Xingzhi Song

2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S., Scott, G., Steffen, D., Worley, K. C., Burch, P. E., Okwuonu, G., Hines, S., Lewis, L., Deramo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R., & 211 othersHolt, R. A., Adams, M. D., Amanatides, P. G., Baden-Tillson, H., Barnstead, M., Chin, S., Evans, C. A., Ferriera, S., Fosler, C., Glodek, A., Gu, Z., Jennings, D., Kraft, C. L., Nguyen, T., Pfannkoch, C. M., Sitter, C., Sutton, G. G., Venter, J. C., Woodage, T., Smith, D., Lee, H. M., Gustafson, E., Cahill, P., Kana, A., Doucette-Stamm, L., Weinstock, K., Fechtel, K., Weiss, R. B., Dunn, D. M., Green, E. D., Blakesley, R. W., Bouffard, G. G., de Jong, P. J., Osoegawa, K., Zhu, B., Marra, M., Schein, J., Bosdet, I., Fjell, C., Jones, S., Krzywinski, M., Mathewson, C., Siddiqui, A., Wye, N., McPherson, J., Zhao, S., Fraser, C. M., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, W. C., Havlak, P. H., Chen, R., Durbin, K. J., Egan, A., Ren, Y., Song, X. Z., Li, B., Liu, Y., Qin, X., Cawley, S., Worley, K. C., Cooney, A. J., D'Souza, L. M., Martin, K., Wu, J. Q., Gonzalez-Garay, M. L., Jackson, A. R., Kalafus, K. J., McLeod, M. P., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, D. A., Zhang, Z., Bailey, J. A., Eichler, E. E., Tuzun, E., Birney, E., Mongin, E., Ureta-Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, B. J., Young, J. M., Smith, D., Huang, H., Fechtel, K., Wang, H., Xing, H., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Albà, M. M., Abril, J. F., Guigo, R., Smit, A., Dubchak, I., Rubin, E. M., Couronne, O., Poliakov, A., Hübner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y. A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, H. J., Bromberg, S., Gullings-Handley, J., Jensen-Seaman, M. I., Kwitek, A. E., Lazar, J., Pasko, D., Tonellato, P. J., Twigger, S., Ponting, C. P., Duarte, J. M., Rice, S., Goodstadt, L., Beatson, S. A., Emes, R. D., Winter, E. E., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, R. C., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, T. D., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, S. M., Cooper, G. M., Batzoglou, S., Brudno, M., Sidow, A., Stone, E. A., Venter, J. C., Payseur, B. A., Bourque, G., López-Otín, C., Puente, X. S., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, V. B., Caspi, A., Tesler, S. D. G., Pevzner, P. A., Haussler, S. C. D., Roskin, K. M., Baertsch, R., Clawson, H., Furey, T. S., Hinrichs, A. S., Karolchik, D., Kent, W. J., Rosenbloom, K. R., Trumbower, H., Weirauch, M., Cooper, D. N., Stenson, P. D., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, R. R., Taylor, M. S., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S. & Collins, F., Apr 1 2004, In: Nature. 428, 6982, p. 493-520 28 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1729 Scopus citations

The Atlas genome assembly system

Havlak, P., Chen, R., Durbin, K. J., Egan, A., Ren, Y., Song, X. Z., Weinstock, G. M. & Gibbs, R. A., Apr 2004, In: Genome research. 14, 4, p. 721-732 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

128 Scopus citations

2006

The DNA sequence, annotation and analysis of human chromosome 3

Muzny, D. M., Scherer, S. E., Kaul, R., Wang, J., Yu, J., Sudbrak, R., Buhay, C. J., Chen, R., Cree, A., Ding, Y., Dugan-Rocha, S., Gill, R., Gunaratne, P., Harris, R. A., Hawes, A. C., Hernandez, J., Hodgson, A. V., Hume, J., Jackson, A., Khan, Z. M., & 94 othersKovar-Smith, C., Lewis, L. R., Lozado, R. J., Metzker, M. L., Milosavljevic, A., Miner, G. R., Morgan, M. B., Nazareth, L. V., Scott, G., Sodergren, E., Song, X. Z., Steffen, D., Wei, S., Wheeler, D. A., Wright, M. W., Worley, K. C., Yuan, Y., Zhang, Z., Adams, C. Q., Ansari-Lari, M. A., Ayele, M., Brown, M. J., Chen, G., Chen, Z., Clendenning, J., Clerc-Blankenburg, K. P., Chen, R., Chen, Z., Davis, C., Delgado, O., Dinh, H. H., Dong, W., Draper, H., Ernst, S., Fu, G., Gonzalez-Garay, M. L., Garcia, D. K., Gillett, W., Gu, J., Hao, B., Haugen, E., Havlak, P., He, X., Hennig, S., Hu, S., Huang, W., Jackson, L. R., Jacob, L. S., Kelly, S. H., Kube, M., Levy, R., Li, Z., Liu, B., Liu, J., Liu, W., Lu, J., Maheshwari, M., Nguyen, B. V., Okwuonu, G. O., Palmeiri, A., Pasternak, S., Perez, L. M., Phelps, K. A., Plopper, F. J. H., Qiang, B., Raymond, C., Rodriguez, R., Saenphimmachak, C., Santibanez, J., Shen, H., Shen, Y., Subramanian, S., Tabor, P. E., Verduzco, D., Waldron, L., Wang, J., Wang, J., Wang, Q., Williams, G. A., Wong, G. K. S., Yao, Z., Zhang, J. K., Zhang, X., Zhao, G., Zhou, J., Zhou, Y., Nelson, D., Lehrach, H., Reinhardt, R., Naylor, S. L., Yang, H., Olson, M., Weinstock, G. & Gibbs, R. A., Apr 27 2006, In: Nature. 440, 7088, p. 1194-1198 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

41 Scopus citations

The finished DNA sequence of human chromosome 12

Scherer, S. E., Muzny, D. M., Buhay, C. J., Chen, R., Cree, A., Ding, Y., Dugan-Rocha, S., Gill, R., Gunaratne, P., Harris, R. A., Hawes, A. C., Hernandez, J., Hodgson, A. V., Hume, J., Jackson, A., Khan, Z. M., Kovar-Smith, C., Lewis, L. R., Lozado, R. J., Metzker, M. L., & 54 othersMilosavljevic, A., Miner, G. R., Montgomery, K. T., Morgan, M. B., Nazareth, L. V., Scott, G., Sodergren, E., Song, X. Z., Steffen, D., Lovering, R. C., Wheeler, D. A., Worley, K. C., Yuan, Y., Zhang, Z., Adams, C. Q., Ansari-Lari, M. A., Ayele, M., Brown, M. J., Chen, G., Chen, Z., Clerc-Blankenburg, K. P., Davis, C., Delgado, O., Dinh, H. H., Draper, H., Gonzalez-Garay, M. L., Havlak, P., Jackson, L. R., Jacob, L. S., Kelly, S. H., Li, L., Li, Z., Liu, J., Liu, W., Lu, J., Maheshwari, M., Nguyen, B. V., Okwuonu, G. O., Pasternak, S., Perez, L. M., Plopper, F. J. H., Santibanez, J., Shen, H., Tabor, P. E., Verduzco, D., Waldron, L., Wang, Q., Williams, G. A., Zhang, J. K., Zhou, J., Nelson, D., Kucherlapati, R., Weinstock, G. & Gibbs, R. A., Mar 16 2006, In: Nature. 440, 7082, p. 346-351 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

42 Scopus citations

The genome of the sea urchin Strongylocentrotus purpuratus

Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., Coffman, J. A., Dean, M., Elphick, M. R., Ettensohn, C. A., Foltz, K. R., Hamdoun, A., Hynes, R. O., Klein, W. H., Marzluff, W., McClay, D. R., & 211 othersMorris, R. L., Mushegian, A., Rast, J. P., Smith, L. C., Thorndyke, M. C., Vacquier, V. D., Wessel, G. M., Wray, G., Zhang, L., Elsik, C. G., Ermolaeva, O., Hlavina, W., Hofmann, G., Kitts, P., Landrum, M. J., Mackey, A. J., Maglott, D., Panopoulou, G., Poustka, A. J., Pruitt, K., Sapojnikov, V., Song, X., Souvorov, A., Solovyev, V., Wei, Z., Whittaker, C. A., Worley, K., Durbin, K. J., Shen, Y., Fedrigo, O., Garfield, D., Haygood, R., Primus, A., Satija, R., Severson, T., Gonzalez-Garay, M. L., Jackson, A. R., Milosavljevic, A., Tong, M., Killian, C. E., Livingston, B. T., Wilt, F. H., Adams, N., Bellé, R., Carbonneau, S., Cheung, R., Cormier, P., Cosson, B., Croce, J., Fernandez-Guerra, A., Genevière, A. M., Goel, M., Kelkar, H., Morales, J., Mulner-Lorillon, O., Robertson, A. J., Goldstone, J. V., Cole, B., Epel, D., Gold, B., Hahn, M. E., Howard-Ashby, M., Scally, M., Stegeman, J. J., Allgood, E. L., Cool, J., Judkins, K. M., McCafferty, S. S., Musante, A. M., Obar, R. A., Rawson, A. P., Rossetti, B. J., Gibbons, I. R., Hoffman, M. P., Leone, A., Istrail, S., Materna, S. C., Samanta, M. P., Stolc, V., Tongprasit, W., Tu, Q., Bergeron, K. F., Brandhorst, B. P., Whittle, J., Berney, K., Bottjer, D. J., Calestani, C., Peterson, K., Chow, E., Yuan, Q. A., Elhaik, E., Graur, D., Reese, J. T., Bosdet, I., Heesun, S., Marra, M. A., Schein, J., Anderson, M. K., Brockton, V., Buckley, K. M., Cohen, A. H., Fugmann, S. D., Hibino, T., Loza-Coll, M., Majeske, A. J., Messier, C., Nair, S. V., Pancer, Z., Terwilliger, D. P., Agca, C., Arboleda, E., Chen, N., Churcher, A. M., Hallböök, F., Humphrey, G. W., Idris, M. M., Kiyama, T., Liang, S., Mellott, D., Mu, X., Murray, G., Olinski, R. P., Raible, F., Rowe, M., Taylor, J. S., Tessmar-Raible, K., Wang, D., Wilson, K. H., Yaguchi, S., Gaasterland, T., Galindo, B. E., Gunaratne, H. J., Juliano, C., Kinukawa, M., Moy, G. W., Neill, A. T., Nomura, M., Raisch, M., Reade, A., Roux, M. M., Song, J. L., Su, Y. H., Townley, I. K., Voronina, E., Wong, J. L., Amore, G., Branno, M., Brown, E. R., Cavalieri, V., Duboc, V., Duloquin, L., Flytzanis, C., Gache, C., Lapraz, F., Lepage, T., Locascio, A., Martinez, P., Matassi, G., Matranga, V., Range, R., Rizzo, F., Röttinger, E., Wilson, K., Beane, W., Bradham, C., Byrum, C., Glenn, T., Hussain, S., Loza, M., Manning, G., Miranda, E., Thomason, R., Walton, K., Wikramanayke, A., Whittaker, C., Wu, S. Y., Xu, R., Brown, C. T., Chen, L., Gray, R. F., Lee, P. Y., Nam, J., Oliveri, P., Smith, J., Muzny, D., Bell, S., Chacko, J., Cree, A., Curry, S., Davis, C., Dinh, H., Dugan-Rocha, S., Fowler, J., Gill, R., Hamilton, C., Hernandez, J., Hines, S., Hume, J., Jackson, L. R., Jolivet, A., Kovar, C., Lee, S., Lewis, L., Miner, G., Morgan, M., Nazareth, L. V., Okwuonu, G., Parker, D., Pu, L. L., Thorn, R. & Wright, R., Nov 10 2006, In: Science. 314, 5801, p. 941-952 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

935 Scopus citations

2007

Direct selection of human genomic loci by microarray hybridization

Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., Song, X., Richmond, T. A., Middle, C. M., Rodesch, M. J., Packard, C. J., Weinstock, G. M. & Gibbs, R. A., Nov 2007, In: Nature Methods. 4, 11, p. 903-905 3 p.

Research output: Contribution to journal › Article › peer-review

550 Scopus citations

2008

The complete genome of an individual by massively parallel DNA sequencing

Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y. J., Makhijani, V., Roth, G. T., Gomes, X., Tartaro, K., Niazi, F., Turcotte, C. L., Irzyk, G. P., Lupski, J. R., Chinault, C., Song, X. Z., Liu, Y., Yuan, Y., & 7 othersNazareth, L., Qin, X., Muzny, D. M., Margulies, M., Weinstock, G. M., Gibbs, R. A. & Rothberg, J. M., Apr 17 2008, In: Nature. 452, 7189, p. 872-876 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1445 Scopus citations

The genome of the model beetle and pest Tribolium castaneum

Richards, S., Gibbs, R. A., Weinstock, G. M., Brown, S. J., Denell, R., Beeman, R. W., Bucher, G., Friedrich, M., Grimmelikhuijzen, C. J. P., Klingler, M., Lorenzen, M., Roth, S., Schröder, R., Tautz, D., Zdobnov, E. M., Muzny, D., Attaway, T., Bell, S., Buhay, C. J., Chandrabose, M. N., & 166 othersChavez, D., Clerk-Blankenburg, K. P., Cree, A., Dao, M., Davis, C., Chacko, J., Dinh, H., Dugan-Rocha, S., Fowler, G., Garner, T. T., Garnes, J., Gnirke, A., Hawes, A., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S. N., Joshi, V., Khan, Z. M., Jackson, L., Kovar, C., Kowis, A., Lee, S., Lewis, L. R., Margolis, J., Morgan, M., Nazareth, L. V., Nguyen, N., Okwuonu, G., Parker, D., Ruiz, S. J., Santibanez, J., Savard, J., Scherer, S. E., Schneider, B., Sodergren, E., Vattahil, S., Villasana, D., White, C. S., Wright, R., Park, Y., Lord, J., Oppert, B., Wang, L., Liu, Y., Worley, K., Elsik, C. G., Reese, J. T., Elhaik, E., Landan, G., Graur, D., Arensburger, P., Atkinson, P., Beidler, J., Demuth, J. P., Drury, D. W., Du, Y. Z., Fujiwara, H., Maselli, V., Osanai, M., Robertson, H. M., Tu, Z., Wang, J. J., Wang, S., Song, H., Zhang, L., Werner, D., Stanke, M., Morgenstern, B., Solovyev, V., Kosarev, P., Brown, G., Chen, H. C., Ermolaeva, O., Hlavina, W., Kapustin, Y., Kiryutin, B., Kitts, P., Maglott, D., Pruitt, K., Sapojnikov, V., Souvorov, A., Mackey, A. J., Waterhouse, R. M., Wyder, S., Kriventseva, E. V., Kadowaki, T., Bork, P., Aranda, M., Bao, R., Beermann, A., Berns, N., Bolognesi, R., Bonneton, F., Bopp, D., Butts, T., Chaumot, A., Denell, R. E., Ferrier, D. E. K., Gordon, C. M., Jindra, M., Lan, Q., Lattorff, H. M. G., Laudet, V., Von Levetsow, C., Liu, Z., Lutz, R., Lynch, J. A., Da Fonseca, R. N., Posnien, N., Reuter, R., Schinko, J. B., Schmitt, C., Schoppmeier, M., Shippy, T. D., Simonnet, F., Marques-Souza, H., Tomoyasu, Y., Trauner, J., Van Der Zee, M., Vervoort, M., Wittkopp, N., Wimmer, E. A., Yang, X., Jones, A. K., Sattelle, D. B., Ebert, P. R., Nelson, D., Scott, J. G., Muthukrishnan, S., Kramer, K. J., Arakane, Y., Zhu, Q., Hogenkamp, D., Dixit, R., Jiang, H., Zou, Z., Lu, Z., Marshall, J., Sumathipala, N., Elpidina, E., Oppert, C., Evans, J., Altincicek, B., Vilcinskas, A., Williams, M., Hultmark, D., Hetru, C., Hauser, F., Cazzamali, G., Williamson, M., Li, B., Tanaka, Y., Predel, R., Neupert, S., Schachtner, J., Verleyen, P., Raible, F., Walden, K. K. O., Angeli, S., Forêt, S., Schuetz, S., Maleszka, R., Miller, S. C. & Grossmann, D., Apr 24 2008, In: Nature. 452, 7190, p. 949-955 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1097 Scopus citations

2009

Bos taurus genome assembly

Liu, Y., Qin, X., Song, X. Z. H., Jiang, H., Shen, Y., Durbin, K. J., Lien, S., Kent, M. P., Sodeland, M., Ren, Y., Zhang, L., Sodergren, E., Havlak, P., Worley, K. C., Weinstock, G. M. & Gibbs, R. A., Apr 24 2009, In: BMC genomics. 10, 180.

Research output: Contribution to journal › Article › peer-review

Open Access

117 Scopus citations

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

Gibbs, R. A., Taylor, J. F., Van Tassell, C. P., Barendse, W., Eversole, K. A., Gill, C. A., Green, R. D., Hamernik, D. L., Kappes, S. M., Lien, S., Matukumalli, L. K., McEwan, J. C., Nazareth, L. V., Schnabel, R. D., Weinstock, G. M., Wheeler, D. A., Ajmone-Marsan, P., Barends, W., Boettcher, P. J., Caetano, A. R., & 72 othersGarcia, J. F., OlivierHanotte, Mariani, P., Skow, L. C., Sonstegard, T. S., Williams, J. L., Diallo, B., Hailemariam, L., Hanotte, O., Martinez, M. L., Morris, C. A., Silva, L. O. C., Spelman, R. J., Mulatu, W., Zhao, K., Abbey, C. A., Agaba, M., Araujo, F. R., Bunch, R. J., Burton, J., Gorni, C., Harrison, B. E., Luff, B., Machado, M. A., Mwakaya, J., Plastow, G., Sim, W., Smith, T., Thomas, M. B., Valentini, A., Williams, P., Womack, J., Woolliams, J. A., Liu, Y., Qin, X., Worley, K. C., Gao, C., Jiang, H., Moore, S. S., Ren, Y., Song, X. Z., Bustamante, C. D., Hernandez, R. D., Muzny, D. M., Patil, S., Lucas, A. S., Fu, Q., Kent, M. P., Vega, R., Matukumalli, A., McWilliam, S., Sclep, G., Bryc, K., Choi, J., Gao, H., Grefenstette, J. J., Murdoch, B., Stella, A., Villa-Angulo, R., Wright, M., Aerts, J., Jann, O., Negrini, R., Goddard, M. E., Hayes, B. J., Bradley, D. G., Da Silva, M. B., Lau, L. P. L., Liu, G. E., Lynn, D. J., Panzitta, F. & Dodds, K. G., Apr 24 2009, In: Science. 324, 5926, p. 528-532 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

650 Scopus citations

The genome sequence of taurine cattle: A window to ruminant biology and evolution

Elsik, C. G., Tellam, R. L., Worley, K. C., Gibbs, R. A., Muzny, D. M., Weinstock, G. M., Adelson, D. L., Eichler, E. E., Elnitski, L., Guigó, R., Hamernik, D. L., Kappes, S. M., Lewin, H. A., Lynn, D. J., Nicholas, F. W., Reymond, A., Rijnkels, M., Skow, L. C., Zdobnov, E. M., Schook, L., & 288 othersWomack, J., Alioto, T., Antonarakis, S. E., Astashyn, A., Chappie, C. E., Chen, H. C., Chrast, J., Câmara, F., Ermolaeva, O., Henrichsen, C. N., Hlavina, W., Kapustin, Y., Kiryutin, B., Kitts, P., Kokocinski, F., Landrum, M., Maglott, D., Pruitt, K., Sapojnikov, V., Searle, S. M., Solovyev, V., Souvorov, A., Ucla, C., Wyss, C., Anzola, J. M., Gerlach, D., Elhaik, E., Graur, D., Reese, J. T., Edgar, R. C., McEwan, J. C., Payne, G. M., Raison, J. M., Junier, T., Kriventseva, E. V., Eyras, E., Plass, M., Donthu, R., Larkin, D. M., Reecy, J., Yang, M. Q., Chen, L., Cheng, Z., Chitko-McKown, C. G., Liu, G. E., Matukumalli, L. K., Song, J., Zhu, B., Bradley, D. G., Brinkman, F. S. L., Lau, L. P. L., Whiteside, M. D., Walker, A., Wheeler, T. T., Casey, T., German, J. B., Lemay, D. G., Maqbool, N. J., Molenaar, A. J., Seo, S., Stothard, P., Baldwin, C. L., Baxter, R., Brinkmeyer-Larigford, C. L., Brown, W. C., Childers, C. P., Connelley, T., Ellis, S. A., Fritz, K., Glass, E. J., Herzig, C. T. A., Livanainen, A., Lahmers, K. K., Bennett, A. K., Dickens, C. M., Gilbert, J. G. R., Hagen, D. E., Salih, H., Aerts, J., Caetano, A. R., Dalrymple, B., Garcia, J. F., Gill, C. A., Hiendleder, S. G., Memili, E., Spurlock, D., Williams, J. L., Alexander, L., Brownstein, M. J., Guan, L., Holt, R. A., Jones, S. J. M., Marra, M. A., Moore, R., Moore, S. S., Roberts, A., Taniguchi, M., Waterman, R. C., Chacko, J., Chandrabose, M. M., Cree, A., Dao, M. D., Dinh, H. H., Gabisi, R. A., Hines, S., Hume, J., Jhangiani, S. N., Joshi, V., Kovar, C. L., Lewis, L. R., Liu, Y. S., Lopez, J., Morgan, M. B., Nguyen, N. B., Okwuonu, G. O., Ruiz, S. J., Santibanez, J., Wright, R. A., Buhay, C., Ding, Y., Dugan-Rocha, S., Herdandez, J., Holder, M., Sabo, A., Egan, A., Goodell, J., Wilczek-Boney, K., Fowler, G. R., Hitchens, M. E., Lozado, R. J., Moen, C., Steffen, D., Warren, J. T., Zhang, J., Chiu, R., Schein, J. E., Durbin, K. J., Havlak, P., Jiang, H., Liu, Y., Qin, X., Ren, Y., Shen, Y., Song, H., Bell, S. N., Davis, C., Johnson, A. J., Lee, S., Nazareth, L. V., Patel, B. M., Pu, L. L., Vattathil, S., Williams, R. L., Curry, S., Hamilton, C., Sodergren, E., Wheeler, D. A., Barris, W., Bennett, G. L., Eggen, A., Green, R. D., Harhay, G. P., Hobbs, M., Jann, O., Keele, J. W., Kent, M. P., Lien, S., McKay, S. D., McWilliam, S., Ratnakumar, A., Schnabel, R. D., Smith, T., Snelling, W. M., Sonstegard, T. S., Stone, R. T., Sugimoto, Y., Takasuga, A., Taylor, J. F., Van Tassell, C. P., MacNeil, M. D., Abatepaulo, A. R. R., Abbey, C. A., Ahola, V., Almeida, L. G., Amadio, A. F., Anatriello, E., Bahadue, S. M., Biase, F. H., Boldt, C. R., Carroll, J. A., Carvalho, W. A., Cervelatti, E. P., Chacko, E., Chapin, J. E., Cheng, Y., Choi, J., Colley, A. J., DeCampos, T. A., De Donato, M., De Miranda Santos, I. K. F., De Oliveira, C. J. F., Deobald, H., Devinoy, E., Donohue, K. E., Dove, P., Eberlein, A., Fitzsimmons, C. J., Franzin, A. M., Garcia, G. R., Genini, S., Gladney, C. J., Grant, J. R., Greaser, M. L., Green, J. A., Hadsell, D. L., Hakimov, H. A., Halgren, R., Harrow, J. L., Hart, E. A., Hastings, N., Hernandez, M., Hu, Z. L., Iivanainen, A., Ingham, A., Iso-Touru, T., Jamis, C., Jensen, K., Kapetis, D., Kerr, T., Khalil, S. S., Khatib, H., Kolbehdari, D., Kumar, C. G., Kumar, D., Leach, R., Lee, J. C. M., Li, C., Logan, K. M., Malinverni, R., Marques, E., Martin, W. F., Martins, N. F., Maruyama, S. R., Mazza, R., McLean, K. L., Medrano, J. F., Moreno, B. T., More, D. D., Muntean, C. T., Nandakumar, H. P., Nogueira, M. F. G., Olsaker, I., Pant, S. D., Panzitta, F., Pastor, R. C. P., Poli, M. A., Poslusny, N., Rachagani, S., Ranganathan, S., Razpet, A., Riggs, P. K., Rincón, G., Rodriguez-Osorio, N., Rodriguez-Zas, S. L., Romero, N. E., Rosenwald, A., Sando, L., Schmutz, S. M., Shen, L., Sherman, L., Southey, B. R., Lutzow, Y. S., Sweedler, J. V., Tammen, I., Telugu, B. P. V. L., Urbanski, J. M., Utsunomiya, Y. T., Verschoor, C. P., Waardenberg, A. J., Wang, Z., Ward, R., WeiKard, R., Welsh, T. H., White, S. N., Wilming, L. G., Wunderlich, K. R., Yang, J. & Zhao, F. Q., Apr 24 2009, In: Science. 324, 5926, p. 522-528 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

942 Scopus citations

2011

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Renfree, M. B., Papenfuss, A. T., Deakin, J. E., Lindsay, J., Heider, T., Belov, K., Rens, W., Waters, P. D., Pharo, E. A., Shaw, G., Wong, E. S. W., Lefèvre, C. M., Nicholas, K. R., Kuroki, Y., Wakefield, M. J., Zenger, K. R., Wang, C., Ferguson-Smith, M., Nicholas, F. W., Hickford, D., & 83 othersYu, H., Short, K. R., Siddle, H. V., Frankenberg, S. R., Chew, K. Y., Menzies, B. R., Stringer, J. M., Suzuki, S., Hore, T. A., Delbridge, M. L., Mohammadi, A., Schneider, N. Y., Hu, Y., O'Hara, W., Al Nadaf, S., Wu, C., Feng, Z. P., Cocks, B. G., Wang, J., Flicek, P., Searle, S. M. J., Fairley, S., Beal, K., Herrero, J., Carone, D. M., Suzuki, Y., Sugano, S., Toyoda, A., Sakaki, Y., Kondo, S., Nishida, Y., Tatsumoto, S., Mandiou, I., Hsu, A., McColl, K. A., Lansdell, B., Weinstock, G., Kuczek, E., McGrath, A., Wilson, P., Men, A., Hazar-Rethinam, M., Hall, A., Davis, J., Wood, D., Williams, S., Sundaravadanam, Y., Muzny, D. M., Jhangiani, S. N., Lewis, L. R., Morgan, M. B., Okwuonu, G. O., Ruiz, S. J., Santibanez, J., Nazareth, L., Cree, A., Fowler, G., Kovar, C. L., Dinh, H. H., Joshi, V., Jing, C., Lara, F., Thornton, R., Chen, L., Deng, J., Liu, Y., Shen, J. Y., Song, X. Z., Edson, J., Troon, C., Thomas, D., Stephens, A., Yapa, L., Levchenko, T., Gibbs, R. A., Cooper, D. W., Speed, T. P., Fujiyama, A., M Graves, J. A., O'Neill, R. J., Pask, A. J., Forrest, S. M. & Worley, K. C., Aug 29 2011, In: Genome biology. 12, 8, R81.

Research output: Contribution to journal › Article › peer-review

Open Access

144 Scopus citations

2013

Assemblathon 2: Evaluating de novo methods of genome assembly in three vertebrate species

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. C., Corbeil, J., Fabbro, C. D., Docking, R. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., & 71 othersGanapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, É., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. W., Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., MacCallum, I., MacManes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. M., Yuan, J., Zhang, G., Zhang, H., Zhou, S. & Korf, I. F., 2013, In: GigaScience. 2, 1, 10.

Research output: Contribution to journal › Article › peer-review

Open Access

468 Scopus citations

Integrated genomic characterization of endometrial carcinoma

Getz, G., Gabriel, S. B., Cibulskis, K., Lander, E., Sivachenko, A., Sougnez, C., Lawrence, M., Kandoth, C., Dooling, D., Fulton, R., Fulton, L., Kalicki-Veizer, J., McLellan, M. D., O'Laughlin, M., Schmidt, H., Wilson, R. K., Ye, K., Li, D., Ally, A., Balasundaram, M., & 256 othersBirol, I., Butterfield, Y. S. N., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H. J. E., Dhalla, N., Guin, R., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Plettner, P., Schein, J. E., Sipahimalani, P., Tam, A., Varhol, R. J., Gordon Robertson, A., Cherniack, A. D., Pashtan, I., Saksena, G., Onofrio, R. C., Schumacher, S. E., Tabak, B., Carter, S. L., Hernandez, B., Gentry, J., Salvesen, H. B., Ardlie, K., Winckler, W., Beroukhim, R., Meyerson, M., Hadjipanayis, A., Lee, S., Mahadeshwar, H. S., Park, P., Protopopov, A., Ren, X., Seth, S., Song, X., Tang, J., Xi, R., Yang, L., Dong, Z., Kucherlapati, R., Chin, L., Zhang, J., Todd Auman, J., Balu, S., Bodenheimer, T., Buda, E., Neil Hayes, D., Hoyle, A. P., Jefferys, S. R., Jones, C. D., Meng, S., Mieczkowski, P. A., Mose, L. E., Parker, J. S., Perou, C. M., Roach, J., Yan, S., Simons, J. V., Soloway, M. G., Tan, D., Topal, M. D., Waring, S., Wu, J., Hoadley, K. A., Baylin, S. B., Bootwalla, M. S., Lai, P. H., Triche, T. J., Van Den Berg, D. J., Weisenberger, D. J., Laird, P. W., Shen, H., Cho, J., Dicara, D., Frazer, S., Heiman, D., Jing, R., Lin, P., Mallard, W., Stojanov, P., Voet, D., Zhang, H., Zou, L., Noble, M., Reynolds, S. M., Shmulevich, I., Arman Aksoy, B., Antipin, Y., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Ladanyi, M., Reva, B., Sander, C., Sinha, R., Onur Sumer, S., Taylor, B. S., Cerami, E., Weinhold, N., Schultz, N., Shen, R., Benz, S., Goldstein, T., Haussler, D., Ng, S., Szeto, C., Stuart, J., Benz, C. C., Yau, C., Zhang, W., Annala, M., Broom, B. M., Casasent, T. D., Ju, Z., Liang, H., Liu, G., Lu, Y., Unruh, A. K., Wakefield, C., Weinstein, J. N., Zhang, N., Liu, Y., Broaddus, R., Akbani, R., Mills, G. B., Adams, C., Barr, T., Black, A. D., Bowen, J., Deardurff, J., Frick, J., Gastier-Foster, J. M., Grossman, T., Harper, H. A., Hart-Kothari, M., Helsel, C., Hobensack, A., Kuck, H., Kneile, K., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Pyatt, R. E., Ramirez, N. C., Tabler, T. R., Vanhoose, N., White, P., Wise, L., Zmuda, E., Barnabas, N., Berry-Green, C., Blanc, V., Boice, L., Button, M., Farkas, A., Green, A., MacKenzie, J., Nicholson, D., Kalloger, S. E., Blake Gilks, C., Karlan, B. Y., Lester, J., Orsulic, S., Borowsky, M., Cadungog, M., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Witkin, G., Nemirovich-Danchenko, E., Potapova, O., Rotin, D., Berchuck, A., Birrer, M., Disaia, P., Monovich, L., Curley, E., Gardner, J., Mallery, D., Penny, R., Dowdy, S. C., Winterhoff, B., Dao, L., Gostout, B., Meuter, A., Teoman, A., Dao, F., Olvera, N., Bogomolniy, F., Garg, K., Soslow, R. A., Abramov, M., Bartlett, J. M. S., Kodeeswaran, S., Parfitt, J., Moiseenko, F., Clarke, B. A., Goodman, M. T., Carney, M. E., Matsuno, R. K., Fisher, J., Huang, M., Kimryn Rathmell, W., Thorne, L., Van Le, L., Dhir, R., Edwards, R., Elishaev, E., Zorn, K., Goodfellow, P. J., Mutch, D., Kahn, A. B., Bell, D. W., Pollock, P. M., Wang, C., Wheeler, D., Shinbrot, E., Gordon Robertson, A., Ding, L., Blake Gilks, C., Mardis, E. R., Ayala, B., Chu, A. L., Jensen, M. A., Kothiyal, P., Pihl, T. D., Pontius, J., Pot, D. A., Snyder, E. E., Srinivasan, D., Mills Shaw, K. R., Sheth, M., Davidsen, T., Eley, G., Ferguson, M. L., Yang, L., Guyer, M. S., Ozenberger, B. A., Sofia, H. J., Gordon Robertson, A. & Levine, D. A., 2013, In: Nature. 497, 7447, p. 67-73 7 p.

Research output: Contribution to journal › Article › peer-review

3646 Scopus citations

The cancer genome atlas pan-cancer analysis project

Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Sander, C., Stuart, J. M., Chang, K., Creighton, C. J., Davis, C., Donehower, L., Drummond, J., Wheeler, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chu, A., Chuah, E., & 316 othersChun, H. J. E., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Robertson, A. G., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, R. J., Beroukhim, R., Bhatt, A. S., Brooks, A. N., Cherniack, A. D., Freeman, S. S., Gabriel, S. B., Helman, E., Jung, J., Meyerson, M., Ojesina, A. I., Pedamallu, C. S., Saksena, G., Schumacher, S. E., Tabak, B., Zack, T., Lander, E. S., Bristow, C. A., Hadjipanayis, A., Haseley, P., Kucherlapati, R., Lee, S., Lee, E., Luquette, L. J., Mahadeshwar, H. S., Pantazi, A., Parfenov, M., Park, P. J., Protopopov, A., Ren, X., Santoso, N., Seidman, J., Seth, S., Song, X., Tang, J., Xi, R., Xu, A. W., Yang, L., Zeng, D., Auman, J. T., Balu, S., Buda, E., Fan, C., Hoadley, K. A., Jones, C. D., Meng, S., Mieczkowski, P. A., Parker, J. S., Perou, C. M., Roach, J., Shi, Y., Silva, G. O., Tan, D., Veluvolu, U., Waring, S., Wilkerson, M. D., Wu, J., Zhao, W., Bodenheimer, T., Hayes, D. N., Hoyle, A. P., Jeffreys, S. R., Mose, L. E., Simons, J. V., Soloway, M. G., Baylin, S. B., Berman, B. P., Bootwalla, M. S., Danilova, L., Herman, J. G., Hinoue, T., Laird, P. W., Rhie, S. K., Shen, H., Triche, T., Weisenberger, D. J., Carter, S. L., Cibulskis, K., Chin, L., Zhang, J., Sougnez, C., Wang, M., Getz, G., Dinh, H., Doddapaneni, H. V., Gibbs, R., Gunaratne, P., Han, Y., Kalra, D., Kovar, C., Lewis, L., Morgan, M., Morton, D., Muzny, D., Reid, J., Xi, L., Cho, J., Dicara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Liu, Y., Noble, M. S., Stojanov, P., Voet, D., Zhang, H., Zou, L., Stewart, C., Bernard, B., Bressler, R., Eakin, A., Iype, L., Knijnenburg, T., Kramer, R., Kreisberg, R., Leinonen, K., Lin, J., Liu, Y., Miller, M., Reynolds, S. M., Rovira, H., Shmulevich, I., Thorsson, V., Yang, D., Zhang, W., Amin, S., Wu, C. J., Wu, C. C., Akbani, R., Aldape, K., Baggerly, K. A., Broom, B., Casasent, T. D., Cleland, J., Dodda, D., Edgerton, M., Han, L., Herbrich, S. M., Ju, Z., Kim, H., Lerner, S., Li, J., Liang, H., Liu, W., Lorenzi, P. L., Lu, Y., Melott, J., Nguyen, L., Su, X., Verhaak, R., Wang, W., Wong, A., Yang, Y., Yao, J., Yao, R., Yoshihara, K., Yuan, Y., Yung, A. K., Zhang, N., Zheng, S., Ryan, M., Kane, D. W., Aksoy, B. A., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Kahles, A., Ladanyi, M., Lee, W., Lehmann, K. V., Miller, M. L., Ramirez, R., Rätsch, G., Reva, B., Schultz, N., Senbabaoglu, Y., Shen, R., Sinha, R., Sumer, S. O., Sun, Y., Taylor, B. S., Weinhold, N., Fei, S., Spellman, P., Benz, C., Carlin, D., Cline, M., Craft, B., Goldman, M., Haussler, D., Ma, S., Ng, S., Paull, E., Radenbaugh, A., Salama, S., Sokolov, A., Swatloski, T., Uzunangelov, V., Waltman, P., Yau, C., Zhu, J., Hamilton, S. R., Abbott, S., Abbott, R., Dees, N. D., Delehaunty, K., Ding, L., Dooling, D. J., Eldred, J. M., Fronick, C. C., Fulton, R., Fulton, L. L., Kalicki-Veizer, J., Kanchi, K. L., Kandoth, C., Koboldt, D. C., Larson, D. E., Ley, T. J., Lin, L., Lu, C., Magrini, V. J., Mardis, E. R., McLellan, M. D., McMichael, J. F., Miller, C. A., O'Laughlin, M., Pohl, C., Schmidt, H., Smith, S. M., Walker, J., Wallis, J. W., Wendl, M. C., Wilson, R. K., Wylie, T., Zhang, Q., Burton, R., Jensen, M. A., Kahn, A., Pihl, T., Pot, D., Wan, Y., Levine, D. A., Black, A. D., Bowen, J., Frick, J., Gastier-Foster, J. M., Harper, H. A., Helsel, C., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Ramirez, N. C., Sharpe, S., Wise, L., Zmuda, E., Chanock, S. J., Davidsen, T., Demchok, J. A., Eley, G., Felau, I., Sheth, M., Sofia, H., Staudt, L., Tarnuzzer, R., Wang, Z., Yang, L., Zhang, J., Omberg, L., Margolin, A., Raphael, B. J., Vandin, F., Wu, H. T., Leiserson, M. D. M., Benz, S. C., Vaske, C. J., Noushmehr, H., Wolf, D., Veer, L. V. T., Anastassiou, D., Yang, T. H. O., Lopez-Bigas, N., Gonzalez-Perez, A., Tamborero, D., Xia, Z., Li, W., Cho, D. Y., Przytycka, T., Hamilton, M., McGuire, S., Nelander, S., Johansson, P., Jörnsten, R. & Kling, T., Oct 1 2013, In: Nature Genetics. 45, 10, p. 1113-1120 8 p.

Research output: Contribution to journal › Article › peer-review

5140 Scopus citations

2014

Characterization of HPV and host genome interactions in primary head and neck cancers

The Cancer Genome Atlas Network, Oct 28 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 43, p. 15544-15549 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

282 Scopus citations

Comprehensive molecular characterization of gastric adenocarcinoma

Cancer Genome Atlas Research Network, Sep 11 2014, In: Nature. 513, 7517, p. 202-209 8 p.

Research output: Contribution to journal › Article › peer-review

4591 Scopus citations

Comprehensive molecular characterization of urothelial bladder carcinoma

Weinstein, J. N., Akbani, R., Broom, B. M., Wang, W., Verhaak, R. G. W., McConkey, D., Lerner, S., Morgan, M., Creighton, C. J., Smith, C., Cherniack, A. D., Kim, J., Pedamallu, C. S., Noble, M. S., Al-Ahmadie, H. A., Reuter, V. E., Rosenberg, J. E., F.Bajorin, D., Bochner, B. H., Solit, D. B., & 273 othersKoppie, T., Robinson, B., Gordenin, D. A., Fargo, D., Klimczak, L. J., Roberts, S. A., Au, J., Laird, P. W., Hinoue, T., Schultz, N., Ramirez, R., Hansel, D., Hoadley, K. A., Kim, W. Y., Damrauer, J. S., Baylin, S. B., Mungall, A. J., Robertson, A. G., Chu, A., Kwiatkowski, D. J., Sougnez, C., Cibulskis, K., Lichtenstein, L., Sivachenko, A., Stewart, C., Lawrence, M. S., Getz, G., Lander, E., Gabrie, S. B., Donehower, L., Carter, S. L., Saksena, G., Schumacher, S. E., Freeman, S. S., Jung, J., Bhatt, A. S., Pugh, T., Beroukhim, R., Meyerson, M., Ally, A., Balasundaram, M., Butterfield, Y. S. N., Dhalla, N., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Wong, T., Wye, N., Bowlby, R., Chuah, E., Guin, R., Shen, H., Bootwalla, M. S., Triche, T., Lai, P. H., Van Den Berg, D. J., Weisenberger, D. J., Balu, S., Bodenheimer, T., Hoyle, A. P., Jefferys, S. R., Meng, S., Mose, L. E., Simons, J. V., Soloway, M. G., Wu, J., Parker, J. S., Hayes, D. N., Roach, J., Buda, E., Jones, C. D., Mieczkowski, P. A., Tan, D., Veluvolu, U., Waring, S., Auman, J. T., Perou, C. M., Wilkerson, M. D., Santoso, N., Parfenov, M., Ren, X., Pantazi, A., Hadjipanayis, A., Seidman, J., Kucherlapati, R., Lee, S., Yang, L., Park, P. J., Xu, A. W., Protopopov, A., Zhang, J., Bristow, C., Mahadeshwar, H. S., Seth, S., Song, X., Tang, J., Zeng, D., Chin, L., Guo, C., Casasent, T. D., Liu, W., Ju, Z., Motter, T., Peng, B., Ryan, M., Su, X., Yang, J. Y., Lorenzi, P. L., Yao, H., Zhang, N., Zhang, J., Mills, G. B., Cho, J., DiCara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Lin, P., Liu, Y., Stojanov, P., Voet, D., Zhang, H., Zou, L., Bernard, B., Kreisberg, D., Reynolds, S., Rovira, H., Shmulevich, I., Gao, J., Jacobsen, A., Aksoy, B. A., Antipin, Y., Ciriello, G., Dresdner, G., Gross, B., Lee, W., Reva, B., Shen, R., Sinha, R., Sumer, S. O., Weinhold, N., Ladanyi, M., Sander, C., Benz, C., Carlin, D., Haussler, D., Ng, S., Paull, E., Stuart, J., Zhu, J., Liu, Y., Zhang, W., Taylor, B. S., Lichtenberg, T. M., Zmuda, E., Barr, T., Black, A. D., George, M., Hanf, B., Helsel, C., McAllister, C., Ramirez, N. C., Tabler, T. R., Weaver, S., Wise, L., Bowen, J., Gastier-Foster, J. M., Jian, W., Tello, S., Ittman, M., Castro, P., McClenden, W. D., Gibbs, R., Saller, C., Tarvin, K., DiPiero, J. M., Owens, J., Bollag, R., Li, Q., Weinberger, P., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Swanson, P., Shelton, T., Curley, E., Gardner, J., Mallery, D., Penny, R., Van Bang, N., Hanh, P. T., Kohl, B., Van Le, X., Phu, B. D., Thorp, R., Tien, N. V., Vinh, L. Q., Sandusky, G., Burks, E., Christ, K., Gee, J., Holway, A., Moinzadeh, A., Sorcini, A., Sullivan, T., Garcia-Grossman, I. R., Regazzi, A. M., Boice, L., Rathmell, W. K., Thorne, L., Bastacky, S., Davies, B., Dhir, R., Gingrich, J., Hrebinko, R., Maranchie, J., Nelson, J., Parwani, A., Bshara, W., Gaudioso, C., Morrison, C., Alexopoulou, V., Bartlett, J., Engel, J., Kodeeswaran, S., Antic, T., O'Donnell, P. H., Smith, N. D., Steinberg, G. D., Egea, S., Gomez-Fernandez, C., Herbert, L., Jorda, M., Soloway, M., Beaver, A., Carter, S., Kapur, P., Lewis, C., Lotan, Y., Bondaruk, J., Czerniak, B., Skinner, E., Aldape, K., Jensen, M. A., Kahn, A. B., Pihl, T. D., Pot, D. A., Srinivasan, D., Wan, Y., Ferguson, M. L., Zenklusen, J. C., Davidsen, T., Demchok, J. A., Shaw, K. R. M., Sheth, M., Tarnuzzer, R., Wang, Z., Yang, L., Hutter, C., Ozenberger, B. A., Sofia, H. J. & Eley, G., 2014, In: Nature. 507, 7492, p. 315-322 8 p.

Research output: Contribution to journal › Article › peer-review

2314 Scopus citations

Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network

Collisson, E. A., Campbell, J. D., Brooks, A. N., Berger, A. H., Lee, W., Chmielecki, J., Beer, D. G., Cope, L., Creighton, C. J., Danilova, L., Ding, L., Getz, G., Hammerman, P. S., Hayes, D. N., Hernandez, B., Herman, J. G., Heymach, J. V., Jurisica, I., Kucherlapati, R., Kwiatkowski, D., & 290 othersLadanyi, M., Robertson, G., Schultz, N., Shen, R., Sinha, R., Sougnez, C., Tsao, M. S., Travis, W. D., Weinstein, J. N., Wigle, D. A., Wilkerson, M. D., Chu, A., Cherniack, A. D., Hadjipanayis, A., Rosenberg, M., Weisenberger, D. J., Laird, P. W., Radenbaugh, A., Ma, S., Stuart, J. M., Byers, L. A., Baylin, S. B., Govindan, R., Meyerson, M., Gabriel, S. B., Cibulskis, K., Kim, J., Stewart, C., Lichtenstein, L., Lander, E. S., Lawrence, M. S., Getz, E., Fulton, R., Fulton, L. L., McLellan, M. D., Wilson, R. K., Ye, K., Fronick, C. C., Maher, C. A., Miller, C. A., Wendl, M. C., Cabanski, C., Mardis, E., Wheeler, D., Balasundaram, M., Butterfield, Y. S. N., Carlsen, R., Chuah, E., Dhalla, N., Guin, R., Hirst, C., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, A. J., Schein, J. E., Sipahimalani, P., Tam, A., Varhol, R., Robertson, A. G., Wye, N., Thiessen, N., Holt, R. A., Jones, S. J. M., Marra, M. A., Imielinski, M., Onofrio, R. C., Hodis, E., Zack, T., Helman, E., Pedamallu, C. S., Mesirov, J., Saksena, G., Schumacher, S. E., Carter, S. L., Garraway, L., Beroukhim, R., Lee, S., Mahadeshwar, H. S., Pantazi, A., Protopopov, A., Ren, X., Seth, S., Song, X., Tang, J., Yang, L., Zhang, J., Chen, P. C., Parfenov, M., Xu, A. W., Santoso, N., Chin, L., Park, P. J., Hoadley, K. A., Auman, J. T., Meng, S., Shi, Y., Buda, E., Waring, S., Veluvolu, U., Tan, D., Mieczkowski, P. A., Jones, C. D., Simons, J. V., Soloway, M. G., Bodenheimer, T., Jefferys, S. R., Roach, J., Hoyle, A. P., Wu, J., Balu, S., Singh, D., Prins, J. F., Marron, J. S., Parker, J. S., Perou, C. M., Liu, J., Maglinte, D. T., Lai, P. H., Bootwalla, M. S., Van Den Berg, D. J., Triche, T., Cho, J., DiCara, D., Heiman, D., Lin, P., Mallard, W., Voet, D., Zhang, H., Zou, L., Noble, M. S., Gehlenborg, N., Thorvaldsdottir, H., Nazaire, M. D., Robinson, J., Aksoy, B. A., Ciriello, G., Taylor, B. S., Dresdner, G., Gao, J., Gross, B., Seshan, V. E., Reva, B., Sumer, S. O., Weinhold, N., Sander, C., Ng, S., Zhu, J., Benz, C. C., Yau, C., Haussler, D., Spellman, P. T., Kimes, P. K., Broom, B. M., Wang, J., Lu, Y., Ng, P. K. S., Diao, L., Liu, W., Amos, C. I., Akbani, R., Mills, G. B., Curley, E., Paulauskis, J., Lau, K., Morris, S., Shelton, T., Mallery, D., Gardner, J., Penny, R., Saller, C., Tarvin, K., Richards, W. G., Cerfolio, R., Bryant, A., Raymond, D. P., Pennell, N. A., Farver, C., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Brown, J., Bauer, T., Dolzhanskiy, C. O., Potapova, O., Rotin, D., Voronina, O., Nemirovich-Danchenko, E., Fedosenko, K. V., Gal, A., Behera, M., Ramalingam, S. S., Sica, G., Flieder, D., Boyd, J., Weaver, J. E., Kohl, B., Thinh, D. H. Q., Sandusky, G., Juhl, H., Duhig, E., Illei, P., Gabrielson, E., Shin, J., Lee, B., Rogers, K., Trusty, D., Brock, M. V., Williamson, C., Burks, E., Rieger-Christ, K., Holway, A., Sullivan, T., Asiedu, M. K., Kosari, F., Rekhtman, N., Zakowski, M., Rusch, V. W., Zippile, P., Suh, J., Pass, H., Goparaju, C., Owusu-Sarpong, Y., Bartlett, J. M. S., Kodeeswaran, S., Parfitt, J., Sekhon, H., Albert, M., Eckman, J., Myers, J. B., Morrison, C., Gaudioso, C., Borgia, J. A., Bonomi, P., Pool, M., Liptay, M. J., Moiseenko, F., Zaytseva, I., Dienemann, H., Meister, M., Schnabel, P. A., Muley, T. R., Peifer, M., Gomez-Fernandez, C., Herbert, L., Egea, S., Huang, M., Thorne, L. B., Boice, L., Salazar, A. H., Funkhouser, W. K., Rathmell, W. K., Dhir, R., Yousem, S. A., Dacic, S., Schneider, F., Siegfried, J. M., Hajek, R., Watson, M. A., McDonald, S., Meyers, B., Clarke, B., Yang, I. A., Fong, K. M., Hunter, L., Windsor, M., Bowman, R. V., Peters, S., Letovanec, I., Khan, K. Z., Jensen, M. A., Snyder, E. E., Srinivasan, D., Kahn, A. B., Baboud, J., Pot, D. A., Shaw, K. R. M., Sheth, M., Davidsen, T., Demchok, J. A., Yang, L., Wang, Z., Tarnuzzer, R., Zenklusen, J. C., Ozenberger, B. A., Sofia, H. J. & Cheney, R., 2014, In: Nature. 511, 7511, p. 543-550 8 p.

Research output: Contribution to journal › Article › peer-review

3986 Scopus citations

Finding the missing honey bee genes: Lessons learned from a genome upgrade

HGSC production teams, Jan 30 2014, In: BMC genomics. 15, 1, 86.

Research output: Contribution to journal › Article › peer-review

315 Scopus citations

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

Agrawal, N., Akbani, R., Aksoy, B. A., Ally, A., Arachchi, H., Asa, S. L., Auman, J. T., Balasundaram, M., Balu, S., Baylin, S. B., Behera, M., Bernard, B., Beroukhim, R., Bishop, J. A., Black, A. D., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J., Bowlby, R., & 223 othersBristow, C. A., Brookens, R., Brooks, D., Bryant, R., Buda, E., Butterfield, Y. S. N., Carling, T., Carlsen, R., Carter, S. L., Carty, S. E., Chan, T. A., Chen, A. Y., Cherniack, A. D., Cheung, D., Chin, L., Cho, J., Chu, A., Chuah, E., Cibulskis, K., Ciriello, G., Clarke, A., Clayman, G. L., Cope, L., Copland, J. A., Covington, K., Danilova, L., Davidsen, T., Demchok, J. A., DiCara, D., Dhalla, N., Dhir, R., Dookran, S. S., Dresdner, G., Eldridge, J., Eley, G., El-Naggar, A. K., Eng, S., Fagin, J. A., Fennell, T., Ferris, R. L., Fisher, S., Frazer, S., Frick, J., Gabriel, S. B., Ganly, I., Gao, J., Garraway, L. A., Gastier-Foster, J. M., Getz, G., Gehlenborg, N., Ghossein, R., Gibbs, R. A., Giordano, T. J., Gomez-Hernandez, K., Grimsby, J., Gross, B., Guin, R., Hadjipanayis, A., Harper, H. A., Hayes, D. N., Heiman, D. I., Herman, J. G., Hoadley, K. A., Hofree, M., Holt, R. A., Hoyle, A. P., Huang, F. W., Huang, M., Hutter, C. M., Ideker, T., Iype, L., Jacobsen, A., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Kasaian, K., Kebebew, E., Khuri, F. R., Kim, J., Kramer, R., Kreisberg, R., Kucherlapati, R., Kwiatkowski, D. J., Ladanyi, M., Lai, P. H., Laird, P. W., Lander, E., Lawrence, M. S., Lee, D., Lee, E., Lee, S., Lee, W., Leraas, K. M., Lichtenberg, T. M., Lichtenstein, L., Lin, P., Ling, S., Liu, J., Liu, W., Liu, Y., LiVolsi, V. A., Lu, Y., Ma, Y., Mahadeshwar, H. S., Marra, M. A., Mayo, M., McFadden, D. G., Meng, S., Meyerson, M., Mieczkowski, P. A., Miller, M., Mills, G., Moore, R. A., Mose, L. E., Mungall, A. J., Murray, B. A., Nikiforov, Y. E., Noble, M. S., Ojesina, A. I., Owonikoko, T. K., Ozenberger, B. A., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Paull, E. O., Pedamallu, C. S., Perou, C. M., Prins, J. F., Protopopov, A., Ramalingam, S. S., Ramirez, N. C., Ramirez, R., Raphael, B. J., Rathmell, W. K., Ren, X., Reynolds, S. M., Rheinbay, E., Ringel, M. D., Rivera, M., Roach, J., Robertson, A. G., Rosenberg, M. W., Rosenthal, M., Sadeghi, S., Saksena, G., Sander, C., Santoso, N., Schein, J. E., Schultz, N., Schumacher, S. E., Seethala, R. R., Seidman, J., Senbabaoglu, Y., Seth, S., Sharpe, S., Shaw, K. R. M., Shen, J. P., Shen, R., Sherman, S., Sheth, M., Shi, Y., Shmulevich, I., Sica, G. L., Simons, J. V., Sinha, R., Sipahimalani, P., Smallridge, R. C., Sofia, H. J., Soloway, M. G., Song, X., Sougnez, C., Stewart, C., Stojanov, P., Stuart, J. M., Sumer, S. O., Sun, Y., Tabak, B., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B. S., Thiessen, N., Thorne, L., Thorsson, V., Tuttle, R. M., Umbricht, C. B., Van Den Berg, D. J., Vandin, F., Veluvolu, U., Verhaak, R. G. W., Vinco, M., Voet, D., Walter, V., Wang, Z., Waring, S., Weinberger, P. M., Weinhold, N., Weinstein, J. N., Weisenberger, D. J., Wheeler, D., Wilkerson, M. D., Wilson, J., Williams, M., Winer, D. A., Wise, L., Wu, J., Xi, L., Xu, A. W., Yang, L., Yang, L., Zack, T. I., Zeiger, M. A., Zeng, D., Zenklusen, J. C., Zhao, N., Zhang, H., Zhang, J., Zhang, J., Zhang, W., Zmuda, E. & Zou, L., Oct 23 2014, In: Cell. 159, 3, p. 676-690 15 p.

Research output: Contribution to journal › Article › peer-review

2166 Scopus citations

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

Zhang, J., Fujimoto, J., Zhang, J., Wedge, D. C., Song, X., Zhang, J., Seth, S., Chow, C. W., Cao, Y., Gumbs, C., Gold, K. A., Kalhor, N., Little, L., Mahadeshwar, H., Moran, C., Protopopov, A., Sun, H., Tang, J., Wu, X., Ye, Y., & 7 othersWilliam, W. N., Lee, J. J., Heymach, J. V., Hong, W. K., Swisher, S., Wistuba, I. I. & Futreal, P. A., Oct 10 2014, In: Science. 346, 6206, p. 256-259 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

758 Scopus citations

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

The Cancer Genome Atlas Research Network, Aug 14 2014, In: Cell. 158, 4, p. 929-944 16 p.

Research output: Contribution to journal › Article › peer-review

1097 Scopus citations

Recurrent PTPRB and PLCG1 mutations in angiosarcoma

Behjati, S., Tarpey, P. S., Sheldon, H., Martincorena, I., Van Loo, P., Gundem, G., Wedge, D. C., Ramakrishna, M., Cooke, S. L., Pillay, N., Vollan, H. K. M., Papaemmanuil, E., Koss, H., Bunney, T. D., Hardy, C., Joseph, O. R., Martin, S., Mudie, L., Butler, A., Teague, J. W., & 30 othersPatil, M., Steers, G., Cao, Y., Gumbs, C., Ingram, D., Lazar, A. J., Little, L., Mahadeshwar, H., Protopopov, A., Al Sannaa, G. A., Seth, S., Song, X., Tang, J., Zhang, J., Ravi, V., Torres, K. E., Khatri, B., Halai, D., Roxanis, I., Baumhoer, D., Tirabosco, R., Amary, M. F., Boshoff, C., McDermott, U., Katan, M., Stratton, M. R., Futreal, P. A., Flanagan, A. M., Harris, A. & Campbell, P. J., Apr 2014, In: Nature Genetics. 46, 4, p. 376-379 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

240 Scopus citations

The somatic genomic landscape of chromophobe renal cell carcinoma

The Cancer Genome Atlas Research Network, 2014, In: Cancer cell. 26, 3, p. 319-330 12 p.

Research output: Contribution to journal › Article › peer-review

582 Scopus citations

2015

Co-clinical assessment identifies patterns of BRAF inhibitor resistance in melanoma

Kwong, L. N., Boland, G. M., Frederick, D. T., Helms, T. L., Akid, A. T., Miller, J. P., Jiang, S., Cooper, Z. A., Song, X., Seth, S., Kamara, J., Protopopov, A., Mills, G. B., Flaherty, K. T., Wargo, J. A. & Chin, L., Apr 1 2015, In: Journal of Clinical Investigation. 125, 4, p. 1459-1470 12 p.

Research output: Contribution to journal › Article › peer-review

93 Scopus citations

Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas

Brat, D. J., Verhaak, R. G. W., Aldape, K. D., Yung, W. K. A., Salama, S. R., Cooper, L. A. D., Rheinbay, E., Miller, C. R., Vitucci, M., Morozova, O., Robertson, A. G., Noushmehr, H., Laird, P. W., Cherniack, A. D., Akbani, R., Huse, J. T., Ciriello, G., Poisson, L. M., Barnholtz-Sloan, J. S., Berger, M. S., & 287 othersBrennan, C., Colen, R. R., Colman, H., Flanders, A. E., Giannini, C., Grifford, M., Iavarone, A., Jain, R., Joseph, I., Kim, J., Kasaian, K., Mikkelsen, T., Murray, B. A., O'Neill, B. P., Pachter, L., Parsons, D. W., Sougnez, C., Sulman, E. P., Vandenberg, S. R., Van Meir, E. G., Von Deimling, A., Zhang, H., Crain, D., Lau, K., Mallery, D., Morris, S., Paulauskis, J., Penny, R., Shelton, T., Sherman, M., Yena, P., Black, A., Bowen, J., Dicostanzo, K., Gastier-Foster, J., Leraas, K. M., Lichtenberg, T. M., Pierson, C. R., Ramirez, N. C., Taylor, C., Weaver, S., Wise, L., Zmuda, E., Davidsen, T., Demchok, J. A., Eley, G., Ferguson, M. L., Hutter, C. M., Shaw, K. R. M., Ozenberger, B. A., Sheth, M., Sofia, H. J., Tarnuzzer, R., Wang, Z., Yang, L., Zenklusen, J. C., Ayala, B., Baboud, J., Chudamani, S., Jensen, M. A., Liu, J., Pihl, T., Raman, R., Wan, Y., Wu, Y., Ally, A., Auman, J. T., Balasundaram, M., Balu, S., Baylin, S. B., Beroukhim, R., Bootwalla, M. S., Bowlby, R., Bristow, C. A., Brooks, D., Butterfield, Y., Carlsen, R., Carter, S., Chin, L., Chu, A., Chuah, E., Cibulskis, K., Clarke, A., Coetzee, S. G., Dhalla, N., Fennell, T., Fisher, S., Gabriel, S., Getz, G., Gibbs, R., Guin, R., Hadjipanayis, A., Hayes, D. N., Hinoue, T., Hoadley, K., Holt, R. A., Hoyle, A. P., Jefferys, S. R., Jones, S., Jones, C. D., Kucherlapati, R., Lai, P. H., Lander, E., Lee, S., Lichtenstein, L., Ma, Y., Maglinte, D. T., Mahadeshwar, H. S., Marra, M. A., Mayo, M., Meng, S., Meyerson, M. L., Mieczkowski, P. A., Moore, R. A., Mose, L. E., Mungall, A. J., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Perou, C. M., Protopopov, A., Ren, X., Roach, J., Sabedot, T. S., Schein, J., Schumacher, S. E., Seidman, J. G., Seth, S., Shen, H., Simons, J. V., Sipahimalani, P., Soloway, M. G., Song, X., Sun, H., Tabak, B., Tam, A., Tan, D., Tang, J., Thiessen, N., Triche, T., Van Den Berg, D. J., Veluvolu, U., Waring, S., Weisenberger, D. J., Wilkerson, M. D., Wong, T., Wu, J., Xi, L., Xu, A. W., Yang, L., Zack, T. I., Zhang, J., Aksoy, B. A., Arachchi, H., Benz, C., Bernard, B., Carlin, D., Cho, J., DiCara, D., Frazer, S., Fuller, G. N., Gao, J. J., Gehlenborg, N., Haussler, D., Heiman, D. I., Iype, L., Jacobsen, A., Ju, Z., Katzman, S., Kim, H., Knijnenburg, T., Kreisberg, R. B., Lawrence, M. S., Lee, W., Leinonen, K., Lin, P., Ling, S., Liu, W., Liu, Y., Liu, Y., Lu, Y., Mills, G., Ng, S., Noble, M. S., Paull, E., Rao, A., Reynolds, S., Saksena, G., Sanborn, Z., Sander, C., Schultz, N., Senbabaoglu, Y., Shen, R., Shmulevich, I., Sinha, R., Stuart, J., Sumer, S. O., Sun, Y., Tasman, N., Taylor, B. S., Voet, D., Weinhold, N., Weinstein, J. N., Yang, D., Yoshihara, K., Zheng, S., Zhang, W., Zou, L., Abel, T., Sadeghi, S., Cohen, M. L., Eschbacher, J., Hattab, E. M., Raghunathan, A., Schniederjan, M. J., Aziz, D., Barnett, G., Barrett, W., Bigner, D. D., Boice, L., Brewer, C., Calatozzolo, C., Campos, B., Carlotti, C. G., Chan, T. A., Cuppini, L., Curley, E., Cuzzubbo, S., Devine, K., DiMeco, F., Duell, R., Elder, J. B., Fehrenbach, A., Finocchiaro, G., Friedman, W., Fulop, J., Gardner, J., Hermes, B., Herold-Mende, C., Jungk, C., Kendler, A., Lehman, N. L., Lipp, E., Liu, O., Mandt, R., McGraw, M., Mclendon, R., McPherson, C., Neder, L., Nguyen, P., Noss, A., Nunziata, R., Ostrom, Q. T., Palmer, C., Perin, A., Pollo, B., Potapov, A., Potapova, O., Rathmell, W. K., Rotin, D., Scarpace, L., Schilero, C., Senecal, K., Shimmel, K., Shurkhay, V., Sifri, S., Singh, R., Sloan, A. E., Smolenski, K., Staugaitis, S. M., Steele, R., Thorne, L., Tirapelli, D. P. C., Unterberg, A., Vallurupalli, M., Wang, Y., Warnick, R., Williams, F., Wolinsky, Y., Bell, S., Rosenberg, M., Stewart, C., Huang, F., Grimsby, J. L., Radenbaugh, A. J. & Zhang, J., Jun 25 2015, In: New England Journal of Medicine. 372, 26, p. 2481-2498 18 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2282 Scopus citations

Comprehensive genomic characterization of head and neck squamous cell carcinomas

The Cancer Genome Atlas Network, Jan 29 2015, In: Nature. 517, 7536, p. 576-582 7 p.

Research output: Contribution to journal › Article › peer-review

2897 Scopus citations

Genomic Classification of Cutaneous Melanoma

The Cancer Genome Atlas Network, Jun 20 2015, In: Cell. 161, 7, p. 1681-1696 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2251 Scopus citations

The Molecular Taxonomy of Primary Prostate Cancer

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., & 292 othersBodenheimer, 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., Nov 5 2015, In: Cell. 163, 4, p. 1011-1025 15 p.

Research output: Contribution to journal › Article › peer-review

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2138 Scopus citations

2016

Genomic heterogeneity of multiple synchronous lung cancer

Liu, Y., Zhang, J., Li, L., Yin, G., Zhang, J., Zheng, S., Cheung, H., Wu, N., Lu, N., Mao, X., Yang, L., Zhang, J., Zhang, L., Seth, S., Chen, H., Song, X., Liu, K., Xie, Y., Zhou, L., Zhao, C., & 24 othersHan, N., Chen, W., Zhang, S., Chen, L., Cai, W., Shen, M., Xu, N., Cheng, S., Yang, H., Lee, J. J., Correa, A., Fujimoto, J., Behrens, C., Chow, C. W., William, W. N., Heymach, J. V., Hong, W. K., Swisher, S., Wistuba, I. I., Wang, J., Lin, D., Liu, X., Futreal, P. A. & Gao, Y., Oct 21 2016, In: Nature communications. 7, 13200.

Research output: Contribution to journal › Article › peer-review

Open Access

132 Scopus citations

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Ceccarelli, M., Barthel, F. P., Malta, T. M., Sabedot, T. S., Salama, S. R., Murray, B. A., Morozova, O., Newton, Y., Radenbaugh, A., Pagnotta, S. M., Anjum, S., Wang, J., Manyam, G., Zoppoli, P., Ling, S., Rao, A. A., Grifford, M., Cherniack, A. D., Zhang, H., Poisson, L., & 188 othersCarlotti, C. G., Tirapelli, D. P. D. C., Uppore Kukkillaya, A. R., Mikkelsen, T., Lau, C. C., Yung, W. K. A., Rabadan, R., Huse, J., Brat, D. J., Lehman, N. L., Barnholtz-Sloan, J. S., Zheng, S., Hess, K. R., Rao, G., Meyerson, M., Beroukhim, R., Cooper, L., Akbani, R., Wrensch, M., Haussler, D., Aldape, K. D., Laird, P. W., Gutmann, D. H., Noushmehr, H., Arachchi, H., Auman, J. T., Balasundaram, M., Balu, S., Barnett, G., Baylin, S., Bell, S., Benz, C., Bir, N., Black, K. L., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J., Bristow, C. A., Butterfield, Y. S. N., Chen, Q. R., Chin, L., Cho, J., Chuah, E., Chudamani, S., Coetzee, S. G., Cohen, M. L., Colman, H., Couce, M., D'Angelo, F., Davidsen, T., Davis, A., Demchok, J. A., Devine, K., Ding, L., Duell, R., Elder, J. B., Eschbacher, J. M., Fehrenbach, A., Ferguson, M., Frazer, S., Fuller, G., Fulop, J., Gabriel, S. B., Garofano, L., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Getz, G., Giannini, C., Gibson, W. J., Hadjipanayis, A., Hayes, D. N., Heiman, D. I., Hermes, B., Hilty, J., Hoadley, K. A., Hoyle, A. P., Huang, M., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Ju, Z., Kastl, A., Kendler, A., Kim, J., Kucherlapati, R., Lai, P. H., Lawrence, M. S., Lee, S., Leraas, K. M., Lichtenberg, T. M., Lin, P., Liu, Y., Liu, J., Ljubimova, J. Y., Lu, Y., Ma, Y., Maglinte, D. T., Mahadeshwar, H. S., Marra, M. A., McGraw, M., McPherson, C., Meng, S., Mieczkowski, P. A., Miller, C. R., Mills, G. B., Moore, R. A., Mose, L. E., Mungall, A. J., Naresh, R., Naska, T., Neder, L., Noble, M. S., Noss, A., O'Neill, B. P., Ostrom, Q. T., Palmer, C., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Perou, C. M., Pierson, C. R., Pihl, T., Protopopov, A., Radenbaugh, A., Ramirez, N. C., Rathmell, W. K., Ren, X., Roach, J., Robertson, A. G., Saksena, G., Schein, J. E., Schumacher, S. E., Seidman, J., Senecal, K., Seth, S., Shen, H., Shi, Y., Shih, J., Shimmel, K., Sicotte, H., Sifri, S., Silva, T., Simons, J. V., Singh, R., Skelly, T., Sloan, A. E., Sofia, H. J., Soloway, M. G., Song, X., Sougnez, C., Souza, C., Staugaitis, S. M., Sun, H., Sun, C., Tan, D., Tang, J., Tang, Y., Thorne, L., Trevisan, F. A., Triche, T., Van Den Berg, D. J., Veluvolu, U., Voet, D., Wan, Y., Wang, Z., Warnick, R., Weinstein, J. N., Weisenberger, D. J., Wilkerson, M. D., Williams, F., Wise, L., Wolinsky, Y., Wu, J., Xu, A. W., Yang, L., Yang, L., Zack, T. I., Zenklusen, J. C., Zhang, J., Zhang, W., Zhang, J., Zmuda, E., Noushmehr, H., Iavarone, A. & Verhaak, R., Jan 28 2016, In: Cell. 164, 3, p. 550-563 14 p.

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Open Access

1452 Scopus citations

2017

A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations

Zhang, Y., Kwok-Shing Ng, P., Kucherlapati, M., Chen, F., Liu, Y., Tsang, Y. H., de Velasco, G., Jeong, K. J., Akbani, R., Hadjipanayis, A., Pantazi, A., Bristow, C. A., Lee, E., Mahadeshwar, H. S., Tang, J., Zhang, J., Yang, L., Seth, S., Lee, S., Ren, X., & 22 othersSong, X., Sun, H., Seidman, J., Luquette, L. J., Xi, R., Chin, L., Protopopov, A., Westbrook, T. F., Shelley, C. S., Choueiri, T. K., Ittmann, M., Van Waes, C., Weinstein, J. N., Liang, H., Henske, E. P., Godwin, A. K., Park, P. J., Kucherlapati, R., Scott, K. L., Mills, G. B., Kwiatkowski, D. J. & Creighton, C. J., Jun 12 2017, In: Cancer cell. 31, 6, p. 820-832.e3

Research output: Contribution to journal › Article › peer-review

Open Access

386 Scopus citations

Copy number alterations detected as clonal hematopoiesis of indeterminate potential

Takahashi, K., Wang, F., Kantarjian, H., Song, X., Patel, K., Neelapu, S., Gumbs, C., Little, L., Tippen, S., Thornton, R., DiNardo, C. D., Ravandi, F., Bueso-Ramos, C., Zhang, J., Wu, X., Garcia-Manero, G. & Andrew Futreal, P., Jun 27 2017, In: Blood Advances. 1, 15, p. 1031-1036 6 p.

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Open Access

30 Scopus citations

DNA methylation intratumor heterogeneity in localized lung adenocarcinomas

Quek, K., Li, J., Estecio, M., Zhang, J., Fujimoto, J., Roarty, E., Little, L., Chow, C. W., Song, X., Behrens, C., Chen, T., William, W. N., Swisher, S., Heymach, J., Wistuba, I., Zhang, J., Futreal, A. & Zhang, J., 2017, In: Oncotarget. 8, 13, p. 21994-22002 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

32 Scopus citations

Genomic and immune heterogeneity are associated with differential responses to therapy in melanoma

Reuben, A., Spencer, C. N., Prieto, P. A., Gopalakrishnan, V., Reddy, S. M., Miller, J. P., Mao, X., De Macedo, M. P., Chen, J., Song, X., Jiang, H., Chen, P. L., Beird, H. C., Garber, H. R., Roh, W., Wani, K., Chen, E., Haymaker, C., Forget, M. A., Little, L. D., & 34 othersGumbs, C., Thornton, R. L., Hudgens, C. W., Chen, W. S., Austin-Breneman, J., Sloane, R. S., Nezi, L., Cogdill, A. P., Bernatchez, C., Roszik, J., Hwu, P., Woodman, S. E., Chin, L., Tawbi, H., Davies, M. A., Gershenwald, J. E., Amaria, R. N., Glitza, I. C., Diab, A., Patel, S. P., Hu, J., Lee, J. E., Grimm, E. A., Tetzlaff, M. T., Lazar, A. J., Wistuba, I. I., Clise-Dwyer, K., Carter, B. W., Zhang, J., Futreal, P. A., Sharma, P., Allison, J. P., Cooper, Z. A. & Wargo, J. A., Dec 1 2017, In: npj Genomic Medicine. 2, 1, 10.

Research output: Contribution to journal › Article › peer-review

112 Scopus citations

Integrated genomic and molecular characterization of cervical cancer

The Cancer Genome Atlas Research Network, Mar 16 2017, In: Nature. 543, 7645, p. 378-384 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

993 Scopus citations

Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma

Robertson, A. G., Shih, J., Yau, C., Gibb, E. A., Oba, J., Mungall, K. L., Hess, J. M., Uzunangelov, V., Walter, V., Danilova, L., Lichtenberg, T. M., Kucherlapati, M., Kimes, P. K., Tang, M., Penson, A., Babur, O., Akbani, R., Bristow, C. A., Hoadley, K. A., Iype, L., & 150 othersChang, M. T., Abdel-Rahman, M. H., Ally, A., Auman, J. T., Balasundaram, M., Balu, S., Benz, C., Beroukhim, R., Birol, I., Bodenheimer, T., Bowen, J., Bowlby, R., Brooks, D., Carlsen, R., Cebulla, C. M., Cherniack, A. D., Chin, L., Cho, J., Chuah, E., Chudamani, S., Cibulskis, C., Cibulskis, K., Cope, L., Coupland, S. E., Defreitas, T., Demchok, J. A., Desjardins, L., Dhalla, N., Esmaeli, B., Felau, I., Ferguson, M. L., Frazer, S., Gabriel, S. B., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Gershenwald, J. E., Getz, G., Griewank, K. G., Grimm, E. A., Hayes, D. N., Hegde, A. M., Heiman, D. I., Helsel, C., Hobensack, S., Holt, R. A., Hoyle, A. P., Hu, X., Hutter, C. M., Jager, M. J., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Kandoth, C., Kasaian, K., Kim, J., Kucherlapati, R., Lander, E., Lawrence, M. S., Lazar, A. J., Lee, S., Leraas, K. M., Lin, P., Liu, J., Liu, W., Lolla, L., Lu, Y., Ma, Y., Mahadeshwar, H. S., Mariani, O., Marra, M. A., Mayo, M., Meier, S., Meng, S., Meyerson, M., Mieczkowski, P. A., Mills, G. B., Moore, R. A., Mose, L. E., Mungall, A. J., Murray, B. A., Naresh, R., Noble, M. S., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Perou, C. M., Pihl, T., Pilarski, R., Protopopov, A., Radenbaugh, A., Rai, K., Ramirez, N. C., Ren, X., Reynolds, S. M., Roach, J., Roman-Roman, S., Roszik, J., Sadeghi, S., Saksena, G., Sastre, X., Schadendorf, D., Schein, J. E., Schoenfield, L., Schumacher, S. E., Seidman, J., Seth, S., Sethi, G., Sheth, M., Shi, Y., Shields, C., Shmulevich, I., Simons, J. V., Singh, A. D., Sipahimalani, P., Skelly, T., Sofia, H., Soloway, M. G., Song, X., Stern, M. H., Stuart, J., Sun, Q., Sun, H., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B. S., Thiessen, N., Thorsson, V., Tse, K., Veluvolu, U., Verhaak, R., Voet, D., Wan, Y., Wang, Z., Weinstein, J. N., Wilkerson, M. D., Williams, M. D., Wise, L., Woodman, S. E., Wong, T., Wu, Y., Yang, L., Yang, L., Zenklusen, J. C., Zhang, J., Zhang, H. & Zmuda, E., Aug 14 2017, In: Cancer cell. 32, 2, p. 204-220.e15

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567 Scopus citations

Oncogenic Kras drives invasion and maintains metastases in colorectal cancer

Boutin, A. T., Liao, W. T., Wang, M., Hwang, S. S., Karpinets, T. V., Cheung, H., Chu, G. C., Jiang, S., Hu, J., Chang, K., Vilar, E., Song, X., Zhang, J., Kopetz, S., Futreal, A., Wang, Y. A., Kwong, L. N. & DePinho, R. A., Feb 15 2017, In: Genes and Development. 31, 4, p. 370-382 13 p.

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Open Access

127 Scopus citations

Systematic analysis of telomere length and somatic alterations in 31 cancer types

Barthel, F. P., Wei, W., Tang, M., Martinez-Ledesma, E., Hu, X., Amin, S. B., Akdemir, K. C., Seth, S., Song, X., Wang, Q., Lichtenberg, T., Hu, J., Zhang, J., Zheng, S. & Verhaak, R. G. W., Mar 1 2017, In: Nature Genetics. 49, 3, p. 349-357 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

402 Scopus citations

2018

A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases

Zhang, Y., Yang, L., Kucherlapati, M., Chen, F., Hadjipanayis, A., Pantazi, A., Bristow, C. A., Lee, E. A., Mahadeshwar, H. S., Tang, J., Zhang, J., Seth, S., Lee, S., Ren, X., Song, X., Sun, H., Seidman, J., Luquette, L. J., Xi, R., Chin, L., & 5 othersProtopopov, A., Li, W., Park, P. J., Kucherlapati, R. & Creighton, C. J., Jul 10 2018, In: Cell Reports. 24, 2, p. 515-527 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

61 Scopus citations

Clearance of somatic mutations at remission and the risk of relapse in acute myeloid leukemia

Morita, K., Kantarjian, H. M., Wang, F., Yan, Y., Bueso-Ramos, C., Sasaki, K., Issa, G. C., Wang, S., Jorgensen, J., Song, X., Zhang, J., Tippen, S., Thornton, R., Coyle, M., Little, L., Gumbs, C., Pemmaraju, N., Daver, N., DiNardo, C. D., Konopleva, M., & 9 othersAndreeff, M., Ravandi, F., Cortes, J. E., Kadia, T., Jabbour, E., Garcia-Manero, G., Patel, K. P., Futreal, P. A. & Takahashi, K., Jun 20 2018, In: Journal of Clinical Oncology. 36, 18, p. 1788-1797 10 p.

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Open Access

145 Scopus citations

Clinical implications of cancer gene mutations in patients with chronic lymphocytic leukemia treated with lenalidomide

Takahashi, K., Hu, B., Wang, F., Yan, Y., Kim, E., Vitale, C., Patel, K. P., Strati, P., Gumbs, C., Little, L., Tippen, S., Song, X., Zhang, J., Jain, N., Thompson, P., Garcia-Manero, G., Kantarjian, H., Estrov, Z., Do, K. A., Keating, M., & 4 othersBurger, J. A., Wierda, W. G., Andrew Futreal, P. & Ferrajoli, A., Apr 19 2018, In: Blood. 131, 16, p. 1820-1832 13 p.

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Open Access

37 Scopus citations

Combined analysis of antigen presentation and T-cell recognition reveals restricted immune responses in melanoma

Kalaora, S., Wolf, Y., Feferman, T., Barnea, E., Greenstein, E., Reshef, D., Tirosh, I., Reuben, A., Patkar, S., Levy, R., Quinkhardt, J., Omokoko, T., Qutob, N., Golani, O., Zhang, J., Mao, X., Song, X., Bernatchez, C., Haymaker, C., Forget, M. A., & 13 othersCreasy, C., Greenberg, P., Carter, B. W., Cooper, Z. A., Rosenberg, S. A., Lotem, M., Sahin, U., Shakhar, G., Ruppin, E., Wargo, J. A., Friedman, N., Admon, A. & Samuels, Y., Nov 2018, In: Cancer discovery. 8, 11, p. 1366-1375 10 p.

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Open Access

73 Scopus citations

Genomic profiling of dedifferentiated liposarcoma compared to matched well-differentiated liposarcoma reveals higher genomic complexity and a common origin

Beird, H. C., Wu, C. C., Ingram, D. R., Wang, W. L., Alimohamed, A., Gumbs, C., Little, L., Song, X., Feig, B. W., Roland, C. L., Zhang, J., Benjamin, R. S., Hwu, P., Lazar, A. J., Futreal, P. A. & Somaiah, N., Apr 2018, In: Cold Spring Harbor Molecular Case Studies. 4, 2, a002386.

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Open Access

48 Scopus citations

Impact of the number of mutations in survival and response outcomes to hypomethylating agents in patients with myelodysplastic syndromes or myelodysplastic/myeloproliferative neoplasms

Montalban-Bravo, G., Takahashi, K., Patel, K., Wang, F., Xingzhi, S., Nogueras, G. M., Huang, X., Pierola, A. A., Jabbour, E., Colla, S., Gañan-Gomez, I., Borthakur, G., Daver, N., Estrov, Z., Kadia, T., Pemmaraju, N., Ravandi, F., Bueso-Ramos, C., Chamseddine, A., Konopleva, M., & 4 othersZhang, J., Kantarjian, H., Futreal, A. & Garcia-Manero, G., 2018, In: Oncotarget. 9, 11, p. 9714-9727 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

53 Scopus citations

Toll-like receptor 4: A target for chemoprevention of hepatocellular carcinoma in obesity and steatohepatitis

Nguyen, J., Jiao, J., Smoot, K., Watt, G. P., Zhao, C., Song, X., Stevenson, H. L., McCormick, J. B., Fisher-Hoch, S. P., Zhang, J., Andrew Futreal, P. & Beretta, L., Jun 29 2018, In: Oncotarget. 9, 50, p. 29495-29507 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

2019

A pilot study of pembrolizumab in smoldering myeloma: Report of the clinical, immune, and genomic analysis

Manasanch, E. E., Han, G., Mathur, R., Qing, Y., Zhang, Z., Lee, H., Weber, D. M., Amini, B., Berkova, Z., Eterovic, K., Zhang, S., Zhang, J., Song, X., Mao, X., Morgan, M., Feng, L., Baladandayuthapani, V., Futreal, A., Wang, L., Neelapu, S. S., & 1 othersOrlowski, R. Z., 2019, In: Blood Advances. 3, 15, p. 2400-2408 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

27 Scopus citations

Global impact of somatic structural variation on the DNA methylome of human cancers

Zhang, Y., Yang, L., Kucherlapati, M., Hadjipanayis, A., Pantazi, A., Bristow, C. A., Lee, E. A., Mahadeshwar, H. S., Tang, J., Zhang, J., Seth, S., Lee, S., Ren, X., Song, X., Sun, H., Seidman, J., Luquette, L. J., Xi, R., Chin, L., Protopopov, A., & 3 othersPark, P. J., Kucherlapati, R. & Creighton, C. J., Oct 15 2019, In: Genome biology. 20, 1, 209.

Research output: Contribution to journal › Article › peer-review

Open Access

23 Scopus citations

Late relapse in acute myeloid leukemia (AML): clonal evolution or therapy-related leukemia?

Yilmaz, M., Wang, F., Loghavi, S., Bueso-Ramos, C., Gumbs, C., Little, L., Song, X., Zhang, J., Kadia, T., Borthakur, G., Jabbour, E., Pemmaraju, N., Short, N., Garcia-Manero, G., Estrov, Z., Kantarjian, H., Futreal, A., Takahashi, K. & Ravandi, F., Feb 1 2019, In: Blood cancer journal. 9, 2, 7.

Research output: Contribution to journal › Article › peer-review

Open Access

62 Scopus citations

Xingzhi Song

Research output

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