Howard Y. Chang

Publications

• Systematic Discovery of Xist RNA Binding Proteins
  Chu, C., Zhang, Q. C., da Rocha, S. T., Flynn, R. A., Bharadwaj, M., & Chang, H. Y. (2015). Systematic Discovery of Xist RNA Binding Proteins. CELL, 161(2), 404-416.
• Structural imprints in vivo decode RNA regulatory mechanisms.
  Spitale, R. C., Flynn, R. A., Zhang, Q. C., Crisalli, P., Lee, B., & Chang, H. Y. (2015). Structural imprints in vivo decode RNA regulatory mechanisms. Nature, 519(7544), 486-490.
• m(6)A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells
  Batista, P. J., Molinie, B., Wang, J., Qu, K., Zhang, J., & Chang, H. Y. (2014). m(6)A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells. CELL STEM CELL, 15(6), 707-719.
• Landscape and variation of RNA secondary structure across the human transcriptome. Wan, Y., Qu, K., Zhang, Q. C., Flynn, R. A., Manor, O., & Chang, H. Y. (2014). Landscape and variation of RNA secondary structure across the human transcriptome. Nature, 505(7485), 706-709.
  
• Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature methods, 10(12), 1213-1218.
  
• Long Noncoding RNAs: Cellular Address Codes in Development and Disease Batista, P. J., & Chang, H. Y. (2013). Long Noncoding RNAs: Cellular Address Codes in Development and Disease. CELL, 152(6), 1298-1307.
  
• Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Grow, E. J., Flynn, R. A., Chavez, S. L., Bayless, N. L., Wossidlo, M., & Wysocka, J. (2015). Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature, 522(7555), 221-225.
  
• Long Noncoding RNA in Hematopoiesis and Immunity Satpathy, A. T., & Chang, H. Y. (2015). Long Noncoding RNA in Hematopoiesis and Immunity. IMMUNITY, 42(5), 792-804.
  
• Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark Corley, M., Solem, A., Qu, K., Chang, H. Y., & Laederach, A. (2015). Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. NUCLEIC ACIDS RESEARCH, 43(3), 1859-1868.
  
• RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Calo, E., Flynn, R. A., Martin, L., Spitale, R. C., Chang, H. Y., & Wysocka, J. (2015). RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature, 518(7538), 249-253.
  
• Structure and Thermodynamics of N-6-Methyladenosine in RNA: A Spring-Loaded Base Modification Roost, C., Lynch, S. R., Batista, P. J., Qu, K., Chang, H. Y., & Kool, E. T. (2015). Structure and Thermodynamics of N-6-Methyladenosine in RNA: A Spring-Loaded Base Modification. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137(5), 2107-2115.
  
• Dissecting noncoding and pathogen RNA-protein interactomes Flynn, R. A., Martin, L., Spitale, R. C., Do, B. T., Sagan, S. M., & Chang, H. Y. (2015). Dissecting noncoding and pathogen RNA-protein interactomes. RNA-A PUBLICATION OF THE RNA SOCIETY, 21(1), 135-143.
  
• Technologies to probe functions and mechanisms of long noncoding RNAs Chu, C., Spitale, R. C., & Chang, H. Y. (2015). Technologies to probe functions and mechanisms of long noncoding RNAs. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 22(1), 29-35.
  
• RNA structural analysis by evolving SHAPE chemistry Spitale, R. C., Flynn, R. A., Torre, E. A., Kool, E. T., & Chang, H. Y. (2014). RNA structural analysis by evolving SHAPE chemistry. WILEY INTERDISCIPLINARY REVIEWS-RNA, 5(6), 867-881.
  
• An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development Benitez, C. M., Qu, K., Sugiyama, T., Pauerstein, P. T., Liu, Y., & Kim, S. K. (2014). An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development. PLOS GENETICS, 10(10).
  
• Physiological roles of long noncoding RNAs: insight from knockout mice Li, L., & Chang, H. Y. (2014). Physiological roles of long noncoding RNAs: insight from knockout mice. TRENDS IN CELL BIOLOGY, 24(10), 594-602.
  
• RNA switch at enhancers. Quinn, J. J., & Chang, H. Y. (2014). RNA switch at enhancers. Nature genetics, 46(9), 929-931.
  
• Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification Quinn, J. J., Ilik, I. A., Qu, K., Georgiev, P., Chu, C., & Chang, H. Y. (2014). Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. NATURE BIOTECHNOLOGY, 32(9), 933-940.
  
• Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. Zheng, G. Xy., Do, B. T., Webster, D. E., Khavari, P. A., & Chang, H. Y. (2014). Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. Nature structural & molecular biology, 21(7), 585-590.
  
• Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs Zheng, G. Xy., Do, B. T., Webster, D. E., Khavari, P. A., & Chang, H. Y. (2014). Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 21(7), 585-590.
  
• Long Noncoding RNAs in Cell-Fate Programming and Reprogramming Flynn, R. A., & Chang, H. Y. (2014). Long Noncoding RNAs in Cell-Fate Programming and Reprogramming. CELL STEM CELL, 14(6), 752-761.
  
• Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Buenrostro, J. D., Araya, C. L., Chircus, L. M., Layton, C. J., Chang, H. Y., & Greenleaf, W. J. (2014). Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nature biotechnology, 32(6), 562-568.
  
• Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes Buenrostro, J. D., Araya, C. L., Chircus, L. M., Layton, C. J., Chang, H. Y., & Greenleaf, W. J. (2014). Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. NATURE BIOTECHNOLOGY, 32(6), 562-?.
  
• Identification of Genes Promoting Skin Youthfulness by Genome-Wide Association Study Chang, A. Ls., Atzmon, G., Bergman, A., Brugmann, S., Atwood, S. X., & Barzilai, N. (2014). Identification of Genes Promoting Skin Youthfulness by Genome-Wide Association Study. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 134(3), 651-657.
  
• Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency Yang, Y. W., Flynn, R. A., Chen, Y., Qu, K., Wan, B., & Chang, H. Y. (2014). Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. ELIFE, 3.
  
• Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. Yang, Y. W., Flynn, R. A., Chen, Y., Qu, K., Wan, B., & Chang, H. Y. (2014). Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. eLife, 3.
  
• Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Quinn, J. J., Ilik, I. A., Qu, K., Georgiev, P., Chu, C., & Chang, H. Y. (2014). Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nature biotechnology, 32(9), 933-40.
  
• Identification of a Selective Polymerase Enables Detection of N-6-Methyladenosine in RNA Harcourt, E. M., Ehrenschwender, T., Batista, P. J., Chang, H. Y., & Kool, E. T. (2013). Identification of a Selective Polymerase Enables Detection of N-6-Methyladenosine in RNA. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135(51), 19079-19082.
  
• Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons Wapinski, O. L., Vierbuchen, T., Qu, K., Lee, Q. Y., Chanda, S., & Wernig, M. (2013). Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons. CELL, 155(3), 621-635.
  
• Augmenting Endogenous Wnt Signaling Improves Skin Wound Healing Whyte, J. L., Smith, A. A., Liu, B., Manzano, W. R., Evans, N. D., & Helms, J. A. (2013). Augmenting Endogenous Wnt Signaling Improves Skin Wound Healing. PLOS ONE, 8(10).
  
• Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression Li, L., Liu, B., Wapinski, O. L., Tsai, M.-C., Qu, K., & Chang, H. Y. (2013). Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression. CELL REPORTS, 5(1), 3-12.
  
• HOXB13 Mediates Tamoxifen Resistance and Invasiveness in Human Breast Cancer by Suppressing ERa and Inducing IL-6 Expression. Shah, N., Jin, K., Cruz, L.-A., Park, S., Sadik, H., & Sukumar, S. (2013). HOXB13 Mediates Tamoxifen Resistance and Invasiveness in Human Breast Cancer by Suppressing ERa and Inducing IL-6 Expression. Cancer research, 73(17), 5449-5458.
  
• Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila Ilik, I. A., Quinn, J. J., Georgiev, P., Tavares-Cadete, F., Maticzka, D., & Akhtar, A. (2013). Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. MOLECULAR CELL, 51(2), 156-173.
  
• A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics Rapicavoli, N. A., Qu, K., Zhang, J., Mikhail, M., Laberge, R.-M., & Chang, H. Y. (2013). A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. ELIFE, 2.
  
• Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing Wan, Y., Qu, K., Ouyang, Z., & Chang, H. Y. (2013). Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. NATURE PROTOCOLS, 8(5), 849-869.
  
• Cytotopic localization by long noncoding RNAs Batista, P. J., & Chang, H. Y. (2013). Cytotopic localization by long noncoding RNAs. CURRENT OPINION IN CELL BIOLOGY, 25(2), 195-199.
  
• The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-gamma Locus Gomez, J. A., Wapinski, O. L., Yang, Y. W., Bureau, J.-F., Gopinath, S., & Kirkegaard, K. (2013). The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-gamma Locus. CELL, 152(4), 743-754.
  
• Rejuvenation of Gene Expression Pattern of Aged Human Skin by Broadband Light Treatment: A Pilot Study Chang, A. L. S., Bitter, P. H., Qu, K., Lin, M., Rapicavoli, N. A., & Chang, H. Y. (2013). Rejuvenation of Gene Expression Pattern of Aged Human Skin by Broadband Light Treatment: A Pilot Study. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 133(2), 394-402.
  
• SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data Ouyang, Z., Snyder, M. P., & Chang, H. Y. (2013). SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. GENOME RESEARCH, 23(2), 377-387.
  
• Control of somatic tissue differentiation by the long non-coding RNA TINCR. Kretz, M., Siprashvili, Z., Chu, C., Webster, D. E., Zehnder, A., & Khavari, P. A. (2013). Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature, 493(7431), 231-235.
  
• Control of somatic tissue differentiation by the long non-coding RNA TINCR Kretz, M., Siprashvili, Z., Chu, C., Webster, D. E., Zehnder, A., & Khavari, P. A. (2013). Control of somatic tissue differentiation by the long non-coding RNA TINCR. NATURE, 493(7431), 231-U245.
  
• RNA SHAPE analysis in living cells. Spitale, R. C., Crisalli, P., Flynn, R. A., Torre, E. A., Kool, E. T., & Chang, H. Y. (2013). RNA SHAPE analysis in living cells. Nature chemical biology, 9(1), 18-20.
  
• Systematic reconstruction of RNA functional motifs with high-throughput microfluidics Martin, L., Meier, M., Lyons, S. M., Sit, R. V., Marzluff, W. F., & Chang, H. Y. (2012). Systematic reconstruction of RNA functional motifs with high-throughput microfluidics. NATURE METHODS, 9(12), 1192-U85.
  
• Identification of proteins binding coding and non-coding human RNAs using protein microarrays Siprashvili, Z., Webster, D. E., Kretz, M., Johnston, D., Rinn, J. L., & Khavari, P. A. (2012). Identification of proteins binding coding and non-coding human RNAs using protein microarrays. BMC GENOMICS, 13.
  
• Genome-wide Measurement of RNA Folding Energies Wan, Y., Qu, K., Ouyang, Z., Kertesz, M., Li, J., & Chang, H. Y. (2012). Genome-wide Measurement of RNA Folding Energies. MOLECULAR CELL, 48(2), 169-181.
  
• Detection of Long Non-Coding RNA in Archival Tissue: Correlation with Polycomb Protein Expression in Primary and Metastatic Breast Carcinoma Chisholm, K. M., Wan, Y., Li, R., Montgomery, K. D., Chang, H. Y., & West, R. B. (2012). Detection of Long Non-Coding RNA in Archival Tissue: Correlation with Polycomb Protein Expression in Primary and Metastatic Breast Carcinoma. PLOS ONE, 7(10).
  
• Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts Lee, C. S., Ungewickell, A., Bhaduri, A., Qu, K., Webster, D. E., & Khavari, P. A. (2012). Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. BLOOD, 120(16), 3288-3297.
  
• A Molecular Signature for Purified Definitive Endoderm Guides Differentiation and Isolation of Endoderm from Mouse and Human Embryonic Stem Cells Wang, P., McKnight, K. D., Wong, D. J., Rodriguez, R. T., Sugiyama, T., & Kim, S. K. (2012). A Molecular Signature for Purified Definitive Endoderm Guides Differentiation and Isolation of Endoderm from Mouse and Human Embryonic Stem Cells. STEM CELLS AND DEVELOPMENT, 21(12), 2273-2287.
  
• The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression Littlepage, L. E., Adler, A. S., Kouros-Mehr, H., Huang, G., Chou, J., & Werb, Z. (2012). The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression. CANCER DISCOVERY, 2(7), 638-651.
  
• Uncovering the role of genomic "dark matter" in human disease Martin, L., & Chang, H. Y. (2012). Uncovering the role of genomic "dark matter" in human disease. JOURNAL OF CLINICAL INVESTIGATION, 122(5), 1589-1595.
  
• Identification of genes promoting exceptional skin youthfulness Chang, A. S., Atzmon, G., Bergman, A., Chang, H. Y., & Barzilai, N. (2012). Identification of genes promoting exceptional skin youthfulness. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 132, S65-S65.
  
• Active chromatin and noncoding RNAs: an intimate relationship Flynn, R. A., & Chang, H. Y. (2012). Active chromatin and noncoding RNAs: an intimate relationship. CURRENT OPINION IN GENETICS & DEVELOPMENT, 22(2), 172-178.
  
• Chromatin Isolation by RNA Purification (ChIRP) Chu, C., Quinn, J., & Chang, H. Y. (2012). Chromatin Isolation by RNA Purification (ChIRP). JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, (61).
  
• Suppression of progenitor differentiation requires the long noncoding RNA ANCR Kretz, M., Webster, D. E., Flockhart, R. J., Lee, C. S., Zehnder, A., & Khavari, P. A. (2012). Suppression of progenitor differentiation requires the long noncoding RNA ANCR. GENES & DEVELOPMENT, 26(4), 338-343.
  
• Aging, Rejuvenation, and Epigenetic Reprogramming: Resetting the Aging Clock Rando, T. A., & Chang, H. Y. (2012). Aging, Rejuvenation, and Epigenetic Reprogramming: Resetting the Aging Clock. CELL, 148(1-2), 46-57.
  
• High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation Wu, A. R., Kawahara, T. La., Rapicavoli, N. A., van Riggelen, J., Shroff, E. H., & Quake, S. R. (2012). High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. LAB ON A CHIP, 12(12), 2190-2198.
  
• Genome Regulation by Long Noncoding RNAs Rinn, J. L., & Chang, H. Y. (2012). Genome Regulation by Long Noncoding RNAs. ANNUAL REVIEW OF BIOCHEMISTRY, VOL 81, 81, 145-166.
  
• Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers Brunner, A. L., Beck, A. H., Edris, B., Sweeney, R. T., Zhu, S. X., & West, R. B. (2012). Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. GENOME BIOLOGY, 13(8).
  
• Chromatin isolation by RNA purification (ChIRP). Chu, C., Quinn, J., & Chang, H. Y. (2012). Chromatin isolation by RNA purification (ChIRP). Journal of visualized experiments : JoVE, (61).
  
• Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions Chu, C., Qu, K., Zhong, F. L., Artandi, S. E., & Chang, H. Y. (2011). Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions. MOLECULAR CELL, 44(4), 667-678.
  
• Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons Marro, S., Pang, Z. P., Yang, N., Tsai, M.-C., Qu, K., & Wernig, M. (2011). Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons. CELL STEM CELL, 9(4), 374-382.
  
• Molecular Mechanisms of Long Noncoding RNAs Wang, K. C., & Chang, H. Y. (2011). Molecular Mechanisms of Long Noncoding RNAs. MOLECULAR CELL, 43(6), 904-914.
  
• Disruption of PPAR gamma/beta-catenin-mediated regulation of apelin impairs BMP-induced mouse and human pulmonary arterial EC survival Alastalo, T.-P., Li, M., Perez, V. D. J., Pham, D., Sawada, H., & Rabinovitch, M. (2011). Disruption of PPAR gamma/beta-catenin-mediated regulation of apelin impairs BMP-induced mouse and human pulmonary arterial EC survival. JOURNAL OF CLINICAL INVESTIGATION, 121(9), 3735-3746.
  
• Understanding the transcriptome through RNA structure Wan, Y., Kertesz, M., Spitale, R. C., Segal, E., & Chang, H. Y. (2011). Understanding the transcriptome through RNA structure. NATURE REVIEWS GENETICS, 12(9), 641-655.
  
• Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding Chen, Y., Wan, B., Wang, K. C., Cao, F., Yang, Y., & Lei, M. (2011). Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding. EMBO REPORTS, 12(8), 797-803.
  
• Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters Hung, T., Wang, Y., Lin, M. F., Koegel, A. K., Kotake, Y., & Chang, H. Y. (2011). Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. NATURE GENETICS, 43(7), 621-U196.
  
• Long noncoding RNAs and human disease Wapinski, O., & Chang, H. Y. (2011). Long noncoding RNAs and human disease. TRENDS IN CELL BIOLOGY, 21(6), 354-361.
  
• Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging-Related Transcriptional Networks Kawahara, T. La., Rapicavoli, N. A., Wu, A. R., Qu, K., Quake, S. R., & Chang, H. Y. (2011). Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging-Related Transcriptional Networks. PLOS GENETICS, 7(6).
  
• RNA templating the epigenome Long noncoding RNAs as molecular scaffolds Spitale, R. C., Tsai, M.-C., & Chang, H. Y. (2011). RNA templating the epigenome Long noncoding RNAs as molecular scaffolds. EPIGENETICS, 6(5), 539-543.
  
• A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression Wang, K. C., Yang, Y. W., Liu, B., Sanyal, A., Corces-Zimmerman, R., & Chang, H. Y. (2011). A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. NATURE, 472(7341), 120-U158.
  
• Long Intergenic Noncoding RNAs: New Links in Cancer Progression Tsai, M.-C., Spitale, R. C., & Chang, H. Y. (2011). Long Intergenic Noncoding RNAs: New Links in Cancer Progression. CANCER RESEARCH, 71(1), 3-7.
  
• Noncoding RNA Landmarks of Pluripotency and Reprogramming Ouyang, Z., Zheng, G. Xy., & Chang, H. Y. (2010). Noncoding RNA Landmarks of Pluripotency and Reprogramming. CELL STEM CELL, 7(6), 649-650.
  
• G1 arrest and differentiation can occur independently of Rb family function Wirt, S. E., Adler, A. S., Gebala, V., Weimann, J. M., Schaffer, B. E., & Sage, J. (2010). G1 arrest and differentiation can occur independently of Rb family function. JOURNAL OF CELL BIOLOGY, 191(4), 809-825.
  
• Genome-wide measurement of RNA secondary structure in yeast Kertesz, M., Wan, Y., Mazor, E., Rinn, J. L., Nutter, R. C., & Segal, E. (2010). Genome-wide measurement of RNA secondary structure in yeast. NATURE, 467(7311), 103-107.
  
• Long noncoding RNA in genome regulation Prospects and mechanisms Hung, T., & Chang, H. Y. (2010). Long noncoding RNA in genome regulation Prospects and mechanisms. RNA BIOLOGY, 7(5), 582-585.
  
• HOTAIR Flight of noncoding RNAs in cancer metastasis Wan, Y., & Chang, H. Y. (2010). HOTAIR Flight of noncoding RNAs in cancer metastasis. CELL CYCLE, 9(17), 3391-3392.
  
• Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes Tsai, M.-C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., & Chang, H. Y. (2010). Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes. SCIENCE, 329(5992), 689-693.
  
• Tumor suppression by the histone demethylase UTX Tsai, M.-C., Wang, J. K., & Chang, H. Y. (2010). Tumor suppression by the histone demethylase UTX. CELL CYCLE, 9(11), 2043-2044.
  
• Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis Gupta, R. A., Shah, N., Wang, K. C., Kim, J., Horlings, H. M., & Chang, H. Y. (2010). Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. NATURE, 464(7291), 1071-U148.
  
• A TGF beta-Responsive Gene Signature Is Associated with a Subset of Diffuse Scleroderma with Increased Disease Severity Sargent, J. L., Milano, A., Bhattacharyya, S., Varga, J., Connolly, M. K., & Whitfield, M. L. (2010). A TGF beta-Responsive Gene Signature Is Associated with a Subset of Diffuse Scleroderma with Increased Disease Severity. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 130(3), 694-705.
  
• The histone demethylase UTX enables RB-dependent cell fate control Wang, J. K., Tsai, M.-C., Poulin, G., Adler, A. S., Chen, S., & Chang, H. Y. (2010). The histone demethylase UTX enables RB-dependent cell fate control. GENES & DEVELOPMENT, 24(4), 327-332.
  
• Anatomic Demarcation of Cells: Genes to Patterns Chang, H. Y. (2009). Anatomic Demarcation of Cells: Genes to Patterns. SCIENCE, 326(5957), 1206-1207.
  
• Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells Chan, K. S., Espinosa, I., Chao, M., Wong, D., Ailles, L., & Weissman, I. L. (2009). Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(33), 14016-14021.
  
• Gene dates, parties and galas Symposium on Chromatin Dynamics and Higher Order Organization Chang, H. Y., Cuvier, O., & Dekker, J. (2009). Gene dates, parties and galas Symposium on Chromatin Dynamics and Higher Order Organization. EMBO REPORTS, 10(7), 689-693.
  
• Tumor Vasculature Is Regulated by PHD2-Mediated Angiogenesis and Bone Marrow-Derived Cell Recruitment Chan, D. A., Kawahara, T. La., Sutphin, P. D., Chang, H. Y., Chi, J.-T., & Giaccia, A. J. (2009). Tumor Vasculature Is Regulated by PHD2-Mediated Angiogenesis and Bone Marrow-Derived Cell Recruitment. CANCER CELL, 15(6), 527-538.
  
• Modeling Inducible Human Tissue Neoplasia Identifies an Extracellular Matrix Interaction Network Involved in Cancer Progression Reuter, J. A., Ortiz-Urda, S., Kretz, M., Garcia, J., Scholl, F. A., & Khavari, P. A. (2009). Modeling Inducible Human Tissue Neoplasia Identifies an Extracellular Matrix Interaction Network Involved in Cancer Progression. CANCER CELL, 15(6), 477-488.
  
• Regeneration, repair and remembering identity: the three Rs of Hox gene expression Wang, K. C., Helms, J. A., & Chang, H. Y. (2009). Regeneration, repair and remembering identity: the three Rs of Hox gene expression. TRENDS IN CELL BIOLOGY, 19(6), 268-275.
  
• Hierarchical Maintenance of MLL Myeloid Leukemia Stem Cells Employs a Transcriptional Program Shared with Embryonic Rather Than Adult Stem Cells Somervaille, T. Cp., Matheny, C. J., Spencer, G. J., Iwasaki, M., Rinn, J. L., & Cleary, M. L. (2009). Hierarchical Maintenance of MLL Myeloid Leukemia Stem Cells Employs a Transcriptional Program Shared with Embryonic Rather Than Adult Stem Cells. CELL STEM CELL, 4(2), 129-140.
  
• Molecular Framework for Response to Imatinib Mesylate in Systemic Sclerosis Chung, L., Fiorentino, D. F., Benbarak, M. J., Adler, A. S., Mariano, M. M., & Robinson, W. H. (2009). Molecular Framework for Response to Imatinib Mesylate in Systemic Sclerosis. ARTHRITIS AND RHEUMATISM, 60(2), 584-591.
  
• ING4 Mediates Crosstalk between Histone H3 K4 Trimethylation and H3 Acetylation to Attenuate Cellular Transformation Hung, T., Binda, O., Champagne, K. S., Kuo, A. J., Johnson, K., & Gozani, O. (2009). ING4 Mediates Crosstalk between Histone H3 K4 Trimethylation and H3 Acetylation to Attenuate Cellular Transformation. MOLECULAR CELL, 33(2), 248-256.
  
• SIRT6 Links Histone H3 Lysine 9 Deacetylation to NF-kappa B-Dependent Gene Expression and Organismal Life Span Kawahara, T. La., Michishita, E., Adler, A. S., Damian, M., Berber, E., & Chua, K. F. (2009). SIRT6 Links Histone H3 Lysine 9 Deacetylation to NF-kappa B-Dependent Gene Expression and Organismal Life Span. CELL, 136(1), 62-74.
  
• Genome-Wide Views of Chromatin Structure Rando, O. J., & Chang, H. Y. (2009). Genome-Wide Views of Chromatin Structure. ANNUAL REVIEW OF BIOCHEMISTRY, 78, 245-271.
  
• Global Expression Profiling in Atopic Eczema Reveals Reciprocal Expression of Inflammatory and Lipid Genes Saaf, A. M., Tengvall-Linder, M., Chang, H. Y., Adler, A. S., Wahlgren, C.-F., & Bradley, M. (2008). Global Expression Profiling in Atopic Eczema Reveals Reciprocal Expression of Inflammatory and Lipid Genes. PLOS ONE, 3(12).
  
• Stemness, cancer and cancer stem cells Wong, D. J., Segal, E., & Chang, H. Y. (2008). Stemness, cancer and cancer stem cells. CELL CYCLE, 7(23), 3622-3624.
  
• Combining biological gene expression signatures in predicting outcome in breast cancer: An alternative to supervised classification Nuyten, D. Sa., Hastie, T., Chi, J.-T. A., Chang, H. Y., & van de Vijver, M. J. (2008). Combining biological gene expression signatures in predicting outcome in breast cancer: An alternative to supervised classification. EUROPEAN JOURNAL OF CANCER, 44(15), 2319-2329.
  
• Deletional tolerance mediated by extrathymic Aire-expressing cells Gardner, J. M., DeVoss, J. J., Friedman, R. S., Wong, D. J., Tan, Y. X., & Anderson, M. S. (2008). Deletional tolerance mediated by extrathymic Aire-expressing cells. SCIENCE, 321(5890), 843-847.
  
• Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3 Sen, G. L., Webster, D. E., Barragan, D. I., Chang, H. Y., & Khavari, P. A. (2008). Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. GENES & DEVELOPMENT, 22(14), 1865-1870.
  
• Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire Su, M. A., Giang, K., Zumer, K., Jiang, H., Oven, I., & Anderson, M. S. (2008). Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire. JOURNAL OF CLINICAL INVESTIGATION, 118(5), 1712-1726.
  
• Module map of stem cell genes guides creation of epithelial cancer stem cells Wong, D. J., Liu, H., Ridky, T. W., Cassarino, D., Segal, E., & Chang, H. Y. (2008). Module map of stem cell genes guides creation of epithelial cancer stem cells. CELL STEM CELL, 2(4), 333-344.
  
• A systems biology approach to anatomic diversity of skin Rinn, J. L., Wang, J. K., Liu, H., Montgomery, K., van de Rijn, M., & Chang, H. Y. (2008). A systems biology approach to anatomic diversity of skin. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 128(4), 776-782.
  
• SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin Michishita, E., McCord, R. A., Berber, E., Kioi, M., Padilla-Nash, H., & Chua, K. F. (2008). SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. NATURE, 452(7186), 492-U16.
  
• Systematic functional characterization of cis-regulatory motifs in human core promoters Sinha, S., Adler, A. S., Field, Y., Chang, H. Y., & Segal, E. (2008). Systematic functional characterization of cis-regulatory motifs in human core promoters. GENOME RESEARCH, 18(3), 477-488.
  
• Reversal of aging by NF kappa B blockade Adler, A. S., Kawahara, T. La., Segal, E., & Chang, H. Y. (2008). Reversal of aging by NF kappa B blockade. CELL CYCLE, 7(5), 556-559.
  
• A dermal HOX transcriptional program regulates site-specific epidermal fate Rinn, J. L., Wang, J. K., Allen, N., Brugmann, S. A., Mikels, A. J., & Chang, H. Y. (2008). A dermal HOX transcriptional program regulates site-specific epidermal fate. GENES & DEVELOPMENT, 22(3), 303-307.
  
• CSN5 isopeptidase activity links COP9 signalosome activation to breast cancer progression Adler, A. S., Littlepage, L. E., Lin, M., Kawahara, T. La., Wong, D. J., & Chang, H. Y. (2008). CSN5 isopeptidase activity links COP9 signalosome activation to breast cancer progression. CANCER RESEARCH, 68(2), 506-515.
  
• Revealing targeted therapy for human cancer by gene module maps Wong, D. J., Nuyten, D. Sa., Regev, A., Lin, M., Adler, A. S., & Chang, H. Y. (2008). Revealing targeted therapy for human cancer by gene module maps. CANCER RESEARCH, 68(2), 369-378.
  
• Motif module map reveals enforcement of aging by continual NF-kappa B activity Adler, A. S., Sinha, S., Kawahara, T. La., Zhang, J. Y., Segal, E., & Chang, H. Y. (2007). Motif module map reveals enforcement of aging by continual NF-kappa B activity. GENES & DEVELOPMENT, 21(24), 3244-3257.
  
• A histone H3 lysine 27 demethylase regulates animal posterior development Lan, F., Bayliss, P. E., Rinn, J. L., Whetstine, J. R., Wang, J. K., & Shi, Y. (2007). A histone H3 lysine 27 demethylase regulates animal posterior development. NATURE, 449(7163), 689-U3.
  
• Turning skin into embryonic stem cells Chang, H. Y., & Cotsarelis, G. (2007). Turning skin into embryonic stem cells. NATURE MEDICINE, 13(7), 783-784.
  
• Functional demarcation of active and silent chromatin domains in human HOX loci by Noncoding RNAs Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X., & Chang, H. Y. (2007). Functional demarcation of active and silent chromatin domains in human HOX loci by Noncoding RNAs. CELL, 129(7), 1311-1323.
  
• Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs O'Geen, H., Squazzo, S. L., Iyengar, S., Blahnik, K., Rinn, J. L., & Farnham, P. J. (2007). Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLOS GENETICS, 3(6), 916-926.
  
• A transcriptional program mediating entry into cellular quiescence Liu, H., Adler, A. S., Segal, E., & Chang, H. Y. (2007). A transcriptional program mediating entry into cellular quiescence. PLOS GENETICS, 3(6), 996-1008.
  
• Decoding global gene expression programs in liver cancer by noninvasive imaging Segal, E., Sirlin, C. B., Ooi, C., Adler, A. S., Gollub, J., & Kuo, M. D. (2007). Decoding global gene expression programs in liver cancer by noninvasive imaging. NATURE BIOTECHNOLOGY, 25(6), 675-680.
  
• Patterning skin pigmentation via dickkopf Chang, H. Y. (2007). Patterning skin pigmentation via dickkopf. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 127(5), 994-995.
  
• GSK3 beta mediates suppression of cyclin D2 expression by tumor suppressor PTEN Huang, W., Chang, H. Y., Fei, T., Wu, H., & Chen, Y.-G. (2007). GSK3 beta mediates suppression of cyclin D2 expression by tumor suppressor PTEN. ONCOGENE, 26(17), 2471-2482.
  
• Spontaneous autoimmunity prevented by thymic expression of a single self-antigen DeVoss, J., Hou, Y., Johannes, K., Lu, W., Liou, G. I., & Anderson, M. S. (2006). Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. JOURNAL OF EXPERIMENTAL MEDICINE, 203(12), 2727-2735.
  
• Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation Sneddon, J. B., Zhen, H. H., Montgomery, K., van de Rijn, M., Tward, A. D., & Brown, P. O. (2006). Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103(40), 14842-14847.
  
• MYC can induce DNA breaks in vivo and in vitro independent of reactive oxygen species Ray, S., Atkuri, K. R., Deb-Basu, D., Adler, A. S., Chang, H. Y., & Felsher, D. W. (2006). MYC can induce DNA breaks in vivo and in vitro independent of reactive oxygen species. CANCER RESEARCH, 66(13), 6598-6605.
  
• Anatomic demarcation by positional variation in fibroblast gene expression programs Rinn, J. L., Bondre, C., Gladstone, H. B., Brown, P. O., & Chang, H. Y. (2006). Anatomic demarcation by positional variation in fibroblast gene expression programs. PLOS GENETICS, 2(7), 1084-1096.
  
• From description to causality - Mechanisms of gene expression signatures in cancer Adler, A. S., & Chang, H. Y. (2006). From description to causality - Mechanisms of gene expression signatures in cancer. CELL CYCLE, 5(11), 1148-1151.
  
• Genetic regulators of large-scale transcriptional signatures in cancer Adler, A. S., Lin, M. H., Horlings, H., Nuyten, D. Sa., Van de Vijver, M. J., & Chang, H. Y. (2006). Genetic regulators of large-scale transcriptional signatures in cancer. NATURE GENETICS, 38(4), 421-430.
  
• Microarray analysis of stem cells and differentiation Chang, H. Y., Thomson, J. A., & Chen, X. (2006). Microarray analysis of stem cells and differentiation. STEM CELL TOOLS AND OTHER EXPERIMENTAL PROTOCOLS, 420, 225-254.
  
• Predicting a local recurrence after breast-conserving therapy by gene expression profiling Nuyten, D. Sa., Kreike, B., Hart, A. Am., Chi, J.-T. A., Sneddon, J. B., & van de Vijver, M. J. (2006). Predicting a local recurrence after breast-conserving therapy by gene expression profiling. BREAST CANCER RESEARCH, 8(5).
  
• Learning more from microarrays: Insights from modules and networks Wong, D. J., & Chang, H. Y. (2005). Learning more from microarrays: Insights from modules and networks. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 125(2), 175-182.
  
• Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival Chang, H. Y., Nuyten, D. Sa., Sneddon, J. B., Hastie, T., Tibshirani, R., & van de Vijver, M. J. (2005). Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102(10), 3738-3743.
  
• Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. Chang, H. Y., Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., & Brown, P. O. (2004). Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS biology, 2(2), E7-?.
  
• Gene expression signature of fibroblast serum response predicts human cancer progression: Similarities between tumors and wounds Chang, H. Y., Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., & Brown, P. O. (2004). Gene expression signature of fibroblast serum response predicts human cancer progression: Similarities between tumors and wounds. PLOS BIOLOGY, 2(2), 206-214.
  
• Kinetics and specificity of Fas ligand induction in toxic epidermal necrolysis Chang, H. Y., Cooper, Z. A., Swetter, S. A., & Marinkovich, M. P. (2004). Kinetics and specificity of Fas ligand induction in toxic epidermal necrolysis. ARCHIVES OF DERMATOLOGY, 140(2), 242-244.
  
• Endothelial cell diversity revealed by global expression profiling Chi, J. T., Chang, H. Y., Haraldsen, G., Jahnsen, F. L., Troyanskaya, O. G., & Brown, P. O. (2003). Endothelial cell diversity revealed by global expression profiling. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(19), 10623-10628.
  
• Eruptive xanthomas associated with olanzapine use Chang, H. Y., Ridky, T. W., Kimball, A. B., Hughes, E., & Oro, A. E. (2003). Eruptive xanthomas associated with olanzapine use. ARCHIVES OF DERMATOLOGY, 139(8), 1045-1048.
  
• Myelogenous leukemia cutis resembling stasis dermatitis Chang, H. Y., Wong, K. M., Bosenberg, M., McKee, P. H., & Haynes, H. A. (2003). Myelogenous leukemia cutis resembling stasis dermatitis. JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY, 49(1), 128-129.
  
• Genomewide view of gene silencing by small interfering RNAs Chi, J. T., Chang, H. Y., Wang, N. N., Chang, D. S., Dunphy, N., & Brown, P. O. (2003). Genomewide view of gene silencing by small interfering RNAs. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(11), 6343-6346.
  
• Diversity, topographic differentiation, and positional memory in human fibroblasts Chang, H. Y., Chi, J. T., Dudoit, S., Bondre, C., van de Rijn, M., & Brown, P. O. (2002). Diversity, topographic differentiation, and positional memory in human fibroblasts. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99(20), 12877-12882.
  
• Proteases for cell suicide: Functions and regulation of caspases Chang, H. Y., & Yang, X. L. (2000). Proteases for cell suicide: Functions and regulation of caspases. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 64(4), 821-?.
  
• Dissecting Fas signaling with an altered-specificity death-domain mutant: Requirement of FADD binding for apoptosis but not Jun N-terminal kinase activation Chang, H. Y., Yang, X. L., & Baltimore, D. (1999). Dissecting Fas signaling with an altered-specificity death-domain mutant: Requirement of FADD binding for apoptosis but not Jun N-terminal kinase activation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 96(4), 1252-1256.
  
• Activation of apoptosis signal regulating kinase 1 (ASK1) by the adapter protein Daxx Chang, H. Y., Nishitoh, H., Yang, X. L., ICHIJO, H., & Baltimore, D. (1998). Activation of apoptosis signal regulating kinase 1 (ASK1) by the adapter protein Daxx. SCIENCE, 281(5384), 1860-1863.
  
• Essential role of CED-4 oligomerization in CED-3 activation and apoptosis Yang, X. L., Chang, H. Y., & Baltimore, D. (1998). Essential role of CED-4 oligomerization in CED-3 activation and apoptosis. SCIENCE, 281(5381), 1355-1357.
  
• Autoproteolytic activation of pro-caspases by oligomerization Yang, X. L., Chang, H. Y., & Baltimore, D. (1998). Autoproteolytic activation of pro-caspases by oligomerization. MOLECULAR CELL, 1(2), 319-325.
  
• Daxx, a novel Fas-binding protein that activates JNK and apoptosis Yang, X. L., KHOSRAVIFAR, R., Chang, H. Y., & Baltimore, D. (1997). Daxx, a novel Fas-binding protein that activates JNK and apoptosis. CELL, 89(7), 1067-1076.
  
• ASYMMETRIC RETRACTION OF GROWTH CONE FILOPODIA FOLLOWING FOCAL INACTIVATION OF CALCINEURIN Chang, H. Y., Takei, K., SYDOR, A. M., Born, T., Rusnak, F., & Jay, D. G. (1995). ASYMMETRIC RETRACTION OF GROWTH CONE FILOPODIA FOLLOWING FOCAL INACTIVATION OF CALCINEURIN. NATURE, 376(6542), 686-690.
  
• ACTIVATION OF CLN1 AND CLN2 G(1) CYCLIN GENE-EXPRESSION BY BCK2 DICOMO, C. J., Chang, H., & Arndt, K. T. (1995). ACTIVATION OF CLN1 AND CLN2 G(1) CYCLIN GENE-EXPRESSION BY BCK2. MOLECULAR AND CELLULAR BIOLOGY, 15(4), 1835-1846.
  
• ACTIVE-SITE MUTANTS OF HUMAN CYCLOPHILIN-A SEPARATE PEPTIDYL-PROLYL ISOMERASE ACTIVITY FROM CYCLOSPORINE-A BINDING AND CALCINEURIN INHIBITION ZYDOWSKY, L. D., Etzkorn, F. A., Chang, H. Y., Ferguson, S. B., STOLZ, L. A., & Walsh, C. T. (1992). ACTIVE-SITE MUTANTS OF HUMAN CYCLOPHILIN-A SEPARATE PEPTIDYL-PROLYL ISOMERASE ACTIVITY FROM CYCLOSPORINE-A BINDING AND CALCINEURIN INHIBITION. PROTEIN SCIENCE, 1(9), 1092-1099.
  
• CYCLOSPORINE-MEDIATED INHIBITION OF BOVINE CALCINEURIN BY CYCLOPHILIN-A AND CYCLOPHILIN-B SWANSON, S. Kh., Born, T., ZYDOWSKY, L. D., Cho, H. J., Chang, H. Y., & Rusnak, F. (1992). CYCLOSPORINE-MEDIATED INHIBITION OF BOVINE CALCINEURIN BY CYCLOPHILIN-A AND CYCLOPHILIN-B. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 89(9), 3741-3745.