Publications by authors named "Howard Y Chang"

100Publications

Structural modularity of the XIST ribonucleoprotein complex.

Nat Commun 2020 12 2;11(1):6163. Epub 2020 Dec 2.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.

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December 2020

Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.

Mol Cell 2020 12 25;80(5):903-914.e8. Epub 2020 Nov 25.

Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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December 2020

Prrx1 Fibroblasts Represent a Pro-fibrotic Lineage in the Mouse Ventral Dermis.

Cell Rep 2020 Nov;33(6):108356

Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA 94305, USA. Electronic address:

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November 2020

Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity.

Cell Rep 2020 Sep;32(12):108180

Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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September 2020

Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies.

Cell 2020 Oct 21;183(1):126-142.e17. Epub 2020 Sep 21.

Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. Electronic address:

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October 2020

Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2.

Cell Host Microbe 2020 10 3;28(4):516-525.e5. Epub 2020 Sep 3.

Department of Pathology, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA. Electronic address:

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October 2020

The road ahead in genetics and genomics.

Nat Rev Genet 2020 10 24;21(10):581-596. Epub 2020 Aug 24.

Center for Genome Engineering, Institute for Basic Science, Daejon, Republic of Korea.

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October 2020

RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus.

Cell Syst 2020 07 20;11(1):102-108.e3. Epub 2020 Jun 20.

Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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July 2020

Long Noncoding RNAs: Molecular Modalities to Organismal Functions.

Annu Rev Biochem 2020 06;89:283-308

Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA.

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June 2020

Diverse lncRNA mechanisms in brain development and disease.

Curr Opin Genet Dev 2020 Dec 14;65:42-46. Epub 2020 Jun 14.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA. Electronic address:

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December 2020

RNA-GPS Predicts SARS-CoV-2 RNA Localization to Host Mitochondria and Nucleolus.

bioRxiv 2020 Apr 28. Epub 2020 Apr 28.

Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA.

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April 2020

Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation.

Cold Spring Harb Symp Quant Biol 2019 1;84:31-45. Epub 2020 Jun 1.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA.

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June 2020

Single-cell RNA sequencing in cardiovascular development, disease and medicine.

Nat Rev Cardiol 2020 08 30;17(8):457-473. Epub 2020 Mar 30.

Stanford Cardiovascular Institute, Stanford, CA, USA.

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August 2020

Pro-neuronal activity of Myod1 due to promiscuous binding to neuronal genes.

Nat Cell Biol 2020 04 30;22(4):401-411. Epub 2020 Mar 30.

Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, Stanford University, Stanford, CA, USA.

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April 2020

RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing.

RNA 2020 07 27;26(7):851-865. Epub 2020 Mar 27.

Department of Computer Science, Stanford University, Stanford, California 94305, USA.

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July 2020

CRISPRpic: fast and precise analysis for CRISPR-induced mutations via prefixed index counting.

NAR Genom Bioinform 2020 Jun 21;2(2):lqaa012. Epub 2020 Feb 21.

Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.

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June 2020

Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes.

Nat Biotechnol 2020 05 24;38(5):573-576. Epub 2020 Feb 24.

Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.

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May 2020

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications.

Genome Biol 2019 12 20;20(1):292. Epub 2019 Dec 20.

Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA.

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December 2019

Tracking the immune response with single-cell genomics.

Vaccine 2020 Jun 16;38(28):4487-4490. Epub 2019 Dec 16.

Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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June 2020

N6-Methyladenosine Modification Controls Circular RNA Immunity.

Mol Cell 2019 10 29;76(1):96-109.e9. Epub 2019 Aug 29.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA. Electronic address:

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October 2019

The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation.

EMBO Rep 2019 10 27;20(10):e48019. Epub 2019 Aug 27.

Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR3215, INSERM U934, PSL University, Paris, France.

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October 2019

Atlas of Subcellular RNA Localization Revealed by APEX-Seq.

Cell 2019 07 20;178(2):473-490.e26. Epub 2019 Jun 20.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address:

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July 2019

RNA structure maps across mammalian cellular compartments.

Nat Struct Mol Biol 2019 04 18;26(4):322-330. Epub 2019 Mar 18.

MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.

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April 2019

A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells.

Immunity 2019 02 29;50(2):362-377.e6. Epub 2019 Jan 29.

Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

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February 2019

TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment.

Cell Stem Cell 2019 02 24;24(2):271-284.e8. Epub 2019 Jan 24.

Program in Epithelial Biology and Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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February 2019

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.

Cell 2019 01 20;176(1-2):361-376.e17. Epub 2018 Dec 20.

Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA. Electronic address:

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January 2019

The RNA Base-Pairing Problem and Base-Pairing Solutions.

Cold Spring Harb Perspect Biol 2018 12 3;10(12). Epub 2018 Dec 3.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305.

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December 2018

Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders.

J Invest Dermatol 2019 03 10;139(3):605-614. Epub 2018 Oct 10.

Department of Dermatology, Stanford University School of Medicine, Redwood City, California, USA. Electronic address:

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March 2019

ChIRP-MS: RNA-Directed Proteomic Discovery.

Methods Mol Biol 2018 ;1861:37-45

Stanford University School of Medicine, Stanford, CA, USA.

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June 2019

A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas.

Cell Syst 2018 09 22;7(3):310-322.e4. Epub 2018 Aug 22.

Department of Developmental Biology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA. Electronic address:

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September 2018

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations.

Proc Natl Acad Sci U S A 2018 07 9;115(30):7723-7728. Epub 2018 Jul 9.

Department of Statistics, Stanford University, Stanford, CA 94305;

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July 2018

An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1.

Cell 2018 06 24;174(1):218-230.e13. Epub 2018 May 24.

Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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June 2018

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Cell 2018 05 26;173(6):1535-1548.e16. Epub 2018 Apr 26.

Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94025, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address:

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May 2018

ATAC Primer Tool for targeted analysis of accessible chromatin.

Nat Methods 2018 04;15(5):304-305

Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.

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April 2018

Epigenomics: Technologies and Applications.

Circ Res 2018 04;122(9):1191-1199

From the Program in Epithelial Biology (K.C.W., H.Y.C.).

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April 2018

Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders.

Nature 2018 02 24;554(7690):112-117. Epub 2018 Jan 24.

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA.

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February 2018

Rapid chromatin repression by Aire provides precise control of immune tolerance.

Nat Immunol 2018 02 15;19(2):162-172. Epub 2018 Jan 15.

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

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February 2018

mA mRNA methylation sustains Treg suppressive functions.

Cell Res 2018 Feb 5;28(2):253-256. Epub 2018 Jan 5.

Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, PR China.

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February 2018

LncRNA Seduction of GOT2 Goes Viral.

Immunity 2017 12;47(6):1021-1023

Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305. Electronic address:

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December 2017

Preleukemic Hematopoietic Stem Cells in Human Acute Myeloid Leukemia.

Front Oncol 2017 6;7:263. Epub 2017 Nov 6.

Program in Cancer Biology, Cancer Institute, Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center, Stanford University School of Medicine, Stanford, CA, United States.

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November 2017

The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline.

Elife 2017 10 31;6. Epub 2017 Oct 31.

Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States.

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October 2017

Mechanistic insights in X-chromosome inactivation.

Philos Trans R Soc Lond B Biol Sci 2017 Nov;372(1733)

Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA

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November 2017

Gene regulation in the immune system by long noncoding RNAs.

Nat Immunol 2017 Aug;18(9):962-972

Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.

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August 2017

IL-4Rα Inhibitor for Atopic Disease.

Cell 2017 Jul;170(2):222

Stanford University School of Medicine, Stanford University, Stanford, CA, USA. Electronic address:

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July 2017

Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs.

Circ Res 2017 Aug 29;121(4):376-391. Epub 2017 Jun 29.

From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA.

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August 2017

Transcription coactivator and lncRNA duet evoke Hox genes.

PLoS Genet 2017 06 29;13(6):e1006797. Epub 2017 Jun 29.

Program in Epithelial Biology and Department of Dermatology, Stanford University School of Medicine, Stanford, California, United States of America.

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June 2017

Sensing Self and Foreign Circular RNAs by Intron Identity.

Mol Cell 2017 Jul 15;67(2):228-238.e5. Epub 2017 Jun 15.

Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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July 2017

Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors.

Cancer Cell 2017 07 15;32(1):27-41.e4. Epub 2017 Jun 15.

Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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July 2017

The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity.

Cell 2017 Jun;169(6):1051-1065.e18

Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address:

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June 2017