ArticleNature communications2020
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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
17 citing papers in PubMed.
- LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing.bioRxiv : the preprint server for biology · 2026Article
- Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.bioRxiv : the preprint server for biology · 2026Article
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- Graph-based deep reinforcement learning for haplotype assembly with Ralphi.Genome research · 2025Article
- HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.International journal of molecular sciences · 2025Article
- Impact of Allele-Specific Expression on Ripening and Quality Characteristics of ABB Banana Fruit.International journal of molecular sciences · 2025Article
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- An efficient genotyper and star-allele caller for pharmacogenomics.Genome research · 2023Article
- Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges.Methods in molecular biology (Clifton, N.J.) · 2023Article
- CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project.The Journal of molecular diagnostics : JMD · 2022Article
- flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines.Frontiers in immunology · 2022Article
- Reconstruction of evolving gene variants and fitness from short sequencing reads.Nature chemical biology · 2021Article
- Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.Cell systems · 2021Article
- A Python-based programming language for high-performance computational genomics.Nature biotechnology · 2021Article
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Authors and funding
8 authors.
Funding
Abstract
Haplotype reconstruction of distant genetic variants remains an unsolved problem due to the short-read length of common sequencing data. Here, we introduce HapTree-X, a probabilistic framework that utilizes latent long-range information to reconstruct unspecified haplotypes in diploid and polyploid organisms. It introduces the observation that differential allele-specific expression can link genetic variants from the same physical chromosome, thus even enabling using reads that cover only individual variants. We demonstrate HapTree-X's feasibility on in-house sequenced Genome in a Bottle RNA-seq and various whole exome, genome, and 10X Genomics datasets. HapTree-X produces more complete phases (up to 25%), even in clinically important genes, and phases more variants than other methods while maintaining similar or higher accuracy and being up to 10× faster than other tools. The advantage of HapTree-X's ability to use multiple lines of evidence, as well as to phase polyploid genomes in a single integrative framework, substantially grows as the amount of diverse data increases.
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Registered trials
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