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Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.
Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M. Ibrahim B, et al. Among authors: schonhuth a. Viruses. 2018 May 14;10(5):256. doi: 10.3390/v10050256. Viruses. 2018. PMID: 29757994 Free PMC article.
Snowball: strain aware gene assembly of metagenomes.
Gregor I, Schönhuth A, McHardy AC. Gregor I, et al. Among authors: schonhuth a. Bioinformatics. 2016 Sep 1;32(17):i649-i657. doi: 10.1093/bioinformatics/btw426. Bioinformatics. 2016. PMID: 27587685
Eleven grand challenges in single-cell data science.
Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowska A, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Lähnemann D, et al. Among authors: schonhuth a. Genome Biol. 2020 Feb 7;21(1):31. doi: 10.1186/s13059-020-1926-6. Genome Biol. 2020. PMID: 32033589 Free PMC article. Review.
OGRE: Overlap Graph-based metagenomic Read clustEring.
Balvert M, Luo X, Hauptfeld E, Schönhuth A, Dutilh BE. Balvert M, et al. Among authors: schonhuth a. Bioinformatics. 2021 May 17;37(7):905-912. doi: 10.1093/bioinformatics/btaa760. Bioinformatics. 2021. PMID: 32871010 Free PMC article.
Viral quasispecies assembly via maximal clique enumeration.
Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N. Töpfer A, et al. Among authors: schonhuth a. PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515. eCollection 2014 Mar. PLoS Comput Biol. 2014. PMID: 24675810 Free PMC article.
Repeat- and error-aware comparison of deletions.
Wittler R, Marschall T, Schönhuth A, Mäkinen V. Wittler R, et al. Among authors: schonhuth a. Bioinformatics. 2015 Sep 15;31(18):2947-54. doi: 10.1093/bioinformatics/btv304. Epub 2015 May 15. Bioinformatics. 2015. PMID: 25979471
De novo assembly of viral quasispecies using overlap graphs.
Baaijens JA, Aabidine AZE, Rivals E, Schönhuth A. Baaijens JA, et al. Among authors: schonhuth a. Genome Res. 2017 May;27(5):835-848. doi: 10.1101/gr.215038.116. Epub 2017 Apr 10. Genome Res. 2017. PMID: 28396522 Free PMC article.
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