Publikationen

Ausgewählte Literatur zum Thema

 

Brinkmann A, Andrusch A, Belka A, et al., Beer M, Nitsche A. (2019) Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico hight-throughput sequencing data sets. J. Clin. Microbiol. DOI:10.1128/JCM.00466-19

Grützke J, Malorny B, Hammerl JA, Busch A, Tausch SH, Tomaso H, Deneke C. (2019) Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing. Front Microbiol 10:1805 DOI:10.3389/fmicb.2019.01805

Wylezich C, Belka A, Hanke D, Beer M, Blome S, Höper D. (2019) Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples. Int. J. Parasitol.

doi.org/10.1016/j.ijpara.2019.04.007

Wylezich C, Papa A, Beer M, Höper D. (2018) A versatile sample processing workflow for diagnostic metagenomics. Sci Rep 8:13108. 10.1038/s41598-018-31496-1

Belka, A, Fischer M, Pohlmann A, Beer M, Höper D. (2018) LVQ-KNN: Composition-based DNA/RNA binning of short nucleotide sequences utilizing a prototype-based k-nearest neighbor approach. Virus Res 258S:55. 10.1016/j.virusres.2018.10.002

Kirstahler P, Bjerrum SS, Friis-Møller A, la Cour M, Aarestrup FM, Westh H, SJ Pamp. (2108) Genomics-based identification of microorganisms in human ocular body fluid. Sci Rep 8:4126. 10.1038/s41598-018-22416-4

Tausch SH, Strauch B, Andrusch A, Loka TP, Lindner MS, Nitsche A, Renard BY. (2018) LiveKraken-real-time metagenomic classification of illumina data. Bioinformatics 34:3750-3752 DOI: 10.1093/bioinformatics/bty433

Andrusch A, Dabrowski PW, Klenner J, Tausch SH, Kohl C, Osman AA, Renard BY, Nitsche A. (2018) PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples. Bioinformatics 34:715-721 DOI: 10.1093/bioinformatics/bty595

Höper D, Wylezich C, Beer M. (2017) Loeffler 4.0: Diagnostic Metagenomics in Loeffler’s footsteps viral genomics in the era of high-throughput sequencing. (eds Beer M & Höper D). ADV Viral Res, Elsevier 99:17–37. 10.1016/bs.aivir.2017.08.001

Höper D, Mettenleiter TC, Beer M. (2016) Metagenomic approaches to identifying infectious agents. Review. Rev Sci Tech. 35:83-93. doi: 10.20506/rst.35.1.2419.

Schlottau K, Schulze C, Bilk S, Hanke D, Höper D, Beer M, Hoffmann B. (2016) Detection of a Novel Bovine Astrovirus in a Cow with Encephalitis. Transbound Emerg Dis. 63:253-9. doi: 10.1111/tbed.12493.

Hoffmann B, Tappe D, Höper D, Herden C, Boldt A, Mawrin C, Niederstraßer O, Müller T, Jenckel M, van der Grinten E, Lutter C, Abendroth B, Teifke JP, Cadar D, Schmidt-Chanasit J, Ulrich RG, Beer M. (2015) A Variegated Squirrel Bornavirus Associated with Fatal Human Encephalitis. N Engl J Med. 373:154-62. doi: 10.1056/NEJMoa1415627.

Scheuch M, Höper D, Beer M. (2015) RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. BMC Bioinf. 16:69. doi: 10.1186/s12859-015-0503-6.

Hoffmann B, Scheuch M, Höper D, Jungblut R, Holsteg M, Schirrmeier H, Eschbaumer M, Goller KV, Wernike K, Fischer M, Breithaupt A, Mettenleiter TC, Beer M. (2012) Novel orthobunyavirus in Cattle, Europe, 2011. Emerg Infect Dis. 18:469-72. doi: 10.3201/eid1803.111905.

Deneke C, Rentzsch R, Renard BY. (2017) PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data. Sci Rep 7:39194 DOI: 10.1038/srep39194

Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K. (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ 5:e3138 DOI: 10.7717/peerj.3138