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., Xu, J., Luo, X., & Schönhuth, A. (2023). Hybrid-hybrid correction of errors in long reads with HERO. Genome Biology , 24(1), 275. https://doi.org/10.1186/s13059-023-03112-7
    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 . https://doi.org/10.1038/s42256-022-00604-2
    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. https://doi.org/10.1038/s41467-022-34381-8
    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. https://doi.org/10.3389/fgene.2022.868280
    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. https://doi.org/10.1093/nar/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. https://doi.org/10.1186/s13059-021-02587-6
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [48]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967245
    Ray, S., Lall, S., Mukhopadhyay, A., Bandyopadhyay, S., & Schönhuth, A. (2022). Deep variational graph autoencoders for novel host-directed therapy options against COVID-19. Artificial Intelligence in Medicine, 134, 102418. https://doi.org/10.1016/j.artmed.2022.102418
    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. https://doi.org/10.1186/s13059-021-02512-x
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [46]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952469
    Metselaar, P. I., Mendoza-Maldonado, L., Li Yim, A. Y. F., Abarkan, I., Henneman, P., Te Velde, A. A., Schönhuth, A., et al. (2021). Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome. Scientific reports, 11(1), 4541. https://doi.org/10.1038/s41598-021-83660-9
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [45]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959624 OA
    Lahnemann, D., Koster, J., Fischer, U., Borkhardt, A., McHardy, A. C., & Schönhuth, A. (2021). Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo. Nature Communications, 12(1), 6744. https://doi.org/10.1038/s41467-021-26938-w
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [44]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945617
    Lopez-Rincon, A., Mendoza-Maldonado, L., Martinez-Archundia, M., Schönhuth, A., Kraneveld, A. D., Garssen, J., & Tonda, A. (2020). Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification. Cancers, 12(7), 1785. https://doi.org/10.3390/cancers12071785
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [43]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2943113
    Koster, J., Dijkstra, L. J., Marschall, T., & Schönhuth, A. (2020). Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery. Genome biology, 21(1). https://doi.org/10.1186/s13059-020-01993-6
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [42]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941754
    Baaijens, J. A., Van der Roest, B., Köster, J., Stougie, L., & Schönhuth, A. (2019). Full-length de novo viral quasispecies assembly through variation graph construction. Bioinformatics, 35(24), 5086-5094. doi:10.1093/bioinformatics/btz443
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [41]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756
    Yin, B., Balvert, M., van der Spek, R. A. A., Dutilh, B. E., Bohté, S., Veldink, J., & Schönhuth, A. (2019). Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype. Bioinformatics, 35(14), i538-i547. doi:10.1093/bioinformatics/btz369
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [40]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760
    Lopez-Rincon, A., Martinez-Archundia, M., Martinez-Ruiz, G. U., Schönhuth, A., & Tonda, A. (2019). Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection. BMC Bioinformatics, 20(1), 480. doi:10.1186/s12859-019-3050-8
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [39]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941677
    Denti, L., Previtali, M., Bernardini, G., Schönhuth, A., & Bonizzoni, P. (2019). MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants. iScience, 18, 20-27. doi:10.1016/j.isci.2019.07.011
    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), 4281-4289. doi:10.1093/bioinformatics/btz255
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [37]
    2019 | Preprint | Veröffentlicht | PUB-ID: 2941762
    Balvert, M., Hauptfeld, T., Schönhuth, A., & Dutilh, B. E. (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., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., et al. (2019). 12 Grand Challenges in Single-Cell Data Science. PeerJ
    PUB
     
  • [34]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941769
    Ibrahim, B., Arkhipova, K., Andeweg, A., Posada-Céspedes, S., Enault, F., Gruber, A., Koonin, E., et al. (2018). Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting. Viruses, 10(5), 256. doi:10.3390/v10050256
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [33]
    2018 | Preprint | Veröffentlicht | PUB-ID: 2941767
    Baaijens, J. A., Van der Roest, B., Köster, J., Stougie, L., & Schönhuth, A. (2018). Full-length de novo viral quasispecies assembly through variation graph construction. bioRxiv
    PUB | Preprint
     
  • [32]
    2018 | Preprint | Veröffentlicht | PUB-ID: 2941768
    Yin, B., Balvert, M., Zambrano, D., Schönhuth, A., & Bohte, S. (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., Aabidine, A. Z. E., Rivals, E., & Schönhuth, A. (2017). De novo assembly of viral quasispecies using overlap graphs. Genome Research, 27(5), 835-848. doi:10.1101/gr.215038.116
    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. doi:10.7717/peerj-cs.117
    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), 4015-4023. doi:10.1093/bioinformatics/btx020
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [27]
    2017 | Preprint | Veröffentlicht | PUB-ID: 2941789
    Dijkstra, L. J., Köster, J., Marschall, T., & Schönhuth, A. (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., Cretu-Stancu, M., Garimella, K. V., Fromer, M., Kloosterman, W. P., Samocha, K. E., Neale, B. M., et al. (2016). A framework for the detection of de novo mutations in family-based sequencing data. European Journal of Human Genetics, 25(2), 227-233. doi:10.1038/ejhg.2016.147
    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), i649-i657. doi:10.1093/bioinformatics/btw426
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [24]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790
    Hehir-Kwa, J. Y., Marschall, T., Kloosterman, W. P., Francioli, L. C., Baaijens, J. A., Dijkstra, L. J., Abdellaoui, A., et al. (2016). A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications, 7(1), 12989. doi:10.1038/ncomms12989
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [23]
    2016 | Preprint | Veröffentlicht | PUB-ID: 2941794
    Martin, M., Patterson, M., Garg, S., O Fischer, S., Pisanti, N., Klau, G. W., Schönhuth, A., et al. (2016). WhatsHap: fast and accurate read-based phasing. bioRxiv
    PUB | Preprint
     
  • [22]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807
    Palamara, P. F., Francioli, L. C., Wilton, P. R., Genovese, G., Gusev, A., Finucane, H. K., Sankararaman, S., et al. (2015). Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. The American Journal of Human Genetics, 97(6), 775-789. https://doi.org/10.1016/j.ajhg.2015.10.006
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [21]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797
    Kloosterman, W. P., Francioli, L. C., Hormozdiari, F., Marschall, T., Hehir-Kwa, J. Y., Abdellaoui, A., Lameijer, E. - W., et al. (2015). Characteristics of de novo structural changes in the human genome. Genome Research, 25(6), 792-801. doi:10.1101/gr.185041.114
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [20]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798
    Leung, W. Y., Marschall, T., Paudel, Y., Falquet, L., Mei, H., Schönhuth, A., & Maoz, T. Y. (2015). SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines. BMC Genomics, 16(1), 238. doi:10.1186/s12864-015-1376-9
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [19]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941804
    van Leeuwen, E. M., Karssen, L. C., Deelen, J., Isaacs, A., Medina-Gomez, C., Mbarek, H., Kanterakis, A., et al. (2015). Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nature Communications, 6(1), 6065. doi:10.1038/ncomms7065
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [18]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941799
    Patterson, M., Marschall, T., Pisanti, N., van Iersel, L., Stougie, L., Klau, G. W., & Schönhuth, A. (2015). WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Journal of Computational Biology, 22(6), 498-509. doi:10.1089/cmb.2014.0157
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [17]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803
    van Leeuwen, E. M., Kanterakis, A., Deelen, P., Kattenberg, M. V., Slagboom, P. E., de Bakker, P. I. W., Wijmenga, C., et al. (2015). Population-specific genotype imputations using minimac or IMPUTE2. Nature Protocols, 10(9), 1285-1296. doi:10.1038/nprot.2015.077
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [16]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805
    Francioli, L. C., Polak, P. P., Koren, A., Menelaou, A., Chun, S., Renkens, I., van Duijn, C. M., et al. (2015). Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics, 47(7), 822-826. doi:10.1038/ng.3292
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [15]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612 OA
    Wittler, R., Marschall, T., Schönhuth, A., & Makinen, V. (2015). Repeat- and error-aware comparison of deletions. Bioinformatics, 31(18), 2947-2954. doi:10.1093/bioinformatics/btv304
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [14]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941795
    Cijvat, R., Manegold, S., Kersten, M., Klau, G. W., Schönhuth, A., Marschall, T., & Zhang, Y. (2015). Genome sequence analysis with MonetDB. Datenbank-Spektrum, 15(3), 185-191. doi:10.1007/s13222-015-0198-x
    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., Menelaou, A., van Leeuwen, E. M., Kanterakis, A., van Dijk, F., Medina-Gomez, C., Francioli, L. C., 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), 1321-1326. doi:10.1038/ejhg.2014.19
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [11]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810
    Töpfer, A., Marschall, T., Bull, R. A., Luciani, F., Schönhuth, A., & Beerenwinkel, N. (2014). Viral Quasispecies Assembly via Maximal Clique Enumeration. PLoS Computational Biology, 10(3), e1003515. doi:10.1371/journal.pcbi.1003515
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [10]
    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941835
    El-Kebir, M., Marschall, T., Wohlers, I., Patterson, M., Heringa, J., Schönhuth, A., & Klau, G. W. (2013). Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics, 14(S15), S18. doi:10.1186/1471-2105-14-s15-s18
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [9]
    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941837
    Allhoff, M., Schönhuth, A., Martin, M., Costa, I. G., Rahmann, S., & Marschall, T. (2013). Discovering motifs that induce sequencing errors. BMC Bioinformatics, 14(Suppl 5), S1. doi:10.1186/1471-2105-14-s5-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), 3143-3150. doi:10.1093/bioinformatics/btt556
    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., Costa, I. G., Canzar, S., Bauer, M., Klau, G. W., Schliep, A., & Schönhuth, A. (2012). CLEVER: clique-enumerating variant finder. Bioinformatics, 28(22), 2875-2882. doi:10.1093/bioinformatics/bts566
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [5]
    2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840
    Hajirasouliha, I., Schönhuth, A., de Juan, D., Valencia, A., & Sahinalp, S. C. (2012). Mirroring co-evolving trees in the light of their topologies. Bioinformatics, 28(9), 1202-1208. doi:10.1093/bioinformatics/bts109
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [4]
    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941841
    Singer, M., Engström, A., Schönhuth, A., & Pachter, L. (2011). Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains. Statistical Applications in Genetics and Molecular Biology, 10(1), 759. doi:10.2202/1544-6115.1677
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [3]
    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842
    Hafemeister, C., Costa, I. G., Schönhuth, A., & Schliep, A. (2011). Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. Bioinformatics, 27(7), 946-952. doi:10.1093/bioinformatics/btr037
    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), 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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