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Items: 1 to 50 of 97

1.

Phage tail-like particles are versatile bacterial nanomachines - A mini-review.

Patz S, Becker Y, Richert-Pöggeler KR, Berger B, Ruppel S, Huson DH, Becker M.

J Adv Res. 2019 Apr 23;19:75-84. doi: 10.1016/j.jare.2019.04.003. eCollection 2019 Sep. Review.

2.

Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN.

Bağcı C, Beier S, Górska A, Huson DH.

Methods Mol Biol. 2019;1910:591-604. doi: 10.1007/978-1-4939-9074-0_19.

PMID:
31278678
3.

Estimating the association between antibiotic exposure and colonization with extended-spectrum β-lactamase-producing Gram-negative bacteria using machine learning methods: a multicentre, prospective cohort study.

Tacconelli E, Górska A, De Angelis G, Lammens C, Restuccia G, Schrenzel J, Huson DH, Carević B, Preoţescu L, Carmeli Y, Kazma M, Spanu T, Carrara E, Malhotra-Kumar S, Gladstone BP.

Clin Microbiol Infect. 2019 May 23. pii: S1198-743X(19)30247-2. doi: 10.1016/j.cmi.2019.05.013. [Epub ahead of print]

PMID:
31128285
4.

Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.

Herp S, Brugiroux S, Garzetti D, Ring D, Jochum LM, Beutler M, Eberl C, Hussain S, Walter S, Gerlach RG, Ruscheweyh HJ, Huson D, Sellin ME, Slack E, Hanson B, Loy A, Baines JF, Rausch P, Basic M, Bleich A, Berry D, Stecher B.

Cell Host Microbe. 2019 May 8;25(5):681-694.e8. doi: 10.1016/j.chom.2019.03.004. Epub 2019 Apr 18.

PMID:
31006637
5.

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data.

Arumugam K, Bağcı C, Bessarab I, Beier S, Buchfink B, Górska A, Qiu G, Huson DH, Williams RBH.

Microbiome. 2019 Apr 16;7(1):61. doi: 10.1186/s40168-019-0665-y.

6.

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes.

Poole AC, Goodrich JK, Youngblut ND, Luque GG, Ruaud A, Sutter JL, Waters JL, Shi Q, El-Hadidi M, Johnson LM, Bar HY, Huson DH, Booth JG, Ley RE.

Cell Host Microbe. 2019 Apr 10;25(4):553-564.e7. doi: 10.1016/j.chom.2019.03.001.

PMID:
30974084
7.

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.

Huson DH, Albrecht B, Bağcı C, Bessarab I, Górska A, Jolic D, Williams RBH.

Biol Direct. 2018 Apr 20;13(1):6. doi: 10.1186/s13062-018-0208-7.

8.

Dynamics of the human gut phageome during antibiotic treatment.

Górska A, Peter S, Willmann M, Autenrieth I, Schlaberg R, Huson DH.

Comput Biol Chem. 2018 Jun;74:420-427. doi: 10.1016/j.compbiolchem.2018.03.011. Epub 2018 Mar 14.

PMID:
29567068
9.

Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico.

Vågene ÅJ, Herbig A, Campana MG, Robles García NM, Warinner C, Sabin S, Spyrou MA, Andrades Valtueña A, Huson D, Tuross N, Bos KI, Krause J.

Nat Ecol Evol. 2018 Mar;2(3):520-528. doi: 10.1038/s41559-017-0446-6. Epub 2018 Jan 15.

PMID:
29335577
10.

Genome Sequence of Galleria mellonella (Greater Wax Moth).

Lange A, Beier S, Huson DH, Parusel R, Iglauer F, Frick JS.

Genome Announc. 2018 Jan 11;6(2). pii: e01220-17. doi: 10.1128/genomeA.01220-17.

11.

Soil biochar amendment affects the diversity of nosZ transcripts: Implications for N2O formation.

Harter J, El-Hadidi M, Huson DH, Kappler A, Behrens S.

Sci Rep. 2017 Jun 13;7(1):3338. doi: 10.1038/s41598-017-03282-y.

12.

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery.

Alanjary M, Kronmiller B, Adamek M, Blin K, Weber T, Huson D, Philmus B, Ziemert N.

Nucleic Acids Res. 2017 Jul 3;45(W1):W42-W48. doi: 10.1093/nar/gkx360.

13.

SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?

Balvočiūtė M, Huson DH.

BMC Genomics. 2017 Mar 14;18(Suppl 2):114. doi: 10.1186/s12864-017-3501-4.

14.

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.

Nature. 2017 Apr 20;544(7650):357-361. doi: 10.1038/nature21674. Epub 2017 Mar 8.

PMID:
28273061
15.

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys.

Xie C, Goi CL, Huson DH, Little PF, Williams RB.

BMC Bioinformatics. 2016 Dec 22;17(Suppl 19):508. doi: 10.1186/s12859-016-1378-x.

16.

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Huson DH, Tappu R, Bazinet AL, Xie C, Cummings MP, Nieselt K, Williams R.

Microbiome. 2017 Jan 25;5(1):11. doi: 10.1186/s40168-017-0233-2.

17.

A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples.

Huson DH, Steel M, El-Hadidi M, Mitra S, Peter S, Willmann M.

J Biotechnol. 2017 May 20;250:45-50. doi: 10.1016/j.jbiotec.2016.10.020. Epub 2016 Oct 27.

18.

Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2).

Talens-Perales D, Górska A, Huson DH, Polaina J, Marín-Navarro J.

PLoS One. 2016 Dec 8;11(12):e0168035. doi: 10.1371/journal.pone.0168035. eCollection 2016.

19.

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.

Nat Microbiol. 2016 Nov 21;2:16215. doi: 10.1038/nmicrobiol.2016.215.

PMID:
27869789
20.

A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil.

Weigold P, El-Hadidi M, Ruecker A, Huson DH, Scholten T, Jochmann M, Kappler A, Behrens S.

Sci Rep. 2016 Jun 29;6:28958. doi: 10.1038/srep28958.

21.

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.

Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R.

PLoS Comput Biol. 2016 Jun 21;12(6):e1004957. doi: 10.1371/journal.pcbi.1004957. eCollection 2016 Jun.

22.

Intestinal Dysbiosis, Barrier Dysfunction, and Bacterial Translocation Account for CKD-Related Systemic Inflammation.

Andersen K, Kesper MS, Marschner JA, Konrad L, Ryu M, Kumar Vr S, Kulkarni OP, Mulay SR, Romoli S, Demleitner J, Schiller P, Dietrich A, Müller S, Gross O, Ruscheweyh HJ, Huson DH, Stecher B, Anders HJ.

J Am Soc Nephrol. 2017 Jan;28(1):76-83. doi: 10.1681/ASN.2015111285. Epub 2016 May 5.

23.

Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

Harter J, Weigold P, El-Hadidi M, Huson DH, Kappler A, Behrens S.

Sci Total Environ. 2016 Aug 15;562:379-390. doi: 10.1016/j.scitotenv.2016.03.220. Epub 2016 Apr 18.

PMID:
27100017
24.

Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.

Lange A, Beier S, Steimle A, Autenrieth IB, Huson DH, Frick JS.

Genome Biol Evol. 2016 Apr 25;8(4):1197-207. doi: 10.1093/gbe/evw070.

25.

Autumn Algorithm-Computation of Hybridization Networks for Realistic Phylogenetic Trees.

Huson DH, Linz S.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Mar-Apr;15(2):398-410. doi: 10.1109/TCBB.2016.2537326. Epub 2016 Mar 2.

PMID:
26955052
26.

Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing.

Louis S, Tappu RM, Damms-Machado A, Huson DH, Bischoff SC.

PLoS One. 2016 Feb 26;11(2):e0149564. doi: 10.1371/journal.pone.0149564. eCollection 2016.

27.

Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics.

Willmann M, El-Hadidi M, Huson DH, Schütz M, Weidenmaier C, Autenrieth IB, Peter S.

Antimicrob Agents Chemother. 2015 Dec;59(12):7335-45. doi: 10.1128/AAC.01504-15. Epub 2015 Sep 14.

28.

Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption.

Damms-Machado A, Mitra S, Schollenberger AE, Kramer KM, Meile T, Königsrainer A, Huson DH, Bischoff SC.

Biomed Res Int. 2015;2015:806248. doi: 10.1155/2015/806248. Epub 2015 Feb 1.

29.

Fast and sensitive protein alignment using DIAMOND.

Buchfink B, Xie C, Huson DH.

Nat Methods. 2015 Jan;12(1):59-60. doi: 10.1038/nmeth.3176. Epub 2014 Nov 17.

PMID:
25402007
30.

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.

Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK, Guichon RA, Wolfe Steadman DL, Cook DC, Niemann S, Behr MA, Zumarraga M, Bastida R, Huson D, Nieselt K, Young D, Parkhill J, Buikstra JE, Gagneux S, Stone AC, Krause J.

Nature. 2014 Oct 23;514(7523):494-7. doi: 10.1038/nature13591. Epub 2014 Aug 20.

31.

Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing.

Mitra S, Förster-Fromme K, Damms-Machado A, Scheurenbrand T, Biskup S, Huson DH, Bischoff SC.

BMC Genomics. 2013;14 Suppl 5:S16. doi: 10.1186/1471-2164-14-S5-S16. Epub 2013 Oct 16.

32.

Endotoxicity of lipopolysaccharide as a determinant of T-cell-mediated colitis induction in mice.

Gronbach K, Flade I, Holst O, Lindner B, Ruscheweyh HJ, Wittmann A, Menz S, Schwiertz A, Adam P, Stecher B, Josenhans C, Suerbaum S, Gruber AD, Kulik A, Huson D, Autenrieth IB, Frick JS.

Gastroenterology. 2014 Mar;146(3):765-75. doi: 10.1053/j.gastro.2013.11.033. Epub 2013 Nov 21.

33.

Microbial community analysis using MEGAN.

Huson DH, Weber N.

Methods Enzymol. 2013;531:465-85. doi: 10.1016/B978-0-12-407863-5.00021-6.

PMID:
24060133
34.

Comparing terracotta and earthenware for multiple functionalities in microbial fuel cells.

Winfield J, Greenman J, Huson D, Ieropoulos I.

Bioprocess Biosyst Eng. 2013 Dec;36(12):1913-21. doi: 10.1007/s00449-013-0967-6. Epub 2013 Jun 1.

PMID:
23728836
35.

A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA.

Huson DH, Xie C.

Bioinformatics. 2014 Jan 1;30(1):38-9. doi: 10.1093/bioinformatics/btt254. Epub 2013 May 7.

36.

Identifying a species tree subject to random lateral gene transfer.

Steel M, Linz S, Huson DH, Sanderson MJ.

J Theor Biol. 2013 Apr 7;322:81-93. doi: 10.1016/j.jtbi.2013.01.009. Epub 2013 Jan 20.

PMID:
23340439
37.

CREST--classification resources for environmental sequence tags.

Lanzén A, Jørgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, Øvreås L, Urich T.

PLoS One. 2012;7(11):e49334. doi: 10.1371/journal.pone.0049334. Epub 2012 Nov 8.

38.

Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.

Huson DH, Scornavacca C.

Syst Biol. 2012 Dec 1;61(6):1061-7. doi: 10.1093/sysbio/sys062. Epub 2012 Jul 10.

PMID:
22780991
39.

Introduction to the analysis of environmental sequences: metagenomics with MEGAN.

Huson DH, Mitra S.

Methods Mol Biol. 2012;856:415-29. doi: 10.1007/978-1-61779-585-5_17.

PMID:
22399469
40.

Analysis of 16S rRNA environmental sequences using MEGAN.

Mitra S, Stärk M, Huson DH.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S17. doi: 10.1186/1471-2164-12-S3-S17. Epub 2011 Nov 30.

41.

Fast computation of minimum hybridization networks.

Albrecht B, Scornavacca C, Cenci A, Huson DH.

Bioinformatics. 2012 Jan 15;28(2):191-7. doi: 10.1093/bioinformatics/btr618. Epub 2011 Nov 9.

PMID:
22072387
42.

LOCAS--a low coverage assembly tool for resequencing projects.

Klein JD, Ossowski S, Schneeberger K, Weigel D, Huson DH.

PLoS One. 2011;6(8):e23455. doi: 10.1371/journal.pone.0023455. Epub 2011 Aug 15.

43.

Integrative analysis of environmental sequences using MEGAN4.

Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC.

Genome Res. 2011 Sep;21(9):1552-60. doi: 10.1101/gr.120618.111. Epub 2011 Jun 20.

44.

Tanglegrams for rooted phylogenetic trees and networks.

Scornavacca C, Zickmann F, Huson DH.

Bioinformatics. 2011 Jul 1;27(13):i248-56. doi: 10.1093/bioinformatics/btr210.

45.

Reference-guided assembly of four diverse Arabidopsis thaliana genomes.

Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D.

Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10249-54. doi: 10.1073/pnas.1107739108. Epub 2011 Jun 6.

46.

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.

Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S21. doi: 10.1186/1471-2105-12-S1-S21.

47.

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project.

Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R.

Stand Genomic Sci. 2010 Dec 25;3(3):243-8. doi: 10.4056/sigs.1433550.

48.

A survey of combinatorial methods for phylogenetic networks.

Huson DH, Scornavacca C.

Genome Biol Evol. 2011;3:23-35. doi: 10.1093/gbe/evq077. Epub 2010 Nov 15.

49.

Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters.

van Iersel L, Kelk S, Rupp R, Huson D.

Bioinformatics. 2010 Jun 15;26(12):i124-31. doi: 10.1093/bioinformatics/btq202.

50.

Comparison of multiple metagenomes using phylogenetic networks based on ecological indices.

Mitra S, Gilbert JA, Field D, Huson DH.

ISME J. 2010 Oct;4(10):1236-42. doi: 10.1038/ismej.2010.51. Epub 2010 Apr 29.

PMID:
20428222

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