Searching journal content for articles similar to Pelizzola et al. 18 (10): 1652.

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Method: Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
- Mark D. Robinson,
- Clare Stirzaker,
- Aaron L. Statham,
- Marcel W. Coolen,
- Jenny Z. Song,
- Shalima S. Nair,
- Dario Strbenac,
- Terence P. Speed,
- and Susan J. Clark
Genome Res. December 2010 20: 1719-1729; Published in Advance November 2, 2010, doi:10.1101/gr.110601.110
...noted that the observed CpG density bias is not unique to the Affymetrix platform, since unamplified MeDIP-enriched fully methylated DNA samples analyzed on a NimbleGen platform (Gal-Yam et al. 2008) also exhibit attenuation over probes with a broad range of GC contents (Supplemental Fig. 6). Since some...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...imprinting, and tissue-specific gene expression. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA methylomes. This includes one of the most widely applied technologies for measuring DNA methylation: methylated DNA immunoprecipitation followed...
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Method: Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
- Michael Stevens,
- Jeffrey B. Cheng,
- Daofeng Li,
- Mingchao Xie,
- Chibo Hong,
- Cécile L. Maire,
- Keith L. Ligon,
- Martin Hirst,
- Marco A. Marra,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1541-1553; Published in Advance June 26, 2013, doi:10.1101/gr.152231.112
...heuristics makes WGBS seem straightforward. Similarly, enrichment-based data are also derived from true methylation states. However, current analytical methods for enrichment-based data usually calculate enrichment scores that are indicative of regional DNA methylation levels corrected by local Cp...
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Method: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
- Lukas Chavez,
- Justyna Jozefczuk,
- Christina Grimm,
- Jörn Dietrich,
- Bernd Timmermann,
- Hans Lehrach,
- Ralf Herwig,
- and James Adjaye
Genome Res. October 2010 20: 1441-1450; Published in Advance August 27, 2010, doi:10.1101/gr.110114.110
...and Baylin 2007; Irizarry et al. 2009). Furthermore, distinct -wide methylation patterns distinguish different cell-types (Eckhardt et al. 2006; Rakyan et al. 2008). Sequencing-based DNA methylation data are an emerging technology for analyzing epigenetic modifications (Laird 2010). Methylated DNA...
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Method: Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15
- Andrew J. Sharp,
- Eugenia Migliavacca,
- Yann Dupre,
- Elisavet Stathaki,
- Mohammad Reza Sailani,
- Alessandra Baumer,
- Albert Schinzel,
- Deborah J. Mackay,
- David O. Robinson,
- Gilda Cobellis,
- Luigi Cobellis,
- Han G. Brunner,
- Bernhard Steiner,
- and Stylianos E. Antonarakis
Genome Res. September 2010 20: 1271-1278; Published in Advance July 14, 2010, doi:10.1101/gr.108597.110
...disomy (UPD) provides a system that allows the two parental chromosomes to be studied independently. We profiled the paternal and maternal methylation on chromosome 15 using immunoprecipitation of methylated DNA and hybridization to tiling oligonucleotide arrays. Comparison of six individuals...
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Methods: Genome-wide screen of promoter methylation identifies novel markers in melanoma
- Yasuo Koga,
- Mattia Pelizzola,
- Elaine Cheng,
- Michael Krauthammer,
- Mario Sznol,
- Stephan Ariyan,
- Deepak Narayan,
- Annette M. Molinaro,
- Ruth Halaban,
- and Sherman M. Weissman
Genome Res. August 2009 19: 1462-1470; Published in Advance June 2, 2009, doi:10.1101/gr.091447.109
...of -wide promoter methylation We performed comprehensive DNA methylation profiling of gene promoters in normal newborn and adult melanocytes and eight melanoma cell strains (Table 1). DNAmethylation was determined using MeDIP (Weber et al. 2005) followed by hybridization to NimbleGen tiling microarray...

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