ArticleCell reports2015
Differential DNA Methylation Analysis without a Reference Genome.
Article in Cell reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 37 citations in OpenAlex.
- Epigenetic Signatures of Ageing in Asian Elephants Revealed by Reduced Representation Bisulphite Sequencing.Evolutionary applications · 2026Article
- Functional genomics in Spiralia.Briefings in functional genomics · 2023Article
- Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species.Nature communications · 2023Article
- Integrated Multiomic Profiling Identifies the Epigenetic Regulator PRC2 as a Therapeutic Target to Counteract Leukemia Immune Escape and Relapse.Cancer discovery · 2022Article
- Gene expression and epigenetic responses of the marine Cladoceran,Ecology and evolution · 2021Article
- Ten Years of EWAS.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- Acute social isolation alters neurogenomic state in songbird forebrain.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A Global Gene Body Methylation Measure Correlates Independently with Overall Survival in Solid Cancer Types.Cancers · 2020Article
- DNA methylation QTL analysis identifies new regulators of human longevity.Human molecular genetics · 2020Article
- MUW researcher of the month.Wiener klinische Wochenschrift · 2019Article
- The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease.Cancer cell · 2019Article
- Profiling DNA methylation patterns of zebrafish liver associated with parental high dietary arachidonic acid.PloS one · 2019Article
- Epigenetic Changes Associated with Early Life Experiences: Saliva, A Biospecimen for DNA Methylation Signatures.Current genomics · 2018Article
- The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space.Nature medicine · 2018Article
- Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species.Epigenetics & chromatin · 2018Article
- Parental micronutrient deficiency distorts liver DNA methylation and expression of lipid genes associated with a fatty-liver-like phenotype in offspring.Scientific reports · 2018Article
- Maximizing ecological and evolutionary insight in bisulfite sequencing data sets.Nature ecology & evolution · 2017Review
- DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma.Nature medicine · 2017Article
- Acute and chronic gregarisation are associated with distinct DNA methylation fingerprints in desert locusts.Scientific reports · 2016Article
- Integrating Epigenomics into the Understanding of Biomedical Insight.Bioinformatics and biology insights · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
Abstract
Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish). Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org). The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.