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Alexander Schönhuth
Utrecht University
83Publications
22H-index
1,712Citations
Publications 85
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Personalizing drug prescriptions in cancer care based on genomic information requires associating genomic markers with treatment effects. This is an unsolved challenge requiring genomic patient data in yet unavailable volumes as well as appropriate quantitative methods. We attempt to solve this challenge for an experimental proxy for which sufficient data is available: 42 drugs tested on 1018 cancer cell lines. Our goal is to develop a method to identify the drug that is most promising based on ...
Telomere length (TL) regulation is an important factor in ageing, reproduction and cancer development. Genetic, hereditary and environmental factors regulating TL are currently widely investigated, however, their relative contribution to TL variability is still understudied. We have used whole genome sequencing data of 250 family trios from the Genome of the Netherlands project to perform computational measurement of TL and a series of regression and genome-wide association analyses to reveal TL...
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#1Jasmijn A. Baaijens (CWI: Centrum Wiskunde & Informatica)H-Index: 4
#2Alexander Schönhuth (UU: Utrecht University)H-Index: 22
htmlabstract Motivation: Haplotype-aware genome assembly plays an important role in genetics, medicine and various other disciplines, yet generation of haplotype-resolved de novo assemblies remains a major challenge. Beyond distinguishing between errors and true sequential variants, one needs to assign the true variants to the different genome copies. Recent work has pointed out that the enormous quantities of traditional NGS read data have been greatly underexploited in terms of haplotig comput...
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#1Johannes Köster (University of Duisburg-Essen)H-Index: 13
#2Louis Dijkstra (Leibniz Association)H-Index: 4
Last.Alexander Schönhuth (CWI: Centrum Wiskunde & Informatica)H-Index: 22
view all 4 authors...
Abstract As witnessed by various population-scale cancer genome sequencing projects, accurate discovery of somatic variants has become of central importance in modern cancer research. However, count statistics on somatic insertions and deletions (indels) discovered so far point out that large amounts of discoveries must have been missed. The reason is that the combination of uncertainties relating to, for example, gap and alignment ambiguities, twilight zone indels, cancer heterogeneity, sample ...
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#1David Laehnemann (HHU: University of Düsseldorf)H-Index: 1
#2Johannes Köster (University of Duisburg-Essen)H-Index: 13
Last.Alexander Schönhuth (UU: Utrecht University)H-Index: 22
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1 CitationsSource
Aug 1, 2019 in RECOMB (Research in Computational Molecular Biology)
#1Luca Denti (University of Milan)H-Index: 3
#2Marco Previtali (University of Milan)H-Index: 5
Last.PaolaBonizzoni (University of Milan)H-Index: 19
view all 5 authors...
Abstract The amount of genetic variation discovered in human populations is growing rapidly leading to challenging computational tasks, such as variant calling. Standard methods for addressing this problem include read mapping, a computationally expensive procedure, thus mapping-free tools have been proposed in recent years. These tools focus on isolated, bi-allelic SNPs, providing limited support for multi-allelic SNPs and short insertions and deletions of nucleotides (indels). Here we introduc...
1 CitationsSource
#1Bojian Yin (CWI: Centrum Wiskunde & Informatica)H-Index: 1
#2Marleen Balvert (UU: Utrecht University)H-Index: 1
Last.Alexander Schönhuth (UU: Utrecht University)H-Index: 22
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textabstractMotivation: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by aberrations in the genome. While several disease-causing variants have been identified, a major part of heritability remains unexplained. ALS is believed to have a complex genetic basis where non-additive combinations of variants constitute disease, which cannot be picked up using the linear models employed in classical genotype-phenotype association studies. Deep learning on the other hand is hi...
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#1Jasmijn A. Baaijens (CWI: Centrum Wiskunde & Informatica)H-Index: 4
#2Bastiaan van der Roest (UU: Utrecht University)H-Index: 1
Last.Alexander Schönhuth (UU: Utrecht University)H-Index: 22
view all 5 authors...
3 CitationsSource
#1Jasmijn A. Baaijens (CWI: Centrum Wiskunde & Informatica)H-Index: 4
#2Leen Stougie (VU: VU University Amsterdam)H-Index: 36
Last.Alexander Schönhuth (UU: Utrecht University)H-Index: 22
view all 3 authors...
Viral quasispecies assembly aims to reconstruct all mutant strains populating an infected patient and to provide corresponding abundance estimates. We provide a reference-genome-independent solution based on the construction of a variation graph, capturing all quasispecies diversity present in the sample. We solve the contig abundance estimation problem and propose a greedy algorithm to efficiently build full-length haplotypes. Finally, we obtain accurate frequency estimates for the reconstructe...
1 CitationsSource
#1Marleen Balvert (CWI: Centrum Wiskunde & Informatica)H-Index: 4
#2Tina Hauptfeld (WUR: Wageningen University and Research Centre)
Last.Bas E. Dutilh (UU: Utrecht University)H-Index: 37
view all 4 authors...
textabstractThe microbes that live in an environment can be identified from the genomic material that is present, also referred to as the metagenome. Using Next Generation Sequencing techniques this genomic material can be obtained from the environment, resulting in a large set of sequencing reads. A proper assembly of these reads into contigs or even full genomes allows one to identify the microbial species and strains that live in the environment. Assembling a metagenome is a challenging task ...
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