Yi Xing

发表

The Bifunctional microRNA miR-9/miR-9* Regulates REST and CoREST and Is Downregulated in Huntington's Disease

Yi Xing, Lesley Jones, Y. Xing, 2008, The Journal of Neuroscience.

Post-transcriptional regulation of cystic fibrosis transmembrane conductance regulator expression and function by microRNAs.

Ashley M. Jacobi, M. Welsh, M. Behlke, 2013, American journal of respiratory cell and molecular biology.

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

Lan Lin, Ying Nian Wu, Yi Xing, 2014, Proceedings of the National Academy of Sciences.

Structure and activity of putative intronic miRNA promoters.

Ji Wan, Yi Xing, Ryan M Spengler, 2010, RNA.

Human transcriptome array for high-throughput clinical studies

John D. Storey, Tyson A. Clark, A. Schweitzer, 2011, Proceedings of the National Academy of Sciences.

BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing.

Pengyuan Yang, Xiangdong Fu, J. Qiu, 2014, Molecular cell.

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

Y. Xing, W. Thompson, B. Barres, 2008, The Journal of Neuroscience.

HDAC Inhibition Impedes Epithelial-Mesenchymal Plasticity and Suppresses Metastatic, Castration-Resistant Prostate Cancer

L. Tran, P. Nelson, Hong Wu, 2015, Oncogene.

m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells.

Yi Xing, Howard Y. Chang, Marius Wernig, 2014, Cell stem cell.

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self‐renewal

Xiaohui S. Xie, Raja Jothi, Lingjie Weng, 2014, The EMBO journal.

Fip 1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

Xiaohui S. Xie, Raja Jothi, Lingjie Weng, 2014 .

Global analysis of alternative splicing differences between humans and chimpanzees.

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

Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes

Christopher J. Lee, Y. Xing, Yi Xing, 2006, Nature Reviews Genetics.

Underlying the Metabolic Syndrome in the Lyon Hypertensive Rat Systems Biology With High-Throughput Sequencing Reveals Genetic Mechanisms

John Man-shun Ma, Y. Xing, Lan Lin, 2015 .

Transcriptome-wide Discovery of microRNA Binding Sites in Human Brain

Yi Xing, Christopher A. Ross, Brian L. Gilmore, 2014, Neuron.

Solving the Problem of Trans-Genomic Query with Alignment Tables

Douglas Stott Parker, Yi Xing, Christopher J. Lee, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures.

Yi Xing, Christopher J. Lee, Christopher Lee, 2004, Genome research.

Genome-Wide Detection of Alternative Splicing in Expressed Sequences Using Partial Order Multiple Sequence Alignment Graphs

Yi Xing, Christopher J. Lee, Catherine S. Grasso, 2003, Pacific Symposium on Biocomputing.

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

Y. Xing, W. Wong, K. Au, 2010, Nucleic acids research.

Depolarization and CaM Kinase IV Modulate NMDA Receptor Splicing through Two Essential RNA Elements

Douglas L Black, Yi Xing, Christopher J. Lee, 2007, PLoS biology.

An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs

Yi Xing, Christopher J. Lee, Christopher Lee, 2006, Nucleic acids research.

Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy

Yi Xing, Christopher J. Lee, Christopher Lee, 2004, Genome Biology.

Population and allelic variation of A-to-I RNA editing in human transcriptomes

Lan Lin, Eddie Park, Shihao Shen, 2017, Genome Biology.

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

Juw Won Park, Y. Xing, R. Carstens, 2012, Nucleic acids research.

Human-specific microRNA regulation of FOXO1: implications for microRNA recognition element evolution.

Ryan M Spengler, Y. Xing, B. Davidson, 2014, Human molecular genetics.

Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes.

Lan Lin, B. Davidson, Shihao Shen, 2009, Human molecular genetics.

Evidence of functional selection pressure for alternative splicingevents that accelerate evolution of protein subsequences

Yi Xing, Christopher J. Lee, Christopher Lee, 2005, Genome Biology.

Kinetics of mRNA nuclear export regulate innate immune response gene expression

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

Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs.

Yi Xing, Nicholas Van Wittenberghe, Y. Xing, 2017, Cell reports.

Identification and characterization of m6A circular RNA epitranscriptomes

Joshua V. Pondick, B. Molinie, C. Giallourakis, 2017, bioRxiv.

m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome

Yi Xing, Peter Dedon, Nicholas Van Wittenberghe, 2016, Nature Methods.

m[superscript 6]A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

Howard Y. Chang, Pedro J. Batista, Ryan A. Flynn, 2014 .

Determination of a Comprehensive Alternative Splicing Regulatory Network and Combinatorial Regulation by Key Factors during the Epithelial-to-Mesenchymal Transition

Yi Xing, Yang Guo, Claude C. Warzecha, 2016, Molecular and Cellular Biology.

Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins.

B. Cieply, Juw Won Park, Angela Nakauka-Ddamba, 2016, Cell reports.

Widespread establishment and regulatory impact of Alu exons in human genes

James J. Cai, Y. Xing, Lan Lin, 2011, Proceedings of the National Academy of Sciences.

Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization

Yi Xing, Shihao Shen, Michael D. Henry, 2014, Molecular Cancer Research.

Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

Ji Wan, Yi Xing, Shihao Shen, 2012, Molecular and Cellular Biology.

An ESRP‐regulated splicing programme is abrogated during the epithelial–mesenchymal transition

Yi Xing, Shihao Shen, Claude C. Warzecha, 2010, The EMBO journal.

The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events

Claude C. Warzecha, Y. Xing, R. Carstens, 2009, RNA biology.

αCP Poly(C) Binding Proteins Act as Global Regulators of Alternative Polyadenylation

S. Liebhaber, Ji Wan, X. Ji, 2013, Molecular and Cellular Biology.

SURVIV for survival analysis of mRNA isoform variation

Y. Xing, Chengyang Wang, Shihao Shen, 2016, Nature Communications.

Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS.

C. Tokheim, Shihao Shen, Yi Xing, 2013, Methods in molecular biology.

Ablation of the epithelial‐specific splicing factor Esrp1 results in ureteric branching defects and reduced nephron number

B. Cieply, T. Bebee, R. Carstens, 2016, Developmental dynamics : an official publication of the American Association of Anatomists.

rMAPS: RNA map analysis and plotting server for alternative exon regulation

Eric C. Rouchka, Yi Xing, Juw Won Park, 2016, Nucleic Acids Res..

The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development

Claude C. Warzecha, B. Cieply, T. Bebee, 2015, eLife.

The RNA Binding Protein RBM38 (RNPC1) Regulates Splicing during Late Erythroid Differentiation

B. Cieply, R. Carstens, Shihao Shen, 2013, PloS one.

Genetic variation of pre‐mRNA alternative splicing in human populations

Yi Xing, Zhi-xiang Lu, Peng Jiang, 2012, Wiley interdisciplinary reviews. RNA.

Transcriptome landscape of the human placenta

Yi Xing, Keyan Zhao, Jeffrey C Murray, 2012, BMC Genomics.

The Expanding Landscape of Alternative Splicing Variation in Human Populations

Y. Xing, Lan Lin, Eddie Park, 2018, American journal of human genetics.

Can RNA selection pressure distort the measurement of Ka/Ks?

Christopher J. Lee, Yi Xing, 2006, Gene.

SEASTAR: systematic evaluation of alternative transcription start sites in RNA

Xuegong Zhang, Y. Xing, P. Stoilov, 2018, Nucleic acids research.

Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring

D. Black, Kyu-Hyeon Yeom, Chia-Ho Lin, 2020, bioRxiv.

Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR

Yi Xing, Kelsey C. Martin, Douglas L. Black, 2016, Cell.

Chromatin and epigenetic regulation of pre-mRNA processing.

Yi Xing, Peter Stoilov, P. Stoilov, 2012, Human molecular genetics.

Concerted effects of heterogeneous nuclear ribonucleoprotein C1/C2 to control vitamin D-directed gene transcription and RNA splicing in human bone cells

Juw Won Park, Y. Xing, J. Adams, 2016, Nucleic acids research.

Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains

Yi Xing, Christopher J. Lee, Christopher Lee, 2003, FEBS letters.

Transcriptome-wide analyses of CstF64–RNA interactions in global regulation of mRNA alternative polyadenylation

Ji Wan, Yi Xing, Lingjie Weng, 2012, Proceedings of the National Academy of Sciences.

Discover hidden splicing variations by mapping personal transcriptomes to personal genomes

Juw Won Park, Y. Xing, Zhi-xiang Lu, 2015, Nucleic acids research.

The contribution of Alu exons to the human proteome

Lan Lin, P. Ping, M. Lam, 2016, Genome Biology.

CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome

Yi Xing, Zijun Zhang, Zijun Zhang, 2017, Nucleic acids research.

Assessing the impact of alternative splicing on domain interactions in the human proteome.

Yi Xing, Christopher J. Lee, Robert Riley, 2004, Journal of proteome research.

Assessing the application of Ka/Ks ratio test to alternatively spliced exons

Yi Xing, Christopher J. Lee, Yi Xing, 2005, Bioinform..

Exon arrays provide accurate assessments of gene expression

Yi Xing, Wing Hung Wong, Karen Kapur, 2007, Genome Biology.

Protein Modularity of Alternatively Spliced Exons Is Associated with Tissue-Specific Regulation of Alternative Splicing

Christopher J. Lee, Y. Xing, Yi Xing, 2005, PLoS genetics.

Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation.

Yi Xing, Christopher J. Lee, Alexander Alekseyenko, 2004, Nucleic acids research.

Adenosine deamination in human transcripts generates novel microRNA binding sites

Yi Xing, Debashish Bhattacharya, Glen M. Borchert, 2009, Human molecular genetics.

Evolution of alternative splicing in primate brain transcriptomes.

Y. Xing, Lan Lin, B. Davidson, 2010, Human molecular genetics.

Predicting Functional Alternative Splicing by Measuring RNA Selection Pressure from Multigenome Alignments

Lan Lin, Yi Xing, Hongchao Lu, 2009, PLoS Comput. Biol..

Genomic analysis of RNA alternative splicing in cancers.

Yi Xing, Y. Xing, Yi Xing, 2007, Frontiers in bioscience : a journal and virtual library.

ASAP: the Alternative Splicing Annotation Project

Yi Xing, Christopher J. Lee, Barmak Modrek, 2003, Nucleic Acids Res..

Context-dependent robustness to 5' splice site polymorphisms in human populations.

James J. Cai, Y. Xing, P. Jiang, 2011, Human molecular genetics.

Mis-splicing in Huntington’s disease: harnessing the power of comparative transcriptomics

B. Davidson, Robert Wang, Yi Xing, 2021, Trends in Neurosciences.

Elucidating dynamics and regulation of alternative splicing in osteogenic differentiation

Lan Lin, Yuanyuan Wang, Samir Adhikari, 2020, bioRxiv.

αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome

Yi Xing, Juw Won Park, Y. Xing, 2016, Nucleic acids research.

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

Dan Wang, Peng Jiang, Song Liu, 2010, Nucleic Acids Res..

MADS+: discovery of differential splicing events from Affymetrix exon junction array data

Shihao Shen, Claude C. Warzecha, Russ P. Carstens, 2009, Bioinform..

Using high-density exon arrays to profile gene expression in closely related species

Junhee Seok, Yi Xing, Wing Hung Wong, 2009, Nucleic acids research.

Cross-hybridization modeling on Affymetrix exon arrays

Wing Hung Wong, Yi Xing, Hui Jiang, 2008, Bioinform..

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

Yi Xing, Shihao Shen, Beverly L. Davidson, 2008, PLoS genetics.

Isolation and Transcriptional Profiling of Purified Hepatic Cells Derived from Human Embryonic Stem Cells

M. Elazar, J. Glenn, W. H. Wong, 2008, Stem cells.

MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays.

Hui Jiang, Douglas L Black, Yi Xing, 2008, RNA.

Probe Selection and Expression Index Computation of Affymetrix Exon Arrays

Y. Xing, W. Wong, K. Kapur, 2006, PloS one.

Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes

Yi Xing, Emad Bahrami-Samani, Emad Bahrami-Samani, 2018, bioRxiv.

Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3′ processing

J. Yates, Xiaohui Xie, Lingjie Weng, 2013, RNA.

Reconstruction of full-length isoforms from splice graphs.

Christopher J. Lee, Y. Xing, Yi Xing, 2008, Methods in molecular biology.

Relating alternative splicing to proteome complexity and genome evolution.

Christopher J. Lee, Y. Xing, Yi Xing, 2007, Advances in experimental medicine and biology.

The effect of intron length on exon creation ratios during the evolution of mammalian genomes.

Christopher J. Lee, Y. Xing, Meenakshi Roy, 2008, RNA.

Evolutionary Divergence of Exon Flanks: A Dissection of Mutability and Selection

Yi Xing, Christopher J. Lee, Christopher Lee, 2006, Genetics.

Species-specific exon loss in human transcriptomes.

C. Tokheim, Zhi-xiang Lu, Jinkai Wang, 2015, Molecular biology and evolution.

Assessing the conservation of mammalian gene expression using high-density exon arrays.

Y. Xing, M. Scott, W. Wong, 2007, Molecular biology and evolution.

Nonallele-specific silencing of mutant and wild-type huntingtin demonstrates therapeutic efficacy in Huntington's disease mice.

I. Martins, B. Davidson, J. McBride, 2009, Molecular therapy : the journal of the American Society of Gene Therapy.

processing ′ mammalian mRNA 3 in τ Overlapping and distinct functions of CstF 64 and CstF 64 Material Supplemental

J. Yates, Xiaohui Xie, Lingjie Weng, 2013 .

The nuclear experience of CPEB: implications for RNA processing and translational control.

Yi Xing, Shihao Shen, Shihao Shen, 2010, RNA.

GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data

Yi Xing, Keyan Zhao, Qing Zhou, 2013, Genome Biology.

variation of alternative splicing using RNA-seq data

Keyan Zhao, Qing Zhou, Zhi-xiang Lu, 2013 .

rMATS‐DVR: rMATS discovery of differential variants in RNA

Lan Lin, Shihao Shen, Yi Xing, 2017, Bioinform..

METTL4 is an snRNA m6Am methyltransferase that regulates RNA splicing

Hao Wu, R. Gregory, Yang Shi, 2020, Cell Research.

Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease.

Yi Xing, Shihao Shen, Olga Pletnikova, 2016, Human molecular genetics.

Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin

Yi Xing, Wei Zou, Jing Huang, 2003, Proceedings of the National Academy of Sciences of the United States of America.

PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data

Yi Xing, Collin Tokheim, Juw Won Park, 2014, Genom. Proteom. Bioinform..

Systems Biology With High-Throughput Sequencing Reveals Genetic Mechanisms Underlying the Metabolic Syndrome in the Lyon Hypertensive Rat

Lan Lin, A. Kwitek, T. Aitman, 2015, Circulation. Cardiovascular genetics.

“Radiotranscriptomics”: A synergy of imaging and transcriptomics in clinical assessment

Yi Xing, William Hsu, Amal Katrib, 2016, Quantitative Biology.

Global analysis of alternative splicing differences between humans and chimpanzees

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

Population and allelic variation of A-to-I RNA editing in human transcriptomes

Yi Xing, Shihao Shen, Levon Demirdjian, 2017, Genome Biology.

Strand specific RNA-seq data for higher specificity

Yi Xing, Julia H. Chariker, Juw Won Park, 2015, RACS.

Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants.

Emad Bahrami-Samani, Shayna Stein, Yi Xing, 2017, Methods in molecular biology.

Genetic variation of pre‐mRNA alternative splicing in human populations

Zhi-xiang Lu, Yi Xing, Peng Jiang, 2012, Wiley interdisciplinary reviews. RNA.

Context-dependent robustness to 5' splice site polymorphisms in human populations.

James J. Cai, Zhi-xiang Lu, Yi Xing, 2011, Human molecular genetics.

m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells.

Howard Y. Chang, Pedro J. Batista, Ryan A. Flynn, 2014, Cell stem cell.

An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs

Christopher J. Lee, Meenakshi Roy, Ying Nian Wu, 2006, Nucleic acids research.

m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome

P. Dedon, Zhi-xiang Lu, B. Molinie, 2016, Nature Methods.

Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

R. Carstens, Shihao Shen, K. Dittmar, 2012, Molecular and Cellular Biology.

Solving the Problem of Trans-Genomic Query with Alignment Tables

Christopher J. Lee, D. S. Parker, Alissa M. Resch, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Human transcriptome array for high-throughput clinical studies

John D. Storey, Tyson A. Clark, A. Schweitzer, 2011, Proceedings of the National Academy of Sciences of the United States of America.

METTL4 is an snRNA m6Am methyltransferase that regulates RNA splicing

Y. Xing, Hao Wu, R. Gregory, 2020, Cell Research.

A panoramic view of RNA modifications: exploring new frontiers

Lan Lin, Eddie Park, Zijun Zhang, 2018, Genome Biology.