List of works by Alexander Goesmann

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

A Predator Unmasked: Life Cycle of Bdellovibrio bacteriovorus from a Genomic Perspective

scientific article

A detailed view of the intracellular transcriptome of Listeria monocytogenes in murine macrophages using RNA-seq

scientific article

A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study

scientific article

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

scientific article (publication date: 10 March 2009)

A reference genome of the Chinese hamster based on a hybrid assembly strategy

article

A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies.

scientific article

ADAR1 Is Required for Dendritic Cell Subset Homeostasis and Alveolar Macrophage Function

scientific article published on 16 January 2019

AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization

scientific article

ALLocator: an interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis

scientific article

ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates

scientific article published on 05 March 2020

Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants

scientific article published on 24 August 2020

An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery.

scientific article

An evaluation framework for statistical tests on microarray data

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

Antidiabetic profiling of veramycins, polyketides accessible by biosynthesis, chemical synthesis and precursor-directed modification ⬇️

scientific article published on 9 February 2022

Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite

scientific article published on 6 March 2015

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

scientific article

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser

scientific article

Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing

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

Big Data in der Biologie: kein Problem mehr!

scientific article published on 05 February 2019

Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes

scientific article

Bioinformatics for NGS-based metagenomics and the application to biogas research.

scientific article

Bioinformatics support for high-throughput proteomics

scientific article published on December 2003

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

scientific article

CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks

scientific article published on 24 August 2010

CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium

scientific article

CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3',3'-cGAMP Nucleotide Levels during Development in Myxococcus xanthus

scientific article published on 15 February 2022

Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria

scientific article published on 10 August 2014

Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling ⬇️

article

Changes in root bacterial communities associated to two different development stages of canola (Brassica napus L. var oleifera) evaluated through next-generation sequencing technology

scientific article

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

scientific article published on 20 December 2011

Chinese hamster genome sequenced from sorted chromosomes

scientific article published in August 2013

Chromosomal Locations of mcr-1 and bla CTX-M-15 in Fluoroquinolone-Resistant Escherichia coli ST410.

scientific article published on 15 September 2016

Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany

scientific article published on 12 May 2016

Colistin resistance gene mcr-1 in extended-spectrum β-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany.

scientific article published on 7 January 2016

Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease

scientific article

Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms

scientific article published on 6 June 2008

Comparative analysis of plasmids in the genus Listeria

scientific article

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.

scientific article

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

scientific article

Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum

scientific article

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds ⬇️

scientific article published on 28 May 2014

Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence

scientific article published on 13 August 2010

Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars

scientific article published on 3 February 2012

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

scientific article

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

scientific article

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.

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 Bacteroides ovatus V975

scientific article published on December 2016

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 Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035

scholarly article published 25 April 2019

Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713.

scientific article

Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing

scientific article published on 5 October 2017

Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T

scientific article published on 09 September 2019

Complete Genome Sequence of the Probiotic Enterococcus faecalis Symbioflor 1 Clone DSM 16431.

scientific article published on January 2013

Complete Sequence of Probiotic Symbioflor 2 Escherichia coli Strain G3/10 and Draft Sequences of Symbioflor 2 E. coli Strains G1/2, G4/9, G5, G6/7, and G8

scientific article published on 5 March 2015

Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a selective capacity to utilize plant glucans

scientific article

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

scientific article

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 Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry.

scientific article published on 18 September 2009

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

scientific article published on 8 January 2010

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 clinical isolate Pantoea ananatis LMG 5342.

scientific article published on March 2012

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 fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp.

scientific article

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

scientific article

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 myxobacterium Sorangium cellulosum

scientific article

Complete genome sequence of the porcine isolate Enterococcus faecalis D32.

scientific article

Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363.

scientific article published on 16 February 2007

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

Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40.

scientific article

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

scientific article published on 25 January 2012

Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii

scientific article

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

scientific article published on 10 January 2014

Conveyor: a workflow engine for bioinformatic analyses.

scientific article

Correction: Bioinformatic Analysis Reveals High Diversity of Bacterial Genes for Laccase-Like Enzymes.

scientific article

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

scientific article

Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node

scientific article published in 2021

Criblamydia sequanensis Harbors a Megaplasmid Encoding Arsenite Resistance

scientific article published on 23 October 2014

Cyclophilin Inhibitors Restrict Middle East Respiratory Syndrome Coronavirus Via Interferon λ In Vitro And In Mice

scientific article published on 02 July 2020

De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite

scientific article published on 9 December 2015

Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacle Balanus amphitrite

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

Development of joint application strategies for two microbial gene finders

scientific article published on 26 February 2004

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

scientific article

DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes.

scientific article

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 Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c.

scientific article published on 10 December 2015

Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71.

scientific article published on 26 October 2017

Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10.

scientific article published on December 2012

Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594

scientific article published on 21 September 2016

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

EDGAR 2.0: an enhanced software platform for comparative gene content analyses

scientific article

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

Ecological genomics of marine Roseobacters

scientific article published on 25 May 2007

Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response

Elucidation of insertion elements carried on plasmids and in vitro construction of shuttle vectors from the toxic cyanobacterium Planktothrix.

scientific article published on 6 June 2014

Enterobacter bugandensis: a novel enterobacterial species associated with severe clinical infection.

scientific article published on 29 March 2018

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

scientific article published on 09 April 2007

Erratum: Corrigendum: Updating benchtop sequencing performance comparison

scholarly article published in Nature Biotechnology

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

scientific article

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

Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex

scientific article published on 02 June 2022

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

scientific article published on 30 March 2011

Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family

scientific article published on 04 January 2021

Fabry disease: Detection of Alu-mediated exon duplication by NGS

scientific article published on 29 March 2019

Flexible metagenome analysis using the MGX framework.

scientific article published on 24 April 2018

From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet

scientific article

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers

scientific article

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

scientific article

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

scientific article published on 8 April 2008

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 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 of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica serovar weltevreden

scientific article published on 4 February 2011

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

scientific article

Genome sequence of Fibrella aestuarina BUZ 2(T), a filamentous marine bacterium

scientific article published on July 2012

Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities

scientific article published on 23 February 2012

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 biocontrol agent Pantoea vagans strain C9-1.

scientific article

Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize

scientific article published on 29 May 2018

Genome sequence of the filamentous bacterium Fibrisoma limi BUZ 3T.

scientific article published on August 2012

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

scientific article

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

scientific article published on 20 April 2010

Genomic avenue to avian colisepticemia

scientific article

Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara

scientific article published on December 2007

Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein

scientific article published on 4 March 2013

Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134.

scientific article published on 14 October 2011

Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans DsijT.

scientific article

High diversity of Vibrio spp. associated with different ecological niches in a marine aquaria system and description of Vibrio aquimaris sp. nov

scientific article published on 18 July 2020

High-quality genome sequence of Pichia pastoris CBS7435

How animals distribute themselves in space: energy landscapes of Antarctic avian predators

scientific article published on 17 May 2021

Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10

scientific article

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

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

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

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 completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage.

scientific article published on 20 March 2012

Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment.

scientific article published on 29 September 2014

Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14.

scientific article published on 28 December 2015

Lausannevirus, a giant amoebal virus encoding histone doublets

scientific article published on 9 March 2011

Learning to Classify Organic and Conventional Wheat - A Machine Learning Driven Approach Using the MeltDB 2.0 Metabolomics Analysis Platform.

scientific article published on 24 March 2015

Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora.

scientific article

Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella

scientific article published on 12 December 2017

MSEA: metabolite set enrichment analysis in the MeltDB metabolomics software platform: metabolic profiling of Corynebacterium glutamicum as an example

article

Massive parallel insertion site sequencing of an arrayed Sinorhizobium meliloti signature-tagged mini-Tn 5 transposon mutant library

scientific article

MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula

scientific article

MeltDB 2.0-advances of the metabolomics software system

scientific article

MeltDB: a software platform for the analysis and integration of metabolomics experiment data

scientific article

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

scientific article published on 29 September 2012

Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT.

scientific article

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

scientific article

Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems

scientific article published on 13 February 2014

Microbial diversity in different compartments of an aquaponics system.

scientific article published on 10 January 2017

Multi-label classification for multi-drug resistance prediction of Escherichia coli

scientific article published in 2022

Multidimension cultivation analysis by standard and omics methods for optimization of therapeutics production.

scientific article published on 4 December 2013

Multilineage murine stem cells generate complex organoids to model distal lung development and disease

scientific article published on 28 September 2020

NFDI4Microbiota – national research data infrastructure for microbiota research

New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics

scientific article published on 3 April 2013

Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots

scientific article published on 28 March 2016

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

Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica.

scientific article published on 23 October 2015

Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila

scientific article published on 13 April 2016

PathFinder: reconstruction and dynamic visualization of metabolic pathways

scientific article published on January 2002

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

scientific article

Phylogenetic classification of short environmental DNA fragments

scientific article (publication date: April 2008)

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

scientific article published on 29 May 2013

Phylogenomic grouping of Listeria monocytogenes

scientific article

Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores

scientific article published on 24 June 2020

Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions

Presence of a widely disseminated Listeria monocytogenes serotype 4b clone in India

scientific article published on 8 June 2016

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

Protein turnover quantification in a multilabeling approach: from data calculation to evaluation

scientific article

Pseudomonas bubulae sp. nov., isolated from beef

scientific article

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

Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments

scientific article published on 6 October 2009

RAPYD--rapid annotation platform for yeast data.

scientific article

Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana

scientific article published on 28 April 2013

Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.

scientific article

ReadXplorer 2-detailed read mapping analysis and visualization from one single source.

scientific article

ReadXplorer--visualization and analysis of mapped sequences

scientific article published on 30 April 2014

Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome

scientific article

Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production

scientific article

ReferenceSeeker: rapid determination of appropriate reference genomes

scientific article published on 04 February 2020

RhizoRegNet--a database of rhizobial transcription factors and regulatory networks

scientific article published on 16 November 2010

Root metabolic response of rice (Oryza sativa L.) genotypes with contrasting tolerance to zinc deficiency and bicarbonate excess

article

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

scientific article published on 19 February 2015

Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8.

scientific article

Streptomyces ciscaucasicus Sveshnikova et al. 1983 is a later subjective synonym of Streptomyces canus Heinemann et al. 1953.

scientific article

Streptomyces dysideae sp. nov., isolated from a marine Mediterranean sponge Dysidea tupha

scientific article published in 2019

Streptomyces phaeopurpureus Shinobu 1957 (Approved Lists 1980) and Streptomyces griseorubiginosus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (Approved Lists 1980) are heterotypic subjective synonyms.

scientific article published on 10 August 2017

Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean

scientific article published on 30 March 2011

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

scientific article published on 10 August 2017

TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

scientific article

TRUNCATULIX--a data warehouse for the legume community

scientific article

Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov.

scientific article

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

scientific article published on 20 June 2008

Temporal variation in brain transcriptome is associated with the expression of female mimicry as a sequential male alternative reproductive tactic in fish.

scientific article

The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of th

scientific article published on 10 January 2003

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand

scientific article

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 Waddlia genome: a window into chlamydial biology

scientific article (publication date: 28 May 2010)

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 Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence ⬇️

scientific article

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

scientific article

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 of the recently domesticated crop plant sugar beet (Beta vulgaris)

scientific article

The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP)

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 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 multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established α, β and δ sub-groups

scholarly article by Martin Iain Bahl et al published July 2007 in Plasmid

The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract

scientific article published in December 2015

The status of the genus Prolinoborus (Pot et al. 1992) and the species Prolinoborus fasciculus (Pot et al. 1992)

scientific article published on 26 August 2020

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 subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

scientific article

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

Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation

scientific article

Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format

scientific article published on 21 July 2009

Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula

article

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

Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

scientific article

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

scientific article

Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation

scientific article

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

Updating benchtop sequencing performance comparison

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