Totalomics Solutions

TotalOmics

스몰 RNA 전사체 해독 관련 논문

2010년

  • Jima DD. et al., Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood. 2010 Aug 23. [Epub ahead of print]
  • Burroughs AM. et al., A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Genome Res. 2010 Oct;20(10):1398-410. Epub 2010 Aug 18.
  • Taft RJ. et al., Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol. 2010 Aug;17(8):1030-4. Epub 2010 Jul 11.
  • Kapranov P. et al., New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature. 2010 Jul 29;466(7306):642-6.
  • Mondal T. et al., Characterization of the RNA content of chromatin. Genome Res. 2010 Jul;20(7):899-907. Epub 2010 Apr 19.
  • Kuchen S. et al., Regulation of microRNA expression and abundance during lymphopoiesis. Immunity. 2010 Jun 25;32(6):828-39. Epub 2010 Jun 3.
  • Chen X. et al., Identification and characterization of microRNAs in raw milk during different periods of lactation, commercial fluid, and powdered milk products. Cell Res. 2010 Oct;20(10):1128-37. Epub 2010 Jun 15.
  • Brinkman AB. et al., Whole-genome DNA methylation profiling using MethylCap-seq. Methods. 2010 Jun 11. [Epub ahead of print]
  • Cock JM. et al., The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature. 2010 Jun 3;465(7298):617-21.
  • Dunoyer P. et al., An endogenous, systemic RNAi pathway in plants. EMBO J. 2010 May 19;29(10):1699-712. Epub 2010 Apr 22.
  • Chiang HR. et al., Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 2010 May 15;24(10):992-1009. Epub 2010 Apr 22.
  • Molnar A. et al., Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science. 2010 May 14;328(5980):872-5. Epub 2010 Apr 22.
  • Wu L. et al., DNA methylation mediated by a microRNA pathway. Mol Cell. 2010 May 14;38(3):465-75. Epub 2010 Apr 8.
  • Chinni SV. et al., Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi. Nucleic Acids Res. 2010 Sep 1;38(17):5893-908. Epub 2010 May 11.
  • Y. et al., Genomic analysis of miRNAs in an extreme mammalian hibernator, the Arctic ground squirrel. Physiol Genomics. 2010 Sep;42(1):39-51. Epub 2010 May 4.
  • Filiatrault MJ. et al., Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. J Bacteriol. 2010 May;192(9):2359-72. Epub 2010 Feb 26.
  • Lee HC. et al., Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell. 2010 Jun 25;38(6):803-14. Epub 2010 Apr 22.
  • Montgomery SB. et al., Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 2010 Apr 1;464(7289):773-7. Epub 2010 Mar 10.
  • Gent JI. et al., Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. Mol Cell. 2010 Mar 12;37(5):679-89. Epub 2010 Jan 28.
  • Schutz K. et al., Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates. RNA. 2010 Mar;16(3):621-31. Epub 2010 Jan 14.
  • Buck AH. et al., Post-transcriptional regulation of miR-27 in murine cytomegalovirus infection. RNA. 2010 Feb;16(2):307-15. Epub 2010 Jan 4.
  • Hao L. et al., Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum. BMC Genomics. 2010 Jan 21;11:55.
  • Beck AH. et al., 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One. 2010 Jan 19;5(1):e8768.
  • Bolduc F. et al., In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection. BMC Mol Biol. 2010 Feb 16;11:16.
  • Wang Z. et al., An "in-depth" description of the small non-coding RNA population of Schistosoma japonicum schistosomulum. PLoS Negl Trop Dis. 2010 Feb 9;4(2):e596.
  • Creighton CJ. et al., Discovery of novel microRNAs in female reproductive tract using next generation sequencing. PLoS One. 2010 Mar 10;5(3):e9637.
  • Stark MS. et al., Characterization of the Melanoma miRNAome by Deep Sequencing. PLoS One. 2010 Mar 12;5(3):e9685.
  • Moldovan D. et al., Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. J Exp Bot. 2010;61(1):165-77.
  • Wurtzel O. et al., A single-base resolution map of an archaeal transcriptome. Genome Res. 2010 Jan;20(1):133-41. Epub 2009 Nov 2.
  • Sharbati S. et al., Deciphering the porcine intestinal microRNA transcriptome. BMC Genomics. 2010 Apr 30;11:275.
  • Liao JY. et al., Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PLoS One. 2010 May 14;5(5):e10563.
  • Xu AG. et al., Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol. 2010 Jul 1;6:e1000843.
  • Umbach JL. et al., In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J Virol. 2010 Jan;84(2):695-703. Epub 2009 Nov 4.
  • Umbach JL. et al., Identification of viral microRNAs expressed in human sacral ganglia latently infected with herpes simplex virus 2. J Virol. 2010 Jan;84(2):1189-92. Epub 2009 Nov 4.


2009년

  • Chen X. et al., Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol. 2009;10(7):R78. Epub 2009 Jul 17.
  • Zhang Y. et al., Insect-Specific microRNA involved in the development of the silkworm Bombyx mori. PLoS One. 2009;4(3):e4677. Epub 2009 Mar 5.
  • Shoji M. et al., The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline. Dev Cell. 2009 Dec;17(6):775-87.
  • Czech B. et al., Hierarchical rules for Argonaute loading in Drosophila. Mol Cell. 2009 Nov 13;36(3):445-56.
  • Wang Y. et al., Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics. 2009 Nov 5;10:512.
  • Pang M. et al., Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biol. 2009;10(11):R122. Epub 2009 Nov 4.
  • Forrest AR. et al., Annotating non-coding transcription using functional genomics strategies. Brief Funct Genomic Proteomic. 2009 Nov;8(6):437-43.
  • Zhang L. et al., A genome-wide characterization of microRNA genes in maize. PLoS Genet. 2009 Nov;5(11):e1000716. Epub 2009 Nov 20.
  • Jia Y. et al., Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. PLoS Genet. 2009 Nov;5(11):e1000737. Epub 2009 Nov 20.
  • Hsieh LC. et al., Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol. 2009 Dec;151(4):2120-32. Epub 2009 Oct 23.
  • Tuteja JH. et al., Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in glycine max seed coats. Plant Cell. 2009 Oct;21(10):3063-77. Epub 2009 Oct 9.
  • Stoeckius M. et al., Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nat Methods. 2009 Oct;6(10):745-51. Epub 2009 Sep 6.
  • Persson H. et al., The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs. Nat Cell Biol. 2009 Oct;11(10):1268-71. Epub 2009 Sep 13.
  • Umbach JL. et al., Analysis of human alphaherpesvirus microRNA expression in latently infected human trigeminal ganglia. J Virol. 2009 Oct;83(20):10677-83. Epub 2009 Aug 5.
  • De Paoli E. et al., Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA. 2009 Nov;15(11):1965-70. Epub 2009 Sep 23.
  • Rao PK. et al., Loss of cardiac microRNA-mediated regulation leads to dilated cardiomyopathy and heart failure. Circ Res. 2009 Sep 11;105(6):585-94. Epub 2009 Aug 13.
  • Stadler PF. et al., Evolution of vault RNAs. Mol Biol Evol. 2009 Sep;26(9):1975-91. Epub 2009 Jun 2.
  • Jones MR. et al., Zcchc11-dependent uridylation of microRNA directs cytokine expression. Nat Cell Biol. 2009 Sep;11(9):1157-63. Epub 2009 Aug 23.
  • Ma L. et al., GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PLoS Genet. 2009 Sep;5(9):e1000635. Epub 2009 Sep 4.
  • Mayr C. et al., Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell. 2009 Aug 21;138(4):673-84.
  • Rechavi O. et al., Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs. Genes Dev. 2009 Aug 15;23(16):1971-9.
  • Armisen J. et al., Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. Genome Res. 2009 Oct;19(10):1766-75. Epub 2009 Jul 23.
  • Wei B. et al., Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Funct Integr Genomics. 2009 Nov;9(4):499-511. Epub 2009 Jun 5.
  • Kreuze JF. et al., Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology. 2009 May 25;388(1):1-7. Epub 2009 Apr 23.
  • Li C. et al., Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell. 2009 May 1;137(3):509-21. Epub 2009 Apr 23.
  • 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.
  • Rathjen T. et al., High throughput sequencing of microRNAs in chicken somites. FEBS Lett. 2009 May 6;583(9):1422-6. Epub 2009 Mar 27.
  • Ebhardt HA. et al., Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res. 2009 May;37(8):2461-70. Epub 2009 Mar 2.
  • 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.
  • Wei Y. et al., Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol. 2009;10(1):R6. Epub 2009 Jan 16.
  • Ben-Ami O. et al., A regulatory interplay between miR-27a and Runx1 during megakaryopoiesis. Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):238-43. Epub 2008 Dec 29.
  • Glazov EA. et al., Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS One. 2009 Jul 27;4(7):e6349.
  • Zhang H. et al., Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PLoS One. 2009 Sep 2;4(9):e6849.
  • Kwak PB. et al., Enrichment of a set of microRNAs during the cotton fiber development. BMC Genomics. 2009 Sep 29;10:457.
  • Navarro B. et al., Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One. 2009 Nov 5;4(11):e7686.
  • Huang J. et al., Genome-wide identification of Schistosoma japonicum microRNAs using a deep-sequencing approach. PLoS One. 2009 Dec 8;4(12):e8206.



2008년

  • Chen X. et al., Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res. 2008 Oct;18(10):997-1006.
  • Mi S. et al., Sorting of small RNAs into arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell. 2008 Apr 4;133(1):116-27. Epub 2008 Mar 13.
  • Montgomery TA. et al., Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell. 2008 Apr 4;133(1):128-41. Epub 2008 Mar 13.
  • Morin RD. et al., Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cell. Genome Res. 2008 Apr;18(4):610-21. Epub 2008 Feb 19.
  • Hafner M. et al., Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods. 2008 Jan;44(1):3-12.
  • Myles KM. et al., Alphavirus-derived small RNAs modulate pathogenesis in disease vector mosquitoes. Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19938-43. Epub 2008 Dec 1.
  • He Y. et al., The antisense transcriptomes of human cells. Science. 2008 Dec 19;322(5909):1855-7. Epub 2008 Dec 4.
  • Ender C. et al., A human snoRNA with microRNA-like functions. Mol Cell. 2008 Nov 21;32(4):519-28.
  • 't Hoen PA. et al., Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008 Dec;36(21):e141. Epub 2008 Oct 15.
  • Chen X. et al., Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res. 2008 Oct;18(10):997-1006.
  • Grimson A. et al., Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature. 2008 Oct 30;455(7217):1193-7. Epub 2008 Oct 1.
  • Zhu QH. et al., A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res. 2008 Sep;18(9):1456-65. Epub 2008 Aug 7.
  • 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.
  • German MA. et al., Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol. 2008 Aug;26(8):941-6. Epub 2008 Jun 9.
  • Glazov EA. et al., A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res. 2008 Jun;18(6):957-64. Epub 2008 May 9.
  • Czech B. et al., An endogenous small interfering RNA pathway in Drosophila. Nature. 2008 Jun 5;453(7196):798-802. Epub 2008 May 7.
  • Lister R. et al., Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008 May 2;133(3):523-36.
  • Nagalakshmi U. et al., The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 Jun 6;320(5881):1344-9. Epub 2008 May 1.
  • Ghildiyal M. et al., Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science. 2008 May 23;320(5879):1077-81. Epub 2008 Apr 10.
  • Tam OH. et al., Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature. 2008 May 22;453(7194):534-8. Epub 2008 Apr 10.
  • Mi S. et al., Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell. 2008 Apr 4;133(1):116-27. Epub 2008 Mar 13.
  • Morin RD. et al., Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008 Apr;18(4):610-21. Epub 2008 Feb 19.
  • Wold B. et al., Sequence census methods for functional genomics. Nat Methods. 2008 Jan;5(1):19-21. Epub 2007 Dec 19.
  • Stark A. et al., A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 2008 Jan 1;22(1):8-13.
  • Tyler DM. et al., Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 2008 Jan 1;22(1):26-36.




2007년

  • Calabrese JM. et al., RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18097-102. Epub 2007 Nov 7.



2006년

  • Ruby JG. et al., Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell. 2006 Dec 15;127(6):1193-207.