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List of works by Alfred Pühler

5.2 Functional -Omics for Cell Lines and Processes: The -Omics Technologies on the Example of CHO Cells

<i>Corynebacterium glutamicum</i>DNA is subjected to methylation-restriction in<i>Escherichia coli</i>

scientific article published in 1994

A Rhizobium Meliloti Ferredoxin (FdxN) Purified from Escherichia Coli Donates Electrons to Rhodobacter Capsulatus Nitrogenase

scientific article published in 1995

A community proposal to integrate proteomics activities in ELIXIR

scientific article

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 comprehensive proteome map of the lipid-requiring nosocomial pathogen Corynebacterium jeikeium K411.

scientific article published on April 2007

A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti

scientific article published on 11 July 2016

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

scientific article

A maltose-regulated large genomic region is activated by the transcriptional regulator MalT in Actinoplanes sp. SE50/110

scientific article published on 28 September 2020

A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data

scientific article (publication date: 10 March 2009)

A propionate-inducible expression system based on the Corynebacterium glutamicum prpD2 promoter and PrpR activator and its application for the redirection of amino acid biosynthesis pathways

scientific article

Absence of the highly expressed small carbohydrate-binding protein Cgt improves the acarbose formation in Actinoplanes sp. SE50/110

scientific article published on 28 April 2020

Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques

scientific article published on May 2005

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant

scientific article

Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021

scientific article

Antibiotic multiresistance plasmid pRSB101 isolated from a wastewater treatment plant is related to plasmids residing in phytopathogenic bacteria and carries eight different resistance determinants including a multidrug transport system

scientific article published in November 2004

Applying DNA affinity chromatography to specifically screen for sucrose-related DNA-binding transcriptional regulators of Xanthomonas campestris

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

BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

scientific article published on 28 October 2004

Back to the Future of Soil Metagenomics

scientific article

Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7.

scientific article published on 29 September 2008

Basis of Transposition and Gene Amplification by Tn1721 and Related Tetracycline-resistance Transposons ⬇️

scientific article published on January 1, 1981

Bioinformatics support for high-throughput proteomics

scientific article published on December 2003

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

scientific article

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology

scientific article

Carbon source dependent biosynthesis of acarviose metabolites in Actinoplanes sp. SE50/110

scientific article published on 26 August 2014

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors.

scientific article

Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.

scientific article published on 20 December 2011

Characterization of the LacI-type transcriptional repressor RbsR controlling ribose transport in Corynebacterium glutamicum ATCC 13032.

scientific article

Characterization of the Xanthomonas campestris pv. campestris lipopolysaccharide substructures essential for elicitation of an oxidative burst in tobacco cells

scientific article published in July 2005

Chinese hamster genome sequenced from sorted chromosomes

scientific article published in August 2013

Classification of hyper-variable Corynebacterium glutamicum surface-layer proteins by sequence analyses and atomic force microscopy.

scientific article

Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry.

scientific article

Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific Medicago truncatula lectin genes

scientific article published in August 2005

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 RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media

Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing

scientific article

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

scientific article

Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11.

scientific article published on 9 May 2008

Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

scientific article

Comparative genomics identified two conserved DNA modules in a corynebacterial plasmid family present in clinical isolates of the opportunistic human pathogen Corynebacterium jeikeium

scientific article published in September 2004

Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions

scientific article

Comparative proteome analysis of Actinoplanes sp. SE50/110 grown with maltose or glucose shows minor differences for acarbose biosynthesis proteins but major differences for saccharide transporters.

scientific article

Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase

article

Comparative transcriptome analysis of the biocontrol strain Bacillus amyloliquefaciens FZB42 as response to biofilm formation analyzed by RNA sequencing

scientific article

Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'.

scientific article published in January 2004

Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses

scientific article published on 30 July 2015

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 of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.

scientific article published on 22 October 2006

Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora

scientific article

Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion

scientific article

Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria

scientific article published on 8 January 2010

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 Pseudomonas sp. strain VLB120 a solvent tolerant, styrene degrading bacterium, isolated from forest soil

scientific article published on 24 October 2013

Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae

scientific article

Complete genome sequence of the actinobacterium Actinoplanes friuliensis HAG 010964, producer of the lipopeptide antibiotic friulimycin

scientific article published on 15 March 2014

Complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) consisting of a linear chromosome and one linear plasmid

scientific article published on 9 December 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 kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids

scientific article

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

scientific article published on 28 September 2014

Complete genome sequence of the myxobacterium Sorangium cellulosum

scientific article

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

Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032

scientific article

Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster.

scientific article

Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines

scientific article published on 25 January 2012

Conjugal Transfer of Megaplasmid 2 between Rhizobium meliloti Strains in Alfalfa Nodules.

scientific article published on August 1990

Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression

article

Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula

scientific article published in March 2004

Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines

scientific article published on 10 January 2014

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

CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data

scientific article

Corynebacterium striatumChloramphenicol Resistance Transposon Tn5564:Genetic Organization and Transposition inCorynebacterium glutamicum ⬇️

scientific article published on September 1, 1998

DNA microarray analysis of the nitrogen starvation response of Corynebacterium glutamicum

article

Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV

scientific article

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant

scientific article published on 30 July 2015

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms

scientific article published on 4 April 2013

Detection of 140 clinically relevant antibiotic-resistance genes in the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to selected antibiotics

scientific article published on 23 April 2009

Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source

scientific article

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

Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses

scientific article published in November 2006

Development of joint application strategies for two microbial gene finders

scientific article published on 26 February 2004

Different molecular rearrangements in the integron of the IncP-1 beta resistance plasmid pB10 isolated from a wastewater treatment plant result in elevated beta-lactam resistance levels

scientific article published on 16 September 2004

Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing

scientific article

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

scientific article

Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes

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 Pseudomonas aeruginosa Strain WS394, a Multidrug-Resistant and Highly Cytotoxic Wound Isolate from Chronic Ulcus Cruris.

scientific article published on 18 December 2014

Draft genome of the xanthan producer Xanthomonas campestris NRRL B-1459 (ATCC 13951).

scientific article published on 9 April 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 Wickerhamomyces ciferrii NRRL Y-1031 F-60-10.

scientific article published on December 2012

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

scientific article published on 24 September 2012

EDGAR: a software framework for the comparative analysis of prokaryotic genomes

scientific article

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

scientific article

EMMA: a platform for consistent storage and efficient analysis of microarray data

scientific article

EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods

scientific article published on 21 June 2005

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

scientific article published on 03 June 2019

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

Efficient electrotransformation of corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1.

scientific article

Electron Microscopy and Computerized Evaluation of Some Partially Denatured Group P Resistance Plasmids

scientific article published on March 1, 1978

Erratum to “Size exclusion chromatography—An improved method to harvest Corynebacterium glutamicum cells for the analysis of cytosolic metabolites” [J. Biotechnol. 154 (2–3) (2011) 171–178]

scholarly article published in Journal of Biotechnology

Erratum: Corrigendum: Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

scientific article published on 09 April 2007

Essentiality of the Maltase AmlE in Maltose Utilization and Its Transcriptional Regulation by the Repressor AmlR in the Acarbose-Producing Bacterium Actinoplanes sp. SE50/110

scientific article published on 29 October 2019

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

Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100.

scientific article published on 6 February 2013

Evaluation of vector systems and promoters for overexpression of the acarbose biosynthesis gene acbC in Actinoplanes sp. SE50/110

scientific article published on 28 June 2019

Expression of plant tumor-specific proteins in minicells of Escherichia coli: a fusion protein of lysopine dehydrogenase with chloramphenicol acetyltransferase ⬇️

scientific article published on October 24, 1981

Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program.

scientific article

Finding novel genes in bacterial communities isolated from the environment

article

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

Functional genome research on bacteria relevant for agriculture, environment and biotechnology

scientific article published on 01 March 2009

Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction

scientific article

GISMO--gene identification using a support vector machine for ORF classification

scientific article published on 14 December 2006

GenDB--an open source genome annotation system for prokaryote genomes

scientific article

Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris

scientific article

Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

scientific article published on 09 August 2019

Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant.

scientific article published on 8 April 2008

Genetic engineering in Actinoplanes sp. SE50/110 - development of an intergeneric conjugation system for the introduction of actinophage-based integrative vectors

scientific article published on 12 May 2016

Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays

scientific article

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 Sequence of Sinorhizobium meliloti Rm41.

scientific article published on 15 January 2013

Genome Sequence of the Acute Urethral Catheter Isolate Pseudomonas aeruginosa MH38.

scientific article

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 Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T

scientific article published on 26 January 2017

Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19.

scientific article published on 12 March 2015

Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21.

scientific article published on 16 July 2015

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 improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis

scientific article

Genome research in the light of ultrafast sequencing technologies

scientific article published on 26 June 2008

Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems.

scientific article published on December 2003

Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide

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 a Neisseria meningitidis capsule null locus strain from the clonal complex of sequence type 198.

scientific article published on September 2012

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

scientific article published on 17 February 2014

Genome sequence of the soybean symbiont Sinorhizobium fredii HH103.

scientific article

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

scientific article

Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan

scientific article

Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum

scientific article published in September 2003

Genome-based microbiology—From -omics research to systems and synthetic biology ⬇️

scientific article published on July 31, 2012

Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling

scientific article

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

scientific article

Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids

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 insights into symbiotic nitrogen fixation

scientific article

Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool

scientific article published on 6 June 2007

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

scientific article published on 20 June 2016

Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions

scientific article published in March 2004

Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress

scientific article published on 21 November 2020

High-quality genome sequence of Pichia pastoris CBS7435

High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum

scientific article published on 25 October 2012

Highlights from ECB10-Biotechnology and Society

scientific article published in September 2002

Host genes involved in nodulation preference in common bean (Phaseolus vulgaris)-rhizobium etli symbiosis revealed by suppressive subtractive hybridization

scientific article published in April 2008

ISR1: An Insertion Element Isolated from the Soil Bacterium Rhizobium lupini ⬇️

scientific article published on 01 January 1981

Identification and characterization of the last two unknown genes, dapC and dapF, in the succinylase branch of the L-lysine biosynthesis of Corynebacterium glutamicum

scientific article published on September 2003

Identification and functional analysis of six mycolyltransferase genes of Corynebacterium glutamicum ATCC 13032: the genes cop1, cmt1, and cmt2 can replace each other in the synthesis of trehalose dicorynomycolate, a component of the mycolic acid la

scientific article published on 10 May 2003

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

scientific article

Identification of Oxygen-Responsive Transcripts in the Silage Inoculant Lactobacillus buchneri CD034 by RNA Sequencing

scientific article published on 31 July 2015

Identification of Xanthomonas campestris pv. campestris galactose utilization genes from transcriptome data

scientific article

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

Identification of two prpDBC gene clusters in Corynebacterium glutamicum and their involvement in propionate degradation via the 2-methylcitrate cycle

scientific journal article

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases

scientific article published on 13 January 2021

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

Improving biotechnology communication ⬇️

scientific article published on June 26, 2013

Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts

scientific article published on 15 March 2014

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

scientific article

IncP-1-beta plasmid pGNB1 isolated from a bacterial community from a wastewater treatment plant mediates decolorization of triphenylmethane dyes

scientific article

Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology

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 Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

scientific article

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

Insights into the genome of the xanthan-producing phytopathogen Xanthomonas arboricola pv. pruni 109 by comparative genomic hybridization

scientific article published on 01 May 2011

Intramolecular amplification of the tetracycline resistance determinant of transposon Tn1771 in Escherichia coli ⬇️

scientific article published on 01 June 1979

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

scientific article published on 7 March 2016

Involvement of bacterial TonB-dependent signaling in the generation of an oligogalacturonide damage-associated molecular pattern from plant cell walls exposed to Xanthomonas campestris pv. campestris pectate lyases

scientific article

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

Mapping and comprehensive analysis of the extracellular and cell surface proteome of the human pathogen Corynebacterium diphtheriae

scientific article published on 01 April 2006

MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets

scientific article published on 29 September 2012

Metabolic flux pattern of glucose utilization by Xanthomonas campestris pv. campestris: prevalent role of the Entner-Doudoroff pathway and minor fluxes through the pentose phosphate pathway and glycolysis

scientific article

Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling

scientific article published on 20 July 2013

Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation

scientific article

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.

scientific article published on 30 April 2018

Mobilizable IncQ-related plasmid carrying a new quinolone resistance gene, qnrS2, isolated from the bacterial community of a wastewater treatment plant

scientific article published on September 2006

Molecular basics of mycorrhizal symbioses

scientific article published on 13 November 2006

Molecular characterization of PrpR, the transcriptional activator of propionate catabolism in Corynebacterium glutamicum

NFDI4Microbiota – national research data infrastructure for microbiota research

New Frontiers in Microbial Genome Research ⬇️

scientific article published on August 20, 2011

Next-generation sequencing of the CHO cell transcriptome

scientific article

Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering

scientific article

Novel macrolide resistance module carried by the IncP-1beta resistance plasmid pRSB111, isolated from a wastewater treatment plant

scientific article published on 13 November 2006

Occurrence of integron-associated resistance gene cassettes located on antibiotic resistance plasmids isolated from a wastewater treatment plant

scientific article published in August 2003

On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria

scientific article

Overlaps in the transcriptional profiles of Medicago truncatula roots inoculated with two different Glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza

scientific article

Phylogenetic Analysis of Bacterial Communities Associated with Leaves of the Seagrass Halophila stipulacea by a Culture-Independent Small-Subunit rRNA Gene Approach

scientific article

Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing

scientific article

Plasmid pB8 is closely related to the prototype IncP-1beta plasmid R751 but transfers poorly to Escherichia coli and carries a new transposon encoding a small multidrug resistance efflux protein

scientific article

Plasmids in Corynebacterium glutamicum and their molecular classification by comparative genomics

scientific article

Prevalence of pSmeSM11a-like plasmids in indigenous Sinorhizobium meliloti strains isolated in the course of a field release experiment with genetically modified S. meliloti strains

scientific article published on 20 November 2007

Production of nodulation factors by Rhizobium meliloti: fermentation, purification and characterization of glycolipids

scientific article published on 01 December 1997

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing

scientific article published on 8 February 2012

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

Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway

scientific journal article

Rational design of a Corynebacterium glutamicum pantothenate production strain and its characterization by metabolic flux analysis and genome-wide transcriptional profiling

scientific article

Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data.

scientific article

Regulation of succinoglycan and galactoglucan biosynthesis in Sinorhizobium meliloti.

scientific article

Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete

scientific article

Research on Industrial Biotechnology within the CLIB-Graduate Cluster – Part II

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

scientific article published on 07 April 2014

Rhizobium favelukesii sp. nov., isolated from the root nodules of alfalfa (Medicago sativa L).

scientific article

Role of the regulatory gene rirA in the transcriptional response of Sinorhizobium meliloti to iron limitation

scientific article

Sequence analysis of the 181-kb accessory plasmid pSmeSM11b, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment

scientific article published on 27 April 2007

Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements

scientific article published on 9 December 2004

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology

scientific article published on 23 April 2011

Single molecule force spectroscopy on ligand-DNA complexes: from molecular binding mechanisms to biosensor applications.

scientific article published in August 2004

Size exclusion chromatography: an improved method to harvest Corynebacterium glutamicum cells for the analysis of cytosolic metabolites

scientific article published on 9 September 2010

Spontaneous degradation of pRD1 DNA into unique size classes is recA dependent ⬇️

scientific article published on March 9, 1979

Stationary-phase mutants of Sinorhizobium meliloti are impaired in stationary-phase survival or in recovery to logarithmic growth ⬇️

scientific article published on October 1, 1997

Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library

scientific article

Targeted genome editing in the rare actinomycete Actinoplanes sp. SE50/110 by using the CRISPR/Cas9 System

scientific article published in June 2016

Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

scientific article

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

Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor

scientific article published on 20 June 2008

The 27.8-kb R-plasmid pTET3 from Corynebacterium glutamicum encodes the aminoglycoside adenyltransferase gene cassette aadA9 and the regulated tetracycline efflux system Tet 33 flanked by active copies of the widespread insertion sequence IS6100.

scientific article published on September 2002

The Corynebacterium glutamicum cglIM gene encoding a 5-cytosine methyltransferase enzyme confers a specific DNA methylation pattern in an McrBC-deficient Escherichia coli strain ⬇️

scientific article published on December 12, 1997

The Corynebacterium glutamicum gene pmt encoding a glycosyltransferase related to eukaryotic protein-O-mannosyltransferases is essential for glycosylation of the resuscitation promoting factor (Rpf2) and other secreted proteins

scientific article published on 01 June 2006

The DeoR-type transcriptional regulator SugR acts as a repressor for genes encoding the phosphoenolpyruvate:sugar phosphotransferase system (PTS) in Corynebacterium glutamicum

scientific article

The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum

scientific article

The GlxR regulon of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcription regulator

scientific article published on 3 June 2008

The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum

scientific article published on 26 January 2007

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 LacI/GalR family transcriptional regulator UriR negatively controls uridine utilization of Corynebacterium glutamicum by binding to catabolite-responsive element (cre)-like sequences

scientific article

The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110.

scientific article published on 25 July 2017

The McbR repressor modulated by the effector substance S-adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism of Corynebacterium glutamicum ATCC 13032.

scientific article

The Medicago truncatula sucrose synthase gene MtSucS1 is activated both in the infected region of root nodules and in the cortex of roots colonized by arbuscular mycorrhizal fungi

scientific article published in October 2003

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 Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies

scientific article

The Sinorhizobium fredii HH103 genome: a comparative analysis with S. fredii strains differing in their symbiotic behaviour with soybean

scientific article published on 15 June 2015

The Sinorhizobium meliloti MucR protein, which is essential for the production of high-molecular-weight succinoglycan exopolysaccharide, binds to short DNA regions upstream of exoH and exoY ⬇️

scientific article published on February 1, 1998

The Sinorhizobium meliloti fur gene regulates, with dependence on Mn(II), transcription of the sitABCD operon, encoding a metal-type transporter

scientific article

The alanine racemase gene alr is an alternative to antibiotic resistance genes in cloning systems for industrial Corynebacterium glutamicum strains

scientific article published in October 2002

The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties

scientific article

The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins

scientific article

The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.

scientific article

The complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) carrying gene clusters for the biosynthesis of tetracenomycin C, 5`-hydroxy streptomycin, and acarbose

scientific article published on 13 September 2017

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 complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere

scientific article

The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti

scientific article

The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor

scientific article published on 5 June 2017

The crystal structures of apo and cAMP-bound GlxR from Corynebacterium glutamicum reveal structural and dynamic changes upon cAMP binding in CRP/FNR family transcription factors

scientific journal article

The cytosolic and extracellular proteomes of Actinoplanes sp. SE50/110 led to the identification of gene products involved in acarbose metabolism

scientific article

The cytosolic, cell surface and extracellular proteomes of the biotechnologically important soil bacterium Corynebacterium efficiens YS-314 in comparison to those of Corynebacterium glutamicum ATCC 13032

scientific article published on 01 January 2006

The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules

scientific article

The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase

scientific article published on 23 November 2020

The extracytoplasmic function-type sigma factor SigM of Corynebacterium glutamicum ATCC 13032 is involved in transcription of disulfide stress-related genes

scientific article published on 4 May 2007

The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis

scientific article

The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity

scientific article (publication date: March 2008)

The glycosylated cell surface protein Rpf2, containing a resuscitation-promoting factor motif, is involved in intercellular communication of Corynebacterium glutamicum

scientific article published on 3 August 2004

The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences

scientific article

The influence of a modified lipopolysaccharide O-antigen on the biosynthesis of xanthan in Xanthomonas campestris pv. campestris B100

scientific article

The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing

scientific article

The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology

scientific article published on 27 May 2008

The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae

scientific article

The nodulation of alfalfa by the acid-tolerant Rhizobium sp. strain LPU83 does not require sulfated forms of lipochitooligosaccharide nodulation signals

scientific article

The promoter of the Vicia faba L. leghemoglobin gene VfLb29 is specifically activated in the infected cells of root nodules and in the arbuscule-containing cells of mycorrhizal roots from different legume and nonlegume plants

scientific article

The promoter of the leghaemoglobin gene VfLb29: functional analysis and identification of modules necessary for its activation in the infected cells of root nodules and in the arbuscule-containing cells of mycorrhizal roots

scientific article published on 24 January 2005

The putative transcriptional repressor McbR, member of the TetR-family, is involved in the regulation of the metabolic network directing the synthesis of sulfur containing amino acids in Corynebacterium glutamicum

scientific article published in June 2003

The role of sigma factor RpoH1 in the pH stress response of Sinorhizobium meliloti ⬇️

scientific article published on October 18, 2010

The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms

scientific article published on 03 July 2015

The surface (S)-layer gene cspB of Corynebacterium glutamicum is transcriptionally activated by a LuxR-type regulator and located on a 6 kb genomic island absent from the type strain ATCC 13032.

scientific article published in April 2006

The time course of the transcriptomic response of Sinorhizobium meliloti 1021 following a shift to acidic pH.

scientific article

The transcriptional regulator SsuR activates expression of the Corynebacterium glutamicum sulphonate utilization genes in the absence of sulphate

scientific article

The transcriptional regulatory repertoire of Corynebacterium glutamicum: reconstruction of the network controlling pathways involved in lysine and glutamate production

scientific article published on 04 December 2009

The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis.

scientific article published on 27 July 2011

Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.).

scientific article published on 5 March 2014

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

scientific article

Transcriptome profiling in root nodules and arbuscular mycorrhiza identifies a collection of novel genes induced during Medicago truncatula root endosymbioses

scientific article

Triple transcriptional control of the resuscitation promoting factor 2 (rpf2) gene of Corynebacterium glutamicum by the regulators of acetate metabolism RamA and RamB and the cAMP-dependent regulator GlxR

scientific journal article

Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids

scientific article

Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression

scientific article published on 30 June 2006

Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing

scientific article

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates

scientific article

Unusual structure of the tonB-exb DNA region of Xanthomonas campestris pv. campestris: tonB, exbB, and exbD1 are essential for ferric iron uptake, but exbD2 is not ⬇️

scientific article published on November 1, 1997

Versatile Low-Copy-Number Plasmids for Temperature-Inducible Overexpression of Bacterial Genes in Escherichia coli ⬇️

scientific article published on 01 March 1998

What can bacterial genome research teach us about bacteria-plant interactions?

scientific article published on April 2004

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

Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique

scientific article

Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes

scientific article published on 25 August 2006

Xanthan gum biosynthesis and application: a biochemical /genetic perspective ⬇️

scientific article published on August 1, 1998

Xanthomonas campestris pv. campestris lpsI and lpsJ genes encoding putative proteins with sequence similarity to the α- and β-subunits of 3-oxoacid CoA-transferases are involved in LPS biosynthesis ⬇️

scientific article published on December 1, 1997

de.NBI Cloud federation through ELIXIR AAI

scientific article published on 10 June 2019

pSETT4, an Improved φC31-Based Integrative Vector System for Actinoplanes sp. SE50/110

scientific article published on 24 September 2020

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