Publications

Research Group for Environmental Genomics and Systems Biology

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A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics

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Plant Pathology, 66, 7. 1094-1102. Peer reviewed.

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Cherries: Botany, Production and Uses

: Bacterial Diseases.

Wallingford, UK: CAB International.

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Comparative genomics-informed design of two LAMP detection assays for detection of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae and discrimination of isolates belonging to the pandemic biovar 3

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Plant Pathology, 66, 1. 140-9. Peer reviewed.

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Complete genome sequence of Pseudomonas viridiflava CFBP 1590, isolated from diseased cherry in France

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Genome Announcements, 5, 30. e00662-17. Peer reviewed.

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

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PLoS ONE, 12, 5. e0178195. Peer reviewed.

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Draft genome sequences of seven Streptococcus agalactiae strains isolated from Camelus dromedarius at the horn of Africa

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Genome Announcements, 5, 28. e00525-17. Peer reviewed.

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Microbial diversity in different compartments of an aquaponics system

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Archives of Microbiology, 199, 4. 613-620. Peer reviewed.

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Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella

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Antonie van Leeuwenhoek, 110, 10. 1287-1309. Peer reviewed.

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Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two new species within the Pseudomonas putida group isolated from forest soil

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International Journal of Systematic and Evolutionary Microbiology, 67 2853-2861. Peer reviewed.

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Role of the type VI secretion systems during disease interactions of Erwinia amylovora with its plant host

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BMC Genomics, 16 628. Peer reviewed.

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Characterization and genetic diversity of causal agent of stone fruit bacterial canker Pseudomonas cerasi, a new pathogen of cherry

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Acta Horticulturae, 1149 9-14.

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Diversity and host range of Pseudomonas in fruit tree species in Latvia

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Acta horticulturae, 1149: 25-29.

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

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International Journal of Systematic and Evolutionary Microbiology, 66, 3. 1583-1592. Peer reviewed.

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Fire blight disease reactome: RNA-seq transcriptional profile of apple host plant defence responses to Erwinia amylovora pathogen infection

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Scientific Reports, 6 21600. Peer reviewed.

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Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics

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The ISME Journal, 10 2527-2542. Peer reviewed.

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Kleinsäuger mit Haarproben zuverlässig bestimmen

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Vierteljahrsschrift der Naturforschenden Gesellschaft in Zürich NGZH, 1/2016, 161. 9-11.

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

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Infection, Genetics and Evolution, 40 389-397. Peer reviewed.

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Pararhizobium polonicum sp. nov. isolated from tumors on stone fruit rootstocks

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Systematic and Applied Microbiology, 39 164-169. Peer reviewed.

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Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry

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Systematic and Applied Microbiology, 39, 6. 370-377. Peer reviewed.

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Specific surface glycan decorations enable antimicrobial peptide resistance in plant-beneficial pseudomonads with insect-pathogenic properties

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Environmental Microbiology, 18, 11. 4265-4281. Peer reviewed.

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Complete genome sequence of the cyanogenic phosphate-solubilizing Pseudomonas sp. strain CCOS 191, a close relative of Pseudomonas mosseli

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Genome Announcements, 3, 3. e00616-15. Peer reviewed.

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Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c

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Genome Announcements, 3, 6. e01448-15. Peer reviewed.

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Evaluation of a real-time PCR and a loop-mediated isothermal amplification for detection of Xanthomonas arboricola pv. pruni in plant tissue samples

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Journal of Microbiological Methods, 112 36-39. Peer reviewed.

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Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis

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Frontiers in Microbiology, 6 576. Peer reviewed.

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Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

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Applied Microbiology and Biotechnology, 99, 13. 5547-5562. Peer reviewed.

Rezzonico, Fabio; Smits, Theo H.M.; Holliger, Eduard (Hg.). ().

Proceedings of the 13th International Workshop on Fire Blight

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Leuven (Belgium): International Society for Horticultural Sciences.

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A novel plasmid pEA68 of Erwinia amylovora and the description of a new family of plasmids

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Archives of Microbiology, 196, 12. 891-899. Peer reviewed.

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Comparative genomics of Erwinia amylovora isolates from Mexico

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Acta Horticulturae, 1056: 173-177.

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Detection of the causative agent of fire blight - Erwinia amylovora (Burrill) Winslow et al. - in the southeast of Kazakhstan

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Acta Horticulturae, 1056: 129-132.

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Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum)

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International Journal of Systematic and Evolutionary Microbiology, 64 768-774. Peer reviewed.

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Direct plantlet inoculation with soil or insect-associated fungi may control cabbage root fly maggots

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Journal of Invertebrate Pathology, Volume, 120. 59-66. Peer reviewed.

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Draft genome sequences for the onion center roth pathogen Pantoea ananatis PA4 and maize brown stalk rot pathogen P. ananatis BD442

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Genome Announcements, 2, 4. e00750-14. Peer reviewed.

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Phenotypic comparison of clinical and plant-beneficial strains of Pantoea agglomerans

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International Microbiology, 17: 81-90. Peer reviewed.

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

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Environmental Microbiology, 16: 2112-2125. Peer reviewed.

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Prevalence of type III secretion system in effective biocontrol pseudomonads

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Research in Microbiology, 165: 300-304. Peer reviewed.

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Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization

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Microbial Biotechnology, 7, 6. 528–544. Peer reviewed.

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Whole-genome sequencing of Erwinia amylovora strains from México detects SNPs in rpsL conferring streptomycin resistance and in the avrRpt2 effector altering host interactions

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Genome Announcements, 2:, 1. e01229-13. Peer reviewed.

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

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PLoS One, 8 e55644. Peer reviewed.

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Comparative RNA-Seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni

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PLoS ONE, 8, e54196. Peer reviewed.

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Complete sequence of Erwinia piriflorinigrans plasmids pEPIR37 and pEPIR5 and role of pEPIR37 in pathogen virulence

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Plant Pathology, 62 786-798. Peer reviewed.

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

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Journal of Microbiological Methods, 92: 332-339. Peer reviewed.

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Genomics-informed design of loop-mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. pruni at the intraspecific level

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Plant Pathology, 62 475-484. Peer reviewed.

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Identification of a major QTL for Xanthomonas arboricola pv. pruni resistance in apricot

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Tree Genetics and Genomes, 9 409-421. Peer reviewed.

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

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Systematic and Applied Microbiology, 36: 449-456. Peer reviewed.

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Thirteenth Int'l Workshop on Fire Blight

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Chronica Horticulturae, 53, 4. 40-41.

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Xanthomonas arboricola pv. fragariae: what's in a name?

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Plant Pathology, 62 1123-1131. Peer reviewed.