Paperbase

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

Craig Nelson

Nelson Craig

ORCID: 0000-0003-2525-3496

http://www.soest.hawaii.edu/oceanography/faculty/Nelson.html

Fluorescent dissolved organic matter as a multivariate biogeochemical tracer of submarine groundwater discharge in coral reef ecosystems 10.1016/j.marchem.2015.06.026

Global microbialization of coral reefs 10.1038/nmicrobiol.2016.42

Using viromes to predict novel immune proteins in non-model organisms 10.1098/rspb.2016.1200

Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities 10.1111/1758-2229.12541

Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean 10.1111/1462-2920.13825

Comparisons of stable isotope (C, H, N) signatures for revealing organic matter sources and trophic relationships in headwater streams 10.1139/cjfas-2016-0322

Exploring the occurrence of and explanations for nighttime spikes in dissolved oxygen across coral reef environments 10.7287/peerj.preprints.2935v2

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

Primer selection impacts specific population abundances but not community dynamics in a monthly time‐series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton 10.1111/1462-2920.14091

Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research 10.1128/mSystems.00159-17

Ecosystem Microbiology of Coral Reefs: Linking Genomic, Metabolomic, and Biogeochemical Dynamics from Animal Symbioses to Reefscape Processes 10.1128/mSystems.00162-17

Fluorescent organic exudates of corals and algae in tropical reefs are compositionally distinct and increase with nutrient enrichment 10.1002/lol2.10074

Nutrient pollution disrupts key ecosystem functions on coral reefs 10.1098/rspb.2017.2718

Elevated p CO 2 alters marine heterotrophic bacterial community composition and metabolic potential in response to a pulse of phytoplankton organic matter 10.1111/1462-2920.14484

Kū Hou Kuapā: Cultural Restoration Improves Water Budget and Water Quality Dynamics in Heʻeia Fishpond 10.3390/su11010161

Diel population and functional synchrony of microbial communities on coral reefs 10.1038/s41467-019-09419-z

Exploring the occurrence of and explanations for nighttime spikes in dissolved oxygen across coral reef environments 10.7287/peerj.preprints.2935v1

Fluorescent organic exudates of corals and algae in tropical reefs are compositionally distinct and increase with nutrient enrichment 10.7287/peerj.preprints.3372v1

Macroalgal biomass, growth rates, and diversity are influenced by submarine groundwater discharge and local hydrodynamics in tropical reefs 10.3354/meps12992

Species-Specific Differences in the Microbiomes and Organic Exudates of Crustose Coralline Algae Influence Bacterioplankton Communities 10.3389/fmicb.2019.02397

An Island Mass Effect Resolved Near Mo’orea, French Polynesia 10.3389/fmars.2020.00016

Ecomimicry in Indigenous resource management: optimizing ecosystem services to achieve resource abundance, with examples from Hawaiʻi 10.5751/es-11539-250226

Distinct bacterial communities in tropical island aquifers 10.1371/journal.pone.0232265

Coral reef benthic community structure is associated with the spatiotemporal dynamics of submarine groundwater discharge chemistry 10.1002/lno.11596

Differential resistance and acclimation of two coral species to chronic nutrient enrichment reflect life‐history traits 10.1111/1365-2435.13780

Marine heatwaves depress metabolic activity and impair cellular acid–base homeostasis in reef‐building corals regardless of bleaching susceptibility 10.1111/gcb.15622

Experimental reef communities persist under future ocean acidification and warming 10.21203/rs.3.rs-640089/v1

Brandon Stephens

Stephens Brandon

ORCID: 0000-0001-7351-2750

Terrestrial and marine perspectives on modeling organic matter degradation pathways 10.1111/gcb.12987

DOM characteristics along the continuum from river to receiving basin: a comparison of freshwater and saline transects 10.1007/s00027-010-0144-9

Dissolved organic matter characteristics within the Lake Superior watershed http://dx.doi.org/10.1016/j.orggeochem.2008.08.001

Sorption of Isoxaflutole Diketonitrile Degradate (DKN) and Dicamba in Unsaturated Soil 10.1080/03601230600850903

Carotenoids are the likely precursor of a significant fraction of marine dissolved organic matter 10.1126/sciadv.1602976

Mesoscale ocean fronts enhance carbon export due to gravitational sinking and subduction 10.1073/pnas.1609435114

Nonsinking Organic Matter Production in the California Current 10.1029/2018GB005930

Dissolved organic matter characteristics within the Lake Superior watershed 10.1016/j.orggeochem.2008.08.001

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

CCE V: Primary production, mesozooplankton grazing, and the biological pump in the California Current Ecosystem: Variability and response to El Niño https://doi.org/10.1016/j.dsr.2018.07.012

Recent Increases in Water Column Denitrification in the Seasonally Suboxic Bottom Waters of the Santa Barbara Basin 10.1029/2019GL082075

Euphotic zone nitrification in the California Current Ecosystem 10.1002/lno.11348

Sorption of a hydrophilic pesticides: Effects of soil water content 10.2136/sssaj2006.0091

CCE V: Primary production, mesozooplankton grazing, and the biological pump in the California Current Ecosystem: Variability and response to El Niño 10.1016/j.dsr.2018.07.012

Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa 10.3389/fmars.2020.590273

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