ArticleNature methods2014
Multiscale representation of genomic signals.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- Evaluating ensemble learning approaches for horizontal gene transfer detection.Scientific reports · 2026Article
- Genome-wide profiling of DNA repair proteins in single cells.Nature communications · 2024Article
- Computational Methods for Single-cell DNA Methylome Analysis.Genomics, proteomics & bioinformatics · 2023Review
- XCVATR: detection and characterization of variant impact on the Embeddings of single -cell and bulk RNA-sequencing samples.BMC genomics · 2022Article
- Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.Microbiome · 2022Article
- EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements.Bioinformatics (Oxford, England) · 2020Article
- Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis.Nature microbiology · 2020Article
- The DNA-binding protein HTa fromeLife · 2019Article
- Colocalization analyses of genomic elements: approaches, recommendations and challenges.Bioinformatics (Oxford, England) · 2019Article
- Selection-Corrected Statistical Inference for Region Detection With High-Throughput Assays.Journal of the American Statistical Association · 2019Article
- DNA methylation loss in late-replicating domains is linked to mitotic cell division.Nature genetics · 2018Article
- Network assessment of demethylation treatment in melanoma: Differential transcriptome-methylome and antigen profile signatures.PloS one · 2018Article
- MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain.PLoS genetics · 2017Article
- Multi-scale chromatin state annotation using a hierarchical hidden Markov model.Nature communications · 2017Article
- Precision medicine driven by cancer systems biology.Cancer metastasis reviews · 2017Article
- Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions.Biophysical journal · 2017Article
- Article
- DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks.BMC bioinformatics · 2016Article
- FocalScan: Scanning for altered genes in cancer based on coordinated DNA and RNA change.Nucleic acids research · 2016Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Genomic information is encoded on a wide range of distance scales, ranging from tens of bases to megabases. We developed a multiscale framework to analyze and visualize the information content of genomic signals. Different types of signals, such as G+C content or DNA methylation, are characterized by distinct patterns of signal enrichment or depletion across scales spanning several orders of magnitude. These patterns are associated with a variety of genomic annotations. By integrating the information across all scales, we demonstrated improved prediction of gene expression from polymerase II chromatin immunoprecipitation sequencing (ChIP-seq) measurements, and we observed that gene expression differences in colorectal cancer are related to methylation patterns that extend beyond the single-gene scale. Our software is available at https://github.com/tknijnen/msr/.
Indexed as
Identifiers
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.