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Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block

Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J. W. Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H. Medema Ulrike Müller Roel Bovenberg Dick B. Janssen Eriko Takano

ACS Synthetic Biology, 2015-7

https://doi.org/10.1021/sb500368w

Mark Loznik

Loznik Mark

ORCID: 0000-0001-9245-703X

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Controlling Optical and Catalytic Activity of Genetically Engineered Proteins by Ultrasound 10.1002/anie.202010324

Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block 10.1021/sb500368w

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DNA hybridization as a general method to enhance the cellular uptake of nanostructures 10.1039/d0nr02405h

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Electrostatically PEGylated DNA enables salt-free hybridization in water 10.1039/c9sc02598g

Mechanochemical bond scission for the activation of drugs. 10.1038/s41557-020-00624-8

Carrier-free micellar CpG interacting with cell membrane for enhanced immunological treatment of HIV-1 10.1016/j.biomaterials.2021.121081

Eriko Takano

Takano Eriko

ORCID: 0000-0002-6791-3256

Synthetic biology advances for pharmaceutical production 10.1016/j.copbio.2015.02.004

Butyrolactone signalling circuits for synthetic biology 10.1016/j.cbpa.2015.06.024

Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block 10.1021/sb500368w

Judging synthetic biology risks 10.1126/science.aaa5253

Ribosylhopane, a novel bacterial hopanoid, as precursor of C35 bacteriohopanepolyols in Streptomyces coelicolor A3(2) 10.1002/cbic.201402261

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters 10.1016/j.cell.2014.06.034

Synthetic Biology of Natural Products 10.1002/9781118794623.ch19

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A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis 10.1371/journal.pcbi.1004016

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products 10.1371/journal.pcbi.1003822

Design-based re-engineering of biosynthetic gene clusters: Plug-and-play in practice 10.1016/j.copbio.2013.03.006

Modeling challenges in the synthetic biology of secondary metabolism 10.1021/sb4000228

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antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers. 10.1093/nar/gkt449

Detecting sequence homology at the gene cluster level with multigeneblast 10.1093/molbev/mst025

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Characterisation of a natural variant of the -butyrolactone signalling receptor 10.1186/1756-0500-5-379

Metabolomics methods for the synthetic biology of secondary metabolism 10.1016/j.febslet.2012.02.008

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A turning point for natural product discovery--ESF-EMBO research conference: synthetic biology of antibiotic production. 10.1111/j.1365-2958.2012.07984.x

Computational tools for the synthetic design of biochemical pathways 10.1038/nrmicro2717

Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2) 10.1002/pmic.201100254

Exploring the metabolic state of microorganisms using metabolomics 10.4155/bio.11.248

Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor 10.1186/1756-0500-4-325

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism 10.1016/j.febslet.2011.06.014

Convergent transcription in the butyrolactone regulon in streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis 10.1371/journal.pone.0021974

AntiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences 10.1093/nar/gkr466

Synthetic biology in streptomyces bacteria 10.1016/B978-0-12-385075-100021-4

Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus 10.1111/j.1751-7915.2010.00226.x

Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2) 10.1111/j.1751-7915.2010.00232.x

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The sequence of a 1.8-Mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways 10.1093/gbe/evq013

Genome-wide inference of regulatory networks in Streptomyces coelicolor 10.1186/1471-2164-11-578

Deletion of a regulatory gene within the cpk gene cluster reveals novel antibacterial activity in Streptomyces coelicolor A3(2) 10.1099/mic.0.038281-0

Metabolomic characterization of the salt stress response in streptomyces coelicolor 10.1128/AEM.01992-09

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor 10.1186/1471-2164-11-202

Genome-based phylogenetic analysis of Streptomyces and its relatives 10.1016/j.ympev.2009.11.019

Noncoding RNA of glutamine synthetase I modulates antibiotic production in Streptomyces coelicolor A3(2) 10.1128/JB.01374-09

The dynamic architecture of the metabolic switch in Streptomyces coelicolor 10.1186/1471-2164-11-10

Analysis of Two Additional Signaling Molecules in Streptomyces coelicolor and the Development of a Butyrolactone-Specific Reporter System 10.1016/j.chembiol.2009.08.010

Chapter 6 Regulation of Antibiotic Production by Bacterial Hormones 10.1016/S0076-6879(09)04806-X

A bistable gene switch for antibiotic biosynthesis: The butyrolactone regulon in Streptomyces coelicolor 10.1371/journal.pone.0002724

The border sequence of the balhimycin biosynthesis gene cluster from Amycolatopsis balhimycina contains bbr, encoding a StrR-like pathway-specific regulator 10.1159/000103599

ScbA from Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize γ-butyrolactones 10.1099/mic.0.2006/004432-0

A cryptic type I polyketide synthase (cpk) gene cluster in Streptomyces coelicolor A3(2) 10.1007/s00203-006-0176-7

Identification of genes involved in siderophore transport in Streptomyces coelicolor A3(2) 10.1111/j.1574-6968.2006.00362.x

γ-Butyrolactones: Streptomyces signalling molecules regulating antibiotic production and differentiation 10.1016/j.mib.2006.04.003

A bacterial hormone (the SCB1) directly controls the expression of a pathway-specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor 10.1111/j.1365-2958.2005.04543.x

A rare leucine codon in adpA is implicated in the morphological defect of bldA mutants of Streptomyces coelicolor 10.1046/j.1365-2958.2003.03728.x

A complex role for the γ-butyrolactone SCB1 in regulating antibiotic production in Streptomyces coelicolor A3(2) 10.1046/j.1365-2958.2001.02562.x

A single amino acid substitution in region 1.2 of the principal σ factor of Streptomyces coelicolor A3(2) results in pleiotropic loss of antibiotic production 10.1046/j.1365-2958.2000.02022.x

Purification and structural determination of SCB1, a γ-butyrolactone that elicits antibiotic production in Streptomyces coelicolor A3(2) 10.1074/jbc.275.15.11010

redD and actII-ORF4, pathway-specific regulatory genes for antibiotic production in Streptomyces coelicolor A3(2), are transcribed in vitro by an RNA polymerase holoenzyme containing ?^hrdD 10.1128/jb.178.11.3402-3405.1996

Construction of thiostrepton-inducible, high-copy-number expression vectors for use in Streptomyces spp. 10.1016/0378-1119(95)00545-2

Stationary?phase production of the antibiotic actinorhodin in Streptomyces coelicolor A3(2) is transcriptionally regulated 10.1111/j.1365-2958.1993.tb01174.x

Transcriptional regulation of the redD transcriptional activator gene accounts for growth?phase?dependent production of the antibiotic undecylprodigiosin in Streptomyces coelicolor A3(2) 10.1111/j.1365-2958.1992.tb01459.x

Purification and properties of a prokaryote type glutamine synthetase from the bialaphos producer Streptomyces hygroscopicus SF1293 10.1016/0922-338X(90)90032-R

The bialaphos resistance gene (bar) plays a role in both self-defense and bialaphos biosynthesis in streptomyces hygroscopicus 10.7164/antibiotics.41.1838

Replacement of streptomyces hygroscopicus genomic segments with in vitro altered DNA sequences 10.7164/antibiotics.41.226

The bialaphos biosynthetic genes of streptomyces hygroscopicus: Cloning and analysis of the genes involved in the alanylation step 10.7164/antibiotics.41.538

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Enzymatic Menthol Production: One-Pot Approach Using Engineered Escherichia coli 10.1021/acssynbio.5b00092

AntiSMASH 3.0-A comprehensive resource for the genome mining of biosynthetic gene clusters 10.1093/nar/gkv437

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Selenzyme: Enzyme selection tool for pathway design 10.1101/188979

Orthogonal Regulatory Circuits for Escherichia coli Based on the γ-Butyrolactone System of Streptomyces coelicolor 10.1021/acssynbio.7b00425

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SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli 10.1021/acssynbio.8b00399

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Non-covalent protein-based adhesives for transparent substrates—bovine serum albumin vs. recombinant spider silk 10.1016/j.mtbio.2020.100068

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Host Systems for the Production of Recombinant Spider Silk 10.1016/j.tibtech.2020.09.007

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Blood, Sweat and Tears: Extraterrestrial Regolith Biocomposites with in Vivo Binders 10.26434/chemrxiv.14769369

Blood, sweat, and tears: extraterrestrial regolith biocomposites with in vivo binders 10.1016/j.mtbio.2021.100136

Roy Goodacre

Goodacre Roy

ORCID: 0000-0003-2230-645X

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The Metabolomics Standards Initiative [3] 10.1038/nbt0807-846b

The metabolomics standards initiative (MSI) 10.1007/s11306-007-0070-6

Quantitative detection of metabolites using matrix-assisted laser desorption/ionization mass spectrometry with 9-aminoacridine as the matrix 10.1002/rcm.3063

Quantification of casein phosphorylation with conformational interpretation using Raman spectroscopy 10.1039/b702944f

Proteome and metabolome analyses for monitoring food quality and authenticity 10.3920/978-90-8686-606-9

Proposed minimum reporting standards for data analysis in metabolomics 10.1007/s11306-007-0081-3

Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI) 10.1007/s11306-007-0082-2

Metabolic footprinting as a tool for discriminating between brewing yeasts 10.1002/yea.1499

Metabolic fingerprinting as a diagnostic tool 10.2217/14622416.8.9.1243

Laser desorption/ionization mass spectrometry on porous silicon for metabolome analyses: Influence of surface oxidation 10.1002/rcm.3078

From phenotype to genotype: Whole tissue profiling for plant breeding 10.1007/s11306-007-0062-6

Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis 10.1111/j.1365-313X.2007.03307.x

Using metabolic fingerprinting of plants for evaluating nitrogen deposition impacts on the landscape level 10.1111/j.1365-2486.2006.01190.x

ToF-SIMS studies of Bacillus using multivariate analysis with possible identification and taxonomic applications 10.1016/j.apsusc.2006.02.237

The rapid differentiation of Streptomyces isolates using Fourier transform infrared spectroscopy 10.1016/j.vibspec.2005.09.006

Surface-enhanced Raman scattering for the rapid discrimination of bacteria 10.1039/b506413a

Rapid discrimination of the causal agents of urinary tract infection using ToF-SIMS with chemometric cluster analysis 10.1016/j.apsusc.2006.02.153

Rapid characterization of microbial biodegradation pathways by FT-IR spectroscopy 10.1016/j.mimet.2006.04.009

Rapid analysis of microbiological systems using SERS 10.1007/11663898_21

Quantitative detection and identification methods for microbial spoilage 10.1533/9781845691417.1.3

PYCHEM: A multivariate analysis package for python 10.1093/bioinformatics/btl416

Metabonomic evaluation of idiosyncrasy-like liver injury in rats cotreated with ranitidine and lipopolysaccharide 10.1016/j.taap.2005.06.021

Metabolomics: Current technologies and future trends 10.1002/pmic.200600106

Metabolomic approaches reveal that phosphatidic and phosphatidyl glycerol phospholipids are major discriminatory non-polar metabolites in responses by Brachypodium distachyon to challenge by Magnaporthe grisea 10.1111/j.1365-313X.2006.02692.x

Metabolic fingerprints of Mycobacterium bovis cluster with molecular type: Implications for genotype-phenotype links 10.1099/mic.0.28986-0

Metabolic fingerprinting in disease diagnosis: Biomedical applications of infrared and Raman spectroscopy 10.1039/b602376m

Matrix-suppressed laser desorption/ionisation mass spectrometry and its suitability for metabolome analyses 10.1002/rcm.2434

Direct infusion electrospray ionization mass spectra of crude cell extracts for microbial characterizations: Influence of solvent conditions on the detection of proteins 10.1002/rcm.2263

An improved fluorescemt amplified fragment length polymorphism method for typing Mycobacterium tuberculosis [2] 10.1128/JCM.44.1.288-289.2006

Understanding the behaviour of pathogenic cells: Proteome and metabolome analyses 10.1533/9781845690229.1.3

The use of chemical profiling for monitoring metabolic changes in artificial soil slurries caused by horizontal gene transfer 10.1007/s11306-005-0011-1

Rapid monitoring of antibiotics using Raman and surface enhanced Raman spectroscopy 10.1039/b502540k

Rapid identification of closely related muscle foods by vibrational spectroscopy and machine learning 10.1039/b511484e

Monitoring the mode of action of antibiotics using raman spectroscopy: Investigating subinhibitory effects of amikacin on Pseudomonas aeruginosa 10.1021/ac048147m

Metabolomics shows the way new discoveries 10.1186/gb-2005-6-11-354

Metabolomics - The way forward 10.1007/s11306-005-1111-7

Metabolome analyses: Strategies for systems biology 10.1007/0-387-25240-1

Metabolic fingerprinting for bio-indication of nitrogen responses in Calluna vulgaris heath communities 10.1007/s11306-005-0004-0

Making sense of the metabolome using evolutionary computation: Seeing the wood with the trees 10.1093/jxb/eri043

Introduction: Metabolome analyses for systems biology 10.1007/0-387-25240-1_1

Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics 10.1105/tpc.105.031542

High-throughput microbial characterizations using electrospray ionization mass spectrometry and its role in functional genomics 10.1002/0471748641.ch11

Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data 10.1093/bioinformatics/bti102

Discrimination and identification of microorganisms by pyrolysis mass spectrometry: From burning ambitions to cooling embers - A historical perspective 10.1002/0471748641.ch15

A metabolome pipeline: From concept to data to knowledge 10.1007/s11306-005-1106-4

A laser desorption ionisation mass spectrometry approach for high throughput metabolomics 10.1007/s11306-005-0007-x

Whole-organism Fingerprinting of the Genus Carnobacterium using Fourier Transform Infrared Spectroscopy (FT-IR) 10.1078/072320204322881808

Ultra-violet resonance Raman spectroscopy for the rapid discrimination of urinary tract infection bacteria 10.1016/S0378-1097(04)00040-0

The rapid identification of Acinetobacter species using Fourier transform infrared spectroscopy 10.1046/j.1365-2672.2003.02154.x

Surface-enhanced Raman spectroscopy for bacterial discrimination utilizing a scanning electron microscope with a Raman spectroscopy interface 10.1021/ac049663f

Selective detection of proteins in mixtures using electrospray ionization mass spectrometry: Influence of instrumental settings and implications for proteomics 10.1021/ac049684+

Rapid and quantitative detection of the microbial spoilage of beef by Fourier transform infrared spectroscopy and machine learning 10.1016/j.aca.2004.03.060

Metabolomics by numbers: Acquiring and understanding global metabolite data 10.1016/j.tibtech.2004.03.007

Metabolic profiling: Pathways in discovery 10.1016/S1359-6446(04)03027-2

Enhancing Raman spectroscopy for the rapid characterisation of microorganisms 10.1017/S1431927604883946

Discrimination of Bacteria Using Surface-Enhanced Raman Spectroscopy 10.1021/ac034689c

Differentiation of Micromonospora isolates from a coastal sediment in Wales on the basis of fourier transform infrared spectroscopy, 16S rRNA sequence analysis, and the amplified fragment length polymorphism technique 10.1128/AEM.70.11.6619-6627.2004

Comparison of diffuse-reflectance absorbance and attenuated total reflectance FT-IR for the discrimination of bacteria 10.1039/b408169b

Characterization of Microorganisms Using UV Resonance Raman Spectroscopy and Chemometrics 10.1021/ac035110d

Applying metabolic fingerprinting to ecology: The use of Fourier-transform infrared spectroscopy for the rapid screening of plant responses to N deposition 10.1007/s11267-004-3035-z

Application of high-throughput Fourier-transform infrared spectroscopy in toxicology studies: Contribution to a study on the development of an animal model for idiosyncratic toxicity 10.1016/j.toxlet.2003.09.011

A structural and chemical analyser (SCA) identification of bacteria labelled by metallic nanoparticles 10.1017/S1431927604882886

A proposed framework for the description of plant metabolomics experiments and their results 10.1038/nbt1041

Rapid quantitative assessment of the adulteration of virgin olive oils with hazelnut oils using Raman spectroscopy and chemometrics 10.1021/jf034493d

Metabolic fingerprinting of salt-stressed tomatoes 10.1016/S0031-9422(02)00722-7

Investigating plant-plant interference by metabolic fingerprinting 10.1016/S0031-9422(03)00288-7

Functional genomics via metabolic footprinting: Monitoring metabolite secretion by Escherichia coli tryptophan metabolism mutants using FT-IR and direct injection electrospray mass spectrometry 10.1002/cfg.302

Explanatory Optimization of Protein Mass Spectrometry via Genetic Search 10.1021/ac034669a

Explanatory analysis of spectroscopic data using machine learning of simple, interpretable rules 10.1016/S0924-2031(03)00045-6

Chemometric discrimination of unfractionated plant extracts analyzed by electrospray mass spectrometry 10.1016/S0031-9422(02)00718-5

Sample preparation in matrix-assisted laser desorption/ionization mass spectrometry of whole bacterial cells and the detection of high mass (>20 kDa) proteins 10.1002/rcm.713

Rapid and quantitative detection of the microbial spoilage of meat by fourier transform infrared spectroscopy and machine learning 10.1128/AEM.68.6.2822-2828.2002

Progress toward the rapid nondestructive assessment of the floral origin of European honey using dispersive Raman spectroscopy 10.1366/0003702021954980

Monitoring of complex industrial bioprocesses for metabolite concentrations using modern spectroscopies and machine learning: Application to gibberellic acid production 10.1002/bit.10226

Metabolic profiling using direct infusion electrospray ionisation mass spectrometry for the characterisation of olive oils 10.1039/b206037j

Fluorescent amplified fragment length polymorphism probabilistic database for identification of bacterial isolates from urinary tract infections 10.1128/JCM.40.8.2795-2800.2002

Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-throughput bacterial identification 10.1016/S1044-0305(01)00339-7

Rapid and quantitative detection of the microbial spoilage of muscle foods: Current status and future trends 10.1016/S0924-2244(02)00019-5

Discrimination of aerobic endospore-forming bacteria via electrospray-ionization mass spectrometry of whole cell suspensions 10.1021/ac0103524

Degeneration of solventogenic Clostridium strains monitored by Fourier transform infrared spectroscopy of bacterial cells 10.1038/sj.jim.7000146

Contribution of pyrolysis-mass spectrometry (Py-MS) to authenticity testing of honey 10.1016/S0165-2370(00)00163-7

Detection of the dipicolinic acid biomarker in Bacillus spores using curie-point pyrolysis mass spectrometry and fourier transform infrared spectroscopy 10.1021/ac990661i

The detection of caffeine in a variety of beverages using Curie-point pyrolysis mass spectrometry and genetic programming 10.1039/a901062i

Rapid analysis of the expression of heterologous proteins in Escherichia coli using pyrolysis mass spectrometry and Fourier transform infrared spectroscopy with chemometrics: application to α2-interferon production 10.1016/S0168-1656(99)00128-5

Characterisation of intact microorganisms using electrospray ionisation mass spectrometry 10.1016/S0378-1097(99)00212-8

The deconvolution of pyrolysis mass spectra using genetic programming: Application to the identification of some Eubacterium species 10.1016/S0378-1097(98)00038-X

Rapid analysis of microbial systems using vibrational spectroscopy and supervised learning methods: Application to the discrimination between methicillin-resistant and methicillin-susceptible Staphylococcus aureus 10.1117/12.306087

DRASTIC(Diffuse Reflectance Absorbance Spectroscopy Taking In Chemometrics). A novel, rapid, hyperspectral, FT-IR-based approach to screening for biocatalytic activity and metabolite overproduction 10.1016/S0165-3253(98)80010-2

Discrimination between methicillin-resistant and methicillin-susceptible Staphylococcus aureus using pyrolysis mass spectrometry and artificial neural networks 10.1093/jac/41.1.27

Differentiation of brewing yeast strains by pyrolysis mass spectrometry and Fourier transform infrared spectroscopy 10.1002/(SICI)1097-0061(199807)14:10<885::AID-YEA286>3.0.CO;2-G

A DRASTIC (Diffuse Reflectance Absorbance Spectroscopy Taking in Chemometrics) approach for the rapid analysis of microbial fermentation products: Quantification of aristeromycin and neplanocin A in Streptomyces citricolor broths 10.1016/S0165-3253(98)80023-0

On mass spectrometer instrument standardization and interlaboratory calibration transfer using neural networks 10.1016/S0003-2670(97)00062-7

Genetic algorithms as a method for variable selection in multiple linear regression and partial least squares regression, with applications to pyrolysis mass spectrometry 10.1016/S0003-2670(97)00065-2

Diffuse reflectance absorbance spectroscopy taking in chemometrics (DRASTIC), A hyperspectral FT-IR-based approach to rapid screening for metabolite overproduction 10.1016/S0003-2670(97)00237-7

Classification of pyrolysis mass spectra by fuzzy multivariate rule induction-comparison with regression, K-nearest neighbour, neural and decision-tree methods 10.1016/S0003-2670(97)00064-0

Rapid identification of Streptococcus and Enterococcus species using diffuse relfectance-absorbance Fourier transform infrared spectroscopy and artificial neural networks 10.1016/0378-1097(96)00186-3

Pyrolysis mass spectrometry and its applications in biotechnology 10.1016/S0958-1669(96)80090-5

Plant seed classification using pyrolysis mass spectrometry with unsupervised learning: The application of auto-associative and Kohonen artificial neural networks 10.1016/0169-7439(96)00021-4

Identification and discrimination of oral asaccharolytic Eubacterium spp. by Pyrolysis mass spectrometry and artificial neural networks 10.1007/s002849900014

Rapid and quantitative analysis of metabolites in fermentor broths using pyrolysis mass spectrometry with supervised learning: application to the screening of Penicillium chrysogenum fermentations for the overproduction of penicillins 10.1016/0003-2670(95)00170-5

Phenotypic and genotypic differences between certain strains of Clostridium acetobutylicum 10.1016/0378-1097(94)00498-G

The dogs that did not bark 10.1016/0167-7799(94)90016-7

Rapid screening for metabolite overproduction in fermenter broths, using pyrolysis mass spectrometry with multivariate calibration and artificial neural networks 10.1002/bit.260441008

Rapid and quantitative analysis of recombinant protein expression using pyrolysis mass spectrometry and artificial neural networks: application to mammalian cytochrome b5 in Escherichia coli 10.1016/0168-1656(94)90088-4

Rapid and quantitative analysis and bioprocesses using pyrolysis mass spectrometry and neural networks: application to indole production 10.1016/0003-2670(93)85062-O

Quantitative analysis of the pyrolysis-mass spectra of complex mixtures using artificial neural networks: Application to amino acids in glycogen 10.1016/0165-2370(93)85020-Y

Neural networks and olive oil [4] 10.1038/359594a0

The use of pyrolysis-mass spectrometry to detect the fimbrial adhesive antigen F41 from Escherichia coli HB101 (pSLM204) 10.1016/0165-2370(91)85002-O

Detection of small genotypic changes in Escherichia coli by pyrolysis mass spectroscopy 10.1016/0378-1097(90)90045-R

Simultaneous quantification of the boar-taint compounds skatole and androstenone by surface-enhanced Raman scattering (SERS) and multivariate data analysis 10.1007/s00216-015-8945-2

Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block 10.1021/sb500368w

Oxidized phosphatidylcholines suggest oxidative stress in patients with medium-chain acyl-CoA dehydrogenase deficiency 10.1016/j.talanta.2015.02.041

New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition 10.1038/nature14560

UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis 10.1038/nature14559

Phenotypic characterisation of shewanella oneidensis MR-1 exposed to X-radiation 10.1371/journal.pone.0131249

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access 10.1007/s11306-015-0810-y

Combining Raman and FT-IR spectroscopy with quantitative isotopic labeling for differentiation of E. Coli Cells at Community and Single Cell Levels 10.1021/acs.analchem.5b00892

Surveillance for lower airway pathogens in mechanically ventilated patients by metabolomic analysis of exhaled breath: A case-control study 10.1136/thoraxjnl-2014-206273

Metabolic profiling of Geobacter sulfurreducens during industrial bioprocess scale-up 10.1128/AEM.00294-15

Profiling of spatial metabolite distributions in wheat leaves under normal and nitrate limiting conditions 10.1016/j.phytochem.2015.01.007

Untargeted metabolic profiling identifies altered serum metabolites of type 2 diabetes mellitus in a prospective, nested case control study 10.1373/clinchem.2014.228965

Acclimation of metabolism to light in Arabidopsis thaliana: The glucose 6-phosphate/phosphate translocator GPT2 directs metabolic acclimation 10.1111/pce.12495

Making colourful sense of Raman images of single cells 10.1039/c4an02298j

A tutorial review: Metabolomics and partial least squares-discriminant analysis - a marriage of convenience or a shotgun wedding 10.1016/j.aca.2015.02.012

MUSCLE: Automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis 10.1093/bioinformatics/btu740

Application of surface enhanced Raman scattering to the solution based detection of a popular legal high, 5,6-methylenedioxy-2-aminoindane (MDAI) 10.1039/c5an00591d

Detection and quantification of the opioid tramadol in urine using surface enhanced Raman scattering 10.1039/c5an01177a

Monitoring antibody aggregation in early drug development using raman spectroscopy and perturbation-correlation moving windows 10.1021/ac5038329

Considerations in sample preparation, collection, and extraction approaches applied in microbial, plant, and mammalian metabolic profiling 10.1017/CBO9780511996634.004

Detection of early stage changes associated with adipogenesis using Raman spectroscopy under aseptic conditions 10.1002/cyto.a.22777

Biochemical analyses of sorghum varieties reveal differential responses to drought 10.1371/journal.pone.0154423

Exploring the mode of action of dithranol therapy for psoriasis: A metabolomic analysis using HaCaT cells 10.1039/c4mb00739e

Detection of Protein Glycosylation Using Tip-Enhanced Raman Scattering 10.1021/acs.analchem.5b03535

Simultaneous multiplexed quantification of caffeine and its major metabolites theobromine and paraxanthine using surface-enhanced Raman scattering 10.1007/s00216-015-9004-8

Meat, the metabolites: An integrated metabolite profiling and lipidomics approach for the detection of the adulteration of beef with pork 10.1039/c6an00108d

Continued growth, continual progress, and continuous publications 10.1007/s11306-015-0911-7

Say hello to Dr Warwick Dunn! Metabolomics’ new Reviews Editor 10.1007/s11306-016-0978-9

Towards Improving Point-of-Care Diagnosis of Non-malaria Febrile Illness: A Metabolomics Approach 10.1371/journal.pntd.0004480

Achieving optimal SERS through enhanced experimental design 10.1002/jrs.4855

Metabolomics investigation of recombinant mTNFaα production in Streptomyces lividans 10.1186/s12934-015-0350-1

Aseptic Raman spectroscopy can detect changes associated with the culture of human dental pulp stromal cells in osteoinductive culture 10.1039/c5an01595b

Evaluation of metabolomics profiles of grain from maize hybrids derived from near-isogenic GM positive and negative segregant inbreds demonstrates that observed differences cannot be attributed unequivocally to the GM trait 10.1007/s11306-016-1017-6

Progress in Chemometrics and Biostatistics for Plant Applications, or: A Good Red Wine is a Bad White Wine 10.1002/9781444339956.ch10

Fingerprint Spectrometry Methods in Bacillus Systematics 10.1002/9780470696743.ch17

Metabolomics reveals the physiological response of Pseudomonas putida KT2440 (UWC1) after pharmaceutical exposure 10.1039/c5mb00889a

Point-and-shoot: Rapid quantitative detection methods for on-site food fraud analysis-moving out of the laboratory and into the food supply chain 10.1039/c5ay02048d

Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access (Metabolomics, (2015), 10.1007/s11306-015-0810-y) 10.1007/s11306-015-0822-7

Chicken, beams, and Campylobacter: Rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry 10.1039/c5an01945a

Metabolic responses of eukaryotic microalgae to environmental stress limit the ability of FT-IR spectroscopy for species identification 10.1016/j.algal.2015.06.009

Data standards can boost metabolomics research, and if there is a will, there is a way 10.1007/s11306-015-0879-3

High-throughput metabolic screening of microalgae genetic variation in response to nutrient limitation 10.1007/s11306-015-0878-4

Metabolite profiling of CHO cells: Molecular reflections of bioprocessing effectiveness 10.1002/biot.201400664

FUM2, a Cytosolic Fumarase, Is Essential for Acclimation to Low Temperature in Arabidopsis thaliana 10.1104/pp.16.00852

Absolute Quantification of Uric Acid in Human Urine Using Surface Enhanced Raman Scattering with the Standard Addition Method 10.1021/acs.analchem.6b04588

Quantitative detection of codeine in human plasma using surface-enhanced Raman scattering via adaptation of the isotopic labelling principle 10.1039/C7AN00193B

Clinical Spectroscopy: General discussion 10.1039/C6FD90013E

Spectral Pathology: General discussion 10.1039/C6FD90011A

Rapid discrimination of Enterococcus faecium strains using phenotypic analytical techniques 10.1039/c6ay02326f

The role of reporting standards for metabolite annotation and identification in metabolomic studies 10.1186/2047-217X-2-13

Metabolic profiling reveals potential metabolic markers associated with Hypoxia Inducible Factor-mediated signalling in hypoxic cancer cells 10.1038/srep15649

The influence of scaling metabolomics data on model classification accuracy 10.1007/s11306-014-0738-7

Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry 10.1007/s11306-016-1054-1

Ethnic differences in male reproductive hormones and relationships with adiposity and insulin resistance in older men 10.1111/cen.13305

Rapid assessment of the adulteration of virgin olive oils by other seed oils using pyrolysis mass spectrometry and artificial neural networks 10.1002/jsfa.2740630306

Intermittent energy restriction induces changes in breast gene expression and systemic metabolism 10.1186/s13058-016-0714-4

Metabolic fingerprinting of Pseudomonas putida DOT-T1E strains: Understanding the influence of divalent cations in adaptation mechanisms following exposure to toluene 10.3390/metabo6020014

SYNBIOCHEM - A SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals 10.1042/BST20160009

Classification of Bacillus and Brevibacillus species using rapid analysis of lipids by mass spectrometry 10.1007/s00216-016-9890-4

Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms: Via multiple vibrational spectroscopic fingerprinting 10.1039/c6an00883f

Metabolomic analysis of riboswitch containing E. coli recombinant expression system 10.1039/c5mb00624d

A flavour of omics approaches for the detection of food fraud 10.1016/j.cofs.2016.07.002

Fractional Factorial Design of MALDI-TOF-MS Sample Preparations for the Optimized Detection of Phospholipids and Acylglycerols 10.1021/acs.analchem.6b00512

Reverse and Multiple Stable Isotope Probing to Study Bacterial Metabolism and Interactions at the Single Cell Level 10.1021/acs.analchem.6b01602

The androgen receptor gene CAG repeat in relation to 4-year changes in androgen-sensitive endpoints in community-dwelling older European men 10.1530/EJE-16-0447

Label-Free Surface Enhanced Raman Scattering Approach for High-Throughput Screening of Biocatalysts 10.1021/acs.analchem.6b00813

Biofluids and other techniques: General discussion 10.1039/C6FD90014C

Detecting food authenticity and integrity 10.1039/c6ay90015a

Metabolomics analysis reveals the participation of efflux pumps and ornithine in the response of pseudomonas putida DOT-T1E cells to challenge with propranolol 10.1371/journal.pone.0156509

Detection of glycosylation and iron-binding protein modifications using Raman spectroscopy 10.1039/c6an02516a

Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy 10.1007/s11306-016-1147-x

Single cell analysis/data handling: General discussion 10.1039/C6FD90012G

Electronic cigarette exposure triggers neutrophil inflammatory responses 10.1186/s12931-016-0368-x

A systematic analysis of TCA Escherichia coli mutants reveals suitable genetic backgrounds for enhanced hydrogen and ethanol production using glycerol as main carbon source 10.1002/biot.201500005

Partial least squares with structured output for modelling the metabolomics data obtained from complex experimental designs: A study into the ϒ-block coding 10.3390/metabo6040038

SERS of meso-droplets supported on superhydrophobic wires allows exquisitely sensitive detection of dipicolinic acid, an anthrax biomarker, considerably below the infective dose 10.1039/c6cc03521c

Rapid, high-throughput, and quantitative determination of orange juice adulteration by Fourier-transform infrared spectroscopy 10.1039/c6ay01480a

Real-Time Monitoring of Enzyme-Catalysed Reactions using Deep UV Resonance Raman Spectroscopy 10.1002/chem.201701388

Recommendations on the Implementation of Genetic Algorithms for the Directed Evolution of Enzymes for Industrial Purposes 10.1002/cbic.201700013

Quantitative Online Liquid Chromatography–Surface-Enhanced Raman Scattering (LC-SERS) of Methotrexate and its Major Metabolites 10.1021/acs.analchem.7b00916

Two Glycerol-3-Phosphate Dehydrogenases from Chlamydomonas Have Distinct Roles in Lipid Metabolism 10.1104/pp.17.00491

Objective assessment of SERS thin films: comparison of silver on copper via galvanic displacement with commercially available fabricated substrates 10.1039/C7AY01584D

Quantitative detection of isotopically enriched E. coli cells by SERS 10.1039/C7FD00150A

Exhaled Volatile Organic Compounds of Infection: A Systematic Review 10.1021/acsinfecdis.7b00088

Through-container, extremely low concentration detection of multiple chemical markers of counterfeit alcohol using a handheld SORS device 10.1038/s41598-017-12263-0

Exhaled breath analysis: a review of ‘breath-taking’ methods for off-line analysis 10.1007/s11306-017-1241-8

Increased intracellular proteolysis reduces disease severity in an ER stress-associated dwarfism 10.1172/JCI93094

Systems biology guided by XCMS Online metabolomics 10.1038/nmeth.4260

Commentary on "rapid identification of streptococcus and enterococcus species using diffuse reflectance-absorbance fourier transform infrared spectroscopy and artificial neural networks" 10.1093/femsle/fnx018

Probing the action of a novel anti-leukaemic drug therapy at the single cell level using modern vibrational spectroscopy techniques 10.1038/s41598-017-02069-5

Metabolomics for the masses: The future of metabolomics in a personalized world 10.1016/j.nhtm.2017.06.001

From Multistep Enzyme Monitoring to Whole-Cell Biotransformations: Development of Real-Time Ultraviolet Resonance Raman Spectroscopy 10.1021/acs.analchem.7b03742

SERS Detection of Multiple Antimicrobial-Resistant Pathogens Using Nanosensors 10.1021/acs.analchem.7b02653

Towards improved quantitative analysis using surface-enhanced Raman scattering incorporating internal isotope labelling 10.1039/C7AY02527K

Headspace volatile organic compounds from bacteria implicated in ventilator-associated pneumonia analysed by TD-GC/MS 10.1088/1752-7163/aa8efc

Improved Descriptors for the Quantitative Structure–Activity Relationship Modeling of Peptides and Proteins 10.1021/acs.jcim.7b00488

Clinical applications of infrared and Raman spectroscopy: state of play and future challenges 10.1039/C7AN01871A

Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins 10.1128/mBio.02118-17

Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World 10.1177/0003702818764672

TD/GC–MS analysis of volatile markers emitted from mono- and co-cultures of Enterobacter cloacae and Pseudomonas aeruginosa in artificial sputum 10.1007/s11306-018-1357-5

Volatile organic compound signature from co-culture of lung epithelial cell line with Pseudomonas aeruginosa 10.1039/C8AN00759D

pH plays a role in the mode of action of trimethoprim on Escherichia coli 10.1371/journal.pone.0200272

Development of an adaptable headspace sampling method for metabolic profiling of the fungal volatome 10.1039/C8AN00841H

On Splitting Training and Validation Set: A Comparative Study of Cross-Validation, Bootstrap and Systematic Sampling for Estimating the Generalization Performance of Supervised Learning 10.1007/s41664-018-0068-2

Methodological considerations for large-scale breath analysis studies: lessons from the U-BIOPRED severe asthma project 10.1088/1752-7163/aae557

Rapid through-container detection of fake spirits and methanol quantification with handheld Raman spectroscopy 10.1039/C8AN01702F

Detection of the adulteration of fresh coconut water via NMR spectroscopy and chemometrics 10.1039/C8AN01964A

Application of HPLC–PDA–MS metabolite profiling to investigate the effect of growth temperature and day length on blackcurrant fruit 10.1007/s11306-018-1462-5

Ultrasensitive Colorimetric Detection of Murine Norovirus Using NanoZyme Aptasensor 10.1021/acs.analchem.8b03300

Rapid UHPLC-MS metabolite profiling and phenotypic assays reveal genotypic impacts of nitrogen supplementation in oats 10.1007/s11306-019-1501-x

Enhancing Disease Diagnosis: Biomedical Applications of Surface-Enhanced Raman Scattering 10.3390/app9061163

Polymer Pen Lithography-Fabricated DNA Arrays for Highly Sensitive and Selective Detection of Unamplified Ganoderma Boninense DNA 10.3390/polym11030561

The blind men and the elephant: challenges in the analysis of complex natural mixtures 10.1039/C9FD00074G

High resolution techniques: general discussion 10.1039/C9FD90045D

Data mining and visualisation: general discussion 10.1039/C9FD90044F

Future challenges and new approaches: general discussion 10.1039/C9FD90046B

Dealing with complexity: general discussion 10.1039/C9FD90055A

Rapid differentiation of Campylobacter jejuni cell wall mutants using Raman spectroscopy, SERS and mass spectrometry combined with chemometrics 10.1039/C9AN02026H

Development of a sensor device with polymer-coated piezoelectric micro-cantilevers for detection of volatile organic compounds 10.1088/1361-6501/ab4f2f

Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity 10.3390/metabo10030121

Quantification of protein glycation using vibrational spectroscopy 10.1039/C9AN02318F

Raman Spectroscopy to Monitor Post-Translational Modifications and Degradation in Monoclonal Antibody Therapeutics 10.1021/acs.analchem.0c00627

Comparison of liver and plasma metabolic profiles in piglets of different ages as animal models for paediatric population 10.1039/D0AN00254B

Evaluation of Sample Preparation Methods for Inter-Laboratory Metabolomics Investigation of Streptomyces lividans TK24 10.3390/metabo10090379

Detection and quantification of exhaled volatile organic compounds in mechanically ventilated patients – comparison of two sampling methods 10.1039/C9AN01134J

Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing 10.1039/D0AN01482F

Metabolism in action: stable isotope probing using vibrational spectroscopy and SIMS reveals kinetic and metabolic flux of key substrates 10.1039/D0AN02319A

Imaging Isotopically Labeled Bacteria at the Single-Cell Level Using High-Resolution Optical Infrared Photothermal Spectroscopy 10.1021/acs.analchem.0c03967

Marnix H. Medema

Medema Marnix H.

ORCID: 0000-0002-2191-2821

http://www.marnixmedema.nl

antiSMASH 10.1007/978-1-4899-7478-5_703

Bioinformatics Approaches and Software for Detection of Secondary Metabolic Gene Clusters 10.1007/978-1-62703-122-6_2

Synthetic Biology in Streptomyces Bacteria 10.1016/b978-0-12-385075-1.00021-4

Computational approaches to natural product discovery 10.1038/nchembio.1884

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms 10.1038/nrmicro2478

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis 10.1371/journal.pcbi.1004016

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism 10.1016/j.febslet.2011.06.014

MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models 10.1371/journal.pone.0051511

The future of industrial antibiotic production: From random mutagenesis to synthetic biology 10.4161/bbug.2.4.16114

Metabolomics methods for the synthetic biology of secondary metabolism 10.1016/j.febslet.2012.02.008

Computational tools for the synthetic design of biochemical pathways 10.1038/nrmicro2717

A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis 10.1186/1471-2164-11-299

Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus 10.1111/j.1751-7915.2010.00226.x

Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea 10.1111/j.1462-2920.2008.01724.x

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters 10.1016/j.cell.2014.06.034

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products 10.1371/journal.pcbi.1003822

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters 10.1093/nar/gkv437

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice 10.1016/j.copbio.2013.03.006

Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block 10.1021/sb500368w

antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers 10.1093/nar/gkt449

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences 10.1093/nar/gkr466

The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways 10.1093/gbe/evq013

MS/MS networking guided analysis of molecule and gene cluster families 10.1073/pnas.1303471110

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast 10.1093/molbev/mst025

Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii 10.1128/jb.02132-12

NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity 10.1093/nar/gkr323

Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation 10.1128/mmbr.00037-08

Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum. 10.1186/s12864-015-2154-4

Leucanicidin and endophenasides result from methyl-rhamnosylation by the same tailoring enzymes in Kitasatospora sp. MBT66 10.1021/acschembio.5b00801

Computational strategies for genome-based natural product discovery and engineering in fungi 10.1016/j.fgb.2016.01.006

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters 10.1093/nar/gkw960

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides 10.1038/nmicrobiol.2016.197

Editorial: Synthetic biology and bioinformatics 10.1039/c6np90031c

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters 10.1093/nar/gkx305

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus 10.1186/s12864-017-3966-1

Mining prokaryotes for antimicrobial compounds: from diversity to function 10.1093/femsre/fux014

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters 10.1093/bib/bbx146

Standardization for natural product synthetic biology 10.1039/c6np00030d

Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways 10.1039/c6np00035e

Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium , Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin 10.1128/genomea.00453-17

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria 10.1093/bioinformatics/btx400

Collaborating with Undergraduates To Contribute to Biochemistry Community Resources 10.1021/acs.biochem.7b00872

Road MAPs to engineer host microbiomes. 10.1016/j.mib.2017.11.023

Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens. 10.1111/1462-2920.13927

Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution. 10.1073/pnas.1705567114

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. 10.1093/nar/gkx319

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. 10.1016/j.fgb.2016.01.012

Exploration and exploitation of the environment for novel specialized metabolites. 10.1016/j.copbio.2018.01.017

Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology 10.1128/mSystems.00182-17

Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics. 10.1016/j.chembiol.2018.02.008

HEx: A heterologous expression platform for the discovery of fungal natural products. 10.1126/sciadv.aar5459

luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria. 10.1128/msystems.00208-17

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology. 10.1021/jacs.7b13292

Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium. 10.3389/fmicb.2018.01158

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. 10.1038/s41396-018-0186-x

Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH. 10.1007/978-1-4939-7874-8_15

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences 10.1186/s40793-018-0318-y

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters 10.1093/nar/gky1060

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1101/463620

Mining bacterial genomes to reveal secret synergy 10.1074/jbc.H118.006669

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters 10.1038/s42003-019-0333-6

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1111/tpj.14292

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters 10.1186/s13104-019-4222-3

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline 10.1093/nar/gkz310

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools 10.1101/654459

BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs 10.1101/gr.243477.118

Genome Mining Approaches to Bacterial Natural Product Discovery 10.1016/b978-0-12-409547-2.14627-x

Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines 10.1039/C9NP00021F

PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters 10.1101/083535

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools 10.3390/metabo9070144

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L. 10.3389/fpls.2019.00846

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome 10.1126/science.aaw9285

MIBiG 2.0: a repository for biosynthetic gene clusters of known function 10.1093/nar/gkz882

A metabolic pathway for bile acid dehydroxylation by the gut microbiome 10.1101/758557

Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines 10.1101/669291

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery 10.1021/acscentsci.9b00806

Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology 10.1038/s41564-019-0588-1

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia 10.1101/856955

Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae 10.1111/nph.16338

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat 10.1098/rspb.2019.2527

Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota 10.1101/2020.03.06.976126

RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery 10.1101/2020.03.14.992123

Linking genomics and metabolomics to chart specialized metabolic diversity 10.1039/D0CS00162G

Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota 10.1099/mgen.0.000373

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining 10.1093/nar/gkaa374

Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products 10.1101/2020.05.19.104752

Ecology and genomics of Actinobacteria: new concepts for natural product discovery 10.1038/s41579-020-0379-y

The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms 10.1038/s42003-020-0993-2

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters 10.1101/2020.08.17.240838

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia 10.1074/jbc.RA120.013528

Microbial natural product databases: moving forward in the multi-omics era 10.1039/D0NP00053A

Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms 10.1038/s42003-020-01228-1

RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery 10.1128/mSystems.00267-20

Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms 10.1038/s42003-020-01271-y

BiG-FAM: the biosynthetic gene cluster families database 10.1093/nar/gkaa812

Coevolution-based prediction of protein–protein interactions in polyketide biosynthetic assembly lines 10.1093/bioinformatics/btaa595

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes 10.1093/nar/gkaa978

Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order 10.1038/s41598-020-77723-6

BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes 10.1101/2020.12.14.422671

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides 10.1371/journal.pbio.3001026

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters 10.1093/gigascience/giaa154

The year 2020 in natural product bioinformatics: an overview of the latest tools and databases 10.1039/D0NP00090F

Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis 10.1101/2021.02.11.430889

A systematic analysis of metabolic pathways in the human gut microbiota 10.1101/2021.02.25.432841

Omics-based strategies to discover novel classes of RiPP natural products 10.1016/j.copbio.2020.12.008

Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria 10.1038/s41467-021-21163-x

The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range 10.3389/fbioe.2021.623701

Mining metagenomes for natural product biosynthetic gene clusters: unlocking new potential with ultrafast techniques 10.1101/2021.01.20.427441

Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes 10.3389/fmicb.2020.574053

A mammalian commensal of the oropharyngeal cavity produces antibiotic and antiviral valinomycin in vivo 10.21203/rs.3.rs-126949/v1

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters 10.1016/j.chembiol.2020.11.009

cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters 10.1101/2020.11.08.370601

antiSMASH 6.0: improving cluster detection and comparison capabilities 10.1093/nar/gkab335

The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota 10.1093/nar/gkab353

Mining genomes to illuminate the specialized chemistry of life 10.1038/s41576-021-00363-7

Dominant drivers of the human plasma metabolome 10.21203/rs.3.rs-688716/v1

A global survey of specialized metabolic diversity encoded in bacterial genomes 10.1101/2021.08.11.455920

cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters 10.1093/bioadv/vbab016

Jason Micklefield

Micklefield Jason

ORCID: 0000-0001-8951-4873

Changing the Selectivity of Biocatalysts 10.1002/chemv.201600027

A Flavin-Dependent Decarboxylase-Dehydrogenase-Monooxygenase Assembles the Warhead of α,β-Epoxyketone Proteasome Inhibitors 10.1021/jacs.6b01619

An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins 10.1021/jacs.5b10928

A Structure-Guided Switch in the Regioselectivity of a Tryptophan Halogenase 10.1002/cbic.201600051

Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase 10.1002/anie.201508287

Recent advances in engineering nonribosomal peptide assembly lines 10.1039/c5np00099h

Dual transcriptional-translational cascade permits cellular level tuneable expression control. 10.1093/nar/gkv912

Rational Re-engineering of a Transcriptional Silencing PreQ1 Riboswitch. 10.1021/jacs.5b03405

Engineered biosynthesis of enduracidin lipoglycopeptide antibiotics using the ramoplanin mannosyltransferase Ram29 10.1099/mic.0.000095

Enzymatic enantioselective decarboxylative protonation of heteroaryl malonates 10.1002/chem.201406014

Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block 10.1021/sb500368w

A High-Throughput Assay for Arylamine Halogenation Based on a Peroxidase-Mediated Quinone-Amine Coupling with Applications in the Screening of Enzymatic Halogenations 10.1002/chem.201403953

Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species 10.1021/ja502873j

Generation of orthogonally selective bacterial riboswitches by targeted mutagenesis and in vivo screening 10.1007/978-1-62703-755-6_8

Nucleic acids: New life, new materials 10.1039/c3ob90017g

S-Adenosyl-Methionine-Dependent Methyltransferases: Highly Versatile Enzymes in Biocatalysis, Biosynthesis and Other Biotechnological Applications 10.1002/cbic.201200556

Introduction of a non-natural amino acid into a nonribosomal peptide antibiotic by modification of adenylation domain specificity 10.1002/anie.201202043

Probing riboswitch-ligand interactions using thiamine pyrophosphate analogues 10.1039/c2ob07116a

Bioengineering natural product biosynthetic pathways for therapeutic applications 10.1016/j.copbio.2012.03.008

Thermal bifunctionality of bacterial phenylalanine aminomutase and ammonia lyase enzymes 10.1002/anie.201200669

Orthogonal riboswitches for tuneable coexpression in bacteria 10.1002/anie.201109106

A methodology for preparing nanostructured biomolecular interfaces with high enzymatic activity 10.1039/c1nr11443c

Biophysical and cellular-uptake properties of mixed-sequence pyrrolidine-amide oligonucleotide mimics 10.1002/chem.201101950

Protein micro- and nanopatterning using aminosilanes with protein-resistant photolabile protecting groups 10.1021/ja1103662

Borrelidin modulates the alternative splicing of VEGF in favour of anti-angiogenic isoforms. 10.1039/C0SC00297F

Active site modification of the β-ketoacyl-ACP synthase FabF3 of Streptomyces coelicolor affects the fatty acid chain length of the CDA lipopeptides 10.1039/c0cc03444d

Parallel scanning near-field photolithography: The snomipede 10.1021/nl1018782

Nanoscale biomolecular structures on self-assembled monolayers generated from modular pegylated disulfides 10.1002/chem.200902439

A non-enzymatic, dna template-directed morpholino primer extension approach 10.1002/chem.200902237

Reengineering orthogonally selective riboswitches 10.1073/pnas.0911209107

Site-selective immobilisation of functional enzymes on to polystyrene nanoparticles 10.1039/b916773k

Chemical modification of oligonucleotides for therapeutic, bioanalytical and other applications 10.1002/cbic.200900341

Selective covalent protein immobilization: Strategies and applications 10.1021/cr8004668

Micrometer-and nanometer-scale photopatterning using 2- nitrophenylpropyloxycarbonyl-protected aminosiloxane monolayers 10.1021/ja807612y

Structure-guided directed evolution of alkenyl and arylmalonate decarboxylases 10.1002/anie.200904112

Chapter 14 Biosynthesis of Nonribosomal Peptide Precursors 10.1016/S0076-6879(09)04814-9

Direct site-selective covalent protein immobilization catalyzed by a phosphopantetheinyl transferase 10.1021/ja8030278

Subsurface biomolecular imaging of Streptomyces coelicolor using secondary ion mass spectrometry 10.1021/ac701921e

Auxotrophic-precursor directed biosynthesis of nonribosomal lipopeptides with modified tryptophan residues 10.1039/b718766c

Structure and mechanism of an unusual malonate decarboxylase and related racemases 10.1002/chem.200800918

Engineered biosynthesis of nonribosomal lipopeptides with modified fatty acid side chains 10.1021/ja074331o

RNA-selective cross-pairing of backbone-extended pyrrolidine-amide oligonucleotide mimics (bePOMs) 10.1039/b714580m

Cellular targets of natural products 10.1039/b616808f

NMR confirmation that tryptophan dehydrogenation occurs with syn stereochemistry during the biosynthesis of CDA in Streptomyces coelicolor 10.1021/jo701660v

Stereospecific enzymatic transformation of α-ketoglutarate to (2S,3R)-3-methyl glutamate during acidic lipopeptide biosynthesis 10.1021/ja074427i

Mining and engineering natural-product biosynthetic pathways 10.1038/nchembio.2007.7

Precursor-directed biosynthesis of nonribosomal lipopeptides with modified glutamate residues 10.1039/b706224a

Stereochemical course of tryptophan dehydrogenation during biosynthesis of the calcium-dependent lipopeptide antibiotics 10.1021/ol0701619

An asparagine oxygenase (AsnO) and a 3-hydroxyasparaginyl phosphotranferase (HasP) are involved in the biosynthesis of calcium-dependent lipopeptide antibiotics 10.1099/mic.0.2006/002725-0

Homopolymeric pyrrolidine-amide oligonucleotide mimics: Fmoc-synthesis and DNA/RNA binding properties 10.1039/b613384n

Mixed-sequence pyrrolidine-amide oligonucleotide mimics: Boc(Z) synthesis and DNA/RNA binding properties 10.1039/b613386j

Biosynthesis of the (2S,3R)-3-methyl glutamate residue of nonribosomal lipopeptides 10.1021/ja062960c

Stereospecific backbone methylation of pyrrolidine-amide oligonucleotide mimics (POM) 10.1039/b518171b

Nature's protection racket 10.1016/j.chembiol.2005.06.002

Metabolic flux analysis for calcium dependent antibiotic (CDA) production in Streptomyces coelicolor 10.1016/j.ymben.2004.04.001

Biotransformations in low-boiling hydrofluorocarbon solvents 10.1002/anie.200460082

Daptomycin structure and mechanism of action revealed 10.1016/j.chembiol.2004.07.001

NMR structure determination and calcium binding effects of lipopeptide antibiotic daptomycin 10.1039/b402722a

Active-Site Modifications of Adenylation Domains Lead to Hydrolysis of Upstream Nonribosomal Peptidyl Thioester Intermediates 10.1021/ja048778y

Nucleic acid binding properties of thyminyl and adeninyl pyrrolidine-amide oligonucleotide mimics (POM). 10.1039/b315768g

Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide oligonucleotide mimics (POM) 10.1039/b306156f

Structure, biosynthetic origin, and engineered biosynthesis of calcium-dependent antibiotics from Streptomyces coelicolor 10.1016/S1074-5521(02)00252-1

Backbone modification of nucleic acids: synthesis, structure and therapeutic applications. 10.2174/0929867013372391

Kinetically selective binding of single stranded RNA over DNA by a pyrrolidine-amide oligonucleotide mimic (POM) 10.1081/NCN-100002512

Haem d1: Stereoselective synthesis of the macrocycle to establish its absolute configuration as 2R,7R 10.1039/a700655a

Haem d1: Development of a new coupling procedure leading to the synthesis of isobacteriochlorins 10.1039/a700654c

Stereochemical Course of Malonate Decarboxylation in Malonomonas rubra 10.1021/ja00108a042

The Snomipede: A parallel platform for scanning near-field photolithography 10.1557/jmr.2011.370

A dynamic combinatorial screen for novel imine reductase activity 10.1016/j.tet.2003.10.114

Lipase-catalysed kinetic resolutions of secondary alcohols in pressurised liquid hydrofluorocarbons 10.1016/j.tetlet.2009.03.037

7.19 C-X Bond Formation: Enzymatic Enantioselective Decarboxylative Protonation and C-C Bond Formation 10.1016/B978-0-08-095167-6.00724-2

Biosynthesis and biosynthetic engineering of calcium-dependent lipopeptide antibiotics 10.1351/PAC-CON-08-08-29

Site-specific bioalkylation of rapamycin by the RapM 16-O-methyltransferase 10.1039/c5sc00164a

Extending the biocatalytic scope of regiocomplementary flavin-dependent halogenase enzymes 10.1039/c5sc00913h

Sulfamide replacement of the phosphodiester linkage in dinucleotides: Synthesis and conformational analysis 10.1016/S0040-4020(97)10421-5

Synthesis of sulfamide linked dinucleotide analogues 10.1016/S0040-4039(97)01179-9

A novel stereoselective synthesis of the macrocycle of haem d1 that establishes its absolute configuration as 2R,7R 10.1039/C39930000275

Reagents for carbonyl methylenation in organic synthesis 10.2174/1570179053545396

Alkylation and acylation of 5-phenylsulphonyl- and 5-cyanobutyrolactones 10.1016/S0040-4020(01)90365-5

Integrated catalysis opens new arylation pathways via regiodivergent enzymatic C–H activation 10.1038/ncomms11873

Rewiring Riboswitches to Create New Genetic Circuits in Bacteria 10.1016/bs.mie.2016.02.022

SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. 10.1042/BST20160009

Real-Time Monitoring of Enzyme-Catalysed Reactions using Deep UV Resonance Raman Spectroscopy 10.1002/chem.201701388

Development of Halogenase Enzymes for Use in Synthesis 10.1021/acs.chemrev.7b00032

RadH: A Versatile Halogenase for Integration into Synthetic Pathways 10.1002/anie.201706342

RadH: A Versatile Halogenase for Integration into Synthetic Pathways 10.1002/ange.201706342

From Multistep Enzyme Monitoring to Whole-Cell Biotransformations: Development of Real-Time Ultraviolet Resonance Raman Spectroscopy 10.1021/acs.analchem.7b03742

An Engineered Tryptophan Synthase Opens New Enzymatic Pathways to β-Methyltryptophan and Derivatives 10.1002/cbic.201600471

Recent advances in methyltransferase biocatalysis 10.1016/j.cbpa.2017.01.020

Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes 10.1039/c6ob01861k

Orthogonal Riboswitches for Tuneable Coexpression in Bacteria 10.1002/ange.201109106

Thermal Bifunctionality of Bacterial Phenylalanine Aminomutase and Ammonia Lyase Enzymes 10.1002/ange.201200669

Introduction of a Non-Natural Amino Acid into a Nonribosomal Peptide Antibiotic by Modification of Adenylation Domain Specificity 10.1002/ange.201202043

Orthogonal riboswitches as tools for controlling gene expression in bacteria 10.1135/css201112086

Structure-Guided Directed Evolution of Alkenyl and Arylmalonate Decarboxylases 10.1002/ange.200904112

Nucleic acid redesign and recognition: the pyrrolidine-amide oligonucleotide mimics (POMs) 10.1135/css200810206

SYNBIOCHEM Synthetic Biology Research Centre, Manchester - A UK foundry for fine and speciality chemicals production. 10.1016/j.synbio.2016.07.001

The cycloaspeptides: uncovering a new model for methylated nonribosomal peptide biosynthesis 10.1039/C8SC00717A

De novo Biosynthesis of “Non-Natural” Thaxtomin Phytotoxins 10.1002/anie.201801525

De novo Biosynthesis of “Non-Natural” Thaxtomin Phytotoxins 10.1002/ange.201801525

Structure and Biocatalytic Scope of Coclaurine N ‐Methyltransferase 10.1002/ange.201805060

Structure and Biocatalytic Scope of Coclaurine N-Methyltransferase 10.1002/anie.201805060

A vitamin K-dependent carboxylase orthologue is involved in antibiotic biosynthesis 10.1038/s41929-018-0178-2

Daptomycin NMR Structure 10.2210/pdb1xt7/pdb

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals 10.1038/s42003-018-0076-9

Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli 10.1371/journal.pbio.3000347

Streamlined recycling of S-adenosylmethionine 10.1038/s41929-019-0323-6

Engineering enzymatic assembly lines to produce new antibiotics 10.1016/j.mib.2019.10.007

Engineering Orthogonal Methyltransferases to Create Alternative Bioalkylation Pathways 10.1002/ange.202004963

Engineering Orthogonal Methyltransferases to Create Alternative Bioalkylation Pathways 10.1002/anie.202004963

Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol 10.1093/synbio/ysaa012

Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers 10.1016/j.ymben.2020.04.008

Editorial overview: Biocatalysis and biotransformations 10.1016/j.cbpa.2020.04.019

Harnessing and engineering amide bond forming ligases for the synthesis of amides 10.1016/j.cbpa.2019.12.004

Nicholas Rattray

Rattray Nicholas

ORCID: 0000-0002-3528-6905

https://pureportal.strath.ac.uk/en/persons/3e0c2ac1-5aa6-4ab5-93ca-5bca98e1608e

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals 10.1038/s42003-018-0076-9

Metabolomics guided pathway analysis reveals link between cancer metastasis, cholesterol sulfate, and phospholipids 10.1186/s40170-017-0171-2

Environmental influences in the etiology of colorectal cancer 10.1007/s40495-017-0088-z

Re-engineering and evaluation of anti-DNA autoantibody 3E10 for therapeutic applications 10.1016/j.bbrc.2018.01.139

Beyond genomics 10.1186/s40246-018-0134-x

Engineering the “missing link” in biosynthetic (−)-menthol production 10.1021/acscatal.7b04115

Yale School of Public Health Symposium on tissue imaging mass spectrometry 10.1186/s40246-018-0142-x

Analytical medicine 10.1038/528193c

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