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Publications

Unlocking the secrets of the genome.

Celniker SE., Dillon LA., Gerstein MB., Gunsalus KC., Henikoff S., Karpen GH., Kellis M., Lai EC., Lieb JD., MacAlpine DM., Micklem G., Piano F., Snyder M., Stein L., White KP., Waterston RH.,
Nature 2009

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Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB., Lu ZJ., Van Nostrand EL., Cheng C., Arshinoff BI., Liu T., Yip KY., Robilotto R., Rechtsteiner A., Ikegami K., Alves P., Chateigner A., Perry M., Morris M., Auerbach RK., Feng X., Leng J., Vielle A., Niu W., Rhrissorrakrai K., Agarwal A., Alexander RP., Barber G., Brdlik CM., Brennan J., Brouillet JJ., Carr A., Cheung MS., Clawson H., Contrino S., Dannenberg LO., Dernburg AF., Desai A., Dick L., Dosé AC., Du J., Egelhofer T., Ercan S., Euskirchen G., Ewing B., Feingold EA., Gassmann R., Good PJ., Green P., Gullier F., Gutwein M., Guyer MS., Habegger L., Han T., Henikoff JG., Henz SR., Hinrichs A., Holster H., Hyman T., Iniguez AL., Janette J., Jensen M., Kato M., Kent WJ., Kephart E., Khivansara V., Khurana E., Kim JK., Kolasinska-Zwierz P., Lai EC., Latorre I., Leahey A., Lewis S., Lloyd P., Lochovsky L., Lowdon RF., Lubling Y., Lyne R., MacCoss M., Mackowiak SD., Mangone M., McKay S., Mecenas D., Merrihew G., Miller DM., Muroyama A., Murray JI., Ooi SL., Pham H., Phippen T., Preston EA., Rajewsky N., Rätsch G., Rosenbaum H., Rozowsky J., Rutherford K., Ruzanov P., Sarov M., Sasidharan R., Sboner A., Scheid P., Segal E., Shin H., Shou C., Slack FJ., Slightam C., Smith R., Spencer WC., Stinson EO., Taing S., Takasaki T., Vafeados D., Voronina K., Wang G., Washington NL., Whittle CM., Wu B., Yan KK., Zeller G., Zha Z., Zhong M., Zhou X., Ahringer J., Strome S., Gunsalus KC., Micklem G., Liu XS., Reinke V., Kim SK., Hillier LW., Henikoff S., Piano F., Snyder M., Stein L., Lieb JD., Waterston RH.,
Science 2010

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Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Roy S., Ernst J., Kharchenko PV., Kheradpour P., Negre N., Eaton ML., Landolin JM., Bristow CA., Ma L., Lin MF., Washietl S., Arshinoff BI., Ay F., Meyer PE., Robine N., Washington NL., Di Stefano L., Berezikov E., Brown CD., Candeias R., Carlson JW., Carr A., Jungreis I., Marbach D., Sealfon R., Tolstorukov MY., Will S., Alekseyenko AA., Artieri C., Booth BW., Brooks AN., Dai Q., Davis CA., Duff MO., Feng X., Gorchakov AA., Gu T., Henikoff JG., Kapranov P., Li R., MacAlpine HK., Malone J., Minoda A., Nordman J., Okamura K., Perry M., Powell SK., Riddle NC., Sakai A., Samsonova A., Sandler JE., Schwartz YB., Sher N., Spokony R., Sturgill D., van Baren M., Wan KH., Yang L., Yu C., Feingold E., Good P., Guyer M., Lowdon R., Ahmad K., Andrews J., Berger B., Brenner SE., Brent MR., Cherbas L., Elgin SC., Gingeras TR., Grossman R., Hoskins RA., Kaufman TC., Kent W., Kuroda MI., Orr-Weaver T., Perrimon N., Pirrotta V., Posakony JW., Ren B., Russell S., Cherbas P., Graveley BR., Lewis S., Micklem G., Oliver B., Park PJ., Celniker SE., Henikoff S., Karpen GH., Lai EC., MacAlpine DM., Stein LD., White KP., Kellis M.,
Science 2010

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modMine: flexible access to modENCODE data

Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G.
Nucleic Acids Res. 2012

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