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Publications

Publications from the Huson lab, sorted by year and author.

2017

Harter, J, El-Hadidi, M, Huson, DH, Kappler, A, and Behrens, S (2017).
Soil biochar amendment affects the diversity of nosZ transcripts: Implications for N2O formation
Scientific Reports, 7(1):3338.

Huson, DH, Tappu, R, Bazinet, AL, Xie, C, Cummings, MP, Nieselt, K, and Williams, RB (2017).
Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads
Microbiome, 20175:11.

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, and Cooper, A (2017).
Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus
Nature, advance online publication.

2016

Andersen, K, Kesper, MS, Marschner, JA, Konrad, L, Ryu, M, Kumar Vr, S, Kulkarni, OP, Mulay, SR, Romoli, S, Demleitner, J, and others (2016).
Intestinal dysbiosis, barrier dysfunction, and bacterial translocation account for CKD-related systemic inflammation
J Am Soc Nephrol.

Beier, S, Gorska, A, Grupp, P, Harbig, TA, Flade, I, and Huson, DH (2016).
Bioinformatics support for the Tubiom community gut microbiome project
PeerJ Preprints, 4:e2382v1.

Brugiroux, S, Beutler, M, Pfann, C, Garzetti, D, Ruscheweyh, H, 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, and Stecher, B (2016).
Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium
Nature Microbiology, 2:16215.

Harter, J, Weigold, P, El-Hadidi, M, Huson, DH, Kappler, A, and Behrens, S (2016).
Soil biochar amendment shapes the composition of N 2 O-reducing microbial communities
Science of The Total Environment, 562:379–390.

Huson, D and Linz, S (2016).
Autumn algorithm - Computation of Hybridization Networks on Realistic Phylogenetic Trees
Transactions in Computational Biology and Bioinformatics.

Huson, D, Beier, S, Flade, I, G\'orska, A, El-Hadidi, M, Mitra, S, Ruscheweyh, H, and Rewati Tappu, D (2016).
MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data
PLoS Comput Biol, 12(6):e1004957.

Huson, DH, Steel, M, El-Hadidi, M, Mitra, S, Peter, S, and Willmann, M (2016).
A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples
Journal of Biotechnology, In press.

Lange, A, Beier, S, Steimle, A, Autenrieth, IB, Huson, DH, and Frick, J (2016).
Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk
Genome Biology and Evolution, 8(4):1197–1207.

Louis, S, Tappu, RM, Damms-Machado, A, Huson, DH, and Bischoff, SC (2016).
Characterization of the gut microbial community of obese patients following a weight-loss intervention using whole metagenome shotgun sequencing
PLoS ONE(2):1–18.

Talens-Perales, D, Górska, A, Huson, DH, Polaina, J, and Marín-Navarro, J (2016).
Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2)
PLOS ONE, 11(12):1-17.

Weigold, P, El-Hadidi, M, Ruecker, A, Huson, DH, Scholten, T, Jochmann, M, Kappler, A, and Behrens, S (2016).
A metagenomic-based survey of microbial (de) halogenation potential in a German forest soil
Scientific Reports, 6.

Xie, C, Goi, CL, Huson, DH, Little, PF, and Williams, RB (2016).
RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
BMC Bioinformatics, 17(19):277–282.

2015

Buchfink, B, Xie, C, and Huson, DH (2015).
Fast and Sensitive Protein Alignment using DIAMOND
Nature Methods, 12:59-60.

Damms-Machado, A, Mitra, S, Schollenberger, AE, Kramer, KM, Meile, T, Koenigsrainer, A, Huson, DH, and Bischoff, SC (2015).
Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption
BioMed Research International, 2015.

Huson, DH (2015).
MEtaGenome ANalyzer (MEGAN): Metagenomic Expert Resource
In: Encyclopedia of Metagenomics, pp. 383–389, Springer US.

Willmann, M, El-Hadidi, M, Huson, DH, Schuetz, M, Weidenmaier, C, Autenrieth, IB, and Peter, S (2015).
Antibiotic selection pressure determination through sequence-based metagenomics
Antimicrobial Agents and Chemotherapy.

2014

Bos, KI and et al (2014).
Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis
Nature, 514(7523):494-497.

Flade, I, Holst, O, Ruscheweyh, HJ, Wittmann, A, and et al (2014).
Endotoxicity of Lipopolysaccharide as a Determinant of T-Cell-Mediated Colitis Induction in Mice
Gastroenterology, 146(3):765-775.

2013

Huson, DH and Chao Xie, D (2013).
A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA
Bioinformatics:doi: 10.1093/bioinformatics/btt254.

Lange, A, Beier, S, Huson, D, Henz, S, Hantke, K, Autenrieth, I, and Frick, J (2013).
Different survival strategies of gut commensal bacteria in IBD
International Journal for Medical Microbiology, 303:99.

Mitra, S and others (2013).
Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing
BMC Genomics, 14(Suppl 5):S16.

Steel, M, Linz, S, Huson, DH, and Michael J. Sanderson, D (2013).
Identifying a species tree subject to random lateral gene transfer
Journal of Theoretical Biology, 322:81-93.