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.
    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, 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.
    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 PI, Mendoza-Maldonado L, Li Yim AYF, Abarkan I, Henneman P, Te Velde AA, Schönhuth A, Bosch JA, Kraneveld AD, Lopez-Rincon A (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, Koster J, Fischer U, Borkhardt A, McHardy AC, Schönhuth A (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, Mendoza-Maldonado L, Martinez-Archundia M, Schönhuth A, Kraneveld AD, Garssen J, Tonda A (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, Dijkstra LJ, Marschall T, Schönhuth A (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 JA, 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.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [41]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756
    Yin B, Balvert M, van der Spek RAA, Dutilh BE, 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.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [40]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760
    Lopez-Rincon A, Martinez-Archundia M, Martinez-Ruiz GU, Schönhuth A, Tonda A (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, Previtali M, Bernardini G, Schönhuth A, Bonizzoni P (2019)
    MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants.
    iScience 18: 20-27.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [38]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941761
    Baaijens JA, Schönhuth A (2019)
    Overlap graph-based generation of haplotigs for diploids and polyploids.
    Bioinformatics 35(21): 4281-4289.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [37]
    2019 | Preprint | Veröffentlicht | PUB-ID: 2941762
    Balvert M, Hauptfeld T, Schönhuth A, Dutilh BE (2019)
    OGRE: Overlap Graph-based metagenomic Read clustEring.
    bioRxiv.
    PUB | Preprint
     
  • [36]
    2019 | Preprint | Veröffentlicht | PUB-ID: 2941763
    Baaijens JA, 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 DJ, Hicks SC, Robinson MD, Vallejos CA, Beerenwinkel N, Campbell KR, Mahfouz A, Pinello L, Skums P, Stamatakis A, Stephan-Otto Attolini C, Aparicio S, Baaijens J, Balvert M, de Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Jessurun Lobo T, Keizer EM, Khatri I, Kiełbasa SM, Korbel JO, Kozlov AM, Kuo T-H, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowski Ł, Reinders M, de Ridder J, Saliba A-E, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A (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, Kupczok A, Lemey P, McHardy A, McMahon D, Pickett B, Robertson D, Scheuermann R, Zhernakova A, Zwart M, Schönhuth A, Dutilh B, Marz M (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 JA, 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 JA, Aabidine AZE, Rivals E, Schönhuth A (2017)
    De novo assembly of viral quasispecies using overlap graphs.
    Genome Research 27(5): 835-848.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [29]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941785
    Dröge J, Schönhuth A, McHardy AC (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): 4015-4023.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [27]
    2017 | Preprint | Veröffentlicht | PUB-ID: 2941789
    Dijkstra LJ, 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 LC, Cretu-Stancu M, Garimella KV, Fromer M, Kloosterman WP, Samocha KE, Neale BM, Daly MJ, Banks E, DePristo MA, de Bakker PIW, Schönhuth A (2016)
    A framework for the detection of de novo mutations in family-based sequencing data.
    European Journal of Human Genetics 25(2): 227-233.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [25]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793
    Gregor I, Schönhuth A, McHardy AC (2016)
    Snowball: strain aware gene assembly of metagenomes.
    Bioinformatics 32(17): i649-i657.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [24]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790
    Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer E-W, van Dijk F, Hormozdiari F, Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PIW, Swertz MA, Wijmenga C, van Ommen G-JB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V (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, Patterson M, Garg S, O Fischer S, Pisanti N, Klau GW, Schönhuth A, Marschall T (2016)
    WhatsHap: fast and accurate read-based phasing.
    bioRxiv.
    PUB | Preprint
     
  • [22]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807
    Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S, Sunyaev SR, de Bakker PIW, Wakeley J, Pe’er I, Price AL, Schönhuth A (2015)
    Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.
    The American Journal of Human Genetics 97(6): 775-789.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [21]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797
    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, Arp P, Karssen LC, Coe BP, Handsaker RE, Suchiman ED, Cuppen E, Thung DT, McVey M, Wendl MC, Uitterlinden A, van Duijn CM, Swertz MA, Wijmenga C, van Ommen GJB, Slagboom PE, Boomsma DI, Schönhuth A, Eichler EE, de Bakker PIW, Ye K, Guryev V (2015)
    Characteristics of de novo structural changes in the human genome.
    Genome Research 25(6): 792-801.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [20]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798
    Leung WY, Marschall T, Paudel Y, Falquet L, Mei H, Schönhuth A, Maoz TY (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 EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, Kanterakis A, Trompet S, Postmus I, Verweij N, van Enckevort DJ, Huffman JE, White CC, Feitosa MF, Bartz TM, Manichaikul A, Joshi PK, Peloso GM, Deelen P, van Dijk F, Willemsen G, de Geus EJ, Milaneschi Y, Penninx BWJH, Francioli LC, Menelaou A, Pulit SL, Rivadeneira F, Hofman A, Oostra BA, Franco OH, Leach IM, Beekman M, de Craen AJM, Uh H-W, Trochet H, Hocking LJ, Porteous DJ, Sattar N, Packard CJ, Buckley BM, Brody JA, Bis JC, Rotter JI, Mychaleckyj JC, Campbell H, Duan Q, Lange LA, Wilson JF, Hayward C, Polasek O, Vitart V, Rudan I, Wright AF, Rich SS, Psaty BM, Borecki IB, Kearney PM, Stott DJ, Adrienne Cupples L, Jukema JW, van der Harst P, Sijbrands EJ, Hottenga J-J, Uitterlinden AG, Swertz MA, van Ommen G-JB, de Bakker PIW, Eline Slagboom P, Boomsma DI, Wijmenga C, van Duijn CM, Schönhuth A (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, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A (2015)
    WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
    Journal of Computational Biology 22(6): 498-509.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [17]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803
    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, Hottenga JJ, Schönhuth A (2015)
    Population-specific genotype imputations using minimac or IMPUTE2.
    Nature Protocols 10(9): 1285-1296.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [16]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805
    Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PIW, Sunyaev SR, Schönhuth A (2015)
    Genome-wide patterns and properties of de novo mutations in humans.
    Nature Genetics 47(7): 822-826.
    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.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [14]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941795
    Cijvat R, Manegold S, Kersten M, Klau GW, Schönhuth A, Marschall T, Zhang Y (2015)
    Genome sequence analysis with MonetDB.
    Datenbank-Spektrum 15(3): 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, Menelaou A, van Leeuwen EM, Kanterakis A, van Dijk F, Medina-Gomez C, Francioli LC, Hottenga JJ, Karssen LC, Estrada K, Kreiner-Møller E, Rivadeneira F, van Setten J, Gutierrez-Achury J, Westra H-J, Franke L, van Enckevort D, Dijkstra M, Byelas H, van Duijn CM, de Bakker PIW, Wijmenga C, Swertz MA, Schönhuth A (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.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [11]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810
    Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N (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, Marschall T, Wohlers I, Patterson M, Heringa J, Schönhuth A, Klau GW (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, Schönhuth A, Martin M, Costa IG, Rahmann S, Marschall T (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): 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, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schönhuth A (2012)
    CLEVER: clique-enumerating variant finder.
    Bioinformatics 28(22): 2875-2882.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [5]
    2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840
    Hajirasouliha I, Schönhuth A, de Juan D, Valencia A, Sahinalp SC (2012)
    Mirroring co-evolving trees in the light of their topologies.
    Bioinformatics 28(9): 1202-1208.
    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.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [3]
    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842
    Hafemeister C, Costa IG, Schönhuth A, Schliep A (2011)
    Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.
    Bioinformatics 27(7): 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): 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
     
Markierte Publikation(en)

Suche

Publikationen filtern

Darstellung / Sortierung

Export / Einbettung