Items where Subject is "epigenetics"

Paper

Abel, Haley J, Larson, David E, Regier, Allison A, Chiang, Colby, Das, Indraniel, Kanchi, Krishna L, Layer, Ryan M, Neale, Benjamin M, Salerno, William J, Reeves, Catherine, Buyske, Steven, NHGRI Centers for Common Disease Genomics, Matise, Tara C, Muzny, Donna M, Zody, Michael C, Lander, Eric S, Dutcher, Susan K, Stitziel, Nathan O, Hall, Ira M (July 2020) Mapping and characterization of structural variation in 17,795 human genomes. Nature, 583 (7814). pp. 83-89. ISSN 0028-0836

Abeshouse, A., Ahn, J., Akbani, R., Ally, A., Amin, S., Andry, C. D., Annala, M., Aprikian, A., Armenia, J., Arora, A., Auman, J. T., Balasundaram, M., Balu, S., Barbieri, C. E., Bauer, T., Benz, C. C., Bergeron, A., Beroukhim, R., Berrios, M., Bivol, A., Bodenheimer, T., Boice, L., Bootwalla, M. S., Borges Dos Reis, R., Boutros, P. C., Bowen, J., Bowlby, R., Boyd, J., Bradley, R. K., Breggia, A., Brimo, F., Bristow, C. A., Brooks, D., Broom, B. M., Bryce, A. H., Bubley, G., Burks, E., Butterfield, Y. S. N., Button, M., Canes, D., Carlotti, C. G., Carlsen, R., Carmel, M., Carroll, P. R., Carter, S. L., Cartun, R., Carver, B. S., Chan, J. M., Chang, M. T., Chen, Y., Cherniack, A. D., Chevalier, S., Chin, L., Cho, J., Chu, A., Chuah, E., Chudamani, S., Cibulskis, K., Ciriello, G., Clarke, A., Cooperberg, M. R., Corcoran, N. M., Costello, A. J., Cowan, J., Crain, D., Curley, E., David, K., Demchok, J. A., Demichelis, F., Dhalla, N., Dhir, R., Doueik, A., Drake, B., Dvinge, H., Dyakova, N., Felau, I., Ferguson, M. L., Frazer, S., Freedland, S., Fu, Y., Gabriel, S. B., Gao, J., Gardner, J., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Gerstein, M. B., Getz, G., Godwin, A. K., Gopalan, A., Graefen, M., Graim, K., Gribbin, T., Guin, R., Gupta, M., Hadjipanayis, A., Haider, S., Hamel, L., Hayes, D. N., Heiman, D. I., Hess, J., Hoadley, K. A., Holbrook, A. H., Holt, R. A., Holway, A., Hovens, C. M., Hoyle, A. P., Huang, M., Hutter, C. M., Ittmann, M., Iype, L., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Juhl, H., Kahles, A., Kane, C. J., Kasaian, K., Kerger, M., Khurana, E., Kim, J., Klein, R. J., Kucherlapati, R., Lacombe, L., Ladanyi, M., Lai, P. H., Laird, P. W., Lander, E. S., Latour, M., Lawrence, M. S., Lau, K., Lebien, T., Lee, D., Lee, S., Lehmann, K. V., Leraas, K. M., Leshchiner, I., Leung, R., Libertino, J. A., Lichtenberg, T. M., Lin, P., Linehan, W. M., Ling, S., Lippman, S. M., Liu, J., Liu, W., Lochovsky, L., Loda, M., Logothetis, C., Lolla, L., Longacre, T., Lu, Y., Luo, J., Ma, Y., Mahadeshwar, H. S., Mallery, D., Mariamidze, A., Marra, M. A., Mayo, M., McCall, S., McKercher, G., Meng, S., Mes-Masson, A. M., Merino, M. J., Meyerson, M., Mieczkowski, P. A., Mills, G. B., Shaw, K. R. M., Minner, S., Moinzadeh, A., Moore, R. A., Morris, S., Morrison, C., Mose, L. E., Mungall, A. J., Murray, B. A., Myers, J. B., Naresh, R., Nelson, J., Nelson, M. A., Nelson, P. S., Newton, Y., Noble, M. S., Noushmehr, H., Nykter, M., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Paulauskis, J., Penny, R., Perou, C. M., Piché, A., Pihl, T., Pinto, P. A., Prandi, D., Protopopov, A., Ramirez, N. C., Rao, A., Rathmell, W. K., Rätsch, G., Ren, X., Reuter, V. E., Reynolds, S. M., Rhie, S. K., Rieger-Christ, K., Roach, J., Robertson, A. G., Robinson, B., Rubin, M. A., Saad, F., Sadeghi, S., Saksena, G., Saller, C., Salner, A., Sanchez-Vega, F., Sander, C., Sandusky, G., Sauter, G., Sboner, A., Scardino, P. T., Scarlata, E., Schein, J. E., Schlomm, T., Schmidt, L. S., Schultz, N., Schumacher, S. E., Seidman, J., Neder, L., Seth, S., Sharp, A., Shelton, C., Shelton, T., Shen, H., Shen, R., Sherman, M., Sheth, M., Shi, Y., Shih, J., Shmulevich, I., Simko, J., Simon, R., Simons, J. V., Sipahimalani, P., Skelly, T., Sofia, H. J., Soloway, M. G., Song, X., Sorcini, A., Sougnez, C., Stepa, S., Stewart, C., Stewart, J., Stuart, J. M., Sullivan, T. B., Sun, C., Sun, H., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Tarvin, K., Taylor, B. S., Teebagy, P., Tenggara, I., Têtu, B., Tewari, A., Thiessen, N., Thompson, T., Thorne, L. B., Tirapelli, D. P., Tomlins, S. A., Trevisan, F. A., Troncoso, P., True, L. D., Tsourlakis, M. C., Tyekucheva, S., Van Allen, E., Van Den Berg, D. J., Veluvolu, U., Verhaak, R., Vocke, C. D., Voet, D., Wan, Y., Wang, Q., Wang, W., Wang, Z., Weinhold, N., Weinstein, J. N., Weisenberger, D. J., Wilkerson, M. D., Wise, L., Witte, J., Wu, C. C., Wu, J., Wu, Y., Xu, A. W., Yadav, S. S., Yang, L., Yang, L., Yau, C., Ye, H., Yena, P., Zeng, T., Zenklusen, J. C., Zhang, H., Zhang, J., Zhang, J., Zhang, W., Zhong, Y., Zhu, K., Zmuda, E. (2015) The Molecular Taxonomy of Primary Prostate Cancer. Cell, 163 (4). pp. 1011-1025. ISSN 0092-8674

BRAIN Initiative Cell Census Network (BICCN) (October 2021) A multimodal cell census and atlas of the mammalian primary motor cortex. Nature, 598 (7879). pp. 86-102. ISSN 0028-0836

Bakken, Trygve E, Jorstad, Nikolas L, Hu, Qiwen, Lake, Blue B, Tian, Wei, Kalmbach, Brian E, Crow, Megan, Hodge, Rebecca D, Krienen, Fenna M, Sorensen, Staci A, Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian D, Aldridge, Andrew I, Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa G, Crichton, Kirsten, Daigle, Tanya L, Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas T, Herb, Brian R, Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang Eric, Liu, Christine S, Liu, Hanqing, Lucero, Jacinta D, Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy A, Moussa, Marmar, Nery, Joseph R, Nicovich, Philip R, Niu, Sheng-Yong, Orvis, Joshua, Osteen, Julia K, Owen, Scott, Palmer, Carter R, Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora M, Rimorin, Christine, Rivkin, Angeline, Romanow, William J, Sedeño-Cortés, Adriana E, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna Marie, Zhang, Renee, Ament, Seth A, Behrens, M Margarita, Bravo, Hector Corrada, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick R, Höllt, Thomas, Horwitz, Gregory D, Keene, C Dirk, Kharchenko, Peter V, Ko, Andrew L, Lelieveldt, Boudewijn P, Luo, Chongyuan, Mukamel, Eran A, Pinto-Duarte, António, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard H, Smith, Kimberly, Spain, William J, White, Owen R, Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan Z, McCarroll, Steven A, Ting, Jonathan T, Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph R, Linnarsson, Sten, Lein, Ed S (October 2021) Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature, 598 (7879). pp. 111-119. ISSN 0028-0836

Balasooriya, Gayan, Spector, David (2022) Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. bioRxiv. (Submitted)

Banito, Ana, Li, Xiang, Laporte, Aimée N., Roe, Jae-Seok, Sanchez-Vega, Francisco, Huang, Chun-Hao, Dancsok, Amanda R., Hatzi, Katerina, Chen, Chi-Chao, Tschaharganeh, Darjus F., Chandwani, Rohit, Tasdemir, Nilgun, Jones, Kevin B., Capecchi, Mario R., Vakoc, Christopher R., Schultz, Nikolaus, Ladanyi, Marc, Nielsen, Torsten O., Lowe, Scott W. (March 2018) The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma. Cancer Cell, 33 (3). pp. 527-541. ISSN 1535-6108

Bastow, R., Mylne, J. S., Lister, C., Lippman, Z., Martienssen, R. A., Dean, C. (January 2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 427 (6970). pp. 164-7. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Benoit, M., Drost, H. G., Catoni, M., Gouil, Q., Lopez-Gomollon, S., Baulcombe, D., Paszkowski, J. (September 2019) Environmental and epigenetic regulation of Rider retrotransposons in tomato. PLoS Genet, 15 (9). e1008370. ISSN 1553-7390

Benoit, Matthias (January 2022) Four to the floor: Active DNA demethylation defines somatic epigenetic patterns and impacts quantitative traits. The Plant cell. ISSN 1532-298X

Bergmann, J. H., Rodriguez, M. G., Martins, N. M. C., Kimura, H., Kelly, D. A., Masumoto, H., Larionov, V., Jansen, L. E. T., Earnshaw, W. C. (December 2011) Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore. EMBO Journal, 30 (2). pp. 328-340.

Bhagwat, A. S., Vakoc, C. R. (March 2014) A new bump in the epigenetic landscape. Molecular Cell, 53 (6). pp. 857-8. ISSN 1097-2765

Bhattacharjee, S., Roche, B., Martienssen, R. A. (June 2019) RNA-induced initiation of transcriptional silencing (RITS) complex structure and function. RNA Biol, 16 (9). pp. 1133-1146. ISSN 1547-6286

Borg, M, Jacob, Y., Susaki, D., LeBlanc, C., Buendia, D, Axelsson, E., Kawashima, T., Voigt, P., Boavida, L. C., Becker, J. D., Higashiyama, T., Martienssen, R. A., Berger, F. (June 2020) Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin. Nature Cell Biology, 22 (6). p. 621. ISSN 1465-7392

Borges, F., Martienssen, R. A. (April 2013) Establishing epigenetic variation during genome reprogramming. RNA Biology, 10 (4). pp. 490-4. ISSN 1555-8584 (Electronic)1547-6286 (Linking)

Brennecke, J., Malone, C. D., Aravin, A. A., Sachidanandam, R., Stark, A., Hannon, G. J. (November 2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science, 322 (5906). pp. 1387-92.

Bronstein, R., Kyle, J., Abraham, A. B., Tsirka, S. E. (May 2017) Neurogenic to Gliogenic Fate Transition Perturbed by Loss of HMGB2. Front Mol Neurosci, 10. p. 153. ISSN 1662-5099

Byrne, M., Kidney, C., Martienssen, R. (July 2004) Homeobox genes in Arabidopsis and their epigenetic regulation. Developmental Biology, 271 (2). p. 553. ISSN 0012-1606

Byrne, M. E., Kidner, C. A., Martienssen, R. A. (October 2003) Plant stem cells: divergent pathways and common themes in shoots and roots. Current Opinion in Genetics & Development, 13 (5). pp. 551-7. ISSN 0959-437X

Cable, Jennifer, Heard, Edith, Hirose, Tetsuro, Prasanth, Kannanganattu V, Chen, Ling-Ling, Henninger, Jonathan E, Quinodoz, Sofia A, Spector, David L, Diermeier, Sarah D, Porman, Allison M, Kumar, Dhiraj, Feinberg, Mark W, Shen, Xiaohua, Unfried, Juan Pablo, Johnson, Rory, Chen, Chun-Kan, Wilusz, Jeremy E, Lempradl, Adelheid, McGeary, Sean E, Wahba, Lamia, Pyle, Anna Marie, Hargrove, Amanda E, Simon, Matthew D, Marcia, Marco, Przanowska, Róża K, Chang, Howard Y, Jaffrey, Samie R, Contreras, Lydia M, Chen, Qi, Shi, Junchao, Mendell, Joshua T, He, Lin, Song, Erwei, Rinn, John L, Lalwani, Mukesh Kumar, Kalem, Murat Can, Chuong, Edward B, Maquat, Lynne E, Liu, Xuhang (November 2021) Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals of the New York Academy of Sciences. ISSN 0077-8923

Cao, Zhendong, Budinich, Krista A, Huang, Hua, Ren, Diqiu, Lu, Bin, Zhang, Zhen, Chen, Qingzhou, Zhou, Yeqiao, Huang, Yu-Han, Alikarami‬, Fatemeh, Kingsley, Molly C, Lenard, Alexandra K, Wakabayashi, Aoi, Khandros, Eugene, Bailis, Will, Qi, Jun, Carroll, Martin P, Blobel, Gerd A, Faryabi, Robert B, Bernt, Kathrin M, Berger, Shelley L, Shi, Junwei (August 2021) ZMYND8-regulated IRF8 transcription axis is an acute myeloid leukemia dependency. Molecular Cell. ISSN 1097-2765

Castel, S. E., Martienssen, R. A. (February 2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet, 14 (2). pp. 100-12. ISSN 1471-0064 (Electronic)1471-0056 (Linking)

Choi, K., Zhao, X., Tock, A. J., Lambing, C., Underwood, C. J., Hardcastle, T. J., Serra, H., Kim, J., Cho, H. S., Kim, J., Ziolkowski, P. A., Yelina, N. E., Hwang, I., Martienssen, R. A., Henderson, I. R. (April 2018) Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res, 28 (4). pp. 532-546. ISSN 1088-9051

Ciccone, M. F., Trousdell, M. C., Dos Santos, C. O. (November 2020) Characterization of Organoid Cultures to Study the Effects of Pregnancy Hormones on the Epigenome and Transcriptional Output of Mammary Epithelial Cells. J Mammary Gland Biol Neoplasia, 25 (4). pp. 351-366. ISSN 1083-3021

Cluntun, A. A., Lukey, M. J., Cerione, R. A., Locasale, J. W. (March 2017) Glutamine Metabolism in Cancer: Understanding the Heterogeneity. Trends Cancer, 3 (3). pp. 169-180. ISSN 2405-8033

Creasey, K. M., Zhai, J., Borges, F., Van Ex, F., Regulski, M., Meyers, B. C., Martienssen, R. A. (March 2014) miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature, 508 (7496). pp. 411-415. ISSN 0028-0836

Dos Santos, C. O., Dolzhenko, E., Hodges, E., Smith, A. D., Hannon, G. J. (May 2015) An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland. Cell Reports. ISSN 2211-1247

Duelli, D. M., Hearn, S., Myers, M. P., Lazebnik, Y. (November 2005) A primate virus generates transformed human cells by fusion. J Cell Biol, 171 (3). pp. 493-503. ISSN 0021-9525 (Print)

Dukler, N., Huang, Y-F., Siepel, A. (March 2020) Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data. Mol Biol Evol, 37 (7). pp. 2137-2152. ISSN 0737-4038

Dukler, Noah, Huang, Yi-Fei, Siepel, Adam (September 2019) Phylogenetic modeling of regulatory element turnover based on epigenomic data. BioRxiv. (Unpublished)

Ezhkova, E., Pasolli, H. A., Parker, J. S., Stokes, N., Su, I. H., Hannon, G. J., Tarakhovsky, A., Fuchs, E. (March 2009) Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells. Cell, 136 (6). pp. 1122-1135. ISSN 0092-8674

Ezhkova, E., Tansey, W. P. (February 2004) Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3. Mol Cell, 13 (3). pp. 435-42. ISSN 1097-2765 (Print)

Fiskus, Warren, Mill, Christopher P, Birdwell, Christine, Davis, John A, Das, Kaberi, Boettcher, Steffen, Kadia, Tapan M, DiNardo, Courtney D, Takahashi, Koichi, Loghavi, Sanam, Soth, Michael J, Heffernan, Tim, McGeehan, Gerard M, Ruan, Xinjia, Su, Xiaoping, Vakoc, Christopher R, Daver, Naval, Bhalla, Kapil N (April 2023) Targeting of epigenetic co-dependencies enhances anti-AML efficacy of Menin inhibitor in AML with MLL1-r or mutant NPM1. Blood Cancer Journal, 13 (1). p. 53. ISSN 2044-5385 (Public Dataset)

Froeling, F., Tuveson, D. (May 2018) Pancreatic cancer foiled by a switch of tumour subtype. Nature, 557 (7706). pp. 500-501. ISSN 0028-0836

Gegenhuber, B., Tollkuhn, J. (June 2019) Sex Differences in the Epigenome: A Cause or Consequence of Sexual Differentiation of the Brain? Genes (Basel), 10 (6). E432. ISSN 2073-4425 (Print)2073-4425

Gegenhuber, Bruno, Tollkuhn, Jessica (July 2022) Epigenetic Mechanisms of Brain Sexual Differentiation. Cold Spring Harbor Perspectives in Biology. a039099. ISSN 1943-0264

Gershman, Ariel, Sauria, Michael EG, Guitart, Xavi, Vollger, Mitchell R, Hook, Paul W, Hoyt, Savannah J, Jain, Miten, Shumate, Alaina, Razaghi, Roham, Koren, Sergey, Altemose, Nicolas, Caldas, Gina V, Logsdon, Glennis A, Rhie, Arang, Eichler, Evan E, Schatz, Michael C, O'Neill, Rachel J, Phillippy, Adam M, Miga, Karen H, Timp, Winston (April 2022) Epigenetic patterns in a complete human genome. Science, 376 (6588). eabj5089. ISSN 0036-8075

Gladman, Nicholas, Hufnagel, Barbara, Regulski, Michael, Liu, Zhigang, Wang, Xiaofei, Chougule, Kapeel, Kochian, Leon, Magalhães, Jurandir, Ware, Doreen (May 2022) Sorghum root epigenetic landscape during limiting phosphorus conditions. Plant Direct, 6 (5). e393. ISSN 2475-4455

Gulko, B., Siepel, A. (February 2019) Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nat Genet, 51 (2). pp. 335-342. ISSN 1061-4036

Gulko, B., Siepel, A. (December 2018) An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nat Genet, 51 (2). pp. 335-342. ISSN 1061-4036

Gulko, Brad, Siepel, Adam (May 2018) How Much Information is Provided by Human Epigenomic Data? An Evolutionary View. BioRxiv. (Unpublished)

He, H., Li, Y., Dong, Q., Chang, A. Y., Gao, F., Chi, Z., Su, M., Zhang, F., Ban, H., Martienssen, R., Chen, Y. H., Li, F. (November 2017) Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex. Proc Natl Acad Sci U S A. ISSN 0027-8424

Heard, E., Martienssen, R. A. (March 2014) Transgenerational Epigenetic Inheritance: Myths and Mechanisms. Cell, 157 (1). pp. 95-109. ISSN 0092-8674

Herridge, Rowan P, Dolata, Jakub, Migliori, Valentina, de Santis Alves, Cristiane, Borges, Filipe, Schorn, Andrea J, van Ex, Frédéric, Lin, Ann, Bajczyk, Mateusz, Parent, Jean-Sebastien, Leonardi, Tommaso, Hendrick, Alan, Kouzarides, Tony, Martienssen, Robert A (September 2024) Pseudouridine guides germline small RNA transport and epigenetic inheritance. Nature Structural & Molecular Biology. ISSN 1545-9993 (Public Dataset)

Herridge, Rowan P, Dolata, Jakub, Migliori, Valentina, de Santis Alves, Cristiane, Borges, Filipe, Van Ex, Frédéric, Lin, Ann, Bajczyk, Mateusz, Leonardi, Tommaso, Hendrick, Alan, Schorn, Andrea J, Kouzarides, Tony, Martienssen, Robert A (August 2023) Pseudouridine guides germline small RNA transport and epigenetic inheritance. bioRxiv. (Public Dataset)

Hodges, E., Molaro, A., Dos Santos, C. O., Thekkat, P., Song, Q., Uren, P. J., Park, J. H., Butler, J., Rafii, S., McCombie, W. R., Smith, A. D., Hannon, G. J. (2011) Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment. Molecular Cell, 44 (1). pp. 17-28. ISSN 1097-2765

Hoyt, Savannah J, Storer, Jessica M, Hartley, Gabrielle A, Grady, Patrick GS, Gershman, Ariel, de Lima, Leonardo G, Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias, Altemose, Nicolas, Rhie, Arang, Core, Leighton J, Gerton, Jennifer L, Makalowski, Wojciech, Olson, Daniel, Rosen, Jeb, Smit, Arian FA, Straight, Aaron F, Vollger, Mitchell R, Wheeler, Travis J, Schatz, Michael C, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Miga, Karen H, O'Neill, Rachel J (April 2022) From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science, 376 (6588). eabk3112. ISSN 0036-8075

Hsu, H. C., Stillman, B., Xu, R. M. (June 2005) Structural basis for origin recognition complex 1 protein-silence information regulator 1 protein interaction in epigenetic silencing. Proc Natl Acad Sci U S A, 102 (24). pp. 8519-24. ISSN 0027-8424 (Print)

Irvine, D. V., Goto, D. B., Vaughn, M. W., Nakaseko, Y., McCombie, W. R., Yanagida, M., Martienssen, R. (June 2009) Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome research, 19 (6). pp. 1077-83. ISSN 1088-9051 (Print)1088-9051 (Linking)

Joly-Lopez, Z., Platts, A. E., Gulko, B., Choi, J. Y., Groen, S. C., Zhong, X., Siepel, A., Purugganan, M. D. (February 2020) An inferred fitness consequence map of the rice genome. Nat Plants, 6 (2). pp. 119-130. ISSN 2055-0278 (Public Dataset)

Jones, P. A., Archer, T. K., Baylin, S. B., Beck, S., Berger, S., Bernstein, B. E., Carpten, J. D., Clark, S. J., Costello, J. F., Doerge, R. W., Esteller, M., Feinberg, A. P., Gingeras, T. R., Greally, J. M., Henikoff, S., Herman, J. G., Jackson-Grusby, L., Jenuwein, T., Jirtle, R. L., Kim, Y. J., Laird, P. W., Lim, B., Martienssen, R., Polyak, K., Stunnenberg, H., Tlsty, T. D., Tycko, B., Ushijima, T., Zhu, J., Pirrotta, V., Allis, C. D., Elgin, S. C., Rine, J., Wu, C. (2008) Moving AHEAD with an international human epigenome project. Nature, 454 (7205). pp. 711-715. ISSN 00280836 (ISSN)

Jones, P. A., Martienssen, R. A. (December 2005) A Blueprint for a Human Epigenome Project: The AACR Human Epigenome Workshop. Cancer Res, 65 (24). pp. 11241-6. ISSN 0008-5472 (Print)

Karakida Kawaguchi, Risa, Tang, Ziqi, Fischer, Stephan, Rajesh, Chandana, Tripathy, Rohit, Koo, Peter K, Gillis, Jesse (December 2022) Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. Briefings in Bioinformatics. bbac541. ISSN 1467-5463

Kawaguchi, Risa Karakida, Tang, Ziqi, Fischer, Stephan, Tripathy, Rohit, Koo, Peter, Gillis, Jesse (April 2021) Exploiting marker genes for robust classification and characterization of single-cell chromatin accessibility. bioRxiv. (Unpublished)

Kloc, A., Zaratiegui, M., Nora, E., Martienssen, R. (April 2008) RNA interference guides histone modification during the S phase of chromosomal replication. Current biology, 18 (7). pp. 490-5. ISSN 0960-9822 (Print)0960-9822 (Linking)

Knott, S. R. V., Peace, J. M., Ostrow, A. Z., Gan, Y., Rex, A. E., Viggiani, C. J., Tavaré, S., Aparicio, O. M. (January 2012) Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell, 148 (1-2). pp. 99-111. ISSN 00928674 (ISSN)

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Wrzeszczynski, K. O., Varadan, V., Byrnes, J., Lum, E., Kamalakaran, S., Levine, D. A., Dimitrova, N., Zhang, M. Q., Lucito, R. (December 2011) Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer. PLoS ONE, 6 (12). ISSN 1932-6203

Wrzeszczynski, K. O., Varadan, V., Kamalakaran, S., Levine, D. A., Dimitrova, N., Lucito, R. (August 2013) Integrative prediction of gene function and platinum-free survival from genomic and epigenetic features in ovarian cancer. Methods Mol Biol, 1049. pp. 35-51. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Xiang, Guanjue, He, Xi, Giardine, Belinda M, Weaver, Kathryn J, Taylor, Dylan J, McCoy, Rajiv C, Jansen, Camden, Keller, Cheryl A, Wixom, Alexander Q, Cockburn, April, Miller, Amber, Qi, Qian, He, Yanghua, Li, Yichao, Lichtenberg, Jens, Heuston, Elisabeth F, Anderson, Stacie M, Luan, Jing, Vermunt, Marit W, Yue, Feng, Sauria, Michael EG, Schatz, Michael C, Taylor, James, Göttgens, Berthold, Hughes, Jim R, Higgs, Douglas R, Weiss, Mitchell J, Cheng, Yong, Blobel, Gerd A, Bodine, David, Zhang, Yu, Li, Qunhua, Mahony, Shaun, Hardison, Ross C (April 2023) Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv.

Xu, Y., Milazzo, J. P., Somerville, T. D. D., Tarumoto, Y., Huang, Y. H., Ostrander, E. L., Wilkinson, J. E., Challen, G. A., Vakoc, C. R. (January 2018) A TFIID-SAGA Perturbation that Targets MYB and Suppresses Acute Myeloid Leukemia. Cancer Cell, 33 (1). 13-28 e8. ISSN 1878-3686 (Electronic)1535-6108 (Linking)

Yan, X., Hu, Z., Feng, Y., Hu, X., Yuan, J., Zhao, S. D., Zhang, Y., Yang, L., Shan, W., He, Q., Fan, L., Kandalaft, L. E., Tanyi, J. L., Li, C., Yuan, C. X., Zhang, D., Yuan, H., Hua, K., Lu, Y., Katsaros, D., Huang, Q., Montone, K., Fan, Y., Coukos, G., Boyd, J., Sood, A. K., Rebbeck, T., Mills, G. B., Dang, C. V., Zhang, L. (2015) Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. Cancer Cell, 28 (4). pp. 529-540. ISSN 1535-6108

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Zahid, Huda, Buchholz, Caroline R, Singh, Manjulata, Ciccone, Michael F, Chan, Alice, Nithianantham, Stanley, Shi, Ke, Aihara, Hideki, Fischer, Marcus, Schönbrunn, Ernst, Dos Santos, Camila O, Landry, Joseph W, Pomerantz, William CK (September 2021) New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. Journal of Medicinal Chemistry. ISSN 0022-2623

Zaratiegui, B. M., Irvine, D. V., Martienssen, R. A. (February 2007) Noncoding RNAs and gene silencing. Cell, 128 (4). pp. 763-76. ISSN 0092-8674 (Print)

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Book Section

Hall, I. M., Grewal, S. I. S. (2003) Structure and function of heterochromatin: implications for epigenetic gene silencing and genome organization. In: RNAi : a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. , pp. 205-232. ISBN 978-087969641-2

Martienssen, R. A. (1996) Epigenetic Silencing of Mu Transposable Elements in Maize. In: Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., p. 593. ISBN 0270-1847

Conference or Workshop Item

Anderson, K., Koseki, H., Skarnes, W., Shen, M. (October 2010) MOUSE DEVELOPMENT,GENETICS & GENOMICS. In: 2010 meeting on MOUSE DEVELOPMENT,GENETICS & GENOMICS, October 26–October 30, 2010, Cold Spring Harbor Laboratory.

Austad, S., Campisi, J., Sinclair, D. (September 2010) MOLECULAR GENETICS OF AGING. In: 2010 Meeting of Molecular Genetics of Aging, September 28–October 2, 2010, Cold Spring Harbor.

Bar-Sagi, D., Lees, J., Sherr, C., Weiss, W. (August 2010) MECHANISMS & MODELS OF CANCER. In: 2010 meeting of MECHANISMS & MODELS OF CANCER, August 17–August 21, 2010, Cold Spring Harbor Laboratory.

Bernstein, B., Bulyk, M., Bussemaker, H., Walhout, M. (March 2010) SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION. In: 2010 meeting on SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION, March 23–March 27, 2010.

Beyaz, Semir (May 2016) UTX controls lineage-specific epigenetic program and development of iNKT cells. In: Annual Meeting of the American-Association-of-Immunologists (AAI).

Brauch, H., Deloukas, P., Kroetz, D., Pirmohamed, M. (November 2010) PHARMACOGENOMICS & PERSONALIZED THERAPY. In: 2010 meeting of PHARMACOGENOMICS & PERSONALIZED THERAPY, November 17–November 21, 2010, Cold Spring Harbor Laboratory.

Eppig, J., Fuller, M., Newmark, P. (October 2010) GERM CELLS. In: 2010 Meeting of Germ Cells, October 5–October 9, 2010.

Feigman, Mary J, Moss, Matthew A, Chen, Chen, Cyrill, Samantha L, Ciccone, Michael, Trousdell, Marygrace, Yang, Shih Ting, Frey, Wesley D, Wilkinson, John E, dos Santos, Camila O (June 2020) Pregnancy reprograms the epigenome of mammary epithelial cells and blocks the development of premalignant mammary lesions in response to cMYC-overexpression. In: AACR Special Conference on the Evolving Landscape of Cancer Modeling.

Garipcan, Aybuke, Eskiocak, Onur, Subhash, Santhilal, Ozler, Kadir, Yueh, Brian, Chung, Charlie, Ergin, Ilgin, Gautier, Nelson, Habel, Jill, Rubino, Rachel, Van der Velden, Adrianus WM, Beyaz, Semir (2023) Epigenetic mechanisms of epithelial - immune interactions that shape immune surveillance in the intestinal epithelium. In: UNSPECIFIED.

Gingeras, T. R. (2012) Important lessons from a complex genome. In: 22nd IUBMB & 37th FEBS Congress, Sept 4th-9th 2012, Seville, Spain.

Mills, Alea A, Hwang, Dong-Woo (October 2014) The tumor suppressor CHD5 is an epigenetic regulator of neuronal cell fate. In: AACR Annual Meeting.

Stewart, D., Stillman, B. (2004) Epigenetics. In: Cold Spring Harbor Symposia on Quantitative Biology LXIX: Epigenetics, Cold Spring Harbor.

Thesis

Berube, Benjamin (August 2021) Epigenetic Control of Meiotic Recombination and Drive. PhD thesis, Cold Spring Harbor Laboratory.

Gegenhuber, Bruno (April 2022) Epigenomic organization and activation of brain sex differences. PhD thesis, Cold Spring Harbor Laboratory.

Johnson, David (July 2022) ELUCIDATING THE EFFECTS OF DEPLETING BRPF1 IN HUMAN GBM. PhD thesis, Cold Spring Harbor Laboratory.

Lippman, Z. B. (December 2004) Transposons, heterochromatin, and epigenetic landscapes in Arabidopsis thaliana. PhD thesis, Cold Spring Harbor Laboratory.

Rollins, F. (2011) The genetics and epigenetics of erlotinib resistance in non-small cell lung cancer. PhD thesis, Cold Spring Harbor Laboratory.

Tang, Ziqi (April 2024) Exploring the Representational Power of Genomic Deep Learning Models. PhD thesis, Cold Spring Harbor Laboratory.