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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this...
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Haplotype based testing for a better understanding of the selective architecture
BackgroundThe identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are...
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Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout ageing
Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here we...
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Sparse Phenoty** and Haplotype-Based Models for Genomic Prediction in Rice
The multi-environment genomic selection enables plant breeders to select varieties resilient to diverse environments or particularly adapted to...
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SNP-based and haplotype-based genome-wide association on drug dependence in Han Chinese
BackgroundDrug addiction is a serious problem worldwide and is influenced by genetic factors. The present study aimed to investigate the association...
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A common regulatory haplotype doubles lactoferrin concentration in milk
BackgroundBovine lactoferrin (Lf) is an iron absorbing whey protein with antibacterial, antiviral, and antifungal activity. Lactoferrin is...
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Haplotype diversity of Heterodera koreana (Tylenchida: Heteroderidae), affecting bamboo in Korea
In a survey of plant-parasitic nematodes in agricultural fields, cyst-forming nematodes were found in soil planted bamboo in Korea. The aim of this...
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Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
BackgroundRecent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of...
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CandiHap: a haplotype analysis toolkit for natural variation study
Haplotype blocks greatly assist association-based map** of casual candidate genes by significantly reducing genoty** effort. The gene haplotype...
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Haplotype-aware pantranscriptome analyses using spliced pangenome graphs
Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures,...
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Mitochondrial genetic diversity and haplotype distribution of golden jackal (Canis aureus, Linnaeus 1758) in Iran, a bridge from India to North Europe
Golden jackal ( Canis aureus ) is one of the most common canid in Iran and can be found in habitats from Southeast Asia to Europe. Its rapid range...
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Hitting the Road: Haplotype Diversity of Fire Ants Nesting on Disturbed Atlantic Forest Habitats
Ants of the genus Solenopsis are globally distributed, presenting high diversity and many generalist species. In South America, the dominant species...
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Molecular Characterization and Haplotype Diversity of Aporcelaimellus obtusicaudatus (Bastian, 1865) Altherr, 1968 (Dorylaimida, Aporcelaimidae) from India
AbstractAporcelaimellus obtusicaudatus was recovered from mustard and sugarcane fields of Uttar Pradesh and Uttarakhand, India. The present species...
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Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years
Key messageSelection over 70 years has led to almost complete fixation of a haplotype spanning ~ 250 Mbp of chomosome 5H in European two-rowed spring...
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The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle
BackgroundLow-pass sequencing followed by sequence variant genotype imputation is an alternative to the routine microarray-based genoty** in...
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A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy
BackgroundLow-pass whole-genome sequencing and imputation offer significant cost savings, enabling substantial increases in sample size and...
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Haplotype-resolved genome of Mimosa bimucronata revealed insights into leaf movement and nitrogen fixation
BackgroundMimosa bimucronata originates from tropical America and exhibits distinctive leaf movement characterized by a relative slow speed....
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The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic map** in pigs
Genetic map** to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals...
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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for...
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Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved...
