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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.

Proceedings of the National Academy of Sciences of the United States of America, 2013-6

https://doi.org/10.1073/pnas.1303471110

Bradley Moore

Moore Bradley

ORCID: 0000-0002-4652-1253

Coupled Biosynthesis of Volatiles and Salinosporamide A in Salinispora tropica 10.1002/cbic.201600388

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

Back Cover: Minimization of the Thiolactomycin Biosynthetic Pathway Reveals that the Cytochrome P450 Enzyme TlmF Is Required for Five-Membered Thiolactone Ring Formation (ChemBioChem 12/2017) 10.1002/cbic.201700270

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

Organohalogens Naturally Biosynthesized in Marine Environments and Produced as Disinfection Byproducts Alter Sarco/Endoplasmic Reticulum Ca2+ Dynamics 10.1021/acs.est.8b00512

Enzymatic control of dioxygen binding and functionalization of the flavin cofactor. 10.1073/pnas.1801189115

Natural Product Reports 35 years on. 10.1039/c8np90001a

Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality. 10.1073/pnas.1714381115

Broad-Host-Range Expression Reveals Native and Host Regulatory Elements That Influence Heterologous Antibiotic Production in Gram-Negative Bacteria. 10.1128/mbio.01291-17

Genomic insights into specialized metabolism in the marine actinomycete Salinispora. 10.1111/1462-2920.13867

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

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Biosynthesis of marine natural products: macroorganisms (Part B). 10.1039/b508781n

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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Engineered biosynthesis of phenyl-substituted polyketides. 10.1002/cbic.200400007

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

Characterization of benzoyl coenzyme A biosynthesis genes in the enterocin-producing bacterium "Streptomyces maritimus". 10.1128/jb.185.2.399-404.2003

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Molecular evidence for a uniform microbial community in sponges from different oceans. 10.1128/aem.68.9.4431-4440.2002

Inactivation, complementation, and heterologous expression of encP, a novel bacterial phenylalanine ammonia-lyase gene. 10.1074/jbc.m204171200

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>3.0.co;2-k

Discovery of a new bacterial polyketide biosynthetic pathway. 10.1002/1439-7633(20010105)2:1<35::aid-cbic35>3.3.co;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

http://www.thephelanlab.com

https://pharmacy.cuanschutz.edu/about-us/profile/Phelan-Vanessa-UCD6000230147

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Kit Pogliano

Pogliano Kit / Kit Johnson

ORCID: 0000-0002-7868-3345

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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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MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus 10.1038/ja.2013.99

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Brendan Duggan

Duggan Brendan / Brendan M. Duggan

ORCID: 0000-0002-7034-8374

http://sopnmr.ucsd.edu

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Catalytic detoxification of nerve agent and pesticide organophosphates by butyrylcholinesterase assisted with non-pyridinium oximes 10.1042/bj20121612

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Ultra-high resolution band-selective HSQC for nanomole-scale identification of chlorine-substituted13C in natural products drug discovery 10.1002/mrc.4415

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Detailed Analysis of (−)-Palmyrolide A and Some Synthetic Derivatives as Voltage-Gated Sodium Channel Antagonists 10.1021/np500644k

Conformational dynamics of thyroid hormones by variable temperature nuclear magnetic resonance: The role of side chain rotations and cisoid/transoid interconversions 10.1021/jm9606610

Contribution of increased length and intact capping sequences to the conformational preference for helix in a 31-residue peptide from the C terminus of myohemerythrin 10.1021/bi970038x

1 H and 13 C NMR Relaxation Studies of Molecular Dynamics of the Thyroid Hormones Thyroxine, 3,5,3‘-Triiodothyronine, and 3,5-Diiodothyronine † 10.1021/jm960231+

MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus 10.1038/ja.2013.99

Mollenynes B-E from the Marine Sponge Spirastrella mollis. Band-Selective Heteronuclear Single Quantum Coherence for Discrimination of Bromo-Chloro Regioisomerism in Natural Products 10.1021/jacs.5b07858

Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria 10.1021/acs.jnatprod.5b00301

Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research 10.1038/s41598-017-13923-x

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules 10.1073/pnas.1315492110

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SANE (Structure Assisted NOE Evaluation): An automated model-based approach for NOE assignment 10.1023/A:1011227824104

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

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Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae 10.7554/eLife.24214

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Identification of a 3-alkylpyridinium compound from the red sea sponge Amphimedon chloros with in vitro inhibitory activity against the West Nile Virus NS3 protease 10.3390/molecules23061472

Toward Expanded Diversity of Host–Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives 10.1007/s10953-018-0769-1

Facile synthesis of a diverse library of mono-3-substituted β-cyclodextrin analogues 10.1080/10610278.2018.1562191

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The Pierced Lasso Topology Leptin has a Bolt on Dynamic Domain Composed by the Disordered Loops I and III 10.1016/j.jmb.2020.01.035

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Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating Siderophore 10.1128/mSystems.00161-20

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides 10.1038/nmicrobiol.2017.10

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samina

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Sphingobacterium canadense sp. nov., an isolate from corn roots 10.1016/j.syapm.2007.06.002

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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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Assessment of two carrier materials for phosphate solubilizing biofertilizers and their effect on growth of wheat (Triticum aestivum L.) 10.1016/j.micres.2017.08.011

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Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola), and characterization of osmoregulatory genes in halophilic Bacilli 10.1139/cjm-2017-0544

Genetic and phenotypic diversity of plant growth promoting rhizobacteria isolated from sugarcane plants growing in Pakistan 10.4014/jmb.1005.05014

Isolation and identification of Gluconacetobacter azotocaptans from corn rhizosphere 10.1016/j.syapm.2005.12.001

Role of secondary metabolites in the interaction between Pseudomonas fluorescens and soil microorganisms under iron-limited conditions 10.1093/femsec/fiw107

The contribution of genome mining strategies to the understanding of active principles of PGPR strains 10.1093/femsec/fiw249

The major histocompatibility complex-related Fc receptor for IgG (FcRn) binds albumin and prolongs its lifespan 10.1084/jem.20021829

Isolation and characterization of bacteria associated with the rhizosphere of halophytes (Salsola stocksii and Atriplex amnicola) for production of hydrolytic enzymes 10.1007/s42770-019-00044-y

Lahorenoic acids A-C, ortho-dialkyl-substituted aromatic acids from the biocontrol strain pseudomonas aurantiaca PB-St2 10.1021/np3005166

The systematic investigation of the quorum sensing system of the biocontrol strain pseudomonas chlororaphis subsp. aurantiaca PB-St2 Unveils aurI to Be a biosynthetic origin for 3-Oxo-homoserine lactones 10.1371/journal.pone.0167002

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Identification of plasmid encoded osmoregulatory genes from halophilic bacteria isolated from the rhizosphere of halophytes 10.1016/j.micres.2019.126307

Isolation, characterization, and effect of fluorescent pseudomonads on micropropagated sugarcane 10.1139/W09-050

Rhizotrophs: Plant Growth Promotion to Bioremediation 10.1007/978-981-10-4862-3

Microbial diversity in the rhizosphere of plants growing under extreme environments and its impact on crop improvement 10.1007/s42398-019-00061-5

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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Harnessing the Plant Microbiome for Improved Abiotic Stress Tolerance 10.1007/978-981-10-5514-0_2

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Gluconacetobacter azotocaptans: A Plant Growth-Promoting Bacteria 10.1007/978-981-10-4862-3_1

Isolation and identification of diazotrophic bacteria from rice, wheat and kallar grass 10.1007/978-94-011-5232-7_23

Contribution of non-leguminous biofertilizers to rice biomass, nitrogen fixation and fertilizer-N use efficiency under flooded soil conditions 10.1007/978-94-011-5232-7_7

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Secondary Metabolites of Pseudomonas aurantiaca and Their Role in Plant Growth Promotion 10.1007/978-81-322-1287-4_14

Effect ofAzospirillum zeaeand Seed Priming with Zinc, Manganese and Auxin on Growth and Yield Parameters of Wheat, under Dryland Farming 10.1007/S40003-020-00480-5

Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress 10.1094/PBIOMES-09-19-0057-R

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Gavilan Ronnie / Ronnie G. Gavilan

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Transoceanic spreading of pathogenic strains of Vibrio parahaemolyticus with distinctive genetic signatures in the recA gene 10.1371/journal.pone.0117485

Microbiota of healthy corals are active against fungi in a light-dependent manner 10.1021/cb500432j

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

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

Molecular Epidemiology and Genetic Variation of Pathogenic Vibrio parahaemolyticus in Peru 10.1371/journal.pntd.0002210

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Antimicrobial-producing Pseudoalteromonas from the marine environment of Panama shows a high phylogenetic diversity and clonal structure 10.1002/jobm.201800087

Hidden biodiversity in Neotropical streams: DNA barcoding uncovers high endemicity of freshwater macroinvertebrates at small spatial scales. 10.1371/journal.pone.0231683

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Emergence of ciprofloxacin-resistant Neisseria meningitidis B from asymptomatic carriers during an outbreak in Peru, 2017 10.1099/jmm.0.001245

Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) is an effective alternative for SARS-CoV-2 molecular detection in middle-income countries 10.1101/2020.10.14.20212977

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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

https://orbit.dtu.dk/en/persons/e5edf515-a516-43a0-afa5-fe4a24ca42eb

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 https://doi.org/10.1177/1934578X1901400109

Fungus-Growing Ant’s Microbial Interaction of Streptomyces sp. and Escovopsis sp. through Molecular Networking and MALDI Imaging https://doi.org/10.1177/1934578X1901400117

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

http://www.marnixmedema.nl

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

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

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

Computational approaches to natural product discovery 10.1038/nchembio.1884

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Editorial: Synthetic biology and bioinformatics 10.1039/c6np90031c

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

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

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

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

Standardization for natural product synthetic biology 10.1039/c6np00030d

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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