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Leslie Cope

Associate Professor

20012024

Research activity per year

Search results

  • 2014

    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

    Open Access
    1322 Scopus citations

  • Integrative correlation: Properties and relation to canonical correlations

    Cope, L., Naiman, D. Q. & Parmigiani, G., Jan 2014, In: Journal of Multivariate Analysis. 123, p. 270-280 11 p.

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

    Open Access
    3 Scopus citations

  • Modular network construction using eQTL data: An analysis of computational costs and benefits

    Ho, Y. Y., Cope, L. M. & Parmigiani, G., 2014, In: Frontiers in Genetics. 5, FEB, Article 40.

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

    Open Access
    9 Scopus citations

  • Mutational analysis of BRAF and KRAS in ovarian serous borderline (atypical proliferative) tumours and associated peritoneal implants

    Ardighieri, L., Zeppernick, F., Hannibal, C. G., Vang, R., Cope, L., Junge, J., Kjaer, S. K., Kurman, R. J. & Shih, I. M., Jan 2014, In: Journal of Pathology. 232, 1, p. 16-22 7 p.

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

    Open Access
    38 Scopus citations

  • Novel methylated biomarkers and a robust assay to detect circulating tumor dna in metastatic breast cancer

    Fackler, M. J., Bujanda, Z. L., Umbricht, C., Teo, W. W., Cho, S., Zhang, Z., Visvanathan, K., Jeter, S., Argani, P., Wang, C., Lyman, J. P., De Brot, M., Ingle, J. N., Boughey, J., McGuire, K., King, T. A., Carey, L. A., Cope, L., Wolff, A. C. & Sukumar, S., Apr 15 2014, In: Cancer Research. 74, 8, p. 2160-2170 11 p.

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

    Open Access
    103 Scopus citations

  • Rapamycin rescues ABT-737 efficacy in small cell lung cancer

    Gardner, E. E., Connis, N., Poirier, J. T., Cope, L., Dobromilskaya, I., Gallia, G. L., Rudin, C. M. & Hann, C. L., May 15 2014, In: Cancer Research. 74, 10, p. 2846-2856 11 p.

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

    Open Access
    41 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 othersBrannon, 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
    1823 Scopus citations

  • DNA copy number variations characterize benign and malignant thyroid tumors

    Liu, Y., Cope, L., Sun, W., Wang, Y., Prasad, N., Sangenario, L., Talbot, K., Somervell, H., Westra, W., Bishop, J., Califano, J., Zeiger, M. & Umbricht, C., Mar 2013, In: Journal of Clinical Endocrinology and Metabolism. 98, 3, p. E558-E566

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

    Open Access
    11 Scopus citations

  • Genome-wide methylation profiling and the PI3K-AKT pathway analysis associated with smoking in urothelial cell carcinoma

    Brait, M., Munari, E., LeBron, C., Noordhuis, M. G., Begum, S., Michailidi, C., Gonzalez-Roibon, N., Maldonado, L., Sen, T., Guerrero-Preston, R., Cope, L., Parrellaw, P., Faziow, V. M., Ha, P. K., Netto, G. J., Sidransky, D. & Hoque, M. O., Apr 1 2013, In: Cell Cycle. 12, 7, p. 1058-1070 13 p.

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

    Open Access
    30 Scopus citations

  • High level of chromosomal aberration in ovarian cancer genome correlates with poor clinical outcome

    Cope, L., Wu, R. C., Shih, I. M. & Wang, T. L., Mar 2013, In: Gynecologic oncology. 128, 3, p. 500-505 6 p.

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

    16 Scopus citations

  • HMGA1: A Master Regulator of Tumor Progression in Triple-Negative Breast Cancer Cells

    Shah, S. N., Cope, L., Poh, W., Belton, A., Roy, S., Talbot, C. C., Sukumar, S., Huso, D. L. & Resar, L. M. S., May 2 2013, In: PloS one. 8, 5, e63419.

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

    Open Access
    83 Scopus citations

  • HOXB13 mediates tamoxifen resistance and invasiveness in human breast cancer by suppressing ERα and inducing IL-6 expression

    Shah, N., Jin, K., Cruz, L. A., Park, S., Sadik, H., Cho, S., Goswami, C. P., Nakshatri, H., Gupta, R., Chang, H. Y., Zhang, Z., Cimino-Mathews, A., Cope, L., Umbricht, C. & Sukumar, S., Sep 1 2013, In: Cancer Research. 73, 17, p. 5449-5458 10 p.

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

    Open Access
    60 Scopus citations

  • Methylation of the Claudin 1 Promoter Is Associated with Loss of Expression in Estrogen Receptor Positive Breast Cancer

    Di Cello, F., Cope, L., Li, H., Jeschke, J., Wang, W., Baylin, S. B. & Zahnow, C. A., Jul 3 2013, In: PloS one. 8, 7, e68630.

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

    Open Access
    33 Scopus citations

  • Modeling precision treatment of breast cancer

    Daemen, A., Griffith, O. L., Heiser, L. M., Wang, N. J., Enache, O. M., Sanborn, Z., Pepin, F., Durinck, S., Korkola, J. E., Griffith, M., Hur, J. S., Huh, N., Chung, J., Cope, L., Fackler, M. J., Umbricht, C., Sukumar, S., Seth, P., Sukhatme, V. P., Jakkula, L. R., & 7 othersLu, Y., Mills, G. B., Cho, R. J., Collisson, E. A., van't Veer, L. J., Spellman, P. T. & Gray, J. W., Dec 10 2013, In: Genome biology. 14, 10, R110.

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

    Open Access
    160 Scopus citations

  • Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis

    Fertig, E. J., Markovic, A., Danilova, L. V., Gaykalova, D. A., Cope, L., Chung, C. H., Ochs, M. F. & Califano, J. A., Nov 4 2013, In: PloS one. 8, 11, e78127.

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

    Open Access
    26 Scopus citations
  • 2012

    Biomarkers for detection and prognosis of breast cancer identified by a functional hypermethylome screen

    Jeschke, J., Van Neste, L., Glöckner, S. C., Dhir, M., Calmon, M. F., Deregowski, V., Van Criekinge, W., Vlassenbroeck, I., Koch, A., Chan, T. A., Cope, L., Hooker, C. M., Schuebel, K. E., Gabrielson, E., Winterpacht, A., Baylin, S. B., Herman, J. G. & Ahuja, N., 2012, In: Epigenetics. 7, 7, p. 701-709 9 p.

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

    Open Access
    48 Scopus citations

  • Comprehensive genomic characterization of squamous cell lung cancers

    Hammerman, P. S., Voet, D., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Getz, G., Imielinski, M., Helman, E., Hernandez, B., Pho, N. H., Meyerson, M., Chu, A., Hye-Chun, J. E., Mungall, A. J., & 316 othersPleasance, E., Robertson, A. G., Sipahimalani, P., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, K., Nip, K. M., Olshen, A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T., Zhao, Y., Jones, S. J. M., Marra, M. A., Saksena, G., Cherniack, A. D., Schumacher, S. E., Tabak, B., Carter, S. L., Nguyen, H., Onofrio, R. C., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Protopopov, A., Zhang, J., Hadjipanayis, A., Lee, S., Xi, R., Yang, L., Ren, X., Zhang, H., Shukla, S., Chen, P. C., Haseley, P., Lee, E., Chin, L., Park, P. J., Kucherlapati, R., Socci, N. D., Liang, Y., Schultz, N., Borsu, L., Lash, A. E., Viale, A., Sander, C., Ladanyi, M., Auman, J. T., Hoadley, K. A., Wilkerson, M. D., Shi, Y., Liquori, C., Meng, S., Li, L., Turman, Y. J., Topal, M. D., Tan, D., Waring, S., Buda, E., Walsh, J., Jones, C. D., Mieczkowski, P. A., Singh, D., Wu, J., Gulabani, A., Dolina, P., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Stuart, J., Mose, L. E., Jefferys, S. R., Balu, S., O'Connor, B. D., Chiang, D., Liu, J., Chiang, D. Y., Hayes, D. N., Perou, C. M., Cope, L., Weisenberger, D., Danilova, L., Weisenberger, D. J., Maglinte, D. T., Pan, F., Van Den Berg, D. J., Triche, T., Herman, J. G., Baylin, S. B., Laird, P. W., Noble, M., Gehlenborg, N., DiCara, D., Zhang, J., Wu, C. J., Liu, S. Y., Zou, L., Lin, P., Cho, J., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Sinha, R., Ciriello, G., Cerami, E., Gross, B., Jacobsen, A., Gao, J., Aksoy, B. A., Weinhold, N., Ramirez, R., Taylor, B. S., Antipin, Y., Reva, B., Mo, Q., Seshan, V., Paik, P. K., Akbani, R., Zhang, N., Broom, B. M., Casasent, T., Unruh, A., Wakefield, C., Cason, R. C., Baggerly, K. A., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Ng, S., Goldstein, T., Waltman, P., Sokolov, A., Collisson, E., Ellrott, K., Collisson, E. A., Zerbino, D., Ma, S., Craft, B., Du, Y., Cabanski, C., Walter, V., Marron, J. S., Liu, Y., Wang, K., Prins, J. F., Creighton, C. J., Zhang, Y., Travis, W. D., Rekhtman, N., Yi, J., Aubry, M. C., Cheney, R., Dacic, S., Flieder, D., Funkhouser, W., Illei, P., Myers, J., Tsao, M. S., Penny, R., Mallery, D., Shelton, T., Hatfield, M., Morris, S., Yena, P., Shelton, C., Sherman, M., Paulauskis, J., Govindan, R., Azodo, I., Beer, D., Bose, R., Byers, L. A., Carbone, D., Chang, L. W., Chun, E., Ding, L., Heymach, J., Ida, C., Johnson, B., Jurisica, I., Kaufman, J., Kosari, F., Kwiatkowski, D., Maher, C. A., Pao, W., Peifer, M., Robertson, G., Rusch, V., Siegfried, J., Sougnez, C., Thomas, R. K., Tomaszek, S., Vaske, C., Wheeler, D., Wigle, D. A., Wilks, C., Zhang, J. J., Jensen, M. A., Sfeir, R., Kahn, A. B., Chu, A. L., Kothiyal, P., Wang, Z., Snyder, E. E., Pontius, J., Pihl, T. D., Backus, M., Walton, J., Baboud, J., Berton, D. L., Nicholls, M. C., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P. A., Alonso, S., Sanbhadti, R. N., Barletta, S. P., Greene, J. M., Pot, D. A., Bandarchi-Chamkhaleh, B., Boyd, J., Weaver, J., Azodo, I. A., Tomaszek, S. C., Yang, P., Brock, M. V., Rogers, K., Rutledge, M., Brown, T., Lee, B., Shin, J., Trusty, D., Dhir, R., Siegfried, J. M., Potapova, O., Fedosenko, K. V., Zakowski, M., Nemirovich-Danchenko, E., Iacocca, M. V., Brown, J., Rabeno, B., Czerwinski, C., Petrelli, N., Fan, Z., Todaro, N., Eckman, J., Rathmell, W. K., Thorne, L. B., Huang, M., Boice, L., Hill, A., Curley, E., Morrison, C., Gaudioso, C., Bartlett, J. M. S., Kodeeswaran, S., Zanke, B., Sekhon, H., David, K., Juhl, H., Le, X. V., Kohl, B., Thorp, R., Tien, N. V., Bang, N. V., Sussman, H., Phu, B. D., Hajek, R., Hung, N. P., Khan, K. Z., Muley, T., Mills Shaw, K. R., Sheth, M., Yang, L., Demchok, J. A., Davidsen, T., Buetow, K., Eley, G., Ferguson, M., Dillon, L. A. L., Schaefer, C., Guyer, M. S., Ozenberger, B. A., Palchik, J. D., Peterson, J., Sofia, H. J., Thomson, E., Johnson, B. E. & Shen, R., Sep 27 2012, In: Nature. 489, 7417, p. 519-525 7 p.

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

    Open Access
    2431 Scopus citations

  • Detection of tumor PIK3CA status in metastatic breast cancer using peripheral blood

    Higgins, M. J., Jelovac, D., Barnathan, E., Blair, B., Slater, S., Powers, P., Zorzi, J., Jeter, S. C., Oliver, G. R., Fetting, J., Emens, L., Riley, C., Stearns, V., Diehl, F., Angenendt, P., Huang, P., Cope, L., Argani, P., Murphy, K. M., Bachman, K. E., & 3 othersGreshock, J., Wolff, A. C. & Park, B. H., Jun 15 2012, In: Clinical Cancer Research. 18, 12, p. 3462-3469 8 p.

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

    Open Access
    239 Scopus citations

  • Exploring massive, genome scale datasets with the genometricorr package

    Favorov, A., Mularoni, L., Cope, L. M., Medvedeva, Y., Mironov, A. A., Makeev, V. J. & Wheelan, S. J., May 2012, In: PLoS computational biology. 8, 5, e1002529.

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

    Open Access
    87 Scopus citations

  • HMGA1 Reprograms Somatic Cells into Pluripotent Stem Cells by Inducing Stem Cell Transcriptional Networks

    Shah, S. N., Kerr, C., Cope, L., Zambidis, E., Liu, C., Hillion, J., Belton, A., Huso, D. L. & Resar, L. M. S., Nov 15 2012, In: PloS one. 7, 11, e48533.

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

    Open Access
    60 Scopus citations

  • The HMGA1-COX-2 axis: A key molecular pathway and potential target in pancreatic adenocarcinoma

    Hillion, J., Smail, S. S., Di Cello, F., Belton, A., Shah, S. N., Huso, T., Schuldenfrei, A., Nelson, D. M., Cope, L., Campbell, N., Karikari, C., Aderinto, A., Maitra, A., Huso, D. L. & Resar, L. M. S., 2012, In: Pancreatology. 12, 4, p. 372-379 8 p.

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

    Open Access
    26 Scopus citations
  • 2011

    Elevated microRNA miR-21 levels in pancreatic cyst fluid are predictive of mucinous precursor lesions of ductal adenocarcinoma

    Ryu, J. K., Matthaei, H., Dal Molin, M., Hong, S. M., Canto, M. I., Schulick, R. D., Wolfgang, C., Goggins, M. G., Hruban, R. H., Cope, L. & Maitra, A., Sep 2011, In: Pancreatology. 11, 3, p. 343-350 8 p.

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

    Open Access
    89 Scopus citations

  • Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence

    Fackler, M. J., Umbricht, C. B., Williams, D., Argani, P., Cruz, L. A., Merino, V. F., Teo, W. W., Zhang, Z., Huang, P., Visvananthan, K., Marks, J., Ethier, S., Gray, J. W., Wolff, A. C., Cope, L. M. & Sukumar, S., Oct 1 2011, In: Cancer Research. 71, 19, p. 6195-6207 13 p.

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

    Open Access
    147 Scopus citations

  • Identification of novel phosphorylation motifs through an integrative computational and experimental analysis of the human phosphoproteome

    Amanchy, R., Kandasamy, K., Mathivanan, S., Periaswamy, B., Reddy, R., Yoon, W. H., Joore, J., Beer, M. A., Cope, L. & Pandey, A., 2011, In: Journal of Proteomics and Bioinformatics. 4, 2, p. 22-35 14 p.

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

    Open Access
    26 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 othersMills, 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

    Open Access
    4462 Scopus citations

  • Modeling Liquid Association

    Ho, Y. Y., Parmigiani, G., Louis, T. A. & Cope, L. M., Mar 2011, In: Biometrics. 67, 1, p. 133-141 9 p.

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

    18 Scopus citations

  • Promoter methylation in head and neck squamous cell carcinoma cell lines is significantly different than methylation in primary tumors and xenografts

    Hennessey, P. T., Ochs, M. F., Mydlarz, W. W., Hsueh, W., Cope, L., Yu, W. & Califano, J. A., 2011, In: PloS one. 6, 5, e20584.

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

    Open Access
    46 Scopus citations

  • Subnormal cytokine profile in the tear fluid of keratoconus patients

    Jun, A. S., Cope, L., Speck, C., Feng, X., Lee, S., Meng, H., Hamad, A. & Chakravarti, S., 2011, In: PloS one. 6, 1, e16437.

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

    Open Access
    107 Scopus citations
  • 2010

    Aberrant silencing of cancer-related genes by CpG hypermethylation occurs independently of their spatial organization in the nucleus

    Easwaran, H. P., Van Neste, L., Cope, L., Sen, S., Mohammad, H. P., Pageau, G. J., Lawrence, J. B., Herman, J. G., Schuebel, K. E. & Baylin, S. B., Oct 15 2010, In: Cancer Research. 70, 20, p. 8015-8024 10 p.

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

    Open Access
    25 Scopus citations

  • A bioinformatics pipeline for cancer epigenetics

    van Neste, L., Herman, J. G., Schuebel, K. E., Cope, L., Baylin, S. B., van Criekinge, W. & Ahuja, N., 2010, In: Current Bioinformatics. 5, 3, p. 153-163 11 p.

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

    2 Scopus citations

  • Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells

    Ohm, J. E., Mali, P., Van Neste, L., Berman, D. M., Liang, L., Pandiyan, K., Briggs, K. J., Zhang, W., Argani, P., Simons, B., Yu, W., Matsui, W., Van Criekinge, W., Rassool, F. V., Zambidis, E., Schuebel, K. E., Cope, L., Yen, J., Mohammad, H. P., Cheng, L., & 1 othersBaylin, S. B., Oct 1 2010, In: Cancer Research. 70, 19, p. 7662-7673 12 p.

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

    Open Access
    52 Scopus citations

  • Cross-platform comparison of two pancreatic cancer phenotypes

    Scharpf, R. B., Iacobuzio-Donahue, C. A., Cope, L., Ruczinski, I., Garrett-Mayer, E., Lakkur, S., Campagna, D. & Parmigiani, G., 2010, In: Cancer Informatics. 9, p. 257-264 8 p.

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

    Open Access
    2 Scopus citations

  • Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis

    Shih, I. M., Chen, L., Wang, C. C., Gu, J., Davidson, B., Cope, L., Kurman, R. J., Xuan, J. & Wang, T. L., Dec 2010, In: American journal of obstetrics and gynecology. 203, 6, p. 584.e1-584.e22

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

    Open Access
    42 Scopus citations

  • HMGA1 correlates with advanced tumor grade and decreased survival in pancreatic ductal adenocarcinoma

    Hristov, A. C., Cope, L., Di Cello, F., Reyes, M. D., Singh, M., Hillion, J. A., Belton, A., Joseph, B., Schuldenfrei, A., Iacobuzio-Donahue, C. A., Maitra, A. & Resar, L. M. S., Jan 2010, In: Modern Pathology. 23, 1, p. 98-104 7 p.

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

    Open Access
    62 Scopus citations

  • Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

    Noushmehr, H., Weisenberger, D. J., Diefes, K., Phillips, H. S., Pujara, K., Berman, B. P., Pan, F., Pelloski, C. E., Sulman, E. P., Bhat, K. P., Verhaak, R. G. W., Hoadley, K. A., Hayes, D. N., Perou, C. M., Schmidt, H. K., Ding, L., Wilson, R. K., Van Den Berg, D., Shen, H., Bengtsson, H., & 7 othersNeuvial, P., Cope, L. M., Buckley, J., Herman, J. G., Baylin, S. B., Laird, P. W. & Aldape, K., May 18 2010, In: Cancer cell. 17, 5, p. 510-522 13 p.

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

    Open Access
    1551 Scopus citations

  • Transcriptional regulation of Wnt inhibitory factor-1 by Miz-1/c-Myc

    Licchesi, J. D. F., Van Neste, L., Tiwari, V. K., Cope, L., Lin, X., Baylin, S. B. & Herman, J. G., Nov 4 2010, In: Oncogene. 29, 44, p. 5923-5934 12 p.

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

    33 Scopus citations
  • 2009

    Discussion of: Brownian distance covariance

    Cope, L., Dec 2009, In: Annals of Applied Statistics. 3, 4, p. 1279-1281 3 p.

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

    Open Access
    3 Scopus citations

  • HMGA2 protein expression correlates with lymph node metastasis and increased tumor grade in pancreatic ductal adenocarcinoma

    Hristov, A. C., Cope, L., Reyes, M. D., Singh, M., Iacobuzio-Donahue, C., Maitra, A. & Resar, L. M. S., Jan 2009, In: Modern Pathology. 22, 1, p. 43-49 7 p.

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

    Open Access
    89 Scopus citations

  • The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations

    Lin, X., Afsari, B., Marchionni, L., Cope, L., Parmigiani, G., Naiman, D. & Geman, D., Aug 20 2009, In: BMC Bioinformatics. 10, p. 256 1 p., 1471.

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

    Open Access
    28 Scopus citations
  • 2008

    A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations

    Tiwari, V. K., Cope, L., McGarvey, K. M., Ohm, J. E. & Baylin, S. B., Jul 2008, In: Genome research. 18, 7, p. 1171-1179 9 p.

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

    Open Access
    97 Scopus citations

  • A requirement for DICER to maintain full promoter CpG island hypermethylation in human cancer cells

    Ting, A. H., Suzuki, H., Cope, L., Schuebel, K. E., Lee, B. H., Toyota, M., Imai, K., Shinomura, Y., Tokino, T. & Baylin, S. B., Apr 15 2008, In: Cancer Research. 68, 8, p. 2570-2575 6 p.

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

    Open Access
    46 Scopus citations

  • Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    McLendon, R., Friedman, A., Bigner, D., Van Meir, E. G., Brat, D. J., Mastrogianakis, G. M., Olson, J. J., Mikkelsen, T., Lehman, N., Aldape, K., Yung, W. K. A., Bogler, O., Weinstein, J. N., VandenBerg, S., Berger, M., Prados, M., Muzny, D., Morgan, M., Scherer, S., Sabo, A., & 211 othersNazareth, L., Lewis, L., Hall, O., Zhu, Y., Ren, Y., Alvi, O., Yao, J., Hawes, A., Jhangiani, S., Fowler, G., San Lucas, A., Kovar, C., Cree, A., Dinh, H., Santibanez, J., Joshi, V., Gonzalez-Garay, M. L., Miller, C. A., Milosavljevic, A., Donehower, L., Wheeler, D. A., Gibbs, R. A., Cibulskis, K., Sougnez, C., Fennell, T., Mahan, S., Wilkinson, J., Ziaugra, L., Onofrio, R., Bloom, T., Nicol, R., Ardlie, K., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., McLellan, M. D., Wallis, J., Larson, D. E., Shi, X., Abbott, R., Fulton, L., Chen, K., Koboldt, D. C., Wendl, M. C., Meyer, R., Tang, Y., Lin, L., Osborne, J. R., Dunford-Shore, B. H., Miner, T. L., Delehaunty, K., Markovic, C., Swift, G., Courtney, W., Pohl, C., Abbott, S., Hawkins, A., Leong, S., Haipek, C., Schmidt, H., Wiechert, M., Vickery, T., Scott, S., Dooling, D. J., Chinwalla, A., Weinstock, G. M., Mardis, E. R., Wilson, R. K., Getz, G., Winckler, W., Verhaak, R. G. W., Lawrence, M. S., O'Kelly, M., Robinson, J., Alexe, G., Beroukhim, R., Carter, S., Chiang, D., Gould, J., Gupta, S., Korn, J., Mermel, C., Mesirov, J., Monti, S., Nguyen, H., Parkin, M., Reich, M., Stransky, N., Weir, B. A., Garraway, L., Golub, T., Meyerson, M., Chin, L., Protopopov, A., Zhang, J., Perna, I., Aronson, S., Sathiamoorthy, N., Ren, G., Yao, J., Wiedemeyer, W. R., Kim, H., Sek, W. K., Xiao, Y., Kohane, I. S., Seidman, J., Park, P. J., Kucherlapati, R., Laird, P. W., Cope, L., Herman, J. G., Weisenberger, D. J., Pan, F., Van Den Berg, D., Van Neste, L., Joo, M. Y., Schuebel, K. E., Baylin, S. B., Absher, D. M., Li, J. Z., Southwick, A., Brady, S., Aggarwal, A., Chung, T., Sherlock, G., Brooks, J. D., Myers, R. M., Spellman, P. T., Purdom, E., Jakkula, L. R., Lapuk, A. V., Marr, H., Dorton, S., Yoon, G. C., Han, J., Ray, A., Wang, V., Durinck, S., Robinson, M., Wang, N. J., Vranizan, K., Peng, V., Van Name, E., Fontenay, G. V., Ngai, J., Conboy, J. G., Parvin, B., Feiler, H. S., Speed, T. P., Gray, J. W., Brennan, C., Socci, N. D., Olshen, A., Taylor, B. S., Lash, A., Schultz, N., Reva, B., Antipin, Y., Stukalov, A., Gross, B., Cerami, E., Wei, Q. W., Qin, L. X., Seshan, V. E., Villafania, L., Cavatore, M., Borsu, L., Viale, A., Gerald, W., Sander, C., Ladanyi, M., Perou, C. M., Hayes, D. N., Topal, M. D., Hoadley, K. A., Qi, Y., Balu, S., Shi, Y., Wu, J., Penny, R., Bittner, M., Shelton, T., Lenkiewicz, E., Morris, S., Beasley, D., Sanders, S., Kahn, A., Sfeir, R., Chen, J., Nassau, D., Feng, L., Hickey, E., Barker, A., Gerhard, D. S., Vockley, J., Compton, C., Vaught, J., Fielding, P., Ferguson, M. L., Schaefer, C., Zhang, J., Madhavan, S., Buetow, K. H., Collins, F., Good, P., Guyer, M., Ozenberger, B., Peterson, J. & Thomson, E., Oct 23 2008, In: Nature. 455, 7216, p. 1061-1068 8 p.

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

    Open Access
    5077 Scopus citations

  • Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis

    Chan, T. A., Glockner, S., Joo, M. Y., Chen, W., Van Neste, L., Cope, L., Herman, J. G., Velculescu, V., Schuebel, K. E., Ahuja, N. & Baylin, S. B., May 2008, In: PLoS medicine. 5, 5, p. 823-837 15 p., e114.

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

    Open Access
    126 Scopus citations

  • Cross-study validation and combined analysis of gene expression microarray data

    Garrett-Mayer, E., Parmigiani, G., Zhong, X., Cope, L. & Gabrielson, E., Apr 2008, In: Biostatistics. 9, 2, p. 333-354 22 p.

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

    Open Access
    34 Scopus citations

  • Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells

    McGarvey, K. M., Van Neste, L., Cope, L., Ohm, J. E., Herman, J. G., Van Criekinge, W., Schuebel, K. E. & Baylin, S. B., Jul 15 2008, In: Cancer Research. 68, 14, p. 5753-5759 7 p.

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

    Open Access
    88 Scopus citations

  • Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays

    Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Grønborg, M., Joore, J., Cope, L. & Pandey, A., Sep 2008, In: Journal of proteome research. 7, 9, p. 3900-3910 11 p.

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

    50 Scopus citations

  • Identifying differential correlation in gene/pathway combinations

    Braun, R., Cope, L. & Parmigiani, G., Nov 18 2008, In: BMC Bioinformatics. 9, 488.

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

    Open Access
    19 Scopus citations

  • Therapeutic efficacy of ABT-737, a selective inhibitor of BCL-2, in small cell lung cancer

    Hann, C. L., Daniel, V. C., Sugar, E. A., Dobromilskaya, I., Murphy, S. C., Cope, L., Lin, X., Hierman, J. S., Wilburn, D. L., Watkins, D. N. & Rudin, C. M., Apr 1 2008, In: Cancer Research. 68, 7, p. 2321-2328 8 p.

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

    Open Access
    164 Scopus citations
  • 2007

    A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing

    Ohm, J. E., McGarvey, K. M., Yu, X., Cheng, L., Schuebel, K. E., Cope, L., Mohammad, H. P., Chen, W., Daniel, V. C., Yu, W., Berman, D. M., Jenuwein, T., Pruitt, K., Sharkis, S. J., Watkins, D. N., Herman, J. G. & Baylin, S. B., Feb 2007, In: Nature genetics. 39, 2, p. 237-242 6 p.

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

    Open Access
    812 Scopus citations

  • Comparing the DNA hypermethylome with gene mutations in human colorectal cancer

    Schuebel, K. E., Chen, W., Cope, L., Glöckner, S. C., Suzuki, H., Yi, J. M., Chan, T. A., Van Neste, L., Van Criekinge, W., Van Den Bosch, S., Van Engeland, M., Ting, A. H., Jair, K., Yu, W., Toyota, M., Imai, K., Ahuja, N., Herman, J. G. & Baylin, S. B., Sep 2007, In: PLoS genetics. 3, 9, p. 1709-1723 15 p.

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

    Open Access
    289 Scopus citations