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View article: Structural and transduction patterns of human-specific polymorphic SVA insertions
Structural and transduction patterns of human-specific polymorphic SVA insertions Open
Background SINE variable number tandem repeat Alu elements (SVAs) are a unique group of hominid-specific composite retrotransposons with highly variable internal structure. They represent the youngest TE family in humans and contribute to …
View article: The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics Open
Background The goal of the Fifth Annual Baylor College of Medicine & DNAnexus Structural Variation Hackathon was to push forward the research on structural variants (SVs) by rapidly developing and deploying open-source software. The event …
View article: Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci
Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci Open
The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genom…
View article: Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures
Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures Open
Background The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR) hypothesized to result from replicative repair of DNA due to replication fork collapse. It is often m…
View article: Impact and characterization of serial structural variations across humans and great apes
Impact and characterization of serial structural variations across humans and great apes Open
Modern sequencing technology enables the detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through series of mutations, a phenomenon we term serial SV (sSV), remain understudied si…
View article: Assemblies and alignment data generated for NAHRwhals manuscript.
Assemblies and alignment data generated for NAHRwhals manuscript. Open
This repository contains 56 human assemblies used for a manuscript describing the NAHRwhals SV identifying tool (https://github.com/WHops/NAHRwhals). All underlying raw data as well as half of the assemblies are directly taken from the Hum…
View article: Assemblies and alignment data generated for NAHRwhals manuscript.
Assemblies and alignment data generated for NAHRwhals manuscript. Open
This repository contains 56 human assemblies used for a manuscript describing the NAHRwhals SV identifying tool (https://github.com/WHops/NAHRwhals). All underlying raw data as well as half of the assemblies are directly taken from the Hum…
View article: Inversion polymorphism in a complete human genome assembly
Inversion polymorphism in a complete human genome assembly Open
Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.
View article: Inversion polymorphism in a complete human genome assembly
Inversion polymorphism in a complete human genome assembly Open
Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.
View article: Inversion polymorphism in a complete human genome assembly
Inversion polymorphism in a complete human genome assembly Open
Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.
View article: Additional file 2 of Inversion polymorphism in a complete human genome assembly
Additional file 2 of Inversion polymorphism in a complete human genome assembly Open
Additional file 2: Table S1. Nonredundant inversion callset reported in this study. Table S2. Putative novel inversions with respect to T2T-CHM13 reference. Table S3. Enrichment of inversions in pericentromeric regions. Table S4. List of m…
View article: Assembly of 43 human Y chromosomes reveals extensive complexity and variation
Assembly of 43 human Y chromosomes reveals extensive complexity and variation Open
The uploaded file contains Supplementary Tables S1-S61 for the manuscript "Assembly of 43 human Y chromosomes reveals extensive complexity and variation"
View article: Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation
Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation Open
The prevalence of highly repetitive sequences within the human Y chromosome has led to its incomplete assembly and systematic omission from genomic analyses. Here, we present long-read de novo assemblies of 43 diverse Y chromosomes spannin…
View article: Inversion polymorphism in a complete human genome assembly
Inversion polymorphism in a complete human genome assembly Open
The completion of the human genome significantly improved our ability to discover and interpret genome copy number variation. In order to understand its impact on the characterization of inversion polymorphisms, we remapped data from 41 hu…
View article: The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms Open
In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on struc…
View article: Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders
Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders Open
Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by tw…
View article: Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Haplotype-resolved diverse human genomes and integrated analysis of structural variation Open
Resolving genomic structural variation Many human genomes have been reported using short-read technology, but it is difficult to resolve structural variants (SVs) using these data. These genomes thus lack comprehensive comparisons among in…
View article: <i>De novo</i>assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation
<i>De novo</i>assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation Open
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent–child trio data. We present 64 assembled haplotypes from 32 diverse human genome…
View article: Recurrent inversion toggling and great ape genome evolution
Recurrent inversion toggling and great ape genome evolution Open
This repository contains raw Strand-seq data aligned to GRCh38 that have been used to detect inversions in the study "Recurrent inversion toggling and great ape genome evolution". See Methods section of the above mentioned paper for more d…
View article: Recurrent inversion toggling and great ape genome evolution
Recurrent inversion toggling and great ape genome evolution Open
This repository contains raw Strand-seq data aligned to GRCh38 that have been used to detect inversions in the study "Recurrent inversion toggling and great ape genome evolution". See Methods section of the above mentioned paper for more d…
View article: Recurrent inversion toggling and great ape genome evolution
Recurrent inversion toggling and great ape genome evolution Open
This repository contains raw Strand-seq data aligned to GRCh38 that have been used to detect inversions in the study "Recurrent inversion toggling and great ape genome evolution". See Methods section of the above mentioned paper for more d…
View article: Gene Unprediction with Spurio: A tool to identify spurious protein sequences
Gene Unprediction with Spurio: A tool to identify spurious protein sequences Open
We now have access to the sequences of tens of millions of proteins. These protein sequences are essential for modern molecular biology and computational biology. The vast majority of protein sequences are derived from gene prediction tool…