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The mutational dynamics of short tandem repeats in large, multigenerational families
BackgroundShort tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases...
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Phosphine resistance among stored product insect pests: A global meta-analysis-based perspective
Phosphine is the most common fumigant used for stored product protection, and its use intensified with the global phasing out of methyl bromide due...
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Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database
BackgroundClinically effective and safe genoty** relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project...
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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Accurate variant calling and genoty** represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase...
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Efficient algorithms for polyploid haplotype phasing
BackgroundInference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component...
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Introducing Cysteines into Nanobodies for Site-Specific Labeling
We have developed a generally applicable methodology for cysteine mutagenesis of nanobody (Nb) framework region serine residues. This strategy allows...
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The Way Forward: Management and Policy Actions
Along with the evidence and analyses expounded on in this book, this chapter provides conclusions and suggestions concerning policy implications....
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Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Despite advances in long-read sequencing technologies, constructing a near telomere-to-telomere assembly is still computationally demanding. Here we...
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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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Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly
Draft genomes generated from Oxford Nanopore Technologies (ONT) long reads are known to have a higher error rate. Although existing genome polishers...
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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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A long-read sequencing and SNP haplotype-based novel preimplantation genetic testing method for female ADPKD patient with de novo PKD1 mutation
The autosomal dominant form of polycystic kidney disease (ADPKD) is the most common hereditary disease that causes late-onset renal cyst development...
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Determining Protein Structures Using X-Ray Crystallography
X-ray crystallography is a robust and widely used technique that facilitates the three-dimensional structure determination of proteins at an atomic...
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Map** crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq
Single-cell whole-genome sequencing methods have undergone great improvements over the past decade. However, allele dropout, which means the...
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HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data
BackgroundDe novo mutations (DNMs) are associated with neurodevelopmental and congenital diseases, and their detection can contribute to...
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Determination of the Crystal Structure of the Cell Wall-Anchored Proteins and Pilins
Surface proteins and pili (or pilus) anchored on the Gram-positive bacterial cell wall play a vital role in adhesion, colonization, biofilm...
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MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide...
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A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations
AbstractKey message New fast and accurate method for phasing and imputation of SNP chip genotypes within diploid bi-parental plant populations. ...