Niche partitioning of a pathogenic microbiome driven by chemical gradients
Quinn, Robert A. Comstock, William Zhang, Tianyu Morton, James T. da Silva, Ricardo Tran, Alda Aksenov, Alexander Nothias, Louis-Felix Wangpraseurt, Daniel Melnik, Alexey, V Ackermann, Gail Conrad, Douglas Klapper, Isaac Knight, Rob Dorrestein, Pieter C.
Rob Knight
Knight Rob
ORCID: 0000-0002-0975-9019
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Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice 10.1113/JP277336
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Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes 10.1038/s41396-018-0175-0
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Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice 10.1016/j.cell.2019.05.004
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Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus 10.1038/s41396-018-0214-x
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Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing 10.1021/acs.est.0c07952
Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice 10.3389/fpsyt.2020.00518
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Best practices for analysing microbiomes 10.1038/s41579-018-0029-9
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Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans 10.1016/j.cell.2020.09.009
Microbial biogeography and ecology of the mouth and implications for periodontal diseases 10.1111/prd.12268
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Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome 10.1186/s40168-019-0636-3
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree 10.1038/s41589-020-00677-3
High-throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county 10.1128/MSYSTEMS.00045-21
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians 10.1016/j.cgh.2018.09.017
Coordinating and assisting research at the SARS-CoV-2/ microbiome nexus 10.1128/MSYSTEMS.00999-20
Expanding magnetic organelle biogenesis in the domain Bacteria 10.1186/s40168-020-00931-9
Toward unrestricted use of public genomic data 10.1126/science.aaw1280
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection 10.1186/s40168-021-01026-9
Single-cell transcriptomics reveal a correlation between genome architecture and gene family evolution in ciliates 10.1128/mBio.02524-19
Triclosan leads to dysregulation of the metabolic regulator FGF21 exacerbating high fat diet-induced nonalcoholic fatty liver disease 10.1073/pnas.2017129117
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Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity 10.1093/ibd/izaa262
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Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome 10.1038/s41598-019-49823-5
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SHOGUN: A modular, accurate and scalable framework for microbiome quantification 10.1093/bioinformatics/btaa277
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Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study 10.1111/cts.12785
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IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis 10.1016/j.jid.2019.05.024
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Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) 10.1002/mbo3.716
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes 10.1186/s40168-020-00857-2
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities 10.1016/j.cels.2019.09.004
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Current Concepts, Opportunities, and Challenges of Gut Microbiome-Based Personalized Medicine in Nonalcoholic Fatty Liver Disease 10.1016/j.cmet.2020.11.010
Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi 10.1002/ajp.22989
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Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017 10.1186/s40168-018-0596-z
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Identifying and predicting novelty in microbiome studies 10.1128/mBio.02099-18
Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry 10.1053/j.gastro.2020.09.038
Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media 10.1038/s41597-019-0331-z
High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity 10.1128/mSystems.00166-18
Species-level functional profiling of metagenomes and metatranscriptomes 10.1038/s41592-018-0176-y
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases 10.1038/s41586-019-1237-9
Effects of Diet versus Gastric Bypass on Metabolic Function in Diabetes 10.1056/NEJMoa2003697
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 10.1038/s41467-020-16366-7
Is there convergence of gut microbes in blood-feeding vertebrates? 10.1098/rstb.2018.0249
The genetic basis for adaptation of modeldesigned syntrophic co-cultures 10.1371/journal.pcbi.1006213
Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information 10.1101/gr.260380.119
Red Sea SAR11 and Prochlorococcus single-cell genomes reflect globally distributed pangenomes 10.1128/AEM.00369-19
Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908
ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7
Reply to: Examining microbe–metabolite correlations by linear methods 10.1038/s41592-020-01007-0
Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study 10.1002/ijc.33473
Microbe-metabolite associations linked to the rebounding murine gut microbiome postcolonization with vancomycin-resistant enterococcus faecium 10.1128/mSystems.00452-20
A microbiome-based index for assessing skin health and treatment effects for atopic dermatitis in children 10.1128/mSystems.00293-19
Absence of CCR2 reduces spontaneous intestinal tumorigenesis in the ApcMin/+ mouse model 10.1002/ijc.33477
QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data 10.1002/cpbi.100
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads 10.1186/s13059-019-1834-9
Striped UniFrac: enabling microbiome analysis at unprecedented scale 10.1038/s41592-018-0187-8
Role of the microbiome in human development 10.1136/gutjnl-2018-317503
Qiita: rapid, web-enabled microbiome meta-analysis 10.1038/s41592-018-0141-9
The gut microbiome, aging, and longevity: A systematic review 10.3390/nu12123759
Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media 10.1038/s41597-019-0051-4
Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome 10.3389/fphys.2021.663950
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations 10.1016/j.tim.2018.11.003
A distinct microbiome signature in posttreatment lyme disease patients 10.1128/mBio.02310-20
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.1186/s40168-020-00960-4
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
Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis 10.1177/1352458520924594
Exposure to toxic metals triggers unique responses from the rat gut microbiota 10.1038/s41598-018-24931-w
Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9
Farm-like indoor microbiota in non-farm homes protects children from asthma development 10.1038/s41591-019-0469-4
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules 10.1101/gr.265645.120
Creating a 3D microbial and chemical snapshot of a human habitat. 10.1038/s41598-018-21541-4
Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome. 10.1371/journal.pntd.0006344
Microbiome and metagenome analyses of a closed habitat during human occupation 10.1128/mSystems.00367-20
Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations 10.1371/journal.pone.0224757
Temporal, environmental, and biological drivers of the mucosal microbiome in a Wild Marine Fish, Scomber japonicus 10.1128/MSPHERE.00401-20
Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month 10.1186/s40168-019-0645-2
Altered Gut Microbiota and Host Metabolite Profiles in Women with Human Immunodeficiency Virus 10.1093/cid/ciz1117
Multiple-disease detection and classification across cohorts via microbiome search 10.1128/mSystems.00150-20
Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. 10.1186/s13059-020-01970-z
Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection 10.1084/jem.20192276
Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk 10.1016/j.bbi.2020.10.003
Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary 10.2144/btn-2018-0192
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States 10.1016/j.cell.2021.03.052
Regional variation limits applications of healthy gut microbiome reference ranges and disease models 10.1038/s41591-018-0164-x
The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus 10.1186/s12866-018-1341-2
Learning representations of microbe–metabolite interactions 10.1038/s41592-019-0616-3
Establishing microbial composition measurement standards with reference frames 10.1038/s41467-019-10656-5
Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny 10.1186/s13059-019-1807-z
American Gut: An open platform for citizen science microbiome research 10.1128/MSYSTEMS.00031-18
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities 10.2144/BTN-2020-0153
Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. 10.1038/s41586-018-0304-y
Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing 10.1016/j.envint.2020.105604
Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations 10.1053/j.gastro.2019.11.305
Calour: an Interactive, Microbe-Centric Analysis Tool 10.1128/MSYSTEMS.00269-18
Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects 10.1016/j.schres.2018.09.014
Challenges in the construction of knowledge bases for human microbiome-disease associations 10.1186/s40168-019-0742-2
Evaluating organism-wide changes in the metabolome and microbiome following a single dose of antibiotic 10.1128/MSYSTEMS.00340-20
Links between environment, diet, and the hunter-gatherer microbiome 10.1080/19490976.2018.1494103
Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism 10.1038/s41467-018-05336-9
The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment 10.3389/fmicb.2020.02015
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4
Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1
A novel sparse compositional technique reveals microbial perturbations 10.1128/MSYSTEMS.00016-19
Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study 10.1038/s41598-020-59016-0
Quantifying live microbial load in human saliva samples over time reveals stable composition and dynamic load 10.1128/MSYSTEMS.01182-20
Associations of the fecal microbial proteome composition and proneness to diet-induced obesity 10.1074/mcp.RA119.001623
Vitamin D metabolites and the gut microbiome in older men 10.1038/s41467-020-19793-8
Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics 10.1093/gbe/evy133
Early-life gut dysbiosis linked to juvenile mortality in ostriches 10.1186/s40168-020-00925-7
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
Species abundance information improves sequence taxonomy classification accuracy 10.1038/s41467-019-12669-6
Organ-level protein networks as a reference for the host effects of the microbiome 10.1101/gr.256875.119
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Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota 10.1038/s41597-020-00656-2
Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1128/mSystems.00635-19
Animal Models for Microbiome Research and Drug Discovery 10.1016/j.ddmod.2019.09.001
FXR Regulates Intestinal Cancer Stem Cell Proliferation 10.1016/j.cell.2019.01.036
The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months 10.1093/ajcn/nqaa011
Intermittent hypoxia and hypercapnia reproducibly change the gut microbiome and metabolome across rodent model systems 10.1128/mSystems.00058-19
Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020 10.1186/s40168-020-00951-5
Association between the gut microbiota and blood pressure in a population cohort of 6953 individuals 10.1161/JAHA.120.016641
Longitudinal survey of microbiome associated with particulate matter in a megacity 10.1186/s13059-020-01964-x
Early-career scientists shaping the world 10.1128/mSystems.00196-19
Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm 10.1038/s41467-018-04409-z
The gut-liver axis and the intersection with the microbiome 10.1038/s41575-018-0011-z
A gut bacterial amyloid promotes a-synuclein aggregation and motor impairment in mice 10.7554/eLife.53111
Leveling up citizen science 10.1038/s41587-020-0694-x
Evaluating the information content of shallow shotgun metagenomics 10.1128/mSystems.00069-18
Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study 10.1016/j.envres.2021.111084
Depression in individuals coinfected with HIV and HCV is associated with systematic differences in the gut microbiome and metabolome 10.1128/mSystems.00465-20
Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota 10.1038/s41396-020-00855-0
Microbial ecology of atlantic salmon (Salmo salar) hatcheries: Impacts of the built environment on fish mucosal microbiota 10.1128/AEM.00411-20
Handwashing and detergent treatment greatly reduce SARS-CoV-2 viral load on halloween candy handled by COVID-19 patients 10.1128/mSystems.01074-20
Author Correction: Farm-like indoor microbiota in non-farm homes protects children from asthma development. 10.1038/s41591-019-0546-8
The Effects of Captivity on the Mammalian Gut Microbiome. 10.1093/icb/icx090
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0218-196a
Leukotriene B4-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progression. 10.1080/2162402x.2017.1361593
Genetic influences on the human oral microbiome. 10.1186/s12864-017-4008-8
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. 10.1126/science.aan4834
Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models. 10.1073/pnas.1711235114
Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic Infection. 10.1021/acs.analchem.7b02423
The sponge microbiome project. 10.1093/gigascience/gix077
Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants. 10.1093/icb/icx088
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. 10.1038/nbt.3981
Impacts of the Human Gut Microbiome on Therapeutics. 10.1146/annurev-pharmtox-042017-031849
Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites. 10.1128/msystems.00093-17
Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project. 10.1038/nature24485
Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. 10.1128/mbio.01343-17
Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. 10.1371/journal.pone.0184336
A communal catalogue reveals Earth's multiscale microbial diversity. 10.1038/nature24621
Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. 10.1016/j.chom.2017.10.001
Evaluating the impact of domestication and captivity on the horse gut microbiome. 10.1038/s41598-017-15375-9
Erratum: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. 10.1038/nature25028
Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes. 10.1128/msystems.00092-17
Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. 10.1111/1365-2656.12781
Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics). 10.1128/mbio.01836-17
Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. 10.1128/msystems.00188-17
Expanding our Understanding of the Role of the Microbiome in Health and Disease. 10.1016/j.arcmed.2018.02.002
Bacterial density rather than diversity correlates with hatching success across different avian species. 10.1093/femsec/fiy022
Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. 10.1073/pnas.1712337115
Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. 10.3390/genes9020104
Improving saliva shotgun metagenomics by chemical host DNA depletion. 10.1186/s40168-018-0426-3
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. 10.1128/msystems.00218-17
Bacterial community changes in an industrial algae production system. 10.1016/j.algal.2017.09.010
Earth Microbiome Project and Global Systems Biology. 10.1128/msystems.00217-17
Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. 10.1093/femsec/fiy063
Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space. 10.1089/bfm.2018.29072.rjk
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. 10.1128/msystems.00021-18
Gut microbiota utilize immunoglobulin A for mucosal colonization. 10.1126/science.aaq0926
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. 10.1186/s40168-018-0470-z
Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. 10.1016/j.cels.2018.04.010
Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome. 10.1128/msystems.00020-18
Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. 10.3389/fmicb.2018.02559
Microbiota as in farm homes protect children from asthma 10.1183/13993003.congress-2018.oa337
Diet and the Gut Microbiome in 10–18-Month-Old Children Living in Urban Slums of Mumbai, India (OR01-08-19) 10.1093/cdn/nzz040.or01-08-19
Neighborhoods to Nucleotides—Advances and Gaps for an Obesity Disparities Systems Epidemiology Model 10.1007/s40471-019-00221-5
Global chemical analysis of biology by mass spectrometry 10.1038/s41570-017-0054
Visualizing 'omic feature rankings and log-ratios using Qurro. 10.1093/nargab/lqaa023
A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis. 10.1016/j.cmet.2020.06.005
Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort. 10.1158/1055-9965.epi-20-0824
Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos. 10.1093/ajcn/nqab001
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. 10.21203/
Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. 10.1101/2021.02.06.21251159
The early evolution of the genetic code. 10.1016/s0092-8674(00)80866-1
Measuring adaptation within the genetic code. 10.1016/s0968-0004(99)01531-5
Early fixation of an optimal genetic code. 10.1093/oxfordjournals.molbev.a026331
An amphioxus Krox gene: insights into vertebrate hindbrain evolution. 10.1007/s004270000092
Identification of conserved C2H2 zinc-finger gene families in the Bilateria. 10.1186/gb-2001-2-5-research0016
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. 10.1186/gb-2001-2-4-research0010
Analyzing partially randomized nucleic acid pools: straight dope on doping. 10.1093/nar/gng030
Do universal codon-usage patterns minimize the effects of mutation and translation error? 10.1186/gb-2005-6-11-r91
Information, probability, and the abundance of the simplest RNA active sites. 10.2741/3137
Systems biology: Understanding function from genes to networks 10.2174/157016409788680974
The mind-body-microbial continuum. 10.31887/dcns.2011.13.1/agonzalez
Analytic Strategies for Understanding Host-Associated Microbial Communities: Faster and cheaper DNA sequencing technologies combined with open-access analytic software packages are opening new vistas 10.1128/microbe.6.389.1
Human microbiome science: Vision for the future, Bethesda, MD, July 24 to 26, 2013 10.1186/2049-2618-2-16
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0718-660a
A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. 10.7554/elife.01104
Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy. 10.7554/elife.11405
Robert Quinn
Quinn Robert
ORCID: 0000-0002-9829-3256
Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence 10.1098/rspb.2016.0469
Correction to ‘Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence’ 10.1098/rspb.2016.1485
Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism 10.1098/rspb.2018.1307
Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908
Metabolomic signatures of coral bleaching history 10.1038/s41559-020-01388-7
Review: microbial transformations of human bile acids 10.1186/s40168-021-01101-1
Bridging the Gap between Analytical and Microbial Sciences in Microbiome Research 10.1128/mSystems.00585-21
Ricardo da Silva
da Silva Ricardo
ORCID: 0000-0001-6378-0479
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
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
Louis-Felix NOTHIAS
NOTHIAS Louis-Felix
ORCID: 0000-0001-6711-6719
Jatrophane diterpenes as inhibitors of chikungunya virus replication: structure-activity relationship and discovery of a potent lead. 10.1021/np500271u
Antiviral Activity of Diterpene Esters on Chikungunya Virus and HIV Replication 10.1021/acs.jnatprod.5b00073
LC-MS2-Based dereplication of Euphorbia extracts with anti-Chikungunya virus activity 10.1016/j.fitote.2015.06.021
Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation 10.1021/acs.jnatprod.7b00737
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
Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908
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
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools 10.1101/654459
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools 10.3390/metabo9070144
Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404
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
Ion Identity Molecular Networking in the GNPS Environment 10.1101/2020.05.11.088948
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
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3
Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale 10.1021/jasms.0c00240
The ant fungus garden acts as an external digestive system 10.1101/2020.11.18.389361
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra 10.1038/s41587-020-0740-8
Reply to: Examining microbe–metabolite correlations by linear methods 10.1038/s41592-020-01007-0
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/mSystems.00601-21
Daniel Wangpraseurt
Wangpraseurt Daniel
ORCID: 0000-0003-4834-8981
Light gradients and optical microniches in coral tissues 10.3389/fmicb.2012.00316
The in situ light microenvironment of corals 10.4319/lo.2014.59.3.0917
Direct and diffuse light propagation through coral tissue 10.1117/12.2038339
Spectral Effects on Symbiodinium Photobiology Studied with a Programmable Light Engine 10.1371/journal.pone.0112809
Light Respiratory Processes and Gross Photosynthesis in Two Scleractinian Corals 10.1371/journal.pone.0110814
In Situ Oxygen Dynamics in Coral-Algal Interactions 10.1371/journal.pone.0031192
Monte Carlo Modeling of Photon Propagation Reveals Highly Scattering Coral Tissue 10.3389/fpls.2016.01404
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Flow and Coral Morphology Control Coral Surface pH: Implications for the Effects of Ocean Acidification 10.3389/fmars.2016.00010
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Microenvironment and phylogenetic diversity of Prochloron inhabiting the surface of crustose didemnid ascidians 10.1111/1462-2920.12983
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Optical properties of living corals determined with diffuse reflectance spectroscopy 10.1101/563106
Optical Properties of Corals Distort Variable Chlorophyll Fluorescence Measurements 10.1104/pp.18.01275
In vivo imaging of coral tissue and skeleton with optical coherence tomography 10.1101/088682
Optical Properties of Living Corals Determined With Diffuse Reflectance Spectroscopy 10.3389/fmars.2019.00472
Corrigendum: Flow and Coral Morphology Control Coral Surface pH: Implications for the Effects of Ocean Acidification 10.3389/fmars.2017.00226
Effect of feeding and thermal stress on photosynthesis, respiration and the carbon budget of the scleractinian coral Pocillopora damicornis 10.1101/378059
Bio-optical properties and radiative energy budgets in fed and starved scleractinian corals (Pocillopora damicornis) during thermal bleaching 10.1101/377937
Editorial: Optics and Ecophysiology of Coral Reef Organisms 10.3389/fmars.2019.00742
Bionic 3D printed corals 10.1101/834051
Microscale light management and inherent optical properties of intact corals studied with optical coherence tomography 10.1101/376723
Optics and Ecophysiology of Coral Reef Organisms 10.3389/978-2-88963-436-1
Elevated CO2 leads to enhanced photosynthesis but decreased growth in early life stages of reef building coralline algae 10.3389/fmars.2018.00495
In vivo microscale measurements of light and photosynthesis during coral bleaching: Evidence for the optical feedback loop? 10.3389/fmicb.2017.00059
Correlation of bio-optical properties with photosynthetic pigment and microorganism distribution in microbial mats from Hamelin Pool, Australia 10.1093/femsec/fiy219
Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate bead model 10.1038/s41522-018-0047-4
Author Correction: Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring (Scientific Reports, (2019), 9, 1, (14148), 10.1038/s41598-019-50658-3) 10.1038/s41598-019-54379-5
Bio-optical properties and radiative energy budgets in fed and unfed scleractinian corals (Pocillopora sp.) during thermal bleaching 10.3354/meps13146
Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring 10.1038/s41598-019-50658-3
Symbiodinium-induced formation of microbialites: Mechanistic insights from in Vitro experiments and the prospect of its occurrence in nature 10.3389/fmicb.2018.00998
Structure-based optics of centric diatom frustules: modulation of the in vivo light field for efficient diatom photosynthesis 10.1111/nph.15149
Bionic 3D printed corals 10.1038/s41467-020-15486-4
Bionic 3D printed corals 10.17863/cam.50943
Bionic 3D printed corals. 10.17863/cam.52364
Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring. 10.17863/cam.46835
Light-harvesting in mesophotic corals is powered by a spatially efficient photosymbiotic system between coral host and microalgae 10.1101/2020.12.04.411496
Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae 10.1073/pnas.2025252118