David N. Heller
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View article: Structural variant calling using third-generation sequencing data
Structural variant calling using third-generation sequencing data Open
Structural variants, commonly defined as genomic differences larger than 50 bp, are an important research target due to their large size and great impact on human phenotype and disease. Their unique properties and the weaknesses of traditi…
View article: SVIM-asm: structural variant detection from haploid and diploid genome assemblies
SVIM-asm: structural variant detection from haploid and diploid genome assemblies Open
Motivation With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental …
View article: SVIM-asm: Structural variant detection from haploid and diploid genome assemblies
SVIM-asm: Structural variant detection from haploid and diploid genome assemblies Open
Motivation With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental …
View article: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality
The mole genome reveals regulatory rearrangements associated with adaptive intersexuality Open
Intersexuality in female moles Female moles are intersexual and develop masculinizing ovotestes, a distinctive trait among mammals. Real et al. investigated the origin of this trait by sequencing the Iberian mole genome and applying compar…
View article: Ranbow: A fast and accurate method for polyploid haplotype reconstruction
Ranbow: A fast and accurate method for polyploid haplotype reconstruction Open
Reconstructing haplotypes from sequencing data is one of the major challenges in genetics. Haplotypes play a crucial role in many analyses, including genome-wide association studies and population genetics. Haplotype reconstruction becomes…
View article: SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing
SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing Open
Segmental duplications are important for understanding human diseases and evolution. The challenge to distinguish allelic and duplication sequences has hindered their phased assembly as well as characterization of structural variant calls.…
View article: Genotyping structural variants in pangenome graphs using the vg toolkit
Genotyping structural variants in pangenome graphs using the vg toolkit Open
Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveragi…
View article: vgteam/sv-genotyping-paper: Revised code repository for "Genotyping structural variants in pangenome graphs using the vg toolkit"
vgteam/sv-genotyping-paper: Revised code repository for "Genotyping structural variants in pangenome graphs using the vg toolkit" Open
This repository contains the commands and scripts used for the revised version of our manuscript Genotyping structural variants in pangenome graphs using the vg toolkit, 2019.
View article: Genotyping structural variants in pangenome graphs using the vg toolkit
Genotyping structural variants in pangenome graphs using the vg toolkit Open
Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveragi…
View article: SVIM: structural variant identification using mapped long reads
SVIM: structural variant identification using mapped long reads Open
Motivation Structural variants are defined as genomic variants larger than 50 bp. They have been shown to affect more bases in any given genome than single-nucleotide polymorphisms or small insertions and deletions. Additionally, they have…
View article: SVIM: Structural Variant Identification using Mapped Long Reads
SVIM: Structural Variant Identification using Mapped Long Reads Open
Motivation Structural variants are defined as genomic variants larger than 50bp. They have been shown to affect more bases in any given genome than SNPs or small indels. Additionally, they have great impact on human phenotype and diversity…
View article: ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data Open
RNA-binding proteins (RBPs) play an important role in RNA post-transcriptional regulation and recognize target RNAs via sequence-structure motifs. The extent to which RNA structure influences protein binding in the presence or absence of a…
View article: ssHMM: Extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data
ssHMM: Extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data Open
RNA-binding proteins (RBPs) play important roles in RNA post-transcriptional regulation and recognize target RNAs via sequence-structure motifs. To which extent RNA structure influences protein binding in the presence or absence of a seque…