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List of works by Björn Usadel

A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis.

scientific article

A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley.

scientific article

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

scientific article

A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants

scientific article published on 29 October 2020

A roadmap for a middleware as a federation service for integrative data retrieval of agricultural data

scientific article published in September 2024

A subtilisin-like serine protease essential for mucilage release from Arabidopsis seed coats

scientific article published on 7 February 2008

A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome ⬇️

scientific article

Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species.

scientific article

Algorithm-driven artifacts in median polish summarization of microarray data

scientific article

An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato

scientific article published on 24 October 2009

An orange ripening mutant links plastid NAD(P)H dehydrogenase complex activity to central and specialized metabolism during tomato fruit maturation

scientific article published on 22 June 2010

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

scientific article

Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry.

scientific article

Antisense inhibition of the 2-oxoglutarate dehydrogenase complex in tomato demonstrates its importance for plant respiration and during leaf senescence and fruit maturation

scientific article published on 29 June 2012

Antisense inhibition of the iron-sulphur subunit of succinate dehydrogenase enhances photosynthesis and growth in tomato via an organic acid-mediated effect on stomatal aperture

article

Arabidopsis and primary photosynthetic metabolism - more than the icing on the cake

scientific article published on March 2010

Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm

scientific article

Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools

scientific article

Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives.

scientific article

CSB.DB: a comprehensive systems-biology database

scientific article

Cell wall modification in tobacco by differential targeting of recombinant endoglucanase from Trichoderma reesei.

scientific article

Chloroplast DnaJ-like proteins 3 and 4 (CDJ3/4) from Chlamydomonas reinhardtii contain redox-active Fe-S clusters and interact with stromal HSP70B.

scientific article published on 29 March 2010

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

scientific article published on 27 August 2009

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

scientific article published on 26 June 2013

Computational aspects underlying genome to phenome analysis in plants

article

Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf

scientific article

Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue.

scientific article

Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping

scientific article published on 01 March 2018

Crystal structure and functional characterization of a glucosamine-6-phosphate N-acetyltransferase from Arabidopsis thaliana

scientific article

DataPLAN: A Web-Based Data Management Plan Generator for the Plant Sciences

scientific article published on 24 October 2023

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.

scientific article published on 12 October 2017

De novo sequencing and analysis of the lily pollen transcriptome: an open access data source for an orphan plant species

scientific article

De-regulation of abscisic acid contents causes abnormal endosperm development in the barley mutant seg8.

scientific article published on 5 October 2010

Demethylation of oligogalacturonides by FaPE1 in the fruits of the wild strawberry Fragaria vesca triggers metabolic and transcriptional changes associated with defence and development of the fruit

article

Demethylesterification of cell wall pectins in Arabidopsis plays a role in seed germination.

scientific article published on 5 November 2012

Description and applications of a rapid and sensitive non-radioactive microplate-based assay for maximum and initial activity of D-ribulose-1,5-bisphosphate carboxylase/oxygenase

scientific article published on 01 September 2007

Detecting Inconsistencies in Large Biological Networks with Answer Set Programming

Diurnal changes of polysome loading track sucrose content in the rosette of wild-type arabidopsis and the starchless pgm mutant

scientific article

Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes

scientific article published on 22 March 2017

Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

scientific article published on 14 March 2020

Ethanol inducible expression of a mesophilic cellulase avoids adverse effects on plant development

scientific article published on 16 April 2013

Evolution of a complex locus for terpene biosynthesis in solanum

scientific article published on 11 June 2013

Exploiting the natural variation in tomato to define pathway structure and metabolic regulation of fruit polyphenolics in the lycopersicum complex

scientific article published on 16 April 2020

Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses

scientific article

Extensive Natural Variation in Arabidopsis Seed Mucilage Structure

scientific article published on 07 June 2016

Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris.

scientific article

From plant genomes to phenotypes

article

GMD@CSB.DB: the Golm Metabolome Database

scientific article

GabiPD - The GABI Primary Database integrates plant proteomic data with gene-centric information

scientific article

Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine

scientific article published on 5 August 2009

Genetic and molecular characterization of multicomponent resistance of Pseudomonas against allicin

scientific article published on 31 March 2020

Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping

scientific article published on 4 October 2016

Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties

scientific article published on 24 July 2020

Genome-Wide Analysis of Yield in Europe: Allelic Effects Vary with Drought and Heat Scenarios.

scientific article

Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus

article

Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae)

scientific article published on 13 January 2021

Genotype-phenotype modeling considering intermediate level of biological variation: a case study involving sensory traits, metabolites and QTLs in ripe tomatoes

scientific article

Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes

scientific article

GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology

scientific article

Growing Near Net Shape Components from Renewable Materials

HRE-type genes are regulated by growth-related changes in internal oxygen concentrations during the normal development of potato (Solanum tuberosum) tubers

scientific article published on 27 September 2011

High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads

scientific article

Highly Branched Xylan Made by IRREGULAR XYLEM14 and MUCILAGE-RELATED21 Links Mucilage to Arabidopsis Seeds

scientific article

How to make a tumour: cell type specific dissection of Ustilago maydis-induced tumour development in maize leaves.

scientific article published on 4 January 2018

Identification and characterization of a UDP-D-glucuronate 4-epimerase in Arabidopsis.

scientific article published in July 2004

Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage

scientific article published on 18 September 2018

Identification of RNA-binding Proteins in Macrophages by Interactome Capture

scientific article published on 08 June 2016

Identification of enzyme activity quantitative trait loci in a Solanum lycopersicum x Solanum pennellii introgression line population

scientific article published on 2 September 2011

Improving the utilization of lignocellulosic biomass by polysaccharide modification

article published in 2016

Insights into cell wall structure of Sida hermaphrodita and its influence on recalcitrance.

scientific article published on 20 March 2017

Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior

scientific article published on 27 October 2006

Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes

scientific article published on 17 August 2006

Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance

scientific article published on 23 July 2019

LASSO modeling of the Arabidopsis thaliana seed/seedling transcriptome: a model case for detection of novel mucilage and pectin metabolism genes

scientific article published in October 2012

LOGAN: A framework for LOssless Graph-based ANalysis of high throughput sequence data

Large-scale phenotyping of transgenic tobacco plants (Nicotiana tabacum) to identify essential leaf functions

scientific article

MUCILAGE-RELATED10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage.

scientific article

Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process

scientific article

Measures for interoperability of phenotypic data: minimum information requirements and formatting

scientific article

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

scientific article

Metabolic Adaptation, a Specialized Leaf Organ Structure and Vascular Responses to Diurnal N2 Fixation by Nostoc azollae Sustain the Astonishing Productivity of Azolla Ferns without Nitrogen Fertilizer

scientific article published on 31 March 2017

Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii

scientific article published on May 2008

Modeling Protein Destiny in Developing Fruit

scientific article published on 23 April 2019

Monitoring Polysaccharide Dynamics in the Plant Cell Wall

article

Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range

scientific article

On the current status of Phakopsora pachyrhizi genome sequencing

scientific article

Overexpression of a pectin methylesterase inhibitor in Arabidopsis thaliana leads to altered growth morphology of the stem and defective organ separation

scientific article published on 20 September 2013

PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research

scientific article published on 11 October 2023

PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

scientific article

PlaNet: combined sequence and expression comparisons across plant networks derived from seven species

scientific article published on 25 March 2011

Plant Pathway Databases

article

Plant genome and transcriptome annotations: from misconceptions to simple solutions

scientific article published on 05 January 2017

Plant genome sequencing - applications for crop improvement

scientific article published on 21 September 2013

Pod indehiscence in common bean is associated to the fine regulation of PvMYB26

scientific article published on 28 November 2020

Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer

scientific article published on 24 January 2019

Quantitation in mass-spectrometry-based proteomics

scientific article published on January 2010

Quantitative RT-PCR Platform to Measure Transcript Levels of C and N Metabolism-Related Genes in Durum Wheat: Transcript Profiles in Elevated [CO2] and High Temperature at Different Levels of N Supply

scientific article

RHM2 is involved in mucilage pectin synthesis and is required for the development of the seed coat in Arabidopsis.

scientific article published on 11 December 2003

RNA interference of LIN5 in tomato confirms its role in controlling Brix content, uncovers the influence of sugars on the levels of fruit hormones, and demonstrates the importance of sucrose cleavage for normal fruit development and fertility.

scientific article published on 13 May 2009

RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H.

scientific article published on 6 January 2018

Rapid structural phenotyping of plant cell wall mutants by enzymatic oligosaccharide fingerprinting

scientific article

Reconstructing The Gigabase Plant Genome Of Solanum pennellii Using Nanopore Sequencing

article

Reduced expression of succinyl-coenzyme A ligase can be compensated for by up-regulation of the gamma-aminobutyrate shunt in illuminated tomato leaves

scientific article published on 20 September 2007

Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling

scientific article published on 12 May 2009

Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis.

scientific article published on 28 June 2008

Reverse engineering: a key component of systems biology to unravel global abiotic stress cross-talk

scientific article

Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis.

scientific article published on 13 October 2009

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

scientific article

Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis

scientific article

SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data

scientific article

Smut infection of perennial hosts: the genome and the transcriptome of the Brassicaceae smut fungus Thecaphora thlaspeos reveal functionally conserved and novel effectors

scientific article published on 17 February 2019

Starch as a major integrator in the regulation of plant growth

scholarly article

Starting to gel: how Arabidopsis seed coat epidermal cells produce specialized secondary cell walls

scientific article

Streptomyces thermoautotrophicus does not fix nitrogen

scientific article

Structure and putative function of NFX1-like proteins in plants

scientific article published on May 2010

Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis

scientific article

Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions

scientific article published on 27 July 2011

TRM4 is essential for cellulose deposition in Arabidopsis seed mucilage by maintaining cortical microtubule organization and interacting with CESA3

scientific article

Temporal kinetics of the transcriptional response to carbon depletion and sucrose readdition in Arabidopsis seedlings.

scientific article published on 19 September 2015

Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings

article

The FRIABLE1 gene product affects cell adhesion in Arabidopsis

scientific article

The Metabolic Signature of Biomass Formation in Barley.

scientific article

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability

scientific article (publication date: September 2013)

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

scientific article

The art of growing plants for experimental purposes: a practical guide for the plant biologist

article

The genetic architecture of photosynthesis and plant growth-related traits in tomato

scientific article published on 18 October 2017

The genome of the stress-tolerant wild tomato species Solanum pennellii.

scientific article published on 27 July 2014

The giant diploid faba genome unlocks variation in a global protein crop

scientific article published in 2023

The inositol oxygenase gene family of Arabidopsis is involved in the biosynthesis of nucleotide sugar precursors for cell-wall matrix polysaccharides ⬇️

scientific article published on 20 January 2005

The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis.

scientific article

The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula

scientific article published on 12 January 2007

The plant growth promoting substance, lumichrome, mimics starch, and ethylene-associated symbiotic responses in lotus and tomato roots

scientific article

The plant transcriptome-from integrating observations to models

scientific article published on 11 March 2013

The role of COBRA-LIKE 2 function, as part of the complex network of interacting pathways regulating Arabidopsis seed mucilage polysaccharide matrix organization

scientific article published on 15 February 2018

Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function

scientific article

Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species

scientific article published on 22 October 2021

Towards positional isolation of three quantitative trait loci conferring resistance to powdery mildew in two Spanish barley landraces

scientific article

Towards recommendations for metadata and data handling in plant phenotyping.

scientific article published on 4 June 2015

Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis

article

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum).

scientific article

Trimmomatic: a flexible trimmer for Illumina sequence data

2014 scientific article, published in Bioinformatics

VisualisationVISUALISATION of Transcriptomic TRANSCRIPTOMICS s Data in Metabolic Pathways

Visualizing large, high-throughput datasets based on the cognitive representation of biological pathways

scholarly article published 10 February 2011

Xeml Lab: a tool that supports the design of experiments at a graphical interface and generates computer-readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy

scientific article published on 19 February 2009

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