54 Publikationen
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2023 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2969521Luo, X., Kang, X. & Schönhuth, A. (2023). Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks. Nature Machine Intelligence . Springer Nature. doi:10.1038/s42256-022-00604-2.
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2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2963686Luo, X., Kang, X. & Schönhuth, A. (2022). Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Frontiers in Genetics, 13: 868280. Frontiers Media. doi:10.3389/fgene.2022.868280.
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2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2964174Kang, X., Luo, X. & Schönhuth, A. (2022). StrainXpress: strain aware metagenome assembly from short reads. Nucleic Acids Research , 50(17): gkac543. Oxford University Press. doi:10.1093/nar/gkac543.
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2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2960849Luo, X., Kang, X. & Schönhuth, A. (2022). Strainline: full-length de novo viral haplotype reconstruction from noisy long reads. Genome Biology , 23(1): 29. BioMed Central. doi:10.1186/s13059-021-02587-6.
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2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967245Ray, 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. Elsevier. doi:10.1016/j.artmed.2022.102418.
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2958717Luo, X., Kang, X. & Schönhuth, A. (2021). phasebook: haplotype-aware de novo assembly of diploid genomes from long reads. Genome Biology, 22(1): 299. BioMed Central. doi:10.1186/s13059-021-02512-x.
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952469Metselaar, P.I., Mendoza-Maldonado, L., Li Yim, A.Y.F., Abarkan, I., Henneman, P., Te Velde, A.A., Schönhuth, A., Bosch, J.A., Kraneveld, A.D. & 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. Springer Nature. doi:10.1038/s41598-021-83660-9.
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959624Lahnemann, 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. Nature. doi:10.1038/s41467-021-26938-w.
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2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945617Lopez-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. MDPI. doi:10.3390/cancers12071785.
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2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2943113Koster, 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). BioMed Central. doi:10.1186/s13059-020-01993-6.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941754Baaijens, 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. Oxford University Press (OUP). doi:10.1093/bioinformatics/btz443.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756Yin, 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. Oxford University Press (OUP). doi:10.1093/bioinformatics/btz369.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760Lopez-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. BioMed Central. doi:10.1186/s12859-019-3050-8.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941677Denti, L., Previtali, M., Bernardini, G., Schönhuth, A. & Bonizzoni, P. (2019). MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants. iScience, 18, 20-27. Elsevier BV. doi:10.1016/j.isci.2019.07.011.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941761Baaijens, J.A. & Schönhuth, A. (2019). Overlap graph-based generation of haplotigs for diploids and polyploids. Bioinformatics, 35(21), 4281-4289. Oxford University Press (OUP). doi:10.1093/bioinformatics/btz255.
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2019 | Preprint | Veröffentlicht | PUB-ID: 2941764Laehnemann, D., Köster, J., Szczurek, E., McCarthy, D.J., Hicks, S.C., Robinson, M.D., Vallejos, C.A., Beerenwinkel, N., Campbell, K.R., 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, B.E., Florescu, M., Guryev, V., Holmer, R., Jahn, K., Jessurun Lobo, T., Keizer, E.M., Khatri, I., Kiełbasa, S.M., Korbel, J.O., Kozlov, A.M., Kuo, T.-H., Lelieveldt, B.P.F., Mandoiu, I.I., Marioni, J.C., Marschall, T., Mölder, F., Niknejad, A., Rączkowski, Ł., Reinders, M., de Ridder, J., Saliba, A.-E., Somarakis, A., Stegle, O., Theis, F.J., Yang, H., Zelikovsky, A., McHardy, A.C., Raphael, B.J., Shah, S.P. & Schönhuth, A. (2019). 12 Grand Challenges in Single-Cell Data Science. PeerJ. PeerJ.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941769Ibrahim, 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. MDPI AG. doi:10.3390/v10050256.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941784Baaijens, 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. Cold Spring Harbor Laboratory. doi:10.1101/gr.215038.116.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941786Ebler, J., Schönhuth, A. & Marschall, T. (2017). Genotyping inversions and tandem duplications. Bioinformatics, 33(24), 4015-4023. Oxford University Press (OUP). doi:10.1093/bioinformatics/btx020.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941788Francioli, L.C., Cretu-Stancu, M., Garimella, K.V., Fromer, M., Kloosterman, W.P., Samocha, K.E., Neale, B.M., Daly, M.J., Banks, E., DePristo, M.A., de Bakker, P.I.W. & 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. Nature Publishing Group. doi:10.1038/ejhg.2016.147.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793Gregor, I., Schönhuth, A. & McHardy, A.C. (2016). Snowball: strain aware gene assembly of metagenomes. Bioinformatics, 32(17), i649-i657. Oxford University Press (OUP). doi:10.1093/bioinformatics/btw426.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790Hehir-Kwa, J.Y., Marschall, T., Kloosterman, W.P., Francioli, L.C., Baaijens, J.A., Dijkstra, L.J., Abdellaoui, A., Koval, V., Thung, D.T., Wardenaar, R., Renkens, I., Coe, B.P., Deelen, P., de Ligt, J., Lameijer, E.-W., van Dijk, F., Hormozdiari, F., Uitterlinden, A.G., van Duijn, C.M., Eichler, E.E., de Bakker, P.I.W., Swertz, M.A., Wijmenga, C., van Ommen, G.-J.B., Slagboom, P.E., Boomsma, D.I., 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. Nature Publishing Group. doi:10.1038/ncomms12989.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807Palamara, P.F., Francioli, L.C., Wilton, P.R., Genovese, G., Gusev, A., Finucane, H.K., Sankararaman, S., Sunyaev, S.R., de Bakker, P.I.W., Wakeley, J., Pe’er, I., Price, A.L. & Schönhuth, A. (2015). Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. The American Journal of Human Genetics, 97(6), 775-789. Elsevier BV. doi:10.1016/j.ajhg.2015.10.006.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797Kloosterman, W.P., Francioli, L.C., Hormozdiari, F., Marschall, T., Hehir-Kwa, J.Y., Abdellaoui, A., Lameijer, E.-W., Moed, M.H., Koval, V., Renkens, I., van Roosmalen, M.J., Arp, P., Karssen, L.C., Coe, B.P., Handsaker, R.E., Suchiman, E.D., Cuppen, E., Thung, D.T., McVey, M., Wendl, M.C., Uitterlinden, A., van Duijn, C.M., Swertz, M.A., Wijmenga, C., van Ommen, G.J.B., Slagboom, P.E., Boomsma, D.I., Schönhuth, A., Eichler, E.E., de Bakker, P.I.W., Ye, K. & Guryev, V. (2015). Characteristics of de novo structural changes in the human genome. Genome Research, 25(6), 792-801. Cold Spring Harbor Laboratory. doi:10.1101/gr.185041.114.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798Leung, 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. BioMed Central. doi:10.1186/s12864-015-1376-9.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941804van Leeuwen, E.M., Karssen, L.C., Deelen, J., Isaacs, A., Medina-Gomez, C., Mbarek, H., Kanterakis, A., Trompet, S., Postmus, I., Verweij, N., van Enckevort, D.J., Huffman, J.E., White, C.C., Feitosa, M.F., Bartz, T.M., Manichaikul, A., Joshi, P.K., Peloso, G.M., Deelen, P., van Dijk, F., Willemsen, G., de Geus, E.J., Milaneschi, Y., Penninx, B.W.J.H., Francioli, L.C., Menelaou, A., Pulit, S.L., Rivadeneira, F., Hofman, A., Oostra, B.A., Franco, O.H., Leach, I.M., Beekman, M., de Craen, A.J.M., Uh, H.-W., Trochet, H., Hocking, L.J., Porteous, D.J., Sattar, N., Packard, C.J., Buckley, B.M., Brody, J.A., Bis, J.C., Rotter, J.I., Mychaleckyj, J.C., Campbell, H., Duan, Q., Lange, L.A., Wilson, J.F., Hayward, C., Polasek, O., Vitart, V., Rudan, I., Wright, A.F., Rich, S.S., Psaty, B.M., Borecki, I.B., Kearney, P.M., Stott, D.J., Adrienne Cupples, L., Jukema, J.W., van der Harst, P., Sijbrands, E.J., Hottenga, J.-J., Uitterlinden, A.G., Swertz, M.A., van Ommen, G.-J.B., de Bakker, P.I.W., Eline Slagboom, P., Boomsma, D.I., Wijmenga, C., van Duijn, C.M. & Schönhuth, A. (2015). Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nature Communications, 6(1): 6065. Nature Publishing Group. doi:10.1038/ncomms7065.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941799Patterson, 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. Mary Ann Liebert . doi:10.1089/cmb.2014.0157.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803van Leeuwen, E.M., Kanterakis, A., Deelen, P., Kattenberg, M.V., Slagboom, P.E., de Bakker, P.I.W., Wijmenga, C., Swertz, M.A., Boomsma, D.I., van Duijn, C.M., Karssen, L.C., Hottenga, J.J. & Schönhuth, A. (2015). Population-specific genotype imputations using minimac or IMPUTE2. Nature Protocols, 10(9), 1285-1296. Nature Publishing Group. doi:10.1038/nprot.2015.077.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805Francioli, L.C., Polak, P.P., Koren, A., Menelaou, A., Chun, S., Renkens, I., van Duijn, C.M., Swertz, M., Wijmenga, C., van Ommen, G., Slagboom, P.E., Boomsma, D.I., Ye, K., Guryev, V., Arndt, P.F., Kloosterman, W.P., de Bakker, P.I.W., Sunyaev, S.R. & Schönhuth, A. (2015). Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics, 47(7), 822-826. Nature Publishing Group. doi:10.1038/ng.3292.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612Wittler, R., Marschall, T., Schönhuth, A. & Makinen, V. (2015). Repeat- and error-aware comparison of deletions. Bioinformatics, 31(18), 2947-2954. OXFORD UNIV PRESS. doi:10.1093/bioinformatics/btv304.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941816Deelen, P., Menelaou, A., van Leeuwen, E.M., Kanterakis, A., van Dijk, F., Medina-Gomez, C., Francioli, L.C., Hottenga, J.J., Karssen, L.C., 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, C.M., de Bakker, P.I.W., Wijmenga, C., Swertz, M.A. & 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. Nature Publishing Group. doi:10.1038/ejhg.2014.19.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810Töpfer, 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. Public Library of Science (PLoS). doi:10.1371/journal.pcbi.1003515.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941835El-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. BioMed Central. doi:10.1186/1471-2105-14-s15-s18.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941837Allhoff, 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. BioMed Central. doi:10.1186/1471-2105-14-s5-s1.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941836Marschall, T., Hajirasouliha, I. & Schönhuth, A. (2013). MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics, 29(24), 3143-3150. Oxford University Press (OUP). doi:10.1093/bioinformatics/btt556.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941839Marschall, 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. Oxford University Press (OUP). doi:10.1093/bioinformatics/bts566.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840Hajirasouliha, 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. Oxford University Press (OUP). doi:10.1093/bioinformatics/bts109.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941841Singer, 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. Walter de Gruyter. doi:10.2202/1544-6115.1677.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842Hafemeister, 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. Oxford University Press (OUP). doi:10.1093/bioinformatics/btr037.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941814Schönhuth, A. (2011). Generic identification of binary-valued hidden Markov processes. Journal of Algebraic Statistics, 5(1), 72-99. Marmara Univ. Instanbul.
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