List of works by Rainer Breitling

17beta-hydroxysteroid dehydrogenase type 7--an ancient 3-ketosteroid reductase of cholesterogenesis.

scientific article

A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior

scientific article

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments

scientific article published on 18 January 2008

A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments

scientific article

A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments

A lock-and-key model for protein-protein interactions

scientific article

A second gene for peroxisomal HMG-CoA reductase? A genomic reassessment

scientific article

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

scientific article published on 23 June 2008

A transatlantic perspective on 20 emerging issues in biological engineering.

scientific article published on 14 November 2017

A turning point for natural product discovery--ESF-EMBO research conference: synthetic biology of antibiotic production

scientific article published on 8 February 2012

A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat

scientific article

Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data

scientific article

Adaptation of cancer cells from different entities to the MDM2 inhibitor nutlin-3 results in the emergence of p53-mutated multi-drug-resistant cancer cells.

scientific article published on 15 December 2011

An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways

article

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals

scientific article published on 08 June 2018

Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series

scientific article

Analysis of Tiling Microarray Data by Learning Vector Quantization and Relevance Learning

Anti-cancer effects of artesunate in a panel of chemoresistant neuroblastoma cell lines

scientific article

Apex peptide elution chain selection: a new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples

scientific article published on 30 September 2010

Bacterial Microcompartments: Biomaterials for Synthetic Biology-Based Compartmentalization Strategies

scholarly article by Ashley Chessher et al published 26 May 2015 in ACS biomaterials science & engineering

Bayesian Approaches for Mass Spectrometry-Based Metabolomics

Bioengineering horizon scan 2020

scientific article published on 29 May 2020

Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle

scientific article published on 17 May 2016

Biological master games: using biologists' reasoning to guide algorithm development for integrated functional genomics

scientific article

Biological microarray interpretation: the rules of engagement

scientific article

Biologically valid linear factor models of gene expression

scientific article published on 16 June 2004

Biomodel Engineering – From Structure to Behavior

Butyrolactone signalling circuits for synthetic biology

scientific article published on 08 July 2015

C. elegans model identifies genetic modifiers of alpha-synuclein inclusion formation during aging

scientific article

Chemoresistance acquisition induces a global shift of expression of aniogenesis-associated genes and increased pro-angogenic activity in neuroblastoma cells

scientific article published on 29 September 2009

Closing the gap: identification of human 3-ketosteroid reductase, the last unknown enzyme of mammalian cholesterol biosynthesis

scientific journal article

CodonGenie: optimised ambiguous codon design tools

article by Neil Swainston et al published 10 July 2017 in PeerJ Computer Science

CodonGenie: optimised ambiguous codon design tools

scholarly article published 9 February 2017

CodonGenie: optimised ambiguous codon design tools

scholarly article published 9 February 2017

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

article

Computation: A New Open Access Journal of Computational Chemistry, Computational Biology and Computational Engineering

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters

article

Computational modelling of kinase signalling cascades.

scientific article published in January 2010

Computational tools for the synthetic design of biochemical pathways

scientific article published on 23 January 2012

Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply

scientific article

Current challenges in quantitative modeling of epidermal growth factor signaling

scientific article

Defining informative priors for ensemble modeling in systems biology

article

Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2) ⬇️

scientific article published on 8 December 2010

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

scientific article

Detecting sequence homology at the gene cluster level with MultiGeneBlast

scientific article published on 14 February 2013

Determination of cDNA, gene structure and chromosomal localization of the novel human 17beta-hydroxysteroid dehydrogenase type 7(1)

scientific journal article

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

scientific article

Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning

scholarly article

Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism

scientific article (publication date: 2012)

East meets West: on the true identity ofCheiracanthium rupestreandXysticus albomaculatus(Arachnida: Araneae: Eutichuridae, Thomisidae)

scholarly article by Rainer Breitling et al published 30 September 2016 in Arachnologische Mitteilungen

Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS.

scientific article

Embryonic expression of cholesterogenic genes is restricted to distinct domains and colocalizes with apoptotic regions in mice

scientific article published on July 2003

Erratum to: Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis

scholarly article published in Analytical and Bioanalytical Chemistry

Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis

scientific article published on 19 August 2013

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms

article

Exploring the metabolic state of microorganisms using metabolomics

scientific article

Expression quantitative trait loci are highly sensitive to cellular differentiation state

scientific article published on 16 October 2009

FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes

scientific article

Feature Selection and the Class Imbalance Problem in Predicting Protein Function from Sequence

Feature selection and the class imbalance problem in predicting protein function from sequence.

scientific article

FrankSum: new feature selection method for protein function prediction

scientific article published on August 2005

GeneRank: using search engine technology for the analysis of microarray experiments

scientific article

Generalizing genetical genomics: getting added value from environmental perturbation

scientific article published on 04 September 2008

Genetical genomics: spotlight on QTL hotspots

scientific article

Genome-based phylogenetic analysis of Streptomyces and its relatives

scientific article published on 3 December 2009

Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus ⬇️

scientific article published on 2 November 2010

Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans

scientific article

Graph-based iterative Group Analysis enhances microarray interpretation

scientific article

Greased hedgehogs: new links between hedgehog signaling and cholesterol metabolism

scientific article published on November 2007

Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei

scientific article (publication date: 2013)

Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries

scientific article published on 29 October 2019

Human 17beta-hydroxysteroid dehydrogenase type 5 is inhibited by dietary flavonoids

scientific article published in January 2002

Human neuroblastoma cells with acquired resistance to the p53 activator RITA retain functional p53 and sensitivity to other p53 activating agents.

scientific article

IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data

scientific article

Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets

scientific article published on 2 February 2015

Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap

scientific article

Inhibition of 17beta-hydroxysteroid dehydrogenases by phytoestrogens: comparison with other steroid metabolizing enzymes.

scientific article

Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships

scientific article published on 11 September 2019

Interspecies comparison of gene structure and computational analysis of gene regulation of 17beta-hydroxysteroid dehydrogenase type 1.

scientific article

Isopentenyl-diphosphate isomerases in human and mouse: evolutionary analysis of a mammalian gene duplication

scientific article published in September 2003

Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments

scientific article

Judging synthetic biology risks

scientific article published in Science

LC-MS metabolomics from study design to data-analysis - using a versatile pathogen as a test case

scientific article

LC-MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes

scientific article

Loss of compartmentalization causes misregulation of lysine biosynthesis in peroxisome-deficient yeast cells

scientific article

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli

scientific article published on 07 January 2019

Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans

article

Mapping determinants of gene expression plasticity by genetical genomics in C. elegans

scientific article

Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics

scientific article (publication date: 26 May 2012)

MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.

scientific article

MetaNetter: inference and visualization of high-resolution metabolomic networks.

scientific article published on 14 November 2007

Metabolic adaptations of Leishmania donovani in relation to differentiation, drug resistance, and drug pressure

scientific article

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

scientific article

Metabolomic Systems Biology of Protozoan Parasites

Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2)

article

Metabolomic characterization of the salt stress response in Streptomyces coelicolor ⬇️

scientific article

Metabolomic systems biology of trypanosomes

scientific article published on 17 February 2010

Metabolomics for secondary metabolite research

scientific article

Metabolomics methods for the synthetic biology of secondary metabolism

scientific article

Metabolomics to unveil and understand phenotypic diversity between pathogen populations

scientific article

Microarray challenges in ecology

scientific article published on 12 February 2007

Minimum Information about a Biosynthetic Gene cluster.

scientific article published on August 2015

Mobilising ion mobility mass spectrometry for metabolomics

article

Modeling challenges in the synthetic biology of secondary metabolism

scientific article published on 20 May 2013

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

scientific article

Natural Products: Tools and More Special Issue

Network theory to understand microarray studies of complex diseases

scientific article published on September 2006

Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms

scientific article

New surveyor tools for charting microbial metabolic maps.

scientific article published on February 2008

Origin of the paired domain

scientific article published on 01 December 2000

Orthogonal Regulatory Circuits for Escherichia coli Based on the γ-Butyrolactone System of Streptomyces coelicolor. ⬇️

scientific article published on 6 March 2018

Pathogenesis of peroxisomal deficiency disorders (Zellweger syndrome) may be mediated by misregulation of the GABAergic system via the diazepam binding inhibitor

scientific article

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis

scientific article

Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products

scientific article

Phantom spiders 2: More notes on dubious spider species from Europe

scientific article published in 2016

Phantom spiders: notes on dubious spider species from Europe

scientific article published in 2015

Phosphoenolpyruvate carboxylase identified as a key enzyme in erythrocytic Plasmodium falciparum carbon metabolism

scientific article (publication date: 2014)

Physiological adaptation of the bacterium Lactococcus lactis in response to the production of human CFTR.

scientific article

Precision mapping of the metabolome.

scientific article published on 24 October 2006

Predicting protein function by machine learning on amino acid sequences--a critical evaluation

scientific article

Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor

scientific article

Probabilistic assignment of formulas to mass peaks in metabolomics experiments

scientific article

Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose

scientific article

Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

scientific article

Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data

scientific article

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

article

Rational cell culture optimization enhances experimental reproducibility in cancer cells

scientific article published on 14 February 2018

Rational cell culture optimization enhances experimental reproducibility in cancer cells

article

Regulation of ubiquitin-binding proteins by monoubiquitination

scientific article

Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology

scientific article published on 13 January 2017

Robust signaling networks of the adipose secretome

scientific article published on 17 October 2008

SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals

scientific article

SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli

scientific article published on 18 March 2019

Selection of a highly invasive neuroblastoma cell population through long-term human cytomegalovirus infection

scientific article

Selenzyme: Enzyme selection tool for pathway design

Separating the wheat from the chaff: a prioritisation pipeline for the analysis of metabolomics datasets

scientific article published on 31 July 2011

Sequence polymorphisms cause many false cis eQTLs

scientific article

Simple data-reduction method for high-resolution LC-MS data in metabolomics

scientific article

Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation

scientific article published on 25 September 2012

Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks

scientific article

Steps towards the synthetic biology of polyketide biosynthesis

scientific article published on 07 January 2014

Stoffwechselwege vom Reißbrett: neue Ansätze der Naturstoffbiochemie

Structure-based phylogenetic analysis of short-chain alcohol dehydrogenases and reclassification of the 17beta-hydroxysteroid dehydrogenase family

scientific article

Synthetic Biology in Streptomyces Bacteria

scholarly article by Marnix H Medema et al published 2011 in Methods in Enzymology

Synthetic Biology of Antibiotic Production

article

Synthetic Biology of Natural Products

scientific article

Synthetic Biology of Natural Products

scholarly article published 28 March 2014

Synthetic biology advances for pharmaceutical production

scientific article

System-wide molecular evidence for phenotypic buffering in Arabidopsis

article

The Yeast Vacuolar Membrane Proteome

The dynamic architecture of the metabolic switch in Streptomyces coelicolor.

scientific article

The exact probability distribution of the rank product statistics for replicated experiments

scientific article

The future of industrial antibiotic production: from random mutagenesis to synthetic biology

scientific article published on July 2011

The latent process decomposition of cDNA microarray data sets

scientific article

The potassium-dependent transcriptome of Arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling

scientific article published on 3 September 2004

The potential of metabolomics for Leishmania research in the post-genomics era.

scientific article published on 29 January 2010

The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways

scientific article published on 12 July 2010

The silicon trypanosome.

scientific article published on 06 May 2010

The silicon trypanosome: a test case of iterative model extension in systems biology

scientific article published on January 2014

The “Three Cs” of Novel Antibiotic Discovery and Production through Synthetic Biology: Biosynthetic Gene Clusters, Heterologous Chassis, and Synthetic Microbial Consortia

article

Theridion zonulatum Thorell 1890, a senior synonym of Theridion zebrinusum Zhu 1998 ⬇️

Toward global metabolomics analysis with hydrophilic interaction liquid chromatography-mass spectrometry: improved metabolite identification by retention time prediction

scientific article

Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis

scientific article

Towards synthesis of monoterpenes and derivatives using synthetic biology

scientific article

Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins.

scientific article

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

scientific article

Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling

scientific article published on 10 July 2020

Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds

scientific article

What is systems biology?

scientific article published on 21 May 2010

antiSMASH

antiSMASH

antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers

scientific article published on 3 June 2013

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters

scientific article published on 6 May 2015

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification

scientific article published on 28 April 2017

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

scientific article published on 14 June 2011

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

scientific article published on 14 July 2017

designGG: an R-package and web tool for the optimal design of genetical genomics experiments

scientific article

msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies

scientific article

mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

scientific article

reGenotyper: Detecting mislabeled samples in genetic data

scientific article (publication date: 2017)

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