BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach
暂无分享,去创建一个
Andrea Riebler | Mark D Robinson | Clare Stirzaker | Mirco Menigatti | Jenny Z Song | Aaron L Statham | Nadiya Mahmud | Charles A Mein | Susan J Clark | M. Robinson | A. Riebler | S. Clark | C. Mein | C. Stirzaker | A. Statham | Jenny Song | M. Menigatti | Nadiya Mahmud
[1] Huidong Shi,et al. Analyzing the cancer methylome through targeted bisulfite sequencing. , 2013, Cancer letters.
[2] Gerben Menschaert,et al. Quality Evaluation of Methyl Binding Domain Based Kits for Enrichment DNA-Methylation Sequencing , 2013, PloS one.
[3] M. Robinson,et al. A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.
[4] Lee E. Edsall,et al. Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.
[5] H. Bayley,et al. Continuous base identification for single-molecule nanopore DNA sequencing. , 2009, Nature nanotechnology.
[6] Susan J Clark,et al. DNA methylation and gene silencing in cancer: which is the guilty party? , 2002, Oncogene.
[7] G. Tsujimoto,et al. Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing , 2010, BMC Genomics.
[8] David Serre,et al. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome , 2009, Nucleic acids research.
[9] P. Laird. Principles and challenges of genome-wide DNA methylation analysis , 2010, Nature Reviews Genetics.
[10] Zachary D. Smith,et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution , 2010, Nature Methods.
[11] Rafael A. Irizarry,et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays , 2014, Bioinform..
[12] Boris Lenhard,et al. Genome-wide DNA methylation profiling of non-small cell lung carcinomas , 2012, Epigenetics & Chromatin.
[13] Richard A. Stein,et al. Epigenetics--the link between infectious diseases and cancer. , 2011, JAMA.
[14] Lu Zhang,et al. Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. , 2011, Genome research.
[15] Dario Strbenac,et al. Copy-number-aware differential analysis of quantitative DNA sequencing data , 2012, Genome research.
[16] Dario Strbenac,et al. Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias , 2011, Epigenetics.
[17] A. Feinberg,et al. Increased methylation variation in epigenetic domains across cancer types , 2011, Nature Genetics.
[18] Nengjun Yi,et al. Statistical Quantification of Methylation Levels by Next-Generation Sequencing , 2011, PloS one.
[19] Stephan Beck,et al. Methylome analysis using MeDIP-seq with low DNA concentrations , 2012, Nature Protocols.
[20] Dario Strbenac,et al. Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. , 2010, Genome research.
[21] Natalie Jäger,et al. Genome-wide mapping of DNA methylation : a quantitative technology comparison , 2012 .
[22] P. Deloukas,et al. A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip® for Methylome Profiling , 2012, PloS one.
[23] Joseph K. Pickrell,et al. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions , 2011, Bioinform..
[24] Margaret R. Karagas,et al. Copy number variation has little impact on bead-array-based measures of DNA methylation , 2009, Bioinform..
[25] K. Hansen,et al. Removing technical variability in RNA-seq data using conditional quantile normalization , 2012, Biostatistics.
[26] Milton Abramowitz,et al. Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables , 1964 .
[27] Jeffrey B. Cheng,et al. Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods , 2013, RECOMB.
[28] Peter A. Jones,et al. A decade of exploring the cancer epigenome — biological and translational implications , 2011, Nature Reviews Cancer.
[29] Natalie Jäger,et al. Genome-wide mapping of DNA methylation: a quantitative technology comparison , 2010, Nature Biotechnology.
[30] S. Swamy,et al. PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data , 2009, Biostatistics.
[31] R. Lister,et al. Finding the fifth base: genome-wide sequencing of cytosine methylation. , 2009, Genome research.
[32] Ralf Herwig,et al. Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. , 2010, Genome research.
[33] Gavin D. Meredith,et al. High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology , 2011, PloS one.
[34] A. Urban,et al. MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. , 2008, Genome research.
[35] Howard Slomko,et al. Minireview: Epigenetics of obesity and diabetes in humans. , 2012, Endocrinology.
[36] K. Gunderson,et al. High density DNA methylation array with single CpG site resolution. , 2011, Genomics.
[37] Tyson A. Clark,et al. Direct detection of DNA methylation during single-molecule, real-time sequencing , 2010, Nature Methods.
[38] S. Clark,et al. High sensitivity mapping of methylated cytosines. , 1994, Nucleic acids research.
[39] David C. Schmittlein,et al. Technical Note---Why Does the NBD Model Work? Robustness in Representing Product Purchases, Brand Purchases and Imperfectly Recorded Purchases , 1985 .
[40] Trupti Joshi,et al. Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing , 2011, Nucleic acids research.
[41] A. Gnirke,et al. Charting a dynamic DNA methylation landscape of the human genome , 2013, Nature.
[42] M. Kerick,et al. Generation and Analysis of Genome-Wide DNA Methylation Maps , 2012 .
[43] M. Abramowitz,et al. Handbook of Mathematical Functions With Formulas, Graphs and Mathematical Tables (National Bureau of Standards Applied Mathematics Series No. 55) , 1965 .
[44] Peter A. Jones. Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.
[45] R. Durbin,et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis , 2008, Nature Biotechnology.
[46] Peter A. Jones,et al. The Epigenomics of Cancer , 2007, Cell.
[47] Peter S. Fader,et al. A note on modelling underreported Poisson counts , 2000 .
[48] M. Esteller. Cancer epigenomics: DNA methylomes and histone-modification maps , 2007, Nature Reviews Genetics.
[49] Daniel Adkins,et al. MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case--control samples. , 2012, Epigenomics.
[50] T. Speed,et al. Protocol matters: which methylome are you actually studying? , 2010, Epigenomics.
[51] Rainer Winkelmann,et al. Markov chain Monte Carlo analysis of underreported count data with an application to worker absenteeism , 1996 .
[52] Leonhard Held,et al. Gaussian Markov Random Fields: Theory and Applications , 2005 .
[53] Dario Strbenac,et al. Repitools: an R package for the analysis of enrichment-based epigenomic data , 2010, Bioinform..