Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism
Mohammad Tauqeer Alam
Marnix H. Medema
Eriko Takano
Rainer Breitling
FEBS Letters, 2011-7
Eriko Takano
Takano Eriko
ORCID: 0000-0002-6791-3256
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Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
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Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei
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Design-based re-engineering of biosynthetic gene clusters: Plug-and-play in practice
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Metabolic adaptations of Leishmania donovani in relation to differentiation, drug resistance, and drug pressure
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Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis
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Modeling challenges in the synthetic biology of secondary metabolism
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Natural products: Tools and more special issue
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antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.
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Detecting sequence homology at the gene cluster level with multigeneblast
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The exact probability distribution of the rank product statistics for replicated experiments
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Mass appeal: Metabolite identification in mass spectrometry-focused untargeted metabolomics
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MzMatch-ISO: An R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data
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LC-MS metabolomics from study design to data-analysis-using a versatile pathogen as a test case
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MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models
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Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation
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Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS
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Metabolomics methods for the synthetic biology of secondary metabolism
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Separating the wheat from the chaff: A prioritisation pipeline for the analysis of metabolomics datasets
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msCompare: A framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies
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Human neuroblastoma cells with acquired resistance to the p53 activator RITA retain functional p53 and sensitivity to other p53 activating agents
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A turning point for natural product discovery--ESF-EMBO research conference: synthetic biology of antibiotic production.
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Computational tools for the synthetic design of biochemical pathways
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Dynamic modelling under uncertainty: The case of trypanosoma brucei energy metabolism
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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
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Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2)
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Toward global metabolomics analysis with hydrophilic interaction liquid chromatography-mass spectrometry: Improved metabolite identification by retention time prediction
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Exploring the metabolic state of microorganisms using metabolomics
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Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor
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Bayesian Approaches for Mass Spectrometry-Based Metabolomics
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Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism
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AntiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
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Physiological adaptation of the bacterium lactococcus lactis in response to the production of human CFTR
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Synthetic biology in streptomyces bacteria
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PeakML/mzMatch: A file format, Java library, R library, and tool-chain for mass spectrometry data analysis
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Erratum: Towards an unbiased metabolic profiling of protozoan parasites: Optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis (Analytical and Bioanalytical Chemistry DOI: 10.1007/s00216-010-4139-0)
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Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus
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Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2)
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Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms
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What is systems biology?
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Apex peptide elution chain selection: A new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples
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Towards an unbiased metabolic profiling of protozoan parasites: Optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis
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The sequence of a 1.8-Mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways
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DiffCoEx: A simple and sensitive method to find differentially coexpressed gene modules
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Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans
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The silicon trypanosome
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The potential of metabolomics for Leishmania research in the post-genomics era
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Metabolomic systems biology of trypanosomes
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A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior
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Biomodel engineering - From structure to behavior
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Metabolomic characterization of the salt stress response in streptomyces coelicolor
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Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
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Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply
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Genome-based phylogenetic analysis of Streptomyces and its relatives
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Anti-cancer effects of artesunate in a panel of chemoresistant neuroblastoma cell lines
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The dynamic architecture of the metabolic switch in Streptomyces coelicolor
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Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms
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Expression quantitative trait loci are highly sensitive to cellular differentiation state
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Chemoresistance acquisition induces a global shift of expression of aniogenesis-associated genes and increased pro-angogenic activity in neuroblastoma cells
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DesignGG: An R-package and web tool for the optimal design of genetical genomics experiments
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An introduction to BioModel engineering, illustrated for signal transduction pathways
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System-wide molecular evidence for phenotypic buffering in Arabidopsis
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The yeast vacuolar membrane proteome
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Probabilistic assignment of formulas to mass peaks in metabolomics experiments
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Robust signaling networks of the adipose secretome
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Simple data-reduction method for high-resolution LC - MS data in metabolomics
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Prosecutor: Parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources
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Generalizing genetical genomics: getting added value from environmental perturbation
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Genetical genomics: Spotlight on QTL hotspots
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A structured approach for the engineering of biochemical network models, illustrated for signalling pathways
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C. elegans model identifies genetic modifiers of α-synuclein inclusion formation during aging
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New surveyor tools for charting microbial metabolic maps
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A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
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MetaNetter: Inference and visualization of high-resolution metabolomic networks
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Greased hedgehogs: New links between hedgehog signaling and cholesterol metabolism
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Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series
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Sequence polymorphisms cause many false cis eQTLs
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Microarray challenges in ecology
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FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes
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A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat
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Predicting protein function by machine learning on amino acid sequences - A critical evaluation
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Mapping determinants of gene expression plasticity by genetical genomics in C. elegans.
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Precision mapping of the metabolome
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Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data
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Network theory to understand microarray studies of complex diseases
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A lock-and-key model for protein-protein interactions
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Biological microarray interpretation: The rules of engagement
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Interspecies comparison of gene structure and computational analysis of gene regulation of 17beta-hydroxysteroid dehydrogenase type 1
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Regulation of ubiquitin-binding proteins by monoubiquitination
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Current challenges in quantitative modeling of epidermal growth factor signaling
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Feature selection and the class imbalance problem in predicting protein function from sequence
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Biological master games: Using biologists' reasoning to guide algorithm development for integrated functional genomics
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Rank-based methods as a non-parametric alternative of the t-statistic for the analysis of biological microarray data
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GeneRank: Using search engine technology for the analysis of microarray experiments
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FrankSum: New feature selection method for protein function prediction
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Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds
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Inhibition of 17beta-hydroxysteroid dehydrogenases by phytoestrogens: Comparison with other steroid metabolizing enzymes
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The potassium-dependent transcriptome of arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling
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Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments
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Pathogenesis of peroxisomal deficiency disorders (Zellweger syndrome) may be mediated by misregulation of the GABAergic system via the diazepam binding inhibitor
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Closing the gap: Identification of human 3-ketosteroid reductase, the last unknown enzyme of mammalian cholesterol biosynthesis
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Isopentenyl-diphosphate isomerases in human and mouse: Evolutionary analysis of a mammalian gene duplication
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Embryonic expression of cholesterogenic genes is restricted to distinct domains and colocalizes with apoptotic regions in mice
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A second gene for peroxisomal HMG-CoA reductase? A genomic reassessment
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Loss of compartmentalization causes misregulation of lysine biosynthesis in peroxisome-deficient yeast cells
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17β-hydroxysteroid dehydrogenase type 7 - An ancient 3-ketosteroid reductase of cholesterogenesis
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Evolution of 17β-HSD type 4, a multifunctional protein of β-oxidation
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Origin of the paired domain
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Determination of cDNA, gene structure and chromosomal localization of the novel human 17β-hydroxysteroid dehydrogenase type 7
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Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.
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Metabolomics for secondary metabolite research.
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Computational modelling of kinase signalling cascades.
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Feature selection and the class imbalance problem in predicting protein function from sequence.
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Structure-based phylogenetic analysis of short-chain alcohol dehydrogenases and reclassification of the 17beta-hydroxysteroid dehydrogenase family.
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antiSMASH
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antiSMASH
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Synthetic Biology of Antibiotic Production
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Transactions on Computational Systems Biology XII
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Computation: A New Open Access Journal of Computational Chemistry, Computational Biology and Computational Engineering
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The future of industrial antibiotic production: From random mutagenesis to synthetic biology
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Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning
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Analysis of Tiling Microarray Data by Learning Vector Quantization and Relevance Learning
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Bacterial Microcompartments: Biomaterials for Synthetic Biology-Based Compartmentalization Strategies
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Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans
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Towards synthesis of monoterpenes and derivatives using synthetic biology
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Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology
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Rational cell culture optimization enhances experimental reproducibility in cancer cells
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Selenzyme: Enzyme selection tool for pathway design
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Butyrolactone signalling circuits for synthetic biology
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Synthetic biology of natural products
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Advanced LC-MS applications for identification and quantification of the metabolome
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Re Genotyper: Detecting mislabeled samples in genetic data
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East meets west: On the true identity of cheiracanthium rupestre and xysticus albomaculatus (Arachnida: Araneae: Eutichuridae, Thomisidae) | Anmerkung zur wahren identität von cheiracanthium rupestre und xysticus albomaculatus (Arachnida: Araneae: Eutichuridae, Thomisidae)
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Phantom spiders 2: More notes on dubious spider species from Europe | Phantomspinnen 2: Weitere bemerkungen zu zweifelhaften spinnenarten aus Europa
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CodonGenie: Optimised ambiguous codon design tools
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Public DNA barcoding data resolve the status of the genus Arboricaria (araneae: Gnaphosidae) | Öffentliche DNA-barcode-daten klären den Status der gattung arboricaria
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Bioinformatics for the synthetic biology of natural products: Integrating across the Design-Build-Test cycle
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biochem4j: Integrated and extensible biochemical knowledge through graph databases
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SYNBIOCHEM - A SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals
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Phantom spiders: Notes on dubious spider species from Europe | Zusammenfassung. Phantomspinnen: Bemerkungen zu zweifelhaften spinnenarten aus Europa
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AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification
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LC–MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes
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A transatlantic perspective on 20 emerging issues in biological engineering
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CodonGenie: optimised ambiguous codon design tools
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CodonGenie: optimised ambiguous codon design tools
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Rational cell culture optimization enhances experimental reproducibility in cancer cells
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Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins
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Orthogonal Regulatory Circuits for Escherichia coli Based on the γ-Butyrolactone System of Streptomyces coelicolor
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Mobilising ion mobility mass spectrometry for metabolomics
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Defining informative priors for ensemble modeling in systems biology
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The “Three Cs” of Novel Antibiotic Discovery and Production through Synthetic Biology: Biosynthetic Gene Clusters, Heterologous Chassis, and Synthetic Microbial Consortia
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Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters
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SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli
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Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships
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Bioengineering horizon scan 2020
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Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling
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Host Systems for the Production of Recombinant Spider Silk
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Towards engineering and production of artificial spider silk using tools of synthetic biology
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Investigation of the effects of actinorhodin biosynthetic gene cluster expression and a rpoB point mutation on the metabolome of Streptomyces coelicolor M1146
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A completely resolved phylogenetic tree of British spiders
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Blood, Sweat and Tears: Extraterrestrial Regolith Biocomposites with in Vivo Binders
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Blood, Sweat and Tears: Extraterrestrial Regolith Biocomposites with in Vivo Binders
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Blood, sweat, and tears: extraterrestrial regolith biocomposites with in vivo binders
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