Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell-derived hepatic organoids
暂无分享,去创建一个
[1] Junil Kim,et al. A PDX1 cistrome and single-cell transcriptome resource of the developing pancreas. , 2022, Development.
[2] Daniel J. Gaffney,et al. Single-cell atlas of human liver development reveals pathways directing hepatic cell fates , 2022, bioRxiv.
[3] I. Amit,et al. A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion , 2021, Nature Communications.
[4] A. Dejneka,et al. Liver Organoids: Recent Developments, Limitations and Potential , 2021, Frontiers in Medicine.
[5] W. Fujibuchi,et al. Human Cell Atlas and cell-type authentication for regenerative medicine , 2020, Experimental & molecular medicine.
[6] Fidel Ramírez,et al. pyGenomeTracks: reproducible plots for multivariate genomic datasets , 2020, Bioinform..
[7] Kyle J. Gaulton,et al. An atlas of dynamic chromatin landscapes in mouse fetal development , 2020, Nature.
[8] T. Baumert,et al. Single-cell genomics and spatial transcriptomics: Discovery of novel cell states and cellular interactions in liver physiology and disease biology , 2020, Journal of hepatology.
[9] M. Son,et al. Long-Term Expansion of Functional Human Pluripotent Stem Cell-Derived Hepatic Organoids , 2020, International journal of stem cells.
[10] Jiandie D. Lin,et al. hnRNPU/TrkB Defines a Chromatin Accessibility Checkpoint for Liver Injury and Nonalcoholic Steatohepatitis Pathogenesis , 2020, Hepatology.
[11] F. Gonzalez,et al. PPARs as Metabolic Regulators in the Liver: Lessons from Liver-Specific PPAR-Null Mice , 2020, International journal of molecular sciences.
[12] Howard Y. Chang,et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia , 2019, Nature Biotechnology.
[13] R. Majeti,et al. The Phosphatidylethanolamine Biosynthesis Pathway Provides a New Target for Cancer Chemotherapy. , 2019, Journal of hepatology.
[14] R. Irizarry. ggplot2 , 2019, Introduction to Data Science.
[15] Ye Seul Son,et al. Generation of expandable human pluripotent stem cell-derived hepatocyte-like liver organoids. , 2019, Journal of hepatology.
[16] Michael A. Dyer,et al. Nucleome Dynamics during Retinal Development , 2019, Neuron.
[17] Nidhi Sharma,et al. Mitochondrial DNA: Epigenetics and environment , 2019, Environmental and molecular mutagenesis.
[18] K. Kaestner,et al. The Dynamic Chromatin Architecture of the Regenerating Liver , 2019, bioRxiv.
[19] Xiaonan Zhang,et al. Long-term functional maintenance of primary human hepatocytes in vitro , 2019, Science.
[20] Kai Zhang,et al. SnapATAC: A Comprehensive Analysis Package for Single Cell ATAC-seq , 2019, bioRxiv.
[21] J. Spence,et al. Biologically inspired approaches to enhance human organoid complexity , 2019, Development.
[22] Huanbai Xu,et al. Distinct roles of Dlk1 isoforms in bi-potential differentiation of hepatic stem cells , 2019, Stem Cell Research & Therapy.
[23] A. Kundaje,et al. mtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis , 2019, iScience.
[24] Christoph Hafemeister,et al. Comprehensive integration of single cell data , 2018, bioRxiv.
[25] Gary D Bader,et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations , 2018, Nature Communications.
[26] J. Friedman,et al. Mitochondrial role in the neonatal predisposition to developing nonalcoholic fatty liver disease , 2018, The Journal of clinical investigation.
[27] Sungjin Ko,et al. Stat3 Regulates Liver Progenitor Cell-Driven Liver Regeneration in Zebrafish. , 2018, Gene expression.
[28] J. Lee,et al. Single-cell RNA sequencing technologies and bioinformatics pipelines , 2018, Experimental & Molecular Medicine.
[29] D. Waxman,et al. Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver , 2018, eLife.
[30] Pedro M. Baptista,et al. Biotechnology Challenges to In Vitro Maturation of Hepatic Stem Cells. , 2018, Gastroenterology.
[31] A. Miyajima,et al. The transcription factor Klf5 is essential for intrahepatic biliary epithelial tissue remodeling after cholestatic liver injury , 2018, The Journal of Biological Chemistry.
[32] S. Babai,et al. Safety data and withdrawal of hepatotoxic drugs. , 2018, Therapie.
[33] Daniel S. Day,et al. YY1 Is a Structural Regulator of Enhancer-Promoter Loops , 2017, Cell.
[34] Shaoping Ji,et al. Six2 Plays an Intrinsic Role in Regulating Proliferation of Mesenchymal Cells in the Developing Palate , 2017, Front. Physiol..
[35] Yuxia Zhang,et al. Role of early growth response 1 in liver metabolism and liver cancer , 2017, Hepatoma research.
[36] J. Michael Cherry,et al. The Encyclopedia of DNA elements (ENCODE): data portal update , 2017, Nucleic Acids Res..
[37] Y. Ikeda,et al. PDX1, Neurogenin-3, and MAFA: critical transcription regulators for beta cell development and regeneration , 2017, Stem Cell Research & Therapy.
[38] Hyun-soo Cho,et al. A liver‐specific gene expression panel predicts the differentiation status of in vitro hepatocyte models , 2017, Hepatology.
[39] Nuno A. Fonseca,et al. Two independent modes of chromatin organization revealed by cohesin removal , 2017, Nature.
[40] Steven J. M. Jones,et al. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma , 2017, Cell.
[41] H. Binder,et al. Multilineage communication regulates human liver bud development from pluripotency , 2017, Nature.
[42] Russell B. Fletcher,et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics , 2017, BMC Genomics.
[43] R. Stein,et al. Impact of Pdx1‐associated chromatin modifiers on islet β‐cells , 2016, Diabetes, obesity & metabolism.
[44] Nicola K. Wilson,et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. , 2016, Blood.
[45] C. Thummel,et al. The Drosophila HNF4 nuclear receptor promotes glucose-stimulated insulin secretion and mitochondrial function in adults , 2016, eLife.
[46] Andrew D. Rouillard,et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..
[47] N. Lanthier,et al. [SPINK1, hepatic macrophages and progenitor cells: new tools for liver regeneration in alcoholic hepatitis?]. , 2016, Medecine sciences : M/S.
[48] F. Tang,et al. Epigenomic Landscape of Human Fetal Brain, Heart, and Liver* , 2015, The Journal of Biological Chemistry.
[49] J. Itskovitz‐Eldor,et al. Microbial‐derived lithocholic acid and vitamin K2 drive the metabolic maturation of pluripotent stem cells–derived and fetal hepatocytes , 2015, Hepatology.
[50] L. Stanton,et al. PDX1 Binds and Represses Hepatic Genes to Ensure Robust Pancreatic Commitment in Differentiating Human Embryonic Stem Cells , 2015, Stem cell reports.
[51] Michael Q. Zhang,et al. Integrative analysis of haplotype-resolved epigenomes across human tissues , 2015, Nature.
[52] Hans Clevers,et al. Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver , 2015, Cell.
[53] Sharon Y. R. Dent,et al. Chromatin modifiers and remodellers: regulators of cellular differentiation , 2013, Nature Reviews Genetics.
[54] Wei Chen,et al. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence , 2013, Genes & development.
[55] Takanori Takebe,et al. Vascularized and functional human liver from an iPSC-derived organ bud transplant , 2013, Nature.
[56] Ellen T. Gelfand,et al. The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.
[57] David Haussler,et al. The UCSC genome browser and associated tools , 2012, Briefings Bioinform..
[58] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[59] C. Glass,et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.
[60] Stephen Dalton,et al. Highly efficient generation of human hepatocyte–like cells from induced pluripotent stem cells , 2010, Hepatology.
[61] C. Peterson,et al. Chromatin immunoprecipitation (ChIP). , 2009, Cold Spring Harbor protocols.
[62] Jennifer B Dennison,et al. Apparent High CYP3A5 Expression Is Required for Significant Metabolism of Vincristine by Human Cryopreserved Hepatocytes , 2008, Journal of Pharmacology and Experimental Therapeutics.
[63] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[64] T. Ichisaka,et al. Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors , 2007, Cell.
[65] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[66] T. Ochiya,et al. Recapitulation of in vivo gene expression during hepatic differentiation from murine embryonic stem cells , 2005, Hepatology.
[67] S. Specht,et al. Regulation and function of trefoil factor family 3 expression in the biliary tree. , 2004, The American journal of pathology.
[68] J. Brockmöller,et al. The Induction of Cytochrome P450 3A5 (CYP3A5) in the Human Liver and Intestine Is Mediated by the Xenobiotic Sensors Pregnane X Receptor (PXR) and Constitutively Activated Receptor (CAR)* , 2004, Journal of Biological Chemistry.
[69] M. Manns,et al. Quantitative gene expression profiling reveals a fetal hepatic phenotype of murine ES-derived hepatocytes. , 2004, The International journal of developmental biology.
[70] S. Duncan,et al. HNF4: A central regulator of hepatocyte differentiation and function , 2003, Hepatology.
[71] M. Torres-Padilla,et al. Expression of HNF4α isoforms in mouse liver development is regulated by sequential promoter usage and constitutive 3′ end splicing , 2001, Mechanisms of Development.
[72] T. Frayling,et al. A distant upstream promoter of the HNF-4alpha gene connects the transcription factors involved in maturity-onset diabetes of the young. , 2001, Human molecular genetics.
[73] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[74] Ira M. Hall,et al. BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..
[75] Charles A Tilford,et al. Gene set enrichment analysis. , 2009, Methods in molecular biology.
[76] B. Thiers. Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors , 2008 .
[77] Shahhosseini Fatima. POLYMERASE CHAIN REACTION (PCR) , 2003 .
[78] L. Mishra,et al. Elf3 encodes a novel 200-kD beta-spectrin: role in liver development. , 1999, Oncogene.