Lifestyle chemistries from phones for individual profiling
Bouslimani, Amina Melnik, Alexey V. Xu, Zhenjiang Amir, Amnon da Silva, Ricardo R. Wang, Mingxun Bandeira, Nuno Alexandrov, Theodore 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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Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans 10.1016/j.cell.2020.09.009
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Chemically informed analyses of metabolomics mass spectrometry data with Qemistree 10.1038/s41589-020-00677-3
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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
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Single-cell transcriptomics reveal a correlation between genome architecture and gene family evolution in ciliates 10.1128/mBio.02524-19
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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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Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) 10.1002/mbo3.716
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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
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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
zhenjiang xu
xu zhenjiang / Zhenjiang Zech Xu
ORCID: 0000-0003-1080-024X
Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor 10.4161/rna.8.3.14421
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences 10.1093/bioinformatics/btq726
Statistical evaluation of improvement in RNA secondary structure prediction 10.1093/nar/gkr1081
Which is more important for classifying microbial communities: who's there or what they can do? 10.1038/ismej.2014.157
Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance 10.1261/rna.033431.112
Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation 10.1016/j.bbrc.2015.01.074
Structural basis for diversity in the SAM clan of riboswitches 10.1073/pnas.1312918111
Dietary effects on human gut microbiome diversity 10.1017/S0007114514004127
Subsistence strategies in traditional societies distinguish gut microbiomes 10.1038/ncomms7505
Ribosomal RNA, the lens into life 10.1261/rna.050799.115
Meta-analyses of human gut microbes associated with obesity and IBD 10.1016/j.febslet.2014.09.039
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies 10.1128/mSystems.00021-16
Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures 10.1371/journal.pone.0130200
Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota 10.1016/j.chom.2015.08.005
Microbial community assembly and metabolic function during mammalian corpse decomposition 10.1126/science.aad2646
Open-Source Sequence Clustering Methods Improve the State Of the Art 10.1128/mSystems.00003-15
Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project 10.1128/jmbe.v17i1.1034
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision 10.1038/ismej.2015.235
Microbiome-wide association studies link dynamic microbial consortia to disease 10.1038/nature18850
Secondary Structure Prediction of Single Sequences Using RNAstructure 10.1007/978-1-4939-6433-8_2
Experiment-Assisted Secondary Structure Prediction with RNAstructure 10.1007/978-1-4939-6433-8_10
Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113
Normalization and microbial differential abundance strategies depend upon data characteristics 10.1186/s40168-017-0237-y
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns 10.1128/mSystems.00191-16
Evidence for fungal and chemodenitrification based N$_\textrm2$O flux from nitrogen impacted coastal sediments 10.1038/ncomms15595
A communal catalogue reveals Earth's multiscale microbial diversity 10.1038/nature24621
Guiding longitudinal sampling in IBD cohorts 10.1136/gutjnl-2017-315352
Prediction of Secondary Structures Conserved in Multiple RNA Sequences 10.1007/978-1-4939-6433-8_3
Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models 10.3390/genes9020104
Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm 10.1038/s41467-018-04409-z
Exposure to toxic metals triggers unique responses from the rat gut microbiota 10.1038/s41598-018-24931-w
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information 10.1128/mSystems.00021-18
Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction 10.1128/mSystems.00188-17
American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18
Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) 10.1002/mbo3.716
Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism 10.1038/s41467-018-05336-9
Microbiome Tools for Forensic Science 10.1016/j.tibtech.2017.03.006
Striped UniFrac: enabling microbiome analysis at unprecedented scale 10.1038/s41592-018-0187-8
Calour: an Interactive, Microbe-Centric Analysis Tool 10.1128/mSystems.00269-18
A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease 10.1038/s41467-019-09455-9
Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems 10.1128/mSystems.00058-19
Identification of new high affinity targets for Roquin based on structural conservation 10.1093/nar/gky908
Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue 10.1111/1556-4029.13949
Best practices for analysing microbiomes 10.1038/s41579-018-0029-9
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 10.1038/s41587-019-0209-9
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads 10.1186/s13059-019-1834-9
Vitamin D metabolites and the gut microbiome in older men 10.1038/s41467-020-19793-8
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4
Toxicant substitutes in immunological assays for mycotoxins detection: A mini review 10.1016/j.foodchem.2020.128589
Multiple-Disease Detection and Classification across Cohorts via Microbiome Search 10.1128/mSystems.00150-20
Chlorogenic acid attenuates cadmium-induced intestinal injury in Sprague–Dawley rats 10.1016/j.fct.2019.110751
PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community 10.1016/j.gpb.2020.07.005
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
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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