RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
Alexander M. Kloosterman Kyle E. Shelton Gilles P. van Wezel Marnix H. Medema Douglas A. Mitchell Marcelino Gutierrez
mSystems, 2020-10-27
Gilles van Wezel
van Wezel Gilles
ORCID: 0000-0003-0341-1561
Off the wall 10.7554/elife.05427
Novel Aspects of Signaling in Streptomyces Development 10.1016/s0065-2164(04)56002-1
Morphogenesis of Streptomyces in Submerged Cultures 10.1016/b978-0-12-800259-9.00001-9
Structured morphological modeling as a framework for rational strain design of Streptomyces species 10.1007/s10482-012-9760-9
Constitutive expression of ftsZ overrides the whi developmental genes to initiate sporulation of Streptomyces coelicolor 10.1007/s10482-011-9678-7
The evolution of actinomycetes: papers from the 16th International Symposium on the Biology of Actinomycetes 10.1007/s10482-012-9805-0
The SsgA-like proteins in actinomycetes: small proteins up to a big task 10.1007/s10482-008-9225-3
The tmRNA-tagging mechanism and the control of gene expression: a review 10.1002/wrna.48
The regulation of the secondary metabolism of Streptomyces: new links and experimental advances 10.1039/c1np00003a
The tylosin resistance gene tlrB of Streptomyces fradiae encodes a methyltransferase that targets G748 in 23S rRNA 10.1046/j.1365-2958.2000.02046.x
Cell division and DNA segregation in Streptomyces: how to build a septum in the middle of nowhere? 10.1111/j.1365-2958.2012.08107.x
Triggers and cues that activate antibiotic production by actinomycetes 10.1007/s10295-013-1309-z
Altered desferrioxamine-mediated iron utilization is a common trait of bald mutants of Streptomyces coelicolor 10.1039/c4mt00068d
Single particle tracking of dynamically localizing TatA complexes in Streptomyces coelicolor 10.1016/j.bbrc.2013.07.016
A novel plasmid vector that uses the glucose kinase gene (glkA) for the positive selection of stable gene disruptants in Streptomyces 10.1016/s0378-1119(96)00563-x
Chemical, structural and biological studies of cis-[Pt(3-Acpy)2Cl2] 10.1016/j.jinorgbio.2009.06.009
Phenanthroline Derivatives with Improved Selectivity as DNA-Targeting Anticancer or Antimicrobial Drugs 10.1002/cmdc.200800097
Imaging of Streptomyces coelicolor A3(2) with Reduced Autofluorescence Reveals a Novel Stage of FtsZ Localization 10.1371/journal.pone.0004242
Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies 10.1038/nrmicro3178
Correlative Cryo-Fluorescence Light Microscopy and Cryo-Electron Tomography of Streptomyces 10.1016/b978-0-12-801075-4.00010-0
Relative quantification of proteasome activity by activity-based protein profiling and LC-MS/MS 10.1038/nprot.2013.065
Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees 10.1007/s10482-014-0139-y
A novel function of Streptomyces integration host factor (sIHF) in the control of antibiotic production and sporulation in Streptomyces coelicolor 10.1007/s10482-011-9657-z
Analysis of novel kitasatosporae reveals significant evolutionary changes in conserved developmental genes between Kitasatospora and Streptomyces 10.1007/s10482-014-0209-1
Identification and isolation of lantibiotics from culture: a bioorthogonal chemistry approach 10.1039/c2ob26050f
Structure, cytotoxicity, and DNA-cleavage properties of the complex [CuII(pbt)Br2] 10.1021/ic702306f
Analysis of two distinct mycelial populations in liquid-grown Streptomyces cultures using a flow cytometry-based proteomics approach 10.1007/s00253-012-4490-5
The permease gene nagE2 is the key to N-acetylglucosamine sensing and utilization in Streptomyces coelicolor and is subject to multi-level control 10.1111/j.1365-2958.2009.07020.x
Platinum(II) compounds with chelating ligands based on pyridine and pyrimidine: DNA and protein binding studies 10.1016/j.jinorgbio.2009.07.003
DNA cleavage and antitumour activity of platinum(II) and copper(II) compounds derived from 4-methyl-2-N-(2-pyridylmethyl)aminophenol: spectroscopic, electrochemical and biological investigation 10.1039/b911542k
The square-planar cytotoxic [CuII(pyrimol)Cl] complex acts as an efficient DNA cleaver without reductant 10.1021/ja056970+
Transcription of the sporulation gene ssgA is activated by the IcIR-type regulator SsgR in a whi-independent manner in Streptomyces A3(2) 10.1111/j.1365-2958.2004.04186.x
Loss of the controlled localization of growth stage-specific cell-wall synthesis pleiotropically affects developmental gene expression in an ssgA mutant of Streptomyces coelicolor 10.1111/j.1365-2958.2007.05732.x
MreB of Streptomyces coelicolor is not essential for vegetative growth but is required for the integrity of aerial hyphae and spores 10.1111/j.1365-2958.2006.05134.x
Substrate induction and glucose repression of maltose utilization by Streptomyces coelicolor A3(2) is controlled by malR, a member of the lacI-galR family of regulatory genes 10.1046/j.1365-2958.1997.d01-1878.x
Cloning and sequencing of the tuf genes of Streptomyces coelicolor A3(2) 10.1016/0167-4781(94)90085-x
Unsuspected control of siderophore production by N-acetylglucosamine in streptomycetes 10.1111/j.1758-2229.2012.00354.x
SsgA-like proteins determine the fate of peptidoglycan during sporulation of Streptomyces coelicolor 10.1111/j.1365-2958.2005.04883.x
Identification of glucose kinase-dependent and -independent pathways for carbon control of primary metabolism, development and antibiotic production in Streptomyces coelicolor by quantitative proteomics 10.1111/mmi.12072
Unique Ligand-Based Oxidative DNA Cleavage by Zinc(II) Complexes of Hpyramol and Hpyrimol 10.1002/chem.200601525
Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence 10.1038/srep01109
A new piece of an old jigsaw: Glucose kinase is activated posttranslationally in a glucose transport-dependent manner in Streptomyces coelicolor A3(2) 10.1159/000096461
Natural Product Proteomining, a Quantitative Proteomics Platform, Allows Rapid Discovery of Biosynthetic Gene Clusters for Different Classes of Natural Products 10.1016/j.chembiol.2014.03.011
Conserved cis-acting elements upstream of genes composing the chitinolytic system of streptomycetes are DasR-responsive elements 10.1159/000096460
Structure and DNA cleavage properties of two copper(ii) complexes of the pyridine-pyrazole-containing ligands mbpzbpy and Hmpzbpya 10.1039/b704390b
PREDetector: A new tool to identify regulatory elements in bacterial genomes 10.1016/j.bbrc.2007.03.180
From dormant to germinating spores of Streptomyces coelicolor A3(2): New perspectives from the crp null mutant 10.1021/pr050155b
Transfer–messenger RNA controls the translation of cell-cycle and stress proteins in Streptomyces 10.1038/embor.2009.255
Chapter 5 Applying the Genetics of Secondary Metabolism in Model Actinomycetes to the Discovery of New Antibiotics 10.1016/s0076-6879(09)04805-8
Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces 10.1038/embor.2008.83
Engineering of N-acetylglucosamine metabolism for improved antibiotic production in Streptomyces coelicolor A3(2) and an unsuspected role of NagA in glucosamine metabolism 10.4161/bioe.21371
Structure of an MmyB-Like Regulator from C. aurantiacus, Member of a New Transcription Factor Family Linked to Antibiotic Metabolism in Actinomycetes 10.1371/journal.pone.0041359
The Streptomyces coelicolor ssgB gene is required for early stages of sporulation 10.1016/s0378-1097(03)00481-6
Objective comparison of particle tracking methods 10.1038/nmeth.2808
A comparative study of the ribosomal RNA operons of Streptomyces coelicolor A3(2) and sequence analysis of rrnA 10.1093/nar/19.16.4399
Dynamic Localization of Tat Protein Transport Machinery Components in Streptomyces coelicolor 10.1128/jb.01425-12
Positive control of cell division: FtsZ is recruited by SsgB during sporulation of Streptomyces 10.1101/gad.600211
ssgA Is Essential for Sporulation of Streptomyces coelicolor A3(2) and Affects Hyphal Development by Stimulating Septum Formation 10.1128/jb.182.20.5653-5662.2000
Unlocking Streptomyces spp. for Use as Sustainable Industrial Production Platforms by Morphological Engineering 10.1128/aem.01853-06
Elongation Factor Tu3 (EF-Tu3) from the Kirromycin Producer Streptomyces ramocissimus Is Resistant to Three Classes of EF-Tu-Specific Inhibitors 10.1128/jb.01810-06
The chitobiose-binding protein, DasA, acts as a link between chitin utilization and morphogenesis in Streptomyces coelicolor 10.1099/mic.0.2007/011940-0
The Secreted Signaling Protein Factor C Triggers the A-factor Response Regulon in Streptomyces griseus: Overlapping Signaling Routes 10.1074/mcp.m600367-mcp200
Functional Analysis of the N-Acetylglucosamine Metabolic Genes of Streptomyces coelicolor and Role in Control of Development and Antibiotic Production 10.1128/jb.06370-11
The tuf3 gene of Streptomyces coelicolor A3(2) encodes an inessential elongation factor Tu that is apparently subject to positive stringent control 10.1099/13500872-141-10-2519
Lack of A-factor Production Induces the Expression of Nutrient Scavenging and Stress-related Proteins in Streptomyces griseus 10.1074/mcp.m900194-mcp200
Three tuf-like genes in the kirromycin producer Streptomyces ramocissimus 10.1099/00221287-140-4-983
The malEFG gene cluster of Streptomyces coelicolor A3(2): characterization, disruption and transcriptional analysis 10.1007/s004380050458
The ROK Family Regulator Rok7B7 Pleiotropically Affects Xylose Utilization, Carbon Catabolite Repression, and Antibiotic Production in Streptomyces coelicolor 10.1128/jb.02191-12
Unlocking Streptomyces spp. for Use as Sustainable Industrial Production Platforms by Morphological Engineering 10.1128/aem.00808-06
Developmental Regulation of the Streptomyces lividans ram Genes: Involvement of RamR in Regulation of the ramCSAB Operon 10.1128/jb.184.16.4420-4429.2002
The Genome Sequence of Streptomyces lividans 66 Reveals a Novel tRNA-Dependent Peptide Biosynthetic System within a Metal-Related Genomic Island 10.1093/gbe/evt082
The sugar phosphotransferase system of Streptomyces coelicolor is regulated by the GntR-family regulator DasR and links N-acetylglucosamine metabolism to the control of development 10.1111/j.1365-2958.2006.05319.x
Metabolomics in the natural products field - a gateway to novel antibiotics 10.1016/j.ddtec.2015.01.004
A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing 10.1111/mmi.12810
Eliciting antibiotics active against the ESKAPE pathogens in a collection of actinomycetes isolated from mountain soils 10.1099/mic.0.078295-0
Multidimensional view of the bacterial cytoskeleton 10.1128/JB.02194-12
Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes 10.1074/jbc.M109.018564
Characterization of the sporulation control protein SsgA by use of an efficient method to create and screen random mutant libraries in streptoniycetes 10.1128/AEM.02755-06
GlcP constitutes the major glucose of uptake system of Streptomyces coelicolor A3(2) 10.1111/j.1365-2958.2004.04413.x
Glucose kinase of Streptomyces coelicolor A3(2): Large-scale purification and biochemical analysis 10.1023/A:1010234916745
Transcriptional and functional analysis of the gene for factor C, an extracellular signal protein involved in cytodifferentiation of Streptomyces griseus 10.1023/A:1010221407340
Effects of increased and deregulated expression of cell division genes on the morphology and on antibiotic production of Streptomycetes 10.1023/A:1010267708249
Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation. 10.1038/srep10868
Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets. 10.1371/journal.pone.0122479
A novel locus for mycelial aggregation forms a gateway to improved Streptomyces cell factories. 10.1186/s12934-015-0224-6
Identification of novel endophenaside antibiotics produced by Kitasatospora sp. MBT66 10.1038/ja.2015.14
A novel taxonomic marker that discriminates between morphologically complex actinomycetes. 10.1098/rsob.130073
Transcriptional analysis of the cell division-related ssg genes in Streptomyces coelicolor reveals direct control of ssgR by AtrA. 10.1007/s10482-015-0479-2
Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2) 10.1016/j.bbrc.2016.12.183
Discovery of C-Glycosylpyranonaphthoquinones in Streptomyces sp. MBT76 by a Combined NMR-Based Metabolomics and Bioinformatics Workflow 10.1021/acs.jnatprod.6b00478
Genome Sequence of the Filamentous Actinomycete Kitasatospora viridifaciens 10.1128/genomeA.01560-16
Aromatic Polyketide GTRI-02 is a Previously Unidentified Product of the act Gene Cluster in Streptomyces coelicolor A3(2) 10.1002/cbic.201700107
Morphology-driven downscaling of Streptomyces lividans to micro-cultivation 10.1101/159509
SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures 10.1101/159475
Intertwined Precursor Supply during Biosynthesis of the Catecholate–Hydroxamate Siderophores Qinichelins in Streptomyces sp. MBT76 10.1021/acschembio.7b00597
Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity 10.1101/222844
Substrate Inhibition of VanA by d -Alanine Reduces Vancomycin Resistance in a VanX-Dependent Manner 10.1128/AAC.00276-16
Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity 10.1007/s10482-018-1014-z
Healthy scents: microbial volatiles as new frontier in antibiotic research? 10.1016/j.mib.2018.02.011
Classification of the gifted natural product producer Streptomyces roseofaciens sp. nov. by polyphasic taxonomy 10.1101/310888
Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline 10.1002/pmic.201700332
Complete Genome Sequence of Escherichia coli AS19, an Antibiotic-Sensitive Variant of E. coli Strain B REL606 10.1128/genomeA.00385-18
Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era 10.1039/C8NP00012C
Sporulation-specific cell division defects in ylmE mutants of Streptomyces coelicolor are rescued by additional deletion of ylmD 10.1038/s41598-018-25782-1
High-Resolution Analysis of the Peptidoglycan Composition in Streptomyces coelicolor 10.1128/JB.00290-18
Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces 10.1101/450833
Cross-membranes orchestrate compartmentalization and morphogenesis in Streptomyces 10.1038/ncomms11836
Stress-induced formation of cell wall-deficient cells in filamentous actinomycetes 10.1038/s41467-018-07560-9
Discovery of Novel Glycerolated Quinazolinones from Streptomyces sp. MBT27 10.1101/484535
Lugdunomycin, an Angucycline‐Derived Molecule with Unprecedented Chemical Architecture 10.1002/anie.201814581
Lugdunomycin, an Angucycline‐Derived Molecule with Unprecedented Chemical Architecture 10.1002/ange.201814581
Discovery of novel glycerolated quinazolinones from Streptomyces sp. MBT27 10.1007/s10295-019-02140-2
Bagremycin Antibiotics and Ferroverdin iron-chelators are synthetized by the Same Gene Cluster 10.1101/631242
Phylogenomic analyses and distribution of terpene synthases among Streptomyces 10.3762/bjoc.15.115
Antibiotic production in Streptomyces is organized by a division of labour through terminal genomic differentiation 10.1101/560136
Teichoic acids anchor distinct cell wall lamellae in an apically growing bacterium 10.1101/714758
A Single Biosynthetic Gene Cluster Is Responsible for the Production of Bagremycin Antibiotics and Ferroverdin Iron Chelators 10.1128/mBio.01230-19
Spatial structure increases the benefits of antibiotic production in Streptomyces * 10.1111/evo.13817
A microbial expression system for high-level production of scFv HIV-neutralizing antibody fragments in Escherichia coli 10.1007/s00253-019-10145-1
Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species 10.1038/s41396-019-0537-2
Longitudinal cell division is associated with single mutations in the FtsZ-recruiting SsgB in Streptomyces 10.1101/860916
Antibiotic production in Streptomyces is organized by a division of labor through terminal genomic differentiation 10.1126/sciadv.aay5781
Competition sensing alters antibiotic production in Streptomyces 10.1101/2020.01.24.918557
Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production 10.1101/796722
RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery 10.1101/2020.03.14.992123
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
Teichoic acids anchor distinct cell wall lamellae in an apically growing bacterium 10.1038/s42003-020-1038-6
Glycosylated cyclophellitol-derived activity-based probes and inhibitors for cellulases 10.1039/D0CB00045K
Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus 10.1021/acs.joc.0c01210
Iso ‐maleimycin, a Constitutional Isomer of Maleimycin, from Streptomyces sp. QL37 10.1002/ejoc.202000767
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery 10.1128/mSystems.00267-20
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production 10.1016/j.isci.2020.101525
A novel and conserved cell wall enzyme that can substitute for the Lipid II synthase MurG 10.1101/2020.10.12.336396
Prodiginines Postpone the Onset of Sporulation in Streptomyces coelicolor 10.3390/antibiotics9120847
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides 10.1371/journal.pbio.3001026
Branching of sporogenic aerial hyphae in sflA and sflB mutants of Streptomyces coelicolor correlates to ectopic localization of DivIVA and FtsZ in time and space 10.1101/2020.12.26.424426
Omics-based strategies to discover novel classes of RiPP natural products 10.1016/j.copbio.2020.12.008
The nucleoid-associated protein Gbn binds to GATC sequences and affects sporulation and antibiotic production in Streptomyces 10.1101/2021.02.06.430045
Competition Sensing Changes Antibiotic Production in Streptomyces 10.1128/mBio.02729-20
Ectopic positioning of the cell division plane is associated with single amino acid substitutions in the FtsZ-recruiting SsgB in Streptomyces 10.1098/rsob.200409
An Alternative and Conserved Cell Wall Enzyme That Can Substitute for the Lipid II Synthase MurG 10.1128/mBio.03381-20
A novel function of Streptomyces integration host factor (sIHF) in the control of antibiotic production and sporulation in Streptomyces coelicolor http://dx.doi.org/10.1007/s10482-011-9657-z
A novel plasmid vector that uses the glucose kinase gene (glkA) for the positive selection of stable gene disruptants in Streptomyces http://dx.doi.org/10.1016/s0378-1119(96)00563-x
ChemInform Abstract: The Regulation of the Secondary Metabolism of Streptomyces: New Links and Experimental Advances http://dx.doi.org/10.1002/chin.201142269
Chemical, structural and biological studies of cis-[Pt(3-Acpy)2Cl2] http://dx.doi.org/10.1016/j.jinorgbio.2009.06.009
Constitutive expression of ftsZ overrides the whi developmental genes to initiate sporulation of Streptomyces coelicolor http://dx.doi.org/10.1007/s10482-011-9678-7
Control of cell division in Streptomyces http://dx.doi.org/10.1111/j.1365-2958.2012.08107.x
Imaging of Streptomyces coelicolor A3(2) with Reduced Autofluorescence Reveals a Novel Stage of FtsZ Localization http://dx.doi.org/10.1371/journal.pone.0004242
Phenanthroline Derivatives with Improved Selectivity as DNA-Targeting Anticancer or Antimicrobial Drugs http://dx.doi.org/10.1002/cmdc.200800097
Relative quantification of proteasome activity by activity-based protein profiling and LC-MS/MS http://dx.doi.org/10.1038/nprot.2013.065
Structured morphological modeling as a framework for rational strain design of Streptomyces species http://dx.doi.org/10.1007/s10482-012-9760-9
The SsgA-like proteins in actinomycetes: small proteins up to a big task http://dx.doi.org/10.1007/s10482-008-9225-3
The regulation of the secondary metabolism of Streptomyces: new links and experimental advances http://dx.doi.org/10.1039/c1np00003a
The tmRNA-tagging mechanism and the control of gene expression: a review http://dx.doi.org/10.1002/wrna.48
The tylosin resistance gene tlrB of Streptomyces fradiae encodes a methyltransferase that targets G748 in 23S rRNA http://dx.doi.org/10.1046/j.1365-2958.2000.02046.x
antiSMASH 6.0: improving cluster detection and comparison capabilities 10.1093/nar/gkab335
Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics 10.1128/mSystems.01116-20
Adrenaline-mediated activation of antibiotic production in Streptomyces highlights catechol as elicitor of specialized metabolism 10.21203/rs.3.rs-715051/v1
Marnix H. Medema
Medema Marnix H.
ORCID: 0000-0002-2191-2821
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