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Research Output

  • 11540 Citations
  • 65 Article
  • 8 Review article
  • 3 Comment/debate
  • 2 Letter
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Article
2002

Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays

Yu, J., Othman, M. I., Farjo, R., Zareparsi, S., MacNee, S. P., Yoshida, S. & Swaroop, A., Dec 1 2002, In : Molecular vision. 8, p. 130-137 8 p.

Research output: Contribution to journalArticle

62 Scopus citations

Mouse eye gene microarrays for investigating ocular development and disease

Farjo, R., Yu, J., Othman, M. I., Yoshida, S., Sheth, S., Glaser, T., Baehr, W. & Swaroop, A., Mar 5 2002, In : Vision Research. 42, 4, p. 463-470 8 p.

Research output: Contribution to journalArticle

39 Scopus citations
2003

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

Yu, J., Farjo, R., MacNee, S. P., Baehr, W., Stambolian, D. E. & Swaroop, A., 2003, In : Genome biology. 4, 10, p. R65

Research output: Contribution to journalArticle

39 Scopus citations

From disease genes to cellular pathways: A progress report

Yu, J., Mears, A. J., Yoshida, S., Farjo, R., Carter, T. A., Ghosh, D., Hero, A., Barlow, C. & Swaroop, A., Jan 1 2003, In : Novartis Foundation Symposium. 255, p. 147-160 14 p.

Research output: Contribution to journalArticle

4 Scopus citations
2004

Altered expression of genes of the Bmp/Smad and Wnt/calcium signaling pathways in the cone-only Nr1-/- mouse retina, revealed by gene profiling using custom cDNA microarrays

Yu, J., He, S., Friedman, J. S., Akimoto, M., Ghosh, D., Mears, A. J., Hicks, D. & Swaroop, A., Oct 1 2004, In : Journal of Biological Chemistry. 279, 40, p. 42211-42220 10 p.

Research output: Contribution to journalArticle

47 Scopus citations

From disease genes to cellular pathways: a progress report.

Yu, J., Mears, A. J., Yoshida, S., Farjo, R., Carter, T. A., Ghosh, D., Hero, A., Barlow, C. & Swaroop, A., Mar 12 2004, In : Novartis Foundation Symposium. 255, p. 147-160 14 p.

Research output: Contribution to journalArticle

2007

A polycomb repression signature in metastatic prostate cancer predicts cancer outcome

Yu, J., Yu, J., Rhodes, D. R., Tomlins, S. A., Cao, X., Chen, G., Mehra, R., Wang, X., Ghosh, D., Shah, R. B., Varambally, S., Pienta, K. J. & Chinnaiyan, A. M., Nov 15 2007, In : Cancer Research. 67, 22, p. 10657-10663 7 p.

Research output: Contribution to journalArticle

237 Scopus citations

Autoantibody profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma

Chen, G., Wang, X., Yu, J., Varambally, S., Yu, J., Thomas, D. G., Lin, M. Y., Vishnu, P., Wang, Z., Wang, R., Fielhauer, J., Ghosh, D., Giordano, T. J., Giacherio, D., Chang, A. C., Orringer, M. B., El-Hefnawy, T., Bigbee, W. L., Beer, D. G. & Chinnaiyan, A. M., Apr 1 2007, In : Cancer Research. 67, 7, p. 3461-3467 7 p.

Research output: Contribution to journalArticle

68 Scopus citations

Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer

Tomlins, S. A., Laxman, B., Dhanasekaran, S. M., Helgeson, B. E., Cao, X., Morris, D. S., Menon, A., Jing, X., Cao, Q., Han, B., Yu, J., Wang, L., Montie, J. E., Rubin, M. A., Pienta, K. J., Roulston, D., Shah, R. B., Varambally, S., Mehra, R. & Chinnaiyan, A. M., Aug 2 2007, In : Nature. 448, 7153, p. 595-599 5 p.

Research output: Contribution to journalArticle

577 Scopus citations

Feature selection and molecular classification of cancer using genetic programming

Yu, J., Yu, J., Almal, A. A., Dhanasekaran, S. M., Ghosh, D., Worzel, W. P. & Chinnaiyan, A. M., Apr 2007, In : Neoplasia. 9, 4, p. 292-303 12 p.

Research output: Contribution to journalArticle

55 Scopus citations

Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control

Zhao, B., Wei, X., Li, W., Udan, R. S., Yang, Q., Kim, J., Xie, J., Ikenoue, T., Yu, J., Li, L., Zheng, P., Ye, K., Chinnaiyan, A., Halder, G., Lai, Z. C. & Guan, K. L., Nov 1 2007, In : Genes and Development. 21, 21, p. 2747-2761 15 p.

Research output: Contribution to journalArticle

1434 Scopus citations

Integrative Genomics Analysis Reveals Silencing of β-Adrenergic Signaling by Polycomb in Prostate Cancer

Yu, J., Cao, Q., Mehra, R., Laxman, B., Yu, J., Tomlins, S. A., Creighton, C. J., Dhanasekaran, S. M., Shen, R., Chen, G., Morris, D. S., Marquez, V. E., Shah, R. B., Ghosh, D., Varambally, S. & Chinnaiyan, A. M., Nov 13 2007, In : Cancer Cell. 12, 5, p. 419-431 13 p.

Research output: Contribution to journalArticle

156 Scopus citations
2008

A fluorescence in situ hybridization screen for E26 transformation-specific aberrations: Identification of DDX5-ETV4 fusion protein in prostate cancer

Han, B., Mehra, R., Dhanasekaran, S. M., Yu, J., Menon, A., Lonigro, R. J., Wang, X., Gong, Y., Wang, L., Shankar, S., Laxman, B., Shah, R. B., Varambally, S., Palanisamy, N., Tomlins, S. A., Kumar-Sinha, C. & Chinnaiyan, A. M., Sep 15 2008, In : Cancer Research. 68, 18, p. 7629-7637 9 p.

Research output: Contribution to journalArticle

123 Scopus citations

A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival

Yu, J., Yu, J., Cordero, K. E., Johnson, M. D., Ghosh, D., Rae, J. M., Chinnaiyan, A. M. & Lippman, M. E., Jan 2008, In : Neoplasia. 10, 1, p. 79-88 10 p.

Research output: Contribution to journalArticle

27 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 journalArticle

791 Scopus citations

Repression of E-cadherin by the polycomb group protein EZH2 in cancer

Cao, Q., Yu, J., Dhanasekaran, S. M., Kim, J. H., Mani, R. S., Tomlins, S. A., Mehra, R., Laxman, B., Cao, X., Yu, J., Kleer, C. G., Varambally, S. & Chinnaiyan, A. M., Dec 11 2008, In : Oncogene. 27, 58, p. 7274-7284 11 p.

Research output: Contribution to journalArticle

397 Scopus citations

Role of the TMPRSS2-ERG gene fusion in prostate cancer

Tomlins, S. A., Laxman, B., Varambally, S., Cao, X., Yu, J., Helgeson, B. E., Cao, Q., Prensner, J. R., Rubin, M. A., Shah, R. B., Mehra, R. & Chinnaiyan, A. M., Feb 2008, In : Neoplasia. 10, 2, p. 177-188 12 p.

Research output: Contribution to journalArticle

439 Scopus citations

TEAD mediates YAP-dependent gene induction and growth control

Zhao, B., Ye, X., Yu, J., Li, L., Li, W., Li, S., Yu, J., Lin, J. D., Wang, C. Y., Chinnaiyan, A. M., Lai, Z. C. & Guan, K. L., Jul 15 2008, In : Genes and Development. 22, 14, p. 1962-1971 10 p.

Research output: Contribution to journalArticle

1123 Scopus citations
2009

Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer

Wang, Q., Li, W., Zhang, Y., Yuan, X., Xu, K., Yu, J., Chen, Z., Beroukhim, R., Wang, H., Lupien, M., Wu, T., Regan, M. M., Meyer, C. A., Carroll, J. S., Manrai, A. K., Jänne, O. A., Balk, S. P., Mehra, R., Han, B., Chinnaiyan, A. M. & 8 others, Rubin, M. A., True, L., Fiorentino, M., Fiore, C., Loda, M., Kantoff, P. W., Liu, X. S. & Brown, M., Jul 23 2009, In : Cell. 138, 2, p. 245-256 12 p.

Research output: Contribution to journalArticle

581 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 journalArticle

260 Scopus citations

Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression

Sreekumar, A., Poisson, L. M., Rajendiran, T. M., Khan, A. P., Cao, Q., Yu, J., Laxman, B., Mehra, R., Lonigro, R. J., Li, Y., Nyati, M. K., Ahsan, A., Kalyana-Sundaram, S., Han, B., Cao, X., Byun, J., Omenn, G. S., Ghosh, D., Pennathur, S., Alexander, D. C. & 6 others, Berger, A., Shuster, J. R., Wei, J. T., Varambally, S., Beecher, C. & Chinnaiyan, A. M., Feb 12 2009, In : Nature. 457, 7231, p. 910-914 5 p.

Research output: Contribution to journalArticle

1438 Scopus citations

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases

Vellaichamy, A., Sreekumar, A., Strahler, J. R., Rajendiran, T., Yu, J., Varambally, S., Li, Y., Omenn, G. S., Chinnaiyan, A. M. & Nesvizhskii, A. I., Sep 18 2009, In : PloS one. 4, 9, e7075.

Research output: Contribution to journalArticle

37 Scopus citations
2010

An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression

Yu, J., Yu, J., Mani, R. S., Cao, Q., Brenner, C. J., Cao, X., Wang, X., Wu, L., Li, J., Hu, M., Gong, Y., Cheng, H., Laxman, B., Vellaichamy, A., Shankar, S., Li, Y., Dhanasekaran, S. M., Morey, R., Barrette, T., Lonigro, R. J. & 4 others, Tomlins, S. A., Varambally, S., Qin, Z. S. & Chinnaiyan, A. M., May 18 2010, In : Cancer Cell. 17, 5, p. 443-454 12 p.

Research output: Contribution to journalArticle

516 Scopus citations

Cdc42-interacting protein 4 promotes breast cancer cell invasion and formation of invadopodia through activation of N-WASp

Pichot, C. S., Arvanitis, C., Hartig, S. M., Jensen, S. A., Bechill, J., Marzouk, S., Yu, J., Frost, J. A. & Corey, S. J., Nov 1 2010, In : Cancer Research. 70, 21, p. 8347-8356 10 p.

Research output: Contribution to journalArticle

67 Scopus citations

ERG cooperates with androgen receptor in regulating trefoil factor 3 in prostate cancer disease progression

Rickman, D. S., Chen, Y. B., Banerjee, S., Pan, Y., Yu, J., Vuong, T., Perner, S., Lafargue, C. J., Mertz, K. D., Setlur, S. R., Sircar, K., Chinnaiyan, A. M., Bismar, T. A., Rubin, M. A. & Demichelis, F., Jan 1 2010, In : Neoplasia. 12, 12, p. 1031-1040 10 p.

Research output: Contribution to journalArticle

47 Scopus citations

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 journalArticle

82 Scopus citations

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

Hu, M., Yu, J., Taylor, J. M. G., Chinnaiyan, A. M. & Qin, Z. S., Jan 7 2010, In : Nucleic acids research. 38, 7, p. 2154-2167 14 p., gkp1180.

Research output: Contribution to journalArticle

77 Scopus citations

The neuronal repellent SLIT2 is a target for repression by EZH2 in prostate cancer

Yu, J., Cao, Q., Yu, J., Wu, L., Dallol, A., Li, J., Chen, G., Grasso, C., Cao, X., Lonigro, R. J., Varambally, S., Mehra, R., Palanisamy, N., Wu, J. Y., Latif, F. & Chinnaiyan, A. M., Sep 30 2010, In : Oncogene. 29, 39, p. 5370-5380 11 p.

Research output: Contribution to journalArticle

56 Scopus citations

The role of YAP transcription coactivator in regulating stem cell self-renewal and differentiation

Lian, I., Kim, J., Okazawa, H., Zhao, J., Zhao, B., Yu, J., Chinnaiyan, A., Israel, M. A., Goldstein, L. S. B., Abujarour, R., Ding, S. & Guan, K. L., Jun 1 2010, In : Genes and Development. 24, 11, p. 1106-1118 13 p.

Research output: Contribution to journalArticle

395 Scopus citations
2011

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 journalArticle

157 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 1 2011, In : Genome research. 21, 7, p. 1028-1041 14 p.

Research output: Contribution to journalArticle

130 Scopus citations

Definition of a FoxA1 cistrome that is crucial for G 1 to S-phase cell-cycle transit in castration-resistant prostate cancer

Zhang, C., Wang, L., Wu, D., Chen, H., Chen, Z., Thomas-Ahner, J. M., Zynger, D. L., Eeckhoute, J., Yu, J., Luo, J., Brown, M., Clinton, S. K., Nephew, K. P., Huang, T. H. M., Li, W. & Wang, Q., Nov 1 2011, In : Cancer Research. 71, 21, p. 6738-6748 11 p.

Research output: Contribution to journalArticle

63 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 journalArticle

290 Scopus citations

The DEK oncoprotein is a Su(var) that is essential to heterochromatin integrity

Kappes, F., Waldmann, T., Mathew, V., Yu, J., Zhang, L., Khodadoust, M. S., Chinnaiyan, A. M., Luger, K., Erhardt, S., Schneider, R. & Markovitz, D. M., Apr 1 2011, In : Genes and Development. 25, 7, p. 673-678 6 p.

Research output: Contribution to journalArticle

50 Scopus citations
2012

Cell detachment activates the Hippo pathway via cytoskeleton reorganization to induce anoikis

Zhao, B., Li, L., Wang, L., Wang, C. Y., Yu, J. & Guan, K. L., Jan 1 2012, In : Genes and Development. 26, 1, p. 54-68 15 p.

Research output: Contribution to journalArticle

403 Scopus citations

Cooperation between Polycomb and androgen receptor during oncogenic transformation

Zhao, J. C., Yu, J., Runkle, C., Wu, L., Hu, M., Wu, D., Liu, J. S., Wang, Q., Qin, Z. S. & Yu, J., Feb 1 2012, In : Genome research. 22, 2, p. 322-331 10 p.

Research output: Contribution to journalArticle

70 Scopus citations
2013

Androgen receptor-independent function of FoxA1 in prostate cancer metastasis

Jin, H. J., Zhao, J. C., Ogden, I., Bergan, R. C. & Yu, J., Jun 15 2013, In : Cancer Research. 73, 12, p. 3725-3736 12 p.

Research output: Contribution to journalArticle

71 Scopus citations

BRCA1 is a negative modulator of the PRC2 complex

Wang, L., Zeng, X., Chen, S., Ding, L., Zhong, J., Zhao, J. C., Wang, L., Sarver, A., Koller, A., Zhi, J., Ma, Y., Yu, J., Chen, J. & Huang, H., May 29 2013, In : EMBO Journal. 32, 11, p. 1584-1597 14 p.

Research output: Contribution to journalArticle

77 Scopus citations

ERG is a critical regulator of Wnt/LEF1 signaling in prostate cancer

Wu, L., Zhao, J. C., Kim, J., Jin, H. J., Wang, C. Y. & Yu, J., Oct 1 2013, In : Cancer Research. 73, 19, p. 6068-6079 12 p.

Research output: Contribution to journalArticle

44 Scopus citations

The histone methyltransferase MMSET/WHSC1 activates TWIST1 to promote an epithelial-mesenchymal transition and invasive properties of prostate cancer

Ezponda, T., Popovic, R., Shah, M. Y., Martinez-Garcia, E., Zheng, Y., Min, D. J., Will, C., Neri, A., Kelleher, N. L., Yu, J. & Licht, J. D., Jun 6 2013, In : Oncogene. 32, 23, p. 2882-2890 9 p.

Research output: Contribution to journalArticle

76 Scopus citations

TMPRSS2-ERG gene fusions induce prostate tumorigenesis by modulating microRNA miR-200c

Kim, J., Wu, L., Zhao, J. C., Jin, H. J. & Yu, J., Nov 4 2013, In : Oncogene. 33, 44, p. 5183-5192 10 p.

Research output: Contribution to journalArticle

32 Scopus citations
2014

CCN3/NOV gene expression in human prostate cancer is directly suppressed by the androgen receptor

Wu, L., Runkle, C., Jin, H. J., Yu, J., Li, J., Yang, X., Kuzel, T., Lee, C. & Yu, J., Jan 23 2014, In : Oncogene. 33, 4, p. 504-513 10 p.

Research output: Contribution to journalArticle

27 Scopus citations

Cooperativity and equilibrium with FOXA1 define the androgen receptor transcriptional program

Jin, H. J., Zhao, J. C., Wu, L., Kim, J. & Yu, J., May 29 2014, In : Nature communications. 5, 3972.

Research output: Contribution to journalArticle

75 Scopus citations
2015

A miR-130a-YAP positive feedback loop promotes organ size and tumorigenesis

Shen, S., Guo, X., Yan, H., Lu, Y., Ji, X., Li, L., Liang, T., Zhou, D., Feng, X. H., Zhao, J. C., Yu, J., Gong, X. G., Zhang, L. & Zhao, B., Sep 4 2015, In : Cell Research. 25, 9, p. 997-1012 16 p.

Research output: Contribution to journalArticle

49 Scopus citations

LncRNA HOTAIR Enhances the Androgen-Receptor-Mediated Transcriptional Program and Drives Castration-Resistant Prostate Cancer

Zhang, A., Zhao, J. C., Kim, J., Fong, K. W., Yang, Y. A., Chakravarti, D., Mo, Y. Y. & Yu, J., Oct 6 2015, In : Cell reports. 13, 1, p. 209-221 13 p.

Research output: Contribution to journalArticle

128 Scopus citations

miR-573 inhibits prostate cancer metastasis by regulating epithelialmesenchymal transition

Wang, L., Song, G., Tan, W., Qi, M., Zhang, L., Chan, J., Yu, J., Han, J. & Han, B., Jan 1 2015, In : Oncotarget. 6, 34, p. 35978-35990 13 p.

Research output: Contribution to journalArticle

35 Scopus citations

The role of TXNDC5 in castration-resistant prostate cancer - Involvement of androgen receptor signaling pathway

Wang, L., Song, G., Chang, X., Tan, W., Pan, J., Zhu, X., Liu, Z., Qi, M., Yu, J. & Han, B., Sep 3 2015, In : Oncogene. 34, 36, p. 4735-4745 11 p.

Research output: Contribution to journalArticle

19 Scopus citations
2016

FOXA1 acts upstream of GATA2 and AR in hormonal regulation of gene expression

Zhao, J. C., Fong, K. W., Jin, H. J., Yang, Y. A., Kim, J. & Yu, J., Aug 18 2016, In : Oncogene. 35, 33, p. 4335-4344 10 p.

Research output: Contribution to journalArticle

29 Scopus citations

FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function

Yang, Y. A., Zhao, J. C., Fong, K. W., Kim, J., Li, S., Song, C., Song, B., Zheng, B., He, C. & Yu, J., Sep 30 2016, In : Nucleic acids research. 44, 17, p. 8153-8164 12 p.

Research output: Contribution to journalArticle

15 Scopus citations

KAT8 regulates androgen signaling in prostate cancer cells

Kim, J. Y., Yu, J., Abdulkadir, S. A. & Chakravarti, D., Aug 2016, In : Molecular Endocrinology. 30, 8, p. 925-936 12 p.

Research output: Contribution to journalArticle

6 Scopus citations