Table of Contents:

Cell-Free DNA General Background

• Pan et al "Brain Tumor Mutations Detected in Cerebral Spinal Fluid"
• Schilling and Rehli "Global, comparative analysis of tissue-specific promoter CpG methylation"
• Jahr et al "DNA Fragments in the Blood Plasma of Cancer Patients: Quantitations and Evidence for Their Origin from Apoptotic and Necrotic Cells"
• Van der Vaart and Pretorius "Circulating DNAIts Origin and Fluctuation"
• Stroun et al "The Origin and Mechanism of Circulating DNA"
• Gravina et al "The dark side of circulating nucleic acids"
• Sun et al "Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments"
• Wyatt et al "Concordance of Circulating Tumor DNA and MatchedMetastatic Tissue Biopsy in Prostate Cancer"
• Ma et al "Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns"

Cell-Free DNA and Methylation

• Lehman-Werman et al "Identification of tissue-specific cell death using methylation patterns of circulating DNA"
• Synder et al "Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin"
• Jensen et al "Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains"
• Guo et al "Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA"
• Seoighe et al (response to Guo et al)"DNA methylation haplotypes as cancer markers"
• Diep and Zhang (response to Seoighe et al) "Reply to ‘DNA methylation haplotypes as cancer markers'"

Methylation Biology

• Kessler et al "CpG methylation differences between neurons and glia are highly conserved from mouse to human"
• Luck et al "A Stochastic Model for the Formation of Spatial Methylation Patterns"
• Doherty and Couldrey "Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment"
• Intro methylation review: "DNA methylation: a form of epigenetic control of gene expression"
• Koch et al "Analysis of DNA methylation in cancer: location revisited"
• Smith and Meissner "DNA methylation: roles in mammalian development"

Non-CpG Methylation

• Xu and Corces "Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites "

Deconvolution algorithms

• Houseman et al "Reference-free deconvolution of DNA methylation data and mediation by cell composition effects"
• Rahmani et al "Sparse PCA Corrects for Cell-Type Heterogeneity in Epigenome-Wide Association Studies"
• Gond and Szustakowski "DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data"

WGBS Algorithms

• Ziller et al "Coverage recommendations for methylation analysis by whole genome bisulfite sequencing"
• Merkel et al "gemBS - high throughput processing for DNA methylation data from Bisulfite Sequencing "
• Lee et al "An integrative approach for efficient analysis of whole genome bisulfite sequencing data"
• Kunde-Ramamoorty et al "Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing"
• Xi and Li "BSMAP: whole genome bisulfite sequence MAPping program"
• Guo et al []"BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data"](https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-774)
• Krueger and Andrews "Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications"
• Feng et al "Disease prediction by cell-free DNA methylation"