54 Publikationen
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2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2963686Luo, Xiao, Kang, Xiongbin, and Schönhuth, Alexander. 2022. “Enhancing Long-Read-Based Strain-Aware Metagenome Assembly”. Frontiers in Genetics 13: 868280.
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2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967245Ray, Sumanta, Lall, Snehalika, Mukhopadhyay, Anirban, Bandyopadhyay, Sanghamitra, and Schönhuth, Alexander. 2022. “Deep variational graph autoencoders for novel host-directed therapy options against COVID-19”. Artificial Intelligence in Medicine 134: 102418.
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952469Metselaar, Paula I, Mendoza-Maldonado, Lucero, Li Yim, Andrew Yung Fong, Abarkan, Ilias, Henneman, Peter, Te Velde, Anje A, Schönhuth, Alexander, Bosch, Jos A, Kraneveld, Aletta D, and Lopez-Rincon, Alejandro. 2021. “Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome.”. Scientific reports 11 (1): 4541.
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2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2959624Lahnemann, David, Koster, Johannes, Fischer, Ute, Borkhardt, Arndt, McHardy, Alice C, and Schönhuth, Alexander. 2021. “Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo”. Nature Communications 12 (1): 6744.
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2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945617Lopez-Rincon, Alejandro, Mendoza-Maldonado, Lucero, Martinez-Archundia, Marlet, Schönhuth, Alexander, Kraneveld, Aletta D., Garssen, Johan, and Tonda, Alberto. 2020. “Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification”. Cancers 12 (7): 1785.
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2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2943113Koster, Johannes, Dijkstra, Louis J, Marschall, Tobias, and Schönhuth, Alexander. 2020. “Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery.”. Genome biology 21 (1).
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941754Baaijens, Jasmijn A, Van der Roest, Bastiaan, Köster, Johannes, Stougie, Leen, and Schönhuth, Alexander. 2019. “Full-length de novo viral quasispecies assembly through variation graph construction”. Bioinformatics 35 (24): 5086-5094.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941756Yin, Bojian, Balvert, Marleen, van der Spek, Rick A A, Dutilh, Bas E, Bohté, Sander, Veldink, Jan, and Schönhuth, Alexander. 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.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941760Lopez-Rincon, Alejandro, Martinez-Archundia, Marlet, Martinez-Ruiz, Gustavo U., Schönhuth, Alexander, and Tonda, Alberto. 2019. “Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection”. BMC Bioinformatics 20 (1): 480.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941677Denti, Luca, Previtali, Marco, Bernardini, Giulia, Schönhuth, Alexander, and Bonizzoni, Paola. 2019. “MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants”. iScience 18: 20-27.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941761Baaijens, Jasmijn A, and Schönhuth, Alexander. 2019. “Overlap graph-based generation of haplotigs for diploids and polyploids”. Bioinformatics 35 (21): 4281-4289.
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2019 | Preprint | Veröffentlicht | PUB-ID: 2941764Laehnemann, David, Köster, Johannes, Szczurek, Ewa, McCarthy, Davis J, Hicks, Stephanie C, Robinson, Mark D, Vallejos, Catalina A, et al. 2019. “12 Grand Challenges in Single-Cell Data Science”. PeerJ.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941769Ibrahim, Bashar, Arkhipova, Ksenia, Andeweg, Arno, Posada-Céspedes, Susana, Enault, François, Gruber, Arthur, Koonin, Eugene, et al. 2018. “Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting”. Viruses 10 (5): 256.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941784Baaijens, Jasmijn A., Aabidine, Amal Zine El, Rivals, Eric, and Schönhuth, Alexander. 2017. “De novo assembly of viral quasispecies using overlap graphs”. Genome Research 27 (5): 835-848.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941786Ebler, Jana, Schönhuth, Alexander, and Marschall, Tobias. 2017. “Genotyping inversions and tandem duplications”. Bioinformatics 33 (24): 4015-4023.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941788Francioli, Laurent C, Cretu-Stancu, Mircea, Garimella, Kiran V, Fromer, Menachem, Kloosterman, Wigard P, Samocha, Kaitlin E, Neale, Benjamin 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.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941793Gregor, I., Schönhuth, Alexander, and McHardy, A. C. 2016. “Snowball: strain aware gene assembly of metagenomes”. Bioinformatics 32 (17): i649-i657.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941790Hehir-Kwa, Jayne Y., Marschall, Tobias, Kloosterman, Wigard P., Francioli, Laurent C., Baaijens, Jasmijn A., Dijkstra, Louis J., Abdellaoui, Abdel, et al. 2016. “A high-quality human reference panel reveals the complexity and distribution of genomic structural variants”. Nature Communications 7 (1): 12989.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941807Palamara, Pier Francesco, Francioli, Laurent C., Wilton, Peter R., Genovese, Giulio, Gusev, Alexander, Finucane, Hilary K., Sankararaman, Sriram, et al. 2015. “Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates”. The American Journal of Human Genetics 97 (6): 775-789.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941797Kloosterman, Wigard P., Francioli, Laurent C., Hormozdiari, Fereydoun, Marschall, Tobias, Hehir-Kwa, Jayne Y., Abdellaoui, Abdel, Lameijer, Eric-Wubbo, et al. 2015. “Characteristics of de novo structural changes in the human genome”. Genome Research 25 (6): 792-801.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941798Leung, Wai Yi, Marschall, Tobias, Paudel, Yogesh, Falquet, Laurent, Mei, Hailiang, Schönhuth, Alexander, and Maoz, Tiffanie Yael. 2015. “SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines”. BMC Genomics 16 (1): 238.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941804van Leeuwen, Elisabeth M., Karssen, Lennart C., Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, et al. 2015. “Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels”. Nature Communications 6 (1): 6065.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941799Patterson, Murray, Marschall, Tobias, Pisanti, Nadia, van Iersel, Leo, Stougie, Leen, Klau, Gunnar W., and Schönhuth, Alexander. 2015. “WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads”. Journal of Computational Biology 22 (6): 498-509.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941803van Leeuwen, Elisabeth M, Kanterakis, Alexandros, Deelen, Patrick, Kattenberg, Mathijs V, Slagboom, P Eline, de Bakker, Paul I W, Wijmenga, Cisca, et al. 2015. “Population-specific genotype imputations using minimac or IMPUTE2”. Nature Protocols 10 (9): 1285-1296.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941805Francioli, Laurent C, Polak, Paz P, Koren, Amnon, Menelaou, Androniki, Chun, Sung, Renkens, Ivo, van Duijn, Cornelia M, et al. 2015. “Genome-wide patterns and properties of de novo mutations in humans”. Nature Genetics 47 (7): 822-826.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941816Deelen, Patrick, Menelaou, Androniki, van Leeuwen, Elisabeth M, Kanterakis, Alexandros, van Dijk, Freerk, Medina-Gomez, Carolina, Francioli, Laurent 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.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941810Töpfer, Armin, Marschall, Tobias, Bull, Rowena A., Luciani, Fabio, Schönhuth, Alexander, and Beerenwinkel, Niko. 2014. “Viral Quasispecies Assembly via Maximal Clique Enumeration”. PLoS Computational Biology 10 (3): e1003515.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941835El-Kebir, Mohammed, Marschall, Tobias, Wohlers, Inken, Patterson, Murray, Heringa, Jaap, Schönhuth, Alexander, and Klau, Gunnar W. 2013. “Mapping proteins in the presence of paralogs using units of coevolution”. BMC Bioinformatics 14 (S15): S18.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941837Allhoff, Manuel, Schönhuth, Alexander, Martin, Marcel, Costa, Ivan G, Rahmann, Sven, and Marschall, Tobias. 2013. “Discovering motifs that induce sequencing errors”. BMC Bioinformatics 14 (Suppl 5): S1.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941836Marschall, Tobias, Hajirasouliha, Iman, and Schönhuth, Alexander. 2013. “MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels”. Bioinformatics 29 (24): 3143-3150.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941839Marschall, Tobias, Costa, Ivan G., Canzar, Stefan, Bauer, Markus, Klau, Gunnar W., Schliep, Alexander, and Schönhuth, Alexander. 2012. “CLEVER: clique-enumerating variant finder”. Bioinformatics 28 (22): 2875-2882.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941840Hajirasouliha, Iman, Schönhuth, Alexander, de Juan, David, Valencia, Alfonso, and Sahinalp, S. Cenk. 2012. “Mirroring co-evolving trees in the light of their topologies”. Bioinformatics 28 (9): 1202-1208.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941841Singer, Meromit, Engström, Alexander, Schönhuth, Alexander, and Pachter, Lior. 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.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941842Hafemeister, Christoph, Costa, Ivan G., Schönhuth, Alexander, and Schliep, Alexander. 2011. “Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions”. Bioinformatics 27 (7): 946-952.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941814Schönhuth, Alexander. 2011. “Generic identification of binary-valued hidden Markov processes”. Journal of Algebraic Statistics 5 (1): 72-99.
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