Totalomics Solutions

TotalOmics

기타 NGS 관련 논문

2010년

  • Shental N. et al., Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Res. 2010 Aug 10. [Epub ahead of print]
  • Kislyuk AO. et al., A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics. 2010 Aug 1;26(15):1819-26. Epub 2010 Jun 2.
  • Otto TD. et al., Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics. 2010 Jul 15;26(14):1704-7. Epub 2010 Jun 18.
  • Zimmermann B. et al., Genomic SELEX: a discovery tool for genomic aptamers. Methods. 2010 Oct;52(2):125-32. Epub 2010 Jun 9.
  • Miller JR. et al., Assembly algorithms for next-generation sequencing data. Genomics. 2010 Jun;95(6):315-27. Epub 2010 Mar 6.
  • Hajirasouliha I. et al., Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics. 2010 May 15;26(10):1277-83. Epub 2010 Apr 12.
  • 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.
  • Au KF. et al., Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res. 2010 Aug;38(14):4570-8. Epub 2010 Apr 5.
  • Shen Y. et al., A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 2010 Feb;20(2):273-80. Epub 2009 Dec 17.
  • Tanaka Y. et al., Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics. 2010 May 17;11:309.
  • Bueno R. et al., Second generation sequencing of the mesothelioma tumor genome. PLoS One. 2010 May 13;5(5):e10612.
  • Hosseini P. et al., An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets. BMC Res Notes. 2010 Jul 2;3:183.
  • McComish BJ. et al., Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biol Evol. 2010 Jul 12;2:410-24. Print 2010.
  • Horner DS. et al., Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform. 2010 Mar;11(2):181-97. Epub 2009 Oct 27.
  • Wood HM. et al., Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res. 2010 Aug;38(14):e151. Epub 2010 Jun 4.
  • Fowler DM. et al., High-resolution mapping of protein sequence-function relationships. Nat Methods. 2010 Sep;7(9):741-6. Epub 2010 Aug 15.
  • Levin JZ. et al., Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods. 2010 Sep;7(9):709-15. Epub 2010 Aug 15.
  • Shental N. et al., Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Res. 2010 Aug 10. [Epub ahead of print]
  • Adli M. et al., Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat Methods. 2010 Aug;7(8):615-8. Epub 2010 Jul 11.
  • Wang H. et al., Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res. 2010 Jul;20(7):981-8. Epub 2010 May 14.
  • Ni T. et al., A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods. 2010 Jul;7(7):521-7. Epub 2010 May 23.
  • Koboldt DC. et al., Challenges of sequencing human genomes. Brief Bioinform. 2010 Sep;11(5):484-98. Epub 2010 Jun 2.
  • Meyer M. et al., Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5448.
  • 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.
  • Kidd JM. et al., Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods. 2010 May;7(5):365-71.
  • 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.
  • Simpson JT. et al., Copy number variant detection in inbred strains from short read sequence data. Bioinformatics. 2010 Feb 15;26(4):565-7. Epub 2009 Dec 18.
  • Mamanova L. et al., FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods. 2010 Feb;7(2):130-2. Epub 2010 Jan 17.
  • Hiatt JB. et al., Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods. 2010 Feb;7(2):119-22. Epub 2010 Jan 17.
  • Salzberg SL., Mind the gaps. Nat Methods. 2010 Feb;7(2):105-6.
  • Young AL. et al., A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res. 2010 Feb;20(2):249-56.
  • Rosa-Rosa JM. et al., Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting. PLoS One. 2010 Apr 2;5(4):e9976.
  • Fan HC. et al., Sensitivity of noninvasive prenatal detection of fetal aneuploidy from maternal plasma using shotgun sequencing is limited only by counting statistics. PLoS One. 2010 May 3;5(5):e10439.
  • McComish BJ. et al., Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biol Evol. 2010 Jul 12;2:410-24. Print 2010.
  • Cunningham C. et al., Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. J Gen Virol. 2010 Mar;91(Pt 3):605-15. Epub 2009 Nov 11.



2009년

  • 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.
  • Pepke S. et al., Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009 Nov;6(11 Suppl):S22-32.
  • Cho BK. et al., The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol. 2009 Nov;27(11):1043-9. Epub 2009 Nov 1.
  • Spyrou C. et al., BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics. 2009 Sep 21;10:299.
  • van Iterson M. et al., Relative power and sample size analysis on gene expression profiling data. BMC Genomics. 2009 Sep 17;10:439.
  • Schneeberger K. et al., Simultaneous alignment of short reads against multiple genomes. Genome Biol. 2009;10(9):R98. Epub 2009 Sep 17.
  • Alkan C. et al., Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet. 2009 Oct;41(10):1061-7. Epub 2009 Aug 30.
  • Yoon S. et al., Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2009 Sep;19(9):1586-92. Epub 2009 Aug 5.
  • Martínez-Alcántara A. et al., PIQA: pipeline for Illumina G1 genome analyzer data quality assessment. Bioinformatics. 2009 Sep 15;25(18):2438-9. Epub 2009 Jul 14.
  • Birol I. et al., De novo transcriptome assembly with ABySS. Bioinformatics. 2009 Nov 1;25(21):2872-7. Epub 2009 Jun 15.
  • 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.
  • Warren RL. et al., Profiling model T-cell metagenomes with short reads. Bioinformatics. 2009 Feb 15;25(4):458-64. Epub 2009 Jan 9.
  • Wang WC. et al., miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics. 2009 Oct 12;10:328.
  • Zerbino DR. et al., Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS One. 2009 Dec 22;4(12):e8407.
  • Zhao Y. et al., Inferring binding energies from selected binding sites. PLoS Comput Biol. 2009 Dec;5(12):e1000590. Epub 2009 Dec 4.
  • van Opijnen T. et al., Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods. 2009 Oct;6(10):767-72. Epub 2009 Sep 20.
  • van Iterson M. et al., Relative power and sample size analysis on gene expression profiling data. BMC Genomics. 2009 Sep 17;10:439.
  • Yoon S. et al., Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2009 Sep;19(9):1586-92. Epub 2009 Aug 5.
  • Li R. et al., SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009 Aug 1;25(15):1966-7. Epub 2009 Jun 3.
  • Birol I. et al., De novo transcriptome assembly with ABySS. Bioinformatics. 2009 Nov 1;25(21):2872-7. Epub 2009 Jun 15.
  • Kozarewa I. et al., Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods. 2009 Apr;6(4):291-5. Epub 2009 Mar 15.
  • 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.
  • 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.
  • 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.
  • Chaisson MJ. et al., De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res. 2009 Feb;19(2):336-46. Epub 2008 Dec 3.



2008년

  • 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.
  • Huang W. et al., EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res. 2008 Sep;18(9):1538-43. Epub 2008 Jun 11.
  • Chaisson MJ. et al., Short read fragment assembly of bacterial genomes. Genome Res. 2008 Feb;18(2):324-30. Epub 2007 Dec 14.
  • Bashir A. et al., Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol. 2008 Apr 25;4(4):e1000051.