MS/MS networking guided analysis of molecule and gene cluster families
Nguyen, D.D. Wu, C.-H. Moree, W.J. Lamsa, A. Medema, M.H. Zhao, X. Gavilan, R.G. Aparicio, M. Atencio, L. Jackson, C. Ballesteros, J. Sanchez, J. Watrous, J.D. Phelan, V.V. Van De Wiel, C. Kersten, R.D. Mehnaz, S. De Mot, R. Shank, E.A. Charusanti, P. Nagarajan, H. Duggan, B.M. Moore, B.S. Bandeira, N. Palsson, B.Ø. Pogliano, K. Gutieŕrez, M. Dorrestein, P.C.
Bradley Moore
Moore Bradley
ORCID: 0000-0002-4652-1253
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Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse 10.1021/acs.chemrev.6b00571
PCR-Independent Method of Transformation-Associated Recombination Reveals the Cosmomycin Biosynthetic Gene Cluster in an Ocean Streptomycete 10.1021/acs.jnatprod.6b01121
Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols 10.1021/acs.jnatprod.6b00722
Minimization of the Thiolactomycin Biosynthetic Pathway Reveals that the Cytochrome P450 Enzyme TlmF Is Required for Five-Membered Thiolactone Ring Formation 10.1002/cbic.201700090
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A unifying paradigm for naphthoquinone-based meroterpenoid (bio)synthesis 10.1038/nchem.2829
Function-related replacement of bacterial siderophore pathways 10.1038/ismej.2017.137
Enzymatic C−H Oxidation-Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity 10.1002/ange.201705239
Enzymatic C−H Oxidation-Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity 10.1002/anie.201705239
Asymmetric Alkene and Arene Halofunctionalization Reactions in Meroterpenoid Biosynthesis 10.1055/s-0036-1590919
Isolation and structure elucidation of lipopeptide antibiotic taromycin B from the activated taromycin biosynthetic gene cluster 10.1038/ja.2017.146
Biosynthesis of the Antibiotic Bicyclomycin in Soil and Pathogenic Bacteria 10.1021/acs.biochem.7b01204
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Editorial: Are natural products the solution to antimicrobial resistance? 10.1039/c7np90026k
Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. 10.1038/nchembio.2330
Erratum: Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. 10.1038/nmicrobiol.2017.10
Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities. 10.1128/aem.02676-16
Family-wide Structural Characterization and Genomic Comparisons Decode the Diversity-oriented Biosynthesis of Thalassospiramides by Marine Proteobacteria. 10.1074/jbc.m116.756858
Biosynthetic Pathway Connects Cryptic Ribosomally Synthesized Posttranslationally Modified Peptide Genes with Pyrroloquinoline Alkaloids. 10.1016/j.chembiol.2016.10.009
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. 10.1038/nmicrobiol.2016.197
Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters. 10.1099/mic.0.000386
Enzymatic Reductive Dehalogenation Controls the Biosynthesis of Marine Bacterial Pyrroles. 10.1021/jacs.6b08512
Divergent biosynthesis yields a cytotoxic aminomalonate-containing precolibactin. 10.1038/nchembio.2157
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. 10.1038/nbt.3597
Biosynthesis of coral settlement cue tetrabromopyrrole in marine bacteria by a uniquely adapted brominase-thioesterase enzyme pair. 10.1073/pnas.1519695113
A Bacterial Quorum-Sensing Precursor Induces Mortality in the Marine Coccolithophore, Emiliania huxleyi. 10.3389/fmicb.2016.00059
Unusual flavoenzyme catalysis in marine bacteria. 10.1016/j.cbpa.2016.01.001
Recent advances in the biosynthesis of unusual polyketide synthase substrates. 10.1039/c5np00112a
A Peptidyl-Transesterifying Type I Thioesterase in Salinamide Biosynthesis. 10.1002/anie.201508576
Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining. 10.1021/acschembio.5b00658
Erratum: Reinvigorating natural product combinatorial biosynthesis with synthetic biology. 10.1038/nchembio1115-887a
Chemoenzymatic Synthesis of Acyl Coenzyme A Substrates Enables in Situ Labeling of Small Molecules and Proteins. 10.1021/acs.orglett.5b02113
Reinvigorating natural product combinatorial biosynthesis with synthetic biology. 10.1038/nchembio.1893
Minimum Information about a Biosynthetic Gene cluster. 10.1038/nchembio.1890
Biochemical Establishment and Characterization of EncM's Flavin-N5-oxide Cofactor. 10.1021/jacs.5b03983
Microbial and biochemical basis of a Fusarium wilt-suppressive soil. 10.1038/ismej.2015.95
Salinipyrone and Pacificanone Are Biosynthetic By-products of the Rosamicin Polyketide Synthase. 10.1002/cbic.201500177
The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery. 10.1039/c4np00167b
Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. 10.1016/j.chembiol.2015.03.010
Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis. 10.1038/srep09383
Mechanism of action of thalassospiramides, a new class of calpain inhibitors. 10.1038/srep08783
Special issue in honor of William Fenical, a pioneer in marine natural products discovery and drug development. 10.1021/acs.jnatprod.5b00146
Digging for biosynthetic dark matter. 10.7554/elife.06453
Complexity of naturally produced polybrominated diphenyl ethers revealed via mass spectrometry. 10.1021/es505440j
Sioxanthin, a novel glycosylated carotenoid, reveals an unusual subclustered biosynthetic pathway. 10.1111/1462-2920.12669
Direct capture and heterologous expression of Salinispora natural product genes for the biosynthesis of enterocin. 10.1021/np500664q
Correction to “Merochlorins A-D, cyclic meroterpenoid antibiotics biosynthesized in divergent pathways with vanadium-dependent chloroperoxidases”. 10.1021/ja509209d
Characterization of an orphan diterpenoid biosynthetic operon from Salinispora arenicola. 10.1021/np500422d
Targeted capture and heterologous expression of the Pseudoalteromonas alterochromide gene cluster in Escherichia coli represents a promising natural product exploratory platform. 10.1021/sb500280q
A multitasking vanadium-dependent chloroperoxidase as an inspiration for the chemical synthesis of the merochlorins. 10.1002/anie.201405696
One-pot enzymatic synthesis of merochlorin A and B. 10.1002/anie.201405694
NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. 10.1021/np500370c
Fungal polyketide engineering comes of age. 10.1073/pnas.1412946111
Enzymatic synthesis of polybrominated dioxins from the marine environment. 10.1021/cb5004338
Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. 10.1038/nchembio.1564
Enzyme inhibition by hydroamination: design and mechanism of a hybrid carmaphycin-syringolin enone proteasome inhibitor. 10.1016/j.chembiol.2014.04.010
Automated genome mining of ribosomal peptide natural products. 10.1021/cb500199h
Antileukemic activity and mechanism of drug resistance to the marine Salinispora tropica proteasome inhibitor salinosporamide A (Marizomib). 10.1124/mol.114.092114
Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. 10.1073/pnas.1319584111
Biosynthesis: Non-stick natural products. 10.1038/nchem.1828
Flavin-linked oxidase catalyzes pyrrolizine formation of dichloropyrrole-containing polyketide extender unit in chlorizidine A. 10.1021/ja409520v
Genetic basis for the biosynthesis of the pharmaceutically important class of epoxyketone proteasome inhibitors. 10.1021/cb400699p
Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules. 10.1073/pnas.1315492110
Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement. 10.1038/nature12643
MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus. 10.1038/ja.2013.99
Challenges and triumphs to genomics-based natural product discovery. 10.1007/s10295-013-1353-8
Predictive model for epoxide hydrolase-generated stereochemistry in the biosynthesis of nine-membered enediyne antitumor antibiotics. 10.1021/bi400572a
MS/MS networking guided analysis of molecule and gene cluster families. 10.1073/pnas.1303471110
A tandem chemoenzymatic methylation by S-adenosyl-L-methionine. 10.1002/cbic.201300221
Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica. 10.1002/cbic.201300147
Structures and comparative characterization of biosynthetic gene clusters for cyanosporasides, enediyne-derived natural products from marine actinomycetes. 10.1021/ja311065v
Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria. 10.1021/ja3119674
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. 10.1039/c2np20085f
Designed biosynthesis of 36-methyl-FK506 by polyketide precursor pathway engineering. 10.1021/sb3001062
Molecular mechanisms of acquired proteasome inhibitor resistance. 10.1021/jm300434z
Mechanistic studies on CymD: a tryptophan reverse N-prenyltransferase. 10.1021/bi3009054
Pyran formation by an atypical CYP-mediated four-electron oxygenation-cyclization cascade in an engineered aureothin pathway. 10.1002/cbic.201200406
Editorial: structural aspects of biosynthesis themed issue. 10.1039/c2np90032g
Iron acquisition in the marine actinomycete genus Salinispora is controlled by the desferrioxamine family of siderophores. 10.1111/j.1574-6968.2012.02641.x
Primer on agar-based microbial imaging mass spectrometry. 10.1128/jb.00823-12
Flavoenzyme-catalyzed atropo-selective N,C-bipyrrole homocoupling in marinopyrrole biosynthesis. 10.1021/ja305670f
Merochlorins A-D, cyclic meroterpenoid antibiotics biosynthesized in divergent pathways with vanadium-dependent chloroperoxidases. 10.1021/ja305665f
Mass spectral molecular networking of living microbial colonies. 10.1073/pnas.1203689109
Bacterial biosynthesis and maturation of the didemnin anti-cancer agents. 10.1021/ja301735a
The carmaphycins: new proteasome inhibitors exhibiting an α,β-epoxyketone warhead from a marine cyanobacterium. 10.1002/cbic.201200007
Evaluation of Streptomyces coelicolor A3(2) as a heterologous expression host for the cyanobacterial protein kinase C activator lyngbyatoxin A. 10.1111/j.1742-4658.2012.08517.x
Novel phenol-soluble modulin derivatives in community-associated methicillin-resistant Staphylococcus aureus identified through imaging mass spectrometry. 10.1074/jbc.m112.349860
Lessons from the past and charting the future of marine natural products drug discovery and chemical biology. 10.1016/j.chembiol.2011.12.014
Selective overproduction of the proteasome inhibitor salinosporamide A via precursor pathway regulation. 10.1016/j.chembiol.2011.10.014
Beyond ethylmalonyl-CoA: the functional role of crotonyl-CoA carboxylase/reductase homologs in expanding polyketide diversity. 10.1039/c1np00082a
Imaging mass spectrometry and genome mining via short sequence tagging identified the anti-infective agent arylomycin in Streptomyces roseosporus. 10.1021/ja2040877
A mass spectrometry-guided genome mining approach for natural product peptidogenomics. 10.1038/nchembio.684
Bacterial self-resistance to the natural proteasome inhibitor salinosporamide A. 10.1021/cb2002544
Discovery and assembly-line biosynthesis of the lymphostin pyrroloquinoline alkaloid family of mTOR inhibitors in Salinispora bacteria. 10.1021/ja205655w
Connecting chemotypes and phenotypes of cultured marine microbial assemblages by imaging mass spectrometry. 10.1002/anie.201101225
Policing starter unit selection of the enterocin type II polyketide synthase by the type II thioesterase EncL. 10.1016/j.bmc.2011.04.024
Significant natural product biosynthetic potential of actinorhizal symbionts of the genus frankia, as revealed by comparative genomic and proteomic analyses. 10.1128/aem.00038-11
A stereoselective vanadium-dependent chloroperoxidase in bacterial antibiotic biosynthesis. 10.1021/ja201088k
Structure and biosynthesis of the marine streptomycete ansamycin ansalactam A and its distinctive branched chain polyketide extender unit. 10.1021/ja109226s
The discovery of salinosporamide K from the marine bacterium "Salinispora pacifica" by genome mining gives insight into pathway evolution. 10.1002/cbic.201000564
A sea of biosynthesis: marine natural products meet the molecular age. 10.1039/c0np90032j
Biosynthesis of the allylmalonyl-CoA extender unit for the FK506 polyketide synthase proceeds through a dedicated polyketide synthase and facilitates the mutasynthesis of analogues. 10.1021/ja108399b
Salinosporamide natural products: Potent 20 S proteasome inhibitors as promising cancer chemotherapeutics. 10.1002/anie.201000728
Prephenate decarboxylases: a new prephenate-utilizing enzyme family that performs nonaromatizing decarboxylation en route to diverse secondary metabolites. 10.1021/bi101457h
Shared biosynthesis of the saliniketals and rifamycins in Salinispora arenicola is controlled by the sare1259-encoded cytochrome P450. 10.1021/ja105891a
Characterization of 5-chloro-5-deoxy-D-ribose 1-dehydrogenase in chloroethylmalonyl coenzyme A biosynthesis: substrate and reaction profiling. 10.1074/jbc.m110.153833
Exploiting enzymatic promiscuity to engineer a focused library of highly selective antifungal and antiproliferative aureothin analogues. 10.1021/ja102751h
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Engineering fluorometabolite production: fluorinase expression in Salinispora tropica Yields Fluorosalinosporamide. 10.1021/np900719u
Functional characterization of the cyclomarin/cyclomarazine prenyltransferase CymD directs the biosynthesis of unnatural cyclic peptides. 10.1021/np9006876
Total (bio)synthesis: strategies of nature and of chemists. 10.1007/128_2010_79
Function-oriented biosynthesis of beta-lactone proteasome inhibitors in Salinispora tropica. 10.1021/jm901098m
Mechanistic insights into water activation in SAM hydroxide adenosyltransferase (duf-62). 10.1002/cbic.200900369
Genomic basis for natural product biosynthetic diversity in the actinomycetes. 10.1039/b817069j
Biosynthesis of salinosporamides from alpha,beta-unsaturated fatty acids: implications for extending polyketide synthase diversity. 10.1021/ja9042824
Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-L-methionine. 10.1073/pnas.0901237106
Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. 10.1021/ac900114t
Chasing the treasures of the sea - bacterial marine natural products. 10.1016/j.mib.2009.05.002
Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. 10.1038/ismej.2009.58
Exploring the chemistry and biology of vanadium-dependent haloperoxidases. 10.1074/jbc.r109.001602
Alkaloid biosynthesis takes root. 10.1038/nchembio0309-140
In vitro biosynthesis of unnatural enterocin and wailupemycin polyketides. 10.1021/np800598t
Formation of the pyridazine natural product azamerone by biosynthetic rearrangement of an aryl diazoketone. 10.1002/anie.200805140
S-Adenosyl-L-methionine hydrolase (adenosine-forming), a conserved bacterial and archaeal protein related to SAM-dependent halogenases. 10.1002/cbic.200800341
Probing the compatibility of type II ketosynthase-carrier protein partners. 10.1002/cbic.200800198
Advances in and applications of proteasome inhibitors. 10.1016/j.cbpa.2008.06.033
Engineered biosynthesis of antiprotealide and other unnatural salinosporamide proteasome inhibitors. 10.1021/ja8029398
Biosynthesis and structures of cyclomarins and cyclomarazines, prenylated cyclic peptides of marine actinobacterial origin. 10.1021/ja711188x
Unraveling the biosynthesis of the sporolide cyclohexenone building block. 10.1021/ja710488m
Extending the biosynthetic repertoire in ribosomal peptide assembly. 10.1002/anie.200803868
Mutasynthesis of fluorosalinosporamide, a potent and reversible inhibitor of the proteasome. 10.1002/anie.200800177
Discovery and characterization of a marine bacterial SAM-dependent chlorinase. 10.1038/nchembio.2007.56
Enzymatic total synthesis of enterocin polyketides. 10.1038/nchembio.2007.22
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. 10.1073/pnas.0700962104
Molecular basis for chloronium-mediated meroterpene cyclization: cloning, sequencing, and heterologous expression of the napyradiomycin biosynthetic gene cluster. 10.1074/jbc.m611046200
Biosynthetic convergence of salinosporamides A and B in the marine actinomycete Salinispora tropica. 10.1021/ol063102o
Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization. 10.1021/bi061774g
Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. 10.1016/j.chembiol.2006.11.011
Type III polyketide synthase beta-ketoacyl-ACP starter unit and ethylmalonyl-CoA extender unit selectivity discovered by Streptomyces coelicolor genome mining. 10.1021/ja065247w
Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type I fatty acid-type III polyketide synthase. 10.1038/nchembio811
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Structural characterization of in vitro and in vivo intermediates on the loading module of microcystin synthetase. 10.1021/cb500007v
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Binding of two flaviolin substrate molecules, oxidative coupling, and crystal structure of Streptomyces coelicolor A3(2) cytochrome P450 158A2. 10.1074/jbc.m410933200
Exploiting marine actinomycete biosynthetic pathways for drug discovery. 10.1007/s10482-004-6541-0
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Heterologous biosynthesis of truncated hexaketides derived from the actinorhodin polyketide synthase. 10.1021/np0499564
Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates. 10.1074/jbc.m406567200
Context-dependent behavior of the enterocin iterative polyketide synthase; a new model for ketoreduction. 10.1016/j.chembiol.2004.03.018
Cloning, sequencing, and biochemical characterization of the nostocyclopeptide biosynthetic gene cluster: molecular basis for imine macrocyclization. 10.1016/j.gene.2003.09.034
Biosynthesis and structural revision of neomarinone. 10.1021/ol035748b
Expression and characterization of the type III polyketide synthase 1,3,6,8-tetrahydroxynaphthalene synthase from Streptomyces coelicolor A3(2). 10.1007/s10295-003-0075-8
Mutasynthesis of enterocin and wailupemycin analogues. 10.1021/ja035973o
Sequence analysis and biochemical characterization of the nostopeptolide A biosynthetic gene cluster from Nostoc sp. GSV224. 10.1016/s0378-1119(03)00587-0
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Mutational analysis of the enterocin favorskii biosynthetic rearrangement. 10.1021/ol0255155
Biosynthesis and attachment of novel bacterial polyketide synthase starter units. 10.1039/b003939j
A mechanism of benzoic acid biosynthesis in plants and bacteria that mirrors fatty acid beta-oxidation. 10.1002/1439-7633(20011001)2:10<784::aid-cbic784>;2-k
Discovery of a new bacterial polyketide biosynthetic pathway. 10.1002/1439-7633(20010105)2:1<35::aid-cbic35>;2-t
Engineering biodiversity with type II polyketide synthase genes. 10.1023/a:1010273224820
Cloning, sequencing and analysis of the enterocin biosynthesis gene cluster from the marine isolate 'Streptomyces maritimus': evidence for the derailment of an aromatic polyketide synthase. 10.1016/s1074-5521(00)00044-2
Biosynthesis of marine natural products: microorganisms and macroalgae. 10.1039/a805873c
Direct evidence that the rifamycin polyketide synthase assembles polyketide chains processively. 10.1073/pnas.96.16.9051
Ectopic expression of the minimal whiE polyketide synthase generates a library of aromatic polyketides of diverse sizes and shapes. 10.1073/pnas.96.7.3622
Biosynthetic Studies of omega-Cycloheptyl Fatty Acids in Alicyclobacillus cycloheptanicus. Formation of Cycloheptanecarboxylic Acid from Phenylacetic Acid. 10.1021/jo962402o
Oleic Acid and Its Positional Isomer, cis-Vaccinic Acid, in the Appendix of Sauromatum guttatum during Anthesis. 10.1104/pp.107.4.1433
Three new omega-cycloheptyl fatty acids from Alicyclobacillus cycloheptanicus and their biosynthetic interrelationships. 10.1021/np50118a019
Biosynthetic studies on the origin of the cyclohexanecarboxylic acid moiety of ansatrienin A and omega-cyclohexyl fatty acids. 10.1021/np50105a008
Correction to Organohalogens Naturally Biosynthesized in Marine Environments and Produced As Disinfection Byproducts Alter Sarco/Endoplasmic Reticulum Ca2+ Dynamics 10.1021/acs.est.8b03174
Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles 10.1038/s41396-018-0292-9
Structural Elucidation of Trace Components Combining GC/MS, GC/IR, DFT-Calculation and Synthesis-Salinilactones, Unprecedented Bicyclic Lactones from Salinispora Bacteria 10.1002/anie.201807923
Strukturaufklärung von Spurenkomponenten durch Kombination von GC/MS, GC/IR, DFT-Simulationen und Synthese - Salinilactone, neuartige bicyclische Lactone aus Salinispora Bakterien 10.1002/ange.201807923
The chemical cue tetrabromopyrrole induces rapid cellular stress and mortality in phytoplankton 10.1038/s41598-018-33945-3
Total Enzyme Syntheses of Napyradiomycins A1 and B1 10.1021/jacs.8b10134
Insights into Thiotemplated Pyrrole Biosynthesis Gained from the Crystal Structure of Flavin-Dependent Oxidase in Complex with Carrier Protein 10.1021/acs.biochem.8b01177
Enzymatic Cascade Reactions in Biosynthesis 10.1002/anie.201807844
Enzymkaskadenreaktionen in der Biosynthese 10.1002/ange.201807844
Avant-garde assembly-line biosynthesis expands diversity of cyclic lipodepsipeptide products 10.1101/560987
Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom 10.1126/science.aau0382
Synthesis, bioactivity, and enzymatic modification of antibacterial thiotetromycin derivatives 10.1039/C8OB03109F
Scalable Biosynthesis of the Seaweed Neurochemical, Kainic Acid 10.1002/anie.201902910
Scalable Biosynthesis of the Seaweed Neurochemical, Kainic Acid 10.1002/ange.201902910
Biosynthesis of l ‐4‐Chlorokynurenine, an Antidepressant Prodrug and a Non‐Proteinogenic Amino Acid Found in Lipopeptide Antibiotics 10.1002/anie.201901571
Biosynthesis of l ‐4‐Chlorokynurenine, an Antidepressant Prodrug and a Non‐Proteinogenic Amino Acid Found in Lipopeptide Antibiotics 10.1002/ange.201901571
Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges 10.1128/mBio.00821-19
Bacterial Tetrabromopyrrole Debrominase Shares a Reductive Dehalogenation Strategy with Human Thyroid Deiodinase 10.1021/acs.biochem.9b00318
Genetic platforms for heterologous expression of microbial natural products 10.1039/C9NP00025A
Cariogenic Streptococcus mutans produces strain-specific antibiotics that impair commensal colonization 10.1101/755025
Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage 10.1038/s41557-019-0317-7
Pass-back chain extension expands multimodular assembly line biosynthesis 10.1038/s41589-019-0385-4
Cariogenic Streptococcus mutans Produces Tetramic Acid Strain-Specific Antibiotics That Impair Commensal Colonization 10.1021/acsinfecdis.9b00365
Algal Neurotoxin Biosynthesis Repurposes the Terpene Cyclase Structural Fold Into an N-prenyltransferase 10.1101/2020.03.31.014811
Nonlinear Biosynthetic Assembly of Alpiniamide by a Hybrid cis/trans-AT PKS-NRPS 10.1021/acschembio.0c00081
Algal neurotoxin biosynthesis repurposes the terpene cyclase structural fold into anN-prenyltransferase 10.1073/pnas.2001325117
Comparative Genomics and Metabolomics in the Genus Nocardia 10.1128/mSystems.00125-20
Co-Occurrence of Enzyme Domains Guides the Discovery of an Oxazolone Synthetase 10.1101/2020.06.11.147165
Meroterpenoid natural products from Streptomyces bacteria – the evolution of chemoenzymatic syntheses 10.1039/D0NP00018C
Site-Directed Mutagenesis of Large Biosynthetic Gene Clusters via Oligonucleotide Recombineering and CRISPR/Cas9 Targeting 10.1021/acssynbio.0c00265
Biosynthesis of marine toxins 10.1016/j.cbpa.2020.06.009
Genetic examination of the marine bacterium Pseudoalteromonas luteoviolacea and effects of its metamorphosis‐inducing factors 10.1111/1462-2920.15211
Enzymes in natural product total synthesis 10.1039/D0NP90038A
Expansion of gamma-butyrolactone signaling molecule biosynthesis to phosphotriester natural products 10.1101/2020.10.11.335315
Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signaling-molecule diversity 10.1101/2020.10.16.342204
Expansion of Gamma-Butyrolactone Signaling Molecule Biosynthesis to Phosphotriester Natural Products 10.1021/acschembio.0c00824
Discovery and Biosynthesis of Tetrachlorizine Reveals Enzymatic Benzylic Dehydrogenation via an ortho-Quinone Methide 10.1021/jacs.0c12415
Cryptic halogenation reactions in natural product biosynthesis 10.1039/D1NP00010A
Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signalling-molecule diversity 10.1099/mgen.0.000568
Mining genomes to illuminate the specialized chemistry of life 10.1038/s41576-021-00363-7
Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase 10.1038/s41589-021-00808-4
Vanessa Phelan
Phelan Vanessa / Vanessa V Phelan / Vanessa Phelan
ORCID: 0000-0001-7156-9294
Impact of a transposon insertion in phzF2 on the specialized metabolite production and interkingdom interactions of Pseudomonas aeruginosa 10.1128/JB.01258-13
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Complete genome sequence of the sugar cane endophyte Pseudomonas aurantiaca PB-St2, a disease-suppressive bacterium with antifungal activity toward the plant pathogen Colletotrichum falcatum 10.1128/genomeA.e01108-13
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Endophytic Azospirillum for enhancement of growth and yield of wheat 10.1007/s42398-018-0014-2
A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications 10.1007/s42398-018-0006-2
Identification and Quantification of Secondary Metabolites by LC-MS from Plant-associated Pseudomonas aurantiaca and Pseudomonas chlororaphis 10.21769/bioprotoc.2702
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High clustering rates of multidrug-resistant Mycobacterium tuberculosis genotypes in Panama 10.1186/1471-2334-13-442
Imaging Mass Spectrometry of a Coral Microbe Interaction with Fungi 10.1007/s10886-013-0320-1
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Phylogenetic structure of Salmonella Enteritidis provides context for a foodborne outbreak in Peru. 10.1038/s41598-020-78808-y
Pep Charusanti
Charusanti Pep
ORCID: 0000-0003-0009-6615
CRISPR-Cas9 Based Engineering of Actinomycetal Genomes 10.1021/acssynbio.5b00038
Microbial regulatory and metabolic networks 10.1016/j.copbio.2007.07.002
Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant 10.1111/1574-6968.12109
Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes 10.1016/j.tibtech.2014.10.009
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92 10.1186/1752-0509-5-163
A mathematical model of BCR-ABL autophosphorylation, signaling through the CRKL pathway, and Gleevec dynamics in chronic myeloid leukemia 10.3934/dcdsb.2004.4.99
Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features 10.1186/1471-2164-13-679
Capsule deletion via a λ-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578 10.1186/1756-0500-7-13
Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters 10.1186/1752-0509-8-4
Exploiting Adaptive Laboratory Evolution of Streptomyces clavuligerus for Antibiotic Discovery and Overproduction 10.1371/journal.pone.0033727
Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene 10.1371/journal.pgen.1001186
Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites 10.1016/j.biotechadv.2013.10.008
Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC 10.3389/fmicb.2015.00958
Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated ‘Omics and Modeling 10.1007/82_2012_247
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models 10.1038/msb.2010.47
Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations 10.1038/srep16025
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data 10.1073/pnas.1501384112
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 10.1186/1752-0509-5-8
A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933 10.1128/genomea.00821-14
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments 10.1073/pnas.1307797110
MS/MS networking guided analysis of molecule and gene cluster families 10.1073/pnas.1303471110
An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228 10.1128/jb.01218-10
Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites 10.1039/c6np00019c
The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli 10.1016/j.micres.2016.10.006
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. 10.1038/nbt.3597
Dissemination of antibiotic resistance genes from antibiotic producers to pathogens 10.1038/ncomms15784
Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast 10.1016/j.synbio.2020.01.004
Complete genome sequence of the rare actinobacterium Kutzneria sp. Strain CA-103260 10.1128/MRA.00499-21
Marcelino Gutierrez
Gutierrez Marcelino
ORCID: 0000-0003-1423-3772
Uprolides N, O and P from the Panamanian Octocoral Eunicea succinea 10.3390/molecules21060819
Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants 10.1038/s41598-017-05515-6
Antimicrobial‐producing Pseudoalteromonas from the marine environment of Panama shows a high phylogenetic diversity and clonal structure 10.1002/jobm.201800087
Imaging Mass Spectrometry of a Coral Microbe Interaction with Fungi 10.1007/s10886-013-0320-1
Leptolide, a new furanocembranolide diterpene from Leptogorgia alba 10.1021/np049745z
Cannabinomimetic lipid from a marine cyanobacterium 10.1021/np200610t
Structural and synthetic investigations of tanikolide dimer, a SIRT2 selective inhibitor, and tanikolide seco-acid from the Madagascar marine cyanobacterium Lyngbya majuscula 10.1021/jo900578j
Antiprotozoal activity against Plasmodium falciparum and Trypanosoma cruzi of aeroplysinin-1 isolated from the new sponge Aplysina chiriquensis 10.1080/13880200500406503
Antiplasmodial activity of bacilosarcin A isolated from the octocoral-associated bacterium Bacillus sp. collected in Panama 10.4103/0975-7406.92739
Antitrypanosomal alkaloids from the marine bacterium Bacillus pumilus 10.3390/molecules170911146
L-Galactose as a natural product: Isolation from a marine octocoral of the first α-L-galactosyl saponin 10.1016/j.tetlet.2004.08.170
MS/MS networking guided analysis of molecule and gene cluster families 10.1073/pnas.1303471110
Apratoxin D, a potent cytotoxic cyclodepsipeptide from papua new Guinea collections of the marine cyanobacteria Lyngbya majuscula and Lyngbya sordida 10.1021/np800121a
seco-briarellinone and briarellin S, two new eunicellin-based diterpenoids from the panamanian octocoral Briareum asbestinum 10.3390/md10112608
Dudawalamides A-D, Antiparasitic Cyclic Depsipeptides from the Marine Cyanobacterium Moorea producens 10.1021/acs.jnatprod.7b00034
Antiplasmodial metabolites isolated from the marine octocoral Muricea austera 10.1021/np060007f
A pseudopterane diterpene isolated from the octocoral Pseudopterogorgia acerosa inhibits the inflammatory response mediated by TLR-ligands and TNF-alpha in macrophages 10.1371/journal.pone.0084107
Microbiota of healthy corals are active against fungi in a light-dependent manner 10.1021/cb500432j
Toxins and pharmacologically active compounds from species of the family Bufonidae (Amphibia, Anura) 10.1016/j.jep.2016.12.021
Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides 10.1021/ac900114t
Malyngolide dimer, a bioactive symmetric cyclodepside from the panamanian marine cyanobacterium lyngbya majuscula 10.1021/np9005184
Assessment of Novel Curcumin Derivatives as Potent Inhibitors of Inflammation and Amyloid-β Aggregation in Alzheimer's Disease 10.3233/JAD-170071
Pumilacidins from the Octocoral-Associated Bacillus sp. DT001 Display Anti-Proliferative Effects in Plasmodium falciparum 10.3390/molecules23092179
A Marine Diterpenoid Modulates the Proteasome Activity in Murine Macrophages Stimulated with LPS 10.3390/biom8040109
Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking 10.1038/s41598-019-39583-7
Antiparasitic Compounds from the Panamanian Marine Bacterium Pseudomonas aeruginosa
Fungus-Growing Ant’s Microbial Interaction of Streptomyces sp. and Escovopsis sp. through Molecular Networking and MALDI Imaging
New Eunicellin-Type Diterpenes from the Panamanian Octocoral Briareum asbestinum 10.3390/md18020084
Analysis of the antiparasitic and anticancer activity of the coconut palm (Cocos nucifera L. ARECACEAE) from the natural reserve of Punta Patiño, Darién 10.1371/journal.pone.0214193
19-Hydroxy-bufalin, a major bufadienolide isolated from the parotoid gland secretions of the Panamanian endemic toad Rhinella centralis (Bufonidae), inhibits the growth of Trypanosoma cruzi 10.1016/j.toxicon.2020.02.009
Reproducible molecular networking of untargeted mass spectrometry data using GNPS 10.1038/s41596-020-0317-5
Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama 10.3390/md18090456
Metabolites from Microbes Isolated from the Skin of the Panamanian Rocket Frog Colostethus panamansis (Anura: Dendrobatidae) 10.3390/metabo10100406
Antimicrobial Secretions of Toads (Anura, Bufonidae): Bioactive Extracts and Isolated Compounds against Human Pathogens 10.3390/antibiotics9120843
Antibacterial Activity of Volatile Organic Compounds Produced by the Octocoral-Associated Bacteria Bacillus sp. BO53 and Pseudoalteromonas sp. GA327 10.3390/antibiotics9120923
Bufadienolides from the Skin Secretions of the Neotropical Toad Rhinella alata (Anura: Bufonidae): Antiprotozoal Activity against Trypanosoma cruzi 10.3390/molecules26144217
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/
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/
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
Elizabeth Shank
Shank Elizabeth / Elizabeth Anne Shank
ORCID: 0000-0002-4804-1966
MS/MS networking guided analysis of molecule and gene cluster families. 10.1073/pnas.1303471110
Using coculture to detect chemically mediated interspecies interactions. 10.3791/50863
Extracellular signaling and multicellularity in Bacillus subtilis. 10.1016/j.mib.2011.09.016
Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. 10.1073/pnas.1103630108
DNA molecular handles for single-molecule protein-folding studies by optical tweezers. 10.1007/978-1-61779-142-0_18
The folding cooperativity of a protein is controlled by its chain topology. 10.1038/nature09021
New developments in microbial interspecies signaling. 10.1016/j.mib.2009.01.003
Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers. 10.1007/s00249-007-0247-y
Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment. 10.1110/ps.062628607
Direct observation of the three-state folding of a single protein molecule. 10.1126/science.1116702
Inhibition of Cell Differentiation in Bacillus subtilis by Pseudomonas protegens 10.1128/JB.02535-14
Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis. 10.1073/pnas.1414272112
Deconvolving molecular signatures of interactions between microbial colonies. 10.1093/bioinformatics/btv251
Draft Genome Sequence of Bacillus luciferensis Isolated from Soil 10.1128/genomeA.01140-16
Pirated Siderophores Promote Sporulation in Bacillus subtilis 10.1128/AEM.03293-16
Natural-Product Antibiotics: Cues for Modulating Bacterial Biofilm Formation 10.1016/j.tim.2017.06.003
Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology 10.1128/msystems.00040-17
Design of synthetic bacterial communities for predictable plant phenotypes 10.1371/journal.pbio.2003962
Cyclic di-AMP Acts as an Extracellular Signal That Impacts Bacillus subtilis Biofilm Formation and Plant Attachment 10.1128/mBio.00341-18
Considering the Lives of Microbes in Microbial Communities 10.1128/mSystems.00155-17
A Dual-Species Biofilm with Emergent Mechanical and Protective Properties 10.1128/JB.00670-18
Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana 10.1094/PBIOMES-02-20-0019-R
Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides 10.1093/bioinformatics/btz127
Monitoring Bacterial Colonization and Maintenance on Arabidopsis thaliana Roots in a Floating Hydroponic System 10.3791/59517
Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms 10.7554/eLife.56275
EcoFABs: advancing microbiome science through standardized fabricated ecosystems. 10.1038/s41592-019-0465-0