Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum
Salo, O.V.
Ries, M.
Medema, M.H.
Lankhorst, P.P.
Vreeken, R.J.
Bovenberg, R.A.L.
Driessen, A.J.M.
BMC genomics, 2015
Arnold J.M. Driessen
Driessen Arnold J.M.
ORCID: 0000-0001-9258-9104
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Fungal ABC transporter deletion and localization analysis
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The large first periplasmic loop of SecD and SecF plays an important role in SecDF functioning
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Engineering of an endogenous hexose transporter into a specific D-xylose transporter facilitates glucose-xylose co-consumption in Saccharomyces cerevisiae
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Enantioselective artificial metalloenzymes by creation of a novel active site at the protein dimer interface
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Energy transduction and transport processes in thermophilic bacteria
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Bioenergetics and cytoplasmic membrane stability of the extremely acidophilic, thermophilic archaeon Picrophilus oshimae
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NarK is a nitrite-extrusion system involved in anaerobic nitrate respiration by Escherichia coli
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In memoriam: Wilhelmus Nicolaas Konings (1937-2014)
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Co-operation between different targeting pathways during integration of a membrane protein
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A single copy of SecYEG is sufficient for preprotein translocation
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Improved xylose uptake in Saccharomyces cerevisiae due to directed evolution of galactose permease Gal2 for sugar co-consumption
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Domain interactions of the peripheral preprotein Translocase subunit SecA
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Kinetics and Energetics of the Translocation of Maltose Binding Protein Folding Mutants
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Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes
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Insights into ABC Transport in Archaea
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Elucidating the native architecture of the YidC: Ribosome complex
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The lateral gate of SecYEG opens during protein translocation
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SecYEG Proteoliposomes Catalyze the Δψ-Dependent Membrane Insertion of FtsQ
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Comparative study of the extracellular proteome of Sulfolobus species reveals limited secretion
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PrlA4 prevents the rejection of signal sequence defective preproteins by stabilizing the SecA-SecY interaction during the initiation of translocation
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Biosynthetic concepts for the production of β-lactam antibiotics in Penicillium chrysogenum
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UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation
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Mechanisms of YidC-mediated insertion and assembly of multimeric membrane protein complexes
10.1074/jbc.R800029200
The purified E. coli integral membrane protein SecY E is sufficient for reconstitution of SecA-dependent precursor protein translocation
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In vitro pore‐forming activity of the lantibiotic nisin: Role of protonmotive force and lipid composition
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Characterization of the annular lipid shell of the Sec translocon
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The essence of being extremophilic: The role of the unique archaeal membrane lipids
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Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
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Identification of the magnesium-binding domain of the high-affinity ATP- binding site of the Bacillus subtilis and Escherichia coli SecA protein
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Formation of the productive ATP-Mg2+-bound dimer of GlcV, an ABC-ATPase from Sulfolobus solfataricus
10.1016/j.jmb.2003.08.065
Interaction between SecA and SecYEG in micellar solution and formation of the membrane-inserted state
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Proton motive force-dependent Hoechst 33342 transport by the ABC transporter LmrA of Lactococcus lactis
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Identification of Two Interaction Sites in SecY that Are Important for the Functional Interaction with SecA
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The formation of oxytocin dimers is suppressed by the zinc-aspartate-oxytocin complex
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Can the excretion of metabolites by bacteria be manipulated?
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The active protein-conducting channel of Escherichia coli contains an apolar patch
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Phylogenetic analysis of fungal ABC transporters
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An engineered cryptic Hxt11 sugar transporter facilitates glucose-xylose co-consumption in Saccharomyces cerevisiae
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Bacterial solute transport proteins in their lipid environment
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In vitro synthesis and oligomerization of the mechanosensitive channel of large conductance, MscL, into a functional ion channel
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The life of proteins: The good, the mostly good and the ugly
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From casein to cheese: The role of lactococcus lactis
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The bindosome is a structural component of the Sulfolobus solfataricus cell envelope
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In vitro interaction of the housekeeping SecA1 with the accessory SecA2 protein of Mycobacterium tuberculosis
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Isoprenoid biosynthesis in Archaea - Biochemical and evolutionary implications
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Bacteriocins: Mechanism of membrane insertion and pore formation
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Competitive binding of the SecA ATPase and ribosomes to the SecYEG translocon
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The saci_2123 gene of the hyperthermoacidophile Sulfolobus acidocaldarius encodes an ATP-binding cassette multidrug transporter
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The ABC transporter ABC40 encodes a phenylacetic acid export system in Penicillium chrysogenum
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Formation of the ether lipids archaetidylglycerol and archaetidylethanolamine in Escherichia coli
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Outer membrane protein A of Escherichia coli inserts and folds into lipid bilayers by a concerted mechanism
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Nonlinear biosynthetic gene cluster dose effect on penicillin production by Penicillium chrysogenum
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Flagellar motility and structure in the hyperthermoacidophilic archaeon Sulfolobus solfataricus
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SecA supports a constant rate of preprotein translocation
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Components required for membrane assembly of newly synthesized K+ channel KcsA
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Pushing, pulling and trapping - Modes of motor protein supported protein translocation
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Substrate specificity of the SecB chaperone
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Bioenergetics and solute uptake under extreme conditions
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SecB - A chaperone dedicated to protein translocation
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Slow fusion of liposomes composed of membrane-spanning lipids
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SecDFyajC forms a heterotetrameric complex with YidC
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Covalently dimerized SecA is functional in protein translocation
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Hydrophobic membrane thickness and lipid-protein interactions of the leucine transport system of Lactococcus lactis
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The protein-conducting channel SecYEG
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Functional characterization of the Escherichia coli K-12 yiaMNO transport protein genes
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The catalytic cycle of the Escherichia coli SecA ATPase comprises two distinct preprotein translocation events
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Escherichia coli translocase: The unravelling of a molecular machine
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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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Chapter 6 Preprotein Translocase of Escherichia coli: Solubilization, Purification, and Reconstitution of the Integral Membrane Subunits SecY/E
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Generation of Proton‐Motive Force by an archaeal terminal quinol oxidase from Sulfolobus acidocaldarius
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Sec-mediated transport of posttranslationally dehydrated peptides in Lactococcus lactis
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Ciprofloxacin-Photoswitch Conjugates: A Facile Strategy for Photopharmacology
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Interaction of Streptococcus mutans YidC1 and YidC2 with translating and nontranslating ribosomes
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Purification, crystallization and preliminary X-ray diffraction analysis of an archaeal ABC-ATPase
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A single amino acid substitution in SecY stabilizes the interaction with SecA
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Sulfur regulation of the sulfate transporter genes sutA and sutB in Penicillium chrysogenum
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The Bifidobacterium longum NCIMB 702259T ctr gene codes for a novel cholate transporter
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SecY-SecY and SecY-SecG contacts revealed by site-specific crosslinking
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Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane-Distinct translocases and mechanisms
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YidC - An evolutionary conserved device for the assembly of energy-transducing membrane protein complexes
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Chapter 32 Translocation of proteins across the bacterial cytoplasmic membrane
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Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation
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Cellobiose uptake in the hyperthermophilic archaeon Pyrococcus furiosus is mediated by an inducible, high-affinity ABC transporter
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The amino-terminal tail of Hxt11 confers membrane stability to the Hxt2 sugar transporter and improves xylose fermentation in the presence of acetic acid
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Growing Membranes In Vitro by Continuous Phospholipid Biosynthesis from Free Fatty Acids
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Photocontrol of Antibacterial Activity: Shifting from UV to Red Light Activation
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Increased xylose affinity of Hxt2 through gene shuffling of hexose transporters in Saccharomyces cerevisiae
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Deregulation of secondary metabolism in a histone deacetylase mutant of Penicillium chrysogenum
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Synthetic Minimal Cell: Self-Reproduction of the Boundary Layer
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Bacterial MbtH-like Proteins Stimulate Nonribosomal Peptide Synthetase-Derived Secondary Metabolism in Filamentous Fungi
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Continuous expansion of a synthetic minimal cellular membrane
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Efficient, D-glucose insensitive, growth on D-xylose by an evolutionary engineered Saccharomyces cerevisiae strain
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Biochemical characterization of the Nocardia lactamdurans ACV synthetase
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CRISPR-Based Transcriptional Activation Tool for Silent Genes in Filamentous Fungi
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Single‐molecule analysis of dynamics and interactions of the SecYEG translocon
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D-glucose overflow metabolism in an evolutionary engineered high-performance D-xylose consuming Saccharomyces cerevisiae strain
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A promiscuous archaeal cardiolipin synthase generating a variety of cardiolipins and phospholipids
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Identification of a conserved N‐terminal domain in the first module of ACV synthetases
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A promiscuous archaeal cardiolipin synthase enables construction of diverse natural and unnatural phospholipids
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A Unified Approach for the Total Synthesis of cyclo ‐Archaeol, iso ‐Caldarchaeol, Caldarchaeol, and Mycoketide
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A Unified Approach for the Total Synthesis of cyclo ‐Archaeol, iso ‐Caldarchaeol, Caldarchaeol, and Mycoketide
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Back Cover: A Unified Approach for the Total Synthesis of cyclo ‐Archaeol, iso ‐Caldarchaeol, Caldarchaeol, and Mycoketide (Angew. Chem. Int. Ed. 32/2021)
10.1002/anie.202107622
Rücktitelbild: A Unified Approach for the Total Synthesis of cyclo ‐Archaeol, iso ‐Caldarchaeol, Caldarchaeol, and Mycoketide (Angew. Chem. 32/2021)
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Nonribosomal peptide synthetases and their biotechnological potential in Penicillium rubens
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The role of the first transmembrane helix in bacterial YidC: Insights from the crystal structure and molecular dynamics simulations
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A versatile method to separate complex lipid mixtures using 1-butanol as eluent in a reverse-phase UHPLC-ESI-MS system
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Rob Vreeken
Vreeken Rob
/ Rob Vreeken
ORCID: 0000-0003-3568-1371
Potent peptidic fusion inhibitors of influenza virus
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Mass spectrometric recommendations for Quan/Qual analysis using liquid-chromatography coupled to quadrupole time-of-flight mass spectrometry
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The pipelined metabolite identification based on MS fragmentation.
10.1186/1758-2946-2-s1-p53
Comprehensive LC-MS E lipidomic analysis using a shotgun approach and its application to biomarker detection and identification in osteoarthritis patients.
10.1021/pr901094j
The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF).
10.1021/pr9005876
Liquid chromatography with triple-quadrupole and quadrupole-time-of-flight mass spectrometry for the determination of micro-constituents - a comparison.
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Generic solid phase extraction-liquid chromatography-tandem mass spectrometry method for fast determination of drugs in biological fluids.
10.1016/s1570-0232(02)01013-9
Determination of oxytetracycline and its degradation products by high-performance liquid chromatography-tandem mass spectrometry in manure-containing anaerobic test systems.
10.1016/s1570-0232(02)00468-3
Determination of polar organophosphorus pesticides in aqueous samples by direct injection using liquid chromatography-tandem mass spectrometry.
10.1016/s0021-9673(01)00660-4
Capillary electrochromatography/nanoelectrospray mass spectrometry for attomole characterization of peptides.
10.1002/1097-0231(20000830)14:16<1448::aid-rcm44>3.0.co;2-9
Determination of daminozide in apples and apple leaves by liquid chromatography--mass spectrometry.
10.1016/s0021-9673(98)00915-7
Rapid target analysis of microcontaminants in water by on-line single-short-column liquid chromatography combined with atmospheric pressure chemical ionization tandem mass spectrometry.
10.1016/s0021-9673(97)00558-x
On-line post-column Diels-Alder derivatization for the determination of vitamin D3 and its metabolites by liquid chromatography/thermospray mass spectrometry.
10.1002/bms.1200221102
Evaluation of eluents in thermospray liquid chromatography-mass spectrometry for identification and determination of pesticides in environmental samples.
10.1016/s0021-9673(01)88502-2
Deregulation of secondary metabolism in a histone deacetylase mutant of Penicillium chrysogenum.
10.1002/mbo3.598
Development and application of a UHPLC-MS/MS metabolomics based comprehensive systemic and tissue-specific screening method for inflammatory, oxidative and nitrosative stress.
10.1007/s00216-018-0912-2
Integration of Ion Mobility MSE after Fully Automated, Online, High-Resolution Liquid Extraction Surface Analysis Micro-Liquid Chromatography.
10.1021/acs.analchem.7b03512
High sensitivity and selectivity in quantitative analysis of drugs in biological samples using 4-column multidimensional micro-UHPLC-MS enabling enhanced sample loading capacity.
10.1016/j.aca.2017.07.067
Fetal Metabolic Stress Disrupts Immune Homeostasis and Induces Proinflammatory Responses in Human Immunodeficiency Virus Type 1- and Combination Antiretroviral Therapy-Exposed Infants.
10.1093/infdis/jix291
Altered expression of epidermal lipid bio-synthesis enzymes in atopic dermatitis skin is accompanied by changes in stratum corneum lipid composition.
10.1016/j.jdermsci.2017.05.005
Endometriosis is associated with aberrant metabolite profiles in plasma.
10.1016/j.fertnstert.2016.12.032
Quantitative analysis of ceramides using a novel lipidomics approach with three dimensional response modelling.
10.1016/j.bbalip.2016.07.004
Metabolomics profiling of the free and total oxidised lipids in urine by LC-MS/MS: application in patients with rheumatoid arthritis.
10.1007/s00216-016-9742-2
Metabolic characterization of the natural progression of chronic hepatitis B.
10.1186/s13073-016-0318-8
Serum-Based Oxylipins Are Associated with Outcomes in Primary Prevention Implantable Cardioverter Defibrillator Patients.
10.1371/journal.pone.0157035
Identification of a Polyketide Synthase Involved in Sorbicillin Biosynthesis by Penicillium chrysogenum.
10.1128/aem.00350-16
Enhanced performance for the analysis of prostaglandins and thromboxanes by liquid chromatography-tandem mass spectrometry using a new atmospheric pressure ionization source.
10.1016/j.chroma.2016.02.055
Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum.
10.1186/s12864-015-2154-4
Collagen Induced Arthritis in DBA/1J Mice Associates with Oxylipin Changes in Plasma.
10.1155/2015/543541
First-Trimester Serum Acylcarnitine Levels to Predict Preeclampsia: A Metabolomics Approach.
10.1155/2015/857108
Matrix Effect Compensation in Small-Molecule Profiling for an LC-TOF Platform Using Multicomponent Postcolumn Infusion.
10.1021/ac504268y
Modulation of stratum corneum lipid composition and organization of human skin equivalents by specific medium supplements.
10.1111/exd.12740
A mutasynthesis approach with a Penicillium chrysogenum ΔroqA strain yields new roquefortine D analogues.
10.1002/cbic.201402686
Systematic evaluation of commercially available ultra-high performance liquid chromatography columns for drug metabolite profiling: optimization of chromatographic peak capacity.
10.1016/j.chroma.2014.11.037
Testing tuberculosis drug efficacy in a zebrafish high-throughput translational medicine screen.
10.1128/aac.03588-14
Roux-en-Y gastric bypass surgery, but not calorie restriction, reduces plasma branched-chain amino acids in obese women independent of weight loss or the presence of type 2 diabetes.
10.2337/dc14-0195
Gas pressure assisted microliquid-liquid extraction coupled online to direct infusion mass spectrometry: a new automated screening platform for bioanalysis.
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Analysis of oxysterols and vitamin D metabolites in mouse brain and cell line samples by ultra-high-performance liquid chromatography-atmospheric pressure photoionization-mass spectrometry.
10.1016/j.chroma.2014.08.088
Metabolic phenotyping reveals a lipid mediator response to ionizing radiation.
10.1021/pr5005295
Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees.
10.1016/j.foodchem.2014.07.076
Pharmacometabolomics reveals that serotonin is implicated in aspirin response variability.
10.1038/psp.2014.22
Enhanced lipid isomer separation in human plasma using reversed-phase UPLC with ion-mobility/high-resolution MS detection.
10.1194/jlr.d047795
A non-canonical NRPS is involved in the synthesis of fungisporin and related hydrophobic cyclic tetrapeptides in Penicillium chrysogenum.
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Metabolomics profiling for identification of novel potential markers in early prediction of preeclampsia.
10.1371/journal.pone.0098540
A protective lipidomic biosignature associated with a balanced omega-6/omega-3 ratio in fat-1 transgenic mice.
10.1371/journal.pone.0096221
Integrating metabolomics profiling measurements across multiple biobanks.
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Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice.
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The importance of free fatty acid chain length for the skin barrier function in atopic eczema patients.
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Intercellular skin barrier lipid composition and organization in Netherton syndrome patients.
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Novel key metabolites reveal further branching of the roquefortine/meleagrin biosynthetic pathway.
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Postprandial fatty acid specific changes in circulating oxylipins in lean and obese men after high-fat challenge tests.
10.1002/mnfr.201300321
Combined LC/MS-platform for analysis of all major stratum corneum lipids, and the profiling of skin substitutes.
10.1016/j.bbalip.2013.10.002
Three-phase electroextraction: a new (online) sample purification and enrichment method for bioanalysis.
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A branched biosynthetic pathway is involved in production of roquefortine and related compounds in Penicillium chrysogenum.
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Skin barrier dysfunction in non-lesional atopic eczema: the role of stratum corneum lipids.
10.1684/ejd.2013.1973
Lipidomics of familial longevity.
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Plasma oxylipin profiling identifies polyunsaturated vicinal diols as responsive to arachidonic acid and docosahexaenoic acid intake in growing piglets.
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Automated pipeline for de novo metabolite identification using mass-spectrometry-based metabolomics.
10.1021/ac303218u
Gender-dependent associations of metabolite profiles and body fat distribution in a healthy population with central obesity: towards metabolomics diagnostics.
10.1089/omi.2012.0062
Fragmentation trees for the structural characterisation of metabolites.
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Increase in short-chain ceramides correlates with an altered lipid organization and decreased barrier function in atopic eczema patients.
10.1194/jlr.p030338
Increased presence of monounsaturated fatty acids in the stratum corneum of human skin equivalents.
10.1038/jid.2012.262
Quantitative profiling of oxylipins through comprehensive LC-MS/MS analysis: application in cardiac surgery.
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Metabolite identification using automated comparison of high-resolution multistage mass spectral trees.
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A lipidomic analysis approach to evaluate the response to cholesterol-lowering food intake.
10.1007/s11306-011-0384-2
An efficient hydrophilic interaction liquid chromatography separation of 7 phospholipid classes based on a diol column.
10.1016/j.chroma.2011.11.034
The impact of delayed storage on the measured proteome and metabolome of human cerebrospinal fluid.
10.1373/clinchem.2011.167601
Attenuation of Slc27a5 gene expression followed by LC-MS measurement of bile acid reconjugation using metabolomics and a stable isotope tracer strategy.
10.1021/pr200475g
Anacetrapib promotes reverse cholesterol transport and bulk cholesterol excretion in Syrian golden hamsters.
10.1194/jlr.m016410
Identifying static and kinetic lipid phenotypes by high resolution UPLC-MS: unraveling diet-induced changes in lipid homeostasis by coupling metabolomics and fluxomics.
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Elemental composition determination based on MS(n).
10.1093/bioinformatics/btr409
Lamellar lipid organization and ceramide composition in the stratum corneum of patients with atopic eczema.
10.1038/jid.2011.175
Localization of fatty acyl and double bond positions in phosphatidylcholines using a dual stage CID fragmentation coupled with ion mobility mass spectrometry.
10.1007/s13361-011-0172-2
Metabolomics of cerebrospinal fluid reveals changes in the central nervous system metabolism in a rat model of multiple sclerosis.
10.1007/s11306-011-0306-3
LC/MS analysis of stratum corneum lipids: ceramide profiling and discovery.
10.1194/jlr.m014456
The pharmacokinetics and pharmacological effect of (S)-5-OH-DPAT following controlled delivery with transdermal iontophoresis.
10.1002/jps.22492
In vivo D2O labeling to quantify static and dynamic changes in cholesterol and cholesterol esters by high resolution LC/MS.
10.1194/jlr.d009787
Mass spectrometric analysis of intact human monoclonal antibody aggregates fractionated by size-exclusion chromatography.
10.1007/s11095-010-0224-5
Coupling of column liquid chromatography and thermospray mass spectrometry via phase‐system switching with an ion‐exchange trapping column
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Membrane interface for the direct coupling of pyrolysis and mass spectrometry
10.1016/0003-2670(95)00244-T
Nonpolar solvents for normal-phase liquid chromatography and postcolumn extraction in thermospray liquid chromatography/mass spectrometry
10.1021/ac00214a033
The derivatization of fatty acids by (chloro)alkyl chloroformates in non‐aqueous and aqueous media for GC analysis
10.1002/jhrc.1240151203
Coupling of ion-pair liquid chromatography and thermospray mass spectrometry via phase-system switching with a polymeric trapping column
10.1016/0021-9673(93)83065-Z
Coupling of capillary zone electrophoresis to mass spectrometry (MS and MS/MS) via a nanoelectrospray interface for the characterisation of some β-agonists
10.1002/(SICI)1097-0231(19990415)13:7<612::AID-RCM531>3.0.CO;2-D
Capillary electrochromatography/nanoelectrospray mass spectrometry for attomole characterization of peptides
10.1002/1097-0231(20000830)14:16<1448::AID-RCM44>3.0.CO;2-9
Determination of quaternary amine pesticides by thermospray mass spectrometry
10.1016/0021-9673(93)83407-J
Advance in Analysis and Detection Technologies for Phospholipidomics
10.1016/S1872-2040(16)60939-8
Recent developments in sample-pretreatment techniques for mass spectrometry-based metabolomics
10.1016/j.trac.2014.06.003
The influence of citrate, EDTA, and heparin anticoagulants to human plasma LC-MS lipidomic profiling
10.1007/s11306-012-0450-4
Chapter 11. On-Line Post Column Liquid-Solid and Liquid-Liquid Extractions in Environmental Liquid Chromatography- Thermospray-Mass Spectrometry
10.1016/S0301-4770(08)60788-5
The use of mobile phase additives in the determination of 55 (polar) pesticides by column liquid chromatography-thermospray-mass spectrometry
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Ion trap mass spectrometry as detector for capillary electrochromatography of peptides: Possibilities and limitations
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Global profiling of the muscle metabolome: method optimization, validation and application to determine exercise-induced metabolic effects
10.1007/s11306-014-0701-7
Erratum: Localization of fatty acyl and double bond positions in phosphatidylcholines using a dual stage CID fragmentation coupled with ion mobility mass spectrometry (Journal of The American Society for Mass Spectrometry DOI: 10.1007/s13361-011-0172-2)
10.1007/s13361-011-0199-4
Selective analysis of the herbicides glyphosate and aminomethylphosphonic acid in water by on-line solid-phase extraction-high- performance liquid chromatography-electrospray ionization mass spectrometry
10.1016/S0021-9673(97)01129-1
Erratum: Comprehensive LC-MSElipidomic analysis using a shotgun approach and its application to biomarker detection and identification in osteoarthritis patients (Journal of Proteome Research (2010) 9 (2377-2389) DOI: 10.1021/pr901094j)
10.1021/pr200420k
Chloroacetonitrile as eluent additive in thermospray liquid chromatography/negative ion mass spectrometry for the characterization of chlorinated organic pollutants
10.1002/bms.1200190806
Rapid metabolic screening of early zebrafish embryogenesis based on direct infusion-nanoESI-FTMS
10.1007/s11306-012-0493-6
Identification of Artefacts in the Desorption of Active Charcoal Tubes with Carbon Disulphide and Methanol. Reduction of Artefact Formation by Selecting Other Polar Additives
10.1080/03067318808079927
Ionisation efficiencies can be predicted in complicated biological matrices: A proof of concept
10.1016/j.aca.2018.05.072
Cross-Species Molecular Imaging of Bile Salts and Lipids in Liver: Identification of Molecular Structural Markers in Health and Disease
10.1021/acs.analchem.8b01378
Targeted Drug and Metabolite Imaging: Desorption Electrospray Ionization Combined with Triple Quadrupole Mass Spectrometry
10.1021/acs.analchem.8b03857
Development and evaluation of matrix application techniques for high throughput mass spectrometry imaging of tissues in the clinic
10.1016/j.clinms.2019.01.004
Oxylipin profiling in endothelial cells in vitro – Effects of DHA and hydrocortisone upon an inflammatory challenge
10.1016/j.prostaglandins.2019.106352
Quantitative Mass Spectrometry Imaging to Study Drug Distribution in the Intestine Following Oral Dosing
10.1021/acs.analchem.0c03956
Quantitative mass spectrometry imaging of drugs and metabolites: a multiplatform comparison
10.1007/s00216-021-03210-0
Direct nose to brain delivery of small molecules: critical analysis of data from a standardized in vivo screening model in rats.
10.1080/10717544.2020.1837291
2-Methyl-pentanoyl-carnitine (2-MPC): a urine biomarker for patent Ascaris lumbricoides infection.
10.1038/s41598-020-72804-y
Skin of atopic dermatitis patients shows disturbed β-glucocerebrosidase and acid sphingomyelinase activity that relates to changes in stratum corneum lipid composition.
10.1016/j.bbalip.2020.158673
Spatial heterogeneity of nanomedicine investigated by multiscale imaging of the drug, the nanoparticle and the tumour environment.
10.7150/thno.38625
Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective.
10.1016/j.aca.2019.10.043
Enhanced Sensitivity Using MALDI Imaging Coupled with Laser Postionization (MALDI-2) for Pharmaceutical Research.
10.1021/acs.analchem.9b02495
Oxidative stress and abnormal bioactive lipids in early cystic fibrosis lung disease.
10.1016/j.jcf.2019.04.011
High-Resolution Mass Spectrometry Quantification: Impact of Differences in Data Processing of Centroid and Continuum Data.
10.1007/s13361-018-2101-0
Translational safety biomarkers of colonic barrier integrity in the rat.
10.1002/jat.3639
Evaluation of cardiac arrhythmic risks using a rabbit model of left ventricular systolic dysfunction.
10.1016/j.ejphar.2018.05.026
Marnix H. Medema
Medema Marnix H.
ORCID: 0000-0002-2191-2821
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
