Chaolin Zhang

发表

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2.

Michael Q. Zhang, J. Castle, A. Krainer, 2008, Genes & development.

Differential expression of 24 , 426 human alternative splicing events and predicted cis-regulation in 48 tissues and cell lines

Jyoti K. Shah, J. Castle, T. Cooper, 2011 .

Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites

Michael Q. Zhang, A. Krainer, Chaolin Zhang, 2007, Proceedings of the National Academy of Sciences.

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

Michael Q. Zhang, A. Krainer, Chaolin Zhang, 2013, Nucleic acids research.

A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes

Yufeng Shen, Chaolin Zhang, Yufeng Shen, 2016, bioRxiv.

A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes

Yufeng Shen, Chaolin Zhang, 2016, bioRxiv.

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

D. Licatalosi, A. Mele, J. Fak, 2011, Cell.

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

T. Maniatis, Chaolin Zhang, B. Barres, 2014, The Journal of Neuroscience.

The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult.

Chaolin Zhang, Jie Wu, D. Spector, 2012, Cell reports.

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis

A. Mele, J. Darnell, R. Darnell, 2014, Nature Protocols.

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

R. Darnell, Chaolin Zhang, 2011, Nature Biotechnology.

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.

Michael Q. Zhang, Sebastien M. Weyn-Vanhentenryck, P. Silver, 2014, Cell reports.

Proteome-scale analysis of phase-separated proteins in immunofluorescence images.

Chaolin Zhang, Tingting Li, Chunyu Yu, 2021, Briefings in bioinformatics.

Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome

Michael Q. Zhang, Chaolin Zhang, S. Grellscheid, 2011, PloS one.

Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.

Sebastien M. Weyn-Vanhentenryck, A. Krainer, Chaolin Zhang, 2019, Molecular cell.

Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites

Sebastien M. Weyn-Vanhentenryck, Chaolin Zhang, Elise D. Flynn, 2018, bioRxiv.

Functional in Silico Analysis of Gene Regulatory Polymorphism

Michael Q. Zhang, Chaolin Zhang, Xiaoyue Zhao, 2007 .

An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.

Michael Q. Zhang, Michael Q Zhang, Chaolin Zhang, 2006, Human molecular genetics.

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain.

Masato Yano, Robert B Darnell, Chaolin Zhang, 2012, Genes & development.

mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data

Xuegong Zhang, Chaolin Zhang, Xuegong Zhang, 2015, Nature Communications.

Capturing the interactome of newly transcribed RNA

Nan Li, Hao Sun, Wei Wang, 2018, Nature Methods.

Precise temporal regulation of alternative splicing during neural development

Sebastien M. Weyn-Vanhentenryck, Xuegong Zhang, Chaolin Zhang, 2018, bioRxiv.

Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes

Chaolin Zhang, Xiang-Jun Lu, Huijuan Feng, 2022, bioRxiv.

Evolutionary impact of limited splicing fidelity in mammalian genes.

Michael Q. Zhang, A. Krainer, Chaolin Zhang, 2007, Trends in genetics : TIG.

The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice

Taylor T. Johnson, R. Carstens, Chaolin Zhang, 2022, PLoS genetics.

Brain Translation: A Feather Tips the Scale.

Chaolin Zhang, Dmytro Ustianenko, Melissa G McKenzie, 2020, Molecular cell.

Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability

A. Mele, J. Fak, J. Ule, 2012, Neuron.

Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes

Chaolin Zhang, Xiang-Jun Lu, Huijuan Feng, 2022, bioRxiv.

Trans-cellular control of synapse properties by a cell type-specific splicing regulator

J. Bischofberger, D. Schreiner, P. Scheiffele, 2022, bioRxiv.

Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

J. Darnell, R. Darnell, T. Maniatis, 2018, Genome Biology.

Muscleblind-like 2-Mediated Alternative Splicing in the Developing Brain and Dysregulation in Myotonic Dystrophy

M. Ares, R. Darnell, M. Cline, 2012, Neuron.

Gain of toxic function by long-term AAV9-mediated SMN overexpression in the sensory-motor circuit

G. Mentis, Chaolin Zhang, Meaghan Van Alstyne, 2021, Nature Neuroscience.

LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs.

Sebastien M. Weyn-Vanhentenryck, Pavel Sumazin, G. Meister, 2018, Molecular cell.

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome

Michael Q. Zhang, Chaolin Zhang, Zhenyu Xuan, 2006, Nucleic acids research.

Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators

Sebastien M. Weyn-Vanhentenryck, Chaolin Zhang, Jia Qian Wu, 2015, Proceedings of the National Academy of Sciences of the United States of America.

NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure

J. Fak, R. Darnell, Chaolin Zhang, 2013, eLife.

Genome Signals and Evolution for Fidelity and Regulation of Pre-mRNA Splicing

Chaolin Zhang, Chaolin Zhang, 2008 .

FMRP binding to a ranked subset of long genes is revealed by coupled CLIP and TRAP in specific neuronal cell types

Christopher Y. Park, J. Fak, J. Darnell, 2019, bioRxiv.

Precise temporal regulation of alternative splicing during neural development

Sebastien M. Weyn-Vanhentenryck, Chaolin Zhang, M. Swanson, 2018, Nature Communications.

Systematic reconstruction of autism biology from massive genetic mutation profiles

Chaolin Zhang, C. Brouwer, Yong-hui Jiang, 2018, Science Advances.

Systematic Reconstruction of Autism Biology with Multi-Level Whole Exome Analysis

Chaolin Zhang, C. Brouwer, Weijun Luo, 2016, bioRxiv.

Alternative splicing at neuroligin site A regulates glycan interaction and synaptogenic activity

Steven A. Connor, Chaolin Zhang, O. Thoumine, 2020, eLife.

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

Michael Q. Zhang, Chaolin Zhang, K. Zaret, 2011, PLoS genetics.

LIN28 selectively modulates a subclass of let-7 microRNAs

Sebastien M. Weyn-Vanhentenryck, Pavel Sumazin, Chaolin Zhang, 2017, bioRxiv.

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

D. Licatalosi, A. Mele, J. Fak, 2010, Science.

Endothelial Notch signaling directly regulates the small GTPase RND1 to facilitate Notch suppression of endothelial migration

Chaolin Zhang, P. Sims, Raphael Kopan, 2022, Scientific Reports.

Prediction of clustered RNA-binding protein motif sites in the mammalian genome

Chaolin Zhang, Maurice S. Swanson, R. Darnell, 2013, Nucleic acids research.

Loss of MBNL leads to disruption of developmentally regulated alternative polyadenylation in RNA-mediated disease.

Chaolin Zhang, M. Swanson, K. Sobczak, 2014, Molecular cell.

PrePPI: A NOVEL STRUCTURE-BASED METHOD FOR PREDICTING PROTEIN-PROTEIN INTERACTIONS

B. Honig, H. Bussemaker, Chaolin Zhang, 2013 .

Profiling alternatively spliced mRNA isoforms for prostate cancer classification

Michael Q. Zhang, Chaolin Zhang, Hai-Ri Li, 2006, BMC Bioinformatics.

11: SYSTEMATIC RECONSTRUCTION OF AUTISM BIOLOGY WITH MULTI-LEVEL WHOLE EXOME ANALYSIS

Chaolin Zhang, C. Brouwer, Weijun Luo, 2016, European Neuropsychopharmacology.

Biomedical Literature Mining

Michael Q. Zhang, Michael Q. Zhang, Chaolin Zhang, 2009 .

Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence

Michael Ruogu Zhang, S. Lowe, Chaolin Zhang, 2022 .

CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data

Chaolin Zhang, Ankeeta Shah, Yingzhi Qian, 2016, Bioinform..

Stage-specific requirement for Mettl3-dependent m6A mRNA methylation during haematopoietic stem cell differentiation

Lei Ding, Suying Bao, Chaolin Zhang, 2019, Nature Cell Biology.

Complexity and graded regulation of neuronal cell-type–specific alternative splicing revealed by single-cell RNA sequencing

V. Menon, Chaolin Zhang, Huijuan Feng, 2021, Proceedings of the National Academy of Sciences.

Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly

Sebastien M. Weyn-Vanhentenryck, H. Wichterle, Chaolin Zhang, 2018, Neuron.

Microexons: discovery, regulation, and function

Sebastien M. Weyn-Vanhentenryck, Chaolin Zhang, Dmytro Ustianenko, 2017, Wiley interdisciplinary reviews. RNA.

mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA-Binding Proteins.

Sebastien M. Weyn-Vanhentenryck, Chaolin Zhang, Chaolin Zhang, 2016, Methods in molecular biology.

RNA landscape of evolution for optimal exon and intron discrimination

Michael Q. Zhang, A. Krainer, Wen-Hsiung Li, 2008, Proceedings of the National Academy of Sciences.

A cell-type-specific alternative splicing regulator shapes synapse properties in a trans-synaptic manner

J. Bischofberger, D. Schreiner, P. Scheiffele, 2023, Cell reports.

The Splicing Code Goes Deep

Suying Bao, Chaolin Zhang, Chaolin Zhang, 2019, Cell.

DAZL Regulates Germ Cell Survival through a Network of PolyA-Proximal mRNA Interactions

Molly M. Hannigan, Leah L. Zagore, Sebastien M. Weyn-Vanhentenryck, 2018, bioRxiv.

Progressive impairment of muscle regeneration in muscleblind-like 3 isoform knockout mice.

R. Darnell, Chaolin Zhang, Michael G. Poulos, 2013, Human molecular genetics.

MBNL Sequestration by Toxic RNAs and RNA Misprocessing in the Myotonic Dystrophy Brain.

Sebastien M. Weyn-Vanhentenryck, L. Buée, Chaolin Zhang, 2015, Cell reports.

Factors Fox-1 and Fox-2 Defining the Regulatory Network of the Tissue-specific Splicing Material Supplemental

Michael Q. Zhang, J. Castle, A. Krainer, 2009 .

Stage-specific requirement for Mettl3-dependent m6A mRNA methylation during haematopoietic stem cell differentiation

J. Hanna, Chaolin Zhang, Shay Geula, 2019, Nature Cell Biology.

A Role for Sensory end Organ-Derived Signals in Regulating Muscle Spindle Proprioceptor Phenotype

T. Jessell, I. Schieren, Chaolin Zhang, 2019, The Journal of Neuroscience.

Proteome-scale analysis of phase-separated proteins in immunofluorescence images

Tingting Li, Minglei Shi, Chaolin Zhang, 2020, Briefings Bioinform..

Precise temporal regulation of alternative splicing during neural development

Sebastien M. Weyn-Vanhentenryck, Xuegong Zhang, Chaolin Zhang, 2018, bioRxiv.

Significance of Gene Ranking for Classification of Microarray Samples

Xuesong Lu, Xuegong Zhang, Chaolin Zhang, 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Systematic dissection of coordinated stromal remodeling identifies Sox10 glial cells as a therapeutic target in myelofibrosis

Chaolin Zhang, G. Bhagat, J. Que, 2023, Cell Stem Cell.

Identification of Splicing Factor Target Genes by High-Throughput Sequencing

Michael Q. Zhang, Chaolin Zhang, 2012 .

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

J. Fak, S. Chi, J. Darnell, 2011, Cell.

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2.

Michael Q. Zhang, J. Castle, A. Krainer, 2008, Genes & development.

LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs.

Sebastien M. Weyn-Vanhentenryck, Pavel Sumazin, G. Meister, 2018, Molecular cell.

Differential expression of 24 , 426 human alternative splicing events and predicted cis-regulation in 48 tissues and cell lines

Jyoti K. Shah, J. Castle, T. Cooper, 2011 .

Bone Marrow Microenvironment Affects The Pathogenesis Of Multiple Myeloma Through Downregulation Of Alternative Splicing Factor Fox2 In Myeloma Cells

Parantu K. Shah, Chaolin Zhang, N. Munshi, 2013 .