Rehan Akbani

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Rehan Akbani

Professor

 https://orcid.org/0000-0003-2686-7721
    Calculated based on number of publications stored in Pure and citations from Scopus
    20032023

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    • Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway

      TCGA Research Network, Feb 2 2021, In: Cell Reports. 34, 5, 108707.

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

      Open Access
      13 Scopus citations

    • Tumour angiogenesis regulation by the miR-200 family

      Pecot, C. V., Rupaimoole, R., Yang, D., Akbani, R., Ivan, C., Lu, C., Wu, S., Han, H. D., Shah, M. Y., Rodriguez-Aguayo, C., Bottsford-Miller, J., Liu, Y., Kim, S. B., Unruh, A., Gonzalez-Villasana, V., Huang, L., Zand, B., Moreno-Smith, M., Mangala, L. S., Taylor, M., & 17 othersDalton, H. J., Sehgal, V., Wen, Y., Kang, Y., Baggerly, K. A., Lee, J. S., Ram, P. T., Ravoori, M. K., Kundra, V., Zhang, X., Ali-Fehmi, R., Gonzalez-Angulo, A. M., Massion, P. P., Calin, G. A., Lopez-Berestein, G., Zhang, W. & Sood, A. K., Sep 10 2013, In: Nature communications. 4, 2427.

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

      Open Access
      340 Scopus citations

    • Tumor-intrinsic SIRPA promotes sensitivity to checkpoint inhibition immunotherapy in melanoma

      Zhou, Z., Chen, M. J. M., Luo, Y., Mojumdar, K., Peng, X., Chen, H., Kumar, S. V., Akbani, R., Lu, Y. & Liang, H., Nov 14 2022, In: Cancer cell. 40, 11, p. 1324-1340.e8

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

      Open Access
      12 Scopus citations

    • The somatic genomic landscape of glioblastoma

      TCGA Research Network, Oct 10 2013, In: Cell. 155, 2, p. 462 1 p.

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

      3492 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

      581 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

      Open Access
      2130 Scopus citations

    • The landscape of viral associations in human cancers

      PCAWG Pathogens & PCAWG Consortium, Mar 1 2020, In: Nature Genetics. 52, 3, p. 320-330 11 p.

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

      Open Access
      219 Scopus citations

    • The Integrated Genomic Landscape of Thymic Epithelial Tumors

      The Cancer Genome Atlas Network, Feb 12 2018, In: Cancer cell. 33, 2, p. 244-258.e10

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

      Open Access
      250 Scopus citations

    • The Immune Landscape of Cancer

      The Cancer Genome Atlas Research Network, Apr 17 2018, In: Immunity. 48, 4, p. 812-830.e14

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

      Open Access
      3139 Scopus citations

    • The Cancer Genome Atlas Project on Muscle-invasive Bladder Cancer

      on behalf of the TCGA Muscle Invasive Bladder Cancer Analysis Working Group, Aug 1 2015, In: European Urology Focus. 1, 1, p. 94-95 2 p.

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

      7 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

      5099 Scopus citations

    • The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

      The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 313-326.e5

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

      Open Access
      514 Scopus citations

    • TCPA v3.0: An integrative platform to explore the pan-cancer analysis of functional proteomic data

      Chen, M. J. M., Li, J., Wang, Y., Akbani, R., Lu, Y., Mills, G. B. & Liang, H., 2019, In: Molecular and Cellular Proteomics. 18, 8, p. S15-S25

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

      Open Access
      42 Scopus citations

    • TCGASpliceSeq a compendium of alternative mRNA splicing in cancer

      Ryan, M., Wong, W. C., Brown, R., Akbani, R., Su, X., Broom, B., Melott, J. & Weinstein, J., 2016, In: Nucleic acids research. 44, D1, p. D1018-D1022

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

      Open Access
      240 Scopus citations

    • Systematic Analysis of Splice-Site-Creating Mutations in Cancer

      The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 270-281.e3

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

      Open Access
      159 Scopus citations

    • Spectral clustering via sparse graph structure learning with application to proteomic signaling networks in cancer

      Banerjee, S., Akbani, R. & Baladandayuthapani, V., Apr 2019, In: Computational Statistics and Data Analysis. 132, p. 46-69 24 p.

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

      7 Scopus citations

    • Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

      The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 181-193.e7

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

      Open Access
      585 Scopus citations

    • Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

      The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 282-296.e4

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

      Open Access
      268 Scopus citations

    • Sex differences in oncogenic mutational processes

      PCAWG Tumour Subtypes and Clinical Translation & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4330.

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

      Open Access
      52 Scopus citations

    • SETD2 Loss and ATR Inhibition Synergize to Promote cGAS Signaling and Immunotherapy Response in Renal Cell Carcinoma

      Liu, X. D., Zhang, Y. T., McGrail, D. J., Zhang, X., Lam, T., Hoang, A., Hasanov, E., Manyam, G., Peterson, C. B., Zhu, H., Kumar, S. V., Akbani, R., Pilie, P. G., Tannir, N. M., Peng, G. & Jonasch, E., Oct 1 2023, In: Clinical Cancer Research. 29, 19, p. 4002-4015 14 p.

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

      3 Scopus citations

    • Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

      MC3 Working Group & The Cancer Genome Atlas Research Network, Mar 28 2018, In: Cell Systems. 6, 3, p. 271-281.e7

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

      Open Access
      446 Scopus citations

    • SAMMI: A semi-Automated tool for the visualization of metabolic networks

      Schultz, A. & Akbani, R., Apr 15 2020, In: Bioinformatics. 36, 8, p. 2616-2617 2 p.

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

      Open Access
      3 Scopus citations

    • RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data

      Shehwana, H., Kumar, S. V., Melott, J. M., Rohrdanz, M. A., Wakefield, C., Ju, Z., Siwak, D. R., Lu, Y., Broom, B. M., Weinstein, J. N., Mills, G. B. & Akbani, R., Nov 15 2022, In: Bioinformatics. 38, 22, p. 5131-5133 3 p.

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

      Open Access
      1 Scopus citations

    • Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

      MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4748.

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

      Open Access
      25 Scopus citations

    • Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

      PCAWG Evolution and Heterogeneity Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 731.

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

      Open Access
      28 Scopus citations

    • Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: A workshop report the RPPA (Reverse Phase Protein Array) Society

      Akbani, R., Becker, K. F., Carragher, N., Goldstein, T., De Koning, L., Korf, U., Liotta, L., Mills, G. B., Nishizuka, S. S., Pawlak, M., Petricoin, E. F., Pollard, H. B., Serrels, B. & Zhu, J., Jul 2014, In: Molecular and Cellular Proteomics. 13, 7, p. 1625-1643 19 p.

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

      134 Scopus citations

    • Prognostically relevant gene signatures of high-grade serous ovarian carcinoma

      Verhaak, R. G. W., Tamayo, P., Yang, J. Y., Hubbard, D., Zhang, H., Creighton, C. J., Fereday, S., Lawrence, M., Carter, S. L., Mermel, C. H., Kostic, A. D., Etemadmoghadam, D., Saksena, G., Cibulskis, K., Duraisamy, S., Levanon, K., Sougnez, C., Tsherniak, A., Gomez, S., Onofrio, R., & 21 othersGabriel, S., Chin, L., Zhang, N., Spellman, P. T., Zhang, Y., Akbani, R., Hoadley, K. A., Kahn, A., Köbel, M., Huntsman, D., Soslow, R. A., Defazio, A., Birrer, M. J., Gray, J. W., Weinstein, J. N., Bowtell, D. D., Drapkin, R., Mesirov, J. P., Getz, G., Levine, D. A. & Meyerson, M., Jan 2 2013, In: Journal of Clinical Investigation. 123, 1, p. 517-525 9 p.

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

      455 Scopus citations

    • Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

      The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 305-320.e10

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

      Open Access
      218 Scopus citations

    • Personalized network modeling of the pan-cancer patient and cell line interactome

      Bhattacharyya, R., Ha, M. J., Liu, Q., Akbani, R., Liang, H. & Baladandayuthapani, V., 2020, In: JCO Clinical Cancer Informatics. 4, p. 399-411 13 p.

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

      Open Access
      11 Scopus citations

    • Personalized Integrated Network Modeling of the Cancer Proteome Atlas

      Ha, M. J., Banerjee, S., Akbani, R., Liang, H., Mills, G. B., Do, K. A. & Baladandayuthapani, V., Dec 1 2018, In: Scientific reports. 8, 1, 14924.

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

      Open Access
      12 Scopus citations

    • Pathway and network analysis of more than 2500 whole cancer genomes

      PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 729.

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

      Open Access
      62 Scopus citations

    • Pathogenic Germline Variants in 10,389 Adult Cancers

      The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 355-370.e14

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

      Open Access
      507 Scopus citations

    • Pan-cancer analysis of whole genomes

      The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Feb 6 2020, In: Nature. 578, 7793, p. 82-93 12 p.

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

      Open Access
      1547 Scopus citations

    • Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

      The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 297-312.e12

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

      Open Access
      189 Scopus citations

    • Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

      The Cancer Genome Atlas Network, Mar 28 2018, In: Cell Systems. 6, 3, p. 282-300.e2

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

      Open Access
      240 Scopus citations

    • Oncogenic Signaling Pathways in The Cancer Genome Atlas

      The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 321-337.e10

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

      Open Access
      1748 Scopus citations

    • NExUS: Bayesian simultaneous network estimation across unequal sample sizes

      Das, P., Peterson, C. B., Do, K. A., Akbani, R. & Baladandayuthapani, V., Feb 1 2020, In: Bioinformatics. 36, 3, p. 798-804 7 p.

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

      Open Access

    • Next-generation characterization of the Cancer Cell Line Encyclopedia

      Ghandi, M., Huang, F. W., Jané-Valbuena, J., Kryukov, G. V., Lo, C. C., McDonald, E. R., Barretina, J., Gelfand, E. T., Bielski, C. M., Li, H., Hu, K., Andreev-Drakhlin, A. Y., Kim, J., Hess, J. M., Haas, B. J., Aguet, F., Weir, B. A., Rothberg, M. V., Paolella, B. R., Lawrence, M. S., & 48 othersAkbani, R., Lu, Y., Tiv, H. L., Gokhale, P. C., de Weck, A., Mansour, A. A., Oh, C., Shih, J., Hadi, K., Rosen, Y., Bistline, J., Venkatesan, K., Reddy, A., Sonkin, D., Liu, M., Lehar, J., Korn, J. M., Porter, D. A., Jones, M. D., Golji, J., Caponigro, G., Taylor, J. E., Dunning, C. M., Creech, A. L., Warren, A. C., McFarland, J. M., Zamanighomi, M., Kauffmann, A., Stransky, N., Imielinski, M., Maruvka, Y. E., Cherniack, A. D., Tsherniak, A., Vazquez, F., Jaffe, J. D., Lane, A. A., Weinstock, D. M., Johannessen, C. M., Morrissey, M. P., Stegmeier, F., Schlegel, R., Hahn, W. C., Getz, G., Mills, G. B., Boehm, J. S., Golub, T. R., Garraway, L. A. & Sellers, W. R., May 23 2019, In: Nature. 569, 7757, p. 503-508 6 p.

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

      Open Access
      1653 Scopus citations

    • Mutational profiles reveal an aberrant TGF-β-CEA regulated pathway in colon adenomas

      Chen, J., Raju, G. S., Jogunoori, W., Menon, V., Majumdar, A., Chen, J. S., Gi, Y. J., Jeong, Y. S., Phan, L., Belkin, M., Gu, S., Kundra, S., Mistry, N. A., Zhang, J., Su, X., Li, S., Lin, S. H., Javle, M., McMurray, J. S., Rahlfs, T. F., & 12 othersMishra, B., White, J., Rashid, A., Beauchemin, N., Weston, B. R., Shafi, M. A., Stroehlein, J. R., Davila, M., Akbani, R., Weinstein, J. N., Wu, X. & Mishra, L., Apr 2016, In: PloS one. 11, 4, e0153933.

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

      Open Access
      18 Scopus citations

    • Multiplatform-based molecular subtypes of non-small-cell lung cancer

      Chen, F., Zhang, Y., Parra, E., Rodriguez, J., Behrens, C., Akbani, R., Lu, Y., Kurie, J. M., Gibbons, D. L., Mills, G. B., Wistuba, I. I. & Creighton, C. J., Mar 1 2017, In: Oncogene. 36, 10, p. 1384-1393 10 p.

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

      Open Access
      94 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

      1093 Scopus citations

    • Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma

      Chen, F., Zhang, Y., Şenbabaoğlu, Y., Ciriello, G., Yang, L., Reznik, E., Shuch, B., Micevic, G., De Velasco, G., Shinbrot, E., Noble, M. S., Lu, Y., Covington, K. R., Xi, L., Drummond, J. A., Muzny, D., Kang, H., Lee, J., Tamboli, P., Reuter, V., & 20 othersShelley, C. S., Kaipparettu, B. A., Bottaro, D. P., Godwin, A. K., Gibbs, R. A., Getz, G., Kucherlapati, R., Park, P. J., Sander, C., Henske, E. P., Zhou, J. H., Kwiatkowski, D. J., Ho, T. H., Choueiri, T. K., Hsieh, J. J., Akbani, R., Mills, G. B., Hakimi, A. A., Wheeler, D. A. & Creighton, C. J., Mar 15 2016, In: Cell Reports. 14, 10, p. 2476-2489 14 p.

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

      Open Access
      264 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.

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

      Open Access
      1446 Scopus citations

    • Molecular heterogeneity at the network level: High-dimensional testing, clustering and a TCGA case study

      Städler, N., Dondelinger, F., Hill, S. M., Akbani, R., Lu, Y., Mills, G. B. & Mukherjee, S., Sep 15 2017, In: Bioinformatics. 33, 18, p. 2890-2896 7 p.

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

      Open Access
      12 Scopus citations

    • Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

      The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 255-269.e4

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

      Open Access
      172 Scopus citations

    • Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

      The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 338-354.e15

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

      Open Access
      1193 Scopus citations

    • Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

      The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 172-180.e3

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

      Open Access
      97 Scopus citations

    • lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

      The Cancer Genome Atlas Research Network, Apr 9 2018, In: Cancer cell. 33, 4, p. 706-720.e9

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

      Open Access
      358 Scopus citations

    • Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines

      Zhao, W., Li, J., Chen, M. J. M., Luo, Y., Ju, Z., Nesser, N. K., Johnson-Camacho, K., Boniface, C. T., Lawrence, Y., Pande, N. T., Davies, M. A., Herlyn, M., Muranen, T., Zervantonakis, I. K., von Euw, E., Schultz, A., Kumar, S. V., Korkut, A., Spellman, P. T., Akbani, R., & 6 othersSlamon, D. J., Gray, J. W., Brugge, J. S., Lu, Y., Mills, G. B. & Liang, H., Dec 14 2020, In: Cancer cell. 38, 6, p. 829-843.e4

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

      Open Access
      31 Scopus citations

    • Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps

      Broom, B. M., Ryan, M. C., Stucky, M., Wakefield, C., Melott, J. M., Akbani, R. & Weinstein, J. N., 2020, In: F1000Research. 8, 1750.

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

      Open Access
      33 Scopus citations