54 Publikationen
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2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985113Hybrid-hybrid correction of errors in long reads with HEROPUB | PDF | DOI | WoS | PubMed | Europe PMC
Kang, Xiongbin, Hybrid-hybrid correction of errors in long reads with HERO. Genome Biology 24 (1). , 2023 -
2023 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2969521Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networksPUB | DOI | WoS
Luo, Xiao, Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks. Nature Machine Intelligence (). , 2023 -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966833VeChat: correcting errors in long reads using variation graphsPUB | PDF | DOI | WoS | PubMed | Europe PMC
Luo, Xiao, VeChat: correcting errors in long reads using variation graphs. Nature Communications 13 (1). , 2022 -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2963686Enhancing Long-Read-Based Strain-Aware Metagenome AssemblyPUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Luo, Xiao, Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Frontiers in Genetics 13 (). , 2022 -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2964174StrainXpress: strain aware metagenome assembly from short readsPUB | PDF | DOI | WoS | PubMed | Europe PMC
Kang, Xiongbin, StrainXpress: strain aware metagenome assembly from short reads. Nucleic Acids Research 50 (17). , 2022 -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2960849Strainline: full-length de novo viral haplotype reconstruction from noisy long readsPUB | PDF | DOI | WoS | PubMed | Europe PMC
Luo, Xiao, Strainline: full-length de novo viral haplotype reconstruction from noisy long reads. Genome Biology 23 (1). , 2022 -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967245Deep variational graph autoencoders for novel host-directed therapy options against COVID-19PUB | DOI | WoS | PubMed | Europe PMC
Ray, Sumanta, Deep variational graph autoencoders for novel host-directed therapy options against COVID-19. Artificial Intelligence in Medicine 134 (). , 2022 -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2958717phasebook: haplotype-aware de novo assembly of diploid genomes from long readsPUB | PDF | DOI | WoS | PubMed | Europe PMC
Luo, Xiao, phasebook: haplotype-aware de novo assembly of diploid genomes from long reads. Genome Biology 22 (1). , 2021 -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952469Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome.PUB | DOI | WoS | PubMed | Europe PMC
Metselaar, Paula I, Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome.. Scientific reports 11 (1). , 2021 -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959624Accurate and scalable variant calling from single cell DNA sequencing data with ProSoloPUB | PDF | DOI | WoS | PubMed | Europe PMC
Lahnemann, David, Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo. Nature Communications 12 (1). , 2021 -
2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945617Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor ClassificationPUB | DOI | WoS | PubMed | Europe PMC
Lopez-Rincon, Alejandro, Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification. Cancers 12 (7). , 2020 -
2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2943113Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery.PUB | DOI | WoS | PubMed | Europe PMC
Koster, Johannes, Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery.. Genome biology 21 (1). , 2020 -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941754Full-length de novo viral quasispecies assembly through variation graph constructionPUB | DOI | WoS | PubMed | Europe PMC
Baaijens, Jasmijn A, Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics 35 (24). , 2019 -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotypePUB | DOI | WoS | PubMed | Europe PMC
Yin, Bojian, Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype. Bioinformatics 35 (14). , 2019 -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selectionPUB | DOI | WoS | PubMed | Europe PMC
Lopez-Rincon, Alejandro, Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection. BMC Bioinformatics 20 (1). , 2019 -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941677MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriantsPUB | DOI | WoS | PubMed | Europe PMC
Denti, Luca, MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants. iScience 18 (). , 2019 -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941761Overlap graph-based generation of haplotigs for diploids and polyploidsPUB | DOI | WoS | PubMed | Europe PMC
Baaijens, Jasmijn A, Overlap graph-based generation of haplotigs for diploids and polyploids. Bioinformatics 35 (21). , 2019 -
2019 | Preprint | Veröffentlicht | PUB-ID: 2941762OGRE: Overlap Graph-based metagenomic Read clustEringPUB | Preprint
Balvert, Marleen, OGRE: Overlap Graph-based metagenomic Read clustEring. bioRxiv (). , 2019 -
2019 | Preprint | Veröffentlicht | PUB-ID: 2941763Strain-aware assembly of genomes from mixed samples using flow variation graphsPUB | Preprint
Baaijens, Jasmijn A., Strain-aware assembly of genomes from mixed samples using flow variation graphs. bioRxiv (). , 2019 -
2019 | Preprint | Veröffentlicht | PUB-ID: 294176412 Grand Challenges in Single-Cell Data SciencePUB
Laehnemann, David, 12 Grand Challenges in Single-Cell Data Science. PeerJ (). , 2019 -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941769Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual MeetingPUB | DOI | WoS | PubMed | Europe PMC
Ibrahim, Bashar, Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting. Viruses 10 (5). , 2018 -
2018 | Preprint | Veröffentlicht | PUB-ID: 2941767Full-length de novo viral quasispecies assembly through variation graph constructionPUB | Preprint
Baaijens, Jasmijn A., Full-length de novo viral quasispecies assembly through variation graph construction. bioRxiv (). , 2018 -
2018 | Preprint | Veröffentlicht | PUB-ID: 2941768An image representation based convolutional network for DNA classificationPUB | arXiv
Yin, Bojian, An image representation based convolutional network for DNA classification. arXiv:1806.04931 (). , 2018 -
2018 | Preprint | Veröffentlicht | PUB-ID: 2941765Dualities in Tree RepresentationsPUB | arXiv
Chikhi, Rayan, Dualities in Tree Representations. arXiv:1804.04263 (). , 2018 -
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941784De novo assembly of viral quasispecies using overlap graphsPUB | DOI | WoS | PubMed | Europe PMC
Baaijens, Jasmijn A., De novo assembly of viral quasispecies using overlap graphs. Genome Research 27 (5). , 2017 -
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941785A probabilistic model to recover individual genomes from metagenomesPUB | DOI | WoS
Dröge, Johannes, A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science 3 (). , 2017 -
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941786Genotyping inversions and tandem duplicationsPUB | DOI | WoS | PubMed | Europe PMC
Ebler, Jana, Genotyping inversions and tandem duplications. Bioinformatics 33 (24). , 2017 -
2017 | Preprint | Veröffentlicht | PUB-ID: 2941789Enhancing sensitivity and controlling false discovery rate in somatic indel discovery using a latent variable modelPUB | Preprint
Dijkstra, Louis J., Enhancing sensitivity and controlling false discovery rate in somatic indel discovery using a latent variable model. bioRxiv (). , 2017 -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941788A framework for the detection of de novo mutations in family-based sequencing dataPUB | DOI | WoS | PubMed | Europe PMC
Francioli, Laurent C, A framework for the detection of de novo mutations in family-based sequencing data. European Journal of Human Genetics 25 (2). , 2016 -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793Snowball: strain aware gene assembly of metagenomesPUB | DOI | WoS | PubMed | Europe PMC
Gregor, I., Snowball: strain aware gene assembly of metagenomes. Bioinformatics 32 (17). , 2016 -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790A high-quality human reference panel reveals the complexity and distribution of genomic structural variantsPUB | DOI | WoS | PubMed | Europe PMC
Hehir-Kwa, Jayne Y., A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications 7 (1). , 2016 -
2016 | Preprint | Veröffentlicht | PUB-ID: 2941794WhatsHap: fast and accurate read-based phasingPUB | Preprint
Martin, Marcel, WhatsHap: fast and accurate read-based phasing. bioRxiv (). , 2016 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion RatesPUB | DOI | WoS | PubMed | Europe PMC
Palamara, Pier Francesco, Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. The American Journal of Human Genetics 97 (6). , 2015 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797Characteristics of de novo structural changes in the human genomePUB | DOI | WoS | PubMed | Europe PMC
Kloosterman, Wigard P., Characteristics of de novo structural changes in the human genome. Genome Research 25 (6). , 2015 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelinesPUB | DOI | WoS | PubMed | Europe PMC
Leung, Wai Yi, SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines. BMC Genomics 16 (1). , 2015 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941804Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levelsPUB | DOI | WoS | PubMed | Europe PMC
van Leeuwen, Elisabeth M., Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nature Communications 6 (1). , 2015 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941799WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing ReadsPUB | DOI | WoS | PubMed | Europe PMC
Patterson, Murray, WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Journal of Computational Biology 22 (6). , 2015 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803Population-specific genotype imputations using minimac or IMPUTE2PUB | DOI | WoS | PubMed | Europe PMC
van Leeuwen, Elisabeth M, Population-specific genotype imputations using minimac or IMPUTE2. Nature Protocols 10 (9). , 2015 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805Genome-wide patterns and properties of de novo mutations in humansPUB | DOI | WoS | PubMed | Europe PMC
Francioli, Laurent C, Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics 47 (7). , 2015 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612Repeat- and error-aware comparison of deletionsPUB | PDF | DOI | WoS | PubMed | Europe PMC
Wittler, Roland, Repeat- and error-aware comparison of deletions. Bioinformatics 31 (18). , 2015 -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941795Genome sequence analysis with MonetDBPUB | DOI
Cijvat, Robin, Genome sequence analysis with MonetDB. Datenbank-Spektrum 15 (3). , 2015 -
2015 | Preprint | PUB-ID: 2941808On Hidden States in Quantum Random WalksPUB | arXiv
Faigle, Ulrich, On Hidden States in Quantum Random Walks. arXiv:1601.02882 (). , 2015 -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941816Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’PUB | DOI | WoS | PubMed | Europe PMC
Deelen, Patrick, Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’. European Journal of Human Genetics 22 (11). , 2014 -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810Viral Quasispecies Assembly via Maximal Clique EnumerationPUB | DOI | WoS | PubMed | Europe PMC
Töpfer, Armin, Viral Quasispecies Assembly via Maximal Clique Enumeration. PLoS Computational Biology 10 (3). , 2014 -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941835Mapping proteins in the presence of paralogs using units of coevolutionPUB | DOI | WoS | PubMed | Europe PMC
El-Kebir, Mohammed, Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics 14 (S15). , 2013 -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941837Discovering motifs that induce sequencing errorsPUB | DOI | WoS | PubMed | Europe PMC
Allhoff, Manuel, Discovering motifs that induce sequencing errors. BMC Bioinformatics 14 (Suppl 5). , 2013 -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941836MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indelsPUB | DOI | WoS | PubMed | Europe PMC
Marschall, Tobias, MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics 29 (24). , 2013 -
2013 | Preprint | Veröffentlicht | PUB-ID: 2941838Sensitive Long-Indel-Aware Alignment of Sequencing ReadsPUB | arXiv
Marschall, Tobias, Sensitive Long-Indel-Aware Alignment of Sequencing Reads. arXiv:1303.3520 (). , 2013 -
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941839CLEVER: clique-enumerating variant finderPUB | DOI | WoS | PubMed | Europe PMC
Marschall, Tobias, CLEVER: clique-enumerating variant finder. Bioinformatics 28 (22). , 2012 -
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840Mirroring co-evolving trees in the light of their topologiesPUB | DOI | WoS | PubMed | Europe PMC
Hajirasouliha, Iman, Mirroring co-evolving trees in the light of their topologies. Bioinformatics 28 (9). , 2012 -
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941841Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov ChainsPUB | DOI | WoS | PubMed | Europe PMC
Singer, Meromit, Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains. Statistical Applications in Genetics and Molecular Biology 10 (1). , 2011 -
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functionsPUB | DOI | WoS | PubMed | Europe PMC
Hafemeister, Christoph, Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. Bioinformatics 27 (7). , 2011 -
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941814Generic identification of binary-valued hidden Markov processesPUB
Schönhuth, Alexander, Generic identification of binary-valued hidden Markov processes. Journal of Algebraic Statistics 5 (1). , 2011 -
2010 | Preprint | Veröffentlicht | PUB-ID: 2941843A Markovian Model for Joint Observations, Bell's Inequality and Hidden StatesPUB | arXiv
Faigle, Ulrich, A Markovian Model for Joint Observations, Bell's Inequality and Hidden States. arXiv:1011.1295 (). , 2010