ArticleNature protocols2013
Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm.
Article in Nature protocols, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed.
- The double life of mammalian DNA replication origins.Genes & development · 2025Review
- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.PLoS computational biology · 2023Article
- Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing.Nature protocols · 2023Review
- OKseqHMM: a genome-wide replication fork directionality analysis toolkit.Nucleic acids research · 2023Article
- Genome-wide mapping of individual replication fork velocities using nanopore sequencing.Nature communications · 2022Article
- Organization of DNA Replication Origin Firing inGenes · 2021Article
- DNA molecular combing-based replication fork directionality profiling.Nucleic acids research · 2021Article
- Article
- FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing.Genome biology · 2020Article
- EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements.Bioinformatics (Oxford, England) · 2020Article
- On the Interplay of the DNA Replication Program and the Intra-S Phase Checkpoint Pathway.Genes · 2019Review
- Exon prediction based on multiscale products of a genomic-inspired multiscale bilateral filtering.PloS one · 2019Article
- Multifractal Desynchronization of the Cardiac Excitable Cell Network During Atrial Fibrillation. II. Modeling.Frontiers in physiology · 2019Article
- Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions.Nucleic acids research · 2018Article
- A journey through the microscopic ages of DNA replication.Protoplasma · 2017Review
- Multi-scale structural community organisation of the human genome.BMC bioinformatics · 2017Article
- Multifractal Desynchronization of the Cardiac Excitable Cell Network During Atrial Fibrillation. I. Multifractal Analysis of Clinical Data.Frontiers in physiology · 2017Article
- Replication landscape of the human genome.Nature communications · 2016Article
- Short Exon Detection via Wavelet Transform Modulus Maxima.PloS one · 2016Article
- Comparative Multifractal Analysis of Dynamic Infrared Thermograms and X-Ray Mammograms Enlightens Changes in the Environment of Malignant Tumors.Frontiers in physiology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this protocol, we describe the use of the LastWave open-source signal-processing command language (http://perso.ens-lyon.fr/benjamin.audit/LastWave/) for analyzing cellular DNA replication timing profiles. LastWave makes use of a multiscale, wavelet-based signal-processing algorithm that is based on a rigorous theoretical analysis linking timing profiles to fundamental features of the cell's DNA replication program, such as the average replication fork polarity and the difference between replication origin density and termination site density. We describe the flow of signal-processing operations to obtain interactive visual analyses of DNA replication timing profiles. We focus on procedures for exploring the space-scale map of apparent replication speeds to detect peaks in the replication timing profiles that represent preferential replication initiation zones, and for delimiting U-shaped domains in the replication timing profile. In comparison with the generally adopted approach that involves genome segmentation into regions of constant timing separated by timing transition regions, the present protocol enables the recognition of more complex patterns of the spatio-temporal replication program and has a broader range of applications. Completing the full procedure should not take more than 1 h, although learning the basics of the program can take a few hours and achieving full proficiency in the use of the software may take days.
Indexed as
Identifiers
23237832What 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.