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19992020

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Article
2020

Microglial Homeostasis Requires Balanced CSF-1/CSF-2 Receptor Signaling

Chitu, V., Biundo, F., Shlager, G. G. L., Park, E. S., Wang, P., Gulinello, M. E., Gokhan, Ş., Ketchum, H. C., Saha, K., DeTure, M. A., Dickson, D. W., Wszolek, Z. K., Zheng, D., Croxford, A. L., Becher, B., Sun, D., Mehler, M. F. & Stanley, E. R., Mar 3 2020, In : Cell Reports. 30, 9, p. 3004-3019.e5

Research output: Contribution to journalArticle

Open Access

NFI transcription factors provide chromatin access to maintain stem cell identity while preventing unintended lineage fate choices

Adam, R. C., Yang, H., Ge, Y., Infarinato, N. R., Gur-Cohen, S., Miao, Y., Wang, P., Zhao, Y., Lu, C. P., Kim, J. E., Ko, J. Y., Paik, S. S., Gronostajski, R. M., Kim, J., Krueger, J. G., Zheng, D. & Fuchs, E., Jun 1 2020, In : Nature Cell Biology. 22, 6, p. 640-650 11 p.

Research output: Contribution to journalArticle

Open Access
2019

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

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

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
1 Scopus citations

GREB1 amplifies androgen receptor output in human prostate cancer and contributes to antiandrogen resistance

Lee, E., Wongvipat, J., Choi, D., Wang, P., Lee, Y. S., Zheng, D., Watson, P. A., Gopalan, A. & Sawyers, C. L., Jan 15 2019, In : eLife. 8, e41913.

Research output: Contribution to journalArticle

2 Scopus citations

Non-catalytic Roles of Tet2 Are Essential to Regulate Hematopoietic Stem and Progenitor Cell Homeostasis

Ito, K., Lee, J., Chrysanthou, S., Zhao, Y., Josephs, K., Sato, H., Teruya-Feldstein, J., Zheng, D., Dawlaty, M. M. & Ito, K., Sep 3 2019, In : Cell Reports. 28, 10, p. 2480-2490.e4

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

PHF19 promotes multiple myeloma tumorigenicity through PRC2 activation and broad H3K27me3 domain formation

Ren, Z., Ahn, J. H., Liu, H., Tsai, Y. H., Bhanu, N. V., Koss, B., Allison, D. F., Ma, A., Storey, A. J., Wang, P., Mackintosh, S. G., Edmondson, R. D., Groen, R. W. J., Martens, A. C., Garcia, B. A., Tackett, A. J., Jin, J., Cai, L., Zheng, D. & Wang, G. G., Oct 3 2019, In : Blood. 134, 14, p. 1176-1189 14 p.

Research output: Contribution to journalArticle

5 Scopus citations

Polycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression

Bar, C., Cohen, I., Zhao, D., Pothula, V., Litskevitch, A., Koseki, H., Zheng, D. & Ezhkova, E., Jul 2 2019, In : Cell Reports. 28, 1, p. 257-266.e5

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

PRC1 preserves epidermal tissue integrity independently of PRC2

Cohen, I., Zhao, D., Menon, G., Nakayama, M., Koseki, H., Zheng, D. & Ezhkova, E., Jan 1 2019, In : Genes and Development. 33, 1-2, p. 55-60 6 p.

Research output: Contribution to journalArticle

6 Scopus citations
Open Access
4 Scopus citations

Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers

Zhao, Y., Wilmarth, P. A., Cheng, C., Limi, S., Fowler, V. M., Zheng, D., David, L. L. & Cvekl, A., Feb 2019, In : Experimental Eye Research. 179, p. 32-46 15 p.

Research output: Contribution to journalArticle

12 Scopus citations

Rinf Regulates Pluripotency Network Genes and Tet Enzymes in Embryonic Stem Cells

Ravichandran, M., Lei, R., Tang, Q., Zhao, Y., Lee, J., Ma, L., Chrysanthou, S., Lorton, B. M., Cvekl, A., Shechter, D., Zheng, D. & Dawlaty, M. M., Aug 20 2019, In : Cell Reports. 28, 8, p. 1993-2003.e5

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis

Liu, Y., Lu, P., Wang, Y., Morrow, B. E., Zhou, B. & Zheng, D., Aug 6 2019, In : Journal of the American Heart Association. 8, 15, e012941.

Research output: Contribution to journalArticle

Open Access

Transcriptomic analysis and novel insights into lens fibre cell differentiation regulated by Gata3

Martynova, E., Zhao, Y., Xie, Q., Zheng, D. & Cvekl, A., Dec 1 2019, In : Open Biology. 9, 12, 190220.

Research output: Contribution to journalArticle

Open Access
2018
10 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

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

7 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. E., Gill, J. B., Zhang, J., Ren, T., Gorlick, R. G. & 2 others, Zi, X. & Hoang, B. H., Dec 1 2018, In : Scientific reports. 8, 1, 14294.

Research output: Contribution to journalArticle

7 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

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

Metabolite differences between glutamate carboxypeptidase II gene knockout mice and their wild-type littermates after traumatic brain injury: A 7-tesla 1H-MRS study 11 Medical and Health Sciences 1109 Neurosciences

Wu, W., Xu, S., Wang, J., Zhang, K., Zhang, M., Cao, Y., Ren, H., Zheng, D. & Zhong, C., Nov 20 2018, In : BMC neuroscience. 19, 1, 75.

Research output: Contribution to journalArticle

PRC1 Fine-tunes Gene Repression and Activation to Safeguard Skin Development and Stem Cell Specification

Cohen, I., Zhao, D., Bar, C., Valdes, V. J., Dauber-Decker, K. L., Nguyen, M. B., Nakayama, M., Rendl, M., Bickmore, W. A., Koseki, H., Zheng, D. & Ezhkova, E., May 3 2018, In : Cell Stem Cell. 22, 5, p. 726-739.e7

Research output: Contribution to journalArticle

30 Scopus citations

Six3 and Six6 Are Jointly Required for the Maintenance of Multipotent Retinal Progenitors through Both Positive and Negative Regulation

Diacou, R., Zhao, Y., Zheng, D., Cvekl, A. & Liu, W., Nov 27 2018, In : Cell Reports. 25, 9, p. 2510-2523.e4

Research output: Contribution to journalArticle

4 Scopus citations

SMARTcleaner: Identify and clean off-target signals in SMART ChIP-seq analysis

Zhao, D. & Zheng, D., Dec 27 2018, In : BMC bioinformatics. 19, 1, 544.

Research output: Contribution to journalArticle

Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression

Adam, R. C., Yang, H., Ge, Y., Lien, W. H., Wang, P., Zhao, Y., Polak, L., Levorse, J., Baksh, S. C., Zheng, D. & Fuchs, E., Mar 1 2018, In : Cell Stem Cell. 22, 3, p. 398-413.e7

Research output: Contribution to journalArticle

18 Scopus citations

The Chromatin Remodeler BPTF Activates a Stemness Gene-Expression Program Essential for the Maintenance of Adult Hematopoietic Stem Cells

Xu, B., Cai, L., Butler, J. M., Chen, D., Lu, X., Allison, D. F., Lu, R., Rafii, S., Parker, J. S., Zheng, D. & Wang, G. G., Mar 13 2018, In : Stem Cell Reports. 10, 3, p. 675-683 9 p.

Research output: Contribution to journalArticle

7 Scopus citations

ZFX Mediates Non-canonical Oncogenic Functions of the Androgen Receptor Splice Variant 7 in Castrate-Resistant Prostate Cancer

Cai, L., Tsai, Y. H., Wang, P., Wang, J., Li, D., Fan, H., Zhao, Y., Bareja, R., Lu, R., Wilson, E. M., Sboner, A., Whang, Y. E., Zheng, D., Parker, J. S., Earp, H. S. & Wang, G. G., Oct 18 2018, In : Molecular Cell. 72, 2, p. 341-354.e6

Research output: Contribution to journalArticle

11 Scopus citations
2017

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

20 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

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

64 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

10 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

Evolutionary origins of Pax6 control of crystallin genes

Cvekl, A., Zhao, Y., McGreal, R., Xie, Q., Gu, X. & Zheng, D., Jan 1 2017, In : Genome Biology and Evolution. 9, 8, p. 2075-2092 18 p.

Research output: Contribution to journalArticle

10 Scopus citations

In utero exposure to a high-fat diet programs hepatic hypermethylation and gene dysregulation and development of metabolic syndrome in male mice

Seki, Y., Suzuki, M., Guo, X., Glenn, A. S., Vuguin, P. M., Fiallo, A., Du, Q., Ko, Y. A., Yu, Y., Susztak, K., Zheng, D., Greally, J. M., Katz, E. B. & Charron, M. J., Sep 1 2017, In : Endocrinology. 158, 9, p. 2860-2872 13 p.

Research output: Contribution to journalArticle

15 Scopus citations

N-myc regulates growth and fiber cell differentiation in lens development

Cavalheiro, G. R., Matos-Rodrigues, G. E., Zhao, Y., Gomes, A. L., Anand, D., Predes, D., de Lima, S., Abreu, J. G., Zheng, D., Lachke, S. A., Cvekl, A. & Martins, R. A. P., Sep 1 2017, In : Developmental Biology. 429, 1, p. 105-117 13 p.

Research output: Contribution to journalArticle

17 Scopus citations

PHB Associates with the HIRA Complex to Control an Epigenetic-Metabolic Circuit in Human ESCs

Zhu, Z., Li, C., Zeng, Y., Ding, J., Qu, Z., Gu, J., Ge, L., Tang, F., Huang, X., Zhou, C., Wang, P., Zheng, D. & Jin, Y., Feb 2 2017, In : Cell Stem Cell. 20, 2, p. 274-289.e7

Research output: Contribution to journalArticle

15 Scopus citations

Reduced dosage of β-catenin provides significant rescue of cardiac outflow tract anomalies in a Tbx1 conditional null mouse model of 22q11.2 deletion syndrome

Racedo, S. E., Hasten, E., Lin, M., Devakanmalai, G. S., Guo, T., Ozbudak, E. M., Cai, C. L., Zheng, D. & Morrow, B. E., Mar 2017, In : PLoS genetics. 13, 3, e1006687.

Research output: Contribution to journalArticle

8 Scopus citations

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer

Shah, N., Wang, P., Wongvipat, J., Karthaus, W. R., Abida, W., Armenia, J., Rockowitz, S., Drier, Y., Bernstein, B. E., Long, H. W., Freedman, M. L., Arora, V. K., Zheng, D. & Sawyers, C. L., Sep 11 2017, In : eLife. 6, e27861.

Research output: Contribution to journalArticle

40 Scopus citations

REST regulates the cell cycle for cardiac development and regeneration

Zhang, D., Wang, Y., Lu, P., Wang, P., Yuan, X., Yan, J., Cai, C., Chang, C. P., Zheng, D., Wu, B. & Zhou, B., Dec 1 2017, In : Nature communications. 8, 1, 1979.

Research output: Contribution to journalArticle

12 Scopus citations
16 Scopus citations
2016

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

58 Scopus citations

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion

Lin, M., Pedrosa, E., Hrabovsky, A., Chen, J., Puliafito, B. R., Gilbert, S. R., Zheng, D. & Lachman, H. M., Nov 15 2016, In : BMC Systems Biology. 10, 1, 105.

Research output: Contribution to journalArticle

30 Scopus citations

Loss of MEN1 activates DNMT1 implicating DNA hypermethylation as a driver of MEN1 tumorigenesis

Yuan, Z., Claros, C. S., Suzuki, M., Maggi, E. C., Kaner, J. D., Kinstlinger, N., Gorecka, J., Quinn, T. J., Geha, R., Corn, A., Pastoriza, J., Jing, Q., Adem, A., Wu, H., Alemu, G., Du, Y. C., Zheng, D., Greally, J. M. & Libutti, S. K., Mar 15 2016, In : Oncotarget. 7, 11, p. 12633-12650 18 p.

Research output: Contribution to journalArticle

11 Scopus citations

MYOSLID is a novel serum response factor-dependent long noncoding RNA that amplifies the vascular smooth muscle differentiation program

Zhao, J., Zhang, W., Lin, M., Wu, W., Jiang, P., Tou, E., Xue, M., Richards, A., Jourd'heuil, D., Asif, A., Zheng, D., Singer, H. A., Miano, J. M. & Long, X., Oct 1 2016, In : Arteriosclerosis, thrombosis, and vascular biology. 36, 10, p. 2088-2099 12 p.

Research output: Contribution to journalArticle

50 Scopus citations

Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts

Zhang, D., Wu, B., Wang, P., Wang, Y., Lu, P., Nechiporuk, T., Floss, T., Greally, J. M., Zheng, D. & Zhou, B., 2016, In : Nucleic Acids Research. 45, 6, p. 3102-3115 14 p.

Research output: Contribution to journalArticle

14 Scopus citations

Pangolin genomes and the evolution of mammalian scales and immunity

Choo, S. W., Rayko, M., Tan, T. K., Hari, R., Komissarov, A., Wee, W. Y., Yurchenko, A. A., Kliver, S., Tamazian, G., Antunes, A., Wilson, R. K., Warren, W. C., Koepfli, K. P., Minx, P., Krasheninnikova, K., Kotze, A., Dalton, D. L., Vermaak, E., Paterson, I. C., Dobrynin, P. & 12 others, Sitam, F. T., Rovie-Ryan, J. J., Johnson, W. E., Yusoff, A. M., Luo, S. J., Karuppannan, K. V., Fang, G., Zheng, D., Gerstein, M. B., Lipovich, L., O'Brien, S. J. & Wong, G. J., Oct 2016, In : Genome research. 26, 10, p. 1312-1322 11 p.

Research output: Contribution to journalArticle

20 Scopus citations

Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers

Sun, J., Zhao, Y., McGreal, R., Cohen-Tayar, Y., Rockowitz, S., Wilczek, C., Ashery-Padan, R., Shechter, D., Zheng, D. & Cvekl, A., Sep 9 2016, In : Epigenetics and Chromatin. 9, 1, 37.

Research output: Contribution to journalArticle

13 Scopus citations

Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development

Perdigoto, C. N., Dauber, K. L., Bar, C., Tsai, P. C., Valdes, V. J., Cohen, I., Santoriello, F. J., Zhao, D., Zheng, D., Hsu, Y. C. & Ezhkova, E., Jul 2016, In : PLoS genetics. 12, 7, e1006151.

Research output: Contribution to journalArticle

20 Scopus citations