PUB - Publikationen an der Universität Bielefeld

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• [56]
  

  2024 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2993654

  HyLight: Strain aware assembly of low coverage metagenomes
  Kang X, Zhang W, Li Y, Luo X, Schönhuth A (2024)
  Nature Communications 15(1): 8665.

  PUB | DOI | PubMed | Europe PMC
   
• [55]
  

  2024 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2990178

  Computing linkage disequilibrium aware genome embeddings using autoencoders
  Tas G, Westerdijk T, Postma E, Veldink JH, Schönhuth A, Balvert M (2024)
  Bioinformatics: btae326.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [54]
  

  2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985113

  Hybrid-hybrid correction of errors in long reads with HERO
  Kang X, Xu J, Luo X, Schönhuth A (2023)
  Genome Biology 24(1): 275.

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

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

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

  PUB | DOI | WoS
   
• [52]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966833

  VeChat: correcting errors in long reads using variation graphs
  Luo X, Kang X, Schönhuth A (2022)
  Nature Communications 13(1): 6657.

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

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2963686

  Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
  Luo X, Kang X, Schönhuth A (2022)
  Frontiers in Genetics 13: 868280.

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

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2964174

  StrainXpress: strain aware metagenome assembly from short reads
  Kang X, Luo X, Schönhuth A (2022)
  Nucleic Acids Research 50(17): gkac543.

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

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2960849

  Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
  Luo X, Kang X, Schönhuth A (2022)
  Genome Biology 23(1): 29.

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

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967245

  Deep variational graph autoencoders for novel host-directed therapy options against COVID-19
  Ray S, Lall S, Mukhopadhyay A, Bandyopadhyay S, Schönhuth A (2022)
  Artificial Intelligence in Medicine 134: 102418.

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

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2958717

  phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
  Luo X, Kang X, Schönhuth A (2021)
  Genome Biology 22(1): 299.

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

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952469

  Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome.
  Metselaar PI, Mendoza-Maldonado L, Li Yim AYF, Abarkan I, Henneman P, Te Velde AA, Schönhuth A, Bosch JA, Kraneveld AD, Lopez-Rincon A (2021)
  Scientific reports 11(1): 4541.

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

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959624

  Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo
  Lahnemann D, Koster J, Fischer U, Borkhardt A, McHardy AC, Schönhuth A (2021)
  Nature Communications 12(1): 6744.

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

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945617

  Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification
  Lopez-Rincon A, Mendoza-Maldonado L, Martinez-Archundia M, Schönhuth A, Kraneveld AD, Garssen J, Tonda A (2020)
  Cancers 12(7): 1785.

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

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2943113

  Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery.
  Koster J, Dijkstra LJ, Marschall T, Schönhuth A (2020)
  Genome biology 21(1).

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

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941754

  Full-length de novo viral quasispecies assembly through variation graph construction
  Baaijens JA, Van der Roest B, Köster J, Stougie L, Schönhuth A (2019)
  Bioinformatics 35(24): 5086-5094.

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

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756

  Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype
  Yin B, Balvert M, van der Spek RAA, Dutilh BE, Bohté S, Veldink J, Schönhuth A (2019)
  Bioinformatics 35(14): i538-i547.

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

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760

  Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection
  Lopez-Rincon A, Martinez-Archundia M, Martinez-Ruiz GU, Schönhuth A, Tonda A (2019)
  BMC Bioinformatics 20(1): 480.

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

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941677

  MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants
  Denti L, Previtali M, Bernardini G, Schönhuth A, Bonizzoni P (2019)
  iScience 18: 20-27.

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

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941761

  Overlap graph-based generation of haplotigs for diploids and polyploids
  Baaijens JA, Schönhuth A (2019)
  Bioinformatics 35(21): 4281-4289.

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

  2019 | Preprint | Veröffentlicht | PUB-ID: 2941762

  OGRE: Overlap Graph-based metagenomic Read clustEring
  Balvert M, Hauptfeld T, Schönhuth A, Dutilh BE (2019)
  bioRxiv.

  PUB | Preprint
   
• [36]
  

  2019 | Preprint | Veröffentlicht | PUB-ID: 2941763

  Strain-aware assembly of genomes from mixed samples using flow variation graphs
  Baaijens JA, Stougie L, Schönhuth A (2019)
  bioRxiv.

  PUB | Preprint
   
• [35]
  

  2019 | Preprint | Veröffentlicht | PUB-ID: 2941764

  12 Grand Challenges in Single-Cell Data Science
  Laehnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Beerenwinkel N, Campbell KR, Mahfouz A, Pinello L, et al. (2019)
  PeerJ.

  PUB
   
• [34]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941769

  Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting
  Ibrahim B, Arkhipova K, Andeweg A, Posada-Céspedes S, Enault F, Gruber A, Koonin E, Kupczok A, Lemey P, McHardy A, McMahon D, et al. (2018)
  Viruses 10(5): 256.

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

  2018 | Preprint | Veröffentlicht | PUB-ID: 2941767

  Full-length de novo viral quasispecies assembly through variation graph construction
  Baaijens JA, Van der Roest B, Köster J, Stougie L, Schönhuth A (2018)
  bioRxiv.

  PUB | Preprint
   
• [32]
  

  2018 | Preprint | Veröffentlicht | PUB-ID: 2941768

  An image representation based convolutional network for DNA classification
  Yin B, Balvert M, Zambrano D, Schönhuth A, Bohte S (2018)
  arXiv:1806.04931.

  PUB | arXiv
   
• [31]
  

  2018 | Preprint | Veröffentlicht | PUB-ID: 2941765

  Dualities in Tree Representations
  Chikhi R, Schönhuth A (2018)
  arXiv:1804.04263.

  PUB | arXiv
   
• [30]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941784

  De novo assembly of viral quasispecies using overlap graphs
  Baaijens JA, Aabidine AZE, Rivals E, Schönhuth A (2017)
  Genome Research 27(5): 835-848.

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

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941785

  A probabilistic model to recover individual genomes from metagenomes
  Dröge J, Schönhuth A, McHardy AC (2017)
  PeerJ Computer Science 3: e117.

  PUB | DOI | WoS
   
• [28]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941786

  Genotyping inversions and tandem duplications
  Ebler J, Schönhuth A, Marschall T (2017)
  Bioinformatics 33(24): 4015-4023.

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

  2017 | Preprint | Veröffentlicht | PUB-ID: 2941789

  Enhancing sensitivity and controlling false discovery rate in somatic indel discovery using a latent variable model
  Dijkstra LJ, Köster J, Marschall T, Schönhuth A (2017)
  bioRxiv.

  PUB | Preprint
   
• [26]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941788

  A framework for the detection of de novo mutations in family-based sequencing data
  Francioli LC, Cretu-Stancu M, Garimella KV, Fromer M, Kloosterman WP, Samocha KE, Neale BM, Daly MJ, Banks E, DePristo MA, de Bakker PIW, et al. (2016)
  European Journal of Human Genetics 25(2): 227-233.

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

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793

  Snowball: strain aware gene assembly of metagenomes
  Gregor I, Schönhuth A, McHardy AC (2016)
  Bioinformatics 32(17): i649-i657.

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

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790

  A high-quality human reference panel reveals the complexity and distribution of genomic structural variants
  Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, et al. (2016)
  Nature Communications 7(1): 12989.

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

  2016 | Preprint | Veröffentlicht | PUB-ID: 2941794

  WhatsHap: fast and accurate read-based phasing
  Martin M, Patterson M, Garg S, O Fischer S, Pisanti N, Klau GW, Schönhuth A, Marschall T (2016)
  bioRxiv.

  PUB | Preprint
   
• [22]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807

  Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates
  Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S, Sunyaev SR, de Bakker PIW, Wakeley J, Pe’er I, et al. (2015)
  The American Journal of Human Genetics 97(6): 775-789.

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

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797

  Characteristics of de novo structural changes in the human genome
  Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer E-W, Moed MH, Koval V, Renkens I, van Roosmalen MJ, et al. (2015)
  Genome Research 25(6): 792-801.

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

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798

  SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines
  Leung WY, Marschall T, Paudel Y, Falquet L, Mei H, Schönhuth A, Maoz TY (2015)
  BMC Genomics 16(1): 238.

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

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941804

  Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels
  van Leeuwen EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, Kanterakis A, Trompet S, Postmus I, Verweij N, van Enckevort DJ, et al. (2015)
  Nature Communications 6(1): 6065.

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

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941799

  WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads
  Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A (2015)
  Journal of Computational Biology 22(6): 498-509.

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

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803

  Population-specific genotype imputations using minimac or IMPUTE2
  van Leeuwen EM, Kanterakis A, Deelen P, Kattenberg MV, Slagboom PE, de Bakker PIW, Wijmenga C, Swertz MA, Boomsma DI, van Duijn CM, Karssen LC, et al. (2015)
  Nature Protocols 10(9): 1285-1296.

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

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805

  Genome-wide patterns and properties of de novo mutations in humans
  Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, et al. (2015)
  Nature Genetics 47(7): 822-826.

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

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612

  Repeat- and error-aware comparison of deletions
  Wittler R, Marschall T, Schönhuth A, Makinen V (2015)
  Bioinformatics 31(18): 2947-2954.

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

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941795

  Genome sequence analysis with MonetDB
  Cijvat R, Manegold S, Kersten M, Klau GW, Schönhuth A, Marschall T, Zhang Y (2015)
  Datenbank-Spektrum 15(3): 185-191.

  PUB | DOI
   
• [13]
  

  2015 | Preprint | PUB-ID: 2941808

  On Hidden States in Quantum Random Walks
  Faigle U, Schönhuth A (2015)
  arXiv:1601.02882.

  PUB | arXiv
   
• [12]
  

  2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941816

  Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’
  Deelen P, Menelaou A, van Leeuwen EM, Kanterakis A, van Dijk F, Medina-Gomez C, Francioli LC, Hottenga JJ, Karssen LC, Estrada K, Kreiner-Møller E, et al. (2014)
  European Journal of Human Genetics 22(11): 1321-1326.

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

  2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810

  Viral Quasispecies Assembly via Maximal Clique Enumeration
  Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N (2014)
  PLoS Computational Biology 10(3): e1003515.

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

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941835

  Mapping proteins in the presence of paralogs using units of coevolution
  El-Kebir M, Marschall T, Wohlers I, Patterson M, Heringa J, Schönhuth A, Klau GW (2013)
  BMC Bioinformatics 14(S15): S18.

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

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941837

  Discovering motifs that induce sequencing errors
  Allhoff M, Schönhuth A, Martin M, Costa IG, Rahmann S, Marschall T (2013)
  BMC Bioinformatics 14(Suppl 5): S1.

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

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941836

  MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels
  Marschall T, Hajirasouliha I, Schönhuth A (2013)
  Bioinformatics 29(24): 3143-3150.

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

  2013 | Preprint | Veröffentlicht | PUB-ID: 2941838

  Sensitive Long-Indel-Aware Alignment of Sequencing Reads
  Marschall T, Schönhuth A (2013)
  arXiv:1303.3520.

  PUB | arXiv
   
• [6]
  

  2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941839

  CLEVER: clique-enumerating variant finder
  Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schönhuth A (2012)
  Bioinformatics 28(22): 2875-2882.

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

  2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840

  Mirroring co-evolving trees in the light of their topologies
  Hajirasouliha I, Schönhuth A, de Juan D, Valencia A, Sahinalp SC (2012)
  Bioinformatics 28(9): 1202-1208.

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

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941841

  Determining Coding CpG Islands by Identifying Regions Significant for Pattern Statistics on Markov Chains
  Singer M, Engström A, Schönhuth A, Pachter L (2011)
  Statistical Applications in Genetics and Molecular Biology 10(1): 759.

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

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842

  Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions
  Hafemeister C, Costa IG, Schönhuth A, Schliep A (2011)
  Bioinformatics 27(7): 946-952.

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

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941814

  Generic identification of binary-valued hidden Markov processes
  Schönhuth A (2011)
  Journal of Algebraic Statistics 5(1): 72-99.

  PUB
   
• [1]
  

  2010 | Preprint | Veröffentlicht | PUB-ID: 2941843

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

  PUB | arXiv