Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
暂无分享,去创建一个
Thomas Lengauer | F. Bäckhed | S. Schreiber | P. Rosenstiel | A. Franke | J. Walter | S. Künzel | J. Baines | A. Luzius | M. Jentzsch | F. Müller | T. Ulas | J. Schultze | F. Sommer | A. Rehman | W. Pan | M. Falk-Paulsen | P. Best | A. Fazio | P. Kachroo | S. Schreiber | Philipp Best | Felix Sommer
[1] P. Legendre. Numerical Ecology , 2019, Encyclopedia of Ecology.
[2] John M Denu,et al. Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. , 2016, Molecular cell.
[3] A. Masotti,et al. How Our Other Genome Controls Our Epi-Genome. , 2016, Trends in microbiology.
[4] Hao Wu,et al. Differential methylation analysis for BS-seq data under general experimental design , 2016, Bioinform..
[5] D. Kasper,et al. How colonization by microbiota in early life shapes the immune system , 2016, Science.
[6] Wolfgang Krebs,et al. The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin , 2016, Cell Research.
[7] V. Rakyan,et al. Assessing DNA methylation in the developing human intestinal epithelium: potential link to inflammatory bowel disease , 2015, Mucosal Immunology.
[8] R. Chen,et al. Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome , 2015, Genome Biology.
[9] Zhaohui S. Qin,et al. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates , 2015, Nucleic acids research.
[10] Olga G. Troyanskaya,et al. FNTM: a server for predicting functional networks of tissues in mouse , 2015, Nucleic Acids Res..
[11] I. Nookaew,et al. Site-specific programming of the host epithelial transcriptome by the gut microbiota , 2015, Genome Biology.
[12] S. Friedman,et al. Epithelial Xbp1 Is Required for Cellular Proliferation and Differentiation during Mammary Gland Development , 2015, Molecular and Cellular Biology.
[13] J. Gordon,et al. Analysis of gene–environment interactions in postnatal development of the mammalian intestine , 2015, Proceedings of the National Academy of Sciences.
[14] Knut Rudi,et al. The composition of the gut microbiota throughout life, with an emphasis on early life , 2015, Microbial ecology in health and disease.
[15] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[16] Lan Lin,et al. rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data , 2014, Proceedings of the National Academy of Sciences.
[17] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[18] R. Eils,et al. Identification of DNA methylation changes at cis-regulatory elements during early steps of HSC differentiation using tagmentation-based whole genome bisulfite sequencing , 2014, Cell cycle.
[19] Gangning Liang,et al. Gene body methylation can alter gene expression and is a therapeutic target in cancer. , 2014, Cancer cell.
[20] Jin He,et al. Tet3 and DNA replication mediate demethylation of both the maternal and paternal genomes in mouse zygotes. , 2014, Cell stem cell.
[21] Roland Eils,et al. circlize implements and enhances circular visualization in R , 2014, Bioinform..
[22] Jenny Chen,et al. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape , 2014, Genome research.
[23] W. Reik,et al. Reprogramming the Methylome: Erasing Memory and Creating Diversity , 2014, Cell stem cell.
[24] Sejal Saglani,et al. Lung microbiota promotes tolerance to allergens in neonates via PD-L1 , 2014, Nature Medicine.
[25] David Artis,et al. Intestinal epithelial cells: regulators of barrier function and immune homeostasis , 2014, Nature Reviews Immunology.
[26] Tom C. Freeman,et al. Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation , 2014, Immunity.
[27] F. Bäckhed,et al. Altered Mucus Glycosylation in Core 1 O-Glycan-Deficient Mice Affects Microbiota Composition and Intestinal Architecture , 2014, PloS one.
[28] F. Bushman,et al. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis , 2013, Nature.
[29] K. McCoy,et al. Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels , 2013, Cell host & microbe.
[30] A. Rudensky,et al. Metabolites produced by commensal bacteria promote peripheral regulatory T cell generation , 2013, Nature.
[31] A. Kaser,et al. Paneth cells as a site of origin for intestinal inflammation , 2013, Nature.
[32] Martin Dugas,et al. Detection of significantly differentially methylated regions in targeted bisulfite sequencing data , 2013, Bioinform..
[33] T. Plösch,et al. CALL FOR PAPERS Fetal and Neonatal Programming: Epigenetic Modification of Phenotype More than just a gut instinct-the potential interplay between a baby's nutrition, its gut microbiome, and the epigenome , 2013 .
[34] J. Doré,et al. Gut bacteria–host metabolic interplay during conventionalisation of the mouse germfree colon , 2012, The ISME Journal.
[35] F. Bäckhed,et al. The gut microbiota — masters of host development and physiology , 2013, Nature Reviews Microbiology.
[36] P. Rosenstiel. Stories of love and hate: innate immunity and host–microbe crosstalk in the intestine , 2013, Current opinion in gastroenterology.
[37] Karin Breuer,et al. InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation , 2012, Nucleic Acids Res..
[38] Anjana Rao,et al. PGC7, H3K9me2 and Tet3: regulators of DNA methylation in zygotes , 2012, Cell Research.
[39] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[40] B. Langmead,et al. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions , 2012, Genome Biology.
[41] Francine E. Garrett-Bakelman,et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.
[42] R. Knight,et al. Diversity, stability and resilience of the human gut microbiota , 2012, Nature.
[43] J. Doré,et al. Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice , 2012, Mucosal Immunology.
[44] T. Down,et al. A functional methylome map of ulcerative colitis , 2012, Genome research.
[45] J. Doré,et al. The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation , 2012, Gut.
[46] Peter A. Jones. Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.
[47] R. Siebert,et al. Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function , 2012, Science.
[48] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[49] J. Neu. Normal gut microbiota modulates brain development and behavior , 2012 .
[50] A. Rao,et al. PGC 7 , H 3 K 9 me 2 and Tet 3 : regulators of DNA methylation in zygotes , 2012 .
[51] V. Tremaroli,et al. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88 , 2011, Gut.
[52] Yang Wang,et al. Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA , 2011, Science.
[53] W. Verstraete,et al. The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept. , 2011, FEMS microbiology reviews.
[54] S. Colgan,et al. Hypoxia and metabolic factors that influence inflammatory bowel disease pathogenesis. , 2011, Gastroenterology.
[55] Felix Krueger,et al. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..
[56] James Versalovic,et al. Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll‐like receptor 2‐knockout mice , 2011, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[57] Kieran Clarke,et al. Regulation of human metabolism by hypoxia-inducible factor , 2010, Proceedings of the National Academy of Sciences.
[58] Annaïg Lan,et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. , 2009, Immunity.
[59] Israel Steinfeld,et al. BMC Bioinformatics BioMed Central , 2008 .
[60] H. Tilg,et al. XBP1 Links ER Stress to Intestinal Inflammation and Confers Genetic Risk for Human Inflammatory Bowel Disease , 2008, Cell.
[61] Sridhar Hannenhalli,et al. Eukaryotic transcription factor binding sites - modeling and integrative search methods , 2008, Bioinform..
[62] P. Chilton,et al. Impaired Bcl3 Up-regulation Leads to Enhanced Lipopolysaccharide-induced Interleukin (IL)-23P19 Gene Expression in IL-10–/– Mice* , 2008, Journal of Biological Chemistry.
[63] E. Berra,et al. The magic of the hypoxia-signaling cascade , 2008, Cellular and Molecular Life Sciences.
[64] T. Yamauchi. Neuronal Ca2+/calmodulin-dependent protein kinase II--discovery, progress in a quarter of a century, and perspective: implication for learning and memory. , 2005, Biological & pharmaceutical bulletin.
[65] T. Bestor,et al. Eukaryotic cytosine methyltransferases. , 2005, Annual review of biochemistry.
[66] U. Bunz. How Are Alkynes Scrambled? , 2005, Science.
[67] István Simon,et al. BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes , 2005, Nucleic acids research.
[68] Y. Chida,et al. Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice , 2004, The Journal of physiology.
[69] Homin K. Lee,et al. Coexpression analysis of human genes across many microarray data sets. , 2004, Genome research.
[70] S. Pradhan,et al. Mammalian DNA (cytosine-5) methyltransferases and their expression. , 2003, Clinical immunology.
[71] Long-Cheng Li,et al. MethPrimer: designing primers for methylation PCRs , 2002, Bioinform..
[72] P. Vertino,et al. DNMT1 is a Component of a Multiprotein DNA Replication Complex , 2002, Cell cycle.
[73] A. Jeltsch,et al. Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA. , 2002, European journal of biochemistry.
[74] S. Dudoit,et al. STATISTICAL METHODS FOR IDENTIFYING DIFFERENTIALLY EXPRESSED GENES IN REPLICATED cDNA MICROARRAY EXPERIMENTS , 2002 .
[75] J. Gordon,et al. Commensal Host-Bacterial Relationships in the Gut , 2001, Science.
[76] D. Haber,et al. DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development , 1999, Cell.
[77] W. Benedict,et al. Retinoblastoma: clues to human oncogenesis. , 1984, Science.
[78] R Holliday,et al. DNA modification mechanisms and gene activity during development , 1975, Science.
[79] Arthur D. Riggs,et al. X inactivation, differentiation, and DNA methylation. , 1975, Cytogenetics and cell genetics.