PUB - Publikationen an der Universität Bielefeld

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• [54]
  

  2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985113

  X. Kang, et al., “Hybrid-hybrid correction of errors in long reads with HERO”, Genome Biology , vol. 24, 2023, : 275.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [53]
  

  2023 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2969521

  X. Luo, X. Kang, and A. Schönhuth, “Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks”, Nature Machine Intelligence , 2023.

  PUB | DOI | WoS
   
• [52]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966833

  X. Luo, X. Kang, and A. Schönhuth, “VeChat: correcting errors in long reads using variation graphs”, Nature Communications, vol. 13, 2022, : 6657.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [51]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2963686

  X. Luo, X. Kang, and A. Schönhuth, “Enhancing Long-Read-Based Strain-Aware Metagenome Assembly”, Frontiers in Genetics, vol. 13, 2022, : 868280.

  PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [50]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2964174

  X. Kang, X. Luo, and A. Schönhuth, “StrainXpress: strain aware metagenome assembly from short reads”, Nucleic Acids Research , vol. 50, 2022, : gkac543.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [49]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2960849

  X. Luo, X. Kang, and A. Schönhuth, “Strainline: full-length de novo viral haplotype reconstruction from noisy long reads”, Genome Biology , vol. 23, 2022, : 29.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [48]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967245

  S. Ray, et al., “Deep variational graph autoencoders for novel host-directed therapy options against COVID-19”, Artificial Intelligence in Medicine, vol. 134, 2022, : 102418.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [47]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2958717

  X. Luo, X. Kang, and A. Schönhuth, “phasebook: haplotype-aware de novo assembly of diploid genomes from long reads”, Genome Biology, vol. 22, 2021, : 299.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [46]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952469

  P.I. Metselaar, et al., “Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome.”, Scientific reports, vol. 11, 2021, : 4541.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [45]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959624

  D. Lahnemann, et al., “Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo”, Nature Communications, vol. 12, 2021, : 6744.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [44]
  

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945617

  A. Lopez-Rincon, et al., “Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification”, Cancers, vol. 12, 2020, : 1785.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [43]
  

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2943113

  J. Koster, et al., “Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery.”, Genome biology, vol. 21, 2020.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [42]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941754

  J.A. Baaijens, et al., “Full-length de novo viral quasispecies assembly through variation graph construction”, Bioinformatics, vol. 35, 2019, pp. 5086-5094.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [41]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756

  B. Yin, et al., “Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype”, Bioinformatics, vol. 35, 2019, pp. i538-i547.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [40]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760

  A. Lopez-Rincon, et al., “Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection”, BMC Bioinformatics, vol. 20, 2019, : 480.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [39]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941677

  L. Denti, et al., “MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants”, iScience, vol. 18, 2019, pp. 20-27.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [38]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941761

  J.A. Baaijens and A. Schönhuth, “Overlap graph-based generation of haplotigs for diploids and polyploids”, Bioinformatics, vol. 35, 2019, pp. 4281-4289.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [37]
  

  2019 | Preprint | Veröffentlicht | PUB-ID: 2941762

  M. Balvert, et al., “OGRE: Overlap Graph-based metagenomic Read clustEring”, bioRxiv, 2019.

  PUB | Preprint
   
• [36]
  

  2019 | Preprint | Veröffentlicht | PUB-ID: 2941763

  J.A. Baaijens, L. Stougie, and A. Schönhuth, “Strain-aware assembly of genomes from mixed samples using flow variation graphs”, bioRxiv, 2019.

  PUB | Preprint
   
• [35]
  

  2019 | Preprint | Veröffentlicht | PUB-ID: 2941764

  D. Laehnemann, et al., “12 Grand Challenges in Single-Cell Data Science”, PeerJ, 2019.

  PUB
   
• [34]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941769

  B. Ibrahim, et al., “Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting”, Viruses, vol. 10, 2018, : 256.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [33]
  

  2018 | Preprint | Veröffentlicht | PUB-ID: 2941767

  J.A. Baaijens, et al., “Full-length de novo viral quasispecies assembly through variation graph construction”, bioRxiv, 2018.

  PUB | Preprint
   
• [32]
  

  2018 | Preprint | Veröffentlicht | PUB-ID: 2941768

  B. Yin, et al., “An image representation based convolutional network for DNA classification”, arXiv:1806.04931, 2018.

  PUB | arXiv
   
• [31]
  

  2018 | Preprint | Veröffentlicht | PUB-ID: 2941765

  R. Chikhi and A. Schönhuth, “Dualities in Tree Representations”, arXiv:1804.04263, 2018.

  PUB | arXiv
   
• [30]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941784

  J.A. Baaijens, et al., “De novo assembly of viral quasispecies using overlap graphs”, Genome Research, vol. 27, 2017, pp. 835-848.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [29]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941785

  J. Dröge, A. Schönhuth, and A.C. McHardy, “A probabilistic model to recover individual genomes from metagenomes”, PeerJ Computer Science, vol. 3, 2017, : e117.

  PUB | DOI | WoS
   
• [28]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941786

  J. Ebler, A. Schönhuth, and T. Marschall, “Genotyping inversions and tandem duplications”, Bioinformatics, vol. 33, 2017, pp. 4015-4023.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [27]
  

  2017 | Preprint | Veröffentlicht | PUB-ID: 2941789

  L.J. Dijkstra, et al., “Enhancing sensitivity and controlling false discovery rate in somatic indel discovery using a latent variable model”, bioRxiv, 2017.

  PUB | Preprint
   
• [26]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941788

  L.C. Francioli, et al., “A framework for the detection of de novo mutations in family-based sequencing data”, European Journal of Human Genetics, vol. 25, 2016, pp. 227-233.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [25]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793

  I. Gregor, A. Schönhuth, and A.C. McHardy, “Snowball: strain aware gene assembly of metagenomes”, Bioinformatics, vol. 32, 2016, pp. i649-i657.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [24]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790

  J.Y. Hehir-Kwa, et al., “A high-quality human reference panel reveals the complexity and distribution of genomic structural variants”, Nature Communications, vol. 7, 2016, : 12989.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [23]
  

  2016 | Preprint | Veröffentlicht | PUB-ID: 2941794

  M. Martin, et al., “WhatsHap: fast and accurate read-based phasing”, bioRxiv, 2016.

  PUB | Preprint
   
• [22]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807

  P.F. Palamara, et al., “Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates”, The American Journal of Human Genetics, vol. 97, 2015, pp. 775-789.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [21]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797

  W.P. Kloosterman, et al., “Characteristics of de novo structural changes in the human genome”, Genome Research, vol. 25, 2015, pp. 792-801.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [20]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798

  W.Y. Leung, et al., “SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines”, BMC Genomics, vol. 16, 2015, : 238.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [19]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941804

  E.M. van Leeuwen, et al., “Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels”, Nature Communications, vol. 6, 2015, : 6065.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [18]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941799

  M. Patterson, et al., “WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads”, Journal of Computational Biology, vol. 22, 2015, pp. 498-509.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [17]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803

  E.M. van Leeuwen, et al., “Population-specific genotype imputations using minimac or IMPUTE2”, Nature Protocols, vol. 10, 2015, pp. 1285-1296.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [16]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805

  L.C. Francioli, et al., “Genome-wide patterns and properties of de novo mutations in humans”, Nature Genetics, vol. 47, 2015, pp. 822-826.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [15]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612

  R. Wittler, et al., “Repeat- and error-aware comparison of deletions”, Bioinformatics, vol. 31, 2015, pp. 2947-2954.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [14]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941795

  R. Cijvat, et al., “Genome sequence analysis with MonetDB”, Datenbank-Spektrum, vol. 15, 2015, pp. 185-191.

  PUB | DOI
   
• [13]
  

  2015 | Preprint | PUB-ID: 2941808

  U. Faigle and A. Schönhuth, “On Hidden States in Quantum Random Walks”, arXiv:1601.02882, 2015.

  PUB | arXiv
   
• [12]
  

  2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941816

  P. Deelen, et al., “Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’”, European Journal of Human Genetics, vol. 22, 2014, pp. 1321-1326.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [11]
  

  2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810

  A. Töpfer, et al., “Viral Quasispecies Assembly via Maximal Clique Enumeration”, PLoS Computational Biology, vol. 10, 2014, : e1003515.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [10]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941835

  M. El-Kebir, et al., “Mapping proteins in the presence of paralogs using units of coevolution”, BMC Bioinformatics, vol. 14, 2013, : S18.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [9]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941837

  M. Allhoff, et al., “Discovering motifs that induce sequencing errors”, BMC Bioinformatics, vol. 14, 2013, : S1.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [8]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941836

  T. Marschall, I. Hajirasouliha, and A. Schönhuth, “MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels”, Bioinformatics, vol. 29, 2013, pp. 3143-3150.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [7]
  

  2013 | Preprint | Veröffentlicht | PUB-ID: 2941838

  T. Marschall and A. Schönhuth, “Sensitive Long-Indel-Aware Alignment of Sequencing Reads”, arXiv:1303.3520, 2013.

  PUB | arXiv
   
• [6]
  

  2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941839

  T. Marschall, et al., “CLEVER: clique-enumerating variant finder”, Bioinformatics, vol. 28, 2012, pp. 2875-2882.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [5]
  

  2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840

  I. Hajirasouliha, et al., “Mirroring co-evolving trees in the light of their topologies”, Bioinformatics, vol. 28, 2012, pp. 1202-1208.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [4]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941841

  M. Singer, et al., “Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains”, Statistical Applications in Genetics and Molecular Biology, vol. 10, 2011, pp. 759.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [3]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842

  C. Hafemeister, et al., “Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions”, Bioinformatics, vol. 27, 2011, pp. 946-952.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [2]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941814

  A. Schönhuth, “Generic identification of binary-valued hidden Markov processes”, Journal of Algebraic Statistics, vol. 5, 2011, pp. 72-99.

  PUB
   
• [1]
  

  2010 | Preprint | Veröffentlicht | PUB-ID: 2941843

  U. Faigle and A. Schönhuth, “A Markovian Model for Joint Observations, Bell's Inequality and Hidden States”, arXiv:1011.1295, 2010.

  PUB | arXiv