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Fast and sensitive protein alignment using DIAMOND.
Buchfink B, Xie C, Huson DH. Buchfink B, et al. Nat Methods. 2015 Jan;12(1):59-60. doi: 10.1038/nmeth.3176. Epub 2014 Nov 17. Nat Methods. 2015. PMID: 25402007
Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.
Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, Morris AG, Alt KW, Caramelli D, Dresely V, Farrell M, Farrer AG, Francken M, Gully N, Haak W, Hardy K, Harvati K, Held P, Holmes EC, Kaidonis J, Lalueza-Fox C, de la Rasilla M, Rosas A, Semal P, Soltysiak A, Townsend G, Usai D, Wahl J, Huson DH, Dobney K, Cooper A. Weyrich LS, et al. Nature. 2017 Apr 20;544(7650):357-361. doi: 10.1038/nature21674. Epub 2017 Mar 8. Nature. 2017. PMID: 28273061
Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics.
Willmann M, El-Hadidi M, Huson DH, Schütz M, Weidenmaier C, Autenrieth IB, Peter S. Willmann M, et al. Antimicrob Agents Chemother. 2015 Dec;59(12):7335-45. doi: 10.1128/AAC.01504-15. Epub 2015 Sep 14. Antimicrob Agents Chemother. 2015. PMID: 26369961 Free PMC article.
Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium.
Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh HJ, Ring D, Diehl M, Herp S, Lötscher Y, Hussain S, Bunk B, Pukall R, Huson DH, Münch PC, McHardy AC, McCoy KD, Macpherson AJ, Loy A, Clavel T, Berry D, Stecher B. Brugiroux S, et al. Nat Microbiol. 2016 Nov 21;2:16215. doi: 10.1038/nmicrobiol.2016.215. Nat Microbiol. 2016. PMID: 27869789
Integrative analysis of environmental sequences using MEGAN4.
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC. Huson DH, et al. Genome Res. 2011 Sep;21(9):1552-60. doi: 10.1101/gr.120618.111. Epub 2011 Jun 20. Genome Res. 2011. PMID: 21690186 Free PMC article.
Microbial community analysis using MEGAN.
Huson DH, Weber N. Huson DH, et al. Methods Enzymol. 2013;531:465-85. doi: 10.1016/B978-0-12-407863-5.00021-6. Methods Enzymol. 2013. PMID: 24060133
A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA.
Huson DH, Xie C. Huson DH, et al. Bioinformatics. 2014 Jan 1;30(1):38-9. doi: 10.1093/bioinformatics/btt254. Epub 2013 May 7. Bioinformatics. 2014. PMID: 23658416 Free PMC article.
Fast computation of minimum hybridization networks.
Albrecht B, Scornavacca C, Cenci A, Huson DH. Albrecht B, et al. Bioinformatics. 2012 Jan 15;28(2):191-7. doi: 10.1093/bioinformatics/btr618. Epub 2011 Nov 9. Bioinformatics. 2012. PMID: 22072387
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