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Items: 50


Evaluating NGS methods for routine monitoring of wild bees: metabarcoding, mitogenomics or NGS barcoding.

Gueuning M, Ganser D, Blaser S, Albrecht M, Knop E, Praz C, Frey JE.

Mol Ecol Resour. 2019 Mar 26. doi: 10.1111/1755-0998.13013. [Epub ahead of print]


Dispersal of harmful fruit fly pests by international trade and a loop-mediated isothermal amplification assay to prevent their introduction.

Blaser S, Heusser C, Diem H, Von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey JE, Frey B, Bühlmann A.

Geospat Health. 2018 Nov 12;13(2). doi: 10.4081/gh.2018.726.


A Loop-mediated Isothermal Amplification (LAMP) Assay for Rapid Identification of Bemisia tabaci.

Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey B, Frey JE, Bühlmann A.

J Vis Exp. 2018 Oct 29;(140). doi: 10.3791/58502.


Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats.

Schmid M, Frei D, Patrignani A, Schlapbach R, Frey JE, Remus-Emsermann MNP, Ahrens CH.

Nucleic Acids Res. 2018 Sep 28;46(17):8953-8965. doi: 10.1093/nar/gky726.


Off-target effects of tribendimidine, tribendimidine plus ivermectin, tribendimidine plus oxantel-pamoate, and albendazole plus oxantel-pamoate on the human gut microbiota.

Schneeberger PHH, Coulibaly JT, Gueuning M, Moser W, Coburn B, Frey JE, Keiser J.

Int J Parasitol Drugs Drug Resist. 2018 Dec;8(3):372-378. doi: 10.1016/j.ijpddr.2018.07.001. Epub 2018 Jul 2.


Global Transcriptomic Effects of Environmentally Relevant Concentrations of the Neonicotinoids Clothianidin, Imidacloprid, and Thiamethoxam in the Brain of Honey Bees ( Apis mellifera).

Christen V, Schirrmann M, Frey JE, Fent K.

Environ Sci Technol. 2018 Jul 3;52(13):7534-7544. doi: 10.1021/acs.est.8b01801. Epub 2018 Jun 14.


Seasonal Dynamics of Glyphosate and AMPA in Lake Greifensee: Rapid Microbial Degradation in the Epilimnion During Summer.

Huntscha S, Stravs MA, Bühlmann A, Ahrens CH, Frey JE, Pomati F, Hollender J, Buerge IJ, Balmer ME, Poiger T.

Environ Sci Technol. 2018 Apr 17;52(8):4641-4649. doi: 10.1021/acs.est.8b00314. Epub 2018 Mar 27.


Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome.

Schneeberger PHH, Coulibaly JT, Panic G, Daubenberger C, Gueuning M, Frey JE, Keiser J.

Parasit Vectors. 2018 Mar 12;11(1):168. doi: 10.1186/s13071-018-2739-2.


Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level.

Schmid M, Muri J, Melidis D, Varadarajan AR, Somerville V, Wicki A, Moser A, Bourqui M, Wenzel C, Eugster-Meier E, Frey JE, Irmler S, Ahrens CH.

Front Microbiol. 2018 Jan 30;9:63. doi: 10.3389/fmicb.2018.00063. eCollection 2018.


From laboratory to point of entry: development and implementation of a loop-mediated isothermal amplification (LAMP)-based genetic identification system to prevent introduction of quarantine insect species.

Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey JE, Bühlmann A.

Pest Manag Sci. 2018 Jun;74(6):1504-1512. doi: 10.1002/ps.4866. Epub 2018 Mar 12.


An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.

Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C, Frey JE, Robinson MD, Wollscheid B, Ahrens CH.

Genome Res. 2017 Dec;27(12):2083-2095. doi: 10.1101/gr.218255.116. Epub 2017 Nov 15.


Development and evaluation of a bioinformatics approach for designing molecular assays for viral detection.

Schneeberger PHH, Pothier JF, Bühlmann A, Duffy B, Beuret C, Utzinger J, Frey JE.

PLoS One. 2017 May 25;12(5):e0178195. doi: 10.1371/journal.pone.0178195. eCollection 2017.


Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites.

Remus-Emsermann MNP, Schmid M, Gekenidis MT, Pelludat C, Frey JE, Ahrens CH, Drissner D.

Stand Genomic Sci. 2016 Sep 26;11:75. doi: 10.1186/s40793-016-0190-6. eCollection 2016.


Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees.

Rezzonico F, Smits THM, Born Y, Blom J, Frey JE, Goesmann A, Cleenwerck I, de Vos P, Bonaterra A, Duffy B, Montesinos E.

Int J Syst Evol Microbiol. 2016 Mar;66(3):1583-1592. doi: 10.1099/ijsem.0.000920. Epub 2016 Jan 26.


Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study.

Schneeberger PHH, Becker SL, Pothier JF, Duffy B, N'Goran EK, Beuret C, Frey JE, Utzinger J.

Infect Genet Evol. 2016 Jun;40:389-397. doi: 10.1016/j.meegid.2015.08.044. Epub 2015 Sep 25.


Biological, Serological, and Molecular Characterization of a Highly Divergent Strain of Grapevine leafroll-associated virus 4 Causing Grapevine Leafroll Disease.

Reynard JS, Schneeberger PH, Frey JE, Schaerer S.

Phytopathology. 2015 Sep;105(9):1262-9. doi: 10.1094/PHYTO-12-14-0386-R. Epub 2015 Aug 28.


Development and Validation of LNA-Based Quantitative Real-Time PCR Assays for Detection and Identification of the Root-Knot Nematode Meloidogyne enterolobii in Complex DNA Backgrounds.

Kiewnick S, Frey JE, Braun-Kiewnick A.

Phytopathology. 2015 Sep;105(9):1245-9. doi: 10.1094/PHYTO-12-14-0364-R. Epub 2015 Aug 28.


Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data.

Qeli E, Omasits U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH.

J Proteomics. 2014 Aug 28;108:269-83. doi: 10.1016/j.jprot.2014.05.011. Epub 2014 May 27.


Restricted streptomycin use in apple orchards did not adversely alter the soil bacteria communities.

Walsh F, Smith DP, Owens SM, Duffy B, Frey JE.

Front Microbiol. 2014 Jan 31;4:383. doi: 10.3389/fmicb.2013.00383. eCollection 2013.


Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites.

Bühlmann A, Dreo T, Rezzonico F, Pothier JF, Smits TH, Ravnikar M, Frey JE, Duffy B.

Environ Microbiol. 2014 Jul;16(7):2112-25. doi: 10.1111/1462-2920.12289. Epub 2013 Oct 17.


Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics.

Smits TH, Rezzonico F, López MM, Blom J, Goesmann A, Frey JE, Duffy B.

Syst Appl Microbiol. 2013 Oct;36(7):449-56. doi: 10.1016/j.syapm.2013.04.003. Epub 2013 May 29.


Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation.

Frey JE, Guillén L, Frey B, Samietz J, Rull J, Aluja M.

BMC Evol Biol. 2013 May 29;13:106. doi: 10.1186/1471-2148-13-106.


Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.

Mann RA, Smits TH, Bühlmann A, Blom J, Goesmann A, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B.

PLoS One. 2013;8(2):e55644. doi: 10.1371/journal.pone.0055644. Epub 2013 Feb 7.


Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight.

Bühlmann A, Pothier JF, Rezzonico F, Smits TH, Andreou M, Boonham N, Duffy B, Frey JE.

J Microbiol Methods. 2013 Mar;92(3):332-9. doi: 10.1016/j.mimet.2012.12.017. Epub 2012 Dec 28.


Comparative analysis of the Hrp pathogenicity island of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element.

Mann RA, Blom J, Bühlmann A, Plummer KM, Beer SV, Luck JE, Goesmann A, Frey JE, Rodoni BC, Duffy B, Smits TH.

Gene. 2012 Aug 1;504(1):6-12. doi: 10.1016/j.gene.2012.05.002. Epub 2012 May 11.


Complete genome sequence of clinical isolate Pantoea ananatis LMG 5342.

De Maayer P, Chan WY, Rezzonico F, Bühlmann A, Venter SN, Blom J, Goesmann A, Frey JE, Smits TH, Duffy B, Coutinho TA.

J Bacteriol. 2012 Mar;194(6):1615-6. doi: 10.1128/JB.06715-11.


Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1.

Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru CA, Frey JE, Stockwell VO, Duffy B.

PLoS One. 2011;6(7):e22247. doi: 10.1371/journal.pone.0022247. Epub 2011 Jul 15.


Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems.

Walsh F, Ingenfeld A, Zampicolli M, Hilber-Bodmer M, Frey JE, Duffy B.

J Microbiol Methods. 2011 Aug;86(2):150-5. doi: 10.1016/j.mimet.2011.04.011. Epub 2011 Apr 23.


Barcoding quarantine nematodes and their close relatives: an update on the QBOL-project.

Holterman MH, Frey JE, Helder H, Mooyman PJ, Rybarczyk KD, Kiewnick S.

Commun Agric Appl Biol Sci. 2011;76(3):403-7.


Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants.

Powney R, Smits TH, Sawbridge T, Frey B, Blom J, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B.

J Bacteriol. 2011 Feb;193(3):785-6. doi: 10.1128/JB.01352-10. Epub 2010 Dec 3.


Genome sequence of the biocontrol agent Pantoea vagans strain C9-1.

Smits TH, Rezzonico F, Kamber T, Goesmann A, Ishimaru CA, Stockwell VO, Frey JE, Duffy B.

J Bacteriol. 2010 Dec;192(24):6486-7. doi: 10.1128/JB.01122-10. Epub 2010 Oct 15.


Genomic and phenotypic characterization of a nonpigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530-kb megaplasmid pPag3.

Smits TH, Rezzonico F, Pelludat C, Goesmann A, Frey JE, Duffy B.

FEMS Microbiol Lett. 2010 Jul 1;308(1):48-54. doi: 10.1111/j.1574-6968.2010.01994.x. Epub 2010 Apr 20.


Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp.

Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Frey JE, Duffy B.

Mol Plant Microbe Interact. 2010 Apr;23(4):384-93. doi: 10.1094/MPMI-23-4-0384.


Broad spectrum microarray for fingerprint-based bacterial species identification.

Pasquer F, Pelludat C, Duffy B, Frey JE.

BMC Biotechnol. 2010 Feb 17;10:13. doi: 10.1186/1472-6750-10-13.


Habitat-specific population structure in native western flower thrips Frankliniella occidentalis (Insecta, Thysanoptera).

Brunner PC, Frey JE.

J Evol Biol. 2010 Apr;23(4):797-804. doi: 10.1111/j.1420-9101.2010.01946.x. Epub 2010 Feb 9.


Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity.

Smits TH, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy B.

BMC Genomics. 2010 Jan 4;11:2. doi: 10.1186/1471-2164-11-2.


Genotypic comparison of Pantoea agglomerans plant and clinical strains.

Rezzonico F, Smits TH, Montesinos E, Frey JE, Duffy B.

BMC Microbiol. 2009 Sep 22;9:204. doi: 10.1186/1471-2180-9-204.


First Report of Root-Knot Nematode Meloidogyne enterolobii on Tomato and Cucumber in Switzerland.

Kiewnick S, Karssen G, Brito JA, Oggenfuss M, Frey JE.

Plant Dis. 2008 Sep;92(9):1370. doi: 10.1094/PDIS-92-9-1370A.


Rapid detection and species identification of Mycobacterium spp. using real-time PCR and DNA-microarray.

Tobler NE, Pfunder M, Herzog K, Frey JE, Altwegg M.

J Microbiol Methods. 2006 Jul;66(1):116-24. Epub 2005 Dec 19.


Quantitative assessment of heteroplasmy levels in Senecio vulgaris chloroplast DNA.

Frey JE, Frey B, Forcioli D.

Genetica. 2005 Mar;123(3):255-61.


Differentiation of Cucumber mosaic virus isolates by hybridization to oligonucleotides in a microarray format.

Deyong Z, Willingmann P, Heinze C, Adam G, Pfunder M, Frey B, Frey JE.

J Virol Methods. 2005 Jan;123(1):101-8.


Host-associated genetic differentiation in Thrips tabaci (Insecta; Thysanoptera), as determined from mtDNA sequence data.

Brunner PC, Chatzivassiliou EK, Katis NI, Frey JE.

Heredity (Edinb). 2004 Oct;93(4):364-70.


Complex relation between triazine-susceptible phenotype and genotype in the weed Senecio vulgaris may be caused by chloroplast DNA polymorphism.

Frey JE, Müller-Schärer H, Frey B, Frei D.

Theor Appl Genet. 1999 Aug;99(3-4):578-86. doi: 10.1007/s001220051271.


Genetic flexibility of plant chloroplasts.

Frey JE.

Nature. 1999 Mar 11;398(6723):115-6. No abstract available.


Differences among sibling speciesRhagoletis mendax andR. pomonella (diptera: ephritidae) in their antennal sensitivity to host fruit compounds.

Frey JE, Bierbaum TJ, Bush GL.

J Chem Ecol. 1992 Nov;18(11):2011-24. doi: 10.1007/BF00981924.


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