Biography
Professional Summary
Education & Certifications
- Fellowship: Stanford University Dept of Dermatology (2004) CA
- Residency: Stanford University Dermatology Residency (2003) CA
- Internship: Santa Clara Valley Medical Center Dept of Medicine (2001) CA
- Board Certification: American Board of Dermatology, Dermatology (2004)
- Medical Education: Harvard Medical School (2000) MA
- Ph.D., MIT, Biology (1998)
- A.B., Harvard, Biochemistry (1994)
Honors & Awards
- Alfred Marchionini Research Prize, Alfred Marchionini Foundation (2011)
- CE.R.I.E.S. Award, Chanel Research and Technology (2010)
- Clinical Scientist Career Development Award (K08), NIH (2004-2009)
- Early Career Scientist, Howard Hughes Medical Institute (2009-2015)
- Elected Member, American Society for Clinical Investigation (2009)
- Investigator, Howard Hughes Medical Institute (2018)
- Judson Daland Prize, American Philosophical Society (2014)
- Member, American Academy of Arts and Sciences (2020)
- Member, National Academy of Medicine (2017)
- Member, National Academy of Sciences (2020)
- Montagna Lecture, Society for Investigative Dermatology (2012)
- NAS Award in Molecular Biology, National Academy of Science (2018)
- New Faculty Award, California Institute for Regenerative Medicine (2008-2013)
- Outstanding Investigator Award, National Cancer Institute (2016)
- Paul Marks Prize for Cancer Research, Memorial Sloan Kettering Cancer Institute (2015)
- Physician-Scientist Career Development Award, Dermatology Foundation (2004)
- Research Scholar Award, American Cancer Society (2007-2010)
- Salvador E. Luria Lecture, Massachusetts Institute of Technology (2012)
- Scholar Award, Damon Runyon Cancer Research Foundation (2006-2008)
- Senior Scholar Award in Aging, Ellison Medical Foundation (2009)
- Vilcek Prize for Creative Promise, Vilcek Foundation (2009)
- Young Investigator Award, American Academy of Dermatology (2003)
Memberships
- Editorial Board, Molecular Cell (2014 - Present)
Administrative Appointments
- Director, NIH Center of Excellence in Genomic Science: Center for Personal Dynamic Regulome (2014 - 2024)
- Member, Stanford Diabetes Research Center (2018 - Present)
Publications
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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-? -
Diversity, topographic differentiation, and positional memory in human fibroblasts
Chang, H. Y., Chi, J. T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., & 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), 12877–82. -
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), 6343–46. -
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. -
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), 1045–48. -
Endothelial cell diversity revealed by global expression profiling
Chi, J. T., Chang, H. Y., Haraldsen, G., Jahnsen, F. L., Troyanskaya, O. G., Chang, D. S., … 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), 10623–28. -
CYCLOSPORINE-MEDIATED INHIBITION OF BOVINE CALCINEURIN BY CYCLOPHILIN-A AND CYCLOPHILIN-B
SWANSON, S. K. H., Born, T., ZYDOWSKY, L. D., Cho, H. J., Chang, H. Y., Walsh, C. T., & 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. -
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., Ho, S. I., & 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. -
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., Montgomery, K., … 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-? -
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), 242–44. -
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival
Chang, H. Y., Nuyten, D. S. A., Sneddon, J. B., Hastie, T., Tibshirani, R., Sorlie, T., … 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), 3738–43. -
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), 175–82. -
Genetic regulators of large-scale transcriptional signatures in cancer
Adler, A. S., Lin, M. H., Horlings, H., Nuyten, D. S. A., Van de Vijver, M. J., & Chang, H. Y. (2006). Genetic regulators of large-scale transcriptional signatures in cancer. NATURE GENETICS, 38(4), 421–30. -
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), 1148–51. -
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., Herzenberg, L. A., & 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), 1084–96. -
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., West, R., … 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), 14842–47. -
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), 2471–82. -
Predicting a local recurrence after breast-conserving therapy by gene expression profiling
Nuyten, D. S. A., Kreike, B., Hart, A. A. M., Chi, J.-T. A., Sneddon, J. B., Wessels, L. F. A., … van de Vijver, M. J. (2006). Predicting a local recurrence after breast-conserving therapy by gene expression profiling. BREAST CANCER RESEARCH, 8(5). -
Spontaneous autoimmunity prevented by thymic expression of a single self-antigen
DeVoss, J., Hou, Y., Johannes, K., Lu, W., Liou, G. I., Rinn, J., … Anderson, M. S. (2006). Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. JOURNAL OF EXPERIMENTAL MEDICINE, 203(12), 2727–35. -
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, 225–54. -
Patterning skin pigmentation via dickkopf
Chang, H. Y. (2007). Patterning skin pigmentation via dickkopf. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 127(5), 994–95. -
Decoding global gene expression programs in liver cancer by noninvasive imaging
Segal, E., Sirlin, C. B., Ooi, C., Adler, A. S., Gollub, J., Chen, X., … Kuo, M. D. (2007). Decoding global gene expression programs in liver cancer by noninvasive imaging. NATURE BIOTECHNOLOGY, 25(6), 675–80. -
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs
O'Geen, H., Squazzo, S. L., Iyengar, S., Blahnik, K., Rinn, J. L., Chang, H. Y., … Farnham, P. J. (2007). Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLOS GENETICS, 3(6), 916–26. -
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. -
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., Brugmann, S. A., … Chang, H. Y. (2007). Functional demarcation of active and silent chromatin domains in human HOX loci by Noncoding RNAs. CELL, 129(7), 1311–23. -
Turning skin into embryonic stem cells
Chang, H. Y., & Cotsarelis, G. (2007). Turning skin into embryonic stem cells. NATURE MEDICINE, 13(7), 783–84. -
A histone H3 lysine 27 demethylase regulates animal posterior development
Lan, F., Bayliss, P. E., Rinn, J. L., Whetstine, J. R., Wang, J. K., Chen, S., … Shi, Y. (2007). A histone H3 lysine 27 demethylase regulates animal posterior development. NATURE, 449(7163), 689–U3. -
Motif module map reveals enforcement of aging by continual NF-kappa B activity
Adler, A. S., Sinha, S., Kawahara, T. L. A., 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), 3244–57. -
Revealing targeted therapy for human cancer by gene module maps
Wong, D. J., Nuyten, D. S. A., Regev, A., Lin, M., Adler, A. S., Segal, E., … Chang, H. Y. (2008). Revealing targeted therapy for human cancer by gene module maps. CANCER RESEARCH, 68(2), 369–78. -
CSN5 isopeptidase activity links COP9 signalosome activation to breast cancer progression
Adler, A. S., Littlepage, L. E., Lin, M., Kawahara, T. L. A., Wong, D. J., Werb, Z., & Chang, H. Y. (2008). CSN5 isopeptidase activity links COP9 signalosome activation to breast cancer progression. CANCER RESEARCH, 68(2), 506–15. -
A dermal HOX transcriptional program regulates site-specific epidermal fate
Rinn, J. L., Wang, J. K., Allen, N., Brugmann, S. A., Mikels, A. J., Liu, H., … Chang, H. Y. (2008). A dermal HOX transcriptional program regulates site-specific epidermal fate. GENES & DEVELOPMENT, 22(3), 303–7. -
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), 477–88. -
Reversal of aging by NF kappa B blockade
Adler, A. S., Kawahara, T. L. A., Segal, E., & Chang, H. Y. (2008). Reversal of aging by NF kappa B blockade. CELL CYCLE, 7(5), 556–59. -
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), 776–82. -
SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin
Michishita, E., McCord, R. A., Berber, E., Kioi, M., Padilla-Nash, H., Damian, M., … Chua, K. F. (2008). SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. NATURE, 452(7186), 492–U16. -
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), 333–44. -
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., Rinn, J. L., … Anderson, M. S. (2008). Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire. JOURNAL OF CLINICAL INVESTIGATION, 118(5), 1712–26. -
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), 1865–70. -
Deletional tolerance mediated by extrathymic Aire-expressing cells
Gardner, J. M., DeVoss, J. J., Friedman, R. S., Wong, D. J., Tan, Y. X., Zhou, X., … Anderson, M. S. (2008). Deletional tolerance mediated by extrathymic Aire-expressing cells. SCIENCE, 321(5890), 843–47. -
Combining biological gene expression signatures in predicting outcome in breast cancer: An alternative to supervised classification
Nuyten, D. S. A., 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), 2319–29. -
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), 3622–24. -
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., Scheynius, A., … Bradley, M. (2008). Global Expression Profiling in Atopic Eczema Reveals Reciprocal Expression of Inflammatory and Lipid Genes. PLOS ONE, 3(12). -
SIRT6 Links Histone H3 Lysine 9 Deacetylation to NF-kappa B-Dependent Gene Expression and Organismal Life Span
Kawahara, T. L. A., Michishita, E., Adler, A. S., Damian, M., Berber, E., Lin, M., … 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. -
Molecular Framework for Response to Imatinib Mesylate in Systemic Sclerosis
Chung, L., Fiorentino, D. F., Benbarak, M. J., Adler, A. S., Mariano, M. M., Paniagua, R. T., … Robinson, W. H. (2009). Molecular Framework for Response to Imatinib Mesylate in Systemic Sclerosis. ARTHRITIS AND RHEUMATISM, 60(2), 584–91. -
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., Chang, H. Y., … Gozani, O. (2009). ING4 Mediates Crosstalk between Histone H3 K4 Trimethylation and H3 Acetylation to Attenuate Cellular Transformation. MOLECULAR CELL, 33(2), 248–56. -
Hierarchical Maintenance of MLL Myeloid Leukemia Stem Cells Employs a Transcriptional Program Shared with Embryonic Rather Than Adult Stem Cells
Somervaille, T. C. P., Matheny, C. J., Spencer, G. J., Iwasaki, M., Rinn, J. L., Witten, D. M., … 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), 129–40. -
Genome-Wide Views of Chromatin Structure
Rando, O. J., & Chang, H. Y. (2009). Genome-Wide Views of Chromatin Structure. ANNUAL REVIEW OF BIOCHEMISTRY, 78, 245–71. -
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), 268–75. -
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., Pasmooij, A. M. G., … Khavari, P. A. (2009). Modeling Inducible Human Tissue Neoplasia Identifies an Extracellular Matrix Interaction Network Involved in Cancer Progression. CANCER CELL, 15(6), 477–88. -
Tumor Vasculature Is Regulated by PHD2-Mediated Angiogenesis and Bone Marrow-Derived Cell Recruitment
Chan, D. A., Kawahara, T. L. A., 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), 527–38. -
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), 689–93. -
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., Diehn, M., … 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), 14016–21. -
Anatomic Demarcation of Cells: Genes to Patterns
Chang, H. Y. (2009). Anatomic Demarcation of Cells: Genes to Patterns. SCIENCE, 326(5957), 1206–7. -
The histone demethylase UTX enables RB-dependent cell fate control
Wang, J. K., Tsai, M.-C., Poulin, G., Adler, A. S., Chen, S., Liu, H., … Chang, H. Y. (2010). The histone demethylase UTX enables RB-dependent cell fate control. GENES & DEVELOPMENT, 24(4), 327–32. -
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., Wong, D. J., … Chang, H. Y. (2010). Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. NATURE, 464(7291), 1071–U148. -
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), 2043–44. -
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Tsai, M.-C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., Lan, F., … Chang, H. Y. (2010). Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes. SCIENCE, 329(5992), 689–93. -
Genome-wide measurement of RNA secondary structure in yeast
Kertesz, M., Wan, Y., Mazor, E., Rinn, J. L., Nutter, R. C., Chang, H. Y., & Segal, E. (2010). Genome-wide measurement of RNA secondary structure in yeast. NATURE, 467(7311), 103–7. -
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), 3391–92. -
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), 582–85. -
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., Saddic, L. A., … Sage, J. (2010). G1 arrest and differentiation can occur independently of Rb family function. JOURNAL OF CELL BIOLOGY, 191(4), 809–25. -
Noncoding RNA Landmarks of Pluripotency and Reprogramming
Ouyang, Z., Zheng, G. X. Y., & Chang, H. Y. (2010). Noncoding RNA Landmarks of Pluripotency and Reprogramming. CELL STEM CELL, 7(6), 649–50. -
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. -
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), 539–43. -
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., Chen, Y., … Chang, H. Y. (2011). A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. NATURE, 472(7341), 120–U158. -
Long noncoding RNAs and human disease
Wapinski, O., & Chang, H. Y. (2011). Long noncoding RNAs and human disease. TRENDS IN CELL BIOLOGY, 21(6), 354–61. -
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters
Hung, T., Wang, Y., Lin, M. F., Koegel, A. K., Kotake, Y., Grant, G. D., … Chang, H. Y. (2011). Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. NATURE GENETICS, 43(7), 621–U196. -
Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging-Related Transcriptional Networks
Kawahara, T. L. A., 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). -
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., Wang, J. K., … 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), 3735–46. -
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), 641–55. -
Molecular Mechanisms of Long Noncoding RNAs
Wang, K. C., & Chang, H. Y. (2011). Molecular Mechanisms of Long Noncoding RNAs. MOLECULAR CELL, 43(6), 904–14. -
Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons
Marro, S., Pang, Z. P., Yang, N., Tsai, M.-C., Qu, K., Chang, H. Y., … Wernig, M. (2011). Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons. CELL STEM CELL, 9(4), 374–82. -
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), 667–78. -
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), 172–78. -
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., Gu, X., … 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), 2273–87. -
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. -
Suppression of progenitor differentiation requires the long noncoding RNA ANCR
Kretz, M., Webster, D. E., Flockhart, R. J., Lee, C. S., Zehnder, A., Lopez-Pajares, V., … Khavari, P. A. (2012). Suppression of progenitor differentiation requires the long noncoding RNA ANCR. GENES & DEVELOPMENT, 26(4), 338–43. -
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). -
High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation
Wu, A. R., Kawahara, T. L. A., Rapicavoli, N. A., van Riggelen, J., Shroff, E. H., Xu, L., … Quake, S. R. (2012). High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. LAB ON A CHIP, 12(12), 2190–98. -
The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression
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Long Noncoding RNA in Hematopoiesis and Immunity
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Single-cell chromatin accessibility reveals principles of regulatory variation.
Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., … Greenleaf, W. J. (2015). Single-cell chromatin accessibility reveals principles of regulatory variation. Nature, 523(7561), 486–90. -
Single-cell chromatin accessibility reveals principles of regulatory variation
Buenostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., … Greenleaf, W. J. (2015). Single-cell chromatin accessibility reveals principles of regulatory variation. NATURE, 523(7561), 486–U264. -
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. -
Structural imprints in vivo decode RNA regulatory mechanisms
Spitale, R. C., Flynn, R. A., Zhang, Q. C., Crisalli, P., Lee, B., Jung, J.-W., … Chang, H. Y. (2015). Structural imprints in vivo decode RNA regulatory mechanisms. NATURE, 519(7544), 486-? -
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), 249–53. -
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
Grow, E. J., Flynn, R. A., Chavez, S. L., Bayless, N. L., Wossidlo, M., Wesche, D. J., … Wysocka, J. (2015). Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. NATURE, 522(7555), 221-? -
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), 867–81. -
Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation
Mazumdar, C., Shen, Y., Xavy, S., Zhao, F., Reinisch, A., Li, R., … Majeti, R. (2015). Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. CELL STEM CELL, 17(6), 1–14. -
Unique features of long non-coding RNA biogenesis and function
Quinn, J. J., & Chang, H. Y. (2016). Unique features of long non-coding RNA biogenesis and function. NATURE REVIEWS GENETICS, 17(1), 47–62. -
Systematic Characterization of Long Noncoding RNAs Reveals the Contrasting Coordination of Cis- and Trans-Molecular Regulation in Human Fetal and Adult Hearts
He, C., Hu, H., Wilson, K. D., Wu, H., Feng, J., Xia, S., … Wu, J. C. (2016). Systematic Characterization of Long Noncoding RNAs Reveals the Contrasting Coordination of Cis- and Trans-Molecular Regulation in Human Fetal and Adult Hearts. CIRCULATION-CARDIOVASCULAR GENETICS, 9(2), 110–18. -
The histone chaperone CAF-1 safeguards somatic cell identity
Cheloufi, S., Elling, U., Hopfgartner, B., Jung, Y. L., Murn, J., Ninova, M., … Hochedlinger, K. (2015). The histone chaperone CAF-1 safeguards somatic cell identity. NATURE, 528(7581), 218-? -
CD44+ Cells in Head and Neck Squamous Cell Carcinoma Suppress T-Cell-Mediated Immunity by Selective Constitutive and Inducible Expression of PD-L1.
Lee, Y., Shin, J. H., Longmire, M., Wang, H., Kohrt, H. E., Chang, H. Y., & Sunwoo, J. B. (2016). CD44+ Cells in Head and Neck Squamous Cell Carcinoma Suppress T-Cell-Mediated Immunity by Selective Constitutive and Inducible Expression of PD-L1. Clinical Cancer Research , 22(14), 3571–81. -
Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human beta Cell Function
Arda, H. E., Li, L., Tsai, J., Torre, E. A., Rosli, Y., Peiris, H., … Kim, S. K. (2016). Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human beta Cell Function. CELL METABOLISM, 23(5), 909–20. -
Decoding the RNA structurome
Lu, Z., & Chang, H. Y. (2016). Decoding the RNA structurome. CURRENT OPINION IN STRUCTURAL BIOLOGY, 36, 142–48. -
A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63.
Bao, X., Rubin, A. J., Qu, K., Zhang, J., Giresi, P. G., Chang, H. Y., & Khavari, P. A. (2015). A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biology, 16(1), 284-? -
7SK-BAF axis controls pervasive transcription at enhancers.
Flynn, R. A., Do, B. T., Rubin, A. J., Calo, E., Lee, B., Kuchelmeister, H., … Chang, H. Y. (2016). 7SK-BAF axis controls pervasive transcription at enhancers. Nature Structural & Molecular Biology, 23(3), 231–38. -
Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.
Flynn, R. A., Zhang, Q. C., Spitale, R. C., Lee, B., Mumbach, M. R., & Chang, H. Y. (2016). Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nature Protocols, 11(2), 273–90. -
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace
Qu, K., Garamszegi, S., Wu, F., Thorvaldsdottir, H., Liefeld, T., Ocana, M., … Mesirov, J. P. (2016). Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. NATURE METHODS, 13(3), 245-? -
Rapid evolutionary turnover underlies conserved lncRNA-genome interactions
Quinn, J. J., Zhang, Q. C., Georgiev, P., Ilik, I. A., Akhtar, A., & Change, H. Y. (2016). Rapid evolutionary turnover underlies conserved lncRNA-genome interactions. GENES & DEVELOPMENT, 30(2), 191–207. -
Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation.
Mazumdar, C., Shen, Y., Xavy, S., Zhao, F., Reinisch, A., Li, R., … Majeti, R. (2015). Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. Cell Stem Cell, 17(6), 675–88. -
Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma.
Tan, J. L., Fogley, R. D., Flynn, R. A., Ablain, J., Yang, S., Saint-André, V., … Zon, L. I. (2016). Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Molecular Cell, 62(1), 34–46. -
Unique features of long non-coding RNA biogenesis and function.
Quinn, J. J., & Chang, H. Y. (2015). Unique features of long non-coding RNA biogenesis and function. Nature Reviews. Genetics, 17(1), 47–62. -
Decoding the RNA structurome.
Lu, Z., & Chang, H. Y. (2016). Decoding the RNA structurome. Current Opinion in Structural Biology, 36, 142–48. -
Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress
Oh, S., Flynn, R. A., Floor, S. N., Purzner, J., Martin, L., Do, B. T., … Cho, Y.-J. (2016). Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. ONCOTARGET, 7(19), 28169–82. -
Single-cell profiling of lncRNAs in the developing human brain
Ma, Q., & Chang, H. Y. (2016). Single-cell profiling of lncRNAs in the developing human brain. GENOME BIOLOGY, 17. -
A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation
Atianand, M. K., Hu, W., Satpathy, A. T., Shen, Y., Ricci, E. P., Alvarez-Dominguez, J. R., … Fitzgerald, K. A. (2016). A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation. CELL, 165(7), 1672–85. -
irCLIP platform for efficient characterization of protein-RNA interactions
Zarnegar, B. J., Flynn, R. A., Shen, Y., Do, B. T., Chang, H. Y., & Khavari, P. A. (2016). irCLIP platform for efficient characterization of protein-RNA interactions. NATURE METHODS, 13(6), 489-? -
An inducible long noncoding RNA amplifies DNA damage signaling.
Schmitt, A. M., Garcia, J. T., Hung, T., Flynn, R. A., Shen, Y., Qu, K., … Chang, H. Y. (2016). An inducible long noncoding RNA amplifies DNA damage signaling. Nature Genetics, 48(11), 1370–76. -
lncRNA Structure: Message to the Heart.
Fazal, F. M., & Chang, H. Y. (2016). lncRNA Structure: Message to the Heart. Molecular Cell, 64(1), 1–2. -
Molecular and Neural Functions of Rai1, the Causal Gene for Smith-Magenis Syndrome.
Huang, W.-H., Guenthner, C. J., Xu, J., Nguyen, T., Schwarz, L. A., Wilkinson, A. W., … Luo, L. (2016). Molecular and Neural Functions of Rai1, the Causal Gene for Smith-Magenis Syndrome. Neuron, 92(2), 392–406. -
HiChIP: efficient and sensitive analysis of protein-directed genome architecture.
Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J., & Chang, H. Y. (2016). HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nature Methods, 13(11), 919–22. -
Structural organization of the inactive X chromosome in the mouse
Giorgetti, L., Lajoie, B. R., Carter, A. C., Attia, M., Zhan, Y., Xu, J., … Dekker, J. (2016). Structural organization of the inactive X chromosome in the mouse. NATURE, 535(7613), 575-? -
HOXC10 Expression Supports the Development of Chemotherapy Resistance by Fine Tuning DNA Repair in Breast Cancer Cells
Sadik, H., Korangath, P., Nguyen, N. K., Gyorffy, B., Kumar, R., Hedayati, M., … Sukumar, S. (2016). HOXC10 Expression Supports the Development of Chemotherapy Resistance by Fine Tuning DNA Repair in Breast Cancer Cells. CANCER RESEARCH, 76(15), 4443–56. -
Individuality and variation of personal regulomes in primary human T cells.
Qu, K., Zaba, L. C., Giresi, P. G., Li, R., Longmire, M., Kim, Y. H., … Chang, H. Y. (2015). Individuality and variation of personal regulomes in primary human T cells. Cell Systems, 1(1), 51–61. -
ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.
Chen, X., Shen, Y., Draper, W., Buenrostro, J. D., Litzenburger, U., Cho, S. W., … Chang, H. Y. (2016). ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nature Methods. -
Single-cell epigenomic variability reveals functional cancer heterogeneity.
Litzenburger, U. M., Buenrostro, J. D., Wu, B., Shen, Y., Sheffield, N. C., Kathiria, A., … Chang, H. Y. (2017). Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biology, 18(1), 15-? -
Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells.
Xu, J., Carter, A. C., Gendrel, A.-V., Attia, M., Loftus, J., Greenleaf, W. J., … Chang, H. Y. (2017). Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Nature Genetics, 49(3), 377–86. -
Individuality and Variation of Personal Regulomes in Primary Human T Cells
Qu, K., Zaba, L. C., Giresi, P. G., Li, R., Longmire, M., Kim, Y. H., … Chang, H. Y. (2015). Individuality and Variation of Personal Regulomes in Primary Human T Cells. CELL SYSTEMS, 1(1), 51–61. -
Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing
Xu, J., Spitale, R. C., Guan, L., Flynn, R. A., Torre, E. A., Li, R., … Chang, A. L. S. (2016). Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing. PLOS ONE, 11(11). -
Comparison of SHAPE reagents for mapping RNA structures inside living cells
Lee, B., Flynn, R. A., Kadina, A., Guo, J. K., Kool, E. T., & Chang, H. Y. (2017). Comparison of SHAPE reagents for mapping RNA structures inside living cells. RNA, 23(2), 169–74. -
Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing.
Xu, J., Spitale, R. C., Guan, L., Flynn, R. A., Torre, E. A., Li, R., … Chang, A. L. S. (2016). Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing. PloS One, 11(11). -
Gpr124 is essential for blood-brain barrier integrity in central nervous system disease
Chang, J., Mancuso, M. R., Maier, C., Liang, X., Yuki, K., Yang, L., … Kuo, C. J. (2017). Gpr124 is essential for blood-brain barrier integrity in central nervous system disease. NATURE MEDICINE, 23(4), 450-? -
The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity.
Simsek, D., Tiu, G. C., Flynn, R. A., Byeon, G. W., Leppek, K., Xu, A. F., … Barna, M. (2017). The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell, 169(6), 1051–65 e18. -
Generation of pure GABAergic neurons by transcription factor programming.
Yang, N., Chanda, S., Marro, S., Ng, Y.-H., Janas, J. A., Haag, D., … Wernig, M. (2017). Generation of pure GABAergic neurons by transcription factor programming. Nature Methods, 14(6), 621–28. -
Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors.
Qu, K., Zaba, L. C., Satpathy, A. T., Giresi, P. G., Li, R., Jin, Y., … Chang, H. Y. (2017). Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors. Cancer Cell. -
Sensing Self and Foreign Circular RNAs by Intron Identity.
Chen, Y. G., Kim, M. V., Chen, X., Batista, P. J., Aoyama, S., Wilusz, J. E., … Chang, H. Y. (2017). Sensing Self and Foreign Circular RNAs by Intron Identity. Molecular Cell. -
Gene regulation in the immune system by long noncoding RNAs.
Chen, Y. G., Satpathy, A. T., & Chang, H. Y. (2017). Gene regulation in the immune system by long noncoding RNAs. Nature Immunology, 18(9), 962–72. -
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.
Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., … Chang, H. Y. (2017). An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature Methods. -
Discovery of stimulation-responsive immune enhancers with CRISPR activation.
Simeonov, D. R., Gowen, B. G., Boontanrart, M., Roth, T. L., Gagnon, J. D., Mumbach, M. R., … Marson, A. (2017). Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature. -
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.
Mumbach, M. R., Satpathy, A. T., Boyle, E. A., Dai, C., Gowen, B. G., Cho, S. W., … Chang, H. Y. (2017). Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nature Genetics. -
Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs.
Liu, Q., Jiang, C., Xu, J., Zhao, M.-T. T., Van Bortle, K., Cheng, X., … Snyder, M. P. (2017). Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs. Circulation Research, 121(4), 376–91. -
Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.
Rubin, A. J., Barajas, B. C., Furlan-Magaril, M., Lopez-Pajares, V., Mumbach, M. R., Howard, I., … Khavari, P. A. (2017). Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nature Genetics, 49(10), 1522–28. -
Factors That May Promote an Effective Local Research Environment
Wang, K., Lee, C. S., Marinkovich, M. P., Chang, H. Y., Oro, A. E., & Khavari, P. A. (2016). Factors That May Promote an Effective Local Research Environment. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 136(8), 1529–31. -
Preleukemic Hematopoietic Stem Cells in Human Acute Myeloid Leukemia
Corces, M. R., Chang, H. Y., & Majeti, R. (2017). Preleukemic Hematopoietic Stem Cells in Human Acute Myeloid Leukemia. FRONTIERS IN ONCOLOGY, 7, 263. -
m(6)A mRNA methylation sustains Treg suppressive functions
Tong, J., Cao, G., Zhang, T., Sefik, E., Vesely, M. C. A., Broughton, J. P., … Li, H.-B. (2018). m(6)A mRNA methylation sustains Treg suppressive functions. CELL RESEARCH, 28(2), 253–56. -
Challenges and recommendations for epigenomics in precision health
Carter, A. C., Chang, H. Y., Church, G., Dombkowski, A., Ecker, J. R., Gil, E., … Wong, W. (2017). Challenges and recommendations for epigenomics in precision health. NATURE BIOTECHNOLOGY, 35(12), 1128–32. -
Expression of the transcription factor ZBTB46 distinguishes human histiocytic disorders of classical dendritic cell origin.
Satpathy, A. T., Brown, R. A., Gomulia, E., Briseño, C. G., Mumbach, M. R., Pan, Z., … Kim, J. (2018). Expression of the transcription factor ZBTB46 distinguishes human histiocytic disorders of classical dendritic cell origin. Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc. -
IL-4R alpha Inhibitor for Atopic Disease
Chang, H. Y., & Nadeau, K. C. (2017). IL-4R alpha Inhibitor for Atopic Disease. CELL, 170(2), 222. -
Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation
Mazumdar, C., Shen, Y., Xavy, S., Zhao, F., Reinisch, A., Li, R., … Majeti, R. (2015). Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. BLOOD. AMER SOC HEMATOLOGY. -
An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1.
Chen, L., Roake, C. M., Freund, A., Batista, P. J., Tian, S., Yin, Y. A., … Artandi, S. E. (2018). An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1. Cell. -
GENOMIC AND EPIGENOMIC ANALYSIS OF ENGRAILED-1 FIBROBLASTS PREDICT FIBROGENIC ROLE IN SCARRING
Hu, M. S., Walmsley, G., Leavitt, T., Litzenburger, U., Marshall, C., Sinha, R., … Longaker, M. (2017). GENOMIC AND EPIGENOMIC ANALYSIS OF ENGRAILED-1 FIBROBLASTS PREDICT FIBROGENIC ROLE IN SCARRING. WOUND REPAIR AND REGENERATION. WILEY. -
Prrx1 Labels the Fibrogenic Fibroblast in the Ventral Dermis
Hu, M., Leavitt, T., Garcia, J., Ransom, R., Litzenburger, U., Walmsley, G., … Longaker, M. (2018). Prrx1 Labels the Fibrogenic Fibroblast in the Ventral Dermis. WOUND REPAIR AND REGENERATION. WILEY. -
Epigenetic Analysis of Scar Forming Fibroblasts Reveals Key Differences in Genes Associated with Fibrosis
Moore, A. L., Marshall, C. D., Litzenburger, U., Barnes, L., Ransom, R. C., Hu, M., … Longaker, M. T. (2017). Epigenetic Analysis of Scar Forming Fibroblasts Reveals Key Differences in Genes Associated with Fibrosis. JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS. ELSEVIER SCIENCE INC. -
The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline
Bailey, A. S., Batista, P. J., Gold, R. S., Chen, Y. G., de Rooij, D. G., Chang, H. Y., & Fuller, M. T. (2017). The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline. ELIFE, 6. -
Rapid chromatin repression by Aire provides precise control of immune tolerance
Koh, A. S., Miller, E. L., Buenrostro, J. D., Moskowitz, D. M., Wang, J., Greenleaf, W. J., … Crabtree, G. R. (2018). Rapid chromatin repression by Aire provides precise control of immune tolerance. NATURE IMMUNOLOGY, 19(2), 162-+. -
Decoding regulatory sequence across skin differentiation with deep learning
Kim, D., Risca, V., Chappell, J., Shi, M., Zhao, Z., Jung, N., … Khavari, P. (2018). Decoding regulatory sequence across skin differentiation with deep learning. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Dynamic morphogen-p63 chromatin interactions that guide epigenetic changes and p63 activity in surface ectoderm commitment
Pattison, J., Melo, S., Piekos, S., Torkelson, J., Mumbach, M. R., Rubin, A., … Oro, A. E. (2018). Dynamic morphogen-p63 chromatin interactions that guide epigenetic changes and p63 activity in surface ectoderm commitment. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Mechanistic insights in X-chromosome inactivation.
Lu, Z., Carter, A. C., & Chang, H. Y. (2017). Mechanistic insights in X-chromosome inactivation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 372(1733). -
Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element.
Cho, S. W., Xu, J., Sun, R., Mumbach, M. R., Carter, A. C., Chen, Y. G., … Chang, H. Y. (2018). Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell, 173(6), 1398. -
Epigenomics: Technologies and Applications.
Wang, K. C., & Chang, H. Y. (2018). Epigenomics: Technologies and Applications. Circulation Research, 122(9), 1191–99. -
Enhancer connectome functionally interrogates GWAS-identified intergenic SNPs associated with inflammatory skin conditions
Jeng, M. Y., Mumbach, M. R., Granja, J. M., Satpathy, A. T., Chang, H., & Chang, A. (2018). Enhancer connectome functionally interrogates GWAS-identified intergenic SNPs associated with inflammatory skin conditions. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Transcription coactivator and lncRNA duet evoke Hox genes
Wang, K. C., & Chang, H. Y. (2017). Transcription coactivator and lncRNA duet evoke Hox genes. PLOS GENETICS, 13(6), e1006797. -
m(6)A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways
Li, H.-B., Tong, J., Zhu, S., Batista, P. J., Duffy, E. E., Zhao, J., … Flavell, R. A. (2017). m(6)A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. NATURE, 548(7667), 338-+. -
ATAC Primer Tool for targeted analysis of accessible chromatin
Yost, K. E., Carter, A. C., Xu, J., Litzenburger, U., & Chang, H. Y. (2018). ATAC Primer Tool for targeted analysis of accessible chromatin. NATURE METHODS, 15(5), 304–5. -
In Situ Imaging of Spatial Organization of Accessible Chromatin at the Nanoscale with ATAC-see and Single-Molecule Super-Resolution Fluorescence Microscopy
Lee, M. Y., Chen, X., Gustavsson, A.-K., Chang, H. Y., & Moerner, W. E. (2018). In Situ Imaging of Spatial Organization of Accessible Chromatin at the Nanoscale with ATAC-see and Single-Molecule Super-Resolution Fluorescence Microscopy. BIOPHYSICAL JOURNAL. CELL PRESS. -
LncRNA Seduction of GOT2 Goes Viral
Chen, Y. G., & Chang, H. Y. (2017). LncRNA Seduction of GOT2 Goes Viral. IMMUNITY, 47(6), 1021–23. -
Long Noncoding RNAs: At the Intersection of Cancer and Chromatin Biology
Schmitt, A. M., & Chang, H. Y. (2017). Long Noncoding RNAs: At the Intersection of Cancer and Chromatin Biology. COLD SPRING HARBOR PERSPECTIVES IN MEDICINE, 7(7). -
Transforming Growth Factor Beta 3 (TGFB3) - a Novel Systemic Sclerosis Susceptibility Locus Involved in Fibrosis and Th17 Cell Development Identified By Genome-Wide Association Study in African Americans from the Genome Research in African American Scleroderma Patients Consortium
Gourh, P., Remmers, E. F., Satpathy, A., Boyden, S., Morgan, N. D., Shah, A. A., … Kastner, D. L. (2017). Transforming Growth Factor Beta 3 (TGFB3) - a Novel Systemic Sclerosis Susceptibility Locus Involved in Fibrosis and Th17 Cell Development Identified By Genome-Wide Association Study in African Americans from the Genome Research in African American Scleroderma Patients Consortium. ARTHRITIS & RHEUMATOLOGY. WILEY. -
Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation
Buenrostro, J. D., Corces, M. R., Lareau, C. A., Wu, B., Schep, A. N., Aryee, M. J., … Greenleaf, W. J. (2018). Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. CELL, 173(6), 1535-+. -
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations.
Duren, Z., Chen, X., Zamanighomi, M., Zeng, W., Satpathy, A. T., Chang, H. Y., … Wong, W. H. (2018). Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations. Proceedings of the National Academy of Sciences of the United States of America. -
SYSTEMATIC IDENTIFICATION OF ESSENTIAL LONG NON-CODING RNA GENES IN GLIOBLASTOMA
Liu, S., Horlbeck, M., Cho, S. W., Birk, H., Malatesta, M., He, D., … Lim, D. (2016). SYSTEMATIC IDENTIFICATION OF ESSENTIAL LONG NON-CODING RNA GENES IN GLIOBLASTOMA. NEURO-ONCOLOGY. OXFORD UNIV PRESS INC. -
Long Non-Coding RNA Expression Levels Correlate with Proliferation Index in Breast Carcinoma.
Chisholm, K. M., Li, R., Wan, Y., Chang, H. Y., & West, R. B. (2011). Long Non-Coding RNA Expression Levels Correlate with Proliferation Index in Breast Carcinoma. MODERN PATHOLOGY. NATURE PUBLISHING GROUP. -
Long Non-Coding RNA and Polycomb Protein Expression Levels Are Increased in Metastatic Versus Primary Breast Carcinoma
Chisholm, K. M., Li, R., Wan, Y., Chang, H., & West, R. B. (2012). Long Non-Coding RNA and Polycomb Protein Expression Levels Are Increased in Metastatic Versus Primary Breast Carcinoma. MODERN PATHOLOGY. NATURE PUBLISHING GROUP. -
Long Non-Coding RNA and Polycomb Protein Expression Levels Are Increased in Metastatic Versus Primary Breast Carcinoma
Chisholm, K. M., Li, R., Wan, Y., Chang, H., & West, R. B. (2012). Long Non-Coding RNA and Polycomb Protein Expression Levels Are Increased in Metastatic Versus Primary Breast Carcinoma. LABORATORY INVESTIGATION. NATURE PUBLISHING GROUP. -
Long Non-Coding RNA Expression Levels Correlate with Proliferation Index in Breast Carcinoma
Chisholm, K. M., Li, R., Wan, Y., Chang, H. Y., & West, R. B. (2011). Long Non-Coding RNA Expression Levels Correlate with Proliferation Index in Breast Carcinoma. LABORATORY INVESTIGATION. NATURE PUBLISHING GROUP. -
Understanding RNA-Chromatin Interactions Using Chromatin Isolation by RNA Purification (ChIRP)
Chu, C., & Chang, H. Y. (2016). Understanding RNA-Chromatin Interactions Using Chromatin Isolation by RNA Purification (ChIRP). POLYCOMB GROUP PROTEINS: METHODS AND PROTOCOLS, 1480, 115–23. -
Genetic determinants of co-accessible chromatin regions in activated T cells across humans
Gate, R. E., Cheng, C. S., Aiden, A. P., Siba, A., Tabaka, M., Lituiev, D., … Regev, A. (2018). Genetic determinants of co-accessible chromatin regions in activated T cells across humans. NATURE GENETICS, 50(8), 1140-+. -
A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas.
Arda, H. E., Tsai, J., Rosli, Y. R., Giresi, P., Bottino, R., Greenleaf, W. J., … Kim, S. K. (2018). A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas. Cell Systems. -
Gender and Gene Regulation in Human Immunity
Longmire, M. R., & Chang, H. (2017). Gender and Gene Regulation in Human Immunity. PRINCIPLES OF GENDER-SPECIFIC MEDICINE: GENDER IN THE GENOMIC ERA, 3RD EDITION, 335–40. -
ChIRP-MS: RNA-Directed Proteomic Discovery.
Chu, C., & Chang, H. Y. (2018). ChIRP-MS: RNA-Directed Proteomic Discovery. Methods in Molecular Biology (Clifton, N.J.), 1861, 37–45. -
Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons
Wapinski, O. L., Lee, Q. Y., Chen, A. C., Li, R., Corces, M. R., Ang, C. E., … Chang, H. Y. (2017). Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons. CELL REPORTS, 20(13), 3236–47. -
Neurogenic lncRNAs mutated in human neurodevelopmental disorders.
Ang, C., Wapinski, O., Ma, Q., Fan, S., Flynn, R. A., Coe, B., … Wernig, M. (2016). Neurogenic lncRNAs mutated in human neurodevelopmental disorders. MOLECULAR BIOLOGY OF THE CELL. AMER SOC CELL BIOLOGY. -
Epidermal tissue differentiation and lipid barrier function requires the long non-coding RNA Linc19A
Kretz, M., Webster, D., Siprashvili, Z., Zehnder, A., Lee, C., Flockhart, R., … Khavari, P. (2011). Epidermal tissue differentiation and lipid barrier function requires the long non-coding RNA Linc19A. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Identification of the Human Skeletal Stem Cell.
Chan, C. K., Gulati, G. S., Sinha, R., Tompkins, J. V., Lopez, M., Carter, A. C., … Longaker, M. T. (2018). Identification of the Human Skeletal Stem Cell. Cell, 175(1), 43. -
Transposition of Native Chromatin for Fast and Sensitive Mulitmodal Analysis of Chromatin Architecture
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2014). Transposition of Native Chromatin for Fast and Sensitive Mulitmodal Analysis of Chromatin Architecture. BIOPHYSICAL JOURNAL. CELL PRESS. -
Enhancer connectome nominates target genes of inherited risk variants from inflammatory skin disorders.
Jeng, M. Y., Mumbach, M. R., Granja, J. M., Satpathy, A. T., Chang, H. Y., & Chang, A. L. (2018). Enhancer connectome nominates target genes of inherited risk variants from inflammatory skin disorders. The Journal of Investigative Dermatology. -
DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions (Retraction of Vol 528, Pg 517, 2015)
Huang, W., Thomas, B., Flynn, R. A., Gavzy, S. J., Wu, L., Kim, S. V., … Littman, D. R. (2018). DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions (Retraction of Vol 528, Pg 517, 2015). NATURE, 562(7725), 150. -
Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders
Calo, E., Gu, B., Bowen, M. E., Aryan, F., Zalc, A., Liang, J., … Wysocka, J. (2018). Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders. NATURE, 554(7690), 112-+. -
Mechanoresponsive stem cells acquire neural crest fate in jaw regeneration.
Ransom, R. C., Carter, A. C., Salhotra, A., Leavitt, T., Marecic, O., Murphy, M. P., … Longaker, M. T. (2018). Mechanoresponsive stem cells acquire neural crest fate in jaw regeneration. Nature. -
The chromatin accessibility landscape of primary human cancers.
Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., … Chang, H. Y. (2018). The chromatin accessibility landscape of primary human cancers. Science (New York, N.Y.), 362(6413). -
Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity.
Chen, X., Litzenburger, U. M., Wei, Y., Schep, A. N., LaGory, E. L., Choudhry, H., … Chang, H. Y. (2018). Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity. Nature Communications, 9(1), 4590. -
Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment.
Pattison, J. M., Melo, S. P., Piekos, S. N., Torkelson, J. L., Bashkirova, E., Mumbach, M. R., … Oro, A. E. (2018). Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. Nature Genetics. -
Discovery of stimulation-responsive immune enhancers with CRISPR activation (vol 549, pg 111, 2017)
Simeonov, D. R., Gowen, B. G., Boontanrart, M., Roth, T. L., Gagnon, J. D., Mumbach, M. R., … Marson, A. (2018). Discovery of stimulation-responsive immune enhancers with CRISPR activation (vol 549, pg 111, 2017). NATURE, 559(7715), E13. -
The RNA Base-Pairing Problem and Base-Pairing Solutions.
Lu, Z., & Chang, H. Y. (2018). The RNA Base-Pairing Problem and Base-Pairing Solutions. Cold Spring Harbor Perspectives in Biology, 10(12). -
Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.
Rubin, A. J., Parker, K. R., Satpathy, A. T., Qi, Y., Wu, B., Ong, A. J., … Khavari, P. A. (2018). Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. Cell. -
Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons.
Luo, C., Lee, Q. Y., Wapinski, O., Castanon, R., Nery, J. R., Mall, M., … Ecker, J. R. (2019). Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. ELife, 8. -
TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment.
Li, L., Wang, Y., Torkelson, J. L., Shankar, G., Pattison, J. M., Zhen, H. H., … Oro, A. E. (2019). TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment. Cell Stem Cell. -
A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells.
Van Gool, F., Nguyen, M. L., Mumbach, M. R., Satpathy, A. T., Rosenthal, W. L., Giacometti, S., … Bluestone, J. A. (2019). A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells. Immunity. -
Long Noncoding RNA and Its Role in the Control of Gene Expression in the Skin
Wang, K. C., & Chang, H. Y. (2018). Long Noncoding RNA and Its Role in the Control of Gene Expression in the Skin. EPIGENETIC REGULATION OF SKIN DEVELOPMENT AND REGENERATION, 197–213. -
Invariant Natural Killer T Cell Subsets Have Diverse Functions: iNKT2 and iNKT17 Protect from Graft-Versus-Host-Disease, Whereas iNKT1 Have Antitumor Potential
Maas-Bauer, K., Simonetta, F., Hirai, T., Wenokur, A., Fazal, F., Kambham, N., … Negrin, R. S. (2018). Invariant Natural Killer T Cell Subsets Have Diverse Functions: iNKT2 and iNKT17 Protect from Graft-Versus-Host-Disease, Whereas iNKT1 Have Antitumor Potential. BLOOD. AMER SOC HEMATOLOGY. -
Foxp3 domain-swap interface is required to suppress T helper type 2 transcriptional program in Regulatory T cells.
Van Gool, F., Nguyen, M. L., Mumbach, M. R., Satpathy, A. T., Anderson, M. S., Marson, A., … Bluestone, J. A. (2018). Foxp3 domain-swap interface is required to suppress T helper type 2 transcriptional program in Regulatory T cells. JOURNAL OF IMMUNOLOGY. AMER ASSOC IMMUNOLOGISTS. -
RNA structure maps across mammalian cellular compartments.
Sun, L., Fazal, F. M., Li, P., Broughton, J. P., Lee, B., Tang, L., … Zhang, Q. C. (2019). RNA structure maps across mammalian cellular compartments. Nature Structural & Molecular Biology. -
Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation
Lopez-Pajares, V., Rubin, A., Barajas, B., Furlan-Magaril, M., Mumbach, M., Greenleaf, W., … Khavari, P. A. (2017). Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
The BAF/SWI/SNF complex controls genome accessibility to p63 during epidermal differentiation
Bao, X., Rubin, A., Qu, K., Zhang, J., Giresi, P., Chang, H., & Khavari, P. (2015). The BAF/SWI/SNF complex controls genome accessibility to p63 during epidermal differentiation. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Reversal of epidermal aging by NF-kappa B blockade
Adler, A. S., Kawahara, T. L., Zhang, J. Y., Segal, E., Chua, K. F., & Chang, H. Y. (2008). Reversal of epidermal aging by NF-kappa B blockade. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Site-specific induction of epidermal fates by dermal HOX transcriptional program
Rinn, J. L., Wang, J. K., Allen, N., Mikels, A. J., Nusse, R., Helms, J. A., & Chang, H. Y. (2007). Site-specific induction of epidermal fates by dermal HOX transcriptional program. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Asymmetric regulation of gene expression in the response of fibroblasts to serum deprivation
Liu, H., Segal, E., & Chang, H. Y. (2006). Asymmetric regulation of gene expression in the response of fibroblasts to serum deprivation. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Gene-expression profiling of lesional and atopy patched tested skin in patients with atopic dermatitis using cDNA microarrays
Saaf, A., Bradley, M., Tengvall-Linder, M., Chang, H. Y., Wahlgren, C. F., Scheynius, A., … Brown, P. O. (2005). Gene-expression profiling of lesional and atopy patched tested skin in patients with atopic dermatitis using cDNA microarrays. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
Molecular anatomy of human fibroblast diversity
Rinn, J. L., Bondre, C., van De Rijn, M., Brown, P., & Chang, H. Y. (2005). Molecular anatomy of human fibroblast diversity. JOURNAL OF INVESTIGATIVE DERMATOLOGY. BLACKWELL PUBLISHING INC. -
Reproducibility of several gene expression signatures in predicting outcome in breast cancer
Nuyten, D. S., Chang, H. Y., Sneddon, J. B., Hart, G. A., van 't Veer, L. J., Peterse, H. L., … van de Vijver, M. J. (2004). Reproducibility of several gene expression signatures in predicting outcome in breast cancer. BREAST CANCER RESEARCH AND TREATMENT. SPRINGER. -
Finding specific drug targets by applying gene module analysis in patients categorized by previously established prognostic gene expression signature in early stage breast cancer.
Nuyten, D. S., Lin, M., Adler, A. A., Bartelink, H., Van de Vijver, M. J., & Chang, H. Y. (2006). Finding specific drug targets by applying gene module analysis in patients categorized by previously established prognostic gene expression signature in early stage breast cancer. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Genome Regulation by Long Noncoding RNAs
Chang, H. Y. (2016). Genome Regulation by Long Noncoding RNAs. FASEB JOURNAL. FEDERATION AMER SOC EXP BIOL. -
Genome Regulation by Long Noncoding RNAs
Chang, H. Y. (2016). Genome Regulation by Long Noncoding RNAs. FASEB JOURNAL. FEDERATION AMER SOC EXP BIOL. -
Comment on "Hotair Is Dispensable for Mouse Development"
Li, L., Helms, J. A., & Chang, H. Y. (2016). Comment on "Hotair Is Dispensable for Mouse Development". PLOS GENETICS, 12(12), e1006406. -
Analysis Of T Helper Cell Gene Regulation In Asthma By Genome-Wide Chromatin Accessibility Profiling In Monozygotic Twins
Bauer, R. N., Satpathy, A. T., Qu, K., Ho, T., Chinthrajah, R. S., Miller, R. L., … Nadeau, K. C. (2016). Analysis Of T Helper Cell Gene Regulation In Asthma By Genome-Wide Chromatin Accessibility Profiling In Monozygotic Twins. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. AMER THORACIC SOC. -
Genome regulation by long noncoding RNAs
Chang, H. Y. (2016). Genome regulation by long noncoding RNAs. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
The Homeobox Protein H0XC10 Is Overexpressed in Breast Cancer and Confers Resistance to Chemotherapy
Sadik, H., Shah, N., Gupta, R. A., Chang, H. Y., & Sukumar, S. (2010). The Homeobox Protein H0XC10 Is Overexpressed in Breast Cancer and Confers Resistance to Chemotherapy. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Long Noncoding RNAs in Breast Cancer Progression
Chang, H. Y. (2010). Long Noncoding RNAs in Breast Cancer Progression. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Tumor as wound: gene expression signature of fibroblast serum response predicts human cancer progression
Chang, H. Y., Sneddon, J. B., van de Rijn, M., & Brown, P. O. (2004). Tumor as wound: gene expression signature of fibroblast serum response predicts human cancer progression. JOURNAL OF INVESTIGATIVE DERMATOLOGY. BLACKWELL PUBLISHING INC. -
LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes
Carlson, H. L., Quinn, J. J., Yang, Y. W., Thornburg, C. K., Chang, H. Y., & Stadler, H. S. (2015). LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes. PLOS GENETICS, 11(12), e1005680. -
Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing.
Wan, Y., Qu, K., Ouyang, Z., & Chang, H. Y. (2016). Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing. Methods in Molecular Biology (Clifton, N.J.), 1361, 141–60. -
Hyaluronan synthase 2 antisense transcript level associates with human skin youthfulness as identified by transcriptome sequencing
Xu, J., Flynn, R. A., Spitale, R., Torre, E., Li, R., Kern, D. G., … Chang, A. S. (2015). Hyaluronan synthase 2 antisense transcript level associates with human skin youthfulness as identified by transcriptome sequencing. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Montagna Symposium 2014-Skin Aging: Molecular Mechanisms and Tissue Consequences
Gilchrest, B. A., Campisi, J., Chang, H. Y., Fisher, G. J., & Kulesz-Martin, M. F. (2015). Montagna Symposium 2014-Skin Aging: Molecular Mechanisms and Tissue Consequences. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 135(4), 950–53. -
Cohesin Complex Mutations Impair Differentiation of Human Hematopoietic Stem and Progenitor Cells
Mazumdar, C., Li, R., Buenrostro, J., Chang, H. Y., & Majeti, R. (2014). Cohesin Complex Mutations Impair Differentiation of Human Hematopoietic Stem and Progenitor Cells. BLOOD. AMER SOC HEMATOLOGY. -
PALMOPLANTAR SPECIFIC LONG NCRNA HOTAIR DRIVES MYOFIBROBLASTS SPECIFIC SIGNATURE IN SYSTEMIC SCLEROSIS
Abignano, G., Hermes, H., Esteves, F., Gillespie, J., Chang, H. Y., Jimenez, S. A., … Del Galdo, F. (2013). PALMOPLANTAR SPECIFIC LONG NCRNA HOTAIR DRIVES MYOFIBROBLASTS SPECIFIC SIGNATURE IN SYSTEMIC SCLEROSIS. ANNALS OF THE RHEUMATIC DISEASES. BMJ PUBLISHING GROUP. -
Epigenomic maps in faithful tissue context of skin cell types
Zaba, L., Longmire, M., Zhang, J., & Chang, H. Y. (2014). Epigenomic maps in faithful tissue context of skin cell types. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Genome regulation by long noncoding RNAs
Chang, H. Y. (2013). Genome regulation by long noncoding RNAs. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Regulation of the DNA Damage Response by an Inducible Long Noncoding RNA
Schmitt, A., Hung, T., Flynn, R., Payumo, A., Peres-da-Silva, A., Broz, D. K., … Chang, H. (2013). Regulation of the DNA Damage Response by an Inducible Long Noncoding RNA. INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS. ELSEVIER SCIENCE INC. -
GENE REGULATION Long RNAs wire up cancer growth
Schmitt, A. M., & Chang, H. Y. (2013). GENE REGULATION Long RNAs wire up cancer growth. NATURE, 500(7464), 536–37. -
Sustained beta-catenin activity leads to dermal fibrosis by promoting expression of various pro-fibrotic mediators
Hamburg, E., Chen, D., Torres, E., Chang, H., & Atit, R. (2013). Sustained beta-catenin activity leads to dermal fibrosis by promoting expression of various pro-fibrotic mediators. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
The transcription factor ZNF217 is an oncogene that promotes an increase in progenitor cells, increases metastasis, and acts via the AKT pathway
Littlepage, L. E., Kouros-Mehr, H., Adler, A. S., Chou, J., Huang, G., Collins, C. C., … Werb, Z. (2011). The transcription factor ZNF217 is an oncogene that promotes an increase in progenitor cells, increases metastasis, and acts via the AKT pathway. MOLECULAR BIOLOGY OF THE CELL. AMER SOC CELL BIOLOGY. -
Rejuvenation of gene expression patterns in aged human skin with broadband light treatment
Chang, A. S., Bitter, P., Qu, K., & Chang, H. Y. (2012). Rejuvenation of gene expression patterns in aged human skin with broadband light treatment. JOURNAL OF INVESTIGATIVE DERMATOLOGY. NATURE PUBLISHING GROUP. -
Microarray Analysis of Stem Cells and Differentiation
Chang, H. Y., & Chen, X. (2009). Microarray Analysis of Stem Cells and Differentiation. ESSENTIALS OF STEM CELL BIOLOGY, 2ND EDITION, 449–57. -
Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA.
Xu, J., Nuno, K., Litzenburger, U. M., Qi, Y., Corces, M. R., Majeti, R., & Chang, H. Y. (2019). Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA. ELife, 8. -
Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.
Oh, S., Flynn, R. A., Floor, S. N., Purzner, J., Martin, L., Do, B. T., … Cho, Y.-J. J. (2016). Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget, 7(19), 28169–82. -
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. -
Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA
Xu, J., Nuno, K., Litzenburger, U. M., Qi, Y., Corces, M. R., Majeti, R., & Chang, H. Y. (2019). Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA. ELIFE, 8. -
Identification of the Human Skeletal Stem Cell
Chan, C. K. F., Gulati, G. S., Sinha, R., Tompkins, J. V., Lopez, M., Carter, A. C., … Longaker, M. T. (2018). Identification of the Human Skeletal Stem Cell. CELL, 175(1), 43-+. -
RNA structure maps across mammalian cellular compartments
Sun, L., Fazal, F. M., Li, P., Broughton, J. P., Lee, B., Tang, L., … Zhang, Q. C. (2019). RNA structure maps across mammalian cellular compartments. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 26(4), 322-+. -
Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks
Rubin, A. J., Parker, K. R., Satpathy, A. T., Qi, Y., Wu, B., Ong, A. J., … Khavari, P. A. (2019). Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. CELL, 176(1-2), 361-+. -
Mechanoresponsive stem cells acquire neural crest fate in jaw regeneration
Ransom, R. C., Carter, A. C., Salhotra, A., Leavitt, T., Marecic, O., Murphy, M. P., … Longaker, M. T. (2018). Mechanoresponsive stem cells acquire neural crest fate in jaw regeneration. NATURE, 563(7732), 514-+. -
ChIRP-MS: RNA-Directed Proteomic Discovery
Chu, C., & Chang, H. Y. (2018). ChIRP-MS: RNA-Directed Proteomic Discovery. X-CHROMOSOME INACTIVATION: METHODS AND PROTOCOLS, 1861, 37–45. -
Promoter of IncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element
Cho, S. W., Xu, J., Sun, R., Mumbach, M. R., Carter, A. C., Chen, Y. G., … Chang, H. Y. (2018). Promoter of IncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. CELL, 173(6), 1398-+. -
Mechanistic insights in X-chromosome inactivation
Lu, Z., Carter, A. C., & Chang, H. Y. (2017). Mechanistic insights in X-chromosome inactivation. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 372(1733). -
A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells
Van Gool, F., Nguyen, M. L. T., Mumbach, M. R., Satpathy, A. T., Rosenthal, W. L., Giacometti, S., … Bluestone, J. A. (2019). A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells. IMMUNITY, 50(2), 362-+. -
TFAP2C-and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment
Li, L., Wang, Y., Torkelson, J. L., Shankar, G., Pattison, J. M., Zhen, H. H., … Oro, A. E. (2019). TFAP2C-and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment. CELL STEM CELL, 24(2), 271-+. -
Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Luo, C., Lee, Q. Y., Wapinski, O., Castanon, R., Nery, J. R., Malin, M., … Ecker, J. R. (2019). Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. ELIFE, 8. -
The novel lncRNA lnc-NR2F1 is proneurogenic and mutated in human neurodevelopmental disorders
Ang, C. E., Ma, Q., Wapinski, O. L., Fan, S. H., Flynn, R. A., Lee, Q. Y., … Chang, H. Y. (2019). The novel lncRNA lnc-NR2F1 is proneurogenic and mutated in human neurodevelopmental disorders. ELIFE, 8. -
The RNA Base-Pairing Problem and Base-Pairing Solutions
Lu, Z., & Chang, H. Y. (2018). The RNA Base-Pairing Problem and Base-Pairing Solutions. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY, 10(12). -
Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment
Pattison, J. M., Melo, S. P., Piekos, S. N., Torkelson, J. L., Bashkirova, E., Mumbach, M. R., … Oro, A. E. (2018). Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. NATURE GENETICS, 50(12), 1658-+. -
Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity
Chen, X., Litzenburger, U. M., Wei, Y., Schep, A. N., LaGory, E. L., Choudhry, H., … Chang, H. Y. (2018). Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity. NATURE COMMUNICATIONS, 9. -
Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders
Jeng, M. Y., Mumbach, M. R., Granja, J. M., Satpathy, A. T., Chang, H. Y., & Chang, A. L. S. (2019). Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 139(3), 605–14. -
A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas
Arda, H. E., Tsai, J., Rosli, Y. R., Giresi, P., Bottino, R., Greenleaf, W. J., … Kim, S. K. (2018). A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas. CELL SYSTEMS, 7(3), 310-+. -
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations
Duren, Z., Chen, X., Zamanighomi, M., Zeng, W., Satpathy, A. T., Chang, H. Y., … Wong, W. H. (2018). Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115(30), 7723–28. -
An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1
Chen, L., Roake, C. M., Freund, A., Batista, P. J., Tian, S., Yin, Y. A., … Artandi, S. E. (2018). An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1. CELL, 174(1), 218-+. -
Expression of the transcription factor ZBTB46 distinguishes human histiocytic disorders of classical dendritic cell origin
Satpathy, A. T., Brown, R. A., Gomulia, E., Briseno, C. G., Mumbach, M. R., Pan, Z., … Kim, J. (2018). Expression of the transcription factor ZBTB46 distinguishes human histiocytic disorders of classical dendritic cell origin. MODERN PATHOLOGY, 31(9), 1479–86. -
Epigenomics Technologies and Applications
Wang, K. C., & Chang, H. Y. (2018). Epigenomics Technologies and Applications. CIRCULATION RESEARCH, 122(9), 1191–99. -
Unraveling keratinocyte gene regulatory networks with single-cell cripsr screening and epigenomic profiling
Ramanathan, M., Rubin, A., Parker, K., Satpathy, A., Greenleaf, W., Chang, H., & Khavari, P. (2019). Unraveling keratinocyte gene regulatory networks with single-cell cripsr screening and epigenomic profiling. JOURNAL OF INVESTIGATIVE DERMATOLOGY. ELSEVIER SCIENCE INC. -
HiChIRP reveals RNA-associated chromosome conformation.
Mumbach, M. R., Granja, J. M., Flynn, R. A., Roake, C. M., Satpathy, A. T., Rubin, A. J., … Chang, H. Y. (2019). HiChIRP reveals RNA-associated chromosome conformation. Nature Methods. -
Engineering AP1 to combat CAR T cell exhaustion
Lynn, R. C., Weber, E. W., Gennert, D., Sotillo, E., Jones, R., Xu, P., … Mackall, C. L. (2018). Engineering AP1 to combat CAR T cell exhaustion. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Genome regulation by long noncoding RNAs
Chang, H. Y. (2018). Genome regulation by long noncoding RNAs. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Atlas of Subcellular RNA Localization Revealed by APEX-Seq.
Fazal, F. M., Han, S., Parker, K. R., Kaewsapsak, P., Xu, J., Boettiger, A. N., … Ting, A. Y. (2019). Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell. -
Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy.
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An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development.
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Chromatin accessibility landscape in healthy and scleroderma skin nominate dendritic cells in disease pathogenesis
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Intrinsic Chromatin State and Extrinsic Wound-Related Cues Can Coordinate to Activate Fibroblasts for Scarring
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Circular ecDNA promotes accessible chromatin and high oncogene expression.
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c-Jun overexpression in CAR T cells induces exhaustion resistance.
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Functional significance of U2AF1 S34F mutations in lung adenocarcinomas.
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Chromatin accessibility dynamics in a model of human forebrain development.
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CRISPR-engineered T cells in patients with refractory cancer.
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Long non-coding RNA HOTAIR drives EZH2-dependent myofibroblast activation in systemic sclerosis through miRNA 34a-dependent activation of NOTCH.
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RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing.
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Single-cell RNA sequencing in cardiovascular development, disease and medicine.
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Pro-neuronal activity of Myod1 due to promiscuous binding to neuronal genes.
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Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.
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A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by T-reg cells
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Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation.
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Diverse lncRNA mechanisms in brain development and disease.
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RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus.
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Functional annotation of human long noncoding RNAs via molecular phenotyping.
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Endogenous Retrovirus-Derived lncRNA BANCR Promotes Cardiomyocyte Migration in Humans and Non-human Primates.
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Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2.
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Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers.
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Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2.
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Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies.
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Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity.
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Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases.
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Prrx1 Fibroblasts Represent a Pro-fibrotic Lineage in the Mouse Ventral Dermis.
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Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis.
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Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
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Structural modularity of the XIST ribonucleoprotein complex.
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Distinct Immune Regulatory Potential of Invariant Natural Killer T (iNKT) Cell Subsets: iNKT2 and iNKT17, but Not iNKT1, Protect from Graft-Versus-Host-Disease
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Deciphering Warburg effect: hypoxia inhibits tumor cell differentiation through reducing acetyl-CoA generation and chromatin accessibility
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Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.
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B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells.
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Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling.
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BABEL enables cross-modality translation between multiomic profiles at single-cell resolution.
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Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.
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Recruiting T cells in cancer immunotherapy.
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Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE
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Invariant Natural Killer T Cell Subsets Have Diverse Graft-Versus-Host-Disease-Preventing and Anti-Tumor Effects.
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Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection.
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Dynamic chromatin regulatory landscape of human CAR T cell exhaustion.
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LKB1 inactivation modulates chromatin accessibility to drive metastatic progression.
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Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution.
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Structured elements drive extensive circular RNA translation.
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fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
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Locus specific epigenetic modalities of random allelic expression imbalance.
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JUN promotes hypertrophic skin scarring via CD36 in preclinical in vitro and in vivo models.
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Integrated spatial multiomics reveals fibroblast fate during tissue repair.
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The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation.
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Extrachromosomal DNA: An Emerging Hallmark in Human Cancer.
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NOT-Gated CD93 CAR T Cells Effectively Target AML with Minimized Endothelial Cross-Reactivity.
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Cancer-Associated Fibroblasts Share Highly Conserved Phenotypes and Functions Across Tumor Types and Species
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ecDNA hubs drive cooperative intermolecular oncogene expression.
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GPC2-CAR Tcells tuned for low antigen density mediate potent activity against neuroblastoma without toxicity.
Heitzeneder, S., Bosse, K. R., Zhu, Z., Zhelev, D., Majzner, R. G., Radosevich, M. T., … Mackall, C. L. (1800). GPC2-CAR Tcells tuned for low antigen density mediate potent activity against neuroblastoma without toxicity. Cancer Cell. -
Identification of Protein-RNA Interactions in Mouse Testis Tissue Using fRIP
Bailey, A., Batista, P., Chang, H., & Fuller, M. (2022). Identification of Protein-RNA Interactions in Mouse Testis Tissue Using fRIP. BIO-PROTOCOL, 12(01). -
Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility.
Meijer, M., Agirre, E., Kabbe, M., van Tuijn, C. A., Heskol, A., Zheng, C., … Castelo-Branco, G. (1800). Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility. Neuron. -
GPC2-CAR T cells tuned for low antigen density mediate potent activity against neuroblastoma without toxicity
Heitzeneder, S., Bosse, K. R., Zhu, Z., Zhelev, D., Majzner, R. G., Radosevich, M. T., … Mackall, C. L. (2022). GPC2-CAR T cells tuned for low antigen density mediate potent activity against neuroblastoma without toxicity. CANCER CELL, 40(1), 53-+. -
Identification of Protein-RNA Interactions in Mouse Testis Tissue Using fRIP.
Bailey, A. S., Batista, P. J., Chang, H. Y., & Fuller, M. T. (2022). Identification of Protein-RNA Interactions in Mouse Testis Tissue Using fRIP. Bio-Protocol, 12(1), e4286. -
Circular RNA migration in agarose gel electrophoresis.
Abe, B. T., Wesselhoeft, R. A., Chen, R., Anderson, D. G., & Chang, H. Y. (2022). Circular RNA migration in agarose gel electrophoresis. Molecular Cell. -
BRD2 compartmentalizes the accessible genome.
Xie, L., Dong, P., Qi, Y., Hsieh, T.-H. S., English, B. P., Jung, S. K., … Liu, Z. (2022). BRD2 compartmentalizes the accessible genome. Nature Genetics. -
Oncogene Convergence in Extrachromosomal DNA Hubs.
Weiser, N. E., Hung, K. L., & Chang, H. Y. (2022). Oncogene Convergence in Extrachromosomal DNA Hubs. Cancer Discovery, OF1–OF4. -
A genetic bottleneck of mitochondrial DNA during human lymphocyte development.
Tang, Z., Lu, Z., Chen, B., Zhang, W., Chang, H. Y., Hu, Z., & Xu, J. (2022). A genetic bottleneck of mitochondrial DNA during human lymphocyte development. Molecular Biology and Evolution. -
Enhanced safety and efficacy of protease-regulated CAR-T cell receptors.
Labanieh, L., Majzner, R. G., Klysz, D., Sotillo, E., Fisher, C. J., Vilches-Moure, J. G., … Mackall, C. L. (2022). Enhanced safety and efficacy of protease-regulated CAR-T cell receptors. Cell. -
The Mettl3 epitranscriptomic writer amplifies p53 stress responses.
Raj, N., Wang, M., Seoane, J. A., Zhao, R. L., Kaiser, A. M., Moonie, N. A., … Attardi, L. D. (2022). The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Molecular Cell. -
Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation.
Kraft, K., Yost, K. E., Murphy, S. E., Magg, A., Long, Y., Corces, M. R., … Chang, H. Y. (2022). Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation. Proceedings of the National Academy of Sciences of the United States of America, 119(22), e2201883119. -
RNA-binding proteins direct myogenic cell fate decisions.
Wheeler, J. R., Whitney, O. N., Vogler, T. O., Nguyen, E. D., Pawlikowski, B., Lester, E., … Olwin, B. B. (2022). RNA-binding proteins direct myogenic cell fate decisions. ELife, 11. -
Engineering circular RNA for enhanced protein production.
Chen, R., Wang, S. K., Belk, J. A., Amaya, L., Li, Z., Cardenas, A., … Chang, H. Y. (2022). Engineering circular RNA for enhanced protein production. Nature Biotechnology. -
Gene regulation on extrachromosomal DNA.
Hung, K. L., Mischel, P. S., & Chang, H. Y. (2022). Gene regulation on extrachromosomal DNA. Nature Structural & Molecular Biology. -
KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress.
Moonen, J.-R. R., Chappell, J., Shi, M., Shinohara, T., Li, D., Mumbach, M. R., … Rabinovitch, M. (2022). KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress. Nature Communications, 13(1), 4941. -
The evolutionary dynamics of extrachromosomal DNA in human cancers.
Lange, J. T., Rose, J. C., Chen, C. Y., Pichugin, Y., Xie, L., Tang, J., … Mischel, P. S. (2022). The evolutionary dynamics of extrachromosomal DNA in human cancers. Nature Genetics. -
Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH.
Hung, K. L., Luebeck, J., Dehkordi, S. R., Colon, C. I., Li, R., Wong, I. T.-L., … Chang, H. Y. (2022). Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. Nature Genetics. -
Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin.
Foster, D. S., Januszyk, M., Delitto, D., Yost, K. E., Griffin, M., Guo, J., … Longaker, M. T. (2022). Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin. Cancer Cell. -
Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases.
Wang, S. K., Nair, S., Li, R., Kraft, K., Pampari, A., Patel, A., … Chang, H. Y. (2022). Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases. Cell Genomics, 2(8). -
Divergent clonal differentiation trajectories of T cell exhaustion.
Daniel, B., Yost, K. E., Hsiung, S., Sandor, K., Xia, Y., Qi, Y., … Satpathy, A. T. (2022). Divergent clonal differentiation trajectories of T cell exhaustion. Nature Immunology. -
Enhanced T cell effector activity by targeting the Mediator kinase module.
Freitas, K. A., Belk, J. A., Sotillo, E., Quinn, P. J., Ramello, M. C., Malipatlolla, M., … Mackall, C. L. (2022). Enhanced T cell effector activity by targeting the Mediator kinase module. Science (New York, N.Y.), 378(6620), eabn5647. -
Profiling oncogenic extra-chromosomal DNA in cancer
Hung, K. L., & Chang, H. Y. (2022). Profiling oncogenic extra-chromosomal DNA in cancer. NATURE GENETICS, 1591–1592. -
Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state.
Daniel, B., Belk, J. A., Meier, S. L., Chen, A. Y., Sandor, K., Czimmerer, Z., … Satpathy, A. T. (2022). Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state. Molecular Cell. -
Engineered cell entry links receptor biology with single-cell genomics.
Yu, B., Shi, Q., Belk, J. A., Yost, K. E., Parker, K. R., Li, R., … Chang, H. Y. (2022). Engineered cell entry links receptor biology with single-cell genomics. Cell. -
The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1.
Haddad Derafshi, B., Danko, T., Chanda, S., Batista, P. J., Litzenburger, U., Lee, Q. Y., … Wernig, M. (2022). The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1. Scientific Reports, 12(1), 22425. -
Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis.
Ma, Q., Yang, L., Tolentino, K., Wang, G., Zhao, Y., Litzenburger, U. M., … Chang, H. Y. (2022). Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis. ELife, 11. -
Long non-coding RNAs: definitions, functions, challenges and recommendations.
Mattick, J. S., Amaral, P. P., Carninci, P., Carpenter, S., Chang, H. Y., Chen, L.-L., … Wu, M. (2023). Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews. Molecular Cell Biology. -
A guide to naming eukaryotic circular RNAs.
Chen, L.-L., Bindereif, A., Bozzoni, I., Chang, H. Y., Matera, A. G., Gorospe, M., … Zhao, F. (2023). A guide to naming eukaryotic circular RNAs. Nature Cell Biology. -
Reversing the Central Dogma: RNA-guided control of DNA in epigenetics and genome editing.
Chang, H. Y., & Qi, L. S. (2023). Reversing the Central Dogma: RNA-guided control of DNA in epigenetics and genome editing. Molecular Cell, 83(3), 442–451. -
Reading and writing extrachromosomal DNA.
Chang, H. Y. (2022). Reading and writing extrachromosomal DNA. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
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. -
Enhanced effector activity of mediator CDK8 kinase module deficient CAR-T Cells
Freitas, K. A., Belk, J. A., Sotillo, E., Daniel, B., Sandor, K., Klysz, D., … Mackall, C. (2022). Enhanced effector activity of mediator CDK8 kinase module deficient CAR-T Cells. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH. -
Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus.
Luebeck, J., Ng, A. W., Galipeau, P. C., Li, X., Sanchez, C. A., Katz-Summercorn, A. C., … Mischel, P. S. (2023). Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus. Nature. -
The AAV capsid can influence the epigenetic marking of rAAV delivered episomal genomes in a species dependent manner.
Gonzalez-Sandoval, A., Pekrun, K., Tsuji, S., Zhang, F., Hung, K. L., Chang, H. Y., & Kay, M. A. (2023). The AAV capsid can influence the epigenetic marking of rAAV delivered episomal genomes in a species dependent manner. Nature Communications, 14(1), 2448. -
Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.
Chamorro González, R., Conrad, T., Stöber, M. C., Xu, R., Giurgiu, M., Rodriguez-Fos, E., … Henssen, A. G. (2023). Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nature Genetics. -
Circular RNA vaccine induces potent T cell responses.
Amaya, L., Grigoryan, L., Li, Z., Lee, A., Wender, P. A., Pulendran, B., & Chang, H. Y. (2023). Circular RNA vaccine induces potent T cell responses. Proceedings of the National Academy of Sciences of the United States of America, 120(20), e2302191120. -
Machine learning modeling of RNA structures: methods, challenges and future perspectives.
Wu, K. E., Zou, J. Y., & Chang, H. (2023). Machine learning modeling of RNA structures: methods, challenges and future perspectives. Briefings in Bioinformatics.
Practice Locations
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Palo Alto, CASkin Cancer Program in Palo Alto
900 Blake Wilbur Drive, 3rd Floor
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Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners are each independent nonprofit organizations that are affiliated with but separate from each other and from Stanford University. The physicians who provide care at facilities operated by Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners are faculty, foundation, or community physicians who are not employees, representatives, or agents of Stanford Health Care, Stanford Health Care Tri- Valley, or Stanford Medicine Partners. Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners do not exercise control over the care provided by such faculty, foundation, and community physicians and are not responsible for their actions.
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