21 Result(s)
within
Alexander Schönhuth
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Article
Open AccessHybrid-hybrid correction of errors in long reads with HERO
Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in ...
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Article
Open AccessPredicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks
Diseases that have a complex genetic architecture tend to suffer from considerable amounts of genetic variants that, although playing a role in the disease, have not yet been revealed as such. Two major causes...
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Article
Open AccessVeChat: correcting errors in long reads using variation graphs
Error correction is the canonical first step in long-read sequencing data analysis. Current self-correction methods, however, are affected by consensus sequence induced biases that mask true variants in haplot...
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Article
Open AccessStrainline: full-length de novo viral haplotype reconstruction from noisy long reads
Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read dat...
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Article
Open AccessAccurate and scalable variant calling from single cell DNA sequencing data with ProSolo
Accurate single cell mutational profiles can reveal genomic cell-to-cell heterogeneity. However, sequencing libraries suitable for genoty** require whole genome amplification, which introduces allelic bias a...
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Article
Open Accessphasebook: haplotype-aware de novo assembly of diploid genomes from long reads
Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly. However, current long-re...
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Article
Open AccessStructural variant detection in cancer genomes: computational challenges and perspectives for precision oncology
Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a kn...
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Article
Open AccessRecursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic disorder characterized by disabling fatigue. Several studies have sought to identify diagnostic biomarkers, with varying results. Here, ...
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Article
Open AccessVarlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and deletions (indels) indicate that large amounts of discoveries ...
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Article
Open AccessEleven grand challenges in single-cell data science
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands—or even millions—of cells analyzed in a si...
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Chapter and Conference Paper
Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs
The goal of strain-aware genome assembly is to reconstruct all individual haplotypes from a mixed sample at the strain level and to provide abundance estimates for the strains.
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Article
Open AccessA high-quality human reference panel reveals the complexity and distribution of genomic structural variants
Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of ...
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Article
Genome sequence analysis with MonetDB
Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but yields terabytes of data to be stored and analyzed. Biolog...
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Article
Open AccessSV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines
Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems app...
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Chapter and Conference Paper
Viral Quasispecies Assembly via Maximal Clique Enumeration
Genetic variability of virus populations within individual hosts is a key determinant of pathogenesis, virulence, and treatment outcome. It is of clinical importance to identify and quantify the intra-host ens...
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Chapter and Conference Paper
WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads
The human genome is diploid, that is each of its chromosomes comes in two copies. This requires to phase the single nucleotide polymorphisms (SNPs), that is, to assign them to the two copies, beyond just detectin...
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Article
Open AccessMap** proteins in the presence of paralogs using units of coevolution
We study the problem of map** proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protei...
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Article
Open AccessDiscovering motifs that induce sequencing errors
Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS)....
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Chapter and Conference Paper
Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties
Although computationally aligning sequence is a crucial step in the vast majority of comparative genomics studies our understanding of alignment biases still needs to be improved. To infer true structural or h...
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Chapter and Conference Paper
Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks
A current major challenge in systems biology is to compute statistics on biomolecular network motifs, since this can reveal significant systemic differences between organisms. We extend the “color coding” techniq...
