ArticleMolecular biology and evolution2021
Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 5 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.
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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
5 citing papers in PubMed.
- AOPxSVM: A Support Vector Machine for Identifying Antioxidant Peptides Using a Block Substitution Matrix and Amino Acid Composition, Transformation, and Distribution Embeddings.Foods (Basel, Switzerland) · 2025Article
- A BERT-based rice enhancer identification model combined with sequence-representation differential entropy interpretation.Frontiers in plant science · 2025Article
- Optimal variable identification for accurate detection of causal expression Quantitative Trait Loci with applications in heart-related diseases.Computational and structural biotechnology journal · 2024Article
- A Machine Learning Method to Identify Umami Peptide Sequences by Using Multiplicative LSTM Embedded Features.Foods (Basel, Switzerland) · 2023Article
- HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes.BMC bioinformatics · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or "haplotypes." However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics, and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here, we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.
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Registered trials
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