相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。MiMeDB: the Human Microbial Metabolome Database
David S. Wishart et al.
NUCLEIC ACIDS RESEARCH (2023)
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota
Andres Aranda-Diaz et al.
CELL HOST & MICROBE (2022)
In vitro interaction network of a synthetic gut bacterial community
Anna S. Weiss et al.
ISME JOURNAL (2022)
Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota
Anna E. Lindell et al.
NATURE REVIEWS MICROBIOLOGY (2022)
Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance
Jason S. L. Yu et al.
NATURE MICROBIOLOGY (2022)
Escherichia colismall heat shock protein IbpA is an aggregation-sensor that self-regulates its own expression at posttranscriptional levels
Tsukumi Miwa et al.
MOLECULAR MICROBIOLOGY (2021)
Combinatorial, additive and dose-dependent drug-microbiome associations
Sofia K. Forslund et al.
NATURE (2021)
Unravelling the collateral damage of antibiotics on gut bacteria
Lisa Maier et al.
NATURE (2021)
Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
Francesco Durazzi et al.
SCIENTIFIC REPORTS (2021)
Towards a mechanistic understanding of reciprocal drug-microbiome interactions
Michael Zimmermann et al.
MOLECULAR SYSTEMS BIOLOGY (2021)
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Francesco Beghini et al.
ELIFE (2021)
A metabolomics pipeline for the mechanistic interrogation of the gut microbiome
Shuo Han et al.
NATURE (2021)
Bioaccumulation of therapeutic drugs by human gut bacteria
Martina Kluenemann et al.
NATURE (2021)
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data
Tianzhi Wu et al.
INNOVATION (2021)
Bayesian inference of distributed time delay in transcriptional and translational regulation
Boseung Choi et al.
BIOINFORMATICS (2020)
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Pierre-Alain Chaumeil et al.
BIOINFORMATICS (2020)
Impact of commonly used drugs on the composition and metabolic function of the gut microbiota
Arnau Vich Vila et al.
NATURE COMMUNICATIONS (2020)
Interaction between drugs and the gut microbiome
Rinse K. Weersma et al.
GUT (2020)
Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump
Elizabeth M. Grimsey et al.
MBIO (2020)
Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome
Bryn C. Taylor et al.
MSYSTEMS (2020)
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis
Sara Vieira-Silva et al.
NATURE (2020)
Personalized Mapping of Drug Metabolism by the Human Gut Microbiome
Bahar Javdan et al.
CELL (2020)
Mechanistic Understanding Enables the Rational Design of Salicylanilide Combination Therapies for Gram-Negative Infections
Janine N. Copp et al.
MBIO (2020)
The functional proteome landscape of Escherichia coli
Andre Mateus et al.
NATURE (2020)
The emergence of antimicrobial resistance in environmental strains of the Bacteroides fragilis group
Sebastian Niestepski et al.
ENVIRONMENT INTERNATIONAL (2019)
A new genomic blueprint of the human gut microbiota
Alexandre Almeida et al.
NATURE (2019)
Separating host and microbiome contributions to drug pharmacokinetics and toxicity
Michael Zimmermann et al.
SCIENCE (2019)
Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese et al.
NATURE COMMUNICATIONS (2019)
Perspective and Guidelines for Metaproteomics in Microbiome Studies
Xu Zhang et al.
JOURNAL OF PROTEOME RESEARCH (2019)
Regulation of the heat shock response in Escherichia coli: history and perspectives
Takashi Yura
GENES & GENETIC SYSTEMS (2019)
Mapping human microbiome drug metabolism by gut bacteria and their genes
Michael Zimmermann et al.
NATURE (2019)
Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism
Kenta Tsutsumi et al.
NATURE COMMUNICATIONS (2019)
Impact of Host DNA and Sequencing Depth on the Taxonomic Resolution of Whole Metagenome Sequencing for Microbiome Analysis
Joana Pereira-Marques et al.
FRONTIERS IN MICROBIOLOGY (2019)
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Luis Pedro Coelho et al.
MICROBIOME (2019)
Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy
Rosina Pryor et al.
CELL (2019)
Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans
Michael L. Patnode et al.
CELL (2019)
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
Guillem Salazar et al.
CELL (2019)
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
Edoardo Pasolli et al.
CELL (2019)
The gut microbiome: Relationships with disease and opportunities for therapy
Juliana Durack et al.
JOURNAL OF EXPERIMENTAL MEDICINE (2019)
Do phenothiazines possess antimicrobial and efflux inhibitory properties?
Elizabeth M. Grimsey et al.
FEMS MICROBIOLOGY REVIEWS (2019)
Ensembl 2018
Daniel R. Zerbino et al.
NUCLEIC ACIDS RESEARCH (2018)
HMDB 4.0: the human metabolome database for 2018
David S. Wishart et al.
NUCLEIC ACIDS RESEARCH (2018)
The Human Gut Microbiome: From Association to Modulation
Thomas S. B. Schmidt et al.
CELL (2018)
Human gut microbiome: hopes, threats and promises
Patrice D. Cani
GUT (2018)
The role of efflux pumps in Bacteroides fragilis resistance to antibiotics
Reza Ghotaslou et al.
MICROBIOLOGICAL RESEARCH (2018)
The fecal metabolome as a functional readout of the gut microbiome
Jonas Zierer et al.
NATURE GENETICS (2018)
Best practices for analysing microbiomes
Rob Knight et al.
NATURE REVIEWS MICROBIOLOGY (2018)
Multidrug efflux pumps: structure, function and regulation
Dijun Du et al.
NATURE REVIEWS MICROBIOLOGY (2018)
Human Gut Microbiome: Function Matters
Anna Heintz-Buschart et al.
TRENDS IN MICROBIOLOGY (2018)
Gut microbiota associations with common diseases and prescription medications in a population-based cohort
Matthew A. Jackson et al.
NATURE COMMUNICATIONS (2018)
Pharmacomicrobiomics: a novel route towards personalized medicine?
Marwah Doestzada et al.
PROTEIN & CELL (2018)
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies
Melanie Tramontano et al.
NATURE MICROBIOLOGY (2018)
Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial
Christina Ludwig et al.
MOLECULAR SYSTEMS BIOLOGY (2018)
Extensive impact of non-antibiotic drugs on human gut bacteria
Lisa Maier et al.
NATURE (2018)
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Donovan H. Parks et al.
NATURE BIOTECHNOLOGY (2018)
Emergent simplicity in microbial community assembly
Joshua E. Goldford et al.
SCIENCE (2018)
Schizophrenia and the microbiome: Time to focus on the impact of antipsychotic treatment on the gut microbiota
Timothy G. Dinan et al.
WORLD JOURNAL OF BIOLOGICAL PSYCHIATRY (2018)
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Chirag Jain et al.
NATURE COMMUNICATIONS (2018)
Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
Kevin D'hoe et al.
ELIFE (2018)
KEGG: new perspectives on genomes, pathways, diseases and drugs
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2017)
Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
Anna Heintz-Buschart et al.
NATURE MICROBIOLOGY (2017)
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Jaime Huerta-Cepas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
Strains, functions and dynamics in the expanded Human Microbiome Project
Jason Lloyd-Price et al.
NATURE (2017)
Shotgun metagenomics, from sampling to analysis
Christopher Quince et al.
NATURE BIOTECHNOLOGY (2017)
Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug
Hao Wu et al.
NATURE MEDICINE (2017)
Gut microbiome interactions with drug metabolism, efficacy, and toxicity
Ian D. Wilson et al.
TRANSLATIONAL RESEARCH (2017)
Navigating the Gut Buffet: Control of Polysaccharide Utilization in Bacteroides spp.
Nathan D. Schwalm et al.
TRENDS IN MICROBIOLOGY (2017)
Assessing species biomass contributions in microbial communities via metaproteomics
Manuel Kleiner et al.
NATURE COMMUNICATIONS (2017)
How to normalize metatranscriptomic count data for differential expression analysis
Heiner Klingenberg et al.
PEERJ (2017)
MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis
Joao F. Matias Rodrigues et al.
BIOINFORMATICS (2017)
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
Jaime Huerta-Cepas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Data-driven hypothesis weighting increases detection power in genome-scale multiple testing
Nikolaos Ignatiadis et al.
NATURE METHODS (2016)
DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan et al.
NATURE METHODS (2016)
The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism
Peter Spanogiannopoulos et al.
NATURE REVIEWS MICROBIOLOGY (2016)
Plasma Proteome Profiling to Assess Human Health and Disease
Philipp E. Geyer et al.
CELL SYSTEMS (2016)
A multi-omic future for microbiome studies
Janet K. Jansson et al.
NATURE MICROBIOLOGY (2016)
Use of Metatranscriptomics in Microbiome Research
Stavros Bashiardes et al.
BIOINFORMATICS AND BIOLOGY INSIGHTS (2016)
Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov et al.
GENOME BIOLOGY (2016)
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
Kristoffer Forslund et al.
NATURE (2015)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities
Karen De Roy et al.
ENVIRONMENTAL MICROBIOLOGY (2014)
Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence
Emma L. Schymanski et al.
ENVIRONMENTAL SCIENCE & TECHNOLOGY (2014)
Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells
Nils A. Kulak et al.
NATURE METHODS (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
NUCLEIC ACIDS RESEARCH (2013)
Pump it up: Occurrence and regulation of multi-drug efflux pumps in Bacteroides fragilis
Hannah M. Wexler
ANAEROBE (2012)
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
Evguenia Kopylova et al.
BIOINFORMATICS (2012)
SprayQc: A Real-Time LC-MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components
Richard A. Scheltema et al.
JOURNAL OF PROTEOME RESEARCH (2012)
APPLICATIONS OF NEXT-GENERATION SEQUENCING The human microbiome: at the interface of health and disease
Ilseung Cho et al.
NATURE REVIEWS GENETICS (2012)
High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection - Time-of-Flight Mass Spectrometry
Tobias Fuhrer et al.
ANALYTICAL CHEMISTRY (2011)
Regulation and control of metabolic fluxes in microbes
Luca Gerosa et al.
CURRENT OPINION IN BIOTECHNOLOGY (2011)
Human nutrition, the gut microbiome and the immune system
Andrew L. Kau et al.
NATURE (2011)
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
J. Gregory Caporaso et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Accelerated Profile HMM Searches
Sean R. Eddy
PLOS COMPUTATIONAL BIOLOGY (2011)
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Frederick A. Matsen et al.
BMC BIOINFORMATICS (2010)
Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt et al.
BMC BIOINFORMATICS (2010)
Glutamate dehydrogenase and glutamine synthetase are regulated in response to nitrogen availability in Myocbacterium smegmatis
Catriona J. Harper et al.
BMC MICROBIOLOGY (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB, which is inhibited by chlorpromazine
Andrew M. Bailey et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2008)
Metformin and the intestine
C. J. Bailey et al.
DIABETOLOGIA (2008)
Bacteroides: the good, the bad, and the nitty-gritty
Hannah M. Wexler
CLINICAL MICROBIOLOGY REVIEWS (2007)
Molecular mechanisms of antibacterial multidrug resistance
Michael N. Alekshun et al.
CELL (2007)
Aggregation of insulin by chlorpromazine
J Bhattacharyya et al.
BIOCHEMICAL PHARMACOLOGY (2001)
分享论文
