Totalomics Solutions

TotalOmics

전사체 해독 관련 논문

2010년

  • Li R. et al., De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010 Feb;20(2):265-72. Epub 2009 Dec 17.
  • Robins HS. et al., Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med. 2010 Sep 1;2(47):47ra64.
  • Guo H. et al., Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature. 2010 Aug 12;466(7308):835-40.
  • Gregg C. et al., Sex-specific parent-of-origin allelic expression in the mouse brain. Science. 2010 Aug 6;329(5992):682-5. Epub 2010 Jul 8.
  • Woodhouse SD. et al., Transcriptome sequencing, microarray, and proteomic analyses reveal cellular and metabolic impact of hepatitis C virus infection in vitro. Hepatology. 2010 Aug;52(2):443-53.
  • Zhang C. et al., Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science. 2010 Jul 23;329(5990):439-43. Epub 2010 Jun 17.
  • McManus CJ. et al., Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12975-9. Epub 2010 Jul 1.
  • Wu T. et al., Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol. 2010 Jul 15;167(11):905-13. Epub 2010 Mar 19.
  • Hansen KD. et al., Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 2010 Jul 1;38(12):e131. Epub 2010 Apr 14.
  • Plessy C. et al., Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods. 2010 Jul;7(7):528-34. Epub 2010 Jun 13.
  • Stamatoyannopoulos JA. et al., Illuminating eukaryotic transcription start sites. Nat Methods. 2010 Jul;7(7):501-3.
  • König J. et al., iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol. 2010 Jul;17(7):909-15. Epub 2010 Jul 4.
  • Martí E. et al., A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing. Nucleic Acids Res. 2010 Jun 30. [Epub ahead of print]
  • Kuchen S. et al., Regulation of microRNA expression and abundance during lymphopoiesis. Immunity. 2010 Jun 25;32(6):828-39. Epub 2010 Jun 3.
  • Yano M. et al., Nova2 regulates neuronal migration through an RNA switch in disabled-1 signaling. Neuron. 2010 Jun 24;66(6):848-58.
  • McManus CJ. et al., Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res. 2010 Jun;20(6):816-25. Epub 2010 Mar 30.
  • Emerson JJ. et al., Natural selection on cis and trans regulation in yeasts. Genome Res. 2010 Jun;20(6):826-36. Epub 2010 May 5.
  • Hammer P. et al., mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain. Genome Res. 2010 Jun;20(6):847-60. Epub 2010 May 7.
  • Gan Q. et al., Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. Cell Res. 2010 Jul;20(7):763-83. 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.
  • Zhang G. et al., Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 2010 May;20(5):646-54. Epub 2010 Mar 19.
  • Yang F. et al., Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res. 2010 May;20(5):614-22. Epub 2010 Apr 2.
  • Guttman M. et al., Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 2010 May;28(5):503-10. Epub 2010 May 2.
  • Trapnell C. et al., Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. Epub 2010 May 2.
  • Kidd JM. et al., Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods. 2010 May;7(5):365-71.
  • Haas BJ. et al., Advancing RNA-Seq analysis. Nat Biotechnol. 2010 May;28(5):421-3.
  • Nicolas FE. et al., Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Res. 2010 Sep;38(16):5535-41. Epub 2010 Apr 28.
  • Wang B. et al., Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res. 2010 Aug;38(15):5075-87. Epub 2010 Apr 14.
  • 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.
  • Siegel TN. et al., Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites. Nucleic Acids Res. 2010 Aug;38(15):4946-57. Epub 2010 Apr 12.
  • Wu H. et al., A splicing-independent function of SF2/ASF in microRNA processing. Mol Cell. 2010 Apr 9;38(1):67-77.
  • Hafner M. et al., Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010 Apr 2;141(1):129-41.
  • Zenoni S. et al., Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol. 2010 Apr;152(4):1787-95. Epub 2010 Jan 29.
  • Pickrell JK. et al., Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010 Apr 1;464(7289):768-72. Epub 2010 Mar 10.
  • Bullard JH. et al., Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5058-63. Epub 2010 Mar 1.
  • Wu JQ. et al., Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5254-9. Epub 2010 Mar 1.
  • Sharma CM. et al., The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010 Mar 11;464(7286):250-5. Epub 2010 Feb 17.
  • Abbas AI. et al., Assessing serotonin receptor mRNA editing frequency by a novel ultra high-throughput sequencing method. Nucleic Acids Res. 2010 Jun;38(10):e118. Epub 2010 Feb 25.
  • Halic M. et al., Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell. 2010 Feb 19;140(4):504-16.
  • Libault M. et al., Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection. Plant Physiol. 2010 Feb;152(2):541-52. Epub 2009 Nov 20.
  • Wilhelm BT. et al., Defining transcribed regions using RNA-seq. Nat Protoc. 2010;5(2):255-66. Epub 2010 Jan 21.
  • Hittinger CT. et al., Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1476-81. Epub 2010 Jan 4.
  • Nechaev S. et al., Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science. 2010 Jan 15;327(5963):335-8. Epub 2009 Dec 10.
  • 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.
  • Vrba L. et al., Role for DNA methylation in the regulation of miR-200c and miR-141 expression in normal and cancer cells. PLoS One. 2010 Jan 13;5(1):e8697.
  • 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.
  • Zhang Y. et al., Expression in aneuploid Drosophila S2 cells. PLoS Biol. 2010 Feb 23;8(2):e1000320.
  • Liu S. et al., MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics. 2010 Mar 3;11:148.
  • David JP. et al., Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology. BMC Genomics. 2010 Mar 31;11:216.
  • Corrêa RL. et al., MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans. PLoS Genet. 2010 Apr 8;6(4):e1000903.
  • Howard BE. et al., Towards reliable isoform quantification using RNA-SEQ data. BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S6.
  • 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.
  • .van Bakel H et al., Most "dark matter" transcripts are associated with known genes. PLoS Biol. 2010 May 18;8(5):e1000371.
  • Beaume M. et al., Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One. 2010 May 20;5(5):e10725.
  • Xiao S. et al., Understanding PRRSV infection in porcine lung based on genome-wide transcriptome response identified by deep sequencing. PLoS One. 2010 Jun 29;5(6):e11377.
  • Bai X. et al., Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines. PLoS One. 2010 Jun 29;5(6):e11370.
  • 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.
  • Larsen PE. et al., Using deep RNA sequencing for the structural annotation of the Laccaria bicolor mycorrhizal transcriptome. PLoS One. 2010 Jul 6;5(7):e9780.
  • Jacob NM. et al., Reaching the depth of the Chinese hamster ovary cell transcriptome. Biotechnol Bioeng. 2010 Apr 1;105(5):1002-9.
  • Filichkin SA. et al., Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 2010 Jan;20(1):45-58. Epub 2009 Oct 26.
  • Cheng X. et al., Screening of human gene promoter activities using transfected-cell arrays. Gene. 2010 Jan 15;450(1-2):48-54.
  • Platts AE. et al., Disease progression and solid tumor survival: a transcriptome decoherence model. Mol Cell Probes. 2010 Feb;24(1):53-60. Epub 2009 Oct 14.
  • Heap GA. et al., Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum Mol Genet. 2010 Jan 1;19(1):122-34.





2009년

  • Maher CA. et al., Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009 Mar 5;458(7234):97-101. Epub 2009 Jan 11.
  • Wang Z. et al., RNA-Seq:a revolutionary tool for transcriptomics. Nat Rev Genet. 2009 Jan;10(1):57-63.
  • Degner JF. et al., Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009 Dec 15;25(24):3207-12. Epub 2009 Oct 6.
  • Hale CR. et al., RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell. 2009 Nov 25;139(5):945-56.
  • Quon G. et al., ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Bioinformatics. 2009 Nov 1;25(21):2882-9. Epub 2009 Jun 19.
  • Ko JH. et al., Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis. Plant J. 2009 Nov;60(4):649-65. Epub 2009 Aug 6.
  • Pepke S. et al., Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009 Nov;6(11 Suppl):S22-32.
  • Lee JH. et al., A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet. 2009 Nov;5(11):e1000718. Epub 2009 Nov 13.
  • Shah SP. et al., Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct 8;461(7265):809-13.
  • Xiao X. et al., Splice site strength-dependent activity and genetic buffering by poly-G runs. Nat Struct Mol Biol. 2009 Oct;16(10):1094-100. Epub 2009 Sep 13.
  • van Iterson M. et al., Relative power and sample size analysis on gene expression profiling data. BMC Genomics. 2009 Sep 17;10:439.
  • Gibbons JG. et al., Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol. 2009 Dec;26(12):2731-44. Epub 2009 Aug 25.
  • Greenway SC. et al., De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot. Nat Genet. 2009 Aug;41(8):931-5. Epub 2009 Jul 13.
  • Hegedus Z. et al., Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol. 2009 Sep;46(15):2918-30. Epub 2009 Jul 24.
  • Ruan MB. et al., Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics. 2009 Oct;94(4):263-8. Epub 2009 Jul 21.
  • Parkhomchuk D. et al., Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Oct;37(18):e123. Epub 2009 Jul 20.
  • Han X. et al., Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing. Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12741-6. Epub 2009 Jul 17.
  • Mosher RA. et al., Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature. 2009 Jul 9;460(7252):283-6. Epub 2009 Jun 3.
  • Shah SP. et al., Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med. 2009 Jun 25;360(26):2719-29. Epub 2009 Jun 10.
  • Birol I. et al., De novo transcriptome assembly with ABySS. Bioinformatics. 2009 Nov 1;25(21):2872-7. Epub 2009 Jun 15.
  • Sackton TB. et al., Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing. BMC Genomics. 2009 Jun 7;10:259.
  • Trapnell C. et al., TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. Epub 2009 Mar 16.
  • 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.
  • 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.
  • Yoder-Himes DR. et al., Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3976-81. Epub 2009 Feb 20.
  • Yassour M. et al., Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3264-9. Epub 2009 Feb 10.
  • Tsuchihara K. et al., Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res. 2009 Apr;37(7):2249-63. Epub 2009 Feb 22.
  • 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.
  • Hillier LW. et al., Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 2009 Apr;19(4):657-66. Epub 2009 Jan 30.
  • Trick M. et al., Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J. 2009 May;7(4):334-46. Epub 2009 Jan 21.
  • Maher CA. et al., Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009 Mar 5;458(7234):97-101. Epub 2009 Jan 11.
  • Fu X. et al., Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics. 2009 Apr 16;10:161.
  • Asmann YW. et al., 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics. 2009 Nov 16;10:531.
  • Oliver HF. et al., Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics. 2009 Dec 30;10:641.
  • McGhee JD. et al., ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol. 2009 Mar 15;327(2):551-65. Epub 2008 Dec 9.
  • Ahsan B. et al., MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. Nucleic Acids Res. 2009 Jan;37(Database issue):D49-53. Epub 2008 Oct 8.




2008년

  • Mortazavi A. et al., Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Epub 2008 May 30.
  • Sultan M. et al., A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science. 2008 Aug 15;321(5891):956-60. Epub 2008 Jul 3.
  • Nagalakshmi. 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.
  • Li H. et al., Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20179-84. Epub 2008 Dec 16.
  • 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.
  • Denoeud F. et al., Annotating genomes with massive-scale RNA sequencing. Genome Biol. 2008;9(12):R175. Epub 2008 Dec 16.
  • International Silkworm Genome Consortium. et al., The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol. 2008 Dec;38(12):1036-45. Epub 2008 Dec 16.
  • He Y. et al., The antisense transcriptomes of human cells. Science. 2008 Dec 19;322(5909):1855-7. Epub 2008 Dec 4.
  • Core LJ. et al., Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008 Dec 19;322(5909):1845-8. Epub 2008 Dec 4.
  • Babak T. et al., Global survey of genomic imprinting by transcriptome sequencing. Curr Biol. 2008 Nov 25;18(22):1735-41.
  • Wang ET. et al., Alternative isoform regulation in human tissue transcriptomes. Nature. 2008 Nov 27;456(7221):470-6.
  • Pan Q. et al., Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008 Dec;40(12):1413-5. Epub 2008 Nov 2.
  • Rosenkranz R. et al., Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics. 2008 Oct;92(4):187-94. Epub 2008 Aug 3.
  • Mortazavi A. et al., Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Epub 2008 May 30.
  • Marioni JC. et al., RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008 Sep;18(9):1509-17. Epub 2008 Jun 11.
  • Wilhelm BT. et al., Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature. 2008 Jun 26;453(7199):1239-43. Epub 2008 May 18.
  • 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.
  • Wold B. et al., Sequence census methods for functional genomics. Nat Methods. 2008 Jan;5(1):19-21. Epub 2007 Dec 19.
  • Mudge J. et al., Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One. 2008;3(11):e3625. Epub 2008 Nov 5.
  • Wang X. et al., Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One. 2008;3(12):e3839. Epub 2008 Dec 4.




2007년

  • Kanehisa M. et al., KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4. Epub 2007 Dec 12.



2006년

  • Ye J. et al., WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7.



2005년

  • Conesa A. et al., Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005 Sep 15;21(18):3674-6. Epub 2005 Aug 4.



1999년

  • Iseli C. et al., ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999:138-48.


1997년

  • Audic S. et al., The significance of digital gene expression profiles. Genome Res. 1997 Oct;7(10):986-95.
  • Pertea G. et al., TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics. 2003 Mar 22;19(5):651-2.