Alexander Schönhuth
- Full Name
- Prof.dr. A. Schönhuth
- Function(s)
- Researcher - Universiteit Utrecht, Scientific Staff Member
- A.Schoenhuth@cwi.nl
- Telephone
- +31 20 592 4113
- Room
- M242
- Department(s)
- Life Sciences and Health
- Homepage
- http://homepages.cwi.nl/~as
Biography
I am a Genome Data Scientist who works at the interfaces of statistics, discrete mathematics and pattern recognition on the one hand and molecular biology and biomedicine on the other hand. I joined CWI in 2010, coming from UC Berkeley where I was a postdoctoral fellow in the Laboratory for Mathematical and Computational Biology in the Department of Mathematics, and I got tenure at CWI in 2014. Prior to UC Berkeley I also was a postdoctoral fellow in the Data Mining and Computational Laboratories of the School of Computing Science at Simon Fraser University in Vancouver. I received my PhD in 2006 from University of Cologne, Germany. On the theoretical end, I am particularly interested in data mining, sequence analysis and machine learning, with a special focus on Markovian and latent variable models. Biomedical questions I address relate to issues in computational genomics, in particular in the areas of pathogen, cancer and single cell biology. Genotyping and phasing variants from next- and third-generation sequencing data is a special focus. I am also concerned with computational pan-genomics, that is, to try to make sense out of -- soon -- millions of sequenced genomes, and with translating genome sequencing data into information that one can make use of in clinical practice, using machine learning methods.
Publications
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Yin, B, Balvert, M, Zambrano, D, Schönhuth, A, & Bohte, S.M. (2018). An image representation based convolutional network for DNA classification. In 6th International Conference on Learning Representations.
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Chikhi, R, & Schönhuth, A. (2018). Dualities in tree representations. In 29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018. doi:10.4230/LIPIcs.CPM.2018.18
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The Computational Pan-Genomics Consortium, Marschall, T, Marz, M, Abeel, T, Dijkstra, L.J, Dutilh, B.E, … Schönhuth, A. (2018). Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19(1), 118–135. doi:10.1093/bib/bbw089
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Ebler, J, Schönhuth, A, & Marschall, T. (2017). Genotyping inversions and tandem duplications. Bioinformatics, 33(24), 4015–4023. doi:10.1093/bioinformatics/btx020
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Dröge, J, Schönhuth, A, & McHardy, A.C. (2017). A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science, 3(e117). doi:10.7717/peerj-cs.117
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Baaijens, J.A, El Aabidine, A.Z, Rivals, E, & Schönhuth, A. (2017). De novo assembly of viral quasispecies using overlap graphs. Genome Research, 27(5), 835–848. doi:10.1101/gr.215038.116
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Hehir-Kwa, J.Y, Schönhuth, A, & et al., . (2016). A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications, 7(12989). doi:10.1038/ncomms129
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Marschall, T, & Schönhuth, A. (2016). Discovering and Genotyping Twilight Zone Deletions. In Computational Methods for Next Generation Sequencing Data Analysis (pp. 149–173).
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Marschall, T, & Schönhuth, A. (2016). Discovering and Genotyping Twilight Zone Deletions. In Computational Methods for Next Generation Sequencing Data Analysis (pp. 149–173). doi:10.1002/9781119272182.ch7
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Gregor, I, Schönhuth, A, & McHardy, A.C. (2016). Snowball: strain aware gene assembly of metagenomes. Bioinformatics, 32(17), i649–i657. doi:10.1093/bioinformatics/btw426
Current projects with external funding
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Statistical Models for Structural Genetic Variants in the Genome of the Netherlands
Professional activities
- Committee member: Member Program Committee - ACM Conference on Bioinformatics,ﾠﾠComputational Biology and Biomedicine [ACM-BCB], 2012, 2017
- Chair: Program Faculty - Computational Genomics Summer Institute [CGSI],ﾠﾠUCLA
- Committee member: Founding Member - Consortium, "Computational Pangenomics"
- Committee member: Member Consortium - "The Genome of the Netherlands"
Grants
- - Summer Semester Stipends, IPAM, UCLA, 2016, 2017 (2016)
- Vidi Innovational Research Grant NWO (2013)
- - Fall Semester Stipend, IPAM, University of California at Los (2011)
Awards
- Faculty of the 1000 paper award (voor "CLEVER: Clique-Enumerating Variant Finder") (2013)