Research graph
References from CDEMI: Characterizing differences in microbial composition and function in microbiome data. Local targets link to admitted publications; unresolved targets remain external evidence.
The state of microbiome science at the intersection of infectious diseases and antimicrobial resistance
10.1093/infdis/jiab020 · 2021 · External reference
10.1038/s41586-021-03707-9
10.1038/s41586-021-03707-9 · External reference
10.1146/annurev-biochem-080320-115307
10.1146/annurev-biochem-080320-115307 · External reference
10.1038/s41586-020-2396-4
10.1038/s41586-020-2396-4 · External reference
10.1038/s41579-020-0438-4
10.1038/s41579-020-0438-4 · External reference
10.1177/0022034515611876
10.1177/0022034515611876 · External reference
10.3390/toxins12040220
10.3390/toxins12040220 · External reference
10.1053/j.gastro.2019.06.048
10.1053/j.gastro.2019.06.048 · External reference
10.1136/gutjnl-2019-320204
10.1136/gutjnl-2019-320204 · External reference
Traditional Chinese medicines differentially modulate the gut microbiota based on their nature (Yao-Xing)
10.1016/j.phymed.2021.153496 · 2021 · External reference
Glyphosate-based herbicides influence antioxidants, reproductive hormones and gut microbiome but not reproduction: a long-term experiment in an avian model
10.1016/j.envpol.2020.115108 · 2020 · External reference
10.1093/nar/gkaa924
10.1093/nar/gkaa924 · External reference
Detecting sparse microbial association signals adaptively from longitudinal microbiome data based on generalized estimating equations
10.1093/bib/bbac149 · 2022 · External reference
10.1038/nrmicro2537
10.1038/nrmicro2537 · External reference
10.1016/j.chom.2020.07.013
10.1016/j.chom.2020.07.013 · External reference
Dysbiotic microbiota interactions in Crohn's disease
10.1080/19490976.2021.1949096 · 2021 · External reference
10.1016/j.chom.2017.03.010
10.1016/j.chom.2017.03.010 · External reference
Advances in understanding the human urinary microbiome and its potential role in urinary tract infection
10.1128/mbio.00218-20 · 2020 · External reference
10.1016/j.tim.2019.08.001
10.1016/j.tim.2019.08.001 · External reference
Correction to: modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health
10.1186/s40168-021-01171-1 · 2021 · External reference
10.1126/science.aay0240
10.1126/science.aay0240 · External reference
gutMEGA: a database of the human gut MEtaGenome Atlas
10.1093/bib/bbaa082 · 2021 · External reference
10.1093/bib/bbaa005
10.1093/bib/bbaa005 · External reference
10.1016/j.tim.2021.04.004
10.1016/j.tim.2021.04.004 · External reference
Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure
10.1186/s40168-022-01319-7 · 2022 · External reference
MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes
10.1038/srep40200 · 2017 · External reference
Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data
10.1038/s41598-020-78511-y · 2020 · External reference
DAnIEL: a user-friendly web server for fungal ITS amplicon sequencing data
10.3389/fmicb.2021.720513 · 2021 · External reference
10.1093/nar/gkw1092
10.1093/nar/gkw1092 · External reference
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups
10.1093/database/baz049 · 2019 · External reference
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes
10.1093/nar/gkv1216 · 2016 · External reference
10.1093/nar/gkx1060
10.1093/nar/gkx1060 · External reference
EasyMap - an interactive web tool for evaluating and comparing associations of clinical variables and microbiome composition
10.3389/fcimb.2022.854164 · 2022 · External reference
VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences
10.1186/1471-2105-11-332 · 2010 · External reference
10.1016/j.gpb.2020.07.005
10.1016/j.gpb.2020.07.005 · External reference
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
10.1093/nar/gkx295 · 2017 · External reference
FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information
10.1093/bioinformatics/btz957 · 2020 · External reference
10.1038/s41586-019-1236-x
10.1038/s41586-019-1236-x · External reference
Structural aspects of lesional and non-lesional skin microbiota reveal key community changes in leprosy patients from India
10.1038/s41598-020-80533-5 · 2021 · External reference
Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy
10.1038/s41598-021-82538-0 · 2021 · External reference
10.1111/1469-0691.12213
10.1111/1469-0691.12213 · External reference
10.1111/brv.12603
10.1111/brv.12603 · External reference
Application of a neutral community model to assess structuring of the human lung microbiome
10.1128/mbio.02284-14 · 2015 · External reference
10.1111/mec.16149
10.1111/mec.16149 · External reference
Visualizing data using t-SNE
2008 · External reference
Differential signature of the microbiome and neutrophils in the oral cavity of HIV-infected individuals
10.3389/fimmu.2021.780910 · 2021 · External reference
Unresolved reference
External reference
The virtual metabolic human database: integrating human and gut microbiome metabolism with nutrition and disease
10.1093/nar/gky992 · 2019 · External reference
10.1016/j.csbj.2022.05.024 · Admitted local publication
GIMICA: host genetic and immune factors shaping human microbiota
10.1093/nar/gkaa851 · 2021 · External reference
gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions
10.1093/nar/gkz843 · 2020 · External reference
Disbiome database: linking the microbiome to disease
10.1186/s12866-018-1197-5 · 2018 · External reference
Database resources of the National Center for Biotechnology Information
10.1093/nar/gkaa892 · 2021 · External reference
10.1016/j.autrev.2019.03.006
10.1016/j.autrev.2019.03.006 · External reference
10.1146/annurev-pathol-020117-043559
10.1146/annurev-pathol-020117-043559 · External reference
10.1093/nar/gkaa971
10.1093/nar/gkaa971 · External reference
10.1093/nar/gkx1089
10.1093/nar/gkx1089 · External reference
Gut microbiota and cardiovascular disease: opportunities and challenges
10.1186/s40168-020-00821-0 · 2020 · External reference
10.1080/19490976.2020.1762520
10.1080/19490976.2020.1762520 · External reference
10.1038/s41577-022-00727-y
10.1038/s41577-022-00727-y · External reference
10.1152/physrev.00045.2009
10.1152/physrev.00045.2009 · External reference
CLOUD: a non-parametric detection test for microbiome outliers
10.1186/s40168-018-0514-4 · 2018 · External reference
10.1016/j.csbj.2022.12.035 · Admitted local publication
Polymicrobial infection and bacterium-mediated epigenetic modification of DNA tumor viruses contribute to pathogenesis
10.1128/mbio.01015-14 · 2014 · External reference
10.1007/s13238-018-0548-1
10.1007/s13238-018-0548-1 · External reference
10.1111/1462-2920.16029
10.1111/1462-2920.16029 · External reference
10.3390/nu11071565
10.3390/nu11071565 · External reference
10.1080/19490976.2020.1848158
10.1080/19490976.2020.1848158 · External reference
10.1111/j.1758-2229.2011.00313.x
10.1111/j.1758-2229.2011.00313.x · External reference
10.1016/j.chom.2013.11.005
10.1016/j.chom.2013.11.005 · External reference
Staphylococcus aureus bloodstream infections: pathogenesis and regulatory mechanisms
10.1016/j.mib.2020.02.005 · 2020 · External reference
Differences in gut microbiota in patients with vs without inflammatory bowel diseases: a systematic review
10.1053/j.gastro.2019.11.294 · 2020 · External reference
Comparison of the ocular microbiomes of dry eye patients with and without autoimmune disease
10.3389/fcimb.2021.716867 · 2021 · External reference
10.1007/s10096-019-03598-9
10.1007/s10096-019-03598-9 · External reference
16S rDNA based skin microbiome data of healthy individuals and leprosy patients from India
10.1038/s41597-019-0232-1 · 2019 · External reference
Streptococcus pyogenes upregulates arginine catabolism to exert its pathogenesis on the skin surface
10.1016/j.celrep.2021.108924 · 2021 · External reference
Alleviation of Pseudomonas aeruginosa infection by propeptide-mediated inhibition of protease IV
10.1128/spectrum.00782-21 · 2021 · External reference
Leprous lesion presents enrichment of opportunistic pathogenic bacteria
10.1186/s40064-015-0955-1 · 2015 · External reference
10.1007/s13238-020-00814-7
10.1007/s13238-020-00814-7 · External reference
Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
10.1186/s13059-020-02104-1 · 2020 · External reference
10.1093/nar/gky379
10.1093/nar/gky379 · External reference
Dysbiosis and implication of the gut microbiota in diabetic retinopathy
10.3389/fcimb.2021.646348 · 2021 · External reference
10.3390/antiox9121244
10.3390/antiox9121244 · External reference
Metabolomic profile of diabetic retinopathy: a GC-TOFMS-based approach using vitreous and aqueous humor
10.1007/s00592-019-01363-0 · 2020 · External reference
10.1007/s40123-020-00278-2
10.1007/s40123-020-00278-2 · External reference
High-coverage serum metabolomics reveals metabolic pathway dysregulation in diabetic retinopathy: a propensity score-matched study
10.3389/fmolb.2022.822647 · 2022 · External reference
10.1016/j.molcel.2016.10.025
10.1016/j.molcel.2016.10.025 · External reference
10.1136/gutjnl-2020-323071
10.1136/gutjnl-2020-323071 · External reference
10.1016/j.lfs.2021.120060
10.1016/j.lfs.2021.120060 · External reference
Alterations of the gut microbiome and metabolome in patients with proliferative diabetic retinopathy
10.3389/fmicb.2021.667632 · 2021 · External reference
Selected pharmacotherapy agents as antiproliferative and anti-inflammatory compounds
10.1002/ddr.21640 · 2020 · External reference
Syphilitic episcleritis and scleritis
10.1016/0002-9394(87)90170-x · 1987 · External reference
Tea polyphenols and Levofloxacin alleviate the lung injury of hepatopulmonary syndrome in common bile duct ligation rats through endotoxin -TNF signaling
10.1016/j.biopha.2021.111263 · 2021 · External reference
10.1002/jcp.28112
10.1002/jcp.28112 · External reference
Endocrine disruptor bisphenol A (BPA) triggers systemic para-inflammation and is sufficient to induce airway allergic sensitization in mice
10.3390/nu12020343 · 2020 · External reference
10.1016/j.etap.2021.103651
10.1016/j.etap.2021.103651 · External reference
