaling to sustain neuroendocrine differentiation and promote small cell lung cancer tumorigenesis von Oser, Matthew G, Sabet, Amin H, Gao, Wenhua, Chakraborty, Abhishek A, Schinzel, Anna C, Jennings, Rebecca B, Fonseca, Raquel, Bonal, Dennis M, Booker, Matthew A, Flaifel, Abdallah, Novak, Jesse S, Christensen, Camilla L, Zhang, Hua, Herbert, Zachary T, Tolstorukov, Michael Y, Buss, Elizabeth J, Wong, Kwok-Kin, Bronson, Roderick T, Nguyen, Quang-De, Signoretti, Sabina, Kaelin, Jr, William G

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Histone Variant H2A.Bbd Is Associated with Active Transcription and mRNA Processing in Human Cells von Tolstorukov, Michael Y., Goldman, Joseph A., Gilbert, Cristele, Ogryzko, Vasily, Kingston, Robert E., Park, Peter J.

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Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters von Tolstorukov, Michael Y., Sansam, Courtney G., Lu, Ping, Koellhoffer, Edward C., Helming, Katherine C., Alver, Burak H., Tillman, Erik J., Evans, Julia A., Wilson, Boris G., Park, Peter J., Roberts, Charles W. M.

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Nature and function of insulator protein binding sites in the Drosophila genome von Schwartz, Yuri B, Linder-Basso, Daniela, Kharchenko, Peter V, Tolstorukov, Michael Y, Kim, Maria, Li, Hua-Bing, Gorchakov, Andrey A, Minoda, Aki, Shanower, Gregory, Alekseyenko, Artyom A, Riddle, Nicole C, Jung, Youngsook L, Gu, Tingting, Plachetka, Annette, Elgin, Sarah C R, Kuroda, Mitzi I, Park, Peter J, Savitsky, Mikhail, Karpen, Gary H, Pirrotta, Vincenzo

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Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming von West, Jason A., Cook, April, Alver, Burak H., Stadtfeld, Matthias, Deaton, Aimee M., Hochedlinger, Konrad, Park, Peter J., Tolstorukov, Michael Y., Kingston, Robert E.

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Regulation of neuroendocrine plasticity by the RNA-binding protein ZFP36L1 von Chen, Hsiao-Yun, Durmaz, Yavuz T., Li, Yixiang, Sabet, Amin H., Vajdi, Amir, Denize, Thomas, Walton, Emily, Laimon, Yasmin Nabil, Doench, John G., Mahadevan, Navin R., Losman, Julie-Aurore, Barbie, David A., Tolstorukov, Michael Y., Rudin, Charles M., Sen, Triparna, Signoretti, Sabina, Oser, Matthew G.

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Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin von Riddle, Nicole C, Minoda, Aki, Kharchenko, Peter V, Alekseyenko, Artyom A, Schwartz, Yuri B, Tolstorukov, Michael Y, Gorchakov, Andrey A, Jaffe, Jacob D, Kennedy, Cameron, Linder-Basso, Daniela, Peach, Sally E, Shanower, Gregory, Zheng, Haiyan, Kuroda, Mitzi I, Pirrotta, Vincenzo, Park, Peter J, Elgin, Sarah C R, Karpen, Gary H

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Lineage-specific canonical and non-canonical activity of EZH2 in advanced prostate cancer subtypes von Venkadakrishnan, Varadha Balaji, Presser, Adam G., Singh, Richa, Booker, Matthew A., Traphagen, Nicole A., Weng, Kenny, Voss, Nathaniel C. E., Mahadevan, Navin R., Mizuno, Kei, Puca, Loredana, Idahor, Osasenaga, Ku, Sheng-Yu, Bakht, Martin K., Borah, Ashir A., Herbert, Zachary T., Tolstorukov, Michael Y., Barbie, David A., Rickman, David S., Brown, Myles, Beltran, Himisha

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A Novel Roll-and-Slide Mechanism of DNA Folding in Chromatin: Implications for Nucleosome Positioning von Tolstorukov, Michael Y., Colasanti, Andrew V., McCandlish, David M., Olson, Wilma K., Zhurkin, Victor B.

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Cancer-associated fibroblasts are the main contributors to epithelial-to-mesenchymal signatures in the tumor microenvironment von Szabo, Peter M., Vajdi, Amir, Kumar, Namit, Tolstorukov, Michael Y., Chen, Benjamin J., Edwards, Robin, Ligon, Keith L., Chasalow, Scott D., Chow, Kin-Hoe, Shetty, Aniket, Bolisetty, Mohan, Holloway, James L., Golhar, Ryan, Kidd, Brian A., Hull, Philip Ansumana, Houser, Jeff, Vlach, Logan, Siemers, Nathan O., Saha, Saurabh

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Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation von Kuzu, Guray, Kaye, Emily G, Chery, Jessica, Siggers, Trevor, Yang, Lin, Dobson, Jason R, Boor, Sonia, Bliss, Jacob, Liu, Wei, Jogl, Gerwald, Rohs, Remo, Singh, Nadia D, Bulyk, Martha L, Tolstorukov, Michael Y, Larschan, Erica

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Genomic and biological study of fusion genes as resistance mechanisms to EGFR inhibitors von Kobayashi, Yoshihisa, Oxnard, Geoffrey R., Cohen, Elizabeth F., Mahadevan, Navin R., Alessi, Joao V., Hung, Yin P., Bertram, Arrien A., Heppner, David E., Ribeiro, Mauricio F., Sacardo, Karina P., Saddi, Rodrigo, Macedo, Mariana P., Blasco, Rafael B., Li, Jiaqi, Kurppa, Kari J., Nguyen, Tom, Voligny, Emma, Ananda, Guruprasad, Chiarle, Roberto, Katz, Artur, Tolstorukov, Michael Y., Sholl, Lynette M., Jänne, Pasi A.

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Enhancer regions show high histone H3.3 turnover that changes during differentiation von Deaton, Aimee M, Gómez-Rodríguez, Mariluz, Mieczkowski, Jakub, Tolstorukov, Michael Y, Kundu, Sharmistha, Sadreyev, Ruslan I, Jansen, Lars Et, Kingston, Robert E

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Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome von Kaye, Emily G., Booker, Matthew, Kurland, Jesse V., Conicella, Alexander E., Fawzi, Nicolas L., Bulyk, Martha L., Tolstorukov, Michael Y., Larschan, Erica

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