Howard Y. Chang
Publications
- Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013; (7431): 231-5
- Long noncoding RNAs: cellular address codes in development and disease. Cell. 2013; (6): 1298-307
- RNA SHAPE analysis in living cells. Nat Chem Biol. 2013; (1): 18-20
- Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock. Cell. 2012; (1-2): 46-57
- A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011; (7341): 120-4
- Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet. 2011; (7): 621-9
- Cytotopic localization by long noncoding RNAs. Curr Opin Cell Biol. 2013; (2): 195-9
- Rejuvenation of gene expression pattern of aged human skin by broadband light treatment: a pilot study. J Invest Dermatol. 2013; (2): 394-402
- SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Res. 2013; (2): 377-87
- The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell. 2013; (4): 743-54
- A molecular signature for purified definitive endoderm guides differentiation and isolation of endoderm from mouse and human embryonic stem cells. Stem Cells Dev. 2012; (12): 2273-87
- Active chromatin and noncoding RNAs: an intimate relationship. Curr Opin Genet Dev. 2012; (2): 172-8
- Chromatin isolation by RNA purification (ChIRP). J Vis Exp. 2012; (61)
- Detection of long non-coding RNA in archival tissue: correlation with polycomb protein expression in primary and metastatic breast carcinoma. PLoS One. 2012; (10): e47998
- Genome-wide measurement of RNA folding energies. Mol Cell. 2012; (2): 169-81
- High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. Lab Chip. 2012; (12): 2190-8
- Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev. 2012; (4): 338-43
- Systematic reconstruction of RNA functional motifs with high-throughput microfluidics. Nat Methods. 2012; (12): 1192-4
- The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression. Cancer Discov. 2012; (7): 638-51
- Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. Blood. 2012; (16): 3288-97
- Direct lineage conversion of terminally differentiated hepatocytes to functional neurons. Cell Stem Cell. 2011; (4): 374-82
- Disruption of PPARγ/β-catenin-mediated regulation of apelin impairs BMP-induced mouse and human pulmonary arterial EC survival. J Clin Invest. 2011; (9): 3735-46
- Dynamic chromatin localization of Sirt6 shapes stress- and aging-related transcriptional networks. PLoS Genet. 2011; (6): e1002153
- Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 2011; (4): 667-78
- Long intergenic noncoding RNAs: new links in cancer progression. Cancer Res. 2011; (1): 3-7
- Long noncoding RNAs and human disease. Trends Cell Biol. 2011; (6): 354-61
- Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011; (6): 904-14
- RNA templating the epigenome: long noncoding RNAs as molecular scaffolds. Epigenetics. 2011; (5): 539-43
- Understanding the transcriptome through RNA structure. Nat Rev Genet. 2011; (9): 641-55
- Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol. 2010 Sep-Oct; (5): 582-5
- G1 arrest and differentiation can occur independently of Rb family function. J Cell Biol. 2010; (4): 809-25
- Genome-wide measurement of RNA secondary structure in yeast. Nature. 2010; (7311): 103-7
- HOTAIR: Flight of noncoding RNAs in cancer metastasis. Cell Cycle. 2010; (17): 3391-2
- Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010; (7291): 1071-6
- Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010; (5992): 689-93
- Noncoding RNA landmarks of pluripotency and reprogramming. Cell Stem Cell. 2010; (6): 649-50
- The histone demethylase UTX enables RB-dependent cell fate control. Genes Dev. 2010; (4): 327-32
- Tumor suppression by the histone demethylase UTX. Cell Cycle. 2010; (11): 2043-4
- Anatomic demarcation of cells: genes to patterns. Science. 2009; (5957): 1206-7
- Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization. EMBO Rep. 2009; (7): 689-93
- Genome-wide views of chromatin structure. Annu Rev Biochem. 2009: 245-71
- Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells. Cell Stem Cell. 2009; (2): 129-40
- ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation. Mol Cell. 2009; (2): 248-56
- Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells. Proc Natl Acad Sci U S A. 2009; (33): 14016-21
- Modeling inducible human tissue neoplasia identifies an extracellular matrix interaction network involved in cancer progression. Cancer Cell. 2009; (6): 477-88
- Molecular framework for response to imatinib mesylate in systemic sclerosis. Arthritis Rheum. 2009; (2): 584-91
- Regeneration, repair and remembering identity: the three Rs of Hox gene expression. Trends Cell Biol. 2009; (6): 268-75
- SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span. Cell. 2009; (1): 62-74
- Tumor vasculature is regulated by PHD2-mediated angiogenesis and bone marrow-derived cell recruitment. Cancer Cell. 2009; (6): 527-38
- A dermal HOX transcriptional program regulates site-specific epidermal fate. Genes Dev. 2008; (3): 303-7
- A systems biology approach to anatomic diversity of skin. J Invest Dermatol. 2008; (4): 776-82
- CSN5 isopeptidase activity links COP9 signalosome activation to breast cancer progression. Cancer Res. 2008; (2): 506-15
- Combining biological gene expression signatures in predicting outcome in breast cancer: An alternative to supervised classification. Eur J Cancer. 2008; (15): 2319-29
- Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. Genes Dev. 2008; (14): 1865-70
- Deletional tolerance mediated by extrathymic Aire-expressing cells. Science. 2008; (5890): 843-7
- Global expression profiling in atopic eczema reveals reciprocal expression of inflammatory and lipid genes. PLoS One. 2008; (12): e4017
- Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire. J Clin Invest. 2008; (5): 1712-26
- Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell. 2008; (4): 333-44
- Revealing targeted therapy for human cancer by gene module maps. Cancer Res. 2008; (2): 369-78
- Reversal of aging by NFkappaB blockade. Cell Cycle. 2008; (5): 556-9
- SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. Nature. 2008; (7186): 492-6
- Stemness, cancer and cancer stem cells. Cell Cycle. 2008; (23): 3622-4
- Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res. 2008; (3): 477-88
- A histone H3 lysine 27 demethylase regulates animal posterior development. Nature. 2007; (7163): 689-94
- A transcriptional program mediating entry into cellular quiescence. PLoS Genet. 2007; (6): e91
- Decoding global gene expression programs in liver cancer by noninvasive imaging. Nat Biotechnol. 2007; (6): 675-80
- Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007; (7): 1311-23
- GSK3 beta mediates suppression of cyclin D2 expression by tumor suppressor PTEN. Oncogene. 2007; (17): 2471-82
- Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet. 2007; (6): e89
- Motif module map reveals enforcement of aging by continual NF-kappaB activity. Genes Dev. 2007; (24): 3244-57
- Patterning skin pigmentation via dickkopf. J Invest Dermatol. 2007; (5): 994-5
- Turning skin into embryonic stem cells. Nat Med. 2007; (7): 783-4
- Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet. 2006; (7): e119
- Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation. Proc Natl Acad Sci U S A. 2006; (40): 14842-7
- From description to causality: mechanisms of gene expression signatures in cancer. Cell Cycle. 2006; (11): 1148-51
- Genetic regulators of large-scale transcriptional signatures in cancer. Nat Genet. 2006; (4): 421-30
- MYC can induce DNA breaks in vivo and in vitro independent of reactive oxygen species. Cancer Res. 2006; (13): 6598-605
- Microarray analysis of stem cells and differentiation. Methods Enzymol. 2006: 225-54
- Predicting a local recurrence after breast-conserving therapy by gene expression profiling. Breast Cancer Res. 2006; (5): R62
- Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. J Exp Med. 2006; (12): 2727-35
- Learning more from microarrays: insights from modules and networks. J Invest Dermatol. 2005; (2): 175-82
- Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A. 2005; (10): 3738-43
- Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol. 2004; (2): E7
- Kinetics and specificity of fas ligand induction in toxic epidermal necrolysis. Arch Dermatol. 2004; (2): 242-4
- Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci U S A. 2003; (19): 10623-8
- Eruptive xanthomas associated with olanzapine use. Arch Dermatol. 2003; (8): 1045-8
- Genomewide view of gene silencing by small interfering RNAs. Proc Natl Acad Sci U S A. 2003; (11): 6343-6
- Myelogenous leukemia cutis resembling stasis dermatitis. J Am Acad Dermatol. 2003; (1): 128-9
- Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci U S A. 2002; (20): 12877-82
- Proteases for cell suicide: functions and regulation of caspases. Microbiol Mol Biol Rev. 2000; (4): 821-46
- Dissecting Fas signaling with an altered-specificity death-domain mutant: requirement of FADD binding for apoptosis but not Jun N-terminal kinase activation. Proc Natl Acad Sci U S A. 1999; (4): 1252-6
- Activation of apoptosis signal-regulating kinase 1 (ASK1) by the adapter protein Daxx. Science. 1998; (5384): 1860-3
- Autoproteolytic activation of pro-caspases by oligomerization. Mol Cell. 1998; (2): 319-25
- Essential role of CED-4 oligomerization in CED-3 activation and apoptosis. Science. 1998; (5381): 1355-7
- Daxx, a novel Fas-binding protein that activates JNK and apoptosis. Cell. 1997; (7): 1067-76
- Activation of CLN1 and CLN2 G1 cyclin gene expression by BCK2. Mol Cell Biol. 1995; (4): 1835-46
- Asymmetric retraction of growth cone filopodia following focal inactivation of calcineurin. Nature. 1995; (6542): 686-90
- Active site mutants of human cyclophilin A separate peptidyl-prolyl isomerase activity from cyclosporin A binding and calcineurin inhibition. Protein Sci. 1992; (9): 1092-9
- Cyclosporin-mediated inhibition of bovine calcineurin by cyclophilins A and B. Proc Natl Acad Sci U S A. 1992; (9): 3741-5
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