Ben Raphael
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Ben Raphael

Princeton University

20032025

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  • 2024

    Current and future directions in network biology

    Zitnik, M., Li, M. M., Wells, A., Glass, K., Gysi, D. M., Krishnan, A., Murali, T. M., Radivojac, P., Roy, S., Baudot, A., Bozdag, S., Chen, D. Z., Cowen, L., Devkota, K., Gitter, A., Gosline, S. J. C., Gu, P., Guzzi, P. H., Huang, H. & Jiang, M. & 17 others, Kesimoglu, Z. N., Koyuturk, M., Ma, J., Pico, A. R., Przulj, N., Przytycka, T. M., Raphael, B. J., Ritz, A., Sharan, R., Shen, Y., Singh, M., Slonim, D. K., Tong, H., Yang, X. H., Yoon, B. J., Yu, H. & Milenkovic, T., 2024, In: Bioinformatics Advances. 4, 1, vbae099.

    Princeton University

    Research output: Contribution to journal › Review article › peer-review

    Open Access
  • 2020

    Eleven grand challenges in single-cell data science

    Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., Pinello, L., Skums, P., Stamatakis, A., Attolini, C. S. O., Aparicio, S., Baaijens, J., Balvert, M., Barbanson, B. D., Cappuccio, A. & Corleone, G. & 31 others, Dutilh, B. E., Florescu, M., Guryev, V., Holmer, R., Jahn, K., Lobo, T. J., Keizer, E. M., Khatri, I., Kielbasa, S. M., Korbel, J. O., Kozlov, A. M., Kuo, T. H., Lelieveldt, B. P. F., Mandoiu, I. I., Marioni, J. C., Marschall, T., Mölder, F., Niknejad, A., Raczkowski, L., Reinders, M., Ridder, J. D., Saliba, A. E., Somarakis, A., Stegle, O., Theis, F. J., Yang, H., Zelikovsky, A., McHardy, A. C., Raphael, B. J., Shah, S. P. & Schönhuth, A., Feb 7 2020, In: Genome biology. 21, 1, 31.

    Princeton University

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    93 Scopus citations
  • 2017

    Network propagation: A universal amplifier of genetic associations

    Cowen, L., Ideker, T., Raphael, B. J. & Sharan, R., Sep 1 2017, In: Nature Reviews Genetics. 18, 9, p. 551-562 12 p.

    Princeton University

    Research output: Contribution to journal › Review article › peer-review

    181 Scopus citations
  • 2015

    Pathway and network analysis of cancer genomes

    Creixell, P., Reimand, J., Haider, S., Wu, G., Shibata, T., Vazquez, M., Mustonen, V., Gonzalez-Perez, A., Pearson, J., Sander, C., Raphael, B. J., Marks, D. S., Ouellette, B. F. F., Valencia, A., Bader, G. D., Boutros, P. C., Stuart, J. M., Linding, R., Lopez-Bigas, N. & Stein, L. D., Jun 30 2015, In: Nature Methods. 12, 7, p. 615-621 7 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    183 Scopus citations
  • 2014

    Expanding the computational toolbox for mining cancer genomes

    Ding, L., Wendl, M. C., McMichael, J. F. & Raphael, B. J., Aug 2014, In: Nature Reviews Genetics. 15, 8, p. 556-570 15 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    128 Scopus citations

  • Identifying driver mutations in sequenced cancer genomes: Computational approaches to enable precision medicine

    Raphael, B. J., Dobson, J. R., Oesper, L. & Vandin, F., Jan 30 2014, In: Genome Medicine. 6, 1, 5.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    113 Scopus citations
  • 2013

    Advances for studying clonal evolution in cancer

    Ding, L., Raphael, B. J., Chen, F. & Wendl, M. C., Nov 1 2013, In: Cancer Letters. 340, 2, p. 212-219 8 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    47 Scopus citations

  • Network analysis of GWAS data

    Leiserson, M. D. M., Eldridge, J. V., Ramachandran, S. & Raphael, B. J., Dec 2013, In: Current Opinion in Genetics and Development. 23, 6, p. 602-610 9 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    56 Scopus citations
  • 2012

    The genetics of alcohol dependence: Advancing towards systems-based approaches

    Palmer, R. H. C., McGeary, J. E., Francazio, S., Raphael, B. J., Lander, A. D., Heath, A. C. & Knopik, V. S., Oct 1 2012, In: Drug and Alcohol Dependence. 125, 3, p. 179-191 13 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    22 Scopus citations
  • 2010

    International network of cancer genome projects

    Hudson, T. J., Anderson, W., Aretz, A., Barker, A. D., Bell, C., Bernabé, R. R., Bhan, M. K., Calvo, F., Eerola, I., Gerhard, D. S., Guttmacher, A., Guyer, M., Hemsley, F. M., Jennings, J. L., Kerr, D., Klatt, P., Kolar, P., Kusuda, J., Lane, D. P. & Laplace, F. & 241 others, Lu, Y., Nettekoven, G., Ozenberger, B., Peterson, J., Rao, T. S., Remacle, J., Schafer, A. J., Shibata, T., Stratton, M. R., Vockley, J. G., Watanabe, K., Yang, H., Yuen, M. M. F., Knoppers, B. M., Bobrow, M., Cambon-Thomsen, A., Dressler, L. G., Dyke, S. O. M., Joly, Y., Kato, K., Kennedy, K. L., Nicolás, P., Parker, M. J., Rial-Sebbag, E., Romeo-Casabona, C. M., Shaw, K. M., Wallace, S., Wiesner, G. L., Zeps, N., Lichter, P., Biankin, A. V., Chabannon, C., Chin, L., Clément, B., Alava, E. D., Degos, F., Ferguson, M. L., Geary, P., Hayes, D. N., Johns, A. L., Kasprzyk, A., Nakagawa, H., Penny, R., Piris, M. A., Sarin, R., Scarpa, A., De Vijver, M. V., Futreal, P. A., Aburatani, H., Bayés, M., Bowtell, D. D. L., Campbel, P. J., Estivill, X., Grimmond, S. M., Gut, I., Hirst, M., López-Otý́n, C., Majumder, P., Marra, M., McPherson, J. D., Ning, Z., Puente, X. S., Ruan, Y., Stunnenberg, H. G., Swerdlow, H., Velculescu, V. E., Wilson, R. K., Xue, H. H., Yang, L., Spellman, P. T., Bader, G. D., Boutros, P. C., Flicek, P., Getz, G., Guigó, R., Guo, G., Haussler, D., Heath, S., Hubbard, T. J., Jiang, T., Jones, S. M., Li, Q., López-Bigas, N., Luo, R., Muthuswamy, L., Ouellette, B. F. F., Pearson, J. V., Quesada, V., Raphael, B. J., Sander, C., Speed, T. P., Stein, L. D., Stuart, J. M., Teague, J. W., Totoki, Y., Tsunoda, T., Valencia, A., Wheeler, D. A., Wu, H., Zhao, S., Zhou, G., Lathrop, M., Thomas, G., Yoshida, T., Axton, M., Gunter, C., Miller, L. J., Zhang, J., Haider, S. A., Wang, J., Yung, C. K., Cross, A., Liang, Y., Gnaneshan, S., Guberman, J., Hsu, J., Chalmers, D. R. C., Hasel, K. W., Kaan, T. S. H., Lowrance, W. W., Masui, T., Rodriguez, L. L., Vergely, C., Bowtel, D. D. L., Cloonan, N., DeFazio, A., Eshleman, J. R., Etemadmoghadam, D., Gardiner, B. A., Kench, J. G., Sutherland, R. L., Tempero, M. A., Waddell, N. J., Wilson, P. J., Gallinger, S., Tsao, M. S., Shaw, P. A., Petersen, G. M., Mukhopadhyay, D., DePinho, R. A., Thayer, S., Shazand, K., Beck, T., Sam, M., Timms, L., Ballin, V., Ji, J., Zhang, X., Chen, F., Hu, X., Yang, Q., Tian, G., Zhang, L., Xing, X., Li, X., Zhu, Z., Yu, Y., Yu, J., Tost, J., Brennan, P., Holcatova, I., Zaridze, D., Brazma, A., Egevad, L., Prokhortchouk, E., Banks, R. E., Uhlén, M., Viksna, J., Ponten, F., Skryabin, K., Futrea, P. A., Birney, E., Borg, A., Børresen-Dale, A. L., Caldas, C., Foekens, J. A., Martin, S., Reis-Filho, J. S., Richardson, A. L., Sotiriou, C., Veer, L. V. T., Birnbaum, D., Blanche, H., Boucher, P., Boyault, S., Masson-Jacquemier, J. D., Pauporté, I., Pivot, X., Vincent-Salomon, A., Tabone, E., Theillet, C., Treilleux, I., Bioulac-Sage, P., Decaens, T., OiseDegos, F., Franco, D., Gut, M., Samuel, D., Zucman-Rossi, J., Eils, R., Brors, B., Korbe, J. O., Korshunov, A., Landgraf, P., Lehrach, H., Pfister, S., Radlwimmer, B., Reifenberger, G., Taylor, M. D., Kalle, C. V., Majumder, P. P., Rao, T. S., Pederzoli, P., Lawlor, R. T., Delledonne, M., Bardelli, A., Gress, T., Klimstra, D., Zamboni, G., Nakamura, Y., Miyano, S., Fujimoto, A., Campo, E., Sanjosé, S. D., Montserrat, E., González-Dý́az, M., Jares, P., Himmelbaue, H., Bea, S., Aparicio, S., Easton, D. F., Collins, F. S., Compton, C. C., Lander, E. S., Burke, W., Green, A. R., Hamilton, S. R., Kallioniemi, O. P., Ley, T. J., Liu, E. T. & Wainwright, B. J., Apr 15 2010, In: Nature. 464, 7291, p. 993-998 6 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    1466 Scopus citations