Global chemical effects of the microbiome include new bile-acid conjugations
Robert A Quinn Alexey V Melnik Alison Vrbanac Ting Fu Kathryn A Patras Mitchell P Christy Zsolt Bodai Pedro Belda-Ferre Anupriya Tripathi Lawton K Chung Michael Downes Ryan D Welch Melissa Quinn Greg Humphrey Morgan Panitchpakdi Kelly C Weldon Alexander Aksenov Ricardo da Silva Julian Avila-Pacheco Clary Clish Sena Bae Himel Mallick Eric A Franzosa Jason Lloyd-Price Robert Bussell Taren Thron Andrew T Nelson Mingxun Wang Eric Leszczynski Fernando Vargas Julia M Gauglitz Michael J Meehan Emily Gentry Timothy D Arthur Alexis C Komor Orit Poulsen Brigid S Boland John T Chang William J Sandborn Meerana Lim Neha Garg Julie C Lumeng Ramnik J Xavier Barbara I Kazmierczak Ruchi Jain Marie Egan Kyung E Rhee David Ferguson Manuela Raffatellu Hera Vlamakis Gabriel G Haddad Dionicio Siegel Curtis Huttenhower Sarkis K Mazmanian Ronald M Evans Victor Nizet Rob Knight Pieter C Dorrestein
Nature, 2020-3
https://doi.org/10.1038/s41586-020-2047-9
Rob Knight
Knight Rob
ORCID: 0000-0002-0975-9019
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Current understanding of the human microbiome. 10.1038/nm.4517
Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California. 10.1080/19490976.2021.1961203
Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. 10.1038/s41396-021-00935-9
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. 10.1101/2020.11.13.370387
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. 10.1101/2020.08.17.238444
Methods for phylogenetic analysis of microbiome data. 10.1038/s41564-018-0156-0
Publisher Correction: Enterotypes in the landscape of gut microbial community composition. 10.1038/s41564-018-0114-x
Enterotypes in the landscape of gut microbial community composition. 10.1038/s41564-017-0072-8
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. 10.1371/journal.pcbi.1009056
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes. 10.1101/gr.275777.121
Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence. 10.1101/2021.07.16.452756
Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 10.1038/s41396-021-01016-7
Structure-based protein function prediction using graph convolutional networks. 10.1038/s41467-021-23303-9
Challenges in benchmarking metagenomic profilers. 10.1038/s41592-021-01141-3
Taxonomic signatures of cause-specific mortality risk in human gut microbiome. 10.1038/s41467-021-22962-y
Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. 10.1111/biom.13481
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition. 10.1128/msystems.01329-20
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Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3
Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models. 10.1038/s41591-018-0219-z
Three-dimensional culture of oral progenitor cells: Effects on small extracellular vesicles production and proliferative function 10.1111/jop.12981
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017 10.1186/s40168-018-0596-z
Human skin, oral, and gut microbiomes predict chronological age 10.1128/mSystems.00630-19
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
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893) 10.1038/nbt0718-660d
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/rs.3.rs-56028/v1
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
Neha Garg
Garg Neha
ORCID: 0000-0002-2760-7123
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
John Chang
Chang John / John T. Chang
ORCID: 0000-0003-0873-6218
Reply to: "CD8+ T cell diversification by asymmetric cell division" 10.1038/ni.3234
Asymmetric Cell Division in T Lymphocyte Fate Diversification 10.1016/j.it.2015.09.004
Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses 10.1038/ni.2842
Regulation of Asymmetric Division and CD8+T Lymphocyte Fate Specification by Protein Kinase Cζ and Protein Kinase Cλ/ι 10.4049/jimmunol.1401652
Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA sequencing 10.1038/ni.3688
Update on Janus Kinase Antagonists in Inflammatory Bowel Disease 10.1016/j.gtc.2014.05.011
Cronkhite Canada Syndrome: Significant Response to Infliximab and a Possible Clue to Pathogenesis 10.1038/ajg.2016.92
Immunodeficiency and Autoimmune Enterocolopathy Linked to NFAT5 Haploinsufficiency 10.4049/jimmunol.1401463
The Real-World Effectiveness and Safety of Vedolizumab for Moderate–Severe Crohn’s Disease: Results From the US VICTORY Consortium 10.1038/ajg.2016.236
A gp130–Src–YAP module links inflammation to epithelial regeneration 10.1038/nature14228
Validation of Gene Expression Biomarker Analysis for Biopsy-based Clinical Trials in Crohnʼs Disease 10.1097/mib.0000000000000264
Regulation of Asymmetric Division by Atypical Protein Kinase C Influences Early Specification of CD8+ T Lymphocyte Fates 10.1038/srep19182
The Microtubule-Associated Protein Lis1 Regulates T Lymphocyte Homeostasis and Differentiation 10.4049/jimmunol.1502410
Molecular regulation of effector and memory T cell differentiation 10.1038/ni.3031
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation 10.1038/ni.3706
Protection One Cell Thick 10.1016/j.immuni.2007.11.009
Asymmetric Proteasome Segregation as a Mechanism for Unequal Partitioning of the Transcription Factor T-bet during T Lymphocyte Division 10.1016/j.immuni.2011.03.017
Asymmetric Division and Stem Cell Renewal without a Permanent Niche: Lessons from Lymphocytes 10.1101/sqb.2008.73.008
Cutting Edge: Asymmetric Memory T Cell Division in Response to Rechallenge 10.4049/jimmunol.1200176
Asymmetric T Lymphocyte Division in the Initiation of Adaptive Immune Responses 10.1126/science.1139393
Should We Divide Crohn's Disease Into Ileum-Dominant and Isolated Colonic Diseases? 10.1016/j.cgh.2019.04.040
Biomarkers Are Associated With Clinical and Endoscopic Outcomes With Vedolizumab Treatment in Ulcerative Colitis. 10.1093/ibd/izy307
Elevated A20 promotes TNF-induced and RIPK1-dependent intestinal epithelial cell death. 10.1073/pnas.1810584115
Development and Validation of a Scoring System to Predict Outcomes of Vedolizumab Treatment in Patients With Crohn's Disease. 10.1053/j.gastro.2018.05.039
Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance. 10.4049/jimmunol.1800112
Hyperbaric oxygen therapy is well tolerated and effective for ulcerative colitis patients hospitalized for moderate-severe flares: a phase 2A pilot multi-center, randomized, double-blind, sham-controlled trial. 10.1038/s41395-018-0005-z
Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. 10.1172/JCI90895
Talin Plays a Critical Role in the Maintenance of the Regulatory T Cell Pool. 10.4049/jimmunol.1601165
Heterogenous Populations of Tissue-Resident CD8+ T Cells Are Generated in Response to Infection and Malignancy. 10.1016/j.immuni.2020.04.007
Early precursors and molecular determinants of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing. 10.1126/sciimmunol.aaz6894
Global chemical effects of the microbiome include new bile-acid conjugations. 10.1038/s41586-020-2047-9
Development and Validation of Clinical Scoring Tool to Predict Outcomes of Treatment With Vedolizumab in Patients With Ulcerative Colitis. 10.1016/j.cgh.2020.02.010
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. 10.1186/s13059-019-1834-9
USP11 Enhances TGFβ-Induced Epithelial-Mesenchymal Plasticity and Human Breast Cancer Metastasis. 10.1158/1541-7786.mcr-17-0723
Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease. 10.1038/ctg.2017.58
Ubiquitylation of CD98 limits cell proliferation and clonal expansion. 10.1242/jcs.178129
Validated gene expression biomarker analysis for biopsy-based clinical trials in ulcerative colitis. 10.1111/apt.12862
Studies in human intestinal tissues: is it time to reemphasize research in human immunology? 10.1053/j.gastro.2014.05.025
Polarity and lymphocyte fate determination. 10.1016/j.ceb.2012.05.002
Loss of T cell CD98 H chain specifically ablates T cell clonal expansion and protects from autoimmunity. 10.4049/jimmunol.1100002
CpG oligonucleotides are potent adjuvants for the activation of autoreactive encephalitogenic T cells in vivo. 10.4049/jimmunol.164.11.5683
The costimulatory effect of IL-18 on the induction of antigen-specific IFN-gamma production by resting T cells is IL-12 dependent and is mediated by up-regulation of the IL-12 receptor beta2 subunit. 10.1002/(sici)1521-4141(200004)30:4&#60;1113::aid-immu1113&#62;3.0.co;2-p
The critical role of IL-12 and the IL-12R beta 2 subunit in the generation of pathogenic autoreactive Th1 cells. 10.1007/bf00812256
Role of costimulation in the induction of the IL-12/IL-12 receptor pathway and the development of autoimmunity. 10.4049/jimmunol.164.1.100
Regulation of interleukin (IL)-12 receptor beta2 subunit expression by endogenous IL-12: a critical step in the differentiation of pathogenic autoreactive T cells. 10.1084/jem.189.6.969
Asymmetric cell division of T cells upon antigen presentation uses multiple conserved mechanisms. 10.4049/jimmunol.0903627
Inducible MHC class II expression by mast cells supports effector and regulatory T cell activation. 10.4049/jimmunol.0803180
Specifying helper T cell fates during immunity. 10.1097/01.mpg.0000313832.47207.0e
Downregulation of 26S proteasome catalytic activity promotes epithelial-mesenchymal transition. 10.18632/oncotarget.7596
Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses. 10.1126/sciimmunol.abb4432
Himel Mallick
Mallick Himel
ORCID: 0000-0003-4956-2429
Hierarchical Models for Genetic Association Studies 10.4172/2155-6180.1000e124
Differences in clinical course, genetics, and the microbiome between familial and sporadic inflammatory bowel diseases 10.1093/ecco-jcc/jjx154
Metatranscriptome of human faecal microbial communities in a cohort of adult men 10.1038/s41564-017-0084-4
Stability of the human faecal microbiome in a cohort of adult men 10.1038/s41564-017-0096-0
Experimental design and quantitative analysis of microbial community multiomics 10.1186/s13059-017-1359-z
A Bayesian method for detecting pairwise associations in compositional data 10.1371/journal.pcbi.1005852
Bayesian group bridge for bi-level variable selection 10.1016/j.csda.2017.01.002
Negative binomial mixed models for analyzing microbiome count data 10.1186/s12859-016-1441-7
EM adaptive LASSO-a multilocus modeling strategy for detecting SNPs associated with zero-inflated count phenotypes 10.3389/fgene.2016.00032
Clinical trial designs incorporating predictive biomarkers 10.1016/j.ctrv.2015.12.008
A genetic association study detects haplotypes associated with obstructive heart defects 10.1007/s00439-014-1453-1
Transcriptomes and shRNA suppressors in a TP53 allele-specific model of early-onset colon cancer in African Americans. 10.1158/1541-7786.mcr-13-0286-t
Multiple comparisons in genetic association studies: A hierarchical modeling approach 10.1515/sagmb-2012-0040
A New Bayesian Lasso. 10.4310/sii.2014.v7.n4.a12
A risk algorithm for assessing short-term mortality for obese black and white men and women 10.1002/oby.20622
Oronasopharyngeal suction versus wiping of the mouth and nose at birth: a randomised equivalency trial. 10.1016/s0140-6736(13)60775-8
Bayesian Methods for High Dimensional Linear Models. 10.4172/2155-6180.s1-005
Mortality and intestinal failure in surgical necrotizing enterocolitis 10.1016/j.jpedsurg.2012.11.028
Bayesian bridge regression 10.1080/02664763.2017.1324565
Group regularization for zero‐inflated negative binomial regression models with an application to health care demand in Germany 10.1002/sim.7804
Group regularization for zero-inflated poisson regression models with an application to insurance ratemaking 10.1080/02664763.2018.1555232
Gut microbiome structure and metabolic activity in inflammatory bowel disease 10.1038/s41564-018-0306-4
A Note on the Adaptive LASSO for Zero-Inflated Poisson Regression 10.1155/2018/2834183
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases 10.1038/s41586-019-1237-9
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences 10.1038/s41467-019-10927-1
Quantile Regression and Beyond in Statistical Analysis of Data 10.1155/2019/2635306
Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men 10.1053/j.gastro.2019.12.029
Editorial: Statistical and Computational Methods for Microbiome Multi-Omics Data 10.3389/fgene.2020.00927
Bayesian reciprocal LASSO quantile regression 10.1080/03610918.2020.1804585
Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9
Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease (Nature Microbiology, (2019), 4, 2, (293-305), 10.1038/s41564-018-0306-4) 10.1038/s41564-019-0442-5
Multivariable Association Discovery in Population-scale Meta-omics Studies 10.1101/2021.01.20.427420
A Statistical Model for Describing and Simulating Microbial Community Profiles 10.1101/2021.03.26.437146
Differential expression of single-cell RNA-seq data using Tweedie models 10.1101/2021.03.28.437378
Omics community detection using multi-resolution clustering 10.1093/bioinformatics/btab317
The reciprocal Bayesian LASSO 10.1002/sim.9098
A statistical model for describing and simulating microbial community profiles 10.1371/journal.pcbi.1008913
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
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
Kathryn Patras
Patras Kathryn
ORCID: 0000-0003-2631-8810
Novel Models of Streptococcus canis Colonization and Disease Reveal Modest Contributions of M-Like (SCM) Protein 10.3390/microorganisms9010183
Global chemical effects of the microbiome include new bile-acid conjugations. 10.1038/s41586-020-2047-9
Determinants of Group B streptococcal virulence potential amongst vaginal clinical isolates from pregnant women. 10.1371/journal.pone.0226699
Cas9 Contributes to Group B Streptococcal Colonization and Disease. 10.3389/fmicb.2019.01930
Host Cathelicidin Exacerbates Group B Streptococcus Urinary Tract Infection. 10.1128/msphere.00932-19
The Fungal Pathogen Candida albicans Promotes Bladder Colonization of Group B Streptococcus. 10.3389/fcimb.2019.00437
Inhibition of Human Neutrophil Extracellular Trap (NET) Production by Propofol and Lipid Emulsion. 10.3389/fphar.2019.00323
Augmentation of Urinary Lactoferrin Enhances Host Innate Immune Clearance of Uropathogenic Escherichia coli. 10.1159/000499342
Multidimensional Proteome Profiling of Blood-Brain Barrier Perturbation by Group B Streptococcus. 10.1128/msystems.00368-20
Group B Streptococcal Maternal Colonization and Neonatal Disease: Molecular Mechanisms and Preventative Approaches. 10.3389/fped.2018.00027
Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic. 10.1128/msystems.00340-20
Developmental Immaturity of Siglec Receptor Expression on Neonatal Alveolar Macrophages Predisposes to Severe Group B Streptococcal Infection. 10.1016/j.isci.2020.101207
Tamm-Horsfall Protein Protects the Urinary Tract against Candida albicans. 10.1128/iai.00451-18
Trichomonas vaginalis Induces NLRP3 Inflammasome Activation and Pyroptotic Cell Death in Human Macrophages. 10.1159/000493585
A Murine Model of Group B Streptococcus Vaginal Colonization. 10.3791/54708
The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus. 10.1186/s12866-018-1341-2
Group B Streptococcus Biofilm Regulatory Protein A Contributes to Bacterial Physiology and Innate Immune Resistance. 10.1093/infdis/jiy341
Tamm-Horsfall glycoprotein engages human Siglec-9 to modulate neutrophil activation in the urinary tract. 10.1038/icb.2017.63
Streptococcus salivarius K12 Limits Group B Streptococcus Vaginal Colonization. 10.1128/iai.00409-15
Group B streptococcal serine-rich repeat proteins promote interaction with fibrinogen and vaginal colonization. 10.1093/infdis/jiu151
Identification of CiaR Regulated Genes That Promote Group B Streptococcal Virulence and Interaction with Brain Endothelial Cells. 10.1371/journal.pone.0153891
A novel C5a-derived immunobiotic peptide reduces Streptococcus agalactiae colonization through targeted bacterial killing. 10.1128/aac.01590-13
Group B Streptococcus CovR regulation modulates host immune signalling pathways to promote vaginal colonization. 10.1111/cmi.12105
Analysis of two-component systems in group B Streptococcus shows that RgfAC and the novel FspSR modulate virulence and bacterial fitness. 10.1128/mbio.00870-14
Hypoxia-Inducible Factor 1 Alpha Is Dispensable for Host Defense of Group B Streptococcus Colonization and Infection. 10.1159/000515739
Characterization of host immunity during persistent vaginal colonization by Group B Streptococcus. 10.1038/mi.2015.23
Ronald Evans
Evans Ronald / Ron Evans
ORCID: 0000-0002-9986-5965
Nuclear receptor coactivators co-ordinate metabolic responses to hormonal and environmental stimuli 10.1142/9789812819178_0018
Establishing Orphan Nuclear Receptors PXR and CAR as Xenobiotic Receptors 10.1002/9780470409107.ch2
Unexpected thymic hyperplasia in transgenic mice harboring a neuronal promoter fused with simian virus 40 large T antigen. 10.1128/MCB.7.9.3178
RXRα deficiency confers genetic susceptibility for aortic sac, conotruncal, atrioventricular cushion, and ventricular muscle defects in mice 10.1172/JCI118920
Nuclear receptors constitutive androstane receptor and pregnane X receptor ameliorate cholestatic liver injury 10.1073/pnas.0409794102
Minireview: Lipid metabolism, metabolic diseases, and peroxisome proliferator-activated receptors 10.1210/en.2003-0288
Intestinal NCoR1, a regulator of epithelial cell maturation, controls neonatal hyperbilirubinemia 10.1073/pnas.1700232114
Arsenic decreases RXRα-dependent transcription of CYP3A and suppresses immune regulators in hepatocytes 10.1016/j.intimp.2012.01.008
The ginsenoside metabolite compound K, a novel agonist of glucocorticoid receptor, induces tolerance to endotoxin-induced lethal shock 10.1111/j.1582-4934.2007.00181.x
Nuclear receptors rock around the clock 10.1002/embr.201338271
Wylie Walker Vale Jr (1941-2012) 10.1038/483542a
Visible light reduces C. elegans longevity 10.1038/s41467-018-02934-5
Nuclear receptor coactivator ACTR is a novel histone acetyltransferase and forms a multimeric activation complex with P/CAF and CBP/p300 10.1016/S0092-8674(00)80516-4
The initiation sites for RNA transcription in Ad2 DNA 10.1016/0092-8674(77)90273-2
Targeting expression of a dominant-negative retinoic acid receptor mutant in the epidermis of transgenic mice results in loss of barrier function 10.1101/gad.9.3.317
PPARs and the complex journey to obesity 10.2302/kjm.53.53
The germ cell nuclear factor mGCNF is expressed in the developing nervous system 10.1159/000111238
O-GlcNAc transferase is involved in glucocorticoid receptor-mediated transrepression 10.1074/jbc.M111.303792
Differential expression and activation of a family of murine peroxisome proliferator-activated receptors 10.1073/pnas.91.15.7355
Cistromic and genetic evidence that the Vitamin D receptor mediates susceptibility to latitude-dependent autoimmune diseases 10.1038/gene.2016.12
Extrahepatic cancer suppresses nuclear receptor-regulated drug metabolism 10.1158/1078-0432.CCR-10-3289
Chromosomal localization of the human retinoid x receptors 10.1006/geno.1994.1193
Effects of peroxisome proliferator-activated receptor δ on placentation, adiposity, and colorectal cancer 10.1073/pnas.012610299
Arsenite decreases CYP3A23 induction in cultured rat hepatocytes by transcriptional and translational mechanisms 10.1016/j.taap.2005.04.008
Retinoid X receptor interacts with nuclear receptors in retinoic acid, thyroid hormone and vitamin D3 signalling. 10.1038/355446a0
Exercise Mimetics: Impact on Health and Performance 10.1016/j.cmet.2016.10.022
Protection from liver fibrosis by a peroxisome proliferator-activated receptor δ agonist 10.1073/pnas.1202464109
Relationship between Drosophila gap gene tailless and a vertebrate nuclear receptor Tlx 10.1038/370375a0
A PML-PPAR-δ pathway for fatty acid oxidation regulates hematopoietic stem cell maintenance 10.1038/nm.2882
A Gpr120-selective agonist improves insulin resistance and chronic inflammation in obese mice 10.1038/nm.3614
Peroxisome proliferator-activated receptor γ controls Muc1 transcription in trophoblasts 10.1128/MCB.24.24.10661-10669.2004
Production of mRNA in chinese hamster cells: Relationship of the rate of synthesis to the cytoplasmic concentration of nine specific mRNA sequences 10.1016/0092-8674(79)90341-6
Zinc fingers: Gilt by association 10.1016/0092-8674(88)90522-3
Evidence for two distinct retinoic acid response pathways for HOXB1 gene regulation 10.1073/pnas.92.2.392
Humanized xenobiotic response in mice expressing nuclear receptor SXR 10.1038/35019116
A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR 10.1016/S1097-2765(03)00104-7
Circadian clock cryptochrome proteins regulate autoimmunity 10.1073/pnas.1619119114
Rescue of a primary myelofibrosis model by retinoid-antagonist therapy 10.1073/pnas.1318974110
Protein kinase C phosphorylation at Thr 654 of the unoccupied EGF receptor and EGF binding regulate functional receptor loss by independent mechanisms 10.1016/0092-8674(86)90006-1
Chromosomal translocation t(15;17) in human acute promyelocytic leukemia fuses RARα with a novel putative transcription factor, PML 10.1016/0092-8674(91)90112-C
Stimulation of noradrenergic sympathetic outflow by calcitonin gene-related peptide 10.1038/305534a0
Calcipotriol targets LRP6 to inhibit wnt signaling in pancreatic cancer 10.1158/1541-7786.MCR-15-0204
Characterization of rat calcitonin mRNA. 10.1073/pnas.77.8.4444
PPARδ regulates glucose metabolism and insulin sensitivity 10.1073/pnas.0511253103
Isoform-specific amino-terminal domains dictate DNA-binding properties of RORα, a novel family of orphan hormone nuclear receptors 10.1101/gad.8.5.538
Retinoic acid is a negative regulator of AP-1-responsive genes 10.1073/pnas.88.14.6092
The synthesis and processing of a nuclear RNA precursor to rat pregrowth hormone messenger RNA 10.1093/nar/6.9.3133
Pituitary hyperplasia induced by ectopic expression of nerve growth factor 10.1073/pnas.89.7.2764
Jun-Fos and receptors for vitamins A and D recognize a common response element in the human osteocalcin gene 10.1016/0092-8674(90)90531-I
Regulation of a xenobiotic sulfonation cascade by nuclear pregnane X receptor (PXR) 10.1073/pnas.212494599
Metabolism: Tick, tock, a Β 2-cell clock 10.1038/466571a
Adenovirus replication is coupled with the dynamic properties of the PML nuclear structure 10.1101/gad.10.2.196
Corepressor SMRT binds the BTB/POZ repressing domain of the LAZ3/BCL6 oncoprotein 10.1073/pnas.94.20.10762
Lymphoma Regression Induced by Ganciclovir in Mice Bearing a Herpes Thymidine Kinase Transgene 10.1089/hum.1990.1.2-125
Interactions between hepatic Mrp4 and Sult2a as revealed by the constitutive androstane receptor and Mrp4 knockout mice 10.1074/jbc.M314111200
PGC-1β controls mitochondrial metabolism to modulate circadian activity, adaptive thermogenesis, and hepatic steatosis 10.1073/pnas.0611623104
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming 10.1038/cr.2011.177
The Bcl6-SMRT/NCoR cistrome represses inflammation to attenuate atherosclerosis 10.1016/j.cmet.2012.02.012
Effective treatment of steatosis and steatohepatitis by fibroblast growth factor 1 in mouse models of nonalcoholic fatty liver disease 10.1073/pnas.1525093113
Genetic profiling defines the xenobiotic gene network controlled by the nuclear receptor pregnane x receptor 10.1210/me.2002-0421
PPARδ Promotes Running Endurance by Preserving Glucose 10.1016/j.cmet.2017.04.006
A novel macromolecular structure is a target of the promyelocyte-retinoic acid receptor oncoprotein 10.1016/0092-8674(94)90340-9
Lethal mitochondrial cardiomyopathy in a hypomorphic Med30 mouse mutant is ameliorated by ketogenic diet 10.1073/pnas.1117835108
Identification of a novel thyroid hormone receptor expressed in the mammalian central nervous system 10.1126/science.3629259
Reciprocal activation of xenobiotic response genes by nuclear receptors SXR/PXR and CAR 10.1101/gad.846800
Role of CBP/P300 in nuclear receptor signalling 10.1038/383099a0
The peroxisome proliferator-activated receptors: Ligands and activators 10.1111/j.1749-6632.1996.tb18621.x
Interactions between the retinoid X receptor and a conserved region of the TATA-binding protein mediate hormone-dependent transactivation 10.1073/pnas.92.18.8288
Adipose-specific peroxisome proliferator-activated receptor γ knockout causes insulin resistance in fat and liver but not in muscle 10.1073/pnas.2536828100
A histone deacetylase corepressor complex regulates the Notch signal transduction pathway 10.1101/gad.12.15.2269
Feeder-dependent and feeder-independent iPS cell derivation from human and mouse adipose stem cells 10.1038/nprot.2010.199
Characterization of an autoregulated response element in the mouse retinoic acid receptor type β gene 10.1073/pnas.87.14.5392
Retinoid X receptor-COUP-TF interactions modulate retinoic acid signaling 10.1073/pnas.89.4.1448
Nuclear receptor TLX prevents retinal dystrophy and recruits the corepressor atrophin1 10.1101/gad.1413606
Nuclear receptors as modulators of the tumor microenvironment 10.1158/1940-6207.CAPR-11-0528
Disease tolerance mediated by microbiome E. coli involves inflammasome and IGF-1 signaling 10.1126/science.aac6468
Deficiency of PPARβ/σ in the epidermis results in defective cutaneous permeability barrier homeostasis and increased inflammation 10.1038/sj.jid.5701026
SMRT repression of nuclear receptors controls the adipogenic set point and metabolic homeostasis 10.1073/pnas.0811012105
High-fat diet and FGF21 cooperatively promote aerobic thermogenesis in mtDNA mutator mice 10.1073/pnas.1509930112
Modulation of the intestinal bile acid/farnesoid X receptor/fibroblast growth factor 15 axis improves alcoholic liver disease in mice 10.1002/hep.29676
Cardiac peroxisome proliferator-activated receptor γ is essential in protecting cardiomyocytes from oxidative damage 10.1016/j.cardiores.2007.06.027
Expression in brain of a messenger RNA encoding a novel neuropeptide homologous to calcitonin gene-related peptide 10.1126/science.2994212
A retinoic acid-triggered cascade of HOXB1 gene activation 10.1073/pnas.92.2.387
Determinants for selective RAR and TR recognition of direct repeat HREs 10.1101/gad.7.7b.1411
Role of the nuclear receptor pregnane X receptor in acetaminophen hepatotoxicity 10.1124/dmd.105.005256
SRF'ing around the clock 10.1016/j.cell.2013.01.028
ERRγ Promotes Angiogenesis, Mitochondrial Biogenesis, and Oxidative Remodeling in PGC1α/β-Deficient Muscle 10.1016/j.celrep.2018.02.047
Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β 10.1038/nature11048
Rosiglitazone activation of PPARg suppresses fractalkine signaling 10.1677/JME-09-0090
The PML nuclear compartment and cancer 10.1016/S0304-419X(96)00028-5
SMRTER, a Drosophila nuclear receptor coregulator, reveals that EcR-mediated repression is critical for development 10.1016/S1097-2765(00)80365-2
Fibroblast growth factor signaling in metabolic regulation 10.3389/fendo.2015.00193
PPARs and LXRs: Atherosclerosis goes nuclear 10.1016/j.tem.2004.03.003
Identification of a nuclear domain with deacetylase activity 10.1073/pnas.97.19.10330
Phosphorylation of CREB at ser-133 induces complex formation with CREB-binding protein via a direct mechanism 10.1128/MCB.16.2.694
Domain structure of human glucocorticoid receptor and its relationship to the v-erb-A oncogene product 10.1038/318670a0
Expression and function of orphan nuclear receptor TLX in adult neural stem cells 10.1038/nature02211
Cytoplasmic recruitment of INI1 and PML on incoming HIV preintegration complexes: Interference with early steps of viral replication 10.1016/S1097-2765(01)00255-6
ERRγ Directs and Maintains the Transition to Oxidative Metabolism in the Postnatal Heart 10.1016/j.cmet.2007.06.007
The steroid and thyroid hormone receptor superfamily 10.1126/science.3283939
Hormonal regulation of the nuclear localization signals of the human glucocorticosteroid receptor 10.1016/0014-4827(92)90352-9
Peroxisome-proliferator-activated receptor δ activates fat metabolism to prevent obesity 10.1016/S0092-8674(03)00269-1
Terminal Differentiation of Human Breast Cancer through PPARγ 10.1016/S1097-2765(00)80047-7
BXR, an embryonic orphan nuclear receptor activated by a novel class of endogenous benzoate metabolites 10.1101/gad.12.9.1269
Corrigendum: Endocrinization of FGF1 produces a neomorphic and potent insulin sensitizer 10.1038/nature14304
Monomeric complex of human orphan estrogen related receptor-2 with DNA: A pseudo-dimer interface mediates extended half-site recognition 10.1016/S0022-2836(03)00183-9
Tlx and Pax6 co-operate genetically to establish the pallio-subpallial boundary in the embryonic mouse telencephalon 10.1242/dev.00328
PPAR-γ dependent and independent effects on macrophage-gene expression in lipid metabolism and inflammation 10.1038/83336
ERRγ Preserves Brown Fat Innate Thermogenic Activity 10.1016/j.celrep.2018.02.061
Discrete cis-active genomic sequences dictate the pituitary cell type-specific expression of rat prolactin and growth hormone genes 10.1038/322557a0
Nuclear receptors, RXR, and the big bang 10.1016/j.cell.2014.03.012
Nuclear Hormone Receptors Activate Direct, Inverted, and Everted Repeats 10.1111/j.1749-6632.1995.tb31366.x
Insights into Negative Regulation by the Glucocorticoid Receptor from Genome-wide Profiling of Inflammatory Cistromes 10.1016/j.molcel.2012.10.013
Journal of Molecular Endocrinology 25th anniversary special issue 10.1530/JME-13-0257
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Expression cloning of human EGF receptor complementary DNA: gene amplification and three related messenger RNA products in A431 cells. 10.1126/science.6326261
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Quantitative and qualitative differences in DNA complementary to avian myeloblastosis virus between normal and leukemic chicken cells. 10.1159/000397570
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Inducible and developmental control of neuroendocrine genes. 10.1101/sqb.1985.050.01.049
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Triptolide targets super-enhancer networks in pancreatic cancer cells and cancer-associated fibroblasts. 10.1038/s41389-020-00285-9
Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas. 10.1158/0008-5472.can-20-0078
Shining Light on the COVID-19 Pandemic: A Vitamin D Receptor Checkpoint in Defense of Unregulated Wound Healing. 10.1016/j.cmet.2020.09.007
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Unified neural pathways that gate affective pain and multisensory innate threat signals to the amygdala 10.21203/rs.3.rs-131308/v1
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Colon cancer checks in when bile acids check out: the bile acid–nuclear receptor axis in colon cancer 10.1042/EBC20210038
Summary of the Sussex-Huawei locomotion-transportation recognition challenge
Observation of a manifold in the chaotic phase space of an asymmetric optical microcavity
Localized temporal variation of Earth's inner-core boundary from high-quality waveform doublets
Off-axis multi-wavelength dispersion controlling metalens for multi-color imaging
Impact of United States political sanctions on international collaborations and research in Iran