Insights into Chinese prostate cancer with RNA-seq

le Sahu, Anirban, Iyer, Matthew K, Chinnaiyan, Arul M
Foilsithe 2012

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

le Iyer, Matthew K., Chinnaiyan, Arul M., Maher, Christopher A.
Foilsithe 2011

Oculus: faster sequence alignment by streaming read compression

le Veeneman, Brendan A, Iyer, Matthew K, Chinnaiyan, Arul M
Foilsithe 2012

TACO produces robust multi-sample transcriptome assemblies from RNA-seq

le Niknafs, Yashar S., Pandian, Balaji, Iyer, Hariharan K., Chinnaiyan, Arul M., Iyer, Matthew K.
Foilsithe in Nat Methods (2016)

Gene Fusions Associated with Recurrent Amplicons Represent a Class of Passenger Aberrations in Breast Cancer

le Kalyana-Sundaram, Shanker, Shankar, Sunita, DeRoo, Scott, Iyer, Matthew K, Palanisamy, Nallasivam, Chinnaiyan, Arul M, Kumar-Sinha, Chandan
Foilsithe 2012

TMPRSS2-ERG-mediated feed-forward regulation of wild-type ERG in human prostate cancers

le Mani, Ram-Shankar, Iyer, Matthew K., Cao, Qi, Brenner, J. Chad, Wang, Lei, Ghosh, Aparna, Cao, Xuhong, Lonigro, Robert J., Tomlins, Scott A., Varambally, Sooryanarayana, Chinnaiyan, Arul M.
Foilsithe 2011

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()()

le 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.
Foilsithe in Neoplasia (2014)

RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

le Widmann, Jeremy, Stombaugh, Jesse, McDonald, Daniel, Chocholousova, Jana, Gardner, Paul, Iyer, Matthew K., Liu, Zongzhi, Lozupone, Catherine A., Quinn, John, Smit, Sandra, Wikman, Shandy, Zaneveld, Jesse R.R., Knight, Rob
Foilsithe 2012

The Long Non-Coding RNA PCAT-1 Promotes Prostate Cancer Cell Proliferation through cMyc()()

le 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.
Foilsithe in Neoplasia (2014)

The lncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer

le Prensner, John R., Sahu, Anirban, Iyer, Matthew K., Malik, Rohit, Chandler, Benjamin, Asangani, Irfan A., Poliakov, Anton, Vergara, Ismael A., Alshalalfa, Mohammed, Jenkins, Robert B., Davicioni, Elai, Feng, Felix Y., Chinnaiyan, Arul M.
Foilsithe 2014

Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin

le 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
Foilsithe in Genome Biol (2015)

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

le 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.
Foilsithe 2012

Transcriptome Sequencing Identifies PCAT-1, a Novel lincRNA Implicated in Prostate Cancer Progression

le Prensner, John R., Iyer, Matthew K., Balbin, O. Alejandro, Dhanasekaran, Saravana M., Cao, Qi, Brenner, J. Chad, Laxman, Bharathi, Asangani, Irfan, Grasso, Catherine, Kominsky, Hal D., Cao, Xuhong, Jing, Xiaojun, Wang, Xiaoju, Siddiqui, Javed, Wei, John T., Robinson, Daniel, Iyer, Hari K., Palanisamy, Nallasivam, Maher, Christopher A., Chinnaiyan, Arul M.
Foilsithe 2011

The Landscape of Long Noncoding RNAs in the Human Transcriptome

le 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.
Foilsithe in Nat Genet (2015)

Nomination and validation of the long noncoding RNA SChLAP1 as a risk factor for metastatic prostate cancer progression: a multi-institutional high-throughput analysis

le Prensner, John R., Zhao, Shuang, Erho, Nicholas, Schipper, Matthew, Iyer, Matthew K., Dhanasekaran, Saravana M., Magi-Galluzzi, Cristina, Mehra, Rohit, Sahu, Anirban, Siddiqui, Javed, Davicioni, Elai, Den, Robert B., Dicker, Adam P., Karnes, R. Jeffrey, Wei, John T., Klein, Eric A., Jenkins, Robert B., Chinnaiyan, Arul M., Feng, Felix Y.
Foilsithe in Lancet Oncol (2014)

Identification of Recurrent NAB2-STAT6 Gene Fusions in Solitary Fibrous Tumor by Integrative Sequencing

le 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.
Foilsithe 2013

PCAT-1, a long noncoding RNA, regulates BRCA2 and controls homologous recombination in cancer

le Prensner, John R., Chen, Wei, Iyer, Matthew K., Cao, Qi, Ma, Teng, Han, Sumin, Sahu, Anirban, Malik, Rohit, Wilder-Romans, Kari, Navone, Nora, 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., Chinnaiyan, Arul M., Feng, Felix Y.
Foilsithe 2014

Prostate Cancer Cell–Stromal Cell Cross-Talk via FGFR1 Mediates Antitumor Activity of Dovitinib in Bone Metastases

le Wan, Xinhai, Corn, Paul G., Yang, Jun, Palanisamy, Nallasivam, Starbuck, Michael W., Efstathiou, Eleni, Li-Ning Tapia, Elsa M., Zurita, Amado J., Aparicio, Ana, Ravoori, Murali K., Vazquez, Elba S., Robinson, Dan R., Wu, Yi-Mi, Cao, Xuhong, Iyer, Matthew K., McKeehan, Wallace, Kundra, Vikas, Wang, Fen, Troncoso, Patricia, Chinnaiyan, Arul M., Logothetis, Christopher J., Navone, Nora M.
Foilsithe in Sci Transl Med (2014)

Oncogenic Role of THOR, a Conserved Cancer/Testis Long Noncoding RNA

le 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
Foilsithe in Cell (2017)

Targeting the MLL complex in castration resistant prostate cancer

le 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.
Foilsithe in Nat Med (2015)