Paperbase

Kyo Bin Kang

Kang Kyo Bin

ORCID: 0000-0003-3290-1017

Email: kbkang@sookmyung.ac.kr

https://www.kyobinkanglab.org

Prediction of tyrosinase inhibitory activities of Morus alba root bark extracts from HPLC fingerprints 10.1016/j.microc.2013.08.012

Anti-Influenza Activity of Betulinic Acid from Zizyphus jujuba on Influenza A/PR/8 Virus 10.4062/biomolther.2015.019

Jubanines F–J, cyclopeptide alkaloids from the roots of Ziziphus jujuba 10.1016/j.phytochem.2015.09.001

Identification of ginsenoside markers from dry purified extract of Panax ginseng by a dereplication approach and UPLC–QTOF/MS analysis 10.1016/j.jpba.2015.02.034

Antiplasmodial activity, cytotoxicity and structure-activity relationship study of cyclopeptide alkaloids 10.3390/molecules22020224

Catechin-Bound Ceanothane-Type Triterpenoid Derivatives from the Roots of Zizyphus jujuba 10.1021/acs.jnatprod.6b01103

Ceanothane- and lupane-type triterpene esters from the roots of Hovenia dulcis and their antiproliferative activity on HSC-T6 cells 10.1016/j.phytochem.2017.06.014

Cytotoxic Ceanothane- and Lupane-Type Triterpenoids from the Roots of Ziziphus jujuba 10.1021/acs.jnatprod.6b00525

UHPLC-ESI-qTOF-MS analysis of cyclopeptide alkaloids in the seeds of Ziziphus jujuba var. Spinosa 10.5478/MSL.2016.7.2.45

Acylphloroglucinolated Catechin and Phenylethyl Isocoumarin Derivatives from Agrimonia pilosa 10.1021/acs.jnatprod.6b00566

Ginsenoside 20(S)-Rh2 exerts anti-cancer activity through targeting IL-6-induced JAK2/STAT3 pathway in human colorectal cancer cells 10.1016/j.jep.2016.08.039

Combined Application of UHPLC-QTOF/MS, HPLC-ELSD and ¹H–NMR Spectroscopy for Quality Assessment of DA-9801, A Standardised Dioscorea Extract 10.1002/pca.2659

Argininosecologanin, a secoiridoid-derived guanidine alkaloid from the roots of Lonicera insularis 10.1080/14786419.2017.1361953

C-Methylated Flavonoid Glycosides from Pentarhizidium orientale Rhizomes and Their Inhibitory Effects on the H1N1 Influenza Virus 10.1021/acs.jnatprod.7b00677

Berchemiosides A–C, 2-Acetoxy-ω-phenylpentaene Fatty Acid Triglycosides from the Unripe Fruits of Berchemia berchemiifolia 10.1021/acs.jnatprod.7b00602

Rhamnellosides A and B, ω-phenylpentaene fatty acid amide diglycosides from the fruits of rhamnella franguloides 10.3390/molecules23040752

Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng 10.1038/s41598-018-30262-7

Genome and evolution of the shade-requiring medicinal herb Panax ginseng 10.1111/pbi.12926

Simultaneous Determination and Stability Test of Two Phthalic Anhydride Derivatives, Senkyunolide A and Z-Ligustilide, in the Water Extract of Cnidium Rhizome from Different Geographical Regions and Species Using HPLC-UVD Analysis 10.1002/bkcs.11471

Chemical and genomic diversity of six Lonicera species occurring in Korea 10.1016/j.phytochem.2018.07.012

Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication 10.1021/acs.jnatprod.8b00292

The complete chloroplast genome sequence of Korean Lonicera japonica and intra-species diversity 10.1080/23802359.2018.1502637

Classficiation of Bupleuri Radix according to Geographical Origins using Near Infrared Spectroscopy (NIRS) Combined with Supervised Pattern Recognition 10.20307/nps.2018.24.3.164

Multiple Targets of 3-Dehydroxyceanothetric Acid 2-Methyl Ester to Protect Against Cisplatin-Induced Cytotoxicity in Kidney Epithelial LLC-PK1 Cells 10.3390/molecules24050878

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

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

Molecular Networking Reveals the Chemical Diversity of Selaginellin Derivatives, Natural Phosphodiesterase-4 Inhibitors from Selaginella tamariscina 10.1021/acs.jnatprod.9b00049

Identification and semi-synthesis of 3-O-protocatechuoylceanothic acid, a novel and natural GPR120 agonist ^† 10.3390/molecules24193487

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

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

Unique triterpenoid of jujube root protects cisplatin-induced damage in kidney epithelial LLC-PK1 cells via autophagy regulation 10.3390/nu12030677

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

Combined MS/MS-NMR Annotation Guided Discovery of Iris lactea var. chinensis Seed as a Source of Viral Neuraminidase Inhibitory Polyphenols 10.3390/molecules25153383

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

A Metabolic Choreography of Maize Plants Treated with a Humic Substance-Based Biostimulant under Normal and Starved Conditions 10.3390/metabo11060403

Chemical and Biological Profiles of Dendrobium in Two Different Species, Their Hybrid, and Gamma-Irradiated Mutant Lines of the Hybrid Based on LC-QToF MS and Cytotoxicity Analysis 10.3390/plants10071376

Elizabeth Brown

Brown Elizabeth

ORCID: 0000-0002-4264-8070

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

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

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

Alyssa Demko

Demko Alyssa / Alyssa M. Demko

ORCID: 0000-0002-6690-8172

Declines in plant palatability from polar to tropical latitudes depend on herbivore and plant identity 10.1002/ecy.1918

Detection of Natural Products and Their Producers in Ocean Sediments 10.1128/aem.02830-18

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

Michael Yoon

Yoon Michael

ORCID: 0000-0002-2900-5257

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

Cathepsin B in neurodegeneration of Alzheimer's disease, traumatic brain injury, and related brain disorders 10.1016/j.bbapap.2020.140428

Assessing the Acceptance of the Pay-For-Performance Model in a Segment of California Pharmacists https://doi.org/10.37901/jcphp17-00011

Differential Neuropeptidomes of Dense Core Secretory Vesicles (DCSV) Produced at Intravesicular and Extracellular pH Conditions by Proteolytic Processing 10.1021/acschemneuro.1c00133

A Clinical-Stage Cysteine Protease Inhibitor blocks SARS-CoV-2 Infection of Human and Monkey Cells 10.1021/acschembio.0c00875

Selective Neutral pH Inhibitor of Cathepsin B Designed Based on Cleavage Preferences at Cytosolic and Lysosomal pH Conditions 10.1021/acschembio.1c00138

Aaron Oom

Oom Aaron / Aaron L. Oom

ORCID: 0000-0003-3300-0333

MicroRNAs: Novel Players in Cancer Diagnosis and Therapies 10.1155/2014/959461

MicroRNA-200b targets protein kinase C and suppresses triple-negative breast cancer metastasis 10.1093/carcin/bgu133

Elicitation of Robust Tier 2 Neutralizing Antibody Responses in Nonhuman Primates by HIV Envelope Trimer Immunization Using Optimized Approaches. 10.1016/j.immuni.2017.05.007

Identification of putative unique immunogenic ZIKV and DENV1-4 peptides for diagnostic cellular based tests 10.1038/s41598-017-05980-z

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

Comparative Analysis of T Cell Spatial Proteomics and the Influence of HIV Expression 10.1101/2021.03.17.435902

Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity 10.1101/2021.04.06.438579

Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity 10.1371/journal.ppat.1009519

Ricardo da Silva

da Silva Ricardo

ORCID: 0000-0001-6378-0479

http://ccbl.fcfrp.usp.br

Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter 10.1007/s13361-018-2069-9

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome 10.1186/s40168-019-0636-3

A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles 10.1371/journal.pone.0207051

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation 10.1021/acs.jnatprod.7b00737

Chemical profiling of two congeneric sea mat corals along the Brazilian coast: adaptive and functional patterns 10.1039/c7cc08411k

Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908

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

Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication 10.1021/acs.jnatprod.8b00292

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples 10.1021/acs.analchem.7b01381

Global chemical analysis of biology by mass spectrometry 10.1038/s41570-017-0054

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter 10.3389/fmars.2017.00405

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols 10.1021/acsjnatprod.6b00722

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung 10.1016/j.chom.2017.10.001

Application of MALDI Mass Spectrometry in Natural Products Analysis 10.1055/s-0042-104800

From Sample to Multi-Omics Conclusions in under 48 Hours 10.1128/mSystems.00038-16

Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113

A metabolomic protocol for plant systematics by matrix-assisted laser-desorption/ionization time-of flight mass spectrometry 10.1016/j.aca.2015.01.002

Illuminating the dark matter in metabolomics 10.1073/pnas.1516878112

Mass spectrometry in plant metabolomics strategies: from analytical platforms to data acquisition and processing 10.1039/c3np70086k

ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics 10.1093/bioinformatics/btu019

Queen signals in a stingless bee: suppression of worker ovary activation and spatial distribution of active compounds 10.1038/srep07449

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

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis 10.1128/MSYSTEMS.00375-19

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

In silico annotation of discriminative markers of three Zanthoxylum species using molecular network derived annotation propagation 10.1016/J.FOODCHEM.2019.05.099

Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation 10.1021/ACS.JNATPROD.8B00916

The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/S12915-019-0660-6

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

Initial Development toward Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin 10.1021/ACS.ANALCHEM.8B05854

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

Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim 10.1021/acsinfecdis.9b00513

Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9

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

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

Time-Scale Shifting of Volatile Semiochemical Levels in Wild Type Lychnophora ericoides (Brazilian arnica) and Pollinator Records 10.1055/a-1320-4556

Distinct photo-oxidation-induced cell death pathways lead to selective killing of human breast cancer cells 10.1038/s41419-020-03275-2

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria 10.3390/md19010020

Convergent evolution of pain-inducing defensive venom components in spitting cobras 10.1126/science.abb9303

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

REDES MOLECULARES: UMA ANÁLISE SOBRE ANOTAÇÕES E DESCOBERTA DE NOVOS ATIVOS 10.21577/0100-4042.20170777

CHAPTER 10. Perspectives for the Future 10.1039/9781788010399-00264

CHAPTER 3. Metabolomics 10.1039/9781788010399-00057

Mass Spectrometry in Chemical Biology 10.1039/9781788010399

Julia Gauglitz

Gauglitz Julia / Julia M. Vraspir

ORCID: 0000-0003-3146-2489

Amphiphilic siderophore production by oil-associating microbes 10.1039/c4mt00047a

Microbial Tailoring of Acyl Peptidic Siderophores 10.1021/bi500266x

A suite of citrate-derived siderophores from a marine Vibrio species isolated following the Deepwater Horizon oil spill 10.1016/j.jinorgbio.2011.10.013

Optical Signatures of Dissolved Organic Matter Transformation in the Global Ocean 10.3389/fmars.2015.00118

Amino acid variability in the peptide composition of a suite of amphiphilic peptide siderophores from an open ocean Vibrio species 10.1007/s00775-013-0995-3

Identification of new members within suites of amphiphilic marine siderophores 10.1007/s10534-010-9378-1

Chemistry of Marine Ligands and Siderophores 10.1146/annurev.marine.010908.163712

Both Incubation Temperature and Posthatching Temperature Affect Swimming Performance and Morphology of Wood Frog Tadpoles ( Rana sylvatica ) 10.1086/498182

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

Untargeted Mass Spectrometry-Based Metabolomics Approach Unveils Molecular Changes in Raw and Processed Foods and Beverages 10.1016/j.foodchem.2019.125290

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1101/790063

Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds 10.1101/824888

A UHPLC-HRMS based metabolomics and chemoinformatics approach to chemically distinguish ‘super foods’ from a variety of plant-based foods 10.1016/j.foodchem.2019.126071

Active nitrogen fixation by Crocosphaera expands their niche despite the presence of ammonium – A case study 10.1038/s41598-019-51378-4

Quantifying Oxygen Management and Temperature and Light Dependencies of Nitrogen Fixation by Crocosphaera watsonii 10.1128/msphere.00531-19

Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales 10.1016/j.ddmod.2019.08.012

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

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

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

Mauricio Caraballo

Caraballo Mauricio / Mauricio Caraballo / Andres M Caraballo-Rodriguez

ORCID: 0000-0001-5499-2728

Amphotericin B as an inducer of griseofulvin-containing guttate in the endophytic fungus Xylaria cubensis FLe9 10.1007/s00049-017-0243-3

Molecular inter-kingdom interactions of endophytes isolated from Lychnophora ericoides 10.1038/s41598-017-05532-5

Expanding the Chemical Repertoire of the Endophyte Streptomyces albospinus RLe7 Reveals Amphotericin B as an Inducer of a Fungal Phenotype 10.1021/acs.jnatprod.6b00870

Endophytic Actinobacteria from the Brazilian Medicinal PlantLychnophora ericoidesMart. and the Biological Potential of Their Secondary Metabolites 10.1002/cbdv.201500225

Protocol for Community‐created Public MS/MS Reference Spectra Within the Global Natural Products Social Molecular Networking Infrastructure 10.1002/rcm.8725

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

Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau 10.1021/acs.jnatprod.9b01128

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

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 10.1038/s41587-019-0209-9

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

The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization 10.1038/s41467-019-09944-x

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

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

Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales 10.1016/j.ddmod.2019.08.012

Chemical signaling involved in plant–microbe interactions 10.1039/c7cs00343a

A Convolutional Neural Network-Based Approach for the Rapid Characterization of Molecularly Diverse Natural Products 10.1021/jacs.9b13786

Gajender Aleti

Aleti Gajender

ORCID: 0000-0002-1867-9758

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease 10.1128/mbio.00321-19

Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage 10.1038/s41598-017-02314-x

Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review 10.1016/j.scitotenv.2018.02.037

The draft genome sequence of Paenibacillus polymyxa strain CCI-25 encompasses high potential for secondary metabolite production 10.1128/genomeA.00366-16

Wake-up-call, a lin-52 paralogue, and Always early, a lin-9 homologue physically interact, but have opposing functions in regulating testis-specific gene expression 10.1016/j.ydbio.2011.04.030

Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis 10.3389/fimmu.2019.02602

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

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity 10.1371/journal.pone.0198107

Surfactin variants mediate species-specific biofilm formation and root colonization in Bacillus 10.1111/1462-2920.13405

Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults 10.1016/j.bbi.2020.02.004

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Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes 10.1016/j.csbj.2015.03.003

A community resource for paired genomic and metabolomic data mining. 10.1038/s41589-020-00724-z

Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma. 10.1007/s00248-020-01596-5

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

Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides 10.1101/2021.08.10.21255754

Irina Koester

Koester Irina

ORCID: 0000-0002-1571-882X

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 10.1038/s41587-019-0209-9

Biological Impacts of the 2013–2015 Warm-Water Anomaly in the Northeast Pacific: Winners, Losers, and the Future 10.5670/oceanog.2016.32

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats 10.1021/acs.analchem.6b03456

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter 10.3389/fmars.2017.00405

Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level 10.3389/fmicb.2016.00321

Spatiotemporal variability in seawater carbon chemistry for a coral reef flat in Kāne‘ohe Bay, Hawai‘i 10.1002/lno.11084

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

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

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC 10.1038/s42256-020-00234-6

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC 10.1038/s42256-020-00259-x

jehad almaliti

almaliti jehad

ORCID: 0000-0002-3562-0846

Apratoxin Kills Cells by Direct Blockade of the Sec61 Protein Translocation Channel 10.1016/j.chembiol.2016.04.008

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

Natural products inspired synthesis of neuroprotective agents against H2O2-induced cell death 10.1016/j.bmcl.2013.01.013

Dudawalamides A–D, Antiparasitic Cyclic Depsipeptides from the Marine Cyanobacterium Moorea producens 10.1021/acs.jnatprod.7b00034

Discovery and Synthesis of Caracolamide A, an Ion Channel Modulating Dichlorovinylidene Containing Phenethylamide from a Panamanian Marine Cyanobacterium cf. Symploca Species 10.1021/acs.jnatprod.7b00367

20S proteasome as a drug target in Trichomonas vaginalis 10.1128/AAC.00448-19

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

Development of a Potent Inhibitor of the Plasmodium Proteasome with Reduced Mammalian Toxicity 10.1021/acs.jmedchem.7b00671

The Proteasome as a Drug Target in the Metazoan Pathogen, Schistosoma mansoni 10.1021/acsinfecdis.9b00237

Exploration of the carmaphycins as payloads in antibody drug conjugate anticancer agents 10.1016/j.ejmech.2018.10.024

Design of Gallinamide A Analogs as Potent Inhibitors of the Cysteine Proteases Human Cathepsin L and Trypanosoma cruzi Cruzain 10.1021/acs.jmedchem.9b00294

Largazole Analogues Embodying Radical Changes in the Depsipeptide Ring: Development of a More Selective and Highly Potent Analogue 10.1021/acs.jmedchem.6b01271

Jacob Wozniak

Wozniak Jacob

ORCID: 0000-0002-2453-0861

Phosphoproteomic analysis of protease-activated receptor-1 biased signaling reveals unique modulators of endothelial barrier function 10.1073/pnas.1917295117

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules 10.1016/j.cell.2017.12.032

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/msystems.00031-18

Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Protein Vpr 10.1074/mcp.m116.066019

Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas 10.1016/j.cels.2018.04.010

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

Quantitative Multiplex Substrate Profiling of Peptidases by Mass Spectrometry 10.1074/mcp.tir118.001099

Optimization of carbon and energy utilization through differential translational efficiency 10.1038/s41467-018-06993-6

EGFR is required for Wnt9a–Fzd9b signalling specificity in haematopoietic stem cells 10.1038/s41556-019-0330-5

Organ-level protein networks as a reference for the host effects of the microbiome 10.1101/gr.256875.119

Quantitative analysis of Mycobacterium avium subsp. hominissuis proteome in response to antibiotics and during exposure to different environmental conditions 10.1186/s12014-019-9260-2

AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions 10.1093/bioinformatics/btz714

PTMphinder: an R package for PTM site localization and motif extraction from proteomic datasets 10.7717/peerj.7046

Functional and Proteomic Analysis of Streptococcus pyogenes Virulence Upon Loss of Its Native Cas9 Nuclease 10.3389/fmicb.2019.01967

Molecular dissection of Chagas induced cardiomyopathy reveals central disease associated and druggable signaling pathways 10.1371/journal.pntd.0007980

Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic Signatures 10.1016/j.cell.2020.07.040

CLK1 reorganizes the splicing factor U1-70K for early spliceosomal protein assembly 10.1073/pnas.2018251118

Heat shock protein 27 activity is linked to endothelial barrier recovery after proinflammatory GPCR-induced disruption 10.1126/scisignal.abc1044

Carlos Molina-Santiago

Molina-Santiago Carlos / Molina-Santiago, C

ORCID: 0000-0002-1131-8917

Differential transcriptional response to antibiotics by Pseudomonas putida DOT-T1E. 10.1111/1462-2920.12775

GtrS and GltR form a two-component system: the central role of 2-ketogluconate in the expression of exotoxin A and glucose catabolic enzymes in Pseudomonas aeruginosa. 10.1093/nar/gku496

Bactericidal and bacteriostatic antibiotics and the Fenton reaction. 10.1111/1751-7915.12120

Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance. 10.1111/1462-2920.12368

Fructooligosacharides reduce Pseudomonas aeruginosa PAO1 pathogenicity through distinct mechanisms. 10.1371/journal.pone.0085772

Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital 10.1371/journal.pone.0081604

Identification of new residues involved in intramolecular signal transmission in a prokaryotic transcriptional repressor. 10.1128/JB.00589-13

Antibiotic adjuvants: identification and clinical use. 10.1111/1751-7915.12044

Evolution of antibiotic resistance, catabolic pathways and niche colonization. 10.1111/j.1751-7915.2012.00335.x

Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440. 10.1128/AAC.05398-11

Directed evolution, natural products for cancer chemotherapy, and micro-biosensing robots. 10.1111/j.1751-7915.2011.00267.x

Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene. 10.1111/1462-2920.13585

Pseudomonas putida as a platform for the synthesis of aromatic compounds. 10.1099/mic.0.000333

A Pseudomonas putida double mutant deficient in butanol assimilation: a promising step for engineering a biological biofuel production platform. 10.1093/femsle/fnw018

Understanding butanol tolerance and assimilation in Pseudomonas putida BIRD-1: an integrated omics approach. 10.1111/1751-7915.12328

Efflux pump-deficient mutants as a platform to search for microbes that produce antibiotics. 10.1111/1751-7915.12295

Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida. 10.1093/femsre/fuv006

Interspecies cross-talk between co-cultured Pseudomonas putida and Escherichia coli 10.1111/1758-2229.12553

Draft whole-genome sequence of the antibiotic-producing soil isolate Pseudomonas sp. strain 250J 10.1111/1758-2229.12245

Diversity of small RNAs expressed in Pseudomonas species 10.1111/1758-2229.12233

Insights in a novel gram‐positive type IV secretion system 10.1111/1462-2920.14296

The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization 10.1038/s41467-019-09944-x

Microbiomes as the new keystone for life sciences development 10.1111/1751-7915.13424

Chemical fertilization: a short‐term solution for plant productivity? 10.1111/1751-7915.13515

Dual functionality of the amyloid protein TasA in Bacillus physiology and fitness on the phylloplane 10.1038/s41467-020-15758-z

Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide. 10.3389/fmicb.2020.00202

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

Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production. 10.1111/1751-7915.13269

The race for antimicrobials in the multidrug resistance era. 10.1111/1751-7915.12884

More than words: the chemistry behind the interactions in the plant holobiont 10.1111/1462-2920.15197