Totalomics Solutions

TotalOmics

후성 유전체 관련 논문


2010년

  • Reyes A. et al., Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010 Jul 15;466(7304):334-8.
  • Walter J. et al., Microbes and Health Sackler Colloquium: Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm. Proc Natl Acad Sci U S A. 2010 Jun 25. [Epub ahead of print]
  • Caporaso JG. et al., Microbes and Health Sackler Colloquium: Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2010 Jun 3. [Epub ahead of print]
  • Coetzee B. et al., Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard. Virology. 2010 May 10;400(2):157-63. Epub 2010 Feb 20.
  • Jones SE. et al., Dormancy contributes to the maintenance of microbial diversity. Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5881-6. Epub 2010 Mar 15.
  • Ettwig KF. et al., Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature. 2010 Mar 25;464(7288):543-8.
  • Qin J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010 Mar 4;464(7285):59-65.
  • Hodges E. et al., High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res. 2009 Sep;19(9):1593-605. Epub 2009 Jul 6.
  • Maunakea AK. et al., Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7.
  • Shoemaker R. et al., Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res. 2010 Jul;20(7):883-9. Epub 2010 Apr 23.
  • Wright KD. et al., To infinium, and beyond! Cancer Cell. 2010 May 18;17(5):419-20.
  • Li N. et al., Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods. 2010 Apr 27. [Epub ahead of print]
  • Feng S. et al., Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A. 2010 May 11;107(19):8689-94. Epub 2010 Apr 15.
  • Bhandare R. et al., Genome-wide analysis of histone modifications in human pancreatic islets. Genome Res. 2010 Apr;20(4):428-33. Epub 2010 Feb 24.
  • Laird PW., Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet. 2010 Feb 2;11(3):191-203. [Epub ahead of print]
  • Gu H. et al., Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods. 2010 Feb;7(2):133-6. Epub 2010 Jan 10.
  • Ruike Y. et al., Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics. 2010 Feb 25;11:137.
  • Daniel JA. et al., PTIP promotes chromatin changes critical for immunoglobulin class switch recombination. Science. 2010 Aug 20;329(5994):917-23. Epub 2010 Jul 29.
  • Elo LL. et al., Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity. 2010 Jun 25;32(6):852-62.
  • Raja SJ. et al., The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell. 2010 Jun 25;38(6):827-41.
  • Aiden AP. et al., Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Cell Stem Cell. 2010 Jun 4;6(6):591-602.
  • Jolma A. et al., Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 2010 Jun;20(6):861-73. Epub 2010 Apr 8.
  • Duan Z. et al., A three-dimensional model of the yeast genome. Nature. 2010 May 20;465(7296):363-7. Epub 2010 May 2.
  • Cheung I. et al., Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc Natl Acad Sci U S A. 2010 May 11;107(19):8824-9. Epub 2010 Apr 26.
  • Thomason HA. et al., Cooperation between the transcription factors p63 and IRF6 is essential to prevent cleft palate in mice. J Clin Invest. 2010 May 3;120(5):1561-9. doi: 10.1172/JCI40266. Epub 2010 Apr 26.
  • Xiang H. et al., Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol. 2010 May;28(5):516-20. Epub 2010 May 2.
  • h.gov/pubmed/20418881 Barski A. et al., Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes. Nat Struct Mol Biol. 2010 May;17(5):629-34. Epub 2010 Apr 25.
  • Oler AJ. et al., Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol. 2010 May;17(5):620-8. Epub 2010 Apr 25.
  • Schmidt D. et al., A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res. 2010 May;20(5):578-88. Epub 2010 Mar 10.
  • Cicatiello L. et al., Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. Am J Pathol. 2010 May;176(5):2113-30. Epub 2010 Mar 26.
  • Floer M. et al., A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell. 2010 Apr 30;141(3):407-18.
  • Ramos YF. et al., Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. Nucleic Acids Res. 2010 Sep;38(16):5396-408. Epub 2010 Apr 30.
  • Huang Y. et al., A feed-forward loop amplifies nutritional regulation of PNPLA3. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7892-7. Epub 2010 Apr 12.
  • Yagi R. et al., The transcription factor GATA3 actively represses RUNX3 protein-regulated production of interferon-gamma. Immunity. 2010 Apr 23;32(4):507-17. Epub 2010 Apr 15.
  • Blackledge NP. et al., CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 2010 Apr 23;38(2):179-90.
  • Cao Y. et al., Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell. 2010 Apr 20;18(4):662-74.
  • Thomson JP. et al., CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature. 2010 Apr 15;464(7291):1082-6.
  • Eaton ML. et al., Conserved nucleosome positioning defines replication origins. Genes Dev. 2010 Apr 15;24(8):748-53. Epub 2010 Mar 29.
  • Masui T. et al., Replacement of Rbpj with Rbpjl in the PTF1 complex controls the final maturation of pancreatic acinar cells. Gastroenterology. 2010 Jul;139(1):270-80. Epub 2010 Apr 14.
  • Drost J. et al., BRD7 is a candidate tumour suppressor gene required for p53 function. Nat Cell Biol. 2010 Apr;12(4):380-9. Epub 2010 Mar 14.
  • Raha D. et al., Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3639-44. Epub 2010 Feb 5.
  • Martens JH. et al., PML-RARalpha/RXR Alters the Epigenetic Landscape in Acute Promyelocytic Leukemia. Cancer Cell. 2010 Feb 17;17(2):173-85.
  • Li G. et al., Jarid2 and PRC2, partners in regulating gene expression. Genes Dev. 2010 Feb 15;24(4):368-80. Epub 2010 Feb 1.
  • Ponts N. et al., Nucleosome landscape and control of transcription in the human malaria parasite. Genome Res. 2010 Feb;20(2):228-38. Epub 2010 Jan 6.
  • Hansen RS. et al., Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44. Epub 2009 Dec 4.
  • Weiner A. et al., High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 2010 Jan;20(1):90-100. Epub 2009 Oct 21.
  • Zhong M. et al., Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010 Feb 19;6(2):e1000848.
  • Day DS. et al., Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 2010;11(6):R69. Epub 2010 Jun 28.
  • MacIsaac KD. et al., A quantitative model of transcriptional regulation reveals the influence of binding location on expression. PLoS Comput Biol. 2010 Apr 29;6(4):e1000773.
  • Tanaka Y. et al., Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics. 2010 May 17;11:309.
  • De Santa F. et al., A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 2010 May 11;8(5):e1000384.
  • Serre D. et al., MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 2010 Jan;38(2):391-9. Epub 2009 Nov 11.
  • Frietze S. et al., Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem. 2010 Jan 8;285(2):1393-403. Epub 2009 Nov 2.



2009년

  • Tyler HL. et al., Confirmation of the sequence of 'Candidatus Liberibacter asiaticus' and assessment of microbial diversity in Huanglongbing-infected citrus phloem using a metagenomic approach. Mol Plant Microbe Interact. 2009 Dec;22(12):1624-34.
  • Angly FE. et al., The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009 Dec;5(12):e1000593. Epub 2009 Dec 11.
  • Lazarevic V. et al., Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods. 2009 Dec;79(3):266-71. Epub 2009 Sep 29.
  • Nusbaum C. et al., Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods. 2009 Jan;6(1):67-9. Epub 2008 Dec 14.
  • Gerlach W. et al., WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics. 2009 Dec 18;10:430.
  • Costello JF. et al., A first look at entire human methylomes. Nat Biotechnol. 2009 Dec;27(12):1130-2.
  • Kanber D. et al., The human retinoblastoma gene is imprinted. PLoS Genet. 2009 Dec;5(12):e1000790. Epub 2009 Dec 24.
  • Lister R. et al., Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009 Nov 19;462(7271):315-22. Epub 2009 Oct 14.
  • Wang Z. et al., Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell. 2009 Sep 4;138(5):1019-31. Epub 2009 Aug 20.
  • Li M. et al., Sensitive digital quantification of DNA methylation in clinical samples. Nat Biotechnol. 2009 Sep;27(9):858-63. Epub 2009 Aug 16.
  • Hollister JD. et al., Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 2009 Aug;19(8):1419-28. Epub 2009 May 28.
  • Li JB. et al., Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res. 2009 Sep;19(9):1606-15. Epub 2009 Jun 12.
  • Gehring M. et al., Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science. 2009 Jun 12;324(5933):1447-51.
  • Hsieh TF. et al., Genome-wide demethylation of Arabidopsis endosperm. Science. 2009 Jun 12;324(5933):1451-4.
  • Smith ZD. et al., High-throughput bisulfite sequencing in mammalian genomes. Methods. 2009 Jul;48(3):226-32. Epub 2009 May 12.
  • Ball MP. et al., Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol. 2009 Apr;27(4):361-8. Epub 2009 Mar 29.
  • Ball MP. et al., Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol. 2009 Apr;27(4):361-8. Epub 2009 Mar 29.
  • Deng J. et al., Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol. 2009 Apr;27(4):353-60. Epub 2009 Mar 29.
  • Brunner AL. et al., Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009 Jun;19(6):1044-56. Epub 2009 Mar 9.
  • Li J. et al., An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics. 2009 May 13;10:223.
  • Xue Y. et al., Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell. 2009 Dec 25;36(6):996-1006.
  • Cheng Y. et al., Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res. 2009 Dec;19(12):2172-84. Epub 2009 Nov 3.
  • Bohnsack MT. et al., Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis. Mol Cell. 2009 Nov 25;36(4):583-92.
  • Fujiwara T. et al., Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell. 2009 Nov 25;36(4):667-81.
  • Yuan P. et al., Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev. 2009 Nov 1;23(21):2507-20.
  • Pepke S. et al., Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009 Nov;6(11 Suppl):S22-32.
  • Sekimata M. et al., CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity. 2009 Oct 16;31(4):551-64. Epub 2009 Oct 8.
  • Lieberman-Aiden E. et al., Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 9;326(5950):289-93.
  • Nishiyama A. et al., Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell. 2009 Oct 2;5(4):420-33.
  • Barski A. et al., Chromatin poises miRNA- and protein-coding genes for expression. Genome Res. 2009 Oct;19(10):1742-51. Epub 2009 Aug 27.
  • Spyrou C. et al., BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics. 2009 Sep 21;10:299.
  • Mirouze M. et al., Selective epigenetic control of retrotransposition in Arabidopsis. Nature. 2009 Sep 17;461(7262):427-30. Epub 2009 Sep 6.
  • Park PJ., ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009 Oct;10(10):669-80. Epub 2009 Sep 8.
  • Seo YK. et al., Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13765-9. Epub 2009 Aug 4.
  • Steiner LA. et al., Chromatin architecture and transcription factor binding regulate expression of erythrocyte membrane protein genes. Mol Cell Biol. 2009 Oct;29(20):5399-412. Epub 2009 Aug 17.
  • Audit B. et al., Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells. Nucleic Acids Res. 2009 Oct;37(18):6064-75. Epub 2009 Aug 10.
  • Zhang Y. et al., Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol. 2009 Aug;16(8):847-52. Epub 2009 Jul 20.
  • Jin C. et al., H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet. 2009 Aug;41(8):941-5. Epub 2009 Jul 26.
  • Gehring M. et al., Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science. 2009 Jun 12;324(5933):1447-51.
  • Wang X. et al., Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell. 2009 Apr;21(4):1053-69. Epub 2009 Apr 17.
  • Siegel TN. et al., Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. Genes Dev. 2009 May 1;23(9):1063-76. Epub 2009 Apr 15.
  • Baugh LR. et al., RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science. 2009 Apr 3;324(5923):92-4. Epub 2009 Feb 26.
  • Wang Z. et al., CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods. 2009 Jul;48(3):287-93. Epub 2009 Mar 9.
  • Field Y. et al., Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet. 2009 Apr;41(4):438-45. Epub 2009 Mar 1.
  • Zhu J. et al., Down-regulation of Gfi-1 expression by TGF-beta is important for differentiation of Th17 and CD103+ inducible regulatory T cells. J Exp Med. 2009 Feb 16;206(2):329-41. Epub 2009 Feb 2.
  • Warren RL. et al., Profiling model T-cell metagenomes with short reads. Bioinformatics. 2009 Feb 15;25(4):458-64. Epub 2009 Jan 9.
  • Ingolia NT. et al., Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009 Apr 10;324(5924):218-23. Epub 2009 Feb 12.
  • Guttman M. et al., Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009 Mar 12;458(7235):223-7. Epub 2009 Feb 1.
  • Lefrançois P. et al., Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics. 2009 Jan 21;10:37.
  • Hoffman BG. et al., Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J Endocrinol. 2009 Apr;201(1):1-13. Epub 2009 Jan 9.
  • Pauler FM. et al., H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res. 2009 Feb;19(2):221-33. Epub 2008 Dec 1.
  • Laajala TD. et al., A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics. 2009 Dec 18;10:618.
  • Gjertsson I. et al., Tolerance induction using lentiviral gene delivery delays onset and severity of collagen II arthritis. Mol Ther. 2009 Apr;17(4):632-40. Epub 2009 Jan 27.



2008년

  • Cokus SJ. et al., Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. Epub 2008 Feb 17.
  • Beck S. et al., The methylome: approaches for global DNA methylation profiling. Trends Genet. 2008 May;24(5):231-7. Epub 2008 Mar 5.
  • Lister R. et al., Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008 May 2;133(3):523-36.
  • Meissner A. et al., Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 7;454(7205):766-70. Epub 2008 Jul 6.
  • Nielsen R. et al., Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev. 2008 Nov 1;22(21):2953-67.
  • Ku M. et al., Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 2008 Oct;4(10):e1000242. Epub 2008 Oct 31.
  • Alekseyenko AA. et al., A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell. 2008 Aug 22;134(4):599-609.
  • Marson A. et al., Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell. 2008 Aug 8;134(3):521-33.
  • Jothi R. et al., Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 2008 Sep;36(16):5221-31. Epub 2008 Aug 6.
  • Wederell ED. et al., Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res. 2008 Aug;36(14):4549-64. Epub 2008 Jul 8.
  • Chen X. et al., Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008 Jun 13;133(6):1106-17.
  • Lister R. et al., Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008 May 2;133(3):523-36.
  • Shivaswamy S. et al., Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 2008 Mar 18;6(3):e65.
  • Schones DE. et al., Dynamic regulation of nucleosome positioning in the human genome. Cell. 2008 Mar 7;132(5):887-98.
  • Wold B. et al., Sequence census methods for functional genomics. Nat Methods. 2008 Jan;5(1):19-21. Epub 2007 Dec 19.



2007년

  • Johnson DS. et al., Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007 Jun 8;316(5830):1497-502. Epub 2007 May 31.