Searching journal content for articles similar to Peiffer et al. 16 (9): 1136.

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  1. Method: Whole-genome bisulfite sequencing with improved accuracy and cost
    • Masako Suzuki,
    • Will Liao,
    • Frank Wos,
    • Andrew D. Johnston,
    • Justin DeGrazia,
    • Jennifer Ishii,
    • Toby Bloom,
    • Michael C. Zody,
    • Soren Germer,
    • and John M. Greally
    Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
    ...for designs targeting the same genomic loci), with the expanded Infinium MethylationEPIC microarray representing a higher proportion of ATAC-seq peaks.We noted the puzzling finding that lambda DNA appeared to have some unconverted cytosines indicating DNA methylation, which should not be occurring...
  2. Methods: PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    • Kai Wang,
    • Mingyao Li,
    • Dexter Hadley,
    • Rui Liu,
    • Joseph Glessner,
    • Struan F.A. Grant,
    • Hakon Hakonarson,
    • and Maja Bucan
    Genome Res. November 2007 17: 1665-1674; Published in Advance October 5, 2007, doi:10.1101/gr.6861907
    ...Chip ( Gunderson et al. 2005 ; Steemers and Gunderson 2007 ), assays more than half a million SNPs in parallel (median SNP distance ∼3 kb), permitting kilobase-resolution detection of CNVs. Several technical advantages in the Illumina Infinium platform make it highly suitable for high-resolution CNV detection...
  3. Research: Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events
    • Jinfeng Liu,
    • William Lee,
    • Zhaoshi Jiang,
    • Zhongqiang Chen,
    • Suchit Jhunjhunwala,
    • Peter M. Haverty,
    • Florian Gnad,
    • Yinghui Guan,
    • Houston N. Gilbert,
    • Jeremy Stinson,
    • Christiaan Klijn,
    • Joseph Guillory,
    • Deepali Bhatt,
    • Steffan Vartanian,
    • Kimberly Walter,
    • Jocelyn Chan,
    • Thomas Holcomb,
    • Peter Dijkgraaf,
    • Stephanie Johnson,
    • Julie Koeman,
    • John D. Minna,
    • Adi F. Gazdar,
    • Howard M. Stern,
    • Klaus P. Hoeflich,
    • Thomas D. Wu,
    • Jeff Settleman,
    • Frederic J. de Sauvage,
    • Robert C. Gentleman,
    • Richard M. Neve,
    • David Stokoe,
    • Zora Modrusan,
    • Somasekar Seshagiri,
    • David S. Shames,
    • and Zemin Zhang
    Genome Res. December 2012 22: 2315-2327; Published in Advance October 2, 2012, doi:10.1101/gr.140988.112
    ...is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole-genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and three lung tumor/normal pairs. Overall, our data show that cell line models exhibit...
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  4. Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
    • Franck Court,
    • Chiharu Tayama,
    • Valeria Romanelli,
    • Alex Martin-Trujillo,
    • Isabel Iglesias-Platas,
    • Kohji Okamura,
    • Naoko Sugahara,
    • Carlos Simón,
    • Harry Moore,
    • Julie V. Harness,
    • Hans Keirstead,
    • Jose Vicente Sanchez-Mut,
    • Eisuke Kaneki,
    • Pablo Lapunzina,
    • Hidenobu Soejima,
    • Norio Wake,
    • Manel Esteller,
    • Tsutomu Ogata,
    • Kenichiro Hata,
    • Kazuhiko Nakabayashi,
    • and David Monk
    Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
    ...Characterization of parent-of-origin methylation profiles in human tissues using high-resolution approaches We combined whole- bisulfite sequencing with Illumina Infinium HumanMethylation 450K BeadChip arrays to generate methylation profiles. To validate this approach, we compared the DNAmethylation profiles...
  5. Research: Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
    • Pedro G. Ferreira,
    • Pedro Jares,
    • Daniel Rico,
    • Gonzalo Gómez-López,
    • Alejandra Martínez-Trillos,
    • Neus Villamor,
    • Simone Ecker,
    • Abel González-Pérez,
    • David G. Knowles,
    • Jean Monlong,
    • Rory Johnson,
    • Victor Quesada,
    • Sarah Djebali,
    • Panagiotis Papasaikas,
    • Mónica López-Guerra,
    • Dolors Colomer,
    • Cristina Royo,
    • Maite Cazorla,
    • Magda Pinyol,
    • Guillem Clot,
    • Marta Aymerich,
    • Maria Rozman,
    • Marta Kulis,
    • David Tamborero,
    • Anaïs Gouin,
    • Julie Blanc,
    • Marta Gut,
    • Ivo Gut,
    • Xose S. Puente,
    • David G. Pisano,
    • José Ignacio Martin-Subero,
    • Nuria López-Bigas,
    • Armando López-Guillermo,
    • Alfonso Valencia,
    • Carlos López-Otín,
    • Elías Campo,
    • and Roderic Guigó
    Genome Res. February 2014 24: 212-226; Published in Advance November 21, 2013, doi:10.1101/gr.152132.112
    ...behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from...
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