Christopher Maher

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Christopher Maher

Professor of Medicine, Professor of Biomedical Engineering

 https://orcid.org/0000-0002-9035-603X

    Willing to Mentor

    Available to Mentor:

    PhD/MSTP Students

    • 25169
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    20012024

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    • 2016

      Mycoplasma Infection Alters Cancer Stem Cell Properties in Vitro

      Gedye, C., Cardwell, T., Dimopoulos, N., Tan, B. S., Jackson, H., Svobodová, S., Anaka, M., Behren, A., Maher, C., Hofmann, O., Hide, W., Caballero, O., Davis, I. D. & Cebon, J., Feb 1 2016, In: Stem Cell Reviews and Reports. 12, 1, p. 156-161 6 p.

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

      Open Access
      15 Scopus citations

    • NFATc1 promotes prostate tumorigenesis and overcomes PTEN loss-induced senescence

      Manda, K. R., Tripathi, P., Hsi, A. C., Ning, J., Ruzinova, M. B., Liapis, H., Bailey, M., Zhang, H., Maher, C. A., Humphrey, P. A., Andriole, G. L., Ding, L., You, Z. & Chen, F., Jun 23 2016, In: Oncogene. 35, 25, p. 3282-3292 11 p.

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

      Open Access
      38 Scopus citations

    • Visualizing tumor evolution with the fishplot package for R

      Miller, C. A., McMichael, J., Dang, H. X., Maher, C. A., Ding, L., Ley, T. J., Mardis, E. R. & Wilson, R. K., Nov 7 2016, In: BMC genomics. 17, 1, 880.

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

      Open Access
      129 Scopus citations
    • 2015

      Genome Modeling System: A Knowledge Management Platform for Genomics

      Griffith, M., Griffith, O. L., Smith, S. M., Ramu, A., Callaway, M. B., Brummett, A. M., Kiwala, M. J., Coffman, A. C., Regier, A. A., Oberkfell, B. J., Sanderson, G. E., Mooney, T. P., Nutter, N. G., Belter, E. A., Du, F., Long, R. L., Abbott, T. E., Ferguson, I. T., Morton, D. L. & Burnett, M. M. & 44 others, Weible, J. V., Peck, J. B., Dukes, A., McMichael, J. F., Lolofie, J. T., Derickson, B. R., Hundal, J., Skidmore, Z. L., Ainscough, B. J., Dees, N. D., Schierding, W. S., Kandoth, C., Kim, K. H., Lu, C., Harris, C. C., Maher, N., Maher, C. A., Magrini, V. J., Abbott, B. S., Chen, K., Clark, E., Das, I., Fan, X., Hawkins, A. E., Hepler, T. G., Wylie, T. N., Leonard, S. M., Schroeder, W. E., Shi, X., Carmichael, L. K., Weil, M. R., Wohlstadter, R. W., Stiehr, G., McLellan, M. D., Pohl, C. S., Miller, C. A., Koboldt, D. C., Walker, J. R., Eldred, J. M., Larson, D. E., Dooling, D. J., Ding, L., Mardis, E. R. & Wilson, R. K., Jul 1 2015, In: PLoS computational biology. 11, 7, e1004274.

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

      Open Access
      65 Scopus citations

    • Optimizing Cancer Genome Sequencing and Analysis

      Griffith, M., Miller, C. A., Griffith, O. L., Krysiak, K., Skidmore, Z. L., Ramu, A., Walker, J. R., Dang, H. X., Trani, L., Larson, D. E., Demeter, R. T., Wendl, M. C., McMichael, J. F., Austin, R. E., Magrini, V., McGrath, S. D., Ly, A., Kulkarni, S., Cordes, M. G. & Fronick, C. C. & 7 others, Fulton, R. S., Maher, C. A., Ding, L., Klco, J. M., Mardis, E. R., Ley, T. J. & Wilson, R. K., Sep 23 2015, In: Cell Systems. 1, 3, p. 210-223 14 p., 35.

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

      Open Access
      145 Scopus citations

    • Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

      Cabanski, C. R., White, N. M., Dang, H. X., Silva-Fisher, J. M., Rauck, C. E., Cicka, D. & Maher, C. A., Jan 1 2015, In: RNA Biology. 12, 6, p. 628-642 15 p.

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

      Open Access
      82 Scopus citations
    • 2014

      CDNA hybrid capture improves transcriptome analysis on low-input and archived samples

      Cabanski, C. R., Magrini, V., Griffith, M., Griffith, O. L., McGrath, S., Zhang, J., Walker, J., Ly, A., Demeter, R., Fulton, R. S., Pong, W. W., Gutmann, D. H., Govindan, R., Mardis, E. R. & Maher, C. A., Jul 2014, In: Journal of Molecular Diagnostics. 16, 4, p. 440-451 12 p.

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

      Open Access
      37 Scopus citations

    • Characterization of the genomic features and expressed fusion genes in micropapillary carcinomas of the breast

      Natrajan, R., Wilkerson, P. M., Marchiò, C., Piscuoglio, S., Ng, C. K. Y., Wai, P., Lambros, M. B., Samartzis, E. P., Dedes, K. J., Frankum, J., Bajrami, I., Kopec, A., Mackay, A., A'Hern, R., Fenwick, K., Kozarewa, I., Hakas, J., Mitsopoulos, C., Hardisson, D. & Lord, C. J. & 7 others, Kumar-Sinha, C., Ashworth, A., Weigelt, B., Sapino, A., Chinnaiyan, A. M., Maher, C. A. & Reis-Filho, J. S., Apr 2014, In: Journal of Pathology. 232, 5, p. 553-565 13 p.

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

      Open Access
      89 Scopus citations

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

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

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

      Open Access
      4307 Scopus citations

    • Loss of Trop2 causes ErbB3 activation through a neuregulin-1-dependent mechanism in the mesenchymal subtype of HNSCC

      Zhang, K., Jones, L., Lim, S., Maher, C. A., Adkins, D., Lewis, J., Kimple, R. J., Fertig, E. J., Chung, C. H., Van Tine, B. A., Ellis, M. J., Herrlich, A. & Michel, L. S., 2014, In: Oncotarget. 5, 19, p. 9281-9294 14 p.

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

      Open Access
      27 Scopus citations

    • SigFuge: Single gene clustering of RNA-seq reveals differential isoform usage among cancer samples

      Kimes, P. K., Cabanski, C. R., Wilkerson, M. D., Zhao, N., Johnson, A. R., Perou, C. M., Makowski, L., Maher, C. A., Liu, Y., Marron, J. S. & Hayes, D. N., Aug 18 2014, In: Nucleic acids research. 42, 14, p. e113

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

      Open Access
      14 Scopus citations

    • Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

      White, N. M., Cabanski, C. R., Silva-Fisher, J. M., Dang, H. X., Govindan, R. & Maher, C. A., 2014, In: Genome biology. 15, 8, p. 429 1 p., 429.

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

      Open Access
      189 Scopus citations
    • 2013

      Characterization of the EZH2-MMSET Histone Methyltransferase Regulatory Axis in Cancer

      Asangani, I. A., Ateeq, B., Cao, Q., Dodson, L., Pandhi, M., Kunju, L. P., Mehra, R., Lonigro, R. J., Siddiqui, J., Palanisamy, N., Wu, Y. M., Cao, X., Kim, J. H., Zhao, M., Qin, Z. S., Iyer, M. K., Maher, C. A., Kumar-Sinha, C., Varambally, S. & Chinnaiyan, A. M., Jan 10 2013, In: Molecular cell. 49, 1, p. 80-93 14 p.

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

      Open Access
      131 Scopus citations

    • Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts

      Li, S., Shen, D., Shao, J., Crowder, R., Liu, W., Prat, A., He, X., Liu, S., Hoog, J., Lu, C., Ding, L., Griffith, O. L., Miller, C., Larson, D., Fulton, R. S., Harrison, M., Mooney, T., McMichael, J. F., Luo, J. & Tao, Y. & 35 others, Goncalves, R., Schlosberg, C., Hiken, J. F., Saied, L., Sanchez, C., Giuntoli, T., Bumb, C., Cooper, C., Kitchens, R. T., Lin, A., Phommaly, C., Davies, S. R., Zhang, J., Kavuri, M. S., McEachern, D., Dong, Y. Y., Ma, C., Pluard, T., Naughton, M., Bose, R., Suresh, R., McDowell, R., Michel, L., Aft, R., Gillanders, W., DeSchryver, K., Wilson, R. K., Wang, S., Mills, G. B., Gonzalez-Angulo, A., Edwards, J. R., Maher, C., Perou, C. M., Mardis, E. R. & Ellis, M. J., Sep 26 2013, In: Cell Reports. 4, 6, p. 1116-1130 15 p.

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

      Open Access
      521 Scopus citations

    • Recurrent rearrangements in prostate cancer: Causes and therapeutic potential

      White, N. M., Feng, F. Y. & Maher, C. A., 2013, In: Current Drug Targets. 14, 4, p. 450-459 10 p.

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

      Open Access
      16 Scopus citations

    • Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia

      Velusamy, T., Palanisamy, N., Kalyana-Sundaram, S., Sahasrabuddhe, A. A., Maher, C. A., Robinson, D. R., Bahler, D. W., Cornell, T. T., Wilson, T. E., Lim, M. S., Chinnaiyan, A. M. & Elenitoba-Johnson, K. S. J., Feb 19 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 8, p. 3035-3040 6 p.

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

      Open Access
      40 Scopus citations

    • Transcription Factors OVOL1 and OVOL2 Induce the Mesenchymal to Epithelial Transition in Human Cancer

      Roca, H., Hernandez, J., Weidner, S., McEachin, R. C., Fuller, D., Sud, S., Schumann, T., Wilkinson, J. E., Zaslavsky, A., Li, H., Maher, C. A., Daignault-Newton, S., Healy, P. N. & Pienta, K. J., Oct 4 2013, In: PloS one. 8, 10, e76773.

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

      Open Access
      193 Scopus citations
    • 2012

      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 others, Pleasance, 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
      3283 Scopus citations

    • From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer

      Lapuk, A. V., Wu, C., Wyatt, A. W., McPherson, A., McConeghy, B. J., Brahmbhatt, S., Mo, F., Zoubeidi, A., Anderson, S., Bell, R. H., Haegert, A., Shukin, R., Wang, Y., Fazli, L., Hurtado-Coll, A., Jones, E. C., Hach, F., Hormozdiari, F., Hajirasouliha, I. & Boutros, P. C. & 12 others, Bristow, R. G., Zhao, Y., Marra, M. A., Fanjul, A., Maher, C. A., Chinnaiyan, A. M., Rubin, M. A., Beltran, H., Cenk Sahinalp, S., Gleave, M. E., Volik, S. V. & Collins, C. C., Jul 2012, In: Journal of Pathology. 227, 3, p. 286-297 12 p.

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

      158 Scopus citations

    • Genetic and epigenetic loss of microRNA-31 leads to feed-forward expression of EZH2 in melanoma

      Asangani, I. A., Harms, P. W., Dodson, L., Pandhi, M., Kunju, L. P., Maher, C. A., Fullen, D. R., Johnson, T. M., Giordano, T. J., Palanisamy, N. & Chinnaiyan, A. M., Sep 2012, In: Oncotarget. 3, 9, p. 1011-1025 15 p.

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

      Open Access
      121 Scopus citations

    • Genomic landscape of non-small cell lung cancer in smokers and never-smokers

      Govindan, R., Ding, L., Griffith, M., Subramanian, J., Dees, N. D., Kanchi, K. L., Maher, C. A., Fulton, R., Fulton, L., Wallis, J., Chen, K., Walker, J., McDonald, S., Bose, R., Ornitz, D., Xiong, D., You, M., Dooling, D. J., Watson, M. & Mardis, E. R. & 1 others, Wilson, R. K., Sep 14 2012, In: Cell. 150, 6, p. 1121-1134 14 p.

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

      Open Access
      1007 Scopus citations

    • Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer

      Wu, C., Wyatt, A. W., Lapuk, A. V., McPherson, A., McConeghy, B. J., Bell, R. H., Anderson, S., Haegert, A., Brahmbhatt, S., Shukin, R., Mo, F., Li, E., Fazli, L., Hurtado-Coll, A., Jones, E. C., Butterfield, Y. S., Hach, F., Hormozdiari, F., Hajirasouliha, I. & Boutros, P. C. & 10 others, Bristow, R. G., Jones, S. J. M., Hirst, M., Marra, M. A., Maher, C. A., Chinnaiyan, A. M., Sahinalp, S. C., Gleave, M. E., Volik, S. V. & Collins, C. C., May 2012, In: Journal of Pathology. 227, 1, p. 53-61 9 p.

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

      63 Scopus citations

    • Next generation sequencing of prostate cancer from a patient identifies a deficiency of methylthioadenosine phosphorylase, an exploitable tumor target

      Collins, C. C., Volik, S. V., Lapuk, A. V., Wang, Y., Gout, P. W., Wu, C., Xue, H., Cheng, H., Haegert, A., Bell, R. H., Brahmbhatt, S., Anderson, S., Fazli, L., Hurtado-Coll, A., Rubin, M. A., Demichelis, F., Beltran, H., Hirst, M., Marra, M. & Maher, C. A. & 5 others, Chinnaiyan, A. M., Gleave, M., Bertino, J. R., Lubin, M. & Wang, Y., Mar 2012, In: Molecular Cancer Therapeutics. 11, 3, p. 775-781 7 p.

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

      Open Access
      31 Scopus citations

    • Whole-genome analysis informs breast cancer response to aromatase inhibition

      Ellis, M. J., Ding, L., Shen, D., Luo, J., Suman, V. J., Wallis, J. W., Van Tine, B. A., Hoog, J., Goiffon, R. J., Goldstein, T. C., Ng, S., Lin, L., Crowder, R., Snider, J., Ballman, K., Weber, J., Chen, K., Koboldt, D. C., Kandoth, C. & Schierding, W. S. & 39 others, McMichael, J. F., Miller, C. A., Lu, C., Harris, C. C., McLellan, M. D., Wendl, M. C., Deschryver, K., Allred, D. C., Esserman, L., Unzeitig, G., Margenthaler, J., Babiera, G. V., Marcom, P. K., Guenther, J. M., Leitch, M., Hunt, K., Olson, J., Tao, Y., Maher, C. A., Fulton, L. L., Fulton, R. S., Harrison, M., Oberkfell, B., Du, F., Demeter, R., Vickery, T. L., Elhammali, A., Piwnica-Worms, H., McDonald, S., Watson, M., Dooling, D. J., Ota, D., Chang, L. W., Bose, R., Ley, T. J., Piwnica-Worms, D., Stuart, J. M., Wilson, R. K. & Mardis, E. R., Jun 21 2012, In: Nature. 486, 7403, p. 353-360 8 p.

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

      Open Access
      883 Scopus citations
    • 2011

      A comparison of single molecule and amplification based sequencing of cancer transcriptomes

      Sam, L. T., Lipson, D., Raz, T., Cao, X., Thompson, J., Milos, P. M., Robinson, D., Chinnaiyan, A. M., Kumar-Sinha, C. & Maher, C. A., 2011, In: PloS one. 6, 3, e17305.

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

      Open Access
      41 Scopus citations

    • A p53/miRNA-34 axis regulates Snail1-dependent cancer cell epithelial-mesenchymal transition

      Kim, N. H., Kim, H. S., Li, X. Y., Lee, I., Choi, H. S., Kang, S. E., Cha, S. Y., Ryu, J. K., Yoon, D., Fearon, E. R., Rowe, R. G., Lee, S., Maher, C. A., Weiss, S. J. & Yook, J. I., Oct 31 2011, In: Journal of Cell Biology. 195, 3, p. 417-433 17 p.

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

      Open Access
      381 Scopus citations

    • ChimeraScan: A tool for identifying chimeric transcription in sequencing data

      Iyer, M. K., Chinnaiyan, A. M. & Maher, C. A., Oct 2011, In: Bioinformatics. 27, 20, p. 2903-2904 2 p., btr467.

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

      Open Access
      226 Scopus citations

    • Coordinated Regulation of Polycomb Group Complexes through microRNAs in Cancer

      Cao, Q., Mani, R. S., Ateeq, B., Dhanasekaran, S. M., Asangani, I. A., Prensner, J. R., Kim, J. H., Brenner, J. C., Jing, X., Cao, X., Wang, R., Li, Y., Dahiya, A., Wang, L., Pandhi, M., Lonigro, R. J., Wu, Y. M., Tomlins, S. A., Palanisamy, N. & Qin, Z. & 4 others, Yu, J., Maher, C. A., Varambally, S. & Chinnaiyan, A. M., Aug 16 2011, In: Cancer Cell. 20, 2, p. 187-199 13 p.

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

      Open Access
      192 Scopus citations

    • Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

      Kim, J. H., Dhanasekaran, S. M., Prensner, J. R., Cao, X., Robinson, D., Kalyana-Sundaram, S., Huang, C., Shankar, S., Jing, X., Iyer, M., Hu, M., Sam, L., Grasso, C., Maher, C. A., Palanisamy, N., Mehra, R., Kominsky, H. D., Siddiqui, J., Yu, J. & Qin, Z. S. & 1 others, Chinnaiyan, A. M., Jul 2011, In: Genome research. 21, 7, p. 1028-1041 14 p.

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

      Open Access
      167 Scopus citations

    • Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer

      Robinson, D. R., Kalyana-Sundaram, S., Wu, Y. M., Shankar, S., Cao, X., Ateeq, B., Asangani, I. A., Iyer, M., Maher, C. A., Grasso, C. S., Lonigro, R. J., Quist, M., Siddiqui, J., Mehra, R., Jing, X., Giordano, T. J., Sabel, M. S., Kleer, C. G., Palanisamy, N. & Natrajan, R. & 4 others, Lambros, M. B., Reis-Filho, J. S., Kumar-Sinha, C. & Chinnaiyan, A. M., Dec 2011, In: Nature medicine. 17, 12, p. 1646-1651 6 p.

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

      290 Scopus citations

    • Genome-wide characterization of the HD-ZIP IV transcription factor family in maize: Preferential expression in the epidermis

      Javelle, M., Klein-Cosson, C., Vernoud, V., Boltz, V., Maher, C., Timmermans, M., Depège-Fargeix, N. & Rogowsky, P. M., Oct 2011, In: Plant Physiology. 157, 2, p. 790-803 14 p.

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

      Open Access
      86 Scopus citations

    • Mechanistic Rationale for Inhibition of Poly(ADP-Ribose) Polymerase in ETS Gene Fusion-Positive Prostate Cancer

      Brenner, J. C., Ateeq, B., Li, Y., Yocum, A. K., Cao, Q., Asangani, I. A., Patel, S., Wang, X., Liang, H., Yu, J., Palanisamy, N., Siddiqui, J., Yan, W., Cao, X., Mehra, R., Sabolch, A., Basrur, V., Lonigro, R. J., Yang, J. & Tomlins, S. A. & 8 others, Maher, C. A., Elenitoba-Johnson, K. S. J., Hussain, M., Navone, N. M., Pienta, K. J., Varambally, S., Feng, F. Y. & Chinnaiyan, A. M., May 17 2011, In: Cancer Cell. 19, 5, p. 664-678 15 p.

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

      Open Access
      374 Scopus citations

    • Targeting of microRNA-142-3p in dendritic cells regulates endotoxin-induced mortality

      Sun, Y., Varambally, S., Maher, C. A., Cao, Q., Chockley, P., Toubai, T., Malter, C., Nieves, E., Tawara, I., Wang, Y., Ward, P. A., Chinnaiyan, A. & Reddy, P., Jun 9 2011, In: Blood. 117, 23, p. 6172-6183 12 p.

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

      Open Access
      129 Scopus citations

    • Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

      Prensner, J. R., Iyer, M. K., Balbin, O. A., Dhanasekaran, S. M., Cao, Q., Brenner, J. C., Laxman, B., Asangani, I. A., Grasso, C. S., Kominsky, H. D., Cao, X., Jing, X., Wang, X., Siddiqui, J., Wei, J. T., Robinson, D., Iyer, H. K., Palanisamy, N., Maher, C. A. & Chinnaiyan, A. M., Aug 2011, In: Nature Biotechnology. 29, 8, p. 742-749 8 p.

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

      900 Scopus citations
    • 2010

      HPeak: An HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

      Qin, Z. S., Yu, J., Shen, J., Maher, C. A., Hu, M., Kalyana-Sundaram, S., Yu, J. & Chinnaiyan, A. M., Jul 2 2010, In: BMC bioinformatics. 11, 369.

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

      Open Access
      87 Scopus citations

    • NGSQC: Cross-platform quality analysis pipeline for deep sequencing data

      Dai, M., Thompson, R. C., Maher, C., Contreras-Galindo, R., Kaplan, M. H., Markovitz, D. M., Omenn, G. & Meng, F., Dec 2 2010, In: BMC genomics. 11, SUPPL. 4, S7.

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

      Open Access
      95 Scopus citations

    • Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma

      Palanisamy, N., Ateeq, B., Kalyana-Sundaram, S., Pflueger, D., Ramnarayanan, K., Shankar, S., Han, B., Cao, Q., Cao, X., Suleman, K., Kumar-Sinha, C., Dhanasekaran, S. M., Chen, Y. B., Esgueva, R., Banerjee, S., Lafargue, C. J., Siddiqui, J., Demichelis, F., Moeller, P. & Bismar, T. A. & 11 others, Kuefer, R., Fullen, D. R., Johnson, T. M., Greenson, J. K., Giordano, T. J., Tan, P., Tomlins, S. A., Varambally, S., Rubin, M. A., Maher, C. A. & Chinnaiyan, A. M., Jul 2010, In: Nature medicine. 16, 7, p. 793-798 6 p.

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

      Open Access
      420 Scopus citations
    • 2009

      A genome-wide characterization of microRNA genes in maize

      Zhang, L., Chia, J. M., Kumari, S., Stein, J. C., Liu, Z., Narechania, A., Maher, C. A., Guill, K., McMullen, M. D. & Ware, D., Nov 2009, In: PLoS genetics. 5, 11, e1000716.

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

      Open Access
      305 Scopus citations

    • Chimeric transcript discovery by paired-end transcriptome sequencing

      Maher, C. A., Palanisamy, N., Brenner, J. C., Cao, X., Kalyana-Sundaram, S., Luo, S., Khrebtukova, I., Barrette, T. R., Grasso, C., Yu, J., Lonigro, R. J., Schroth, G., Kumar-Sinha, C. & Chinnaiyan, A. M., Jul 28 2009, In: Proceedings of the National Academy of Sciences of the United States of America. 106, 30, p. 12353-12358 6 p.

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

      Open Access
      283 Scopus citations

    • miR-24 Inhibits Cell Proliferation by Targeting E2F2, MYC, and Other Cell-Cycle Genes via Binding to "Seedless" 3′UTR MicroRNA Recognition Elements

      Lal, A., Navarro, F., Maher, C. A., Maliszewski, L. E., Yan, N., O'Day, E., Chowdhury, D., Dykxhoorn, D. M., Tsai, P., Hofmann, O., Becker, K. G., Gorospe, M., Hide, W. & Lieberman, J., Sep 11 2009, In: Molecular cell. 35, 5, p. 610-625 16 p.

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

      Open Access
      527 Scopus citations

    • ProbeMatch: Rapid alignment of oligonucleotides to genome allowing both gaps and mismatches

      Kim, Y. J., Teletia, N., Ruotti, V., Maher, C. A., Chinnaiyan, A. M., Stewart, R., Thomson, J. A. & Patel, J. M., Jun 2009, In: Bioinformatics. 25, 11, p. 1424-1425 2 p.

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

      Open Access
      18 Scopus citations

    • The Sorghum bicolor genome and the diversification of grasses

      Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A. K., Chapman, J., Feltus, F. A., Gowik, U. & Grigoriev, I. V. & 25 others, Lyons, E., Maher, C. A., Martis, M., Narechania, A., Otillar, R. P., Penning, B. W., Salamov, A. A., Wang, Y., Zhang, L., Carpita, N. C., Freeling, M., Gingle, A. R., Hash, C. T., Keller, B., Klein, P., Kresovich, S., McCann, M. C., Ming, R., Peterson, D. G., Mehboob-Ur-Rahman, Ware, D., Westhoff, P., Mayer, K. F. X., Messing, J. & Rokhsar, D. S., Jan 29 2009, In: Nature. 457, 7229, p. 551-556 6 p.

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

      Open Access
      2438 Scopus citations

    • The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

      Suzuki, H., Forrest, A. R. R., Van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., De Hoon, M. J. L., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E. & Asada, M. & 140 others, Asahara, H., Bailey, T., Bajic, V. B., Bauer, D., Beckhouse, A. G., Bertin, N., Björkegren, J., Brombacher, F., Bulger, E., Chalk, A. M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P. G., Essack, M., Faulkner, G. J., Fink, J. L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S. M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hörnquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M. C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., MacPherson, C., Maeda, N., Maher, C. A., Maqungo, M., Mar, J., Matigian, N. A., Matsuda, H., Mattick, J. S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schönbach, C., Schwartz, A. S., Semple, C. A., Sera, M., Severin, J., Shirahige, K., Simons, C., St. Laurent, G., Suzuki, M., Suzuki, T., Sweet, M. J., Taft, R. J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M. S., Teasdale, R. D., Tegnér, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C. A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D. A., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J. & Hayashizaki, Y., May 2009, In: Nature Genetics. 41, 5, p. 553-562 10 p.

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

      Open Access
      363 Scopus citations

    • Transcriptome sequencing to detect gene fusions in cancer

      Maher, C. A., Kumar-Sinha, C., Cao, X., Kalyana-Sundaram, S., Han, B., Jing, X., Sam, L., Barrette, T., Palanisamy, N. & Chinnaiyan, A. M., Mar 5 2009, In: Nature. 458, 7234, p. 97-101 5 p.

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

      733 Scopus citations
    • 2008

      Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

      Kim, H. R., Hurwitz, B., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J. C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J. L., Stein, L., Ware, D., Jackson, S. A., Soderlund, C. & Wing, R. A., Feb 28 2008, In: Genome biology. 9, 2, R45.

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

      Open Access
      77 Scopus citations

    • Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)

      Lu, C., Jeong, D. H., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, S. R., Maher, C., Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B. C. & Green, P. J., Mar 25 2008, In: Proceedings of the National Academy of Sciences of the United States of America. 105, 12, p. 4951-4956 6 p.

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

      Open Access
      202 Scopus citations

    • Genome-wide analysis of cancer/testis gene expression

      Hofmann, O., Caballero, O. L., Stevenson, B. J., Chen, Y. T., Cohen, T., Chua, R., Maher, C. A., Panji, S., Schaefer, U., Kruger, A., Lehvaslaiho, M., Carninci, P., Hayashizaki, Y., Jongeneel, C. V., Simpson, A. J. G., Old, L. J. & Hide, W., Dec 23 2008, In: Proceedings of the National Academy of Sciences of the United States of America. 105, 51, p. 20422-20427 6 p.

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

      Open Access
      302 Scopus citations

    • Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer

      Varambally, S., Cao, Q., Mani, R. S., Shankar, S., Wang, X., Ateeq, B., Laxman, B., Cao, X., Jing, X., Ramnarayanan, K., Brenner, J. C., Yu, J., Kim, J. H., Han, B., Tan, P., Kumar-Sinha, C., Lonigro, R. J., Palanisamy, N., Maher, C. A. & Chinnaiyan, A. M., Dec 12 2008, In: Science. 322, 5908, p. 1695-1699 5 p.

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

      Open Access
      947 Scopus citations
    • 2006

      Evolution of Arabidopsis microRNA families through duplication events

      Maher, C., Stein, L. & Ware, D., Apr 2006, In: Genome research. 16, 4, p. 510-519 10 p.

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

      Open Access
      287 Scopus citations
    • 2002

      Creating genetic applications for informal science learning in multi-user virtual environments

      Maher, C. & Corbit, M., 2002, In: Journal of Network and Computer Applications. 25, 4, p. 295-308 14 p.

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

      3 Scopus citations