Ben Raphael

2014

Detecting independent and recurrent copy number aberrations using interval graphs

Wu, H. T., Hajirasouliha, I. & Raphael, B. J., Jun 15 2014, In: Bioinformatics. 30, 12, p. I195-I203

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

Open Access

Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease

Brodsky, A. S., Fischer, A., Miller, D. H., Vang, S., MacLaughlan, S., Wu, H. T., Yu, J., Steinhoff, M., Collins, C., Smith, P. J. S., Raphael, B. J. & Brard, L., Apr 14 2014, In: PLoS One. 9, 4, e94476.

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

Open Access

41 Scopus citations

Integrated analysis of germline and somatic variants in ovarian cancer

Kanchi, K. L., Johnson, K. J., Lu, C., McLellan, M. D., Leiserson, M. D. M., Wendl, M. C., Zhang, Q., Koboldt, D. C., Xie, M., Kandoth, C., McMichael, J. F., Wyczalkowski, M. A., Larson, D. E., Schmidt, H. K., Miller, C. A., Fulton, R. S., Spellman, P. T., Mardis, E. R., Druley, T. E. & Graubert, T. A. & 4 others, Goodfellow, P. J., Raphael, B. J., Wilson, R. K. & Ding, L., Jan 22 2014, In: Nature communications. 5, 3156.

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

Open Access

169 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 others, Bristow, 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

Open Access

1327 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.

Princeton University

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

Open Access

810 Scopus citations

Open adjacencies and k-breaks: Detecting simultaneous rearrangements in cancer genomes

Weinreb, C., Oesper, L. & Raphael, B. J., Oct 17 2014, In: BMC genomics. 15, 6, S4.

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

Open Access

5 Scopus citations

Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data

Oesper, L., Satas, G. & Raphael, B. J., Dec 15 2014, In: Bioinformatics. 30, 24, p. 3532-3540 9 p.

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

Open Access

74 Scopus citations

2013

Comprehensivemolecular characterization of clear cell renal cell carcinoma

Creighton, C. J., Morgan, M., Gunaratne, P. H., Wheeler, D. A., Gibbs, R. A., Robertson, G., Chu, A., Beroukhim, R., Cibulskis, K., Signoretti, S., Vandin, F., Wu, H. T., Raphael, B. J., Verhaak, R. G. W., Tamboli, P., Torres-Garcia, W., Akbani, R., Weinstein, J. N., Reuter, V. & Hsieh, J. J. & 268 others, Brannon, A. R., Hakimi, A. A., Jacobsen, A., Ciriello, G., Reva, B., Ricketts, C. J., Linehan, W. M., Stuart, J. M., Rathmell, W. K., Hui, S., Laird, P. W., Muzny, D., Davis, C., Liu, X., Chang, K., Kakkar, N., Treviño, L. R., Benton, S., Reid, J. G., Morton, D., Doddapaneni, H., Yi, H., Lewis, L., Huyen, D., Kovar, C., Zhu, Y., Santibanez, J., Min, W., Hale, W., Kalra, D., Getz, G., Lawrence, M. S., Sougnez, C., Carter, S. L., Sivachenko, A., Lee, L., Stewart, C., Voet, D., Fisher, S., Gabriel, S. B., Lander, E., Schumacher, S. E., Tabak, B., Saksena, G., Onofrio, R. C., Cherniack, A. D., Gentry, J., Ardlie, K., Meyerson, M., Chun, H. J. E., Mungall, A. J., Sipahimalani, P., Stoll, D., Ally, A., Balasundaram, M., Butterfield, Y. S. N., Carlsen, R., Carter, C., Chuah, E., Coope, R. J. N., Dhalla, N., Gorski, S., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lebovitz, C., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Pleasance, E., Plettner, P., Schein, J. E., Shafiei, A., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R. J., Wye, N., Zhao, Y., Birol, I., Jones, S. J. M., Marra, M. A., Auman, J. T., Tan, D., Jones, C. D., Hoadley, K. A., Mieczkowski, P. A., Mose, L. E., Jefferys, S. R., Topal, M. D., Liquori, C., Turman, Y. J., Yan, S., Waring, S., Buda, E., Walsh, J., Wu, J., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Balu, S., Parker, J. S., Hayes, D. N., Perou, C. M., Kucherlapati, R., Park, P., Triche, T., Weisenberger, D. J., Lai, P. H., Bootwalla, M. S., Maglinte, D. T., Mahurkar, S., Berman, B. P., Van Den Berg, D. J., Cope, L., Baylin, S. B., Noble, M. S., DiCara, D., Zhang, H., Cho, J., Heiman, D. I., Gehlenborg, N., Mallard, W., Pei, L., Frazer, S., Stojanov, P., Liu, Y., Zhou, L., Kim, J., Chin, L., Benz, C., Yau, C., Reynolds, S. M., Shmulevich, I., Vegesna, R., Kim, H., Wei, Z., Cogdell, D., Jonasch, E., Ding, Z., Lu, Y., Zhang, N., Unruh, A. K., Casasent, T. D., Wakefield, C., Tsavachidou, D., Mills, G. B., Gao, J., Cerami, E., Gross, B., Aksoy, B. A., Sinha, R., Weinhold, N., Sumer, S. O., Taylor, B. S., Shen, R., Ostrovnaya, I., Berger, M. F., Ladanyi, M., Sander, C., Fei, S. S., Stout, A., Spellman, P. T., Rubin, D. L., Liu, T. T., Sam, N., Paull, E. O., Carlin, D., Goldstein, T., Waltman, P., Ellrott, K., Jing, Z., Haussler, D., Xiao, W., Shelton, C., Gardner, J., Penny, R., Sherman, M., Mallery, D., Morris, S., Paulauskis, J., Burnett, K., Shelton, T., Kaelin, W. G., Choueiri, T., Atkins, M. B., Curley, E., Tickoo, S., Thorne, L., Boice, L., Mei, H., Fisher, J. C., Vocke, C. D., Peterson, J., Worrell, R., Merino, M. J., Schmidt, L. S., Czerniak, B. A., Aldape, K. D., Wood, C. G., Boyd, J., Weaver, J. E., Iacocca, M. V., Petrelli, N., Witkin, G., Brown, J., Czerwinski, C., Huelsenbeck-Dill, L., Rabeno, B., Myers, J., Morrison, C., Bergsten, J., Eckman, J., Harr, J., Smith, C., Tucker, K., Zach, L. A., Bshara, W., Gaudioso, C., Dhir, R., Maranchie, J., Nelson, J., Parwani, A., Potapova, C. O., Fedosenko, K., Cheville, J. C., Thompson, R. H., Mosquera, J. M., Rubin, M. A., Blute, M. L., Pihl, T., Jensen, M., Sfeir, R., Kahn, A., Chu, A., Kothiyal, P., Snyder, E., Pontius, J., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D., Nicholls, M., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P., Alonso, S., Sanbhadti, R., Barletta, S., Pot, D., Sheth, M., Demchok, J. A., Davidsen, T., Wang, Z., Yang, L., Tarnuzzer, R. W., Zhang, J., Eley, G., Ferguson, M. L., Mills Shaw, K. R., Guyer, M. S., Ozenberger, B. A. & Sofia, H. J., 2013, In: Nature. 499, 7456, p. 43-49 7 p.

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

Open Access

1842 Scopus citations

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

Ley, T. J., Miller, C., Ding, L., Raphael, B. J., Mungall, A. J., Robertson, G., Hoadley, K., Triche, T. J., Laird, P. W., Baty, J. D., Fulton, L. L., Fulton, R., Heath, S. E., Kalicki-Veizer, J., Kandoth, C., Klco, J. M., Koboldt, D. C., Kanchi, K. L., Kulkarni, S. & Lamprecht, T. L. & 119 others, Larson, D. E., Lin, G., Lu, C., McLellan, M. D., McMichael, J. F., Payton, J., Schmidt, H., Spencer, D. H., Tomasson, M. H., Wallis, J. W., Wartman, L. D., Watson, M. A., Welch, J., Wendl, M. C., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Chiu, R., Chu, A., Chuah, E., Chun, H. J., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A., Jones, S., Karsan, A., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, K., Parker, J., Pleasance, E., Plettner, P., Schein, J., Stoll, D., Swanson, L., Tam, A., Thiessen, N., Varhol, R., Wye, N., Zhao, Y., Gabriel, S., Getz, G., Sougnez, C., Zou, L., Leiserson, M. D. M., Vandin, F., Wu, H. T., Applebaum, F., Baylin, S. B., Akbani, R., Broom, B. M., Chen, K., Motter, T. C., Nguyen, K., Weinstein, J. N., Zhang, N., Ferguson, M. L., Adams, C., Black, A., Bowen, J., Gastier-Foster, J., Grossman, T., Lichtenberg, T., Wise, L., Davidsen, T., Demchok, J. A., Mills Shaw, K. R., Sheth, M., Sofia, H. J., Yang, L., Downing, J. R., Eley, G., Alonso, S., Ayala, B., Baboud, J., Backus, M., Barletta, S. P., Berton, D. L., Chu, A. L., Girshik, S., Jensen, M. A., Kahn, A., Kothiyal, P., Nicholls, M. C., Pihl, T. D., Pot, D. A., Raman, R., Sanbhadti, R. N., Snyder, E. E., Srinivasan, D., Walton, J., Wan, Y., Wang, Z., Issa, J. P. J., Beau, M. L., Carroll, M., Kantarjian, H., Kornblau, S., Bootwalla, M. S., Lai, P. H., Shen, H., Van Den Berg, D. J., Weisenberger, D. J., Link, D. C., Walter, M. J., Ozenberger, B. A., Mardis, E. R., Westervelt, P., Graubert, T. A., DiPersio, J. F. & Wilson, R. K., May 30 2013, In: New England Journal of Medicine. 368, 22, p. 2059-2074 16 p.

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

Open Access

2648 Scopus citations

Mutational landscape and significance across 12 major cancer types

Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., Xie, M., Zhang, Q., McMichael, J. F., Wyczalkowski, M. A., Leiserson, M. D. M., Miller, C. A., Welch, J. S., Walter, M. J., Wendl, M. C., Ley, T. J., Wilson, R. K., Raphael, B. J. & Ding, L., 2013, In: Nature. 502, 7471, p. 333-339 7 p.

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

Open Access

2391 Scopus citations

Simultaneous Identification of Multiple Driver Pathways in Cancer

Leiserson, M. D. M., Blokh, D., Sharan, R. & Raphael, B. J., May 2013, In: PLoS computational biology. 9, 5, e1003054.

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

Open Access

147 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 others, Chun, 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

Open Access

2947 Scopus citations

The mutational landscape of adenoid cystic carcinoma

Ho, A. S., Kannan, K., Roy, D. M., Morris, L. G. T., Ganly, I., Katabi, N., Ramaswami, D., Walsh, L. A., Eng, S., Huse, J. T., Zhang, J., Dolgalev, I., Huberman, K., Heguy, A., Viale, A., Drobnjak, M., Leversha, M. A., Rice, C. E., Singh, B. & Iyer, N. G. & 18 others, Leemans, C. R., Bloemena, E., Ferris, R. L., Seethala, R. R., Gross, B. E., Liang, Y., Sinha, R., Peng, L., Raphael, B. J., Turcan, S., Gong, Y., Schultz, N., Kim, S., Chiosea, S., Shah, J. P., Sander, C., Lee, W. & Chan, T. A., Jul 2013, In: Nature genetics. 45, 7, p. 791-798 8 p.

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

Open Access

258 Scopus citations

THetA: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

Oesper, L., Mahmoody, A. & Raphael, B. J., 2013, In: Genome biology. 14, 7, R80.

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

Open Access

142 Scopus citations

2012

Algorithms and genome sequencing: Identifying driver pathways in cancer

Vandin, F., Upfal, E. & Raphael, B. J., Mar 2012, Computer, 45, 3, p. 39-46 8 p.

Research output: Contribution to specialist publication › Article

8 Scopus citations

An integrative probabilistic model for identification of structural variation in sequencing data

Sindi, S. S., Önal, S., Peng, L. C., Wu, H. T. & Raphael, B. J., Mar 27 2012, In: Genome biology. 13, 3, R22.

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

Open Access

94 Scopus citations

Chapter 6: Structural Variation and Medical Genomics

Raphael, B. J., Dec 2012, In: PLoS computational biology. 8, 12, e1002821.

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

Open Access

23 Scopus citations

De novo discovery of mutated driver pathways in cancer

Vandin, F., Upfal, E. & Raphael, B. J., Feb 2012, In: Genome research. 22, 2, p. 375-385 11 p.

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

Open Access

266 Scopus citations

Finding driver pathways in cancer: Models and algorithms

Vandin, F., Upfal, E. & Raphael, B. J., Sep 6 2012, In: Algorithms for Molecular Biology. 7, 1, 23.

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

Open Access

15 Scopus citations

Identification of polymorphic inversions from genotypes

Cáceres, A., Sindi, S. S., Raphael, B. J., Cáceres, M. & González, J. R., Feb 9 2012, In: BMC bioinformatics. 13, 1, 28.

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

Open Access

Quantitative Phosphoproteomics Reveals SLP-76 Dependent Regulation of PAG and Src Family Kinases in T Cells

Cao, L., Ding, Y., Hung, N., Yu, K., Ritz, A., Raphael, B. J. & Salomon, A. R., Oct 11 2012, In: PLoS One. 7, 10, e46725.

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

Open Access

19 Scopus citations

Reconstructing cancer genomes from paired-end sequencing data.

Oesper, L., Ritz, A., Aerni, S. J., Drebin, R. & Raphael, B. J., 2012, In: BMC bioinformatics. 13 Suppl 6, p. S10 S10.

Princeton University

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

Open Access

29 Scopus citations

Reconstructing genome mixtures from partial adjacencies.

Mahmoody, A., Kahn, C. L. & Raphael, B. J., 2012, In: Unknown Journal. 13 Suppl 19, p. S9 S9.

Princeton University

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

Open Access

4 Scopus citations

The mutational landscape of lethal castration-resistant prostate cancer

Grasso, C. S., Wu, Y. M., Robinson, D. R., Cao, X., Dhanasekaran, S. M., Khan, A. P., Quist, M. J., Jing, X., Lonigro, R. J., Brenner, J. C., Asangani, I. A., Ateeq, B., Chun, S. Y., Siddiqui, J., Sam, L., Anstett, M., Mehra, R., Prensner, J. R., Palanisamy, N. & Ryslik, G. A. & 7 others, Vandin, F., Raphael, B. J., Kunju, L. P., Rhodes, D. R., Pienta, K. J., Chinnaiyan, A. M. & Tomlins, S. A., Jul 12 2012, In: Nature. 487, 7406, p. 239-243 5 p.

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

Open Access

1505 Scopus citations

2011

Algorithms for detecting significantly mutated pathways in cancer

Vandin, F., Upfal, E. & Raphael, B. J., Mar 1 2011, In: Journal of Computational Biology. 18, 3, p. 507-522 16 p.

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

256 Scopus citations

Detection of recurrent rearrangement breakpoints from copy number data

Ritz, A., Paris, P. L., Ittmann, M. M., Collins, C. & Raphael, B. J., Apr 21 2011, In: BMC bioinformatics. 12, 114.

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

Open Access

17 Scopus citations

Integrated genomic analyses of ovarian carcinoma

Bell, D., Berchuck, A., Birrer, M., Chien, J., Cramer, D. W., Dao, F., Dhir, R., Disaia, P., Gabra, H., Glenn, P., Godwin, A. K., Gross, J., Hartmann, L., Huang, M., Huntsman, D. G., Iacocca, M., Imielinski, M., Kalloger, S., Karlan, B. Y. & Levine, D. A. & 240 others, Mills, G. B., Morrison, C., Mutch, D., Olvera, N., Orsulic, S., Park, K., Petrelli, N., Rabeno, B., Rader, J. S., Sikic, B. I., Smith-Mccune, K., Sood, A. K., Bowtell, D., Penny, R., Testa, J. R., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Gunaratne, P., Hawes, A. C., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Santibanez, J., Reid, J. G., Trevino, L. R., Wu, Y. Q., Wang, M., Muzny, D. M., Wheeler, D. A., Gibbs, R. A., Getz, G., Lawrence, M. S., Cibulskis, K., Sivachenko, A. Y., Sougnez, C., Voet, D., Wilkinson, J., Bloom, T., Ardlie, K., Fennell, T., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., Koboldt, D. C., McLellan, M. D., Wylie, T., Walker, J., O'Laughlin, M., Dooling, D. J., Fulton, L., Abbott, R., Dees, N. D., Zhang, Q., Kandoth, C., Wendl, M., Schierding, W., Shen, D., Harris, C. C., Schmidt, H., Kalicki, J., Delehaunty, K. D., Fronick, C. C., Demeter, R., Cook, L., Wallis, J. W., Lin, L., Magrini, V. J., Hodges, J. S., Eldred, J. M., Smith, S. M., Pohl, C. S., Vandin, F., Raphael, B. J., Weinstock, G. M., Mardis, E. R., Wilson, R. K., Meyerson, M., Winckler, W., Verhaak, R. G. W., Carter, S. L., Mermel, C. H., Saksena, G., Nguyen, H., Onofrio, R. C., Hubbard, D., Gupta, S., Crenshaw, A., Ramos, A. H., Chin, L., Protopopov, A., Zhang, J., Kim, T. M., Perna, I., Xiao, Y., Zhang, H., Ren, G., Sathiamoorthy, N., Park, R. W., Lee, E., Park, P. J., Kucherlapati, R., Absher, D. M., Waite, L., Sherlock, G., Brooks, J. D., Li, J. Z., Xu, J., Myers, R. M., Laird, P. W., Cope, L., Herman, J. G., Shen, H., Weisenberger, D. J., Noushmehr, H., Pan, F., Triche, T., Berman, B. P., Van Den Berg, D. J., Buckley, J., Baylin, S. B., Spellman, P. T., Purdom, E., Neuvial, P., Bengtsson, H., Jakkula, L. R., Durinck, S., Han, J., Dorton, S., Marr, H., Choi, Y. G., Wang, V., Wang, N. J., Ngai, J., Conboy, J. G., Parvin, B., Feiler, H. S., Speed, T. P., Gray, J. W., Socci, N. D., Liang, Y., Taylor, B. S., Schultz, N., Borsu, L., Lash, A. E., Brennan, C., Viale, A., Sander, C., Ladanyi, M., Hoadley, K. A., Meng, S., Du, Y., Shi, Y., Li, L., Turman, Y. J., Zang, D., Helms, E. B., Balu, S., Zhou, X., Wu, J., Topal, M. D., Hayes, D. N., Perou, C. M., Wu, C. J., Shukla, S., Sivachenko, A., Jing, R., Liu, Y., Noble, M., Carter, H., Kim, D., Karchin, R., Korkola, J. E., Heiser, L. M., Cho, R. J., Hu, Z., Cerami, E., Olshen, A., Reva, B., Antipin, Y., Shen, R., Mankoo, P., Sheridan, R., Ciriello, G., Chang, W. K., Bernanke, J. A., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Sanborn, J. Z., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Wilkerson, M. D., Zhang, N., Akbani, R., Baggerly, K. A., Yung, W. K., Weinstein, J. N., Shelton, T., Grimm, D., Hatfield, M., Morris, S., Yena, P., Rhodes, P., Sherman, M., Paulauskis, J., Millis, S., Kahn, A., Greene, J. M., Sfeir, R., Jensen, M. A., Chen, J., Whitmore, J., Alonso, S., Jordan, J., Chu, A., Barker, A., Compton, C., Eley, G., Ferguson, M., Fielding, P., Gerhard, D. S., Myles, R., Schaefer, C., Mills Shaw, K. R., Vaught, J., Vockley, J. B., Good, P. J., Guyer, M. S., Ozenberger, B., Peterson, J. & Thomson, E., Jun 30 2011, In: Nature. 474, 7353, p. 609-615 7 p.

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

4476 Scopus citations

Integrated genomics of ovarian xenograft tumor progression and chemotherapy response

Stuckey, A., Fischer, A., Miller, D. H., Hillenmeyer, S., Kim, K. K., Ritz, A., Singh, R. K., Raphael, B. J., Brard, L. & Brodsky, A. S., Jul 22 2011, In: BMC cancer. 11, 308.

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

Open Access

9 Scopus citations

Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes

Lim, K. H., Ferraris, L., Filloux, M. E., Raphael, B. J. & Fairbrother, W. G., Jul 5 2011, In: Proceedings of the National Academy of Sciences of the United States of America. 108, 27, p. 11093-11098 6 p.

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

Open Access

166 Scopus citations

2010

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes

Kahn, C. L., Mozes, S. & Raphael, B. J., Jan 4 2010, In: Algorithms for Molecular Biology. 5, 1, 11.

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

Open Access

4 Scopus citations

Gremlin: An interactive visualization model for analyzing genomic rearrangements

O'Brien, T., Ritz, A., Raphael, B. & Laidlaw, D., 2010, In: IEEE Transactions on Visualization and Computer Graphics. 16, 6, p. 918-926 9 p., 5613428.

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

17 Scopus citations

Identification and frequency estimation of inversion polymorphisms from haplotype data

Sindi, S. S. & Raphael, B. J., Mar 1 2010, In: Journal of Computational Biology. 17, 3, p. 517-531 15 p.

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

16 Scopus citations

Optimizing PCR assays for DNA-based cancer diagnostics

Bashir, A., Lu, Q., Carson, D., Raphael, B. J., Liu, Y. T. & Bafna, V., Mar 1 2010, In: Journal of Computational Biology. 17, 3, p. 369-381 13 p.

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

Open Access

3 Scopus citations

Parsimony and likelihood reconstruction of human segmental duplications

Kahn, C. L., Hristov, B. H. & Raphael, B. J., Sep 4 2010, In: Bioinformatics. 26, 18, p. i446-i452 btq368.

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

Open Access

3 Scopus citations

Structural variation analysis with strobe reads

Ritz, A., Bashir, A. & Raphael, B. J., Apr 8 2010, In: Bioinformatics. 26, 10, p. 1291-1298 8 p., btq153.

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

Open Access

26 Scopus citations

2009

A geometric approach for classification and comparison of structural variants

Sindi, S., Helman, E., Bashir, A. & Raphael, B. J., 2009, In: Bioinformatics. 25, 12, p. i222-i230

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

Open Access

121 Scopus citations

A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation

Nguyen, V., Cao, L., Lin, J. T., Hung, N., Ritz, A., Yu, K., Jianu, R., Ulin, S. P., Raphael, B. J., Laidlaw, D. H., Brossay, L. & Salomon, A. R., 2009, In: Molecular and Cellular Proteomics. 8, 11, p. 2418-2431 14 p.

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

Open Access

61 Scopus citations

Computational identification of CDR3 sequence archetypes among immunoglobulin sequences in chronic lymphocytic leukemia

Messmer, B. T., Raphael, B. J., Aerni, S. J., Widhopf, G. F., Rassenti, L. Z., Gribben, J. G., Kay, N. E. & Kipps, T. J., Mar 2009, In: Leukemia Research. 33, 3, p. 368-376 9 p.

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

Open Access

19 Scopus citations

Discovery of phosphorylation motif mixtures in phosphoproteomics data

Ritz, A., Shakhnarovich, G., Salomon, A. R. & Raphael, B. J., Jan 2009, In: Bioinformatics. 25, 1, p. 14-21 8 p.

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

Open Access

29 Scopus citations

2008

Analysis of segmental duplications via duplication distance

Kahn, C. L. & Raphael, B. J., Aug 2008, In: Bioinformatics. 24, 16, p. i133-i138

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

Open Access

10 Scopus citations

A sequence-based survey of the complex structural organization of tumor genomes

Raphael, B. J., Volik, S., Yu, P., Wu, C., Huang, G., Linardopoulou, E. V., Trask, B. J., Waldman, F., Costello, J., Pienta, K. J., Mills, G. B., Bajsarowicz, K., Kobayashi, Y., Sridharan, S., Paris, P. L., Tao, Q., Aerni, S. J., Brown, R. P., Bashir, A. & Gray, J. W. & 6 others, Cheng, J. F., de Jong, P., Nefedov, M., Ried, T., Padilla-Nash, H. M. & Collins, C. C., Mar 25 2008, In: Genome biology. 9, 3, R59.

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

Open Access

31 Scopus citations

Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer

Bashir, A., Volik, S., Collins, C., Bafna, V. & Raphael, B. J., Apr 2008, In: PLoS computational biology. 4, 4, e1000051.

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

Open Access

56 Scopus citations

2007

Optimization of primer design for the detection of variable genomic lesions in cancer

Bashir, A., Liu, Y. T., Raphael, B. J., Carson, D. & Bafna, V., Nov 2007, In: Bioinformatics. 23, 21, p. 2807-2815 9 p.

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

Open Access

16 Scopus citations

Quantitative time-resolved phosphoproteomic analysis of mast cell signaling

Cao, L., Yu, K., Banh, C., Nguyen, V., Ritz, A., Raphael, B. J., Kawakami, Y., Kawakami, T. & Salomon, A. R., Nov 1 2007, In: Journal of Immunology. 179, 9, p. 5864-5876 13 p.

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

Open Access

58 Scopus citations

The Sorcerer II global ocean sampling expedition: Expanding the universe of protein families

Yooseph, S., Sutton, G., Rusch, D. B., Halpern, A. L., Williamson, S. J., Remington, K., Eisen, J. A., Heidelberg, K. B., Manning, G., Li, W., Jaroszewski, L., Cieplak, P., Miller, C. S., Li, H., Mashiyama, S. T., Joachimiak, M. P., Van Belle, C., Chandonia, J. M., Soergel, D. A. & Zhai, Y. & 13 others, Natarajan, K., Lee, S., Raphael, B. J., Bafna, V., Friedman, R., Brenner, S. E., Godzik, A., Eisenberg, D., Dixon, J. E., Taylor, S. S., Strausberg, R. L., Frazier, M. & Venter, J. C., Mar 2007, In: PLoS Biology. 5, 3, p. 432-466 35 p.

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

Open Access

575 Scopus citations

2006

AliWABA: Alignment on the web through an A-Bruijn approach

Jones, N. C., Zhi, D. & Raphael, B. J., Jul 2006, In: Nucleic acids research. 34, WEB. SERV. ISS., p. W613-W616

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

Open Access

4 Scopus citations

Decoding the fine-scale structure of a breast cancer genome and transcriptome

Volik, S., Raphael, B. J., Huang, G., Stratton, M. R., Bignel, G., Murnane, J., Brebner, J. H., Bajsarowicz, K., Paris, P. L., Tao, Q., Kowbel, D., Lapuk, A., Shagin, D. A., Shagina, I. A., Gray, J. W., Cheng, J. F., De Jong, P. J., Pevzner, P. & Collins, C., Mar 2006, In: Genome research. 16, 3, p. 394-404 11 p.

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

Open Access