Unveiling transposable element expression heterogeneity in cell fate regulation at the single-cell level
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A. Hutchins | I. A. Babarinde | Jiekai Chen | Jiangping He | Li Sun | Shuyang Xu | Ruhai Chen | Yuanjie Wei | Yuhao Li | Gang Ma | Q. Zhuang | Zhuang Qiang
[1] J. Jurka. Repbase update: a database and an electronic journal of repetitive elements. , 2000, Trends in genetics : TIG.
[2] S. Yamanaka,et al. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.
[3] C. Feschotte. Transposable elements and the evolution of regulatory networks , 2008, Nature Reviews Genetics.
[4] Timothy L. Bailey,et al. Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data , 2010, BMC Bioinformatics.
[5] J. Kawai,et al. The regulated retrotransposon transcriptome of mammalian cells , 2009, Nature Genetics.
[6] M. Batzer,et al. The impact of retrotransposons on human genome evolution , 2009, Nature Reviews Genetics.
[7] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[8] G. Bourque,et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells , 2010, Nature Genetics.
[9] G. Mizuguchi,et al. Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome , 2010, Cell.
[10] Sandrine Dudoit,et al. GC-Content Normalization for RNA-Seq Data , 2011, BMC Bioinformatics.
[11] D. Selkoe. Alzheimer's disease. , 2011, Cold Spring Harbor perspectives in biology.
[12] S. Salzberg,et al. Repetitive DNA and next-generation sequencing: computational challenges and solutions , 2011, Nature Reviews Genetics.
[13] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[14] C. Burge,et al. Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues , 2012, Science.
[15] Shawn P. Driscoll,et al. ES cell potency fluctuates with endogenous retrovirus activity , 2012, Nature.
[16] Ralf Jauch,et al. glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data , 2014, Cell Regeneration.
[17] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[18] J. Baker,et al. Endogenous retroviruses function as species-specific enhancer elements in the placenta , 2013, Nature Genetics.
[19] H. Deng,et al. Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small-Molecule Compounds , 2013, Science.
[20] J. Dubnau,et al. Activation of transposable elements during aging and neuronal decline in Drosophila , 2013, Nature Neuroscience.
[21] A. Sandelin,et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance , 2014, Nature Genetics.
[22] L. Groop,et al. Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism , 2014, Proceedings of the National Academy of Sciences.
[23] L. Hurst,et al. Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells , 2014, Nature.
[24] Jennifer A. Erwin,et al. Mobile DNA elements in the generation of diversity and complexity in the brain , 2014, Nature Reviews Neuroscience.
[25] G. Bourque,et al. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity , 2014, Nature Structural &Molecular Biology.
[26] Daniel C. Factor,et al. Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency. , 2014, Cell stem cell.
[27] G. Faulkner,et al. L1 retrotransposons and somatic mosaicism in the brain. , 2014, Annual review of genetics.
[28] Helen M. Rowe,et al. Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency , 2014, Genome research.
[29] E. Koonin,et al. Evolution of adaptive immunity from transposable elements combined with innate immune systems , 2014, Nature Reviews Genetics.
[30] Howard Y. Chang,et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells , 2015, Nature.
[31] Haley O. Tucker,et al. Smyd1 Facilitates Heart Development by Antagonizing Oxidative and ER Stress Responses , 2015, PloS one.
[32] Howard Y. Chang,et al. Single-cell chromatin accessibility reveals principles of regulatory variation , 2015, Nature.
[33] A. Hutchins,et al. Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs , 2015, Science bulletin.
[34] B. Bruneau,et al. Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms. , 2015, Cell stem cell.
[35] G. Pan,et al. The oncogene c-Jun impedes somatic cell reprogramming , 2015, Nature Cell Biology.
[36] H. Ng,et al. Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. , 2015, Cell stem cell.
[37] Ying Jin,et al. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets , 2015, Bioinform..
[38] A. Murphy,et al. RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes. , 2016, Cell metabolism.
[39] Haley O. Tucker,et al. The chromatin-binding protein Smyd1 restricts adult mammalian heart growth. , 2016, American journal of physiology. Heart and circulatory physiology.
[40] R. Jaenisch,et al. Molecular Criteria for Defining the Naive Human Pluripotent State , 2016, Cell Stem Cell.
[41] Davis J. McCarthy,et al. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor , 2016, F1000Research.
[42] J. García-Pérez,et al. The impact of transposable elements on mammalian development , 2016, Development.
[43] Charles H. Yoon,et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq , 2016, Science.
[44] C. Feschotte,et al. Regulatory evolution of innate immunity through co-option of endogenous retroviruses , 2016, Science.
[45] J. Ernst,et al. Cooperative Binding of Transcription Factors Orchestrates Reprogramming , 2017, Cell.
[46] Grace X. Y. Zheng,et al. Massively parallel digital transcriptional profiling of single cells , 2016, Nature Communications.
[47] I. Amit,et al. A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease , 2017, Cell.
[48] Howard Y. Chang,et al. Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs , 2017, Circulation research.
[49] Steven D Chang,et al. Single-Cell RNAseq analysis of infiltrating neoplastic cells at the migrating front of human glioblastoma , 2017, bioRxiv.
[50] A. Hutchins,et al. Chromatin Accessibility Dynamics during iPSC Reprogramming. , 2017, Cell stem cell.
[51] A. Hutchins,et al. Models of global gene expression define major domains of cell type and tissue identity , 2017, Nucleic acids research.
[52] J. George,et al. Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes , 2017, Genome research.
[53] Fabian J Theis,et al. SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.
[54] C. Feschotte,et al. Regulatory activities of transposable elements: from conflicts to benefits , 2016, Nature Reviews Genetics.
[55] O. Rando,et al. LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo , 2017, Nature Genetics.
[56] K. Burns. Transposable elements in cancer , 2017, Nature Reviews Cancer.
[57] M. Torres-Padilla,et al. Nimble and Ready to Mingle: Transposon Outbursts of Early Development. , 2018, Trends in genetics : TIG.
[58] James T. Webber,et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris , 2018, Nature.
[59] Z. Bar-Joseph,et al. Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation. , 2018, Cell stem cell.
[60] David A. Knowles,et al. Landscape of stimulation-responsive chromatin across diverse human immune cells , 2018, Nature Genetics.
[61] Principal Investigators,et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris , 2018 .
[62] K. Jung,et al. Isolation of primitive mouse extraembryonic endoderm (pXEN) stem cell lines. , 2018, Stem cell research.
[63] S. Teichmann,et al. A rapid and robust method for single cell chromatin accessibility profiling , 2018 .
[64] G. Pan,et al. Chromatin Accessibility Dynamics during Chemical Induction of Pluripotency. , 2018, Cell stem cell.
[65] G. Bourque,et al. Computational tools to unmask transposable elements , 2018, Nature Reviews Genetics.
[66] Ricardo J. Miragaia,et al. A rapid and robust method for single cell chromatin accessibility profiling , 2018, Nature Communications.
[67] Chao Tang,et al. Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming. , 2018, Cell stem cell.
[68] J. Boeke,et al. Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression , 2018, Proceedings of the National Academy of Sciences.
[69] William S. DeWitt,et al. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility , 2018, Cell.
[70] Xiaohua Shen,et al. A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity , 2018, Cell.
[71] G. Bourque,et al. Ten things you should know about transposable elements , 2018, Genome Biology.
[72] J. Boeke,et al. LINE-1 derepression in senescent cells triggers interferon and inflammaging , 2018, Nature.
[73] Haley O. Tucker,et al. Histone methyltransferase Smyd1 regulates mitochondrial energetics in the heart , 2018, Proceedings of the National Academy of Sciences.
[74] Jason D. Buenrostro,et al. Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution , 2018, Nature Genetics.
[75] J. Boeke,et al. LINE-1 derepression in senescent cells triggers interferon and inflammaging , 2018, Nature.
[76] G. Pan,et al. Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2-Jhdm1b-Mkk6-Glis1-Nanog-Essrb-Sall4. , 2019, Cell reports.
[77] Paul J. Hoffman,et al. Comprehensive Integration of Single-Cell Data , 2018, Cell.
[78] Deanna M. Church,et al. The emergent landscape of the mouse gut endoderm at single-cell resolution , 2019, Nature.
[79] Nakul M. Shah,et al. Transposable elements drive widespread expression of oncogenes in human cancers , 2019, Nature Genetics.
[80] P. Rigollet,et al. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming , 2019, Cell.
[81] Berthold Göttgens,et al. A single-cell molecular map of mouse gastrulation and early organogenesis , 2019, Nature.
[82] K. Burns,et al. Transposable elements in human genetic disease , 2019, Nature Reviews Genetics.
[83] S. Kummerfeld,et al. The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification , 2019, bioRxiv.
[84] Mark Gerstein,et al. GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..
[85] A. del Sol,et al. Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects , 2019, Nature.
[86] Stein Aerts,et al. cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data , 2019, Nature Methods.
[87] G. Pan,et al. Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq. , 2019, Molecular cell.
[88] Oliver H. Tam,et al. Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease , 2019, Mobile DNA.
[89] P. Rigollet,et al. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming , 2019, Cell.
[90] David A. Knowles,et al. Landscape of stimulation-responsive chromatin across diverse human immune cells , 2018, Nature Genetics.
[91] I. Amit,et al. Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma , 2019, Cell.
[92] Y. Loh,et al. Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells , 2019, Nature Communications.
[93] Xudong Fu,et al. Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells , 2019, Nature Cell Biology.