• 11194 Citations
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19992020

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Article

Aberrant Activation of a Gastrointestinal Transcriptional Circuit in Prostate Cancer Mediates Castration Resistance

Shukla, S., Cyrta, J., Murphy, D. A., Walczak, E. G., Ran, L., Agrawal, P., Xie, Y., Chen, Y., Wang, S., Zhan, Y., Li, D., Wong, E. W. P., Sboner, A., Beltran, H., Mosquera, J. M., Sher, J., Cao, Z., Wongvipat, J., Koche, R. P., Gopalan, A. & 5 others, Zheng, D., Rubin, M. A., Scher, H. I., Chi, P. & Chen, Y., Dec 11 2017, In : Cancer Cell. 32, 6, p. 792-806.e7

Research output: Contribution to journalArticle

22 Scopus citations
10 Scopus citations

A computational approach for identifying pseudogenes in the ENCODE regions.

Zheng, D. & Gerstein, M. B., 2006, In : Genome biology. 7 Suppl 1, p. S13.1-10

Research output: Contribution to journalArticle

28 Scopus citations

A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation

Wontakal, S. N., Guo, X., Smith, C., MacCarthy, T., Bresnick, E. H., Bergman, A., Snyder, M. P., Weissman, S. M., Zheng, D. & Skoultchi, A. I., Mar 6 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 10, p. 3832-3837 6 p.

Research output: Contribution to journalArticle

44 Scopus citations

A large gene network in immature Erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1

Wontakal, S. N., Guo, X., Will, B., Shi, M., Raha, D., Mahajan, M. C., Weissman, S., Snyder, M., Steidl, U., Zheng, D. & Skoultchi, A. I., Jun 2011, In : PLoS genetics. 7, 6, e1001392.

Research output: Contribution to journalArticle

30 Scopus citations

Allele-Biased Expression in Differentiating Human Neurons: Implications for Neuropsychiatric Disorders

Lin, M., Hrabovsky, A., Pedrosa, E., Wang, T., Zheng, D. & Lachman, H. M., Aug 30 2012, In : PloS one. 7, 8, e44017.

Research output: Contribution to journalArticle

46 Scopus citations

Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

Wiesner, T., Lee, W., Obenauf, A. C., Ran, L., Murali, R., Zhang, Q. F., Wong, E. W. P., Hu, W., Scott, S. N., Shah, R. H., Landa, I., Button, J., Lailler, N., Sboner, A., Gao, D., Murphy, D. A., Cao, Z., Shukla, S., Hollmann, T. J., Wang, L. & 12 others, Borsu, L., Merghoub, T., Schwartz, G. K., Postow, M. A., Ariyan, C. E., Fagin, J. A., Zheng, D., Ladanyi, M., Busam, K. J., Berger, M. F., Chen, Y. & Chi, P., Oct 15 2015, In : Nature. 526, 7573, p. 453-457 5 p.

Research output: Contribution to journalArticle

104 Scopus citations

Androgen receptor signaling regulates DNA repair in prostate cancers

Polkinghorn, W. R., Parker, J. S., Lee, M. X., Kass, E. M., Spratt, D. E., Iaquinta, P. J., Arora, V. K., Yen, W. F., Cai, L., Zheng, D., Carver, B. S., Chen, Y., Watson, P. A., Shah, N. P., Fujisawa, S., Goglia, A. G., Gopalan, A., Hieronymus, H., Wongvipat, J., Scardino, P. T. & 5 others, Zelefsky, M. J., Jasin, M., Chaudhuri, J., Powell, S. N. & Sawyers, C. L., Nov 2013, In : Cancer discovery. 3, 11, p. 1245-1253 9 p.

Research output: Contribution to journalArticle

209 Scopus citations

An H3K36 Methylation-Engaging Tudor Motif of Polycomb-like Proteins Mediates PRC2 Complex Targeting

Cai, L., Rothbart, S. B., Lu, R., Xu, B., Chen, W. Y., Tripathy, A., Rockowitz, S., Zheng, D., Patel, D. J., Allis, C. D., Strahl, B. D., Song, J. & Wang, G. G., Feb 7 2013, In : Molecular Cell. 49, 3, p. 571-582 12 p.

Research output: Contribution to journalArticle

126 Scopus citations

A PCR method for typing B-L̄II family (class II MHC) alleles in broiler chickens

Zheng, D., O'Keefe, G., Li, L., Johnson, L. W. & Ewald, S. J., Apr 1999, In : Animal Genetics. 30, 2, p. 109-119 11 p.

Research output: Contribution to journalArticle

23 Scopus citations

Architectural niche organization by LHX2 is linked to hair follicle stem cell function

Folgueras, A. R., Guo, X., Pasolli, H. A., Stokes, N., Polak, L., Zheng, D. & Fuchs, E., Sep 5 2013, In : Cell Stem Cell. 13, 3, p. 314-327 14 p.

Research output: Contribution to journalArticle

52 Scopus citations

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

Emanuelsson, O., Nagalakshmi, U., Zheng, D., Rozowsky, J. S., Urban, A. E., Du, J., Lian, Z., Stolc, V., Weissman, S., Snyder, M. & Gerstein, M. B., Jun 2007, In : Genome research. 17, 6, p. 886-897 12 p.

Research output: Contribution to journalArticle

25 Scopus citations
21 Scopus citations

Automated protein fold determination using a minimal NMR constraint strategy

Zheng, D., Huang, Y. J., Moseley, H. N. B., Xiao, R., Aramini, J., Swapna, G. V. T. & Montelione, G. T., Jun 1 2003, In : Protein Science. 12, 6, p. 1232-1246 15 p.

Research output: Contribution to journalArticle

50 Scopus citations

Bidirectional analysis of cryba4-crybb1 nascent transcription and nuclear accumulation of crybb3 mrnas in lens fibers

Limi, S., Zhao, Y., Guo, P., Lopez-Jones, M., Zheng, D., Singer, R. H., Skoultchi, A. I. & Cvekl, A., Jan 1 2019, In : Investigative Ophthalmology and Visual Science. 60, 1, p. 234-244 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis

Zhao, D., Lin, M., Pedrosa, E., Lachman, H. M. & Zheng, D., Nov 10 2017, In : BMC Genomics. 18, 1, 860.

Research output: Contribution to journalArticle

4 Scopus citations

Characterization of human pseudogene-derived non-coding RNAs for functional potential

Guo, X., Lin, M., Rockowitz, S., Lachman, H. M. & Zheng, D., Apr 3 2014, In : PloS one. 9, 4, e93972.

Research output: Contribution to journalArticle

33 Scopus citations

Characterization of the past and current duplication activities in the human 22q11.2 region

Guo, X., Freyer, L., Morrow, B. & Zheng, D., Jan 26 2011, In : BMC Genomics. 12, 71.

Research output: Contribution to journalArticle

16 Scopus citations

Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators

Sun, J., Rockowitz, S., Chauss, D., Wang, P., Kantorow, M., Zheng, D. & Cvekl, A., Aug 28 2015, In : Molecular vision. 21, p. 955-973 19 p.

Research output: Contribution to journalArticle

12 Scopus citations

Colony stimulating factor-1 receptor signaling networks inhibit mouse macrophage inflammatory responses by induction of microRNA-21

Caescu, C. I., Guo, X., Tesfa, L., Bhagat, T. D., Verma, A., Zheng, D. & Stanley, E. R., Feb 19 2015, In : Blood. 125, 8, p. e1-e13

Research output: Contribution to journalArticle

54 Scopus citations

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes

Balasubramanian, S., Zheng, D., Liu, Y. J., Fang, G., Frankish, A., Carriero, N., Robilotto, R., Cayting, P. & Gerstein, M., Jan 5 2009, In : Genome biology. 10, 1, R2.

Research output: Contribution to journalArticle

57 Scopus citations

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions

Rockowitz, S., Lien, W. H., Pedrosa, E., Wei, G., Lin, M., Zhao, K., Lachman, H. M., Fuchs, E. & Zheng, D., Jun 2014, In : PLoS Computational Biology. 10, 6, e1003671.

Research output: Contribution to journalArticle

20 Scopus citations

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: The anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity

Liu, Y. J., Zheng, D., Balasubramanian, S., Carriero, N., Khurana, E., Robilotto, R. & Gerstein, M. B., Oct 16 2009, In : BMC Genomics. 10, p. 480 1 p., 1471.

Research output: Contribution to journalArticle

35 Scopus citations

Comprehensive transcriptional landscape of aging mouse liver

White, R. R., Milholland, B., MacRae, S. L., Lin, M., Zheng, D. & Vijg, J., Nov 5 2015, In : BMC Genomics. 16, 1, 899.

Research output: Contribution to journalArticle

47 Scopus citations
45 Scopus citations

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells

Wang, P., Mokhtari, R., Pedrosa, E., Kirschenbaum, M., Bayrak, C., Zheng, D. & Lachman, H. M., Mar 20 2017, In : Molecular Autism. 8, 1, 11.

Research output: Contribution to journalArticle

69 Scopus citations

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment

Wang, P., Lin, M., Pedrosa, E., Hrabovsky, A., Zhang, Z., Guo, W., Lachman, H. M. & Zheng, D., Dec 2015, In : Molecular Autism. 6, 1, 48.

Research output: Contribution to journalArticle

63 Scopus citations

Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development

Ko, Y. A., Mohtat, D., Suzuki, M., Park, A. S. D., Izquierdo, M. C., Han, S. Y., Kang, H. M., Si, H., Hostetter, T., Pullman, J. M., Fazzari, M., Verma, A., Zheng, D., Greally, J. M. & Susztak, K., Oct 7 2013, In : Genome biology. 14, 10, R108.

Research output: Contribution to journalArticle

136 Scopus citations

Deletion size analysis of 1680 22q11.2DS subjects identifies a new recombination hotspot on chromosome 22q11.2

on behalf of the International Chromosome 22q11.2, International 22q11.2 Brain and Behavior Consortia, Apr 1 2018, In : Human molecular genetics. 27, 7, p. 1150-1163 14 p.

Research output: Contribution to journalArticle

6 Scopus citations

Development of patient-specific neurons in schizophrenia using induced pluripotent stem cells

Pedrosa, E., Sandler, V., Shah, A., Carroll, R., Chang, C., Rockowitz, S., Guo, X., Zheng, D. & Lachman, H. M., Oct 1 2011, In : Journal of Neurogenetics. 25, 3, p. 88-103 16 p.

Research output: Contribution to journalArticle

100 Scopus citations

Differential deployment of REST and CoREST promotes glial subtype specification and oligodendrocyte lineage maturation

Abrajano, J. J., Qureshi, I. A., Gokhan, S., Zheng, D., Bergman, A. & Mehler, M. F., Nov 3 2009, In : PloS one. 4, 11, e7665.

Research output: Contribution to journalArticle

61 Scopus citations

Disruption of interneuron neurogenesis in premature newborns and reversal with Estrogen treatment

Tibrewal, M., Cheng, B., Dohare, P., Hu, F., Mehdizadeh, R., Wang, P., Zheng, D., Ungvari, Z. & Ballabh, P., Jan 31 2018, In : Journal of Neuroscience. 38, 5, p. 1100-1113 14 p.

Research output: Contribution to journalArticle

8 Scopus citations

Dissection of Merkel cell formation in hairy and glabrous skin reveals a common requirement for FGFR2-mediated signalling

Nguyen, M. B., Valdes, V. J., Cohen, I., Pothula, V., Zhao, D., Zheng, D. & Ezhkova, E., Apr 2019, In : Experimental Dermatology. 28, 4, p. 374-382 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

Goldberg, A. D., Banaszynski, L. A., Noh, K. M., Lewis, P. W., Elsaesser, S. J., Stadler, S., Dewell, S., Law, M., Guo, X., Li, X., Wen, D., Chapgier, A., DeKelver, R. C., Miller, J. C., Lee, Y. L., Boydston, E. A., Holmes, M. C., Gregory, P. D., Greally, J. M., Rafii, S. & 9 others, Yang, C., Scambler, P. J., Garrick, D., Gibbons, R. J., Higgs, D. R., Cristea, I. M., Urnov, F. D., Zheng, D. & Allis, C. D., Mar 5 2010, In : Cell. 140, 5, p. 678-691 14 p.

Research output: Contribution to journalArticle

719 Scopus citations

DNA methylation is developmentally regulated for genes essential for cardiogenesis

Chamberlain, A. A., Lin, M., Lister, R. L., Maslov, A. A., Wang, Y., Suzuki, M., Wu, B., Greally, J. M., Zheng, D. & Zhou, B., 2014, In : Journal of the American Heart Association. 3, 3, 000976.

Research output: Contribution to journalArticle

32 Scopus citations

Down-regulation of Skp2 expression inhibits invasion and lung metastasis in osteosarcoma

Zhang, Y., Zvi, Y. S., Batko, B., Zaphiros, N., O’Donnell, E. F., Wang, J., Sato, K., Yang, R., Geller, D. S., Koirala, P., Zhang, W., Du, X., Piperdi, S., Liu, Y., Zheng, D., Roth, M., Gill, J., Zhang, J., Ren, T., Gorlick, R. & 2 others, Zi, X. & Hoang, B. H., Dec 1 2018, In : Scientific reports. 8, 1, 14294.

Research output: Contribution to journalArticle

12 Scopus citations

Drosophila RpS12 controls translation, growth, and cell competition through Xrp1

Ji, Z., Kiparaki, M., Folgado, V., Kumar, A., Blanco, J., Rimesso, G., Chuen, J., Liu, Y., Zheng, D. & Baker, N. E., 2019, In : PLoS genetics. 15, 12, e1008513.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Endocardial cells form the coronary arteries by angiogenesis through myocardial-endocardial VEGF signaling

Wu, B., Zhang, Z., Lui, W., Chen, X., Wang, Y., Chamberlain, A. A., Moreno-Rodriguez, R. A., Markwald, R. R., O'Rourke, B. P., Sharp, D. J., Zheng, D., Lenz, J., Baldwin, H. S., Chang, C. P. & Zhou, B., Nov 21 2012, In : Cell. 151, 5, p. 1083-1096 14 p.

Research output: Contribution to journalArticle

199 Scopus citations

Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons

Wang, P., Zhao, D., Lachman, H. M. & Zheng, D., Dec 1 2018, In : Translational psychiatry. 8, 1, 58.

Research output: Contribution to journalArticle

18 Scopus citations

Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses

Shen, Y., Stanislauskas, M., Li, G., Zheng, D. & Liu, L., Feb 17 2017, In : Scientific reports. 7, 42646.

Research output: Contribution to journalArticle

11 Scopus citations

Epigenetic Perturbations by Arg882-Mutated DNMT3A Potentiate Aberrant Stem Cell Gene-Expression Program and Acute Leukemia Development

Lu, R., Wang, P., Parton, T., Zhou, Y., Chrysovergis, K., Rockowitz, S., Chen, W. Y., Abdel-Wahab, O., Wade, P. A., Zheng, D. & Wang, G. G., Jul 11 2016, In : Cancer Cell. 30, 1, p. 92-107 16 p.

Research output: Contribution to journalArticle

60 Scopus citations

ERF mutations reveal a balance of ETS factors controlling prostate oncogenesis

Bose, R., Karthaus, W. R., Armenia, J., Abida, W., Iaquinta, P. J., Zhang, Z., Wongvipat, J., Wasmuth, E. V., Shah, N., Sullivan, P. S., Doran, M. G., Wang, P., Patruno, A., Zhao, Y., Zheng, D., Schultz, N. & Sawyers, C. L., Jun 29 2017, In : Nature. 546, 7660, p. 671-675 5 p.

Research output: Contribution to journalArticle

23 Scopus citations

ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss

Chen, Y., Chi, P., Rockowitz, S., Iaquinta, P. J., Shamu, T., Shukla, S., Gao, D., Sirota, I., Carver, B. S., Wongvipat, J., Scher, H. I., Zheng, D. & Sawyers, C. L., Aug 2013, In : Nature Medicine. 19, 8, p. 1023-1029 7 p.

Research output: Contribution to journalArticle

166 Scopus citations

ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas

Yang, H., Schramek, D., Adam, R. C., Keyes, B. E., Wang, P., Zheng, D. & Fuchs, E., Nov 21 2015, In : eLife. 4, NOVEMBER2015, e10870.

Research output: Contribution to journalArticle

38 Scopus citations

ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours

Chi, P., Chen, Y., Zhang, L., Guo, X., Wongvipat, J., Shamu, T., Fletcher, J. A., Dewell, S., Maki, R. G., Zheng, D., Antonescu, C. R., Allis, C. D. & Sawyers, C. L., Oct 14 2010, In : Nature. 467, 7317, p. 849-853 5 p.

Research output: Contribution to journalArticle

192 Scopus citations

Evolutionary origins of Pax6 control of crystallin genes

Cvekl, A., Zhao, Y., McGreal, R., Xie, Q., Gu, X. & Zheng, D., 2017, In : Genome Biology and Evolution. 9, 8, p. 2075-2092 18 p.

Research output: Contribution to journalArticle

10 Scopus citations

FOXF1 defines the core-regulatory circuitry in gastrointestinal stromal tumor

Ran, L., Chen, Y., Sher, J., Wong, E. W. P., Murphy, D., Zhang, J. Q., Li, D., Deniz, K., Sirota, I., Cao, Z., Wang, S., Guan, Y., Shukla, S., Li, K. Y., Chramiec, A., Xie, Y., Zheng, D., Koche, R. P., Antonescu, C. R., Chen, Y. & 1 others, Chi, P., Feb 2018, In : Cancer discovery. 8, 2, p. 234-251 18 p.

Research output: Contribution to journalArticle

13 Scopus citations

Gene duplication in the epigenomic era.

Zheng, D., Sep 2008, In : Epigenetics : official journal of the DNA Methylation Society. 3, 5, p. 250-253 4 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage

Lien, W. H., Guo, X., Polak, L., Lawton, L. N., Young, R. A., Zheng, D. & Fuchs, E., Sep 2 2011, In : Cell Stem Cell. 9, 3, p. 219-232 14 p.

Research output: Contribution to journalArticle

134 Scopus citations

Glucocorticoid receptor confers resistance to antiandrogens by bypassing androgen receptor blockade

Arora, V. K., Schenkein, E., Murali, R., Subudhi, S. K., Wongvipat, J., Balbas, M. D., Shah, N., Cai, L., Efstathiou, E., Logothetis, C., Zheng, D. & Sawyers, C. L., Dec 5 2013, In : Cell. 155, 6, p. 1309-1322 14 p.

Research output: Contribution to journalArticle

446 Scopus citations