Alexander Schönhuth
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View article: Correction: A graph neural network-based approach for predicting SARS-CoV-2–human protein interactions from multiview data
Correction: A graph neural network-based approach for predicting SARS-CoV-2–human protein interactions from multiview data Open
[This corrects the article DOI: 10.1371/journal.pone.0332794.].
View article: A graph neural network-based approach for predicting SARS-CoV-2–human protein interactions from multiview data
A graph neural network-based approach for predicting SARS-CoV-2–human protein interactions from multiview data Open
The COVID-19 pandemic has demanded urgent and accelerated action toward developing effective therapeutic strategies. Drug repurposing models (in silico) are in high demand and require accurate and reliable molecular interaction data. While…
View article: GraphAware: Interpretable machine learning on graphs
GraphAware: Interpretable machine learning on graphs Open
Graph Neural Networks (GNNs) have demonstrated state-of-the-art performance in many applications from disease prediction to weather forecasting. However, each GNN layer introduces new trainable parameters that increase its complexity and l…
View article: SBC-SHAP: Increasing the Accessibility and Interpretability of Machine Learning Algorithms for Sepsis Prediction
SBC-SHAP: Increasing the Accessibility and Interpretability of Machine Learning Algorithms for Sepsis Prediction Open
Background Sepsis is a life-threatening condition that is one of the major causes of death worldwide. Early detection of sepsis is required for fast initialization of an appropriate therapy. Complete blood count data containing information…
View article: Genetic features for drug responses in cancer — Investigating an ensemble-feature-selection approach
Genetic features for drug responses in cancer — Investigating an ensemble-feature-selection approach Open
Predicting drug responses using genetic and transcriptomic features is crucial for enhancing personalized medicine. In this study, we implemented an ensemble of machine learning algorithms to analyze the correlation between genetic and tra…
View article: Generating synthetic genotypes using diffusion models
Generating synthetic genotypes using diffusion models Open
Summary In this paper, we introduce the first diffusion model designed to generate complete synthetic human genotypes, which, by standard protocols, one can straightforwardly expand into full-length, DNA-level genomes. The synthetic genoty…
View article: Strain-level metagenomic profiling using pangenome graphs with PanTax
Strain-level metagenomic profiling using pangenome graphs with PanTax Open
Microbes are omnipresent, thriving in a range of habitats, from oceans to soils, and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequentl…
View article: Towards a diagnostic test for sporadic ALS utilising deep learning and SNP microarrays
Towards a diagnostic test for sporadic ALS utilising deep learning and SNP microarrays Open
A variety of common and rare genetic factors have been implicated in the development of amyotrophic lateral sclerosis (ALS), and the evidence is that a genetic component is present in most affected individuals. However, our current underst…
View article: PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases
PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases Open
Motivation Species identification is a critical task in agriculture, food processing, and health-care. The rapid growth of genomic databases — driven in part by the increasing investigation of bacterial genomes in clinical microbiology — h…
View article: DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs Open
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances be…
View article: PhenoEncoder: A Discriminative Embedding Approach to Genomic Data Compression
PhenoEncoder: A Discriminative Embedding Approach to Genomic Data Compression Open
Exploring the heritability of complex genetic traits requires methods that can handle the genome’s vast scale and the intricate re-lationships among genetic markers. Widely accepted association studies overlook non-linear effects (epistasi…
View article: Generating Synthetic Genotypes using Diffusion Models
Generating Synthetic Genotypes using Diffusion Models Open
In this paper, we introduce the first diffusion model designed to generate complete synthetic human genotypes, which, by standard protocols, one can straightforwardly expand into full-length, DNA-level genomes. The synthetic genotypes mimi…
View article: PanTax: Strain-level taxonomic classification of metagenomic data using pangenome graphs
PanTax: Strain-level taxonomic classification of metagenomic data using pangenome graphs Open
Microbes are omnipresent, thriving in a range of habitats from oceans to soils and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequently,…
View article: Algebras of Interaction and Cooperation
Algebras of Interaction and Cooperation Open
Systems of cooperation and interaction are usually studied in the context of real or complex vector spaces. Additional insight, however, is gained when such systems are represented in vector spaces with ultiplicative structures, i.e., in a…
View article: Computing linkage disequilibrium aware genome embeddings using autoencoders
Computing linkage disequilibrium aware genome embeddings using autoencoders Open
Motivation The completion of the genome has paved the way for genome-wide association studies (GWAS), which explained certain proportions of heritability. GWAS are not optimally suited to detect non-linear effects in disease risk, possibly…
View article: HyLight: Strain aware assembly of low coverage metagenomes
HyLight: Strain aware assembly of low coverage metagenomes Open
Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of a microbial community at strain level poses major methodical challenges, because re…
View article: Hybrid-hybrid correction of errors in long reads with HERO
Hybrid-hybrid correction of errors in long reads with HERO Open
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 polyploid and mixed samples. W…
View article: Hybrid-hybrid correction of errors in long reads with HERO
Hybrid-hybrid correction of errors in long reads with HERO Open
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 polyploid and mixed samples. W…
View article: Computing Linkage Disequilibrium Aware Genome Embeddings using Autoencoders
Computing Linkage Disequilibrium Aware Genome Embeddings using Autoencoders Open
Motivation The completion of the human genome has paved the way for genome-wide association studies (GWAS), which have already succeeded in explaining certain proportions of heritability. GWAS are not optimally suited to detect potential n…
View article: Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks
Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks Open
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 for this phenomenon are genet…
View article: Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks
Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks Open
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 for this phenomenon are genet…
View article: VeChat: correcting errors in long reads using variation graphs
VeChat: correcting errors in long reads using variation graphs Open
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 haplotypes of lower frequency showin…
View article: StrainXpress: strain aware metagenome assembly from short reads
StrainXpress: strain aware metagenome assembly from short reads Open
Next-generation sequencing–based metagenomics has enabled to identify microorganisms in characteristic habitats without the need for lengthy cultivation. Importantly, clinically relevant phenomena such as resistance to medication, virulenc…
View article: Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
Enhancing Long-Read-Based Strain-Aware Metagenome Assembly Open
Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biologi…
View article: StrainXpress: strain aware metagenome assembly from short reads
StrainXpress: strain aware metagenome assembly from short reads Open
Next-generation sequencing based metagenomics has enabled to identify microorganisms in characteristic habitats without the need for lengthy cultivation. Importantly, clinically relevant phenomena such as resistance to medication, virulenc…