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

Sebastian Böcker

Böcker Sebastian

ORCID: 0000-0002-9304-8091

http://bio.informatik.uni-jena.de/

SIRIUS~4: a rapid tool for turning tandem mass spectra into metabolite structure information 10.1038/s41592-019-0344-8

Expanding the Use of Spectral Libraries in Proteomics. 10.1021/acs.jproteome.8b00485

Liquid-Chromatography Retention Order Prediction for Metabolite Identification 10.1093/bioinformatics/bty590

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints 10.1093/bioinformatics/bty245

BCD Beam Search: Considering suboptimal partial solutions in Bad Clade Deletion supertrees 10.7717/peerj.4987

Secondary ion mass spectrometry imaging and multivariate data analysis reveal co-aggregation patterns of Populus trichocarpa leaf surface compounds on a micrometer scale 10.1111/tpj.13763

Significance estimation for large scale metabolomics annotations by spectral matching 10.1038/s41467-017-01318-5

Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm 10.1093/molbev/msx191

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis 10.1515/jib-2017-0010

Critical Assessment of Small Molecule Identification 2016: Automated Methods 10.1186/s13321-017-0207-1

Exploring the Limits of the Geometric Copolymerization Model 10.3390/polym9030101

Searching molecular structure databases using tandem MS data: are we there yet? 10.1016/j.cbpa.2016.12.010

Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina). 10.1371/journal.pgen.1006491

Finding approximate gene clusters with Gecko 3. 10.1093/nar/gkw843

Predicting the presence of uncommon elements in unknown biomolecules from isotope patterns 10.1021/acs.analchem.6b01015

Collecting reliable clades using the Greedy Strict Consensus Merger 10.7717/peerj.2172

New Statistical Models for Copolymerization 10.3390/polym8060240

Fast metabolite identification with Input Output Kernel Regression 10.1093/bioinformatics/btw246

Abundance correction for mass discrimination effects in polymer mass spectra 10.1002/rcm.7553

Fragmentation trees reloaded 10.1186/s13321-016-0116-8

Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data. 10.1002/mas.21489

Searching molecular structure databases with tandem mass spectra using CSI:FingerID 10.1073/pnas.1509788112

Collecting reliable clades using the Greedy Strict Consensus Merger 10.7287/peerj.preprints.1297

Correcting mass shifts: A lock-mass-free recalibration procedure for mass spectrometry imaging data 10.1007/s00216-015-8935-4

COCONUT—An Efficient Tool for Estimating Copolymer Compositions from Mass Spectra. 10.1021/acs.analchem.5b00146

Identifying gene clusters by discovering common intervals in indeterminate strings. 10.1186/1471-2164-15-S6-S2

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). 10.1371/journal.pgen.1004496

Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees 10.5702/massspectrometry.S0037

Metabolite Identification through Multiple Kernel Learning on Fragmentation Trees 10.1093/bioinformatics/btu275

New kids on the block: novel informatics methods for natural product discovery. 10.1039/c3np70101h

Mass spectrometry imaging of surface lipids on intact Drosophila melanogaster flies. 10.1002/jms.3331

Statistics for approximate gene clusters 10.1186/1471-2105-14-S15-S14

Munronia pinnata (Wall.) Theob.: unveiling phytochemistry and dual inhibition of 5-lipoxygenase and microsomal prostaglandin E2 synthase (mPGES)-1. 10.1016/j.jep.2013.11.052

Counting glycans revisited 10.1007/s00285-013-0721-3

Molecular Formula Identification with SIRIUS 10.3390/metabo3020506

Finding Maximum Colorful Subtrees in practice 10.1089/cmb.2012.0083

Computational mass spectrometry for small molecules. 10.1186/1758-2946-5-12

Determination of 15N-incorporation into plant proteins and their absolute quantitation: a new tool to study nitrogen flux dynamics and protein pool sizes elicited by plant-herbivore interactions 10.1021/pr300465n

De Novo Analysis of Electron Impact Mass Spectra Using Fragmentation Trees 10.1016/j.aca.2012.06.021

Comment on ''An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses'' by Claesen et al. 10.1007/s13361-012-0402-2

Recovering Symbolically Dated, Rooted Trees from Symbolic Ultrametrics 10.1006/aima.1998.1743

Fast alignment of fragmentation trees 10.1093/bioinformatics/bts207

Identifying the unknowns by aligning fragmentation trees 10.1021/ac300304u

Polynomial Supertree Methods Revisited 10.1155/2011/524182

Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data 10.1089/cmb.2011.0168

Determination of glycan structure from tandem mass spectra. 10.1109/tcbb.2010.129

Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra 10.1002/rcm.5019

Swiftly computing center strings 10.1186/1471-2105-12-106

Comprehensive cluster analysis with Transitivity Clustering 10.1038/nprot.2010.197

Automated Bond Order Assignment as an Optimization Problem 10.1093/bioinformatics/btq718

Computing fragmentation trees from tandem mass spectrometry data 10.1021/ac101825k

Combinatorics of aliphatic amino acids 10.1007/s00114-010-0743-2

Computational mass spectrometry for metabolomics: identification of metabolites and small molecules. 10.1007/s00216-010-4142-5

Partitioning biological data with transitivity clustering 10.1038/nmeth0610-419

Unbiased transcriptional comparisons of generalist and specialist herbivores feeding on progressively defenseless Nicotiana attenuata plants. 10.1371/journal.pone.0008735

De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation 10.1002/elps.200900332

Computation of median gene clusters 10.1089/cmb.2009.0098

On optimal comparability editing with applications to molecular diagnostics 10.1186/1471-2105-10-S1-S61

SIRIUS: Decomposing isotope patterns for metabolite identification 10.1093/bioinformatics/btn603

Peak Intensity Prediction in MALDI-TOF Mass Spectrometry: A Machine Learning Study to Support Quantitative Proteomics 10.1186/1471-2105-9-443

Towards de novo identification of metabolites by analyzing tandem mass spectra 10.1093/bioinformatics/btn270

EPoS: A modular software framework for phylogenetic analysis 10.1093/bioinformatics/btn364

DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem 10.1093/bioinformatics/btm631

Combinatorial Approaches for Mass Spectra Recalibration 10.1109/tcbb.2007.1077

SAMPI: Protein identification with Mass Spectra Alignments 10.1186/1471-2105-8-102

Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry 10.1093/bioinformatics/btl291

Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS 10.1093/nar/gni038

Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+~nt 10.1089/cmb.2004.11.1110

Novel mass spectrometry-based tool for genotypic identification of mycobacteria. 10.1128/JCM.42.1.339-346.2004

High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. 10.1101/gr.1692304

SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry 10.1093/bioinformatics/btg1004

Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. 10.1073/pnas.102165899

Simple but fundamental limitations on supertree and consensus tree methods. 10.1093/sysbio/49.2.363

A golden ratio parameterized algorithm for Cluster Editing 10.1007/978-3-642-25011-8_7

German Conference on Bioinformatics 2012 10.4230/OASIcs.GCB.2012

Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491) 10.4230/DagRep.7.12.1

Computational Metabolomics (Dagstuhl Seminar 15492) 10.4230/DagRep.5.11.180

FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time 10.1007/978-3-642-22685-4_4

Polynomial Supertree Methods Revisited 10.1007/978-3-642-16001-1_16

Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+~nt (extended abstract) 10.1007/b13243

Heuristic algorithms for the Maximum Colorful Subtree problem 10.4230/LIPIcs.WABI.2018.23

Cluster Editing 10.1007/978-3-642-39053-1_5

Inferring peptide composition from molecular formulas 10.1007/978-3-642-02882-3

An Improved Fixed-Parameter Algorithm for Minimum-Flip Consensus Trees 10.1007/978-3-540-79723-4

Computing Bond Types in Molecule Graphs 10.1007/978-3-642-02882-3_28

Annotating fragmentation patterns 10.1007/978-3-642-04241-6

Determination of glycan structure from tandem mass spectra 10.1007/978-3-642-02882-3_26

Exact Algorithms for Cluster Editing: Evaluation and Experiments 10.1007/978-3-540-68552-4_22

Going Weighted: Parameterized Algorithms for Cluster Editing 10.1007/978-3-540-85097-7_1

Computation of Median Gene Clusters 10.1007/978-3-540-78839-3_28

The generalized Robinson-Foulds metric 10.1007/978-3-642-40453-5_13

Decomposing metabolomic isotope patterns 10.1007/11851561_2

A faster fixed-parameter approach to drawing binary tanglegrams 10.1007/978-3-642-11269-0_3

Exact ILP Solutions for Phylogenetic Minimum Flip Problems 10.1145/1854776.1854800

Fragmentation trees reloaded 10.1007/978-3-319-16706-0_10

Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways 10.4230/OASIcs.GCB.2012.12

Collecting reliable clades using the Greedy Strict Consensus Merger 10.7287/peerj.preprints.1297v1

Faster mass decomposition 10.1007/978-3-642-40453-5_5

Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting 10.1007/978-3-540-73060-6_3

Swiftly computing center strings 10.1007/978-3-642-15294-8_27

Finding Characteristic Substructures for Metabolite Classes 10.4230/OASIcs.GCB.2012.23

SOM-based peptide prototyping for mass spectrometry peak intensity prediction 10.2390/biecoll-wsom2007-157

Neural network approach for mass spectrometry prediction by peptide prototyping 10.1007/978-3-540-74695-9

Multiple Mass Spectrometry Fragmentation Trees Revisited: Boosting Performance and Quality 10.1007/978-3-662-44753-6_17

Mapping metabolites from rough terrain: laser ablation electrospray ionization on non-flat samples 10.1039/C6RA26854D

Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting 10.1007/978-3-642-02490-0_63

Computing fragmentation trees from metabolite multiple mass spectrometry data 10.1007/978-3-642-20036-6_36

Speedy Colorful Subtrees 10.1007/978-3-319-21398-9_25

FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time 10.1007/s00453-012-9698-3

A golden ratio parameterized algorithm for Cluster Editing 10.1016/j.jda.2012.04.005

Ten times eighteen 10.2197/ipsjjip.23.258

Even faster parameterized cluster deletion and cluster editing 10.1016/j.ipl.2011.05.003

A Note on Maximal Hierarchies 10.1006/aima.1999.1891

Sequencing from Compomers: The Puzzle 10.1007/s00224-005-1238-y

Exponentially many supertrees 10.1016/S0893-9659(02)00054-X

A Note on the Parameterized Complexity of Unordered Maximum Tree Orientation 10.1016/j.dam.2012.02.017

Patchworks 10.1006/aima.1999.1912

A fast and simple algorithm for the Money Changing Problem 10.1007/s00453-007-0162-8

Mass Spectra Alignments and Their Significance 10.1016/j.jda.2006.11.003

Improved Fixed-Parameter Algorithms for Minimum-Flip Consensus Trees 10.1145/2071379.2071386

Algorithmic aspects of tree amalgamation 10.1006/jagm.2000.1116

Exact Algorithms for Cluster Editing: Evaluation and Experiments 10.1007/s00453-009-9339-7

Computing Bond Orders in Molecule Graphs 10.1016/j.tcs.2010.12.063

Going Weighted: Parameterized Algorithms for Cluster Editing 10.1016/j.tcs.2009.05.006

RNAse T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis 10.1093/nar/gng047

A novel mass spectrometry based tool for genotypic identification of mycobacteria http://jcm.asm.org/cgi/reprint/42/1/339

Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis 10.1080/15427951.2011.604559

Feature-based Molecular Networking in the GNPS Analysis Environment 10.1038/s41592-020-0933-6

Neha Garg

Garg Neha

ORCID: 0000-0002-2760-7123

https://www.garglab-microbiomegt.com/

Creating a 3D microbial and chemical snapshot of a human habitat 10.1038/s41598-018-21541-4

Dereplication of peptidic natural products through database search of mass spectra 10.1038/nchembio.2219

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

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules 10.1128/mSystems.00058-17

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment 10.1128/mSystems.00016-17

Natural products as mediators of disease 10.1039/c6np00063k

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

Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis 10.1021/acschembio.6b01031

Characterization of the Stereochemical Configuration of Lanthionines Formed by the Lanthipeptide Synthetase GeoM 10.1002/bip.22876

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

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome 10.1038/ismej.2015.207

Microbiome-wide association studies link dynamic microbial consortia to disease 10.1038/nature18850

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen 10.1128/mSystems.00139-16

Chemoenzymatic Synthesis of Acyl Coenzyme A Substrates Enables in Situ Labeling of Small Molecules and Proteins 10.1021/acs.orglett.5b02113

Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures 10.1016/j.ijms.2014.06.005

Chemical Rescue and Inhibition Studies to Determine the Role of Arg301 in Phosphite Dehydrogenase 10.1371/journal.pone.0087134

Mass spectrometry of natural products: current, emerging and future technologies 10.1039/c4np00044g

Mode of action and structure-activity relationship studies of geobacillin I 10.1038/ja.2013.112

Specialized Metabolites from the Microbiome in Health and Disease 10.1016/j.cmet.2014.10.016

Substrate Specificity of the Lanthipeptide Peptidase ElxP and the Oxidoreductase ElxO 10.1021/cb5002526

The Intestinal Metabolome: An Intersection Between Microbiota and Host 10.1053/j.gastro.2014.03.001

In vitro activity of the nisin dehydratase NisB 10.1073/pnas.1222488110

Cloning, sequence analysis, expression of Cyathus bulleri laccase in Pichia pastoris and characterization of recombinant laccase 10.1186/1472-6750-12-75

Lantibiotics from Geobacillus thermodenitrificans 10.1073/pnas.1116815109

Production of Lantipeptides in Escherichia coli 10.1021/ja109044r

Mass Spectrometry-Based Integration and Expansion of the Chemical Diversity Harbored Within a Marine Sponge. 10.1007/s13361-019-02207-5

The chemical topology of a bacterial swarm. 10.1074/jbc.H118.003178

Chemoenzymatic Synthesis of Starting Materials and Characterization of Halogenases Requiring Acyl Carrier Protein-Tethered Substrates. 10.1016/bs.mie.2018.01.028

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

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

Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors. 10.3390/md18020124

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

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

Precursor-Guided Mining of Marine Sponge Metabolomes Lends Insight into Biosynthesis of Pyrrole-Imidazole Alkaloids. 10.1021/acschembio.0c00375

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

Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures. 10.1128/msystems.01387-20

LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome. 10.1016/j.cell.2021.04.001

Johannes Rainer

Rainer Johannes

ORCID: 0000-0002-6977-7147

https://github.com/jorainer/

https://twitter.com/jo_rainer

Human Macrophages Preferentially Infiltrate the Superficial Adipose Tissue 10.3390/ijms19051404

3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimic in-vivo conditions 10.18632/oncotarget.22636

Pre-analytic evaluation of volumetric absorptive microsampling and integration in a mass spectrometry-based metabolomics workflow 10.1007/s00216-017-0571-8

Enhancing dopaminergic signaling and histone acetylation promotes long-term rescue of deficient fear extinction 10.1038/tp.2016.231

Computational assessment of feature combinations for pathogenic variant prediction 10.1002/mgg3.214

The AR/NCOA1 axis regulates prostate cancer migration by involvement of PRKD1 10.1530/erc-16-0160

Restricting calcium currents is required for correct fiber type specification in skeletal muscle 10.1242/dev.129676

FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees 10.1093/bioinformatics/btw019

Putative Prostate Cancer Risk SNP in an Androgen Receptor-Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites 10.1002/humu.22909

Quantitative proteomic analysis reveals maturation as a mechanism underlying glucocorticoid resistance in B lineage ALL and re-sensitization by JNK inhibition 10.1111/bjh.13647

Beclin 1 is dispensable for chromosome congression and proper outer kinetochore assembly 10.15252/embr.201540731

miR-22 and miR-29a Are Members of the Androgen Receptor Cistrome Modulating LAMC1 and Mcl-1 in Prostate Cancer 10.1210/me.2014-1358

C10ORF10/DEPP, a transcriptional target of FOXO3, regulates ROS-sensitivity in human neuroblastoma 10.1186/1476-4598-13-224

The synthetic glucocorticoids prednisolone and dexamethasone regulate the same genes in acute lymphoblastic leukemia cells 10.1186/1471-2164-15-662

eIF3a is over-expressed in urinary bladder cancer and influences its phenotype independent of translation initiation 10.1007/s13402-014-0181-9

Translational profiling in childhood acute lymphoblastic leukemia: no evidence for glucocorticoid regulation of mRNA translation 10.1186/1471-2164-14-844

SOCS2 correlates with malignancy and exerts growth-promoting effects in prostate cancer 10.1530/erc-13-0446

EpCAM overexpression prolongs proliferative capacity of primary human breast epithelial cells and supports hyperplastic growth 10.1186/1476-4598-12-56

CLP1 links tRNA metabolism to progressive motor-neuron loss 10.1038/nature11923

An antibody microarray analysis of serum cytokines in neurodegenerative Parkinsonian syndromes 10.1186/1477-5956-10-71

Orphan kinases turn eccentric 10.4161/cc.21592

Elevated mRNA expression of CHAC1 splicing variants is associated with poor outcome for breast and ovarian cancer patients 10.1038/bjc.2011.510

Research Resource: Transcriptional Response to Glucocorticoids in Childhood Acute Lymphoblastic Leukemia 10.1210/me.2011-1213

Establishing a sensitive and specific assay for determination of glucocorticoid bioactivity 10.1007/s00508-011-1562-y

Insights into Global Mechanisms and Disease by Gene Expression Profiling 10.1007/978-1-61779-027-0_13

Comprehensive proteomic and transcriptomic characterization of hepatic expression signatures affected in p14 liver conditional knockout mice 10.1002/pmic.201000400

Glucocorticoid-induced alterations in mitochondrial membrane properties and respiration in childhood acute lymphoblastic leukemia 10.1016/j.bbabio.2010.12.010

ETV6/RUNX1-positive relapses evolve from an ancestral clone and frequently acquire deletions of genes implicated in glucocorticoid signaling 10.1182/blood-2010-03-275347

Expression, regulation and function of phosphofructo-kinase/fructose-biphosphatases (PFKFBs) in glucocorticoid-induced apoptosis of acute lymphoblastic leukemia cells 10.1186/1471-2407-10-638

PLZF/ZBTB16, a glucocorticoid response gene in acute lymphoblastic leukemia, interferes with glucocorticoid-induced apoptosis 10.1016/j.jsbmb.2010.04.019

Functional analyses of Src-like adaptor (SLA), a glucocorticoid-regulated gene in acute lymphoblastic leukemia 10.1016/j.leukres.2009.06.029

Repression of the BH3-only molecule PMAIP1/Noxa impairs glucocorticoid sensitivity of acute lymphoblastic leukemia cells 10.1007/s10495-009-0355-5

Glucocorticoid-regulated microRNAs and mirtrons in acute lymphoblastic leukemia 10.1038/leu.2008.370

The BCL2 rheostat in glucocorticoid-induced apoptosis of acute lymphoblastic leukemia 10.1038/sj.leu.2405039

CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis 10.1093/nar/gkl038

Identification of glucocorticoid-response genes in children with acute lymphoblastic leukemia 10.1182/blood-2005-07-2853

Glucocorticoid-induced apoptosis and glucocorticoid resistance in acute lymphoblastic leukemia 10.1016/j.jsbmb.2004.12.017

Glucocorticoid-induced apoptosis and glucocorticoid resistance: molecular mechanisms and clinical relevance 10.1038/sj.cdd.4401456

Client-Server environment for high-performance gene expression data analysis 10.1093/bioinformatics/btg074

The arrhythmogenic cardiomyopathy-specific coding and non-coding transcriptome in human cardiac stromal cells 10.1186/s12864-018-4876-6

Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees 10.1093/bioinformatics/bty541

ensembldb: an R package to create and use Ensembl-based annotation resources 10.1093/bioinformatics/btz031

Influence of collection tubes during quantitative targeted metabolomics studies in human blood samples 10.1016/j.cca.2018.08.014

The metaRbolomics Toolbox in Bioconductor and beyond 10.3390/metabo9100200

Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404

MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data 10.1101/2020.04.29.067868

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

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data 10.1021/acs.jproteome.0c00313

Metabolic Signature of Arrhythmogenic Cardiomyopathy 10.3390/metabo11040195

Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment 10.1038/s41467-021-23953-9

Pierre-Marie Allard

Allard Pierre-Marie

ORCID: 0000-0003-3389-2191

Email: pierre-marie.allard@unige.ch

Thinking big about small beings--the (yet) underdeveloped microbial natural products chemistry in Brazil. 10.1039/c3np70112c

Antiviral chlorinated daphnane diterpenoid orthoesters from the bark and wood of Trigonostemon cherrieri. 10.1016/j.phytochem.2012.07.023

Trigocherrin A, the first natural chlorinated daphnane diterpene orthoester from Trigonostemon cherrieri. 10.1021/ol2030907

Alkylated flavanones from the bark of Cryptocarya chartacea as dengue virus NS5 polymerase inhibitors. 10.1021/np200715v

Deep metabolome annotation in natural products research: towards a virtuous cycle in metabolite identification 10.1016/j.cbpa.2016.12.022

Pharmacognosy in the digital era: shifting to contextualized metabolomics 10.1016/j.copbio.2018.02.010

Lung Cancer Chemopreventive Activity of Patulin Isolated from Penicillium vulpinum 10.3390/molecules23030636

Searching for original natural products by molecular networking: detection, isolation and total synthesis of chloroaustralasines 10.1039/C8QO00429C

The plant pathogen Pseudomonas aeruginosa triggers a DELLA-dependent seed germination arrest in Arabidopsis 10.7554/eLife.37082

Application of a molecular networking approach for clinical and forensic toxicology exemplified in three cases involving 3‐MeO‐PCP, doxylamine, and chlormequat 10.1002/dta.2550

Characterization, Diversity, and Structure-Activity Relationship Study of Lipoamino Acids from Pantoea sp. and Synthetic Analogues 10.3390/ijms20051083

Taxonomically informed scoring enhances confidence in natural products annotation 10.1101/702308

Metabolomics of Myrcia bella Populations in Brazilian Savanna Reveals Strong Influence of Environmental Factors on Its Specialized Metabolism 10.3390/molecules25122954

In Silico Studies of the Biomolecular Interactions Between Natural Products and SARS-CoV-2 Main Protease 10.26434/chemrxiv.13065206

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Spatial and evolutionary predictability of phytochemical diversity 10.1073/pnas.2013344118

Novel trophic interactions under climate change promote alpine plant coexistence 10.1126/science.abd7015

Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata 10.1101/2021.02.28.433265

A Mass Spectrometry Based Metabolite Profiling Workflow for Selecting Abundant Specific Markers and Their Structurally Related Multi-Component Signatures in Traditional Chinese Medicine Multi-Herb Formulae. 10.3389/fphar.2020.578346

New insights into quetiapine metabolism using molecular networking. 10.1038/s41598-020-77106-x

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

Insights on the Structural and Metabolic Resistance of Potato (Solanum tuberosum) Cultivars to Tuber Black Dot (Colletotrichum coccodes). 10.3389/fpls.2020.01287

Metabolite Profiling of Javanese Ginger Zingiber purpureum and Identification of Antiseizure Metabolites via a Low-Cost Open-Source Zebrafish Bioassay-Guided Isolation. 10.1021/acs.jafc.0c02641

Surface sensing triggers a broad-spectrum antimicrobial response in Pseudomonas aeruginosa. 10.1111/1462-2920.15139

A database of high-resolution MS/MS spectra for lichen metabolites. 10.1038/s41597-019-0305-1

Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation. 10.3389/fpls.2019.01329

Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404

Effects of Sphagnum Leachate on Competitive Sphagnum Microbiome Depend on Species and Time. 10.3389/fmicb.2019.02042

Discovery of Lipid Peroxidation Inhibitors from Bacopa Species Prioritized through Multivariate Data Analysis and Multi-Informative Molecular Networking. 10.3390/molecules24162989

Identification of chemotypes in bitter melon by metabolomics: a plant with potential benefit for management of diabetes in traditional Chinese medicine. 10.1007/s11306-019-1565-7

A case of fatal acebutolol poisoning: an illustration of the potential of molecular networking. 10.1007/s00414-019-02062-9

Targeted Isolation of Monoterpene Indole Alkaloids from Palicourea sessilis. 10.1021/acs.jnatprod.7b00681

Cytotoxic Prenylated Stilbenes Isolated from Macaranga tanarius. 10.1021/acs.jnatprod.7b00409

Bioactive Natural Products Prioritization Using Massive Multi-informational Molecular Networks. 10.1021/acschembio.7b00413

Peptidomic and transcriptomic profiling of four distinct spider venoms. 10.1371/journal.pone.0172966

UHPLC-MS-based HDAC Assay Applied to Bio-guided Microfractionation of Fungal Extracts. 10.1002/pca.2652

Targeted Isolation of Indolopyridoquinazoline Alkaloids from Conchocarpus fontanesianus Based on Molecular Networks. 10.1021/acs.jnatprod.6b00379

Molecular and Functional Analysis of Sunitinib-Resistance Induction in Human Renal Cell Carcinoma Cells 10.3390/ijms22126467

Drug Repurposing to Identify a Synergistic High-Order Drug Combination to Treat Sunitinib-Resistant Renal Cell Carcinoma 10.3390/cancers13163978

Vanessa Phelan

Phelan Vanessa / Vanessa V Phelan / Vanessa Phelan

ORCID: 0000-0001-7156-9294

http://www.thephelanlab.com

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

Impact of a transposon insertion in phzF2 on the specialized metabolite production and interkingdom interactions of Pseudomonas aeruginosa 10.1128/JB.01258-13

Lipophilic mediated assays for ß-hematin inhibitors 10.2174/138620710790980496

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

Phosphonopeptide K-26 biosynthetic intermediates in Astrosporangium hypotensionis 10.1039/b611768f

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome 10.1038/ismej.2015.207

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry 10.1073/pnas.1206855109

Benzodiazepine Biosynthesis in Streptomyces refuineus 10.1016/j.chembiol.2007.05.009

Reassembly of anthramycin biosynthetic gene cluster by using recombinogenic cassettes 10.1002/cbic.200800029

Adenylation Enzyme Characterization Using γ -¹⁸O4-ATP Pyrophosphate Exchange 10.1016/j.chembiol.2009.04.007

Primer on Agar-Based Microbial Imaging Mass Spectrometry 10.1128/JB.00823-12

Benzodiazepine Biosynthesis in Streptomyces refuineus (DOI:10.1016/j.chembiol.2007.05.009) 10.1016/j.chembiol.2007.07.006

Mass spectrometry analysis of pseudomonas aeruginosa treated with azithromycin 10.1007/s13361-015-1101-6

Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle 10.1074/jbc.M110.201350

Microbial metabolic exchangeg-the chemotype-to-phenotype link 10.1038/nchembio.739

Microbial metabolic exchange in 3D 10.1038/ismej.2012.155

Microbiome and metabolome data integration provides insight into health and disease 10.1016/j.trsl.2017.07.001

Natural products as mediators of disease 10.1039/c6np00063k

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads 10.1186/s13059-019-1834-9

Feature-Based Molecular Networking for Metabolite Annotation. 10.1007/978-1-0716-0239-3_13

Exogenous Alginate Protects Staphylococcus aureus from Killing by Pseudomonas aeruginosa. 10.1128/jb.00559-19

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

Artificial Sputum Medium Formulation Impacts Pseudomonas aeruginosa Phenotype and Chemotype 10.1101/2021.01.25.428197

Michael Witting

Witting Michael

ORCID: 0000-0002-1462-4426

Email: michael.witting@helmholtz-muenchen.de

http://www.dr-witting.com

Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past 10.1073/pnas.1500783112

Fast separation and quantification of steroid hormones δ4- and δ7-dafachronic acid in Caenorhabditis elegans 10.1016/j.jchromb.2014.12.005

DI-ICR-FT-MS-based high-throughput deep metabotyping: a case study of the Caenorhabditis elegans-Pseudomonas aeruginosa infection model 10.1007/s00216-014-8331-5

Optimizing a ultrahigh pressure liquid chromatography-time of flight-mass spectrometry approach using a novel sub-2μm core-shell particle for in depth lipidomic profiling of Caenorhabditis elegans 10.1016/j.chroma.2014.07.021

Integrating analytical resolutions in non-targeted wine metabolomics 10.1016/j.tet.2015.02.054

Ultrahigh resolution mass spectrometry based non-targeted microbial metabolomics 10.1007/978-1-4614-1689-0_5

Molecular and structural characterization of dissolved organic matter during and post cyanobacterial bloom in Taihu by combination of NMR spectroscopy and FTICR mass spectrometry 10.1016/j.watres.2014.02.051

Transcriptome and Metabolome Data Integration-Technical Perquisites for Successful Data Fusion and Visualization 10.1016/B978-0-444-62651-6.00018-0

Ultrahigh resolution mass spectrometry-based metabolic characterization reveals cerebellum as a disturbed region in two animal models 10.1016/j.talanta.2013.09.019

Steroid hormone signalling links reproduction to lifespan in dietary-restricted Caenorhabditis elegans 10.1038/ncomms5879

Phenotype of htgA (mbiA), a recently evolved orphan gene of Escherichia coli and Shigella, completely overlapping in antisense to yaaW 10.1111/1574-6968.12288

Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet 10.1038/ismej.2014.79

High-resolution metabolite imaging of light and dark treated retina using MALDI-FTICR mass spectrometry 10.1002/pmic.201300407

Masstrix reloaded: Combined analysis and visualization of tran-scriptome and metabolome data 10.1371/journal.pone.0039860

Metformin impacts cecal bile acid profiles in mice 10.1016/j.jchromb.2018.02.029

Pharmacometabolic response to pirfenidone in pulmonary fibrosis detected by MALDI-FTICR-MSI 10.1183/13993003.02314-2017

Metabotype variation in a field population of tansy plants influences aphid host selection 10.1111/pce.13407

Tandem HILIC-RP liquid chromatography for increased polarity coverage in food analysis 10.1002/elps.201800038

Usage of FT-ICR-MS Metabolomics for Characterizing the Chemical Signatures of Barrel-Aged Whisky. 10.3389/fchem.2018.00029

Mycorrhiza-triggered transcriptomic and metabolomic networks impinge on herbivore fitness 10.1104/pp.17.01810

Bio- and chemoinformatics approaches for metabolomics data analysis 10.1007/978-1-4939-7643-0_4

Identification of molecules from non-targeted analysis 10.1016/j.jchromb.2017.11.030

WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series. 10.1080/21624054.2017.1373939

Comparative analysis of LytS/LytTR-type histidine kinase/response regulator systems in γ-proteobacteria 10.1371/journal.pone.0182993

Identification of a High-Affinity Pyruvate Receptor in Escherichia coli 10.1038/s41598-017-01410-2

LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome 10.1371/journal.pone.0172311

QSRR modeling for metabolite standards analyzed by two different chromatographic columns using multiple linear regression 10.3390/metabo7010007

Amniotic Fluid and Maternal Serum Metabolic Signatures in the Second Trimester Associated with Preterm Delivery 10.1021/acs.jproteome.6b00845

Metabolic profile of human coelomic fluid 10.4155/bio-2016-0223

The role of dafachronic acid signaling in development and longevity in Caenorhabditis elegans: Digging deeper using cutting-edge analytical chemistry 10.3389/fendo.2016.00012

Natural oxygenation of Champagne wine during ageing on lees: A metabolomics picture of hormesis 10.1016/j.foodchem.2016.02.043

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting. 10.1186/s12862-015-0558-z

Computational analysis and ratiometric comparison approaches aimed to assist column selection in hydrophilic interaction liquid chromatography-tandem mass spectrometry targeted metabolomics 10.1016/j.chroma.2015.06.008

The Caenorhabditis elegans lipidome: A primer for lipid analysis in Caenorhabditis elegans 10.1016/j.abb.2015.06.003

High precision mass measurements for wine metabolomics 10.3389/fchem.2014.00102

Modeling meets metabolomics-the wormjam consensus model as basis for metabolic studies in the model organism Caenorhabditis elegans 10.3389/fmolb.2018.00096

Combined nontargeted analytical methodologies for the characterization of the chemical evolution of bottled wines 10.1021/bk-2015-1203.ch002

The sphingolipidome of the model organism Caenorhabditis elegans 10.1016/j.chemphyslip.2019.04.009

Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling 10.1016/j.jchromb.2019.01.016

In-vivo targeted tagging of RNA isolates cell specific transcriptional responses to environmental stimuli and identifies liver-to-adipose RNA transfer 10.1101/670398

The metaRbolomics Toolbox in Bioconductor and beyond 10.3390/metabo9100200

Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404

Current status of retention time prediction in metabolite identification 10.1002/jssc.202000060

Autophagy compensates for defects in mitochondrial dynamics 10.1371/journal.pgen.1008638

Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model 10.3390/metabo10040130

Comprehensive vitamer profiling of folate monoand polyglutamates in baker’s yeast (Saccharomyces cerevisiae) as a function of different sample preparation procedures 10.3390/metabo10080301

Metabolomic adjustments in the orchid mycorrhizal fungus Tulasnella calospora during symbiosis with Serapias vomeracea 10.1111/nph.16812

Using Genome-Scale Metabolic Networks for Analysis, Visualization, and Integration of Targeted Metabolomics Data 10.1007/978-1-0716-0239-3_18

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

iTAG-RNA Isolates Cell-Specific Transcriptional Responses to Environmental Stimuli and Identifies an RNA-Based Endocrine Axis 10.1016/j.celrep.2020.02.020

Reduced peroxisomal import triggers peroxisomal retrograde signaling 10.1016/j.celrep.2020.108653

UHPLC-IM-Q-ToFMS analysis of maradolipids, found exclusively in Caenorhabditis elegans dauer larvae 10.1007/s00216-021-03172-3

HLH‐30‐dependent rewiring of metabolism during starvation in C . elegans 10.1111/acel.13342

Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the Nematode 10.3390/metabo11050284

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

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

Kai Dührkop

Dührkop Kai

ORCID: 0000-0002-9056-0540

Significance estimation for large scale metabolomics annotations by spectral matching 10.1038/s41467-017-01318-5

Searching molecular structure databases with tandem mass spectra using CSI:FingerID 10.1073/pnas.1509788112

Fragmentation trees reloaded 10.1007/978-3-319-16706-0_10

Critical Assessment of Small Molecule Identification 2016: automated methods 10.1186/s13321-017-0207-1

Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints 10.1093/bioinformatics/bty245

Faster mass decomposition 10.1007/978-3-642-40453-5_5

Speedy colorful subtrees 10.1007/978-3-319-21398-9_25

Fragmentation trees reloaded 10.1186/s13321-016-0116-8

Heuristic algorithms for the Maximum Colorful Subtree problem 10.4230/LIPIcs.WABI.2018.23

Metabolite identification through multiple kernel learning on fragmentation trees 10.1093/bioinformatics/btu275

Fast metabolite identification with Input Output Kernel Regression 10.1093/bioinformatics/btw246

Fast alignment of fragmentation trees 10.1093/bioinformatics/bts207

Current challenges in plant Eco-Metabolomics 10.3390/ijms19051385

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information 10.1038/s41592-019-0344-8

Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404

Computational methods for small molecule identification 10.1515/itit-2019-0033

ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules 10.1101/842740

Classes for the masses: Systematic classification of unknowns using fragmentation spectra 10.1101/2020.04.17.046672

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

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

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

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

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra 10.1038/s41587-020-0740-8

Assigning confidence to structural annotations from mass spectra with COSMIC 10.1101/2021.03.18.435634

Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment 10.1038/s41467-021-23953-9

MSNovelist: De novo structure generation from mass spectra 10.1101/2021.07.06.450875

Christian Martin H.

Martin H. Christian

ORCID: 0000-0002-9604-6737

Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking 10.1038/s41598-019-39583-7

Fungus-Growing Ant's Microbial Interaction of Streptomyces sp. and Escovopsis sp. through Molecular Networking and MALDI Imaging 10.1177/1934578x1901400117

Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama 10.3390/md18090456

Metabolites from Microbes Isolated from the Skin of the Panamanian Rocket Frog Colostethus panamansis (Anura: Dendrobatidae) 10.3390/metabo10100406

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

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

Metabolomic signatures of coral bleaching history. 10.1038/s41559-020-01388-7

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

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

audrey Le Gouellec

Le Gouellec audrey

ORCID: 0000-0002-4905-3854

https://www-timc.imag.fr/en

High-Resolution Magic Angle Spinning NMR-Based Metabolomics Revealing Metabolic Changes in Lung of Mice Infected with P. aeruginosa Consistent with the Degree of Disease Severity 10.1021/acs.jproteome.8b00306

A PBP2x from a Clinical Isolate ofStreptococcus pneumoniaeExhibits an Alternative Mechanism for Reduction of Susceptibility to β-Lactam Antibiotics 10.1074/jbc.m313492200

In vitro reconstitution of a trimeric complex of DivIB, DivIC and FtsL, and their transient co-localization at the division site in Streptococcus pneumoniae 10.1111/j.1365-2958.2004.04408.x

Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae. 10.1074/jbc.M408446200

Central domain of DivIB caps the C-terminal regions of the FtsL/DivIC coiled-coil rod. 10.1074/jbc.M109.019471

Optimization of Antitumor Immunotherapy Mediated by Type III Secretion System-based Live Attenuated Bacterial Vectors 10.1097/CJI.0b013e31824747e5

A safe bacterial microsyringe for in vivo antigen delivery and immunotherapy 10.1038/mt.2013.41

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Is tryptophan metabolism involved in sleep apnea-related cardiovascular co-morbidities and cancer progression? 10.1016/j.mehy.2015.06.022

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Live-attenuated bacteria as a cancer vaccine vector 10.1586/14760584.2013.836914

Bacterial vectors for the delivery of tumor antigens 10.1007/978-1-4939-0345-0_33

Poly-functional and long-lasting anticancer immune response elicited by a safe attenuated Pseudomonas aeruginosa vector for antigens delivery 10.1038/mto.2016.33

Targeted release of transcription factors for cell reprogramming by a natural micro-syringe 10.1016/j.ijpharm.2016.09.081

Cibler les mécanismes immunosuppresseurs de la réponse immune antitumorale en onco-hématologie : une nouvelle stratégie thérapeutique ? Immune checkpoint blockade in onco-hematology therapy. 10.1684/ito.2017.0078

Chemobacterial Synthesis of a Sialyl-Tn Cyclopeptide Vaccine Candidate 10.1002/cbic.201700240

Altered humoral immune responses and IgG subtypes in NOX2-deficient mice and patients: A key role for NOX2 in antigen-presenting cells 10.3389/fimmu.2018.01555

Tryptophan catabolism in Pseudomonas aeruginosa and potential for inter-kingdom relationship 10.1186/s12866-016-0756-x

Killed but metabolically active Pseudomonas aeruginosa-based vaccine induces protective humoral- and cell-mediated immunity against Pseudomonas aeruginosa pulmonary infections 10.1016/j.vaccine.2018.02.040

Effect of double-filtration plasmapheresis for antibody-mediated rejection on hemostasis parameters and thrombin generation 10.1016/j.thromres.2018.04.018

Corrigendum to “Effect of double-filtration plasmapheresis for antibody-mediated rejection on hemostasis parameters and thrombin generation” [Thromb. Res. 166 (2018) 113–121](S0049384818303232)(10.1016/j.thromres.2018.04.018) 10.1016/j.thromres.2018.05.033

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data 10.1101/750471

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Ion Identity Molecular Networking in the GNPS Environment 10.1101/2020.05.11.088948

Prebiotic role of softwood hemicellulose in healthy mice model 10.1016/j.jff.2019.103688

Mediation analysis of CRP on the association of physical activity with FEV1 and FVC: the ECRHS study. 10.1183/13993003.congress-2018.pa4483

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

COVID-19: Underlying Adipokine Storm and Angiotensin 1-7 Umbrella 10.3389/fimmu.2020.01714

The role of C-reactive protein levels on the association of physical activity with lung function in adults 10.1371/journal.pone.0222578

Optimal epitope composition after antigen screening using a live bacterial delivery vector application to TRP-2 10.4161/bbug.1.1.9482

Metabotypes of Pseudomonas aeruginosa Correlate with Antibiotic Resistance, Virulence and Clinical Outcome in Cystic Fibrosis Chronic Infections 10.3390/metabo11020063

What We Know So Far about the Metabolite-Mediated Microbiota-Intestinal Immunity Dialogue and How to Hear the Sound of This Crosstalk 10.3390/metabo11060406

Tam Dang

Dang Tam

ORCID: 0000-0002-3602-1917

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

Total Synthesis and Biological Assessment of Novel Albicidins Discovered by Mass Spectrometric Networking 10.1002/chem.201704074

Bioactive Peptide Natural Products as Lead Structures for Medicinal Use 10.1021/acs.accounts.7b00159

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

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

Xavier Cachet

Cachet Xavier

ORCID: 0000-0001-9150-1932

Clerodane furanoditerpenoids as the probable cause of toxic hepatitis induced by Tinospora crispa 10.1038/s41598-018-31815-6

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

4-Deoxyphorbol inhibits HIV-1 infection in synergism with antiretroviral drugs and reactivates viral reservoirs through PKC/MEK activation synergizing with vorinostat 10.1016/j.bcp.2020.113937

Health risk associated with the oral consumption of “Chiniy-tref”, a traditional medicinal preparation used in Martinique (French West Indies): Qualitative and quantitative analyses of aristolochic acids contained therein 10.1016/j.toxicon.2019.10.241

Scale inhibition effect of Hylocereus undatus solution on calcium carbonate formation 10.1016/j.jcrysgro.2019.125161

Environmentally Friendly Procedure Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking for the Discovery of Potent Antiviral Compounds fromEuphorbia semiperfoliata 10.1021/acs.jnatprod.7b00113

Bioactive Natural Products Prioritization Using Massive Multi-informational Molecular Networks 10.1021/acschembio.7b00413

Synthetic Analogue of the Natural Product Piperlongumine as a Potent Inhibitor of Breast Cancer Cell Line Migration 10.21577/0103-5053.20160303

Antiscalant properties of Herniaria glabra aqueous solution 10.1016/j.desal.2017.01.028

A new 3,4-seco-cycloartane from the leaves ofHopea odorataRoxb. 10.1080/14786419.2015.1007975

Antibacterial Labdane Diterpenoids fromVitex vestita 10.1021/acs.jnatprod.5b00206

Toxic hepatitis induced by a herbal medicine: Tinospora crispa 10.1016/j.phymed.2014.04.031

Hiroshi Tsugawa

Tsugawa Hiroshi

ORCID: 0000-0002-2015-3958

The importance of bioinformatics for connecting data-driven lipidomics and biological insights 10.1016/j.bbalip.2017.05.006

Integrated Strategy for Unknown EI–MS Identification Using Quality Control Calibration Curve, Multivariate Analysis, EI–MS Spectral Database, and Retention Index Prediction 10.1021/acs.analchem.7b01010

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics 10.1038/nmeth.4512

A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms 10.1038/s41592-019-0358-2

Publisher Correction: A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms 10.1038/s41592-019-0423-x

Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics 10.3390/metabo9060119

Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404

Characterization of Lipid Profiles after Dietary Intake of Polyunsaturated Fatty Acids Using Integrated Untargeted and Targeted Lipidomics 10.3390/metabo9100241

Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics 10.3390/metabo9110251

MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas 10.1101/2020.02.11.944900

Metabolomics with 15N Labeling for Characterizing Missing Monoterpene Indole Alkaloids in Plants 10.1021/acs.analchem.9b03860

Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software 10.3390/metabo10030101

Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics 10.1021/acs.analchem.9b05765

A lipidome atlas in MS-DIAL 4 10.1038/s41587-020-0531-2

Correlation-Based Deconvolution (CorrDec) To Generate High-Quality MS2 Spectra from Data-Independent Acquisition in Multisample Studies 10.1021/acs.analchem.0c01980

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

Metabolome-Based Discrimination Analysis of Shallot Landraces and Bulb Onion Cultivars Associated with Differences in the Amino Acid and Flavonoid Profiles 10.3390/molecules25225300

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses 10.1016/j.isci.2020.101841

Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis 10.1038/s41467-020-20508-2

Food Lipidomics for 155 Agricultural Plant Products 10.1021/acs.jafc.0c07356

OS-PCA: Orthogonal Smoothed Principal Component Analysis Applied to Metabolome Data 10.3390/metabo11030149

Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment 10.1038/s41467-021-23953-9

Computational mass spectrometry accelerates C=C position-resolved untargeted lipidomics using oxygen attachment dissociation 10.21203/rs.3.rs-727852/v1

Metabolomics and complementary techniques to investigate the plant phytochemical cosmos 10.1039/D1NP00014D