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  • 2021

    To mock or not: A comprehensive comparison of mock IP and DNA input for ChIP-seq

    Xu, J., Kudron, M. M., Victorsen, A., Gao, J., Ammouri, H. N., Navarro, F. C. P., Gevirtzman, L., Waterston, R. H., White, K. P., Reinke, V. & Gerstein, M., Feb 22 2021, In: Nucleic acids research. 49, 3, e17.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    4 Scopus citations
  • 2020

    Expanded encyclopaedias of DNA elements in the human and mouse genomes

    ENCODE Project Consortium, Jul 30 2020, In: Nature. 583, 7818, p. 699-710 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    475 Scopus citations
  • 2018

    The modern resource: genome-wide binding profiles for hundreds of Drosophila and Caenorhabditis elegans transcription factors

    Kudron, M. M., Victorsen, A., Gevirtzman, L., Hillier, L. W., Fisher, W. W., Vafeados, D., Kirkey, M., Hammonds, A. S., Gersch, J., Ammouri, H., Wall, M. L., Moran, J., Steffen, D., Szynkarek, M., Seabrook-Sturgis, S., Jameel, N., Kadaba, M., Patton, J., Terrell, R., Corson, M., & 12 othersDurham, T. J., Park, S., Samanta, S., Han, M., Xu, J., Yan, K. K., Celniker, S. E., White, K. P., Ma, L., Gerstein, M., Reinke, V. & Waterston, R. H., Mar 2018, In: Genetics. 208, 3, p. 937-949 13 p.

    Research output: Contribution to journalArticlepeer-review

    80 Scopus citations
  • 2014

    Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

    Slattery, M., Ma, L., Spokony, R. F., Arthur, R. K., Kheradpour, P., Kundaje, A., Nègre, N., Crofts, A., Ptashkin, R., Zieba, J., Ostapenko, A., Suchy, S., Victorsen, A., Jameel, N., Grundstad, A. J., Gao, W., Moran, J. R., Rehm, E. J., Grossman, R. L., Kellis, M., & 1 othersWhite, K. P., Jul 2014, In: Genome research. 24, 7, p. 1224-1235 12 p.

    Research output: Contribution to journalArticlepeer-review

    24 Scopus citations
  • 2012

    An integrated encyclopedia of DNA elements in the human genome

    Principal investigators (steering committee), Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis), Broad Institute Group (data production and analysis), Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis), Data coordination center at UC Santa Cruz (production data coordination), Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis), Genome Institute of Singapore group (data production and analysis), HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis), Lawrence Berkeley National Laboratory group (targeted experimental validation), NHGRI groups (data production and analysis), Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis), Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis), University of Albany SUNY group (data production and analysis), University of Chicago Stanford group (data production and analysis), University of Heidelberg group (targeted experimental validation), University of Massachusetts Medical School Bioinformatics group (data production and analysis), University of Washington University of Massachusetts Medical Center group (data production and analysis), Data Analysis Center (data analysis), The ENCODE Project Consortium, Data production leads (data production), & 3 othersLead analysts (data analysis), Writing group & NHGRI project management (scientific management), Sep 6 2012, In: Nature. 489, 7414, p. 57-74 18 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    11006 Scopus citations
  • 2011

    A cis-regulatory map of the Drosophila genome

    Négre, N., Brown, C. D., Ma, L., Bristow, C. A., Miller, S. W., Wagner, U., Kheradpour, P., Eaton, M. L., Loriaux, P., Sealfon, R., Li, Z., Ishii, H., Spokony, R. F., Chen, J., Hwang, L., Cheng, C., Auburn, R. P., Davis, M. B., Domanus, M., Shah, P. K., & 20 othersMorrison, C. A., Zieba, J., Suchy, S., Senderowicz, L., Victorsen, A., Bild, N. A., Grundstad, A. J., Hanley, D., MacAlpine, D. M., Mannervik, M., Venken, K., Bellen, H., White, R., Gerstein, M., Russell, S., Grossman, R. L., Ren, B., Posakony, J. W., Kellis, M. & White, K. P., Mar 24 2011, In: Nature. 471, 7339, p. 527-531 5 p.

    Research output: Contribution to journalArticlepeer-review

    380 Scopus citations
  • A user's guide to the Encyclopedia of DNA elements (ENCODE)

    Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X., Wang, L., Issner, R., Coyne, M. J., & 295 othersDurham, T., Ku, M., Truong, T., Ward, L. D., Altshuler, R. C., Lin, M. F., Kellis, M., Davis, C. A., Kapranov, P., Dobin, A., Zaleski, C., Schlesinger, F., Batut, P., Chakrabortty, S., Jha, S., Lin, W., Drenkow, J., Wang, H., Bell, K., Bell, I., Gao, H., Dumais, E., Dumais, J., Antonarakis, S. E., Ucla, C., Borel, C., Guigo, R., Djebali, S., Lagarde, J., Kingswood, C., Ribeca, P., Sammeth, M., Alioto, T., Merkel, A., Tilgner, H., Carninci, P., Hayashizaki, Y., Lassmann, T., Takahashi, H., Abdelhamid, R. F., Hannon, G., Fejes, K. T., Preall, J., Gordon, A., Sotirova, V., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Ruan, Y., Ruan, X., Shahab, A., Poh, W. T., Wei, C. L., Furey, T. S., Boyle, A. P., Sheffield, N. C., Song, L., Shibata, Y., Vales, T., Winter, D., Zhang, Z., London, D., Wang, T., Keefe, D., Iyer, V. R., Lee, B. K., McDaniell, R. M., Liu, Z., Battenhouse, A., Bhinge, A. A., Lieb, J. D., Grasfeder, L. L., Showers, K. A., Giresi, P. G., Kim, S. K. C., Shestak, C., Pauli, F., Reddy, T. E., Gertz, J., Partridge, E. C., Jain, P., Sprouse, R. O., Bansal, A., Pusey, B., Muratet, M. A., Varley, K. E., Bowling, K. M., Newberry, K. M., Nesmith, A. S., Dilocker, J. A., Parker, S. L., Waite, L. L., Thibeault, K., Roberts, K., Absher, D. M., Mortazavi, A., Williams, B., Marinov, G., Trout, D., King, B., McCue, K., Kirilusha, A., DeSalvo, G., Fisher, K. A., Amrhein, H., Pepke, S., Vielmetter, J., Sherlock, G., Sidow, A., Batzoglou, S., Rauch, R., Kundaje, A., Libbrecht, M., Margulies, E. H., Parker, S. C. J., Elnitski, L., Green, E. D., Hubbard, T., Harrow, J., Searle, S., Kokocinski, F., Aken, B., Frankish, A., Hunt, T., Despacio-Reyes, G., Kay, M., Mukherjee, G., Bignell, A., Saunders, G., Boychenko, V., Brent, M., van Baren, M. J., Brown, R. H., Gerstein, M., Khurana, E., Balasubramanian, S., Lam, H., Cayting, P., Robilotto, R., Lu, Z., Derrien, T., Tanzer, A., Knowles, D. G., Mariotti, M., Haussler, D., Harte, R., Diekhans, M., Lin, M., Valencia, A., Tress, M., Landt, S. G., Raha, D., Shi, M., Euskirchen, G., Grubert, F., Kasowski, M., Lian, J., Lacroute, P., Xu, Y., Monahan, H., Patacsil, D., Slifer, T., Yang, X., Charos, A., Reed, B., Wu, L., Auerbach, R. K., Habegger, L., Hariharan, M., Rozowsky, J., Abyzov, A., Weissman, S. M., Struhl, K., Lamarre-Vincent, N., Lindahl-Allen, M., Miotto, B., Moqtaderi, Z., Fleming, J. D., Newburger, P., Farnham, P. J., Frietze, S., O'Geen, H., Xu, X., Blahnik, K. R., Cao, A. R., Iyengar, S., Kaul, R., Thurman, R. E., Wang, H., Navas, P. A., Sandstrom, R., Sabo, P. J., Weaver, M., Canfield, T., Lee, K., Neph, S., Roach, V., Reynolds, A., Johnson, A., Rynes, E., Giste, E., Vong, S., Neri, J., Frum, T., Nguyen, E. D., Ebersol, A. K., Sanchez, M. E., Sheffer, H. H., Lotakis, D., Haugen, E., Humbert, R., Kutyavin, T., Shafer, T., Noble, W. S., Dekker, J., Lajoie, B. R., Sanyal, A., Rosenbloom, K. R., Dreszer, T. R., Raney, B. J., Barber, G. P., Meyer, L. R., Sloan, C. A., Malladi, V. S., Cline, M. S., Learned, K., Swing, V. K., Zweig, A. S., Rhead, B., Fujita, P. A., Roskin, K., Karolchik, D., Kuhn, R. M., Wilder, S. P., Sobral, D., Herrero, J., Beal, K., Lukk, M., Brazma, A., Vaquerizas, J. M., Luscombe, N. M., Bickel, P. J., Boley, N., Brown, J. B., Li, Q., Huang, H., Sboner, A., Yip, K. Y., Cheng, C., Yan, K. K., Bhardwaj, N., Wang, J., Lochovsky, L., Jee, J., Gibson, T., Leng, J., Du, J., Harris, R. S., Song, G., Miller, W., Suh, B., Paten, B., Hoffman, M. M., Buske, O. J., Weng, Z., Dong, X., Wang, J., Xi, H., Tenenbaum, S. A., Doyle, F., Chittur, S., Penalva, L. O., Tullius, T. D., White, K. P., Karmakar, S., Victorsen, A., Jameel, N., Bild, N., Grossman, R. L., Collins, P. J., Trinklein, N. D., Giddings, M. C., Khatun, J., Maier, C., Wang, T., Whitfield, T. W., Chen, X., Yu, Y., Gunawardena, H., Feingold, E. A., Lowdon, R. F., Dillon, L. A. L., Good, P. J. & Risk, B., Apr 1 2011, In: PLoS biology. 9, 4, e1001046.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1113 Scopus citations
  • Evidence of abundant stop codon readthrough in Drosophila and other metazoa

    Jungreis, I., Lin, M. F., Spokony, R., Chan, C. S., Negre, N., Victorsen, A., White, K. P. & Kellis, M., Dec 2011, In: Genome research. 21, 12, p. 2096-2113 18 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    139 Scopus citations