A pressure test to make 10 molecules in 90 days: External evaluation of methods to engineer biology
Casini, Arturo
Chang, Fang-Yuan
Eluere, Raissa
King, Andrew
Young, Eric M.
Dudley, Quentin M.
Karim, Ashty
Pratt, Katelin
Bristol, Cassandra
Forget, Anthony
Ghodasara, Amar
Warden-Rothman, Robert
Gan, Rui
Cristofaro, Alexander
Espah Borujeni, Amin
Ryu, Min-Hyung
Li, Jian
Kwon, Yong Chan
Wang, He
Tatsis, Evangelos
Rodriguez-Lopez, Carlos
O'Connor, Sarah
Medema, Marnix H.
Fischbach, Michael
Jewett, Michael C.
Voigt, Christopher A.
Gordon, D. Benjamin
Arturo Casini
Casini Arturo
ORCID: 0000-0003-2828-5223
R2oDNA designer: computational design of biologically neutral synthetic DNA sequences.
10.1021/sb4001323
One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy.
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Bricks and blueprints: methods and standards for DNA assembly.
10.1038/nrm4014
Organism Engineering for the Bioproduction of the Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG).
10.1021/acssynbio.9b00393
BASIC: A Simple and Accurate Modular DNA Assembly Method.
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A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.
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BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology.
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Four-Step Pathway from Phenylpyruvate to Benzylamine, an Intermediate to the High-Energy Propellant CL-20
10.1021/acssynbio.1c00021
Michael Fischbach
Fischbach Michael
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Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota.
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Signaling in Host-Associated Microbial Communities.
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Synthetic biology to access and expand nature's chemical diversity.
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A Wave of Regulatory T Cells into Neonatal Skin Mediates Tolerance to Commensal Microbes.
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Mammalian Lipopolysaccharide Receptors Incorporated into the Retroviral Envelope Augment Virus Transmission.
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A Phase-Variable Surface Layer from the Gut Symbiont Bacteroides thetaiotaomicron.
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Genome-Directed Lead Discovery: Biosynthesis, Structure Elucidation, and Biological Evaluation of Two Families of Polyene Macrolactams against Trypanosoma brucei.
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Computational approaches to natural product discovery.
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Minimum Information about a Biosynthetic Gene cluster.
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HUMAN MICROBIOTA. Small molecules from the human microbiota.
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A biosynthetic pathway for a prominent class of microbiota-derived bile acids.
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IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.
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MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.
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antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
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A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis.
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Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine.
10.1016/j.chom.2014.09.001
A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.
10.1016/j.cell.2014.08.032
Synthetic microbes as drug delivery systems.
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Propionibacterium-produced coproporphyrin III induces Staphylococcus aureus aggregation and biofilm formation.
10.1128/mbio.01286-14
Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.
10.1016/j.cell.2014.06.034
Key applications of plant metabolic engineering.
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The prevalence of species and strains in the human microbiome: a resource for experimental efforts.
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Diet rapidly and reproducibly alters the human gut microbiome.
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What Lives On Our Skin: Ecology, Genomics and Therapeutic Opportunities Of the Skin Microbiome.
10.1016/j.ddmec.2012.12.003
Production of α-galactosylceramide by a prominent member of the human gut microbiota.
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A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice.
10.1038/ismej.2013.89
antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.
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Cell-based therapeutics: the next pillar of medicine.
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Trehalose biosynthesis promotes Pseudomonas aeruginosa pathogenicity in plants.
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Dyeing to learn more about the gut microbiota.
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Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.
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Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor.
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Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations.
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Microbiota-targeted therapies: an ecological perspective.
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A mass spectrometry-guided genome mining approach for natural product peptidogenomics.
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Eating for two: how metabolism establishes interspecies interactions in the gut.
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Combination therapies for combating antimicrobial resistance.
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antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.
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Community health care: therapeutic opportunities in the human microbiome.
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Draft genome sequence of Streptomyces clavuligerus NRRL 3585, a producer of diverse secondary metabolites.
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A family of pyrazinone natural products from a conserved nonribosomal peptide synthetase in Staphylococcus aureus.
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The next frontier of systems biology: higher-order and interspecies interactions.
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A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations.
10.1016/j.cell.2010.02.027
Natural products version 2.0: connecting genes to molecules.
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Dapdiamides, tripeptide antibiotics formed by unconventional amide ligases.
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Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.
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Antibiotics for emerging pathogens.
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Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin.
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Repurposing libraries of eukaryotic protein kinase inhibitors for antibiotic discovery.
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Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis.
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Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.
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The evolution of gene collectives: How natural selection drives chemical innovation.
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Biosynthetic tailoring of microcin E492m: post-translational modification affords an antibacterial siderophore-peptide conjugate.
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Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes.
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One pathway, many products.
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The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis.
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New antibiotics from bacterial natural products.
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Biochemistry. Directing biosynthesis.
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Structural characterization of enterobactin hydrolase IroE.
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A biosynthetic gene cluster for the acetyl-CoA carboxylase inhibitor andrimid.
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Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms.
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"Oncogenic shock": explaining oncogene addiction through differential signal attenuation.
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A protein interaction surface in nonribosomal peptide synthesis mapped by combinatorial mutagenesis and selection.
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How pathogenic bacteria evade mammalian sabotage in the battle for iron.
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Activity screening of carrier domains within nonribosomal peptide synthetases using complex substrate mixtures and large molecule mass spectrometry.
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Regulation of the nucleotide state of oncogenic ras proteins by nucleoside diphosphate kinase.
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Mixing with bubbles: a practical technology for use with portable microfluidic devices.
10.1039/b510843h
In vitro characterization of salmochelin and enterobactin trilactone hydrolases IroD, IroE, and Fes.
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In vitro characterization of IroB, a pathogen-associated C-glycosyltransferase.
10.1073/pnas.0408463102
Dynamic control of liquid-core/liquid-cladding optical waveguides.
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Natural Products: An Overview
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Observing the invisible through imaging mass spectrometry, a window into the metabolic exchange patterns of microbes
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The biosynthesis of lipooligosaccharide from Bacteroides thetaiotaomicron
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Skin microbiota-host interactions
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Experimental realization of a quantum quincunx by use of linear optical elements
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Enzymatic tailoring of enterobactin alters membrane partitioning and iron acquisition.
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A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology
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Prokaryotic gene clusters: A rich toolbox for synthetic biology
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A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites
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Contextual control of skin immunity and inflammation by Corynebacterium
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Design for mixing using bubbles in branched microfluidic channels
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Quantification of bile acids: a mass spectrometry platform for studying gut microbe connection to metabolic diseases
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Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products
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CRISPR-based functional genomics in human dendritic cells
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Eliciting a potent antitumor immune response by expressing tumor antigens in a skin commensal
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Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
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Fang-Yuan Chang
Chang Fang-Yuan
ORCID: 0000-0001-5819-6454
Characterization of an Environmental DNA-Derived Gene Cluster that Encodes the Bisindolylmaleimide Methylarcyriarubin
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Natural Products from Environmental DNA Hosted in Ralstonia metallidurans
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Discovery and Synthetic Refactoring of Tryptophan Dimer Gene Clusters from the Environment
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Cloning and Characterization of an Environmental DNA-Derived Gene Cluster That Encodes the Biosynthesis of the Antitumor Substance BE-54017
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Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening
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Introducing our Authors
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Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria
10.1128/aem.02169-09
Mutations in the Proteolipid Subunits of the Vacuolar H + -ATPase Provide Resistance to Indolotryptoline Natural Products
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A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology
10.1021/jacs.7b13292
Targeted Metagenomics: Finding Rare Tryptophan Dimer Natural Products in the Environment
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Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters
10.1073/pnas.1507606112
Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases
10.1016/j.cell.2016.12.021
Carlos Rodríguez-López
Rodríguez-López Carlos
ORCID: 0000-0001-9224-0455
A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology
10.1021/jacs.7b13292
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Avocado fruit maturation and ripening: Dynamics of aliphatic acetogenins and lipidomic profiles from mesocarp, idioblasts and seed
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Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae
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High hydrostatic pressure treatments trigger de novo carotenoid biosynthesis in papaya fruit (Carica papaya cv. Maradol)
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Metabolomics Analysis Reveals Tissue-Specific Metabolite Compositions in Leaf Blade and Traps of Carnivorous Nepenthes Plants
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Two bi-functional cytochrome P450 CYP72 enzymes from olive (Olea europaea) catalyze the oxidative C-C bond cleavage in the biosynthesis of secoxy-iridoids - flavor and quality determinants in olive oil
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The evolutionary origins of the cat attractant nepetalactone in catnip
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Two bi‐functional cytochrome P450 CYP72 enzymes from olive ( Olea europaea ) catalyze the oxidative C‐C bond cleavage in the biosynthesis of secoxy‐iridoids – flavor and quality determinants in olive oil
10.1111/nph.16975
Evangelos Tatsis
Tatsis Evangelos
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ORCID: 0000-0002-4013-1537
Unlocking the Diversity of Alkaloids in Catharanthus roseus: Nuclear Localization Suggests Metabolic Channeling in Secondary Metabolism
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Biosynthesis of nudicaulins: A 13CO2-pulse/chase labeling study with papaver nudicaule
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Concentration Kinetics of Secoisolariciresinol Diglucoside and its Biosynthetic Precursor Coniferin in Developing Flaxseed
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Nudicaulins, Yellow Flower Pigments of Papaver nudicaule: Revised Constitution and Assignment of Absolute Configuration
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Identification of the major constituents of Hypericum perforatum by LC/SPE/NMR and/or LC/MS
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Towards a consensus structure of hypericin in solution: direct evidence for a single tautomer and different ionization states in protic and nonprotic solvents by the use of variable temperature gradient H-1 NMR
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Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity
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Unprecedented Utilization of Pelargonidin and Indole for the Biosynthesis of Plant Indole Alkaloids
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Dual Catalytic Activity of a Cytochrome P450 Controls Bifurcation at a Metabolic Branch Point of Alkaloid Biosynthesis in Rauwolfia serpentina
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New developments in engineering plant metabolic pathways
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A three enzyme system to generate the Strychnos alkaloid scaffold from a central biosynthetic intermediate
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Discovery of a short chain dehydrogenase from Catharanthus roseus that produces a novel monoterpene indole alkaloid
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A pressure test to make 10 molecules in 90 days: External evaluation of methods to engineer biology
10.1021/jacs.7b13292
Ashty Karim
Karim Ashty
ORCID: 0000-0002-5789-7715
High-Throughput Optimization Cycle of a Cell-Free Ribosome Assembly and Protein Synthesis System
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In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design
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Cell-free gene expression: an expanded repertoire of applications
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Metabolic engineering of muconic acid production in Saccharomyces cerevisiae
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Cell-free metabolic engineering: Biomanufacturing beyond the cell
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Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications
10.1016/j.ymben.2013.07.001
Characterization of plasmid burden and copy number inSaccharomyces cerevisiaefor optimization of metabolic engineering applications
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Design of synthetic yeast promoters via tuning of nucleosome architecture
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A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery
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A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology
10.1021/jacs.7b13292
Controlling cell-free metabolism through physiochemical perturbations
10.1016/j.ymben.2017.11.005
Cell-Free Synthetic Biology for Pathway Prototyping
10.1016/bs.mie.2018.04.029
Cell-Free Synthetic Systems for Metabolic Engineering and Biosynthetic Pathway Prototyping
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Enhancing control of cell-free metabolism through pH modulation
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Cell-free styrene biosynthesis at high titers
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Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin
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Cell-free prototyping of limonene biosynthesis using cell-free protein synthesis
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In vitro prototyping of limonene biosynthesis using cell-free protein synthesis
10.1016/j.ymben.2020.05.006
Cell-free styrene biosynthesis at high titers
10.1016/j.ymben.2020.05.009
In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design
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Modular cell-free expression plasmids to accelerate biological design in cells
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Cell‐Free Exploration of the Natural Product Chemical Space
10.1002/cbic.202000452
Modular cell-free expression plasmids to accelerate biological design in cells
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Spacer2PAM: A computational framework for identification of functional PAM sequences for endogenous CRISPR systems
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Marnix H. Medema
Medema Marnix H.
ORCID: 0000-0002-2191-2821
antiSMASH
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Bioinformatics Approaches and Software for Detection of Secondary Metabolic Gene Clusters
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Synthetic Biology in Streptomyces Bacteria
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Computational approaches to natural product discovery
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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
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Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism
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MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models
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The future of industrial antibiotic production: From random mutagenesis to synthetic biology
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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
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A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis
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Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus
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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
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antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
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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
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antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers
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antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
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The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways
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MS/MS networking guided analysis of molecule and gene cluster families
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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
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NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity
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Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
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Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum.
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Leucanicidin and endophenasides result from methyl-rhamnosylation by the same tailoring enzymes in Kitasatospora sp. MBT66
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Computational strategies for genome-based natural product discovery and engineering in fungi
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The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters
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Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
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Editorial: Synthetic biology and bioinformatics
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plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
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Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus
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Mining prokaryotes for antimicrobial compounds: from diversity to function
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Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
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Standardization for natural product synthetic biology
10.1039/c6np00030d
Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways
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Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium , Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin
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SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria
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Collaborating with Undergraduates To Contribute to Biochemistry Community Resources
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Road MAPs to engineer host microbiomes.
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Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens.
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Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution.
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antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
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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
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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.
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luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria.
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A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.
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Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.
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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
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PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
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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
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MIBiG 2.0: a repository for biosynthetic gene clusters of known function
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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
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The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
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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
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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
Eric M. Young
Young Eric M.
ORCID: 0000-0001-5276-2873
Curation Principles Derived from the Analysis of the SBOL iGEM Data Set
10.1021/acssynbio.1c00225
Rewiring yeast sugar transporter preference through modifying a conserved protein motif
10.1073/pnas.1311970111
Remaining Challenges in the Metabolic Engineering of Yeasts for Biofuels
10.1016/b978-0-444-59592-8.00012-9
Double dutch: A tool for designing combinatorial libraries of biological systems
10.1021/acssynbio.5b00232
Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae
10.1021/acssynbio.6b00371
Genetic engineering of host organisms for pharmaceutical synthesis
https://doi.org/10.1016/j.copbio.2018.02.001
Genetic engineering of host organisms for pharmaceutical synthesis
10.1016/j.copbio.2018.02.001
A pressure test to make 10 molecules in 90 days: External evaluation of methods to engineer biology
10.1021/jacs.7b13292
Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast
10.1016/j.ymben.2018.05.002
Synthetic biology for bio-derived structural materials
10.1016/j.coche.2019.03.002
Verification of genetic engineering in yeasts with nanopore whole genome sequencing
10.1101/2020.05.05.079368
Genetic circuit design automation for yeast
10.1038/s41564-020-0757-2
Engineered yeast genomes accurately assembled from pure and mixed samples
10.1038/s41467-021-21656-9
A molecular transporter engineering approach to improving xylose catabolism in Saccharomyces cerevisiae
10.1016/j.ymben.2012.03.004
Functional survey for heterologous sugar transport proteins, using Saccharomyces cerevisiae as a host
10.1128/AEM.02651-10
Optimizing pentose utilization in yeast: The need for novel tools and approaches
10.1186/1754-6834-3-24
Synthetic biology: Tools to design, build, and optimize cellular processes
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