Contact and support
Need help, have a question, or want to contact the ResearchHub team?
© 2026 ResearchHub. Built for responsible scholarly connection.
Privacy-aware community infrastructureResearch graph
References from Computational challenges in detection of cancer using cell-free DNA methylation. Local targets link to admitted publications; unresolved targets remain external evidence.
Disease prediction by cell-free DNA methylation
10.1093/bib/bby029 · 2019 · External reference
Finding new cancer epigenetic and genetic biomarkers from cell-free DNA by combining SALP-seq and machine learning: Esophageal cancer as an example
10.1101/2020.01.18.911172 · 2020 · External reference
Techniques of using circulating tumor DNA as a liquid biopsy component in cancer management, Computational and Structural
2018 · External reference
Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease
10.1038/s41467-018-07466-6 · 2018 · External reference
10.1039/c9an00935c
10.1039/c9an00935c · External reference
10.3390/cancers11060805
10.3390/cancers11060805 · External reference
Methods for genome-wide DNA methylation analysis in human cancer
10.1093/bfgp/elw010 · 2016 · External reference
Methylation of cell-free circulating DNA in the diagnosis of cancer
10.3389/fmolb.2015.00013 · 2015 · External reference
Cell-Free DNA: Hope and Potential Application in Cancer
2021 · External reference
Grail and the quest for earlier multi-cancer detection
2018 · External reference
10.3390/cancers11111741
10.3390/cancers11111741 · External reference
10.1111/brv.12413
10.1111/brv.12413 · External reference
10.3390/ijms21218062
10.3390/ijms21218062 · External reference
Characterization of Cell Free Plasma Methyl-DNA From Xenografted Tumors to Guide the Selection of Diagnostic Markers for Early-Stage Cancers
2021 · External reference
10.3390/cancers13040728
10.3390/cancers13040728 · External reference
10.1093/bioinformatics/btaa999
10.1093/bioinformatics/btaa999 · External reference
10.1016/j.bdq.2019.100087
10.1016/j.bdq.2019.100087 · External reference
Kinetics of circulating cell-free DNA for biomedical applications: Critical appraisal of the literature
10.4155/fsoa-2017-0140 · 2018 · External reference
10.3390/biom10121677
10.3390/biom10121677 · External reference
DNA methylation data by sequencing: Experimental approaches and recommendations for tools and pipelines for data analysis
10.1186/s13148-019-0795-x · 2019 · External reference
DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells
10.1093/nar/gkz717 · 2019 · External reference
Absolute quantification of DNA methylation using microfluidic chip-based digital PCR
10.1016/j.bios.2017.05.021 · 2017 · External reference
10.1038/s41598-018-19655-w
10.1038/s41598-018-19655-w · External reference
Circulating cell-free DNA from plasma undergoes less fragmentation during bisulfite treatment than genomic DNA due to low molecular weight
10.1371/journal.pone.0224338 · 2019 · External reference
10.1007/978-1-4939-7774-1_17
10.1007/978-1-4939-7774-1_17 · External reference
10.1016/j.canlet.2012.10.040
10.1016/j.canlet.2012.10.040 · External reference
10.1101/gr.232587.117
10.1101/gr.232587.117 · External reference
10.1016/j.gde.2017.01.017
10.1016/j.gde.2017.01.017 · External reference
10.1038/cr.2015.126
10.1038/cr.2015.126 · External reference
Detection of Colorectal Cancer in Circulating Cell-Free DNA by Methylated CpG Tandem Amplification and Sequencing
10.1373/clinchem.2019.301804 · 2019 · External reference
10.1111/nph.15388
10.1111/nph.15388 · External reference
cfNOMe —A single assay for comprehensive epigenetic analyses of cell-free DNA
10.1186/s13073-020-00750-5 · 2020 · External reference
Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome
2017 · External reference
Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21
10.1038/nm.2312 · 2011 · External reference
Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA
10.1038/s41596-019-0202-2 · 2019 · External reference
10.1038/nprot.2012.012
10.1038/nprot.2012.012 · External reference
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
10.4161/epi.6.1.13313 · 2011 · External reference
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
10.1038/nbt1414 · 2008 · External reference
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
10.1101/gr.110114.110 · 2010 · External reference
10.1126/science.1170116
10.1126/science.1170116 · External reference
10.1126/science.1210944
10.1126/science.1210944 · External reference
10.1038/nchem.2064
10.1038/nchem.2064 · External reference
10.1016/j.cancergen.2015.02.009
10.1016/j.cancergen.2015.02.009 · External reference
10.1038/cr.2017.121
10.1038/cr.2017.121 · External reference
10.1136/gutjnl-2019-318882
10.1136/gutjnl-2019-318882 · External reference
Circulating tumor DNA 5-hydroxymethylcytosine as a novel diagnostic biomarker for esophageal cancer
10.1038/s41422-018-0014-x · 2018 · External reference
10.1126/science.1220671
10.1126/science.1220671 · External reference
10.1016/j.cell.2012.04.027
10.1016/j.cell.2012.04.027 · External reference
10.1021/acsnano.8b03023
10.1021/acsnano.8b03023 · External reference
Pilot study demonstrating changes in DNA hydroxymethylation enable detection of multiple cancers in plasma cell-free DNA, Preprint
10.1101/2020.01.22.20018382 · 2020 · External reference
In Vitro diagnosis of DNA methylation biomarkers with digital PCR in breast tumors
10.1039/c8an00205c · 2018 · External reference
10.1158/1541-7786.mcr-16-0044
10.1158/1541-7786.mcr-16-0044 · External reference
BEAMing Up Personalized Medicine: Mutation Detection in Blood
10.1158/1078-0432.ccr-12-0871 · 2012 · External reference
Digital Droplet PCR for Monitoring Tissue-Specific Cell Death Using DNA Methylation Patterns of Circulating Cell-Free DNA
10.1002/cpmb.90 · 2019 · External reference
Levels of circulating insulin cell-free DNA in women with polycystic ovary syndrome – a longitudinal cohort study
10.1186/s12958-019-0478-7 · 2019 · External reference
10.1042/bsr20181170
10.1042/bsr20181170 · External reference
10.1016/j.jviromet.2014.02.020
10.1016/j.jviromet.2014.02.020 · External reference
ddpcRquant: Threshold determination for single channel droplet digital PCR experiments
10.1007/s00216-015-8773-4 · 2015 · External reference
10.12688/f1000research.9022.1
10.12688/f1000research.9022.1 · External reference
10.1093/bioinformatics/btx308
10.1093/bioinformatics/btx308 · External reference
ddPCRclust: An R package and Shiny app for automated analysis of multiplexed ddPCR data
10.1093/bioinformatics/bty136 · 2018 · External reference
Multiplex quantification of four DNA targets in one reaction with Bio-Rad droplet digital PCR system for GMO detection
10.1038/srep35451 · 2016 · External reference
Circulating cell-free DNA-based epigenetic assay can detect early breast cancer
10.1186/s13058-016-0788-z · 2016 · External reference
10.1016/j.ygyno.2010.11.018
10.1016/j.ygyno.2010.11.018 · External reference
Rapid quantification of DNA methylation by measuring relative peak heights in direct bisulfite-PCR sequencing traces
10.1038/labinvest.2009.132 · 2010 · External reference
10.1016/s1471-4914(02)02355-9
10.1016/s1471-4914(02)02355-9 · External reference
Optimizing methodologies for PCR-based DNA methylation analysis
10.2144/000114087 · 2013 · External reference
The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
10.1373/clinchem.2008.112797 · 2009 · External reference
Pitfalls of Quantitative Real-Time Reverse-Transcription Polymerase Chain Reaction
2004 · External reference
An overview of technical considerations when using quantitative real-time PCR analysis of gene expression in human exercise research
10.1371/journal.pone.0196438 · 2018 · External reference
Normalization of real-time quantitative reverse transcription-PCR data: A model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
10.1158/0008-5472.can-04-0496 · 2004 · External reference
Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper–Excel-based tool using pair-wise correlations
10.1023/b:bile.0000019559.84305.47 · 2004 · External reference
10.1186/gb-2002-3-7-research0034 · Admitted local publication
miRDeepFinder: A miRNA analysis tool for deep sequencing of plant small RNAs
10.1007/s11103-012-9885-2 · 2012 · External reference
ctDNA Detection in Microfluidic Platform: A Promising Biomarker for Personalized Cancer Chemotherapy
10.1155/2020/8353674 · 2020 · External reference
Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing
10.1373/clinchem.2012.196014 · 2013 · External reference
10.1158/1078-0432.ccr-13-3063
10.1158/1078-0432.ccr-13-3063 · External reference
10.1002/ijc.29265
10.1002/ijc.29265 · External reference
Next-generation sequencing in liquid biopsy: Cancer screening and early detection
10.1186/s40246-019-0220-8 · 2019 · External reference
10.1038/s41551-021-00746-5
10.1038/s41551-021-00746-5 · External reference
Field guide to next-generation DNA sequencers: FIELD GUIDE TO NEXT-GEN SEQUENCERS
10.1111/j.1755-0998.2011.03024.x · 2011 · External reference
Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors: Challenges
2020 · External reference
Unresolved reference
External reference
NCBI GEO: Archive for functional genomics data sets—update
10.1093/nar/gks1193 · 2013 · External reference
10.2217/epi.15.114
10.2217/epi.15.114 · External reference
10.1016/j.tig.2013.11.004
10.1016/j.tig.2013.11.004 · External reference
Review of processing and analysis methods for DNA methylation array data
10.1038/bjc.2013.496 · 2013 · External reference
10.1038/nrg2825
10.1038/nrg2825 · External reference
A Toolkit for Quality Control of Next Generation Sequencing Data
10.1371/journal.pone.0030619 · 2012 · External reference
ClinQC: A tool for quality control and cleaning of Sanger and NGS data in clinical research
10.1186/s12859-016-0915-y · 2016 · External reference
10.1093/nar/gky1095
10.1093/nar/gky1095 · External reference
10.1093/nar/gkz830
10.1093/nar/gkz830 · External reference
Methylation plotter: A web tool for dynamic visualization of DNA methylation data
10.1186/1751-0473-9-11 · 2014 · External reference
10.1093/bib/bbs017
10.1093/bib/bbs017 · External reference
WBSA: Web Service for Bisulfite Sequencing Data Analysis
10.1371/journal.pone.0086707 · 2014 · External reference
10.12688/f1000research.7210.1
10.12688/f1000research.7210.1 · External reference
10.1016/j.cell.2010.04.033
10.1016/j.cell.2010.04.033 · External reference
10.3390/diagnostics8020031
10.3390/diagnostics8020031 · External reference
Liquid biopsy and tumor heterogeneity in metastatic solid tumors: The potentiality of blood samples
10.1186/s13046-020-01601-2 · 2020 · External reference
10.1007/s00109-020-01874-2
10.1007/s00109-020-01874-2 · External reference
10.1016/j.gpb.2018.07.002
10.1016/j.gpb.2018.07.002 · External reference
Quantitative comparison of within-sample heterogeneity scores for DNA methylation data
10.1093/nar/gkaa120 · 2020 · External reference
An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line
10.7150/jca.15423 · 2016 · External reference
10.1136/gutjnl-2016-313372
10.1136/gutjnl-2016-313372 · External reference
10.1016/j.molonc.2014.02.005
10.1016/j.molonc.2014.02.005 · External reference
Cell-free DNA as a diagnostic marker for cancer: Current insights
10.2147/ott.s100901 · 2016 · External reference
10.1038/cr.2017.106
10.1038/cr.2017.106 · External reference
Hydroxymethylation and tumors: Can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment?
10.1186/s40246-020-00265-5 · 2020 · External reference
10.1016/j.gpb.2018.06.002
10.1016/j.gpb.2018.06.002 · External reference
5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic and predictive biomarkers for coronary artery disease
10.1186/s13148-020-0810-2 · 2020 · External reference
Liver- and Colon-Specific DNA Methylation Markers in Plasma for Investigation of Colorectal Cancers with or without Liver Metastases
10.1373/clinchem.2018.290304 · 2018 · External reference
10.1093/hmg/ddx275
10.1093/hmg/ddx275 · External reference
10.2217/epi-2016-0153
10.2217/epi-2016-0153 · External reference
10.1186/s12859-017-1511-5
10.1186/s12859-017-1511-5 · External reference
10.1038/nmeth.3337
10.1038/nmeth.3337 · External reference
Cell Mix: A comprehensive toolbox for gene expression deconvolution
10.1093/bioinformatics/btt351 · 2013 · External reference
CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data
10.1371/journal.pcbi.1007510 · 2019 · External reference
TOAST: Improving reference-free cell composition estimation by cross-cell type differential analysis
10.1186/s13059-019-1778-0 · 2019 · External reference
10.1093/bioinformatics/btu029
10.1093/bioinformatics/btu029 · External reference
Epigenome-wide association studies without the need for cell-type composition
10.1038/nmeth.2815 · 2014 · External reference
Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies
10.1038/nmeth.3809 · 2016 · External reference
10.1371/journal.pgen.0030161
10.1371/journal.pgen.0030161 · External reference
10.1038/s41586-018-0703-0
10.1038/s41586-018-0703-0 · External reference
10.1186/s12885-019-6003-8
10.1186/s12885-019-6003-8 · External reference
10.1126/scitranslmed.aax7533
10.1126/scitranslmed.aax7533 · External reference
Circulating cell-free DNA in breast cancer: Size profiling, levels, and methylation patterns lead to prognostic and predictive classifiers
10.1038/s41388-018-0660-y · 2019 · External reference
10.1016/j.annonc.2020.02.011
10.1016/j.annonc.2020.02.011 · External reference
10.1609/aaai.v24i1.7682
10.1609/aaai.v24i1.7682 · External reference
An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping
10.1186/s12859-018-2593-4 · 2019 · External reference
10.1186/1471-2105-10-232
10.1186/1471-2105-10-232 · External reference
10.1093/bioinformatics/btr167
10.1093/bioinformatics/btr167 · External reference
10.1186/1471-2164-14-774
10.1186/1471-2164-14-774 · External reference
Unresolved reference
External reference
BSmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
10.1186/gb-2012-13-10-r83 · 2012 · External reference
MethylCoder: Software pipeline for bisulfite-treated sequences
10.1093/bioinformatics/btr394 · 2011 · External reference
Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
10.1371/journal.pcbi.1000502 · 2009 · External reference
10.1093/bioinformatics/btq057
10.1093/bioinformatics/btq057 · External reference
BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads
10.1093/bioinformatics/bts264 · 2012 · External reference
10.1145/2382936.2382938
10.1145/2382936.2382938 · External reference
The GEM mapper: Fast, accurate and versatile alignment by filtration
10.1038/nmeth.2221 · 2012 · External reference
A mostly traditional approach improves alignment of bisulfite-converted DNA
10.1093/nar/gks275 · 2012 · External reference
Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit
10.1016/j.patter.2020.100127 · 2020 · External reference
TAMeBS: A sensitive bisulfite-sequencing read mapping tool for DNA methylation analysis, in
2014 · External reference
MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
10.1101/gr.080721.108 · 2008 · External reference
Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers
10.1186/2047-217x-1-3 · 2012 · External reference
10.5772/61207
10.5772/61207 · External reference
MethylAction: Detecting differentially methylated regions that distinguish biological subtypes
10.1093/nar/gkv1461 · 2016 · External reference
RnBeads 2.0: Comprehensive analysis of DNA methylation data
10.1186/s13059-019-1664-9 · 2019 · External reference
De novo identification of differentially methylated regions in the human genome
10.1186/1756-8935-8-6 · 2015 · External reference
DMRcaller: A versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts
2018 · External reference
methylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles
10.1186/gb-2012-13-10-r87 · 2012 · External reference
10.1093/bioinformatics/btu339
10.1093/bioinformatics/btu339 · External reference
10.1007/s40484-019-0183-8
10.1007/s40484-019-0183-8 · External reference
msgbsr: An r package for analysing methylation-sensitive restriction enzyme sequencing data
10.1038/s41598-018-19655-w · 2018 · External reference
10.1093/nar/gku457
10.1093/nar/gku457 · External reference
