The landscape of long noncoding RNAs in the human transcriptome von Iyer, Matthew K, Niknafs, Yashar S, Malik, Rohit, Singhal, Udit, Sahu, Anirban, Hosono, Yasuyuki, Barrette, Terrence R, Prensner, John R, Evans, Joseph R, Zhao, Shuang, Poliakov, Anton, Cao, Xuhong, Dhanasekaran, Saravana M, Wu, Yi-Mi, Robinson, Dan R, Beer, David G, Feng, Felix Y, Iyer, Hariharan K, Chinnaiyan, Arul M

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Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1 , an unannotated lincRNA implicated in disease progression von Chinnaiyan, Arul M, Prensner, John R, Iyer, Matthew K, Balbin, O Alejandro, Dhanasekaran, Saravana M, Cao, Qi, Brenner, J Chad, Laxman, Bharathi, Asangani, Irfan A, Grasso, Catherine S, Kominsky, Hal D, Cao, Xuhong, Jing, Xiaojun, Wang, Xiaoju, Siddiqui, Javed, Wei, John T, Robinson, Daniel, Iyer, Hari K, Palanisamy, Nallasivam, Maher, Christopher A

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ChimeraScan: a tool for identifying chimeric transcription in sequencing data von Iyer, Matthew K., Chinnaiyan, Arul M., Maher, Christopher A.

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Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA von Hosono, Yasuyuki, Niknafs, Yashar S., Prensner, John R., Iyer, Matthew K., Dhanasekaran, Saravana M., Mehra, Rohit, Pitchiaya, Sethuramasundaram, Tien, Jean, Escara-Wilke, June, Poliakov, Anton, Chu, Shih-Chun, Saleh, Sahal, Sankar, Keerthana, Su, Fengyun, Guo, Shuling, Qiao, Yuanyuan, Freier, Susan M., Bui, Huynh-Hoa, Cao, Xuhong, Malik, Rohit, Johnson, Timothy M., Beer, David G., Feng, Felix Y., Zhou, Weibin, Chinnaiyan, Arul M.

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Analysis of the androgen receptor–regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression von Zhang, Yajia, Pitchiaya, Sethuramasundaram, Cieślik, Marcin, Niknafs, Yashar S., Tien, Jean C.-Y., Hosono, Yasuyuki, Iyer, Matthew K., Yazdani, Sahr, Subramaniam, Shruthi, Shukla, Sudhanshu K., Jiang, Xia, Wang, Lisha, Liu, Tzu-Ying, Uhl, Michael, Gawronski, Alexander R., Qiao, Yuanyuan, Xiao, Lanbo, Dhanasekaran, Saravana M., Juckette, Kristin M., Kunju, Lakshmi P., Cao, Xuhong, Patel, Utsav, Batish, Mona, Shukla, Girish C., Paulsen, Michelle T., Ljungman, Mats, Jiang, Hui, Mehra, Rohit, Backofen, Rolf, Sahinalp, Cenk S., Freier, Susan M., Watt, Andrew T., Guo, Shuling, Wei, John T., Feng, Felix Y., Malik, Rohit, Chinnaiyan, Arul M.

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Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing von Robinson, Dan R, Wu, Yi-Mi, Kalyana-Sundaram, Shanker, Cao, Xuhong, Lonigro, Robert J, Sung, Yun-Shao, Chen, Chun-Liang, Zhang, Lei, Wang, Rui, Su, Fengyun, Iyer, Matthew K, Roychowdhury, Sameek, Siddiqui, Javed, Pienta, Kenneth J, Kunju, Lakshmi P, Talpaz, Moshe, Mosquera, Juan Miguel, Singer, Samuel, Schuetze, Scott M, Antonescu, Cristina R, Chinnaiyan, Arul M

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Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin von Tsoi, Lam C, Iyer, Matthew K, Stuart, Philip E, Swindell, William R, Gudjonsson, Johann E, Tejasvi, Trilokraj, Sarkar, Mrinal K, Li, Bingshan, Ding, Jun, Voorhees, John J, Kang, Hyun M, Nair, Rajan P, Chinnaiyan, Arul M, Abecasis, Goncalo R, Elder, James T

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RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1 von Prensner, John R, MD, Zhao, Shuang, MSc, Erho, Nicholas, MSc, Schipper, Matthew, PhD, Iyer, Matthew K, PhD, Dhanasekaran, Saravana M, PhD, Magi-Galluzzi, Cristina, MD, Mehra, Rohit, MD, Sahu, Anirban, BSc, Siddiqui, Javed, MSc, Davicioni, Elai, PhD, Den, Robert B, MD, Dicker, Adam P, Prof, Karnes, R Jeffrey, MD, Wei, John T, Prof, Klein, Eric A, Prof, Jenkins, Robert B, Prof, Chinnaiyan, Arul M, Prof, Feng, Felix Y, Dr

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The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex von Prensner, John R, Iyer, Matthew K, Sahu, Anirban, Asangani, Irfan A, Cao, Qi, Patel, Lalit, Vergara, Ismael A, Davicioni, Elai, Erho, Nicholas, Ghadessi, Mercedeh, Jenkins, Robert B, Triche, Timothy J, Malik, Rohit, Bedenis, Rachel, McGregor, Natalie, Ma, Teng, Chen, Wei, Han, Sumin, Jing, Xiaojun, Cao, Xuhong, Wang, Xiaoju, Chandler, Benjamin, Yan, Wei, Siddiqui, Javed, Kunju, Lakshmi P, Dhanasekaran, Saravana M, Pienta, Kenneth J, Feng, Felix Y, Chinnaiyan, Arul M

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PCAT-1, a Long Noncoding RNA, Regulates BRCA2 and Controls Homologous Recombination in Cancer von PRENSNER, John R, WEI CHEN, LOGOTHETIS, Christopher J, ARAUJO, John C, PISTERS, Louis L, TEWARI, Ashutosh K, CANMAN, Christine E, KNUDSEN, Karen E, KITABAYASHI, Naoki, RUBIN, Mark A, DEMICHELIS, Francesca, LAWRENCE, Theodore S, IYER, Matthew K, CHINNAIYAN, Arul M, FENG, Felix Y, QI CAO, TENG MA, SUMIN HAN, SAHU, Anirban, MALIK, Rohit, WILDER-ROMANS, Kari, NAVONE, Nora

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The Long Non-Coding RNA PCAT-1 Promotes Prostate Cancer Cell Proliferation through cMyc von Prensner, John R, Chen, Wei, Han, Sumin, Iyer, Matthew K, Cao, Qi, Kothari, Vishal, Evans, Joseph R, Knudsen, Karen E, Paulsen, Michelle T, Ljungman, Mats, Lawrence, Theodore S, Chinnaiyan, Arul M, Feng, Felix Y

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The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression von Niknafs, Yashar S., Han, Sumin, Ma, Teng, Speers, Corey, Zhang, Chao, Wilder-Romans, Kari, Iyer, Matthew K., Pitchiaya, Sethuramasundaram, Malik, Rohit, Hosono, Yasuyuki, Prensner, John R., Poliakov, Anton, Singhal, Udit, Xiao, Lanbo, Kregel, Steven, Siebenaler, Ronald F., Zhao, Shuang G., Uhl, Michael, Gawronski, Alexander, Hayes, Daniel F., Pierce, Lori J., Cao, Xuhong, Collins, Colin, Backofen, Rolf, Sahinalp, Cenk S., Rae, James M., Chinnaiyan, Arul M., Feng, Felix Y.

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Targeting the MLL complex in castration-resistant prostate cancer von Malik, Rohit, Khan, Amjad P, Asangani, Irfan A, Cieślik, Marcin, Prensner, John R, Wang, Xiaoju, Iyer, Matthew K, Jiang, Xia, Borkin, Dmitry, Escara-Wilke, June, Stender, Rachell, Wu, Yi-Mi, Niknafs, Yashar S, Jing, Xiaojun, Qiao, Yuanyuan, Palanisamy, Nallasivam, Kunju, Lakshmi P, Krishnamurthy, Pranathi M, Yocum, Anastasia K, Mellacheruvu, Dattatreya, Nesvizhskii, Alexey I, Cao, Xuhong, Dhanasekaran, Saravana M, Feng, Felix Y, Grembecka, Jolanta, Cierpicki, Tomasz, Chinnaiyan, Arul M

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The lncRNA PCAT29 inhibits oncogenic phenotypes in prostate cancer von Malik, Rohit, Patel, Lalit, Prensner, John R, Shi, Yang, Iyer, Matthew K, Subramaniyan, Shruthi, Carley, Alexander, Niknafs, Yashar S, Sahu, Anirban, Han, Sumin, Ma, Teng, Liu, Meilan, Asangani, Irfan A, Jing, Xiaojun, Cao, Xuhong, Dhanasekaran, Saravana M, Robinson, Dan R, Feng, Felix Y, Chinnaiyan, Arul M

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A Novel RNA In Situ Hybridization Assay for the Long Noncoding RNA SChLAP1 Predicts Poor Clinical Outcome After Radical Prostatectomy in Clinically Localized Prostate Cancer von Mehra, Rohit, Shi, Yang, Udager, Aaron M, Prensner, John R, Sahu, Anirban, Iyer, Matthew K, Siddiqui, Javed, Cao, Xuhong, Wei, John, Jiang, Hui, Feng, Felix Y, Chinnaiyan, Arul M

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TACO produces robust multisample transcriptome assemblies from RNA-seq von Niknafs, Yashar S, Pandian, Balaji, Iyer, Hariharan K, Chinnaiyan, Arul M, Iyer, Matthew K

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Gene Fusions Associated with Recurrent Amplicons Represent a Class of Passenger Aberrations in Breast Cancer von Kalyana-Sundaram, Shanker, Shankar, Sunita, DeRoo, Scott, Iyer, Matthew K, Palanisamy, Nallasivam, Chinnaiyan, Arul M, Kumar-Sinha, Chandan

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Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers von Kalyana-Sundaram, Shanker, Kumar-Sinha, Chandan, Shankar, Sunita, Robinson, Dan R., Wu, Yi-Mi, Cao, Xuhong, Asangani, Irfan A., Kothari, Vishal, Prensner, John R., Lonigro, Robert J., Iyer, Matthew K., Barrette, Terrence, Shanmugam, Achiraman, Dhanasekaran, Saravana M., Palanisamy, Nallasivam, Chinnaiyan, Arul M.

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TMPRSS2―ERG-Mediated Feed-Forward Regulation of Wild-Type ERG in Human Prostate Cancers von MANI, Ram-Shankar, IYER, Matthew K, CHINNAIYAN, Arul M, QI CAO, CHAD BRENNER, J, LEI WANG, GHOSH, Aparna, XUHONG CAO, LONIGRO, Robert J, TOMLINS, Scott A, VARAMBALLY, Sooryanarayana

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Oculus: faster sequence alignment by streaming read compression von Veeneman, Brendan A, Iyer, Matthew K, Chinnaiyan, Arul M

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