Alexander Schönhuth

aschoen@cebitec.uni-bielefeld.de
ORCID logo https://orcid.org/0000-0003-3529-0856

PEVZ-ID
202729007

54 Publikationen

Alle markieren

  • [54]
    2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985113 OA
    Kang, X., et al., 2023. Hybrid-hybrid correction of errors in long reads with HERO. Genome Biology , 24(1): 275.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [53]
    2023 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2969521
    Luo, X., Kang, X., & Schönhuth, A., 2023. Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks. Nature Machine Intelligence .
    PUB | DOI | WoS
     
  • [52]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966833 OA
    Luo, X., Kang, X., & Schönhuth, A., 2022. VeChat: correcting errors in long reads using variation graphs. Nature Communications, 13(1): 6657.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [51]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2963686 OA
    Luo, X., Kang, X., & Schönhuth, A., 2022. Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Frontiers in Genetics, 13: 868280.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [50]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2964174 OA
    Kang, X., Luo, X., & Schönhuth, A., 2022. StrainXpress: strain aware metagenome assembly from short reads. Nucleic Acids Research , 50(17): gkac543.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [49]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2960849 OA
    Luo, X., Kang, X., & Schönhuth, A., 2022. Strainline: full-length de novo viral haplotype reconstruction from noisy long reads. Genome Biology , 23(1): 29.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [48]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967245
    Ray, S., et al., 2022. Deep variational graph autoencoders for novel host-directed therapy options against COVID-19. Artificial Intelligence in Medicine, 134: 102418.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [47]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2958717 OA
    Luo, X., Kang, X., & Schönhuth, A., 2021. phasebook: haplotype-aware de novo assembly of diploid genomes from long reads. Genome Biology, 22(1): 299.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [46]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952469
    Metselaar, P.I., et al., 2021. Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome. Scientific reports, 11(1): 4541.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [45]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959624 OA
    Lahnemann, D., et al., 2021. Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo. Nature Communications, 12(1): 6744.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [44]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945617
    Lopez-Rincon, A., et al., 2020. Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification. Cancers, 12(7): 1785.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [43]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2943113
    Koster, J., et al., 2020. Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery. Genome biology, 21(1).
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [42]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941754
    Baaijens, J.A., et al., 2019. Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics, 35(24), p 5086-5094.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [41]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756
    Yin, B., et al., 2019. Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype. Bioinformatics, 35(14), p i538-i547.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [40]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760
    Lopez-Rincon, A., et al., 2019. Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection. BMC Bioinformatics, 20(1): 480.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [39]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941677
    Denti, L., et al., 2019. MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants. iScience, 18, p 20-27.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [38]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941761
    Baaijens, J.A., & Schönhuth, A., 2019. Overlap graph-based generation of haplotigs for diploids and polyploids. Bioinformatics, 35(21), p 4281-4289.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [37]
    2019 | Preprint | Veröffentlicht | PUB-ID: 2941762
    Balvert, M., et al., 2019. OGRE: Overlap Graph-based metagenomic Read clustEring. bioRxiv.
    PUB | Preprint
     
  • [36]
    2019 | Preprint | Veröffentlicht | PUB-ID: 2941763
    Baaijens, J.A., Stougie, L., & Schönhuth, A., 2019. Strain-aware assembly of genomes from mixed samples using flow variation graphs. bioRxiv.
    PUB | Preprint
     
  • [35]
    2019 | Preprint | Veröffentlicht | PUB-ID: 2941764
    Laehnemann, D., et al., 2019. 12 Grand Challenges in Single-Cell Data Science. PeerJ.
    PUB
     
  • [34]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941769
    Ibrahim, B., et al., 2018. Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting. Viruses, 10(5): 256.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [33]
    2018 | Preprint | Veröffentlicht | PUB-ID: 2941767
    Baaijens, J.A., et al., 2018. Full-length de novo viral quasispecies assembly through variation graph construction. bioRxiv.
    PUB | Preprint
     
  • [32]
    2018 | Preprint | Veröffentlicht | PUB-ID: 2941768
    Yin, B., et al., 2018. An image representation based convolutional network for DNA classification. arXiv:1806.04931.
    PUB | arXiv
     
  • [31]
    2018 | Preprint | Veröffentlicht | PUB-ID: 2941765
    Chikhi, R., & Schönhuth, A., 2018. Dualities in Tree Representations. arXiv:1804.04263.
    PUB | arXiv
     
  • [30]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941784
    Baaijens, J.A., et al., 2017. De novo assembly of viral quasispecies using overlap graphs. Genome Research, 27(5), p 835-848.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [29]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941785
    Dröge, J., Schönhuth, A., & McHardy, A.C., 2017. A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science, 3: e117.
    PUB | DOI | WoS
     
  • [28]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941786
    Ebler, J., Schönhuth, A., & Marschall, T., 2017. Genotyping inversions and tandem duplications. Bioinformatics, 33(24), p 4015-4023.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [27]
    2017 | Preprint | Veröffentlicht | PUB-ID: 2941789
    Dijkstra, L.J., et al., 2017. Enhancing sensitivity and controlling false discovery rate in somatic indel discovery using a latent variable model. bioRxiv.
    PUB | Preprint
     
  • [26]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941788
    Francioli, L.C., et al., 2016. A framework for the detection of de novo mutations in family-based sequencing data. European Journal of Human Genetics, 25(2), p 227-233.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [25]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793
    Gregor, I., Schönhuth, A., & McHardy, A.C., 2016. Snowball: strain aware gene assembly of metagenomes. Bioinformatics, 32(17), p i649-i657.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [24]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790
    Hehir-Kwa, J.Y., et al., 2016. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications, 7(1): 12989.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [23]
    2016 | Preprint | Veröffentlicht | PUB-ID: 2941794
    Martin, M., et al., 2016. WhatsHap: fast and accurate read-based phasing. bioRxiv.
    PUB | Preprint
     
  • [22]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807
    Palamara, P.F., et al., 2015. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. The American Journal of Human Genetics, 97(6), p 775-789.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [21]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797
    Kloosterman, W.P., et al., 2015. Characteristics of de novo structural changes in the human genome. Genome Research, 25(6), p 792-801.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [20]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798
    Leung, W.Y., et al., 2015. SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines. BMC Genomics, 16(1): 238.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [19]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941804
    van Leeuwen, E.M., et al., 2015. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nature Communications, 6(1): 6065.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [18]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941799
    Patterson, M., et al., 2015. WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Journal of Computational Biology, 22(6), p 498-509.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [17]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803
    van Leeuwen, E.M., et al., 2015. Population-specific genotype imputations using minimac or IMPUTE2. Nature Protocols, 10(9), p 1285-1296.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [16]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805
    Francioli, L.C., et al., 2015. Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics, 47(7), p 822-826.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [15]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612 OA
    Wittler, R., et al., 2015. Repeat- and error-aware comparison of deletions. Bioinformatics, 31(18), p 2947-2954.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [14]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941795
    Cijvat, R., et al., 2015. Genome sequence analysis with MonetDB. Datenbank-Spektrum, 15(3), p 185-191.
    PUB | DOI
     
  • [13]
    2015 | Preprint | PUB-ID: 2941808
    Faigle, U., & Schönhuth, A., 2015. On Hidden States in Quantum Random Walks. arXiv:1601.02882.
    PUB | arXiv
     
  • [12]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941816
    Deelen, P., et al., 2014. 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), p 1321-1326.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [11]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810
    Töpfer, A., et al., 2014. Viral Quasispecies Assembly via Maximal Clique Enumeration. PLoS Computational Biology, 10(3): e1003515.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [10]
    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941835
    El-Kebir, M., et al., 2013. Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics, 14(S15): S18.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [9]
    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941837
    Allhoff, M., et al., 2013. Discovering motifs that induce sequencing errors. BMC Bioinformatics, 14(Suppl 5): S1.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [8]
    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941836
    Marschall, T., Hajirasouliha, I., & Schönhuth, A., 2013. MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics, 29(24), p 3143-3150.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [7]
    2013 | Preprint | Veröffentlicht | PUB-ID: 2941838
    Marschall, T., & Schönhuth, A., 2013. Sensitive Long-Indel-Aware Alignment of Sequencing Reads. arXiv:1303.3520.
    PUB | arXiv
     
  • [6]
    2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941839
    Marschall, T., et al., 2012. CLEVER: clique-enumerating variant finder. Bioinformatics, 28(22), p 2875-2882.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [5]
    2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840
    Hajirasouliha, I., et al., 2012. Mirroring co-evolving trees in the light of their topologies. Bioinformatics, 28(9), p 1202-1208.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [4]
    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941841
    Singer, M., et al., 2011. Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains. Statistical Applications in Genetics and Molecular Biology, 10(1), p 759.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [3]
    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842
    Hafemeister, C., et al., 2011. Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. Bioinformatics, 27(7), p 946-952.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [2]
    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941814
    Schönhuth, A., 2011. Generic identification of binary-valued hidden Markov processes. Journal of Algebraic Statistics, 5(1), p 72-99.
    PUB
     
  • [1]
    2010 | Preprint | Veröffentlicht | PUB-ID: 2941843
    Faigle, U., & Schönhuth, A., 2010. A Markovian Model for Joint Observations, Bell's Inequality and Hidden States. arXiv:1011.1295.
    PUB | arXiv
     
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