X. Xiao

发表

Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis

Gene W. Yeo, Michael B. Stadler, C. Burge, 2006, PLoS genetics.

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

Gene W. Yeo, C. Burge, A. Urban, 2018, Nature Communications.

Widespread RNA editing dysregulation in Autism Spectrum Disorders

Gene W. Yeo, D. Geschwind, X. Xiao, 2018, bioRxiv.

Widespread RNA editing dysregulation in brains from autistic individuals

Eric L Van Nostrand, Gene W Yeo, Xinshu Xiao, 2018, Nature Neuroscience.

Global Approaches to Alternative Splicing and Its Regulation—Recent Advances and Open Questions

X. Xiao, J. Bahn, Y. Hsiao, 2016 .

Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts

Jae-Hyung Lee, X. Xiao, Yibin Wang, 2011, Circulation research.

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.

Jae-Hyung Lee, X. Xiao, J. Bahn, 2012, Genome research.

Genome Sequence-Independent Identification of RNA Editing Sites

X. Xiao, Qing Zhang, Xinshu Xiao, 2015, Nature Methods.

Extensive translation of circular RNAs driven by N6-methyladenosine

Yang Zhang, Xinshu Xiao, Zefeng Wang, 2017, Cell Research.

The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B.

C. Burge, D. Black, P. Stoilov, 2012, RNA.

depletion of the splicing factors SRSF 3 and TRA 2 B The cardiotonic steroid digitoxin regulates alternative splicing through Material Supplemental

C. Burge, D. Black, P. Stoilov, 2012 .

Identification of allele-specific alternative mRNA processing via transcriptome sequencing

Stanley F. Nelson, Xinshu Xiao, Guangdun Peng, 2012, Nucleic acids research.

The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva.

Feng Li, Xinshu Xiao, X. Xiao, 2015, Clinical chemistry.

Global analysis of alternative splicing differences between humans and chimpanzees.

Yi Xing, Christopher J. Lee, Xinshu Xiao, 2007, Genes & development.

RNA editing in nascent RNA affects pre-mRNA splicing

X. Xiao, E. Yang, J. Bahn, 2018, Genome research.

Structure-mediated modulation of mRNA abundance by A-to-I editing

X. Xiao, Anneke Brümmer, Yun Yang, 2017, Nature Communications.

Electronic Theses and Dissertations Title Importance of Mitochondrial Homeostasis in Heart Disease and Its Prevention

X. Xiao, Yibin Wang, R. Avetisyan, 2017 .

A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions.

E. M. Jones, Daniel B. Goodman, S. Kosuri, 2019, Molecular cell.

Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets

Jae-Hyung Lee, X. Xiao, J. Bahn, 2016, Nucleic acids research.

Genetics of white color and iridophoroma in “Lemon Frost” leopard geckos

L. Kruglyak, X. Xiao, S. Sykes, 2020, bioRxiv.

Regulation of RNA editing by RNA-binding proteins in human cells

Gene W. Yeo, X. Xiao, B. Graveley, 2019, Communications Biology.

Catabolic Defect of Branched-Chain Amino Acids Promotes Heart Failure

Christoph D. Rau, Svati H Shah, X. Xiao, 2016, Circulation.

Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing.

X. Xiao, D. Chia, D. Elashoff, 2018, Clinical chemistry.

Wnt11 regulates cardiac chamber development and disease during perinatal maturation.

X. Xiao, G. Coppola, Fuying Gao, 2017, JCI insight.

Detection of two distinct forms of apoC-I in great apes.

X. Xiao, O. Ryder, J. Whitelegge, 2010, Comparative biochemistry and physiology. Part D, Genomics & proteomics.

FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch

X. Xiao, S. White, A. Hilliard, 2018, eLife.

FoxP 2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra

X. Xiao, S. White, Z. D. Burkett, 2022 .

Regulation of NF-κB signaling by oxidized glycerophospholipid and IL-1β induced miRs-21-3p and -27a-5p in human aortic endothelial cells[S]

X. Xiao, A. Lusis, Raffi Hagopian, 2015, Journal of Lipid Research.

Multifaceted role of RNA editing in promoting loss-of-function of PODXL in cancer

X. Xiao, J. Bahn, Ting Fu, 2022, iScience.

Improved Zebra Finch Brain Transcriptome identifies novel proteins with sex differences.

X. Xiao, S. White, Ting Fu, 2022, Gene.

UNIVERSITY OF CALIFORNIA Los Angeles Improved Zebra Finch Brain Transcriptome Using Both Short and Long Read RNA-seq Methods A thesis submitted in satisfaction of the requirements for the degree Master of Science in Physiological Science by

X. Xiao, S. White, B. Schlinger, 2020 .

Title Gene Annotation in Rice Genome Using Homology Permalink

M. Pellegrini, T. Graeber, X. Xiao, 2013 .

p38 mitogen-activated protein kinase regulates chamber specific perinatal growth in heart.

Rajan P Kulkarni, Christoph D. Rau, Rajan P. Kulkarni, 2020, The Journal of clinical investigation.

Loss of MECP2 leads to telomere dysfunction and neuronal stress

M. Pellegrini, P. Jin, X. Xiao, 2017 .

p38 MAP Kinase Regulates Remodeling of Heart via IRE1α During Early Postnatal Development

X. Xiao, J. Tidball, Yibin Wang, 2016 .

Identification of Vascular and Hematopoietic Genes Downstream of etsrp by Deep Sequencing in Zebrafish

Jae-Hyung Lee, X. Xiao, Shuo Lin, 2012, PloS one.

Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in inbred and recombinant inbred mice

E. Eskin, X. Xiao, J. Jentsch, 2022, bioRxiv.

Kinetics of mRNA nuclear export regulate innate immune response gene expression

Erin M. Wissink, D. Black, Y. Xing, 2022, Nature Communications.

Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery

X. Xiao, G. Coppola, Fuying Gao, 2016, Circulation. Cardiovascular genetics.

TAPAS: tool for alternative polyadenylation site analysis

Tao Jiang, Juntao Liu, Xinshu Xiao, 2018, Bioinform..

Coregulation of alternative splicing by hnRNPM and ESRP1 during EMT

S. E. Harvey, Chonghui Cheng, X. Xiao, 2018, bioRxiv.

RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure.

Christoph D. Rau, Douglas J. Chapski, Jae-Hyung Lee, 2015, The Journal of clinical investigation.

Extracellular microRNA 3’ end modification across diverse body fluids

X. Xiao, J. Bahn, K. Koyano, 2020, bioRxiv.

Noncoding RNAs in human saliva as potential disease biomarkers

Xinshu Xiao, X. Xiao, D. Wong, 2015, Front. Genet..

A Long Non-Coding RNA Defines an Epigenetic Checkpoint in Cardiac Hypertrophy

P. Zhang, D. Srivastava, Yen-Sin Ang, 2016 .

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

Paul D Piehowski, Vladislav A Petyuk, Eleazar Eskin, 2016, eLife.

ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation

T. Bebee, R. Carstens, Jae-Hyung Lee, 2015, Nature Communications.

Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation

D. Wong, X. Xiao, I. Spigelman, 2020, PloS one.

Genomic Analysis of ADAR1 Binding and its Involvement in Multiple RNA Processing Pathways

Xinshu Xiao, Jaegyoon Ahn, Mete Civelek, 2015, Nature Communications.

Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing

Chonghui Cheng, Jae-Hyung Lee, M. Peter, 2014, Genes & development.

metastasis via regulating alternative splicing Cell type-restricted activity of hnRNPM promotes breast cancer Material Supplemental

Chonghui Cheng, Jae-Hyung Lee, M. Peter, 2014 .

Differential RNA editing between epithelial and mesenchymal tumors impacts mRNA abundance in immune response pathways

Chonghui Cheng, Jae-Hyung Lee, X. Xiao, 2020, bioRxiv.

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research

Nikita A. Sakhanenko, Michael T. McManus, Andrew R. Jackson, 2019, Cell.

Long Term Maturation of Human Cortical Organoids Matches Key Early Postnatal Transitions

S. Horvath, D. Geschwind, J. Huguenard, 2021, Nature Neuroscience.

RNA editing in cancer impacts mRNA abundance in immune response pathways

Chonghui Cheng, Jae-Hyung Lee, X. Xiao, 2020, Genome biology.

Systems analysis of alternative splicing and its regulation

Xinshu Xiao, Jae-Hyung Lee, X. Xiao, 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins

Xinshu Xiao, X. Xiao, J. Bahn, 2016, Genome research.

Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling

Qing Zhou, Xinshu Xiao, Stephen S Tran, 2020, Bioinform..

The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice

X. Xiao, A. Clark, Kevin Nee, 2015, The EMBO journal.

Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders

Xia Yang, Matteo Pellegrini, Rahul Agrawal, 2016, EBioMedicine.

Fe(III) heme sets an activation threshold for processing distinct groups of pri-miRNAs in mammalian cells

X. Xiao, F. Guo, S. Weiss, 2020, bioRxiv.

Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants.

Xinshu Xiao, Jae-Hyung Lee, X. Xiao, 2013, RNA.

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development

Mark Gerstein, Sung Kim, Xiaoyan Wang, 2018, Bioinform..

L-GIREMI uncovers RNA editing sites in long-read RNA-seq

A. Mortazavi, X. Xiao, Ting Fu, 2022, bioRxiv.

Intronic Splicing Enhancers, Cognate Splicing Factors and Context Dependent Regulation Rules

Zefeng Wang, X. Xiao, Yang Wang, 2012, Nature Structural &Molecular Biology.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity

Howard Y. Chang, S. E. Harvey, Ryan A. Flynn, 2023, bioRxiv.

Allele-specific alternative splicing and its functional genetic variants in human tissues

X. Xiao, E. Yang, J. Bahn, 2021, Genome research.

Allele-specific alternative splicing in human tissues

X. Xiao, E. Yang, J. Bahn, 2020, bioRxiv.

mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.

X. Xiao, Ashley A. Cass, Xinshu Xiao, 2019, Cell systems.

DeepPASTA: deep neural network based polyadenylation site analysis

Tao Jiang, Xinshu Xiao, Ashraful Arefeen, 2019, Bioinform..

Research Resource: Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome.

Matthew J. Fuxjager, Jae-Hyung Lee, X. Xiao, 2016, Molecular endocrinology.

RASER: reads aligner for SNPs and editing sites of RNA

Xinshu Xiao, Jaegyoon Ahn, X. Xiao, 2015, Bioinform..

The difficult calls in RNA editing

Li Yang, Zhiyu Peng, Jin Billy Li, 2012, Nature Biotechnology.

Lipin 1 modulates mRNA splicing during fasting adaptation in liver

X. Xiao, A. Vashisht, J. Wohlschlegel, 2021, JCI insight.

Human tRNA-Derived Small RNAs Modulate Host–Oral Microbial Interactions

X. Xiao, W. Shi, B. Bor, 2018, Journal of dental research.

Widespread RNA hypoediting in schizophrenia and its relevance to mitochondrial function

X. Xiao, J. Bahn, Ting Fu, 2023, Science advances.

Regulation of RNA editing by RNA-binding proteins in human cells

Gene W. Yeo, X. Xiao, B. Graveley, 2019, Communications Biology.

Structure-mediated modulation of mRNA abundance by A-to-I editing

X. Xiao, Anneke Brümmer, Yun Yang, 2017, Nature Communications.

Regulation of RNA editing by RNA-binding proteins in human cells

Gene W. Yeo, X. Xiao, B. Graveley, 2019, Communications Biology.

Decoding the noncoding transcripts in human heart failure.

X. Xiao, Yibin Wang, Marlin Touma, 2014, Circulation.

Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice

E. Eskin, X. Xiao, J. Jentsch, 2023, Cell reports.

scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq

X. Xiao, Ting Fu, Tracey W Chan, 2022, bioRxiv.

Global analysis of alternative splicing differences between humans and chimpanzees

Christopher J. Lee, John A. Calarco, B. Blencowe, 2007 .

A Long Non-Coding RNA Defines an Epigenetic Checkpoint in Cardiac Hypertrophy

D. Srivastava, Yen-Sin Ang, X. Xiao, 2016, Nature Medicine.

Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence

M. Pellegrini, X. Xiao, K. Plath, 2017, bioRxiv.

Modeling Associated Protein-DNA Pattern Discovery with Unified Scores

Kwong-Sak Leung, Man Hon Wong, Leung-Yau Lo, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts

Jae-Hyung Lee, X. Xiao, Guangdun Peng, 2011 .

Loss of MECP2 leads to activation of p53 and neuronal senescence

M. Pellegrini, P. Jin, X. Xiao, 2017, bioRxiv.

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research

Nikita A. Sakhanenko, Michael T. McManus, Andrew R. Jackson, 2019, Cell.

A Long Non-Coding RNA Defines an Epigenetic Checkpoint in Cardiac Hypertrophy

D. Srivastava, Yen-Sin Ang, X. Xiao, 2016, Nature Medicine.

Wnt11 regulates cardiac chamber development and disease during perinatal maturation.

X. Xiao, G. Coppola, Fuying Gao, 2017, JCI insight.

Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts

Jae-Hyung Lee, X. Xiao, Yibin Wang, 2011, Circulation research.

dsRID: Editing-free in silico identification of dsRNA region using long-read RNA-seq data

X. Xiao, Zhiheng Liu, Mudra Choudhury, 2023, bioRxiv.

Single-cell analysis in lung adenocarcinoma implicates RNA editing in cancer innate immunity and patient prognosis.

P. Boutros, X. Xiao, Jack P. Dodson, 2022, Cancer research.

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.

Jae-Hyung Lee, X. Xiao, J. Bahn, 2012, Genome Research.

Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery

X. Xiao, G. Coppola, Fuying Gao, 2016, Circulation. Cardiovascular genetics.