Searching journal content for articles similar to Hoberman et al. 19 (9): 1542.

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  1. RESOURCE: PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data
    • Ken Chen,
    • Michael D. McLellan,
    • Li Ding,
    • Michael C. Wendl,
    • Yumi Kasai,
    • Richard K. Wilson,
    • and Elaine R. Mardis
    Genome Res. May 2007 17: 659-666; Published in Advance April 6, 2007, doi:10.1101/gr.6151507
    ...continues to pose difficult challenges. In this paper, we present PolyScan, an algorithm and software implementation designed to provide de novo heterozygous indel detection and improved SNP identification in the context of high-throughput medical resequencing. Tests on a human diploid PCR-based sequence...
  2. Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
    • Georg Zeller,
    • Richard M. Clark,
    • Korbinian Schneeberger,
    • Anja Bohlen,
    • Detlef Weigel,
    • and Gunnar Rätsch
    Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
    ...-genome oligonucleotide resequencing arrays have allowed the comprehensive discovery of single nucleotide polymorphisms (SNPs) in eukaryotic genomes of moderate to large size. With this technology, the detection rate for isolated SNPs is typically high. However, it is greatly reduced when other polymorphisms are located...
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  3. Resource: A probabilistic disease-gene finder for personal genomes
    • Mark Yandell,
    • Chad Huff,
    • Hao Hu,
    • Marc Singleton,
    • Barry Moore,
    • Jinchuan Xing,
    • Lynn B. Jorde,
    • and Martin G. Reese
    Genome Res. September 2011 21: 1529-1542; Published in Advance June 23, 2011, doi:10.1101/gr.123158.111
    ...-causing genes (Altshuler et al. 2008; Lausch et al. 2008).With the advent of SNPmicroarrays, the principle of linkage disequilibrium was used to identify hundreds of SNPs associated with susceptibility to common diseases (Wellcome Trust Case Control Consortium 2007;Manolio 2009). However, the causes ofmany...
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  4. Resource: An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa
    • Rosaria Scozzari,
    • Andrea Massaia,
    • Beniamino Trombetta,
    • Giovanna Bellusci,
    • Natalie M. Myres,
    • Andrea Novelletto,
    • and Fulvio Cruciani
    Genome Res. March 2014 24: 535-544; Published in Advance January 6, 2014, doi:10.1101/gr.160788.113
    ...An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa Rosaria Scozzari 1 , Andrea Massaia 1 , Beniamino Trombetta 1 , Giovanna Bellusci 2 , Natalie M...
  5. METHODS: Polymorphism Ratio Sequencing: A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping
    • Robert G. Blazej,
    • Brian M. Paegel,
    • and Richard A. Mathies
    Genome Res. February 1, 2003 13: 287-293; doi:10.1101/gr.396203
    ...Polymorphism ratio sequencing (PRS) combines the advantages of high-throughput DNA sequencing with new labeling and pooling schemes to produce a powerful assay for sensitive single nucleotide polymorphism (SNP) discovery, rapid genotyping, and accurate, multiplexed allele frequency determination. In the PRS...
  6. Resource: Dindel: Accurate indel calls from short-read data
    • Cornelis A. Albers,
    • Gerton Lunter,
    • Daniel G. MacArthur,
    • Gilean McVean,
    • Willem H. Ouwehand,
    • and Richard Durbin
    Genome Res. June 2011 21: 961-973; Published in Advance October 27, 2010, doi:10.1101/gr.112326.110
    ...sequences to explain the data with a probabilistic model, thereby combining strengths of both. Accurate inference of indels from short-read data is challenging for a number of reasons. First, compared with SNPs, indels occur at approximately eightfold lower rates (Lunter 2007; Cartwright 2009), which makes...
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  7. Resource: Accurate detection and genotyping of SNPs utilizing population sequencing data
    • Vikas Bansal,
    • Olivier Harismendy,
    • Ryan Tewhey,
    • Sarah S. Murray,
    • Nicholas J. Schork,
    • Eric J. Topol,
    • and Kelly A. Frazer
    Genome Res. April 2010 20: 537-545; Published in Advance February 11, 2010, doi:10.1101/gr.100040.109
    ...to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for single nucleotide polymorphism (SNP) detection...
  8. Method: Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines
    • Eric A. Stone
    Genome Res. May 2012 22: 966-974; Published in Advance February 23, 2012, doi:10.1101/gr.129122.111
    ...Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, et al. 2009. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res 20: 273...
  9. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ...nucleotide polymorphisms (SNPs).View larger version: In this window In a new window Figure 1. Methods to detect -wide 5mC. DNAm can be detected through enrichment, bisulfite conversion, enzymatic modification, or single-molecule approaches. (A) Enrichment methods use restriction enzymes...
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  10. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...14 putative pathogenic SNVs and indels, uncovered newly identified SINE-R/VNTR/Alu elements affecting the APC gene in two familial adenomatous polyposis patients, and demonstrated the utility of off-target reads from adaptive sampling for SNP genotyping, enabling polygenic risk score calculations...
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