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  • 2001
    1 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 journalArticlepeer-review

    3 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 journalArticlepeer-review

    Open Access
    251 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 journalArticlepeer-review

    Open Access
    74 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 journalArticlepeer-review

    Open Access
    175 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 journalArticlepeer-review

    256 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 journalArticlepeer-review

    888 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 journalArticlepeer-review

    Open Access
    262 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 journalArticlepeer-review

    270 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 journalArticlepeer-review

    Open Access
    478 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 journalArticlepeer-review

    Open Access
    16 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 journalArticlepeer-review

    Open Access
    2070 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 journalArticlepeer-review

    340 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 journalArticlepeer-review

    674 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 journalArticlepeer-review

    Open Access
    86 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 journalArticlepeer-review

    Open Access
    80 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 journalArticlepeer-review

    378 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 journalArticlepeer-review

    Open Access
    38 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 journalArticlepeer-review

    Open Access
    336 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 journalArticlepeer-review

    Open Access
    200 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 journalArticlepeer-review

    Open Access
    176 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 journalArticlepeer-review

    Open Access
    153 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 journalArticlepeer-review

    247 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 journalArticlepeer-review

    Open Access
    68 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 journalArticlepeer-review

    Open Access
    333 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 journalArticlepeer-review

    Open Access
    114 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 journalArticlepeer-review

    793 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 journalArticlepeer-review

    Open Access
    2760 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 journalArticlepeer-review

    141 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 journalArticlepeer-review

    Open Access
    108 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 journalArticlepeer-review

    Open Access
    862 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 journalArticlepeer-review

    54 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 journalArticlepeer-review

    Open Access
    29 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 journalArticlepeer-review

    Open Access
    787 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 journalArticlepeer-review

    Open Access
    109 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 journalArticlepeer-review

    Open Access
    427 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 journalArticlepeer-review

    15 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 journalArticlepeer-review

    34 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 journalArticlepeer-review

    Open Access
    149 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 journalArticlepeer-review

    Open Access
    31 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 journalArticlepeer-review

    Open Access
    70 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 journalArticlepeer-review

    Open Access
    3207 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 journalArticlepeer-review

    Open Access
    22 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 journalArticlepeer-review

    Open Access
    12 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 journalArticlepeer-review

    Open Access
    164 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 journalArticlepeer-review

    Open Access
    54 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 journalArticlepeer-review

    Open Access
    123 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 journalArticlepeer-review

    Open Access
    64 Scopus citations
  • 2016

    A genomic case study of mixed fibrolamellar hepatocellular carcinoma

    Griffith, O. L., M.Griffith, K.Krysiak, V.Magrini, A.Ramu, Z.L.Skidmore, J.Kunisaki, R.Austin, S.McGrath, J.Zhang, R.Demeter, T.Graves, J.M.Eldred, J.Walker, D.E.Larson, C.A.Maher, Y.Lin, W.Chapman, A.Mahadevan, R.Miksad & 3 others, I.Nasser, D.W.Hanto & E.R.Mardis, Jun 18 2016, In: Annals of Oncology. 27, 6, p. 1148-1154 7 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    14 Scopus citations
  • An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer

    Ruggles, K. V., Tang, Z., Wang, X., Grover, H., Askenazi, M., Teubl, J., Cao, S., McLellan, M. D., Clauser, K. R., Tabb, D. L., Mertins, P., Slebos, R., Erdmann-Gilmore, P., Li, S., Gunawardena, H. P., Xie, L., Liu, T., Zhou, J. Y., Sun, S., Hoadley, K. A. & 18 others, Perou, C. M., Chen, X., Davies, S. R., Maher, C. A., Kinsinger, C. R., Rodland, K. D., Zhang, H., Zhang, Z., Ding, L., Townsend, R. R., Rodriguez, H., Chan, D., Smith, R. D., Liebler, D. C., Carr, S. A., Payne, S., Ellis, M. J. & Fenyo, D., Mar 2016, In: Molecular and Cellular Proteomics. 15, 3, p. 1060-1071 12 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    78 Scopus citations