ArticleCell systems2018
Statistical Binning for Barcoded Reads Improves Downstream Analyses.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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.
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Who cites it
14 citing papers in PubMed.
- Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.Molecular ecology · 2025Article
- LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.GigaScience · 2024Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- Ariadne: synthetic long read deconvolution using assembly graphs.Genome biology · 2023Article
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.Nucleic acids research · 2022Article
- False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.Genome biology · 2022Article
- CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project.The Journal of molecular diagnostics : JMD · 2022Article
- Article
- The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades.Genome biology and evolution · 2021Article
- Levenshtein Distance, Sequence Comparison and Biological Database Search.IEEE transactions on information theory · 2021Article
- Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets.Nature communications · 2020Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- Seq: A High-Performance Language for Bioinformatics.Proceedings of the ACM on programming languages · 2019Article
- 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
4 authors.
Funding
Abstract
Sequencing technologies are capturing longer-range genomic information at lower error rates, enabling alignment to genomic regions that are inaccessible with short reads. However, many methods are unable to align reads to much of the genome, recognized as important in disease, and thus report erroneous results in downstream analyses. We introduce EMA, a novel two-tiered statistical binning model for barcoded read alignment, that first probabilistically maps reads to potentially multiple "read clouds" and then within clouds by newly exploiting the non-uniform read densities characteristic of barcoded read sequencing. EMA substantially improves downstream accuracy over existing methods, including phasing and genotyping on 10x data, with fewer false variant calls in nearly half the time. EMA effectively resolves particularly challenging alignments in genomic regions that contain nearby homologous elements, uncovering variants in the pharmacogenomically important CYP2D region, and clinically important genes C4 (schizophrenia) and AMY1A (obesity), which go undetected by existing methods. Our work provides a framework for future generation sequencing.
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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.