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Paper

Roe, Jae-Seok, Mercan, Fatih, Rivera, Keith, Pappin, Darryl J, Vakoc, Christopher R (2015) BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Molecular Cell, 58 (6). pp. 1028-1036. ISSN 1097-2765

Shi, J., Wang, E., Milazzo, J. P., Wang, Z., Kinney, J. B., Vakoc, C. R. (2015) Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol, 33 (6). pp. 661-67. ISSN 1546-1696 (Electronic)1087-0156 (Linking)

Trotman, L. C., Nowak, D. G., Cho, H., Herzka, T., Watrud, K., DeMarco, D. V., Wang, V. M., Senturk, S., Fellmann, C., Ding, D., Beinortas, T., Kleinman, D., Chen, M., Sordella, R., Wilkinson, J. E., Castillo-Martin, M., Cordon-Cardo, C., Robinson, B. D. (2015) Myc drives Pten/trp53-deficient proliferation and metastasis due to Il6-secretion and Akt-suppression via Phlpp2. Cancer Discovery, 5 (6). pp. 636-651. ISSN 21598274

Naguib, Adam, Bencze, Gyula, Cho, Hyejin, Zheng, Wu, Tocilj, Ante, Elkayam, Elad, Faehnle, Christopher R, Jaber, Nadia, Pratt, Christopher P, Chen, Muhan, Zong, Wei-Xing, Marks, Michael S, Joshua-Tor, Leemor, Pappin, Darryl J, Trotman, Lloyd C (2015) PTEN Functions by Recruitment to Cytoplasmic Vesicles. Molecular Cell, 58 (2). pp. 255-268. ISSN 1097-2765

Yu, J. R., Tai, Y., Jin, Y., Hammell, M. C., Wilkinson, J. E., Roe, J. S., Vakoc, C. R., Van Aelst, L. (2015) TGF-beta/Smad signaling through DOCK4 facilitates lung adenocarcinoma metastasis. Genes Dev, 29 (3). pp. 250-61. ISSN 0890-9369

Pervouchine, D. D., Djebali, S., Breschi, A., Davis, C. A., Barja, P. P., Dobin, A., Tanzer, A., Lagarde, J., Zaleski, C., See, L. H., Fastuca, M., Drenkow, J., Wang, H., Bussotti, G., Pei, B., Balasubramanian, S., Monlong, J., Harmanci, A., Gerstein, M., Beer, M. A., Notredame, C., Guigo, R., Gingeras, T. R. (2015) Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun, 6. p. 5903. ISSN 2041-1723

Boj, Sylvia F, Hwang, Chang-Il, Baker, Lindsey A, Chio, Iok In Christine, Engle, Dannielle D, Corbo, Vincenzo, Jager, Myrthe, Ponz-Sarvise, Mariano, Tiriac, Hervé, Spector, Mona S, Gracanin, Ana, Oni, Tobiloba, Yu, Kenneth H, van Boxtel, Ruben, Huch, Meritxell, Rivera, Keith D, Wilson, John P, Feigin, Michael E, Öhlund, Daniel, Handly-Santana, Abram, Ardito-Abraham, Christine M, Ludwig, Michael, Elyada, Ela, Alagesan, Brinda, Biffi, Giulia, Yordanov, Georgi N, Delcuze, Bethany, Creighton, Brianna, Wright, Kevin, Park, Youngkyu, Morsink, Folkert H M., Molenaar, I.  Quintus, Borel Rinkes, Inne H, Cuppen, Edwin, Hao, Yuan, Jin, Ying, Nijman, Isaac J, Iacobuzio-Donahue, Christine, Leach, Steven D, Pappin, Darryl J, Hammell, Molly, Klimstra, David S, Basturk, Olca, Hruban, Ralph H, Offerhaus, George Johan, Vries, Robert G J., Clevers, Hans, Tuveson, David A (2015) Organoid Models of Human and Mouse Ductal Pancreatic Cancer. Cell, 160 (1-2). pp. 324-338. ISSN 0092-8674

Naguib, A., Bencze, G., Engle, D. D., Chio, II, Herzka, T., Watrud, K., Bencze, S., Tuveson, D. A., Pappin, D. J., Trotman, L. C. (2014) P53 Mutations Change Phosphatidylinositol Acyl Chain Composition. Cell Reports, 10 (1). pp. 8-19. ISSN 2211-1247

Lin, S., Lin, Y., Nery, J. R., Urich, M. A., Breschi, A., Davis, C. A., Dobin, A., Zaleski, C., Beer, M. A., Chapman, W. C., Gingeras, T. R., Ecker, J. R., Snyder, M. P. (2014) Comparison of the transcriptional landscapes between human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America, 111 (48). pp. 17224-17229. ISSN 0027-8424

Reyes, G., Niederst, M., Cohen-Katsenelson, K., Stender, J. D., Kunkel, M. T., Chen, M., Brognard, J., Sierecki, E., Gao, T., Nowak, D. G., Trotman, L. C., Glass, C. K., Newton, A. C. (2014) Pleckstrin homology domain leucine-rich repeat protein phosphatases set the amplitude of receptor tyrosine kinase output. Proc Natl Acad Sci U S A, 111 (38). E3957-E3965. ISSN 0027-8424

Gerstein, M. B., Rozowsky, J., Yan, K. K., Wang, D., Cheng, C., Brown, J. B., Davis, C. A., Hillier, L., Sisu, C., Li, J. J., Pei, B., Harmanci, A. O., Duff, M. O., Djebali, S., Alexander, R. P., Alver, B. H., Auerbach, R., Bell, K., Bickel, P. J., Boeck, M. E., Boley, N. P., Booth, B. W., Cherbas, L., Cherbas, P., Di, C., Dobin, A., Drenkow, J., Ewing, B., Fang, G., Fastuca, M., Feingold, E. A., Frankish, A., Gao, G., Good, P. J., Guigo, R., Hammonds, A., Harrow, J., Hoskins, R. A., Howald, C., Hu, L., Huang, H., Hubbard, T. J., Huynh, C., Jha, S., Kasper, D., Kato, M., Kaufman, T. C., Kitchen, R. R., Ladewig, E., Lagarde, J., Lai, E., Leng, J., Lu, Z., MacCoss, M., May, G., McWhirter, R., Merrihew, G., Miller, D. M., Mortazavi, A., Murad, R., Oliver, B., Olson, S., Park, P. J., Pazin, M. J., Perrimon, N., Pervouchine, D., Reinke, V., Reymond, A., Robinson, G., Samsonova, A., Saunders, G. I., Schlesinger, F., Sethi, A., Slack, F. J., Spencer, W. C., Stoiber, M. H., Strasbourger, P., Tanzer, A., Thompson, O. A., Wan, K. H., Wang, G., Wang, H., Watkins, K. L., Wen, J., Wen, K., Xue, C., Yang, L., Yip, K., Zaleski, C., Zhang, Y., Zheng, H., Brenner, S. E., Graveley, B. R., Celniker, S. E., Gingeras, T. R., Waterston, R. (2014) Comparative analysis of the transcriptome across distant species. Nature, 512 (7515). pp. 445-8. ISSN 0028-0836

Dago, A. E., Stepansky, A., Carlsson, A., Luttgen, M., Kendall, J., Baslan, T., Kolatkar, A., Wigler, M., Bethel, K., Gross, M. E., Hicks, J., Kuhn, P. (2014) Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells. PLoS One, 9 (8). e101777. ISSN 1932-6203

Perales, R., King, D. M., Aguirre-Chen, C., Hammell, C. M. (2014) LIN-42, the Caenorhabditis elegans PERIOD homolog, Negatively Regulates MicroRNA Transcription. PLoS Genetics, 10 (7). e1004486. ISSN 15537390 (ISSN)

Mazurek, A., Park, Y., Miething, C., Wilkinson, J. E., Gillis, J., Lowe, S. W, Vakoc, C. R, Stillman, B. (2014) Acquired Dependence of Acute Myeloid Leukemia on the DEAD-Box RNA Helicase DDX5. Cell Reports, 7 (6). pp. 1887-1899. ISSN 2211-1247

Li, W., Wu, J., Kim, S. Y., Zhao, M., Hearn, S. A., Zhang, M. Q., Meistrich, M. L., Mills, A. A. (2014) Chd5 orchestrates chromatin remodelling during sperm development. Nature Communications, 5. p. 3812. ISSN 20411723

Miething, C., Scuoppo, C., Bosbach, B., Appelmann, I., Nakitandwe, J., Ma, J., Wu, G., Lintault, L., Auer, M., Premsrirut, P. K., Teruya-Feldstein, J., Hicks, J., Benveniste, H., Speicher, M. R., Downing, J. R., Lowe, S. W. (2014) PTEN action in leukaemia dictated by the tissue microenvironment. Nature, 510 (7505). p. 402. ISSN 0028-0836

Zinovyeva, A. Y., Bouasker, S., Simard, M. J., Hammell, C. M., Ambros, V. (2014) Mutations in Conserved Residues of the C. elegans microRNA Argonaute ALG-1 Identify Separable Functions in ALG-1 miRISC Loading and Target Repression. PLoS Genetics, 10 (4). e1004286. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., Dunham, I., Elnitski, L. L., Farnham, P. J., Feingold, E. A., Gerstein, M., Giddings, M. C., Gilbert, D. M., Gingeras, T. R., Green, E. D., Guigo, R., Hubbard, T., Kent, J., Lieb, J. D., Myers, R. M., Pazin, M. J., Ren, B., Stamatoyannopoulos, J. A., Weng, Z. P., White, K. P., Hardison, R. C. (2014) Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America, 111 (17). pp. 6131-6138. ISSN 0027-8424

Meikar, O., Vagin, V. V., Chalmel, F., Sostar, K., Lardenois, A., Hammell, M., Jin, Y., Da Ros, M., Wasik, K. A., Toppari, J., Hannon, G. J., Kotaja, N. (2014) An atlas of chromatoid body components. RNA, 20 (4). pp. 483-95. ISSN 1355-8382

Goh, W. S. S., Seah, J. W. E., Harrison, E. J., Chen, C., Hammell, C. M., Hannon, G. J. (2014) A genome-wide RNAi screen identifies factors required for distinct stages of C-elegans piRNA biogenesis. Genes & Development, 28 (7). pp. 797-807. ISSN 0890-9369

Cho, H., Herzka, T., Zheng, W., Qi, J., Wilkinson, J. E., Bradner, J. E., Robinson, B. D., Castillo-Martin, M., Cordon-Cardo, C., Trotman, L. C. (2014) RapidCaP, a novel GEM model for analysis and therapy of metastatic prostate cancer, reveals Myc as a driver of Pten-mutant metastasis. Cancer Discovery, 4 (3). pp. 318-33. ISSN 21598274

Streppel, M. M., Lata, S., Delabastide, M., Montgomery, E. A., Wang, J. S., Canto, M. I., Macgregor-Das, A. M., Pai, S., Morsink, F. H., Offerhaus, G. J., Antoniou, E., Maitra, A., McCombie, W. R. (2014) Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barrett's esophagus. Oncogene, 33 (3). pp. 347-57. ISSN 0950-9232

Labbé, D. P., Nowak, D. G., Deblois, G., Lessard, L., Giguère, V., Trotman, L. C., Tremblay, M. L. (2014) Prostate cancer genetic-susceptibility locus on chromosome 20q13 is amplified and coupled to androgen receptor-regulation in metastatic tumors. Molecular Cancer Research, 12 (2). pp. 184-189. ISSN 15417786 (ISSN)

Shi, J., Whyte, W. A., Zepeda-Mendoza, C. J., Milazzo, J. P., Shen, C., Roe, J. S., Minder, J. L., Mercan, F., Wang, E., Eckersley-Maslin, M. A., Campbell, A. E., Kawaoka, S., Shareef, S., Zhu, Z., Kendall, J., Muhar, M., Haslinger, C., Yu, M., Roeder, R. G., Wigler, M. A., Blobel, G. A., Zuber, J., Spector, D. L., Young, R. A., Vakoc, C. R. (2013) Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes and Development, 27 (24). pp. 264-273. ISSN 08909369 (ISSN)

Schlesinger, F., Smith, A. D., Gingeras, T. R., Hannon, G. J., Hodges, E. (2013) De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements. Genome Research, 23 (10). pp. 1601-1614. ISSN 10889051 (ISSN)

Wang, E., Kawaoka, S., Yu, M., Shi, J., Ni, T., Yang, W., Zhu, J., Roeder, R. G., Vakoc, C. R. (2013) Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia. Proceedings of the National Academy of Sciences of the United States of America, 110 (10). pp. 3901-6. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Rozhkov, N. V., Hammell, M., Hannon, G. J. (2013) Multiple roles for Piwi in silencing Drosophila transposons. Genes and Development, 27 (4). pp. 400-412. ISSN 08909369 (ISSN)

Paul, S., Kuo, A., Schalch, T., Vogel, H., Joshua-Tor, L., McCombie, W. R., Gozani, O., Hammell, M., Mills, A. A. (2013) Chd5 Requires PHD-Mediated Histone 3 Binding for Tumor Suppression. Cell Reports, 3 (1). pp. 92-102. ISSN 2211-1247

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T. R. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29 (1). pp. 15-21. ISSN 1367-4803

Shi, J., Wang, E., Zuber, J., Rappaport, A., Taylor, M., Johns, C., Lowe, S. W., Vakoc, C. R. (2013) The Polycomb complex PRC2 supports aberrant self-renewal in a mouse model of MLL-AF9;Nras(G12D) acute myeloid leukemia. Oncogene, 32 (7). pp. 930-938. ISSN 1476-5594 (Electronic)0950-9232 (Linking)

Yu, M., Lin, G., Arshadi, N., Kalatskaya, I., Xue, B., Haider, S., Nguyen, F., Boutros, P. C., Elson, A., Muthuswamy, L. B., Tonks, N. K., Muthuswamy, S. K. (2012) Expression profiling during mammary epithelial cell 3D morphogenesis identifies PTPRO as a novel regulator of morphogenesis and ErbB2 mediated transformation. Mol Cell Biol, 32 (19). pp. 3913-3924. ISSN 1098-5549 (Electronic)0270-7306 (Linking)

Cheng, C., Alexander, R., Min, R. Q., Leng, J., Yip, K. Y., Rozowsky, J., Yan, K. K., Dong, X. J., Djebali, S., Ruan, Y. J., Davis, C. A., Carninci, P., Lassman, T., Gingeras, T. R., Guigo, R., Birney, E., Weng, Z. P., Snyder, M., Gerstein, M. (2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research, 22 (9). pp. 1658-1667. ISSN 1088-9051

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F., Alioto, T., Antoshechkin, I., Baer, M. T., Bar, N. S., Batut, P., Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. J., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L. H., Shahab, A., Skancke, J., Suzuki, A. M., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S. E., Hannon, G., Giddings, M. C., Ruan, Y., Wold, B., Carninci, P., Guig, R., Gingeras, T. R. (2012) Landscape of transcription in human cells. Nature, 489 (7414). pp. 101-108. ISSN 0028-0836

Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., Sanyal, A., Shoresh, N., Simon, J. M., Song, L., Trinklein, N. D., Altshuler, R. C., Birney, E., Brown, J. B., Cheng, C., Djebali, S., Dong, X. J., Ernst, J., Furey, T. S., Gerstein, M., Giardine, B., Greven, M., Hardison, R. C., Harris, R. S., Herrero, J., Hoffman, M. M., Iyer, S., Kellis, M., Kheradpour, P., Lassmann, T., Li, Q. H., Lin, X., Marinov, G. K., Merkel, A., Mortazavi, A., Parker, S. C. J., Reddy, T. E., Rozowsky, J., Schlesinger, F., Thurman, R. E., Wang, J., Ward, L. D., Whitfield, T. W., Wilder, S. P., Wu, W., Xi, H. L. S., Yip, K. Y., Zhuang, J. L., Bernstein, B. E., Green, E. D., Gunter, C., Snyder, M., Pazin, M. J., Lowdon, R. F., Dillon, L. A. L., Adams, L. B., Kelly, C. J., Zhang, J., Wexler, J. R., Good, P. J., Feingold, E. A., Crawford, G. E., Dekker, J., Elnitski, L., Farnham, P. J., Giddings, M. C., Gingeras, T. R., Guigo, R., Hubbard, T. J., Kent, W. J., Lieb, J. D., Margulies, E. H., Myers, R. M., Stamatoyannopoulos, J. A., Tenenbaum, S. A., Weng, Z. P., White, K. P., Wold, B., Yu, Y., Wrobel, J., Risk, B. A., Gunawardena, H. P., Kuiper, H. C., Maier, C. W., Xie, L., Chen, X., Mikkelsen, T. S., Gillespie, S. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836

Hossain, M., Stillman, B. (2012) Meier-Gorlin syndrome mutations disrupt an Orc1 CDK inhibitory domain and cause centrosome reduplication. Genes and Development, 26 (16). pp. 1797-810. ISSN 08909369 (ISSN)

Freed-Pastor, W. A., Mizuno, H., Zhao, X., Langerød, A., Moon, S. H., Rodriguez-Barrueco, R., Barsotti, A., Chicas, A., Li, W., Polotskaia, A., Bissell, M. J., Osborne, T. F., Tian, B., Lowe, S. W., Silva, J. M., Børresen-Dale, A. L., Levine, A. J., Bargonetti, J., Prives, C. (2012) Mutant p53 disrupts mammary tissue architecture via the mevalonate pathway. Cell, 148 (1-2). pp. 244-258. ISSN 00928674 (ISSN)

Muerdter, F., Olovnikov, I., Molaro, A., Rozhkov, N. V., Czech, B., Gordon, A., Hannon, G. J., Aravin, A. A. (2012) Production of artificial piRNAs in flies and mice. RNA, 18 (1). pp. 42-52. ISSN 1355-8382

Mazurek, A., Luo, W., Krasnitz, A., Hicks, J., Powers, R. S., Stillman, B. (2012) DDX5 regulates DNA replication and is required for cell proliferation in a subset of breast cancer cells. Cancer Discovery, 2 (9). pp. 812-825. ISSN 21598274 (ISSN)

Van Stry, M., Oguin Iii, T. H., Cheloufi, S., Vogel, P., Watanabe, M., Pillai, M. R., Dash, P., Thomas, P. G., Hannon, G. J., Bix, M. (2012) Enhanced susceptibility of Ago1/3 double-null mice to influenza a virus infection. Journal of Virology, 86 (8). pp. 4151-4157. ISSN 0022538X (ISSN)

Fang, F., Hodges, E., Molaro, A., Dean, M., Hannon, G. J., Smith, A. D. (2012) Genomic landscape of human allele-specific DNA methylation. Proceedings of the National Academy of Sciences of the United States of America, 109 (19). pp. 7332-7337. ISSN 00278424 (ISSN)

Liu, S., Patel, S. H., Ginestier, C., Ibarra, I., Martin-Trevino, R., Bai, S., McDermott, S. P., Shang, L., Ke, J., Ou, S. J., Heath, A., Zhang, K. J., Korkaya, H., Clouthier, S. G., Charafe-Jauffret, E., Birnbaum, D., Hannon, G. J., Wicha, M. S. (2012) MicroRNA93 regulates proliferation and differentiation of normal and malignant breast stem cells. PLoS Genetics, 8 (6). ISSN 15537390 (ISSN)

Dahlman, K. B., Parker, J. S., Shamu, T., Hieronymus, H., Chapinski, C., Carver, B., Chang, K., Hannon, G. J., Sawyers, C. L. (2012) Modulators of prostate cancer cell proliferation and viability identified by short-hairpin RNA library screening. PLoS One, 7 (4). ISSN 19326203 (ISSN)

Preall, J. B., Czech, B., Guzzardo, P. M., Muerdter, F., Hannon, G. J. (2012) Shutdown is a component of the Drosophila piRNA biogenesis machinery. RNA, 18 (8). pp. 1446-1457. ISSN 13558382 (ISSN)

Lindsay, J., Carone, D. M., Brown, J., Hall, L., Qureshi, S., Mitchell, S. E., Jannetty, N., Hannon, G., Renfree, M., Pask, A., O'Neill, M., O'Neill, R. (2012) Unique small RNA signatures uncovered in the tammar wallaby genome. BMC Genomics, 13. p. 559. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

Chi, S. W., Hannon, G. J., Darnell, R. B. (2012) An alternative mode of microRNA target recognition. Nature Structural and Molecular Biology, 19 (3). pp. 321-327. ISSN 15459993 (ISSN)

Dow, L. E., Premsrirut, P. K., Zuber, J., Fellmann, C., McJunkin, K., Miething, C., Park, Y., Dickins, R. A., Hannon, G. J., Lowe, S. W. (2012) A pipeline for the generation of shRNA transgenic mice. Nature Protocols, 7 (2). pp. 374-393. ISSN 17542189 (ISSN)

Elkayam, E., Kuhn, C. D., Tocilj, A., Haase, A. D., Greene, E. M., Hannon, G. J., Joshua-Tor, L. (2012) The structure of human argonaute-2 in complex with miR-20a. Cell, 150 (1). pp. 100-110. ISSN 00928674 (ISSN)

Liu-Sullivan, N., Zhang, J., Bakleh, A., Marchica, J., Li, J., Siolas, D., Laquerre, S., Degenhardt, Y. Y., Wooster, R., Chang, K., Hannon, G. J., Powers, S. (2011) Pooled shRNA screen for sensitizers to inhibition of the mitotic regulator polo-like kinase (PLK1). Oncotarget, 2 (12). pp. 1254-64. ISSN 1949-2553 (Electronic) 1949-2553 (Linking)

Wu, J., Akerman, M., Sun, S., McCombie, W. R., Krainer, A. R., Zhang, M. Q. (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27 (21). 3010-3016 . ISSN 1367-4803

Chien, Y., Scuoppo, C., Wang, X., Fang, X., Balgley, B., Bolden, J. E., Premsrirut, P., Luo, W., Chicas, A., Lee, C. S., Kogan, S. C., Lowe, S. W. (2011) Control of the senescence-associated secretory phenotype by NF-kappaB promotes senescence and enhances chemosensitivity. Genes Dev, 25 (20). pp. 2125-36. ISSN 1549-5477 (Electronic) 0890-9369 (Linking)

Molaro, A., Hodges, E., Fang, F., Song, Q., McCombie, W. R., Hannon, G. J., Smith, A. D. (2011) Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates. Cell, 146 (6). pp. 1029-1041. ISSN 0092-8674

Albert, F. W., Hodges, E., Jensen, J. D., Besnier, F., Xuan, Z. Y., Rooks, M., Bhattacharjee, A., Brizuela, L., Good, J. M., Green, R. E., Burbano, H. A., Plyusnina, I. Z., Trut, L., Andersson, L., Schoneberg, T., Carlborg, O., Hannon, G. J., Paabo, S. (2011) Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity, 107 (3). pp. 205-214. ISSN 0018-067X

Rangan, P., Malone, Colin D. , Navarro, C., Newbold, S. P, Hayes, P. S, Sachidanandam, R., Hannon, G. J., Lehmann, R. (2011) piRNA Production Requires Heterochromatin Formation in Drosophila. Current Biology, 21 (16). pp. 1373-1379. ISSN 0960-9822

Zuber, J., Shi, J., Wang, E., Rappaport, A. R., Herrmann, H., Sison, E. A., Magoon, D., Qi, J., Blatt, K., Wunderlich, M., Taylor, M. J., Johns, C., Chicas, A., Mulloy, J. C., Kogan, S. C., Brown, P., Valent, P., Bradner, J. E., Lowe, S. W., Vakoc, C. R. (2011) RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature, 478 (7370). pp. 524-528. ISSN 0028-0836

Zuber, J., Rappaport, A. R., Luo, W., Wang, E., Chen, C., Vaseva, A. V., Shi, J., Weissmueller, S., Fellman, C., Taylor, M. J., Weissenboeck, M., Graeber, T. G., Kogan, S. C., Vakoc, C. R., Lowe, S. W. (2011) An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance. Genes & Development, 25 (15). pp. 1628-1640. ISSN 0890-9369

Chen, M. H., Pratt, C. P., Zeeman, M. E., Schultz, N., Taylor, B. S., O'Neill, A., Castillo-Martin, M., Nowak, D. G., Naguib, A., Grace, D. M., Murn, J., Navin, N., Atwal, G. S., Sander, C., Gerald, W. L., Cordon-Cardo, C., Newton, A. C., Carver, B. S., Trotman, L. C. (2011) Identification of PHLPP1 as a Tumor Suppressor Reveals the Role of Feedback Activation in PTEN-Mutant Prostate Cancer Progression. Cancer Cell, 20 (2). pp. 173-186. ISSN 1535-6108

Lin, G., Aranda, V., Muthuswamy, S. K., Tonks, N. K. (2011) Identification of PTPN23 as a novel regulator of cell invasion in mammary epithelial cells from a loss-of-function screen of the 'PTP-ome'. Genes & Development, 25 (13). pp. 1412-1425. ISSN 0890-9369

Erlich, Y., Edvardson, S., Hodges, E., Zenvirt, S., Thekkat, P., Shaag, A., Dor, T., Hannon, G. J., Elpeleg, O. (2011) Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Research, 21 (5). pp. 658-664. ISSN 1088-9051

Premsrirut, P. K., Dow, L. E., Kim, S. Y., Camiolo, M., Malone, C. D., Miething, C., Scuoppo, C. , Zuber, J., Dickins, R. A., Kogan, Scott C, Shroyer, Kenneth R, Sordella, R., Hannon, G. J., Lowe, S. W. (2011) A Rapid and Scalable System for Studying Gene Function in Mice Using Conditional RNA Interference. Cell, 145 (1). pp. 145-158. ISSN 0092-8674

Fellmann, C., Zuber, J., McJunkin, K., Chang, K. , Malone, C. D., Dickins, R. A., Xu, Q., Hengartner, M. O., Elledge, S. J., Hannon, G. J., Lowe, S. W. (2011) Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay. Molecular Cell, 41 (6). pp. 733-746. ISSN 1097-2765

Sawey, E. T., Chanrion, M., Cai, C., Wu, G., Zhang, J., Zender, L., Zhao, A., Busuttil, R. W., Yee, H., Stein, L. D., French, D. M., Finn, Richard S, Lowe, S. W., Powers, S. (2011) Identification of a Therapeutic Strategy Targeting Amplified FGF19 in Liver Cancer by Oncogenomic Screening. Cancer Cell, 19 (3). pp. 347-358. ISSN 1535-6108

Bivona, T. G., Hieronymus, H., Parker, J., Chang, K., Taron, M., Rosell, R., Moonsamy, P., Dahlman, K., Miller, V. A., Costa, C., Hannon, G. J., Sawyers, C. L. (2011) FAS and NF-kappa B signalling modulate dependence of lung cancers on mutant EGFR. Nature, 471 (7339). pp. 523-526. ISSN 0028-0836

Berezikov, E., Robine, N., Samsonova, A., Westholm, J. O., Naqvi, A., Hung, J. H., Okamura, K., Dai, Q., Bortolamiol-Becet, D., Martin, R., Zhao, Y. J., Zamore, P. D., Hannon, G. J., Marra, M. A., Weng, Z. P., Perrimon, N., Lai, E. C. (2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research, 21 (2). pp. 203-215. ISSN 1088-9051

Zuber, J., McJunkin, K., Fellmann, C., Dow, L. E., Taylor, M. J., Hannon, G. J., Lowe, S. W. (2011) Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNA. Nature Biotechnology, 29 (1). pp. 79-85.

Wang, J., Czech, B., Crunk, A., Wallace, A., Mitreva, M., Hannon, G. J., Davis, R. E. (2011) Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. Genome Research, 21 (9). pp. 1462-1477. ISSN 10889051 (ISSN)

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

Lee, S., Paulson, K. G., Murchison, E. P., Afanasiev, O. K., Alkan, C., Leonard, J. H., Byrd, D. R., Hannon, G. J., Nghiem, P. (2011) Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas. Journal of Clinical Virology, 52 (3). pp. 272-275. ISSN 13866532 (ISSN)

Spierings, D. C., McGoldrick, D., Hamilton-Easton, A. M., Neale, G., Murchison, E. P., Hannon, G. J., Green, D. R., Withoff, S. (2011) Ordered progression of stage-specific miRNA profiles in the mouse B2 B-cell lineage. Blood, 117 (20). pp. 5340-5349. ISSN 00064971 (ISSN)

Obad, S., Dos Santos, C. O., Petri, A., Heidenblad, M., Broom, O., Ruse, C., Fu, C., Lindow, M., Stenvang, J., Straarup, E. M., Hansen, H. F., Koch, T., Pappin, D., Hannon, G. J., Kauppinen, S. (2011) Silencing of microRNA families by seed-targeting tiny LNAs. Nature Genetics, 43 (4). pp. 371-380. ISSN 10614036 (ISSN)

Tanaka, T., Hosokawa, M., Vagin, V. V., Reuter, M., Hayashi, E., Mochizuki, A. L., Kitamura, K., Yamanaka, H., Kondoh, G., Okawa, K., Kuramochi-Miyagawa, S., Nakano, T., Sachidanandam, R., Hannon, G. J., Pillai, R. S., Nakatsuji, N., Chuma, S. (2011) Tudor domain containing 7 (Tdrd7) is essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. Proceedings of the National Academy of Sciences of the United States of America, 108 (26). pp. 10579-10584. ISSN 00278424 (ISSN)

Zamparini, A. L., Davis, M. Y., Malone, C. D., Vieira, E., Zavadil, J., Sachidanandam, R., Hannon, G. J., Lehmann, R. (2011) Vreteno, a gonad-specific protein, is essential for germline development and primary pirna biogenesis in Drosophila. Development, 138 (18). pp. 4039-4050. ISSN 09501991 (ISSN)

Ni, J. Q., Zhou, R., Czech, B., Liu, L. P., Holderbaum, L., Yang-Zhou, D., Shim, H. S., Tao, R., Handler, D., Karpowicz, P., Binari, R., Booker, M., Brennecke, J., Perkins, L. A., Hannon, G. J., Perrimon, N. (2011) A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nature Methods, 8 (5). pp. 405-407. ISSN 15487091 (ISSN)

Haase, A. D., Fenoglio, S., Muerdter, F., Guzzardo, P. M., Czech, B., Pappin, D. J., Chen, C., Gordon, A., Hannon, G. J. (2010) Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila. Genes and Development, 24 (22). pp. 2499-2504. ISSN 08909369 (ISSN)

Chong, M. M. W., Zhang, G. A., Cheloufi, S., Neubert, T. A., Hannon, G. J., Littman, D. R. (2010) Canonical and alternate functions of the microRNA biogenesis machinery. Genes & Development, 24 (17). pp. 1951-1960. ISSN 0890-9369

Schreiber, S. L., Shamji, A. F., Clemons, P. A., Hon, C., Koehler, A. N., Munoz, B., Palmer, M., Stern, A. M., Wagner, B. K., Powers, S., Lowe, S. W., Guo, X., Krasnitz, A., Sawey, E. T., Sordella, R., Stein, L. D., Trotman, L. C., Califano, A., Dalla-Favera, R., Ferrando, A., Iavarone, A., Pasqualucci, L., Silva, J., Stockwell, B. R., Hahn, W. C., Chin, L., DePinho, R. A., Boehm, J. S., Gopal, S., Huang, A., Root, D. E., Weir, B. A., Gerhard, D. S., Zenklusen, J. C., Roth, M. G., White, M. A., Minna, J. D., MacMillan, J. B., Posner, B. A. (2010) Towards patient-based cancer therapeutics. Nature Biotechnology, 28 (9). pp. 904-906.

Cheloufi, S., Dos Santos, C. O., Chong, M. M. W., Hannon, G. J. (2010) A Dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature, 465 (7298). 584-U76. ISSN 0028-0836

Burbano, H. A., Hodges, E., Green, R. E., Briggs, A. W., Krause, J., Meyer, M., Good, J. M., Maricic, T., Johnson, P. L. F., Xuan, Z. Y., Rooks, M., Bhattacharjee, A., Brizuela, L., Albert, F. W., De La Rasilla, M., Fortea, J., Rosas, A., Lachmann, M., Hannon, G. J., Paabo, S. (2010) Targeted investigation of the neandertal genome by array-based sequence capture. Science, 328 (5979). pp. 723-725.

Chicas, A., Wang, X., Zhang, C., McCurrach, M. E., Zhao, Z., Mert, O., Dickins, R. A., Narita, M., Zhang, M. Q., Lowe, S. W. (2010) Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence. Cancer Cell, 17 (4). pp. 376-387.

Olmedo-Monfil, V., Durán-Figueroa, N., Arteaga-Vázquez, M., Demesa-Arévalo, E., Autran, D., Grimanelli, D., Slotkin, R. K., Martienssen, R. A., Vielle-Calzada, J. P. (2010) Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature, 464 (7288). pp. 628-632.

Wang, S. M., Zhang, M. Q. (2010) Transcriptome Study for Early Hematopoiesis-Achievement, Challenge and New Opportunity. Journal of Cellular Physiology, 223 (3). pp. 549-552. ISSN 0021-9541

Rosa-Rosa, J. M., Gracia-Aznarez, F. J., Hodges, E., Pita, G., Rooks, M., Xuan, Z., Bhattacharjee, A., Brizuela, L., Silva, J. M., Hannon, G. J., Benitez, J. (2010) Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting. PLoS One, 5 (4). e9976. ISSN 1932-6203

Bandyopadhyay, S., Mitra, R., Maulik, U., Zhang, M. Q. (2010) Development of the human cancer microRNA network. Silence, 1 (1). p. 6. ISSN 1758-907x

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S. M., Belter, E., Du, F., Kim, K., Abbott, R. M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S. M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M. J., McMahan, L., Van Buren, P., Vaughn, M. W. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956). pp. 1112-5. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Smith, A. D., Chung, W. Y., Hodges, E., Kendall, Jude T., Hannon, G. J., Hicks, J. B., Xuan, Z., Zhang, M. Q. (2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25 (21). pp. 2841-2842.

Wei, F., Stein, J. C., Liang, C., Zhang, J., Fulton, R. S., Baucom, R. S., De Paoli, E., Zhou, S., Yang, L., Han, Y., Pasternak, S., Narechania, A., Zhang, L., Yeh, C. T., Ying, K., Nagel, D. H., Collura, K., Kudrna, D., Currie, J., Lin, J., Kim, H., Angelova, A., Scara, G., Wissotski, M., Golser, W., Courtney, L., Kruchowski, S., Graves, T. A., Rock, S. M., Adams, S., Fulton, L. A., Fronick, C., Courtney, W., Kramer, M., Spiegel, L., Nascimento, L., Kalyanaraman, A., Chaparro, C., Deragon, J. M., Miguel, P. S., Jiang, N., Wessler, S. R., Green, P. J., Yu, Y., Schwartz, D. C., Meyers, B. C., Bennetzen, J. L., Martienssen, R. A., McCombie, W. R., Aluru, S., Clifton, S. W., Schnable, P. S., Ware, D., Wilson, R. K., Wing, R. A. (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS genetics, 5 (11). e1000728. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Bric, A., Miething, C., Bialucha, C. U., Scuoppo, C., Zender, L., Krasnitz, A., Xuan, Z., Zuber, J., Wigler, M. H., Hicks, J. B., McCombie, W. R., Hemann, M. T., Hannon, G. J., Powers, S., Lowe, S. W. (2009) Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell, 16 (4). pp. 324-35. ISSN 1535-6108

Hodges, E., Smith, A. D., Kendall, J. T., Xuan, Z., Ravi, K., Rooks, M., Zhang, M. Q., Ye, K., Bhattacharjee, A., Brizuela, L., McCombie, W. R., Wigler, M. H., Hannon, G. J., Hicks, J. B. (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research, 19 (9). pp. 1593-1605. ISSN 1088-9051

Benita, Y., Kikuchi, H., Smith, A. D., Zhang, M. Q., Chung, D. C., Xavier, R. J. (2009) An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res, 37 (14). 4587–4602.

Kim, Y. C., Wu, Q., Chen, J., Xuan, Z., Jung, Y.-C., Zhang, M. Q., Rowley, J. D., Wang, S. M. (2009) The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A, 106 (20). pp. 8278-8283.

Rosenfeld, J. A., Wang, Z., Schones, D. E., Zhao, K., DeSalle, R., Zhang, M. Q. (2009) Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics, 10 (1). p. 143. ISSN 1471-2164

Niida, A., Smith, A. D., Imoto, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (2009) Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinformatics, 10. p. 71. ISSN 1471-2105

Slotkin, R. K., Vaughn, M., Borges, F., Tanurdzic, M., Becker, J. D., Feijo, J. A., Martienssen, R. A. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell, 136 (3). pp. 461-72. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Zhang, M. Q., Waterman, M. S., Zhang, X. (2009) The seventh Asia Pacific bioinformatics conference (APBC2009). BMC Bioinformatics, 10 (SUPPL.).

Rechavi, O., Erlich, Y., Amram, H., Flomenblit, L., Karginov, F. V., Goldstein, I., Hannon, G. J., Kloog, Y. (2009) Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs. Genes and Development, 23 (16). pp. 1971-1979. ISSN 08909369 (ISSN)

Silva, J. M., Ezhkova, E., Silva, J., Heart, S., Castillo, M., Campos, Y., Castro, V., Bonilla, F., Cordon-Cardo, C., Muthuswamy, S. K., Powers, S., Fuchs, E., Hannon, G. J. (2009) Cyfip1 Is a Putative Invasion Suppressor in Epithelial Cancers. Cell, 137 (6). pp. 1047-1061. ISSN 00928674 (ISSN)

Castellano, L., Giamas, G., Jacob, J., Coombes, R. C., Lucchesi, W., Thiruchelvam, P., Barton, G., Jiao, L. R., Wait, R., Waxman, J., Hannon, G. J., Stebbing, J. (2009) The estrogen receptor-α-induced microRNA signature regulates itself and its transcriptional response. Proceedings of the National Academy of Sciences of the United States of America, 106 (37). pp. 15732-15737. ISSN 00278424 (ISSN)

This list was generated on Tue Jun 27 15:16:14 2017 EDT.
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