Paperbase

Jeffrey A. van Santen

van Santen Jeffrey A.

ORCID: 0000-0002-5424-804X

Dispersion Corrections Improve the Accuracy of Both Noncovalent and Covalent Interactions Energies Predicted by a Density-Functional Theory Approximation 10.1021/acs.jpca.5b02809

A computational and experimental re-examination of the reaction of the benzyloxyl radical with DMSO 10.1016/j.comptc.2015.10.030

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

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

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

Bimodal Evans–Polanyi Relationships in Hydrogen Atom Transfer from C(sp3)–H Bonds to the Cumyloxyl Radical. A Combined Time-Resolved Kinetic and Computational Study 10.1021/jacs.1c05566

Development of an NMR-Based Platform for the Direct Structural Annotation of Complex Natural Products Mixtures 10.1021/acs.jnatprod.0c01076

Kai Blin

Blin Kai

ORCID: 0000-0003-3764-6051

https://orbit.dtu.dk/en/persons/3b511204-dc2b-4932-b73d-a0c72c2301e5

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

The bifunctional role of aconitase in Streptomyces viridochromogenes Tu494. 10.1111/1462-2920.12006

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

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

DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. 10.1093/nar/gku1180

Improved lanthipeptide detection and prediction for antiSMASH. 10.1371/journal.pone.0089420

Proteomic approach to reveal the regulatory function of aconitase AcnA in oxidative stress response in the antibiotic producer Streptomyces viridochromogenes Tu494. 10.1371/journal.pone.0087905

Complete genome sequence of the kirromycin producer Streptomyces collinus Tu 365 consisting of a linear chromosome and two linear plasmids. 10.1016/j.jbiotec.2013.10.004

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

Minimum Information about a Biosynthetic Gene cluster 10.1038/nchembio.1890

CRISPy-web 10.1016/j.synbio.2016.01.003

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

Ten Simple Rules for Taking Advantage of Git and GitHub 10.1371/journal.pcbi.1004947

Dissemination of antibiotic resistance genes from antibiotic producers to pathogens 10.1038/ncomms15784

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

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

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery 10.1093/nar/gkx360

Engineering of actinomycetes using CRISPR/Cas9 technologies 10.1055/s-0036-1596147

Recent development of computational resources for new antibiotics discovery 10.1016/j.mib.2017.10.027

CRISPR-Cas9 Toolkit for Actinomycete Genome Editing 10.1007/978-1-4939-7295-1_11

Patscanui: an intuitive web interface for searching patterns in DNA and protein data 10.1093/nar/gky321

Bioconda: sustainable and comprehensive software distribution for the life sciences 10.1038/s41592-018-0046-7

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

CRISPR-BEST: a highly efficient DSB-free base editor for filamentous actinomycetes 10.1101/582403

Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH 10.1007/s10295-018-02131-9

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

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

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

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST 10.1073/pnas.1913493116

Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast 10.1016/j.synbio.2020.01.004

Disclosing the Potential of the SARP-Type Regulator PapR2 for the Activation of Antibiotic Gene Clusters in Streptomycetes 10.3389/fmicb.2020.00225

Designing sgRNAs for CRISPR-BEST base editing applications with CRISPy-web 2.0 10.1016/j.synbio.2020.05.005

CRISPR–Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in streptomycetes 10.1038/s41596-020-0339-z

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

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

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

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

A Regulator Based “Semi-Targeted” Approach to Activate Silent Biosynthetic Gene Clusters 10.3390/ijms22147567

Discovery and Characterization of Epemicins A and B, New 30-Membered Macrolides from Kutzneria sp. CA-103260 10.1021/acschembio.1c00318

Satria Kautsar

Kautsar Satria / Satria A Kautsar / SA Kautsar

ORCID: 0000-0002-9815-511X

http://satriaphd.link

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

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

An application framework for evaluating methods in biometrics systems 10.1109/ICODSE.2014.7062685

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

Genomic identification and analysis of specialized metabolite biosynthetic gene clusters in plants using plantiSMASH 10.1007/978-1-4939-7874-8_15

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

A computational framework to explore large-scale biosynthetic diversity 10.1038/s41589-019-0400-9

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

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

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

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

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

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

Tilmann Weber

Weber Tilmann

ORCID: 0000-0002-8260-5120

http://www.biosustain.dtu.dk/english/research/scientific-sections/nbc

http://www.iimena.org

https://scholar.google.dk/citations?user=KuOZZSAAAAAJ&hl=en

Die Struktur des Cyclodecatriens Collinolacton, seine Biosynthese und semisynthetische Derivate: monopolare Spindeln und Schutz vor intrazellulärem oxidativem Stress 10.1002/ange.202106802

The Structure of Cyclodecatriene Collinolactone, its Biosynthesis, and Semisynthetic Analogues: Effects of Monoastral Phenotype and Protection from Intracellular Oxidative Stress 10.1002/anie.202106802

Complete Genome Sequence of Amycolatopsis sp. CA-230715, Encoding a 35-Module Type I Polyketide Synthase 10.1128/MRA.00805-21

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

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes. 10.1021/acssynbio.5b00038

Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. 10.1016/j.tibtech.2014.10.009

Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024. 10.1186/s12864-016-2369-z

Bioinformatics Tools for the Discovery of New Nonribosomal Peptides. 10.1007/978-1-4939-3375-4_14

The cyclochlorotine mycotoxin is produced by the nonribosomal peptide synthetase CctN in Talaromyces islandicus ("Penicillium islandicum"). 10.1111/1462-2920.13294

CLUSEAN, Overview 10.1007/978-1-4899-7478-5_706

Antibiotics: Biosynthesis, Generation of Novel Compounds 10.1002/9780470054581.eib040

Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites 10.1039/c6np00019c

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production 10.1016/j.synbio.2015.12.002

Introduction to the Special Issue “Bioinformatic tools and approaches for Synthetic Biology of natural products” 10.1016/j.synbio.2016.04.001

CRISPy-web: An online resource to design sgRNAs for CRISPR applications 10.1016/j.synbio.2016.01.003

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

Polyketide bio-derivatization using the promiscuous acyltransferase KirCII. 10.1021/acssynbio.6b00341

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery 10.1093/nar/gkx360

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

Cyanodermella asteris sp. nov. (Ostropales) from the inflorescence axis of Aster tataricus 10.5248/132.107

Dissemination of antibiotic resistance genes from antibiotic producers to pathogens 10.1038/ncomms15784

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

Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production. 10.1002/biot.201700465

Linking secondary metabolites to biosynthesis genes in the fungal endophyte Cyanodermella asteris: The anti-cancer bisanthraquinone skyrin. 10.1016/j.jbiotec.2017.06.410

CRISPR-Cas9 Toolkit for Actinomycete Genome Editing. 10.1007/978-1-4939-7295-1_11

Recent development of computational resources for new antibiotics discovery. 10.1016/j.mib.2017.10.027

Filling the Gaps in the Kirromycin Biosynthesis: Deciphering the Role of Genes Involved in Ethylmalonyl-CoA Supply and Tailoring Reactions 10.1038/s41598-018-21507-6

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms 10.1016/j.mib.2018.03.004

Patscanui: an intuitive web interface for searching patterns in DNA and protein data 10.1093/nar/gky321

Lysoquinone-TH1, a New Polyphenolic Tridecaketide Produced by Expressing the Lysolipin Minimal PKS II in Streptomyces albus 10.3390/antibiotics7030053

Discrete acyltransferases involved in polyketide biosynthesis 10.1039/c2md20048a

Improved Lanthipeptide Detection and Prediction for antiSMASH 10.1371/journal.pone.0089420

Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production 10.1002/biot.201800377

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

CRISPR/Cas-based genome engineering in natural product discovery 10.1039/C8NP00089A

Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH 10.1007/s10295-018-02131-9

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery 10.1016/j.biotechadv.2019.03.005

Depiction of secondary metabolites and antifungal activity of Bacillus velezensis DTU001 10.1101/577817

CRISPR-BEST: a highly efficient DSB-free base editor for filamentous actinomycetes 10.1101/582403

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

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

Engineering of cell factories for the production of natural products 10.1039/C9NP90036E

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST 10.1073/pnas.1913493116

Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets 10.1101/781328

Depiction of secondary metabolites and antifungal activity of Bacillus velezensis DTU001. 10.1016/j.synbio.2019.08.002

The Draft Whole-Genome Sequence of the Antibiotic Producer Empedobacter haloabium ATCC 31962 Provides Indications for Its Taxonomic Reclassification. 10.1128/mra.01120-19

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

Versatile polyketide biosynthesis platform for production of aromatic compounds in yeast 10.1101/618751

Antitumor astins originate from the fungal endophyteCyanodermella asterisliving within the medicinal plantAster tataricus 10.1073/pnas.1910527116

Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast. 10.1016/j.synbio.2020.01.004

Complete Genome Sequences of 13 Bacillus subtilis Soil Isolates for Studying Secondary Metabolite Diversity. 10.1128/MRA.01406-19

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

Designing sgRNAs for CRISPR-BEST base editing applications with CRISPy-web 2.0 10.1016/j.synbio.2020.05.005

CRISPR–Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in streptomycetes 10.1038/s41596-020-0339-z

Distribution of Epsilon-Polylysine Synthetases in Coryneform Bacteria Isolated from Cheese and Human Skin 10.1101/2020.07.24.220772

Genomic and chemical diversity of Bacillus subtilis secondary metabolites against plant pathogenic fungi 10.1101/2020.08.05.238063

CRISPR-nRAGE, a Cas9 nickase-reverse transcriptase assisted versatile genetic engineering toolkit for E. coli 10.1101/2020.09.02.279141

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

Phylogenetic distribution of secondary metabolites in the Bacillus subtilis species complex 10.1101/2020.10.28.358507

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

Characterization and Engineering of Streptomyces griseofuscus DSM 40191 as a Potential Host for Heterologous Expression of Biosynthetic Gene Clusters 10.1101/2020.11.06.372458

High-Quality Sequencing, Assembly, and Annotation of the Streptomyces griseofuscus DSM 40191 Genome 10.1128/MRA.01100-20

Automating Cloning by Natural Transformation 10.1021/acssynbio.0c00240

Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi 10.1128/mSystems.00770-20

Distribution of ε-Poly- l -Lysine Synthetases in Coryneform Bacteria Isolated from Cheese and Human Skin 10.1128/AEM.01841-20

Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex 10.1128/mSystems.00057-21

Recent Advances in Re-engineering Modular PKS and NRPS Assembly Lines 10.1007/s12257-020-0265-5

The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes 10.1042/EBC20200132

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

Complete Genome Sequence of Streptomyces sp. Strain CA-256286 10.1128/MRA.00290-21

A Regulator Based “Semi-Targeted” Approach to Activate Silent Biosynthetic Gene Clusters 10.3390/ijms22147567

Complete Genome Sequence of the Rare Actinobacterium Kutzneria sp. Strain CA-103260 10.1128/MRA.00499-21

Towards the sustainable discovery and development of new antibiotics 10.1038/s41570-021-00313-1

A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing 10.1038/s41467-021-25541-3

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. 10.1186/s13321-021-00546-8

Discovery and Characterization of Epemicins A and B, New 30-Membered Macrolides from Kutzneria sp. CA-103260. 10.1021/acschembio.1c00318

Victoria Pascal Andreu

Pascal Andreu Victoria

ORCID: 0000-0001-9609-9401

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

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

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

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

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

George Lund

Lund George

ORCID: 0000-0001-9099-3461

Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10× metagenomics 10.1128/mSystems.01116-20

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

Justin van der Hooft

van der Hooft Justin / Justin J.J. van der Hooft

ORCID: 0000-0002-9340-5511

Structural elucidation of low abundant metabolites in complex sample matrices 10.1007/s11306-013-0519-8

Non-smoky GLYCOSYLTRANSFERASE1 prevents the release of smoky aroma from tomato fruit 10.1105/tpc.113.114231

Automatic chemical structure annotation of an LC-MSn based metabolic profile from green tea 10.1021/ac400861a

Substructure-based annotation of high-resolution multistage MSn spectral trees 10.1002/rcm.6364

Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts 10.1021/jf300297y

Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake 10.1021/ac3017339

Spectral trees as a robust annotation tool in LC-MS based metabolomics 10.1007/s11306-011-0363-7

Metabolite identification using automated comparison of high-resolution multistage mass spectral trees 10.1021/ac2034216

Inhibitory activity of plumbagin produced by Drosera intermedia on food spoilage fungi 10.1002/jsfa.5522

A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC-MS-SPE-NMR 10.1002/mrc.2833

Thermal diffusivity of periderm from tomatoes of different maturity stages as determined by the concept of the frequency-domain open photoacoustic cell 10.1063/1.3530735

Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation 10.1021/ac102546x

Iridoid and caffeoyl phenylethanoid glycosides of the endangered carnivorous plant Pinguicula lusitanica L. (Lentibulariaceae) 10.1016/j.bse.2009.05.003

Topic modeling for untargeted substructure exploration in metabolomics 10.1073/pnas.1608041113

Propagating annotations of molecular networks using in silico fragmentation 10.1371/journal.pcbi.1006089

Did a plant-herbivore arms race drive chemical diversity in Euphorbia? 10.1101/323014

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa. 10.5702/massspectrometry.S0033

Interactions of blacktea polyphenols with human gut microbiota: implications for gut and cardiovascular health 10.3945/ajcn.113.058263

Identification of a drimenol synthase and drimenol oxidase from Persicaria hydropiper, involved in the biosynthesis of insect deterrent drimanes 10.1111/tpj.13527

Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines 10.3389/fbioe.2015.00026

Rapid and sustained systemic circulation of conjugated gut microbiol catabolites after single-dose black tea extract consumption 10.1021/pr5001253

In Silico Prediction and Automatic LC–MSn Annotation of Green Tea Metabolites in Urine 10.1021/ac403875b

Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose 10.1007/s11306-018-1438-5

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

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra 10.1101/491506

Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics 10.1021/acs.analchem.8b05112

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages 10.1101/347716

Absorption, metabolism, distribution and excretion of (−)-epicatechin: A review of recent findings https://doi.org/10.1016/j.mam.2017.11.002

Metabolite Identification in Complex Mixtures Using Nuclear Magnetic Resonance Spectroscopy 10.1007/978-3-319-28275-6_6-2

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry 10.1093/bioinformatics/btx582

A comprehensive evaluation of the [2-14C](–)-epicatechin metabolome in rats https://doi.org/10.1016/j.freeradbiomed.2016.08.001

The food metabolome: a window over dietary exposure 10.3945/ajcn.113.076133

Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols 10.3945/ajcn.113.058958

Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics 10.1021/acs.analchem.7b01391

A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes 10.18174/FAIRdata2018.16286

Implementations of the chemical structural and compositional similarity metric in R and Python 10.1101/546150

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites 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

The Metabolomics Society—Current State of the Membership and Future Directions 10.3390/metabo9050089

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra 10.1039/C8FD00235E

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

Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli 10.3389/fmicb.2019.00252

Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l. 10.3389/fpls.2019.00846

Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools 10.3390/metabo9070144

In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics 10.3390/metabo9100219

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

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/j.foodchem.2019.125290

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

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow 10.1016/j.phytochem.2020.112292

Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication 10.1126/sciadv.aax6328

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree 10.1101/2020.05.04.077636

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

Reproducible molecular networking of untargeted mass spectrometry data using GNPS 10.1038/s41596-020-0317-5

Decomposing metabolite set activity levels with PALS 10.1101/2020.06.07.138974

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions 10.1101/2020.06.12.148205

Phenylpropane as an Alternative Dearomatizing Unit of Indoles: Discovery of Inaequalisines A and B Using Substructure-Informed Molecular Networking 10.1021/acs.orglett.0c02153

matchms - processing and similarity evaluation of mass spectrometry data 10.1101/2020.08.06.239244

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships 10.1101/2020.08.11.245928

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

matchms - processing and similarity evaluation of mass spectrometry data. 10.21105/joss.02411

ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7

Feature-based molecular networking in the GNPS analysis environment 10.1038/s41592-020-0933-6

Rapid Development of Improved Data-dependent Acquisition Strategies 10.1101/2020.09.11.293092

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree 10.1038/s41589-020-00677-3

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

The ant fungus garden acts as an external digestive system 10.1101/2020.11.18.389361

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

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

Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs 10.1371/journal.ppat.1008932

Comparative Metabologenomics Analysis of Polar Actinomycetes 10.3390/md19020103

Ranking Metabolite Sets by Their Activity Levels 10.3390/metabo11020103

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships 10.1371/journal.pcbi.1008724

Rapid Development of Improved Data-Dependent Acquisition Strategies 10.1021/acs.analchem.0c03895

MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons 10.1101/2021.04.18.440324

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions 10.1371/journal.pcbi.1008920

Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview 10.3390/metabo11070445

Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/mSystems.00601-21

Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery 10.1128/mSystems.00726-21

Jorge Navarro

Navarro Jorge / Jorge C. Navarro-Muñoz / Jorge C. Navarro-Muñoz

ORCID: 0000-0003-2992-1607

Email: j.navarro@wi.knaw.nl

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data 10.1101/445270

Draft Genome Sequence of the Wood-Staining Ascomycete Chlorociboria aeruginascens DSM 107184 10.1128/mra.00249-19

Including transcription factor information in the superparamagnetic clustering of microarray data 10.1016/j.physa.2010.09.006

Designing lattice structures with maximal nearest-neighbor entanglement 10.1088/1751-8113/42/31/315302

Genetic algorithm optimization of entanglement 10.1103/physreva.74.052308

Cinnamic Acid and Sorbic acid Conversion Are Mediated by the Same Transcriptional Regulator in Aspergillus niger 10.3389/fbioe.2019.00249

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

The High-Quality Complete Genome Sequence of the Opportunistic Fungal Pathogen Candida vulturna CBS 14366T 10.1007/s11046-019-00404-0

A computational framework to explore large-scale biosynthetic diversity 10.1038/s41589-019-0400-9

Evolutionary Histories of Type III Polyketide Synthases in Fungi 10.3389/fmicb.2019.03018

The Biosynthesis of Fungal Secondary Metabolites: From Fundamentals to Biotechnological Applications 10.1016/b978-0-12-809633-8.21072-8

Secondary metabolite biosynthetic diversity in the fungal family Hypoxylaceae and Xylaria hypoxylon 10.1016/j.simyco.2021.100118

Vittorio Tracanna

Tracanna Vittorio

ORCID: 0000-0002-7244-567X

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

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs 10.1101/gr.243477.118

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

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics 10.1128/mSystems.01116-20

Barbara Terlouw

Terlouw Barbara

ORCID: 0000-0002-4058-6718

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

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

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics 10.1128/mSystems.01116-20

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

Nelly Selem

Selem Nelly

ORCID: 0000-0003-1697-3862

Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model streptomycetes 10.1093/gbe/evw125

Actinobacteria phylogenomics, selective isolation from an iron oligotrophic environment and siderophore functional characterization, unveil new desferrioxamine traits 10.1093/femsec/fix086

Whole genome sequencing reveals widespread distribution of typhoidal toxin genes and VirB/D4 plasmids in bovine-associated nontyphoidal Salmonella 10.1038/s41598-018-28169-4

The cycad coralloid root contains a diverse endophytic bacterial community including cyanobacteria encoding specific biosynthetic gene clusters 10.1093/gbe/evy266

Expanding primary metabolism helps generate the metabolic robustness to facilitate antibiotic biosynthesis in streptomyces 10.1128/mBio.02283-17

A computational framework to explore large-scale biosynthetic diversity 10.1038/s41589-019-0400-9

EvoMining reveals the origin and fate of natural products biosynthetic enzymes 10.1101/482273

Evolutionary dynamics of natural product biosynthesis in bacteria 10.1039/C9NP00048H

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

ActDES – a Curated Actinobacterial Database for Evolutionary Studies 10.1101/2020.05.20.105536

ActDES – a curated Actinobacterial Database for Evolutionary Studies 10.1099/mgen.0.000498

The confluence of big data and evolutionary genome mining for the discovery of natural products 10.1039/D1NP00013F

Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21 10.1099/mic.0.001084

Roger Linington

Linington Roger / Roger G. Linington

ORCID: 0000-0003-1818-4971

http://linington.chem.sfu.ca/

Biofilm Formation and Detachment in Gram-Negative Pathogens Is Modulated by Select Bile Acids. 10.1371/journal.pone.0149603

The Natural Product N-Palmitoyl-l-leucine Selectively Inhibits Late Assembly of Human Spliceosomes. 10.1074/jbc.M115.673210

Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries. 10.1073/pnas.1507743112

Phenotype-Guided Natural Products Discovery Using Cytological Profiling. 10.1021/acs.jnatprod.5b00455

Genome-Directed Lead Discovery: Biosynthesis, Structure Elucidation, and Biological Evaluation of Two Families of Polyene Macrolactams against Trypanosoma brucei. 10.1021/acschembio.5b00308

Bastimolide A, a Potent Antimalarial Polyhydroxy Macrolide from the Marine Cyanobacterium Okeania hirsuta. 10.1021/acs.joc.5b01264

Optimized quinoline amino alcohols as disruptors and dispersal agents of Vibrio cholerae biofilms. 10.1039/c5ob01134e

Living in the matrix: assembly and control of Vibrio cholerae biofilms. 10.1038/nrmicro3433

Connecting phenotype and chemotype: high-content discovery strategies for natural products research. 10.1021/acs.jnatprod.5b00017

Salinipostins A-K, long-chain bicyclic phosphotriesters as a potent and selective antimalarial chemotype. 10.1021/jo5024409

Abyssomicin 2 reactivates latent HIV-1 by a PKC- and HDAC-independent mechanism. 10.1021/ol503349y

Development of benzo[1,4]oxazines as biofilm inhibitors and dispersal agents against Vibrio cholerae. 10.1039/c4cc07003h

Borrelidin B: isolation, biological activity, and implications for nitrile biosynthesis. 10.1021/np500727g

A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. 10.1016/j.cell.2014.08.032

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

Sloth hair as a novel source of fungi with potent anti-parasitic, anti-cancer and anti-bacterial bioactivity. 10.1371/journal.pone.0084549

An NF-κB-based high-throughput screen identifies piericidins as inhibitors of the Yersinia pseudotuberculosis type III secretion system. 10.1128/AAC.02025-13

Image-based 384-well high-throughput screening method for the discovery of skyllamycins A to C as biofilm inhibitors and inducers of biofilm detachment in Pseudomonas aeruginosa. 10.1128/AAC.01781-13

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

Discovery and biological characterization of the auromomycin chromophore as an inhibitor of biofilm formation in Vibrio cholerae. 10.1002/cbic.201300131

Molecular networking as a dereplication strategy. 10.1021/np400413s

Mechanism of action-based classification of antibiotics using high-content bacterial image analysis. 10.1039/c3mb70027e

Development of quinoline-based disruptors of biofilm formation against Vibrio cholerae. 10.1021/ol400150z

Examination of the mode of action of the almiramide family of natural products against the kinetoplastid parasite Trypanosoma brucei. 10.1021/np300834q

"Function-first" lead discovery: mode of action profiling of natural product libraries using image-based screening. 10.1016/j.chembiol.2012.12.007

Development of antibiotic activity profile screening for the classification and discovery of natural product antibiotics. 10.1016/j.chembiol.2012.09.014

Correction of F508del-CFTR trafficking by the sponge alkaloid latonduine is modulated by interaction with PARP. 10.1016/j.chembiol.2012.08.014

Hit-to-lead development of the chamigrane endoperoxide merulin A for the treatment of African sleeping sickness. 10.1371/journal.pone.0046172

Chemical inhibitors of the type three secretion system: disarming bacterial pathogens. 10.1128/AAC.00975-12

Examining the fish microbiome: vertebrate-derived bacteria as an environmental niche for the discovery of unique marine natural products. 10.1371/journal.pone.0035398

Total synthesis, stereochemical assignment, and antimalarial activity of gallinamide A. 10.1002/chem.201102538

On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds. 10.1038/nchembio.664

Highlights of marine invertebrate-derived biosynthetic products: their biomedical potential and possible production by microbial associants. 10.1016/j.bmc.2011.07.017

Versatile method for the detection of covalently bound substrates on solid supports by DART mass spectrometry. 10.1021/ol201404v

Expedient synthesis of α,α-dimethyl-β-hydroxy carbonyl scaffolds via Evans' aldol reaction with a tertiary enolate. 10.1016/j.tetlet.2011.03.126

An image-based 384-well high-throughput screening method for the discovery of biofilm inhibitors in Vibrio cholerae. 10.1039/c0mb00276c

Identification and characterization of a phosphodiesterase that inversely regulates motility and biofilm formation in Vibrio cholerae. 10.1128/JB.00209-10

Almiramides A-C: discovery and development of a new class of leishmaniasis lead compounds. 10.1021/jm100265s

Dragonamide E, a modified linear lipopeptide from Lyngbya majuscula with antileishmanial activity. 10.1021/np900622m

Dereplication and de novo sequencing of nonribosomal peptides. 10.1038/nmeth.1350

New innovations for an old infection: antimalarial lead discovery from marine natural products during the period 2003-2008. 10.4155/fmc.09.56

Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. 10.1021/ac900114t

Antimalarial peptides from marine cyanobacteria: isolation and structural elucidation of gallinamide A. 10.1021/np8003529

Symplocamide A, a potent cytotoxin and chymotrypsin inhibitor from the marine Cyanobacterium Symploca sp. 10.1021/np070280x

Linking bioprospecting with sustainable development and conservation: the Panama case 10.1007/s10531-007-9214-2

Antimalarial linear lipopeptides from a Panamanian strain of the marine cyanobacterium Lyngbya majuscula. 10.1021/np0700772

Venturamides A and B: antimalarial constituents of the panamanian marine Cyanobacterium Oscillatoria sp. 10.1021/np0605790

Caminosides B-D, antimicrobial glycolipids isolated from the marine sponge Caminus sphaeroconia. 10.1021/np050192h

Stereochemical assignment in acyclic lipids across long distance by circular dichroism: absolute stereochemistry of the aglycone of caminoside A. 10.1002/anie.200461158

Latonduines A and B, new alkaloids isolated from the marine sponge Stylissa carteri: structure elucidation, synthesis, and biogenetic implications. 10.1021/ol034950b

Caminoside A, an antimicrobial glycolipid isolated from the marine sponge Caminus sphaeroconia. 10.1021/ol0268337

Total Synthesis of Glycinocins A-C. 10.1021/acs.joc.7b01959

Total Synthesis of Skyllamycins A-C. 10.1002/chem.201704277

Data-analysis strategies for image-based cell profiling. 10.1038/nmeth.4397

Reply to Skinnider and Magarvey: Rates of novel natural product discovery remain high. 10.1073/pnas.1711139114

Retrospective analysis of natural products provides insights for future discovery trends. 10.1073/pnas.1614680114

Special Issue in Honor of Professor Phil Crews. 10.1021/acs.jnatprod.7b00161

Sansanmycin natural product analogues as potent and selective anti-mycobacterials that inhibit lipid I biosynthesis. 10.1038/ncomms14414

Piericidin A1 Blocks Yersinia Ysc Type III Secretion System Needle Assembly. 10.1128/msphere.00030-17

Discovery of anabaenopeptin 679 from freshwater algal bloom material: Insights into the structure-activity relationship of anabaenopeptin protease inhibitors. 10.1016/j.bmcl.2016.09.008

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. 10.1038/nbt.3597

Erratum for Duncan et al., An NF-κB-Based High-Throughput Screen Identifies Piericidins as Inhibitors of the Yersinia pseudotuberculosis Type III Secretion System. 10.1128/aac.00973-16

Image-Based Screening Approaches to Natural Products Discovery 10.1002/9781118794623.ch20

De Novo Sequencing of Nonribosomal Peptides 10.1007/978-3-540-78839-3_16

De Novo terpenoid biosynthesis by the dendronotid nudibranch Melibe leonina 10.1007/pl00012669

The bioactive lipid (S)-sebastenoic acid impacts motility and dispersion in Vibrio cholerae 10.1139/cjc-2017-0334

Synthetic Studies Toward the Skyllamycins: Total Synthesis and Generation of Simplified Analogues 10.1021/acs.joc.8b00898

Marine Mammal Microbiota Yields Novel Antibiotic with Potent Activity Against Clostridium difficile. 10.1021/acsinfecdis.7b00105

A selective genome-guided method for environmental Burkholderia isolation. 10.1007/s10295-018-02121-x

Genome-Based Identification of a Plant-Associated Marine Bacterium as a Rich Natural Product Source. 10.1002/anie.201805673

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. 10.1039/c7np00064b

Synthesis and evaluation of analogues of the glycinocin family of calcium-dependent antibiotics. 10.1039/c8ob01268g

Maculatic Acids-Sex Attractant Pheromone Components of Bald-Faced Hornets. 10.1002/anie.201804666

Cutibacterium acnes antibiotic production shapes niche competition in the human skin microbiome 10.1101/594010

Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. 10.1039/c8np90041h

Problems in Organic Structure Determination 10.1201/b19329

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

High-Throughput Functional Annotation of Natural Products by Integrated Activity Profiling 10.1101/748129

Isolation, Structure Elucidation, and Total Synthesis of Dolichovespulide, a Sesquiterpene from Dolichovespula Yellowjackets 10.1021/acs.jnatprod.9b00238

Targeting tRNA-Synthetase Interactions towards Novel Therapeutic Discovery Against Eukaryotic Pathogens 10.1101/711697

New methods for isolation and structure determination of natural products 10.1039/c9np90023c

Development of a Custom MALDI-TOF Mass Spectrometric Database for Identification of Environmental Burkholderia and Related Genera. 10.1128/aem.00354-20

Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens. 10.1371/journal.pntd.0007983

The Antimalarial Natural Product Salinipostin A Identifies Essential α/β Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites. 10.1016/j.chembiol.2020.01.001

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

A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles 10.1126/scitranslmed.aay5445

Expansion of Gamma-Butyrolactone Signaling Molecule Biosynthesis to Phosphotriester Natural Products. 10.1021/acschembio.0c00824

Microbial natural product databases: moving forward in the multi-omics era. 10.1039/d0np00053a