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List of works by Daniel Wibberg

<i>Ustilago maydis</i> Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model

scientific article published on 20 May 2022

A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani

scientific article published on 10 May 2019

A framework to assess the quality and impact of bioinformatics training across ELIXIR

scientific article published on 23 July 2020

A research data management (RDM) community for ELIXIR

scientific article published on 30 September 2024

An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH

scientific article

Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids.

scientific article

Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

scientific article

Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

scientific article

Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome.

scientific article published on 22 May 2015

Comparative Transcriptome Analysis Provides Molecular Insights into the Interaction of Beet necrotic yellow vein virus and Beet soil-borne mosaic virus with Their Host Sugar Beet

scientific article published on 08 January 2020

Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats.

scientific article

Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

scientific article

Complete Chloroplast and Mitochondrial Genome Sequences of the Hydrocarbon Oil-Producing Green Microalga Botryococcus braunii Race B (Showa)

scientific article

Complete Genome Sequence of Herbinix luporum SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor

scientific article

Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T).

scientific article published on December 2016

Complete Genome Sequence of the Clinical Strain Acinetobacter baumannii R2090 Carrying the Chromosomally Encoded Metallo-β-Lactamase Gene blaNDM-1.

scientific article published on 10 September 2015

Complete Genome Sequence of the Methanogen Methanoculleus bourgensis BA1 Isolated from a Biogas Reactor.

scientific article

Complete genome analysis of Clostridium bornimense strain M2/40(T): A new acidogenic Clostridium species isolated from a mesophilic two-phase laboratory-scale biogas reactor

scientific article published on 6 August 2015

Complete genome sequence of Peptoniphilus sp. strain ING2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation

scientific article published on 19 September 2014

Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant

scientific article published on 28 August 2014

Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.

scientific article

Complete genome sequence of the hydrogenotrophic Archaeon Methanobacterium sp. Mb1 isolated from a production-scale biogas plant

scientific article published on 29 October 2013

Complete genome sequence of the hydrogenotrophic, methanogenic archaeon Methanoculleus bourgensis strain MS2(T), Isolated from a sewage sludge digester

scientific article (publication date: October 2012)

Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.).

scientific article published on 28 September 2014

Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab-scale biogas reactor

scientific article published on 20 November 2014

Complete genome sequence of the strain Defluviitoga tunisiensis L3, isolated from a thermophilic, production-scale biogas plant

scientific article published on 20 March 2015

Complete genome sequencing of Acinetobacter baumannii str. K50 disclosed the large conjugative plasmid pK50a encoding the carbapenemase OXA-23 and the extended-spectrum β-lactamase GES-11.

scientific article published on 20 February 2018

Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid

article by Daniel Wibberg et al published August 2011 in Journal of Biotechnology

Complete sequence of broad-host-range plasmid pNOR-2000 harbouring the metallo-β-lactamase gene blaVIM-2 from Pseudomonas aeruginosa

scientific article published on 25 January 2013

Corrigendum to "Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant" [J. Biotechnol. 188 (2014) 136-137].

scientific article published on 15 September 2016

Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates

scientific article published on 21 December 2015

Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals

scientific article

Draft Genome Sequence of Propionispora sp. Strain 2/2-37, a New Xylan-Degrading Bacterium Isolated from a Mesophilic Biogas Reactor

scientific article published on 23 June 2016

Draft Genome Sequence of Pseudomonas aeruginosa Strain WS136, a Highly Cytotoxic ExoS-Positive Wound Isolate Recovered from Pyoderma Gangrenosum

scientific article published on 2 July 2015

Draft genome sequence of Herbinix hemicellulosilytica T3/55 T, a new thermophilic cellulose degrading bacterium isolated from a thermophilic biogas reactor.

scientific article published on 4 August 2015

Draft genome sequence of Sinorhizobium meliloti RU11/001, a model organism for flagellum structure, motility and chemotaxis

scientific article

Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation.

scientific article published on 19 August 2013

Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3.

scientific article published on 8 June 2017

Draft genome sequence of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB strain BBA69670

article by Daniel Wibberg et al published March 2016 in Journal of Biotechnology

Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities for forage grasses

scientific article published on 17 August 2016

Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.

scientific article published on 24 September 2012

Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing

scientific article published on 27 May 2014

Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14.

scientific article published on 29 December 2012

Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing.

scientific article published on 6 April 2016

First draft genome sequence of the amylolytic Bacillus thermoamylovorans wild-type strain 1A1 isolated from a thermophilic biogas plant

scientific article published on 28 September 2014

First genomic analysis of the broad-host-range Rhizobium sp. LPU83 strain, a member of the low-genetic diversity Oregon-like Rhizobium sp. group

scientific article published on 15 February 2011

Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing.

scientific article published on 5 April 2018

Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter

scientific article published on 20 December 2019

Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602

scientific article published in 2022

Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection

scientific article published on 23 January 2014

Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes

scientific article

Genome content, metabolic pathways and biotechnological potential of the psychrophilic Arctic bacterium Psychrobacter sp. DAB_AL43B, a source and a host of novel Psychrobacter-specific vectors

scientific article

Genome sequence of Methanobacterium congolense strain Buetzberg, a hydrogenotrophic, methanogenic archaeon, isolated from a mesophilic industrial-scale biogas plant utilizing bio-waste

scientific article published on 16 February 2017

Genome sequence of the acid-tolerant strain Rhizobium sp. LPU83.

scientific article published on 17 February 2014

Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686.

scientific article

Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment

scientific article published on 7 May 2016

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

scientific article published on 13 November 2017

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

scientific article published on 20 June 2016

High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa ⬇️

scholarly article published in 2020

Identification of a novel mycovirus isolated from Rhizoctonia solani (AG 2-2 IV) provides further information about genome plasticity within the order Tymovirales

scientific article published on 12 October 2016

Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system

scientific article

IncH-type plasmid harboring bla CTX-M-15, bla DHA-1, and qnrB4 genes recovered from animal isolates

scientific article

IncP-1β plasmids of Comamonas sp. and Delftia sp. strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet

scientific article

Insight into the structure, function and conjugative transfer of pLPU83a, an accessory plasmid of Rhizobium favelukesii LPU83

scientific article published on 27 March 2019

Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants

scientific article

Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage

scientific article published on 20 March 2012

Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene

scientific article published on 7 March 2016

Kitasatospora fiedleri sp. nov., a novel antibiotic-producing member of the genus Kitasatospora

scientific article published in 2023

Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685.

scientific article published on 30 August 2017

New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing

scientific article

Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions.

scientific article published on 30 April 2018

Pseudomonas carnis sp. nov., isolated from meat

scientific article published on 10 January 2020

Pseudomonas paracarnis sp. nov., isolated from refrigerated beef

scientific article published in 2021

Rhizobial plasmid pLPU83a is able to switch between different transfer machineries depending on its genomic background

scientific article published on 07 April 2014

Streptomyces coriariae sp. nov., a novel streptomycete isolated from actinorhizal nodules of Coriaria intermedia ⬇️

scientific article published on 13 December 2022

Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges

scientific article published on 25 June 2013

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes

scientific article published on 5 January 2016

The IncF plasmid pRSB225 isolated from a municipal wastewater treatment plant's on-site preflooder combining antibiotic resistance and putative virulence functions is highly related to virulence plasmids identified in pathogenic E. coli isolates

scientific article published on 2 December 2012

The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.).

scientific article

The Role of <i>Petrimonas mucosa</i> ING2-E5A<sup>T</sup> in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

scientific article published on 17 December 2020

The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome

scientific article

The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution

scientific article published on 2 February 2012

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

scientific article published on 07 November 2019

Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs).

scientific article

Whole genome sequence of Clostridium bornimense strain M2/40 isolated from a lab-scale mesophilic two-phase biogas reactor digesting maize silage and wheat straw

scientific article published on 4 June 2014

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