Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
Víctor J. Carrión Juan Perez-Jaramillo Viviane Cordovez Vittorio Tracanna Mattias de Hollander Daniel Ruiz-Buck Lucas W. Mendes Wilfred F.J. van Ijcken Ruth Gomez-Exposito Somayah S. Elsayed Prarthana Mohanraju Adini Arifah John van der Oost Joseph N. Paulson Rodrigo Mendes Gilles P. van Wezel Marnix H. Medema Jos M. Raaijmakers
Science (New York, N.Y.), 2019-10
https://doi.org/10.1126/science.aaw9285
Lucas William Mendes
Mendes Lucas William / Mendes LW
ORCID: 0000-0003-0980-7006
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Pérez-Jaramillo Juan Esteban
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Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome 10.1126/science.aaw9285
Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis 10.1007/s00251-019-01142-9
CREPT Promotes Melanoma Progression Through Accelerated Proliferation and Enhanced Migration by RhoA-Mediated Actin Filaments and Focal Adhesion Formation 10.3390/cancers12010033
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Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases 10.1007/s00401-019-02109-6
Gliotoxin, identified from a screen of fungal metabolites, disrupts 7SK snRNP, releases P-TEFb and reverses HIV-1 latency 10.1101/848929
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Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform specific start-loss mutations of essential genes can cause genetic diseases 10.1101/799841
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The mouse KLF1 Nan variant impairs nuclear condensation and erythroid maturation 10.1371/journal.pone.0208659
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Identification of SPRY4 as a Novel Candidate Susceptibility Gene for Familial Nonmedullary Thyroid Cancer 10.1089/thy.2020.0290
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Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control 10.1101/gr.253211.119
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Induction of selective cell death in HIV-1-infected cells by DDX3 inhibitors leads to depletion of the inducible reservoir 10.1101/2020.08.26.266726
SPEN is Required for Xist Upregulation during Initiation of X Chromosome Inactivation 10.1101/2020.12.30.424676
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ACO2 homozygous missense mutation associated with complicated hereditary spastic paraplegia 10.1212/NXG.0000000000000223
Infantile hypertrophic pyloric stenosis in patients with esophageal atresia 10.1002/bdr2.1683
Differentially Methylated Regions in Desmoid-Type Fibromatosis: A Comparison Between CTNNB1 S45F and T41A Tumors 10.3389/fonc.2020.565031
Employed family-based genetic discovery combining linkage analysis and exome sequencing to identify RCL1 as a novel candidate gene for depression, with independent replication in a population-based cohort 10.1038/mp.2018.6
Epigenome analysis links gene regulatory elements in group 2 innate lymphocytes to asthma susceptibility 10.1016/j.jaci.2017.12.1006
Identification of Variants in RET and IHH Pathway Members in a Large Family With History of Hirschsprung Disease 10.1053/j.gastro.2018.03.034
Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness 10.1038/s41588-021-00888-x
Gliotoxin, identified from a screen of fungal metabolites, disrupts 7SK snRNP, releases P-TEFb, and reverses HIV-1 latency 10.1126/sciadv.aba6617
Steroid-resistant human inflammatory ILC2s are marked by CD45RO and elevated in type 2 respiratory diseases 10.1126/SCIIMMUNOL.ABD3489
The Bone-Forming Properties of Periosteum-Derived Cells Differ Between Harvest Sites 10.3389/fcell.2020.554984
Large-Scale Expansion of Human iPSC-Derived Skeletal Muscle Cells for Disease Modeling and Cell-Based Therapeutic Strategies 10.1016/j.stemcr.2018.04.002
Thyroid state regulates gene expression in human whole blood 10.1210/jc.2017-01144
Lewy pathology in Parkinson’s disease consists of a crowded organellar, membranous medley 10.1101/137976
Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus 10.1186/s13148-021-01134-1
Cystic renal-epithelial derived induced pluripotent stem cells from polycystic kidney disease patients 10.1002/sctm.18-0283
In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states 10.1038/s41556-020-0508-x
Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation 10.1093/hmg/ddaa141
Validation of a Combined Transcriptome and T Cell Receptor Alpha/Beta (TRA/TRB) Repertoire Assay at the Single Cell Level for Paucicellular Samples 10.3389/fimmu.2020.01999
Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb 10.1242/dev186338
MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome 10.1016/j.celrep.2020.107647
Orphan CpG islands boost the regulatory activity of poised enhancers and dictate the responsiveness of their target genes 10.1101/2020.08.05.237768
Nimbus: A design-driven analyses suite for amplicon-based NGS data 10.1093/bioinformatics/bty145
Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis 10.1101/2021.02.11.430889
Low Input Targeted Chromatin Capture (Low-T2C) 10.1007/978-1-0716-1597-3_9
High throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by Methylated DNA sequencing (MeD-seq) of LpnPI digested fragments 10.1101/2021.07.12.452012
Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb 10.1242/dev.184861
Victor J Carrion
Carrion Victor J / Carrion VJ
ORCID: 0000-0002-4093-0355
Characterisation of the mgo operon in Pseudomonas syringae pv. syringae UMAF0158 that is required for mangotoxin production 10.1186/1471-2180-12-10
Mangotoxin production of Pseudomonas syringae pv. syringae is regulated by MgoA 10.1186/1471-2180-14-46
Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits 10.1038/ismej.2017.85
Cellulose production in Pseudomonas syringae pv. Syringae: A compromise between epiphytic and pathogenic lifestyles 10.1093/femsec/fiv071
The wild side of plant microbiomes 10.1186/s40168-018-0519-z
The mangotoxin biosynthetic operon (mbo) is specifically distributed within Pseudomonas syringae genomospecies 1 and was acquired only once during evolution 10.1128/AEM.03007-12
The mbo operon is specific and essential for biosynthesis of mangotoxin in pseudomonas syringae 10.1371/journal.pone.0036709
Legacy of land use history determines reprogramming of plant physiology by soil microbiome 10.1038/s41396-018-0300-0
Bioinformatics analysis of the complete genome sequence of the mango tree pathogen Pseudomonas syringae pv. Syringae UMAF0158 reveals traits relevant to virulence and epiphytic lifestyle 10.1371/journal.pone.0136101
Recruitment and rearrangement of three different genetic determinants into a conjugative plasmid increase copper resistance in pseudomonas syringae 10.1128/AEM.02644-12
Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil 10.3389/fmicb.2015.01081
Screening and characterization of potentially suppressive soils against Gaeumannomyces graminis under extensive wheat cropping by Chilean indigenous communities 10.3389/fmicb.2017.01552
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides 10.1038/nmicrobiol.2016.197
Plant phenotypic and transcriptional changes induced by volatiles from the fungal root pathogen Rhizoctonia solani 10.3389/fpls.2017.01262
A Pseudomonas syringae diversity survey reveals a differentiated phylotype of the pathovar syringae associated with the mango host and mangotoxin production 10.1094/PHYTO-04-13-0093-R
Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils 10.1038/s41396-018-0186-x
Microbial community composition in take-All suppressive soils 10.3389/fmicb.2018.02198
darR and darS are regulatory genes that modulate 2-hexyl, 5-propyl resorcinol transcription in Pseudomonas chlororaphis PCL1606 10.1099/mic.0.082677-0
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome 10.1126/science.aaw9285
Atypical spirotetronate polyketides identified in the underexplored genus streptacidiphilus 10.1021/acs.joc.0c01210
A novel and conserved cell wall enzyme that can substitute for the Lipid II synthase MurG 10.1101/2020.10.12.336396
An alternative and conserved cell wall enzyme that can substitute for the lipid II synthase MurG 10.1128/mBio.03381-20
Mitigation of Pseudomonas syringae virulence by signal inactivation 10.1126/sciadv.abg2293
Jos Raaijmakers
Raaijmakers Jos
ORCID: 0000-0003-1608-6614
Involvement of the ABC transporter BcAtrB and the laccase BcLCC2 in defence of Botrytis cinerea against the broad-spectrum antibiotic 2,4-diacetylphloroglucinol 10.1111/j.1462-2920.2007.01531.x
Massetolide a biosynthesis in Pseudomonas fluorescens 10.1128/jb.01563-07
Characterization of CMR5c and CMR12a, novel fluorescent Pseudomonas strains from the cocoyam rhizosphere with biocontrol activity 10.1111/j.1365-2672.2007.03345.x
Cyclic lipopeptide surfactant production by Pseudomonas fluorescens SS101 is not required for suppression of complex Pythium spp. Populations 10.1094/phyto-97-10-1348
Diversity of cultivated endophytic bacteria from sugarcane: Genetic and biochemical characterization of Burkholderia cepacia complex isolates 10.1128/aem.01222-07
Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species 10.1111/j.1365-2958.2006.05525.x
Role of the cyclic lipopeptide massetolide A in biological control of Phytophthora infestans and in colonization of tomato plants by Pseudomonas fluorescens 10.1111/j.1469-8137.2007.02138.x
Special issue: New perspectives and approaches in 'plant growth-promoting rhizobacteria' research - Foreword 10.1007/s10658-007-9114-z
Cyclic lipopeptide production by plant-associated Pseudomonas spp.: Diversity, activity, biosynthesis, and regulation 10.1094/mpmi-19-0699
Assessment of genotypic diversity of antibiotic-producing Pseudomonas species in the rhizosphere by denaturing gradient gel electrophoresis 10.1128/aem.71.2.993-1003.2005
Effect of mixed and single crops on disease suppressiveness of soils 10.1094/phyto-95-1325
Effect of organic management of soils on suppressiveness to Gaeumannomyces graminis var. tritici and its antagonist, Pseudomonas fluorescens 10.1007/s10658-005-5402-7
Influence of plant species on population dynamics, genotypic diversity and antibiotic production in the rhizosphere by indigenous Pseudomonas spp 10.1016/j.femsec.2004.10.007
Defense responses of Fusarium oxysporum to 2,4-diacetylphloroglucinol, a broad-spectrum antibiotic produced by Pseudomonas fluorescens 10.1094/mpmi.2004.17.11.1201
Wheat cultivar-specific selection of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas species from resident soil populations 10.1007/s00248-003-1067-y
Biochemical, genetic, and zoosporicidal properties of cyclic lipopeptide surfactants produced by Pseudomonas fluorescens 10.1128/aem.69.12.7161-7172.2003
Effect of 2,4-diacetylphloroglucinol on Pythium: Cellular responses and variation in sensitivity among propagules and species 10.1094/phyto.2003.93.8.966
Frequency, diversity, and activity of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in Dutch take-all decline soils 10.1094/phyto.2003.93.1.54
Pathogen self-defense: Mechanisms to counteract microbial antagonism 10.1146/annurev.phyto.41.052002.095606
Polymorphisms within the prnD and pltC genes from pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp 10.1016/s0168-6496(02)00414-2
Antibiotic production by bacterial biocontrol agents 10.1023/a:1020501420831
Differential ability of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains to colonize the roots of pea plants 10.1128/aem.68.7.3226-3237.2002
Fungal ABC transporters and microbial interactions in natural environments 10.1094/mpmi.2002.15.11.1165
Microbial populations responsible for specific soil suppressiveness to plant pathogens 10.1146/annurev.phyto.40.030402.110010
Exploiting genotypic diversity of 2,4-diacetylphloroglucinol-producing Pseudomonas spp.: Characterization of superior root-colonizing P-fluorescens strain Q8r1-96 10.1128/aem.67.6.2545-2554.2001
Effect of population density of Pseudomonas fluorescens on production of 2,4-diacetylphloroglucinol in the rhizosphere of wheat 10.1094/phyto.1999.89.6.470
Natural plant protection by 2,4-diacetylphloroglucinol - Producing Pseudomonas spp. in take-all decline soils 10.1094/mpmi.1998.11.2.144
DISPERSAL OF WILD-TYPE AND GENETICALLY-MODIFIED PSEUDOMONAS SPP FROM TREATED SEEDS OR SOIL TO AERIAL PARTS OF RADISH PLANTS 10.1016/0038-0717(95)00065-m
DOSE-RESPONSE RELATIONSHIPS IN BIOLOGICAL-CONTROL OF FUSARIUM-WILT OF RADISH BY PSEUDOMONAS SPP 10.1094/Phyto-85-1075
UTILIZATION OF HETEROLOGOUS SIDEROPHORES AND RHIZOSPHERE COMPETENCE OF FLUORESCENT PSEUDOMONAS SPP 10.1139/m95-017
Challenges and opportunities in harnessing soil disease suppressiveness for sustainable pasture production 10.1016/j.soilbio.2015.12.006
Fungal invasion of the rhizosphere microbiome 10.1038/ismej.2015.82
Comparative genomics and metabolic profiling of the genus Lysobacter 10.1186/s12864-015-2191-z
Cross-kingdom similarities in microbiome functions 10.1038/ismej.2015.7
Diversity and Activity of Lysobacter Species from Disease Suppressive Soils 10.3389/fmicb.2015.01243
Diversity of Aquatic Pseudomonas Species and Their Activity against the Fish Pathogenic Oomycete Saprolegnia 10.1371/journal.pone.0136241
Gac-mediated changes in pyrroloquinoline quinone biosynthesis enhance the antimicrobial activity of Pseudomonas fluorescens SBW25 10.1111/1758-2229.12231
Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp SH-C52 for antimicrobial compounds 10.3389/fmicb.2015.00693
Investigations into the Biosynthesis, Regulation, and Self-Resistance of Toxoflavin in Pseudomonas protegens Pf-5 10.1002/cbic.201500247
Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP 10.1186/s12866-015-0367-y
Molecular and chemical dialogues in bacteria-protozoa interactions 10.1038/srep12837
Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds 10.1016/j.bbrc.2015.04.039
The Novel Lipopeptide Poaeamide of the Endophyte Pseudomonas poae RE star 1-1-14 Is Involved in Pathogen Suppression and Root Colonization 10.1094/MPMI-12-14-0406-R
The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis 10.1111/1751-7915.12190
Volatile affairs in microbial interactions 10.1038/ismej.2015.42
Biosynthetic genes and activity spectrum of antifungal polyynes from Collimonas fungivorans Ter331 10.1111/1462-2920.12440
Biosynthetic Origin of the Antibiotic Cyclocarbamate Brabantamide A (SB-253514) in Plant-Associated Pseudomonas 10.1002/cbic.201300527
Deciphering microbial landscapes of fish eggs to mitigate emerging diseases 10.1038/ismej.2014.44
Discovery of new regulatory genes of lipopeptide biosynthesis in Pseudomonas fluorescens 10.1111/1574-6968.12404
Impact of interspecific interactions on antimicrobial activity among soil bacteria 10.3389/fmicb.2014.00567
Mangotoxin production of Pseudomonas syringae pv. syringae is regulated by MgoA 10.1186/1471-2180-14-46
Unravelling the Microbiome of Eggs of the Endangered Sea Turtle Eretmochelys imbricata Identifies Bacteria with Activity against the Emerging Pathogen Fusarium falciforme 10.1371/journal.pone.0095206
Friend or foe: genetic and functional characterization of plant endophytic Pseudomonas aeruginosa 10.1111/1462-2920.12031
Going back to the roots: the microbial ecology of the rhizosphere 10.1038/nrmicro3109
The Gac regulon of Pseudomonas fluorescens SBW25 10.1111/1758-2229.12061
The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms 10.1111/1574-6976.12028
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions 10.1371/journal.pgen.1002784
Diversity and Natural Functions of Antibiotics Produced by Beneficial and Plant Pathogenic Bacteria 10.1146/annurev-phyto-081211-172908
Genetic and Phenotypic Diversity of Sclerotium rolfsii in Groundnut Fields in Central Vietnam 10.1094/pdis-06-11-0468
Identification of Traits Shared by Rhizosphere-Competent Strains of Fluorescent Pseudomonads 10.1007/s00248-012-0065-3
Involvement of phenazines and lipopeptides in interactions between Pseudomonas species and Sclerotium rolfsii, causal agent of stem rot disease on groundnut 10.1111/j.1365-2672.2011.05205.x
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Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria 10.1126/science.1203980
Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors 10.1038/ismej.2010.196
Diversity and Evolution of the Phenazine Biosynthesis Pathway 10.1128/aem.02009-09
Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics 10.1111/j.1574-6976.2010.00221.x
Cellular Responses of the Late Blight Pathogen Phytophthora infestans to Cyclic Lipopeptide Surfactants and Their Dependence on G Proteins 10.1128/aem.00241-09
Diversity and Functional Analysis of LuxR-Type Transcriptional Regulators of Cyclic Lipopeptide Biosynthesis in Pseudomonas fluorescens 10.1128/aem.00575-09
Functional, genetic and chemical characterization of biosurfactants produced by plant growth-promoting Pseudomonas putida 267 10.1111/j.1365-2672.2009.04244.x
Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt 10.1038/ismej.2009.33
Protozoan-Induced Regulation of Cyclic Lipopeptide Biosynthesis Is an Effective Predation Defense Mechanism for Pseudomonas fluorescens 10.1128/aem.01272-09
Regulation of Cyclic Lipopeptide Biosynthesis in Pseudomonas fluorescens by the ClpP Protease 10.1128/jb.01558-08
The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms 10.1007/s11104-008-9568-6
Diversity and activity of biosurfactant-producing Pseudomonas in the rhizosphere of black pepper in Vietnam 10.1111/j.1365-2672.2007.03618.x
Smelly Fumes: Volatile-Mediated Communication between Bacteria and Other Organisms 10.3389/fmicb.2016.02031
Lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms 10.1099/mic.0.000191
Ectomycorrhizal symbiosis affects functional diversity of rhizosphere fluorescent pseudomonads 10.1111/j.1469-8137.2004.01212.x
Soil immune responses 10.1126/science.aaf3252
Role of the GacS Sensor Kinase in the Regulation of Volatile Production by Plant Growth-Promoting Pseudomonas fluorescens SBW25 10.3389/fpls.2016.01706
Impact of plant domestication on rhizosphere microbiome assembly and functions 10.1007/s11103-015-0337-7
Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina 10.3390/ijms17010140
Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility 10.1111/1462-2920.13288
Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics 10.1038/ismej.2016.5
Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression 10.1111/ele.12567
Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore 10.1093/femsec/fix038
Potential for Biocontrol of Hairy Root Disease by a Paenibacillus Clade 10.3389/fmicb.2017.00447
Membrane Interactions of Natural Cyclic Lipodepsipeptides of the Viscosin Group 10.1016/j.bbamem.2016.12.013
Saving seed microbiomes 10.1038/s41396-017-0028-2
Smelly Fumes: Volatile-Mediated Communication between Bacteria and Other Organisms 10.3389/978-2-88945-222-4
Road MAPs to engineer host microbiomes 10.1016/j.mib.2017.11.023
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
Secondary Metabolism and Interspecific Competition Affect Accumulation of Spontaneous Mutants in the GacS-GacA Regulatory System in Pseudomonas protegens 10.1128/mbio.01845-17
Modulation of plant chemistry by beneficial root microbiota 10.1039/C7NP00057J
Embracing Community Ecology in Plant Microbiome Research 10.1016/j.tplants.2018.03.013
Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region 10.3389/fmicb.2018.00568
Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils 10.1038/s41396-018-0186-x
Healthy scents: microbial volatiles as new frontier in antibiotic research? 10.1016/j.mib.2018.02.011
Impact of Pseudomonas H6 surfactant on all external life cycle stages of the fish parasitic ciliate Ichthyophthirius multifiliis. 10.1111/jfd.12810
Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. 10.1111/nph.15036
Exploring fish microbial communities to mitigate emerging diseases in aquaculture. 10.1093/femsec/fix161
Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils. 10.3389/fmicb.2017.02529
Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens. 10.1111/1462-2920.13927
Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. 10.1038/ismej.2017.158
Plant Phenotypic and Transcriptional Changes Induced by Volatiles from the Fungal Root Pathogen Rhizoctonia solani. 10.3389/fpls.2017.01262
Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. 10.1038/ismej.2017.85
Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil 10.3389/fmicb.2015.01081
Wave-like distribution patterns of gfp-marked Pseudomonas fluorescens along roots of wheat plants grown in two soils. 10.1007/s00248-007-9292-4
Conservation of the response regulator gene gacA in Pseudomonas species. 10.1111/j.1462-2920.2003.00438.x
Genotypic and phenotypic diversity of phlD-containing Pseudomonas strains isolated from the rhizosphere of wheat. 10.1128/aem.66.5.1939-1946.2000
Polymerase chain reaction for verification of fluorescent colonies of Erwinia chrysanthemi and Pseudomonas putida WCS358 in immunofluorescence colony staining. 10.1111/j.1365-2672.1995.tb03178.x
Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces 10.1101/450833
The Minimal Rhizosphere Microbiome 10.1007/978-3-319-08575-3_43
Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation 10.3389/fmicb.2018.01636
The wild side of plant microbiomes 10.1186/s40168-018-0519-z
Linking ecology and plant pathology to unravel the importance of soil-borne fungal pathogens in species-rich grasslands 10.1007/s10658-018-1573-x
Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean 10.1038/s41396-018-0234-6
Volatiles of pathogenic and non-pathogenic soil-borne fungi affect plant development and resistance to insects 10.1007/s00442-019-04433-w
Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity 10.1101/222844
Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome. 10.3389/fmicb.2019.02252
Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. 10.1186/s40168-019-0727-1
Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness 10.1016/j.soilbio.2019.05.020
Ecology and Evolution of Plant Microbiomes. 10.1146/annurev-micro-090817-062524
Priming of Plant Growth Promotion by Volatiles of Root-Associated Microbacterium spp. 10.1128/AEM.01865-18
Erratum: Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. 10.1038/nmicrobiol.2017.10
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. 10.1038/nmicrobiol.2016.197
Minimum Information about a Biosynthetic Gene cluster. 10.1038/nchembio.1890
Isolation, characterization and comparative analysis of plant-associated bacteria for suppression of soil-borne diseases of field-grown groundnut in Vietnam 10.1016/j.biocontrol.2018.03.014
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome 10.1126/science.aaw9285
Harnessing the microbiome to control plant parasitic weeds 10.1016/j.mib.2019.09.006
Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat 10.1098/rspb.2019.2527
No evidence of modulation of indirect plant resistance of Brassica rapa plants by volatiles from soil‐borne fungi 10.1111/een.12906
Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species 10.1038/s41396-019-0537-2
Fungal volatiles influence plant defence against above‐ground and below‐ground herbivory 10.1111/1365-2435.13633
Volatiles from soil‐borne fungi affect directional growth of roots 10.1111/pce.13890
Volatiles from the fungus Fusarium oxysporum affect interactions of Brassica rapa plants with root herbivores 10.1111/een.12956
Plant-soil feedback effects on growth, defense and susceptibility to a soil-borne disease in a cut flower crop: species and functional group effects 10.3389/fpls.2017.02127
Optimizing Biocontrol Activity of Paenibacillus xylanexedens for Management of Hairy Root Disease in Tomato Grown in Hydroponic Greenhouses 10.3390/agronomy11050817
The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots 10.3390/metabo11060357
Molecular Detection and Quantification of the Striga Seedbank in Ethiopian Sorghum Field Soils 10.21203/rs.3.rs-572695/v1
Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10× metagenomics 10.1128/mSystems.01116-20
Disentangling soil microbiome functions by perturbation 10.1111/1758-2229.12989
Adini Qisthi Arifah
Arifah Adini Qisthi / Adini Q Arifah
ORCID: 0000-0002-9283-9713
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. 10.1126/science.aaw9285
SIBR-Cas enables host-independent and universal CRISPR genome engineering in bacteria 10.1101/2021.04.26.441145
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
Summary of the Sussex-Huawei locomotion-transportation recognition challenge
Observation of a manifold in the chaotic phase space of an asymmetric optical microcavity
Localized temporal variation of Earth's inner-core boundary from high-quality waveform doublets
Off-axis multi-wavelength dispersion controlling metalens for multi-color imaging
Impact of United States political sanctions on international collaborations and research in Iran