ReviewGigaScience2015
SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing.
Review in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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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
10 citing papers in PubMed, 16 citations in OpenAlex.
- Uncovering alterations in cancer epigenetics via trans-dimensional Markov chain Monte Carlo and hidden Markov models.Journal of the Royal Statistical Society. Series C, Applied statistics · 2026Article
- Coordinated Transcriptomic and Epigenetic Approach Reveals Molecular Features Underlying Natural Mating Ability in Captive Male Giant Pandas.Ecology and evolution · 2025Article
- Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline.Frontiers in plant science · 2021Review
- DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis.Clinical epigenetics · 2019Review
- CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.Bioinformatics (Oxford, England) · 2018Article
- Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Article
- Integrating DNA Methylation and Hydroxymethylation Data with the Mint Pipeline.Cancer research · 2017Article
- Profiling genome-wide DNA methylation.Epigenetics & chromatin · 2016Review
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA methylation has important roles in the regulation of gene expression and cellular specification. Reduced representation bisulfite sequencing (RRBS) has prevailed in methylation studies due to its cost-effectiveness and single-base resolution. The rapid accumulation of RRBS data demands well designed analytical tools.
findingsTo streamline the data processing of DNA methylation from multiple RRBS samples, we present a flexible pipeline named SMAP, whose features include: (i) handling of single-and/or paired-end diverse bisulfite sequencing data with reduced false-positive rates in differentially methylated regions; (ii) detection of allele-specific methylation events with improved algorithms; (iii) a built-in pipeline for detection of novel single nucleotide polymorphisms (SNPs); (iv) support of multiple user-defined restriction enzymes; (v) conduction of all methylation analyses in a single-step operation when well configured.
conclusionsSimulation and experimental data validated the high accuracy of SMAP for SNP detection and methylation identification. Most analyses required in methylation studies (such as estimation of methylation levels, differentially methylated cytosine groups, and allele-specific methylation regions) can be executed readily with SMAP. All raw data from diverse samples could be processed in parallel and 'packetized' streams. A simple user guide to the methylation applications is also provided.
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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.