Searching journal content for articles similar to Fakhrai-Rad et al. 14 (7): 1404.

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  1. Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
    • Bo Yan,
    • Duan Wang,
    • Romualdas Vaisvila,
    • Zhiyi Sun,
    • and Laurence Ettwiller
    Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
    ...reads) with high coverage (94% of the covered) and high sequence identity (2.21 mismatches per 100 kbp) (Fig. 6A), which was comparable to the performance of the assembler for single-end short read assembly using standard DNA-seq.View larger version: In this window In a new window Figure 6. Methyl-SNP...
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  2. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    ...be done with high-density SNP typing using microarrays (Gentalen and Chee 1999), which facilitates the completion of linkage analysis more rapidly than ever before. The reference sequence of the human and the variation database made “resequencing” approaches possible. Following this, the first decade...
  3. Method: Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair
    • Ryan J. McGinty,
    • Rachel G. Rubinstein,
    • Alexander J. Neil,
    • Margaret Dominska,
    • Denis Kiktev,
    • Thomas D. Petes,
    • and Sergei M. Mirkin
    Genome Res. December 2017 27: 2072-2082; Published in Advance November 7, 2017, doi:10.1101/gr.228148.117
    ...orientation and requires mismatch repair. EMBO J 27: 2896–2906. ↵Lee JA, Carvalho CM, Lupski JR. 2007. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131: 1235–1247. ↵Lee JK, Choi YL, Kwon M, Park PJ. 2016. Mechanisms and consequences of cancer...
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  4. Resource: Genome-wide discovery of human splicing branchpoints
    • Tim R. Mercer,
    • Michael B. Clark,
    • Stacey B. Andersen,
    • Marion E. Brunck,
    • Wilfried Haerty,
    • Joanna Crawford,
    • Ryan J. Taft,
    • Lars K. Nielsen,
    • Marcel E. Dinger,
    • and John S. Mattick
    Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
    ...to the expected background rate of nucleotide substitution. This demonstrates enrichment for SNPs that maintain complementary or wobble binding between the B-box and U2 snRNA. U2 snRNA and B-box base-pairing nucleotide possibilities are indicated in the lower schematic. Branchpoint discovery Genome Research 297...
  5. Resource: VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
    • Daniel C. Koboldt,
    • Qunyuan Zhang,
    • David E. Larson,
    • Dong Shen,
    • Michael D. McLellan,
    • Ling Lin,
    • Christopher A. Miller,
    • Elaine R. Mardis,
    • Li Ding,
    • and Richard K. Wilson
    Genome Res. March 2012 22: 568-576; Published in Advance February 2, 2012, doi:10.1101/gr.129684.111
    ...data from high-density SNP array and WGS approaches. Our results demonstrate the accuracy of VarScan 2 for somatic mutation and CNA detection and enable a new survey of the genetic landscape in ovarian carcinoma. Results The VarScan 2 algorithm reads SAMtools pileup or mpileup output from tumor...
  6. Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
    • Peter A. Audano and
    • Christine R. Beck
    Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
    ...locus in the reference. (B) When a small polymorphism such as a SNP or indel is in the homologous region (red dot), the alignment score is penalized for the mismatching base. If the breakpoint is shifted so that the polymorphism falls inside the inserted sequence, the penalty is eliminated...
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  7. Research: Error-prone polymerase activity causes multinucleotide mutations in humans
    • Kelley Harris and
    • Rasmus Nielsen
    Genome Res. September 2014 24: 1445-1454; Published in Advance July 30, 2014, doi:10.1101/gr.170696.113
    .... However, it is interesting that Pol z appears to create the same mutation types in the human lineage that it creates in yeast with artificial excision repair deficiencies. We are hopeful that MNM can be understood more completely in the future by comparing perfect LD SNPs to de novo mutations from other...
  8. Method: DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly
    • Ilari Scheinin,
    • Daoud Sie,
    • Henrik Bengtsson,
    • Mark A. van de Wiel,
    • Adam B. Olshen,
    • Hinke F. van Thuijl,
    • Hendrik F. van Essen,
    • Paul P. Eijk,
    • François Rustenburg,
    • Gerrit A. Meijer,
    • Jaap C. Reijneveld,
    • Pieter Wesseling,
    • Daniel Pinkel,
    • Donna G. Albertson,
    • and Bauke Ylstra
    Genome Res. December 2014 24: 2022-2032; Published in Advance September 18, 2014, doi:10.1101/gr.175141.114
    ...). For > 20 yr, these alterations have been routinely detected first by -wide comparative genomichybridization (CGH) (Kallioniemi et al. 1992) and subsequently by array-based CGH (Snijders et al. 2001) or single nucleotide polymorphism (SNP) arrays (Ylstra et al. 2006). Nowwhole- sequencing (WGS) offers...
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  9. ARTICLE: Pattern of Sequence Variation Across 213 Environmental Response Genes
    • Robert J. Livingston,
    • Andrew von Niederhausern,
    • Anil G. Jegga,
    • Dana C. Crawford,
    • Christopher S. Carlson,
    • Mark J. Rieder,
    • Sivakumar Gowrisankar,
    • Bruce J. Aronow,
    • Robert B. Weiss,
    • and Deborah A. Nickerson
    Genome Res. October 2004 14: 1821-1831; Published in Advance September 13, 2004, doi:10.1101/gr.2730004
    ...the fidelity of DNA repair and increase the lifetime risk of developing cancer ( Alonso et al. 2001 ; Mathonnet et al. 2003 ; Buchholz et al. 2004 ). The first phase of the EGP is now complete, and herein we report the discovery of 23,443 SNPs in 213 candidate environmental response genes by systematically...
  10. Method: Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
    • Jamie K. Teer,
    • Lori L. Bonnycastle,
    • Peter S. Chines,
    • Nancy F. Hansen,
    • Natsuyo Aoyama,
    • Amy J. Swift,
    • Hatice Ozel Abaan,
    • Thomas J. Albert,
    • NISC Comparative Sequencing Program,
    • Elliott H. Margulies,
    • Eric D. Green,
    • Francis S. Collins,
    • James C. Mullikin,
    • and Leslie G. Biesecker
    Genome Res. October 2010 20: 1420-1431; Published in Advance September 1, 2010, doi:10.1101/gr.106716.110
    ...; of the heterozygous positions identified by each of the capture methods, >99.57% agreed with 1M SNP BeadChip, and >98.840% agreed with the whole-genome shotgun data. In addition, we successfully piloted the genomic enrichment of a set of 12 pooled samples via the MGS method using molecular bar codes. We find...
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