ArticleGenome biology2009
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
- Tracing the evolution of sequencing into the era of genomic medicine.Nature reviews. Genetics · 2025Review
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- Review
- The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data.PeerJ · 2024Article
- INSnet: a method for detecting insertions based on deep learning network.BMC bioinformatics · 2023Article
- Article
- Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings.Frontiers in genetics · 2023Review
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
- Current status of structural variation studies in plants.Plant biotechnology journal · 2021Review
- Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers.BMC bioinformatics · 2021Article
- SIns: A Novel Insertion Detection Approach Based on Soft-Clipped Reads.Frontiers in genetics · 2021Article
- CNV-MEANN: A Neural Network and Mind Evolutionary Algorithm-Based Detection of Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2021Article
- Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing.BMC genetics · 2020Article
- CONY: A Bayesian procedure for detecting copy number variations from sequencing read depths.Scientific reports · 2020Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- Comparison of multiple algorithms to reliably detect structural variants in pears.BMC genomics · 2020Article
- Predicting Local Inversions Using Rectangle Clustering and Representative Rectangle Prediction.IEEE transactions on nanobioscience · 2019Article
- Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine.Science China. Life sciences · 2019Review
- Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota.BMC genomics · 2018Article
- MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples.Scientific reports · 2018Article
57 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Personal-genomics endeavors, such as the 1000 Genomes project, are generating maps of genomic structural variants by analyzing ends of massively sequenced genome fragments. To process these we developed Paired-End Mapper (PEMer; http://sv.gersteinlab.org/pemer). This comprises an analysis pipeline, compatible with several next-generation sequencing platforms; simulation-based error models, yielding confidence-values for each structural variant; and a back-end database. The simulations demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors.
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