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BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes

https://doi.org/10.1101/2020.12.14.422671

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/mnfr.200700412openalex-snapshot

Acrolein: Sources, metabolism, and biomolecular interactions relevant to human health and disease

inferredcites →https://doi.org/10.1002/pol.1984.170220115openalex-snapshot

Acrolein polymerization: Monodisperse, homo, and hybrido microspheres, synthesis, mechanism, and reactions

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Implication of gut microbiota metabolites in cardiovascular and metabolic diseases

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Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis

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Inhibitory effect of Lactobacillus reuteri on periodontopathic and cariogenic bacteria

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Microbiome: Focus on Causation and Mechanism

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Lactobacillus reuteri in bovine milk fermented decreases the oral carriage of mutans streptococci

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The rhizosphere microbiome and plant health

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Cariogenic Streptococcus mutans Produces Tetramic Acid Strain-Specific Antibiotics That Impair Commensal Colonization

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ChemCalc: A Building Block for Tomorrow’s Chemical Infrastructure

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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

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Fast gapped-read alignment with Bowtie 2

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Differential abundance analysis for microbial marker-gene surveys

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Bacterial competition: surviving and thriving in the microbial jungle

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Ethanolamine utilization in bacterial pathogens: roles and regulation

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SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells

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An anaerobic bacterium host system for heterologous expression of natural product biosynthetic gene clusters

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Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

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1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

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Mass spectrometry searches using MASST

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A computational framework to explore large-scale biosynthetic diversity

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Species-level functional profiling of metagenomes and metatranscriptomes

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Feature-based molecular networking in the GNPS analysis environment

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Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

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MetaTrans: an open-source pipeline for metatranscriptomics

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Acrolein contributes strongly to antimicrobial and heterocyclic amine transformation activities of reuterin

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Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans

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The Sequence Alignment/Map format and SAMtools

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BEDTools: a flexible suite of utilities for comparing genomic features

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Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

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Complex heatmaps reveal patterns and correlations in multidimensional genomic data

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Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production

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Mining prokaryotes for antimicrobial compounds: from diversity to function

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Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

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antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

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Regulated functional alternative splicing in Drosophila

inferredcites →https://doi.org/10.1093/nar/gkr988openalex-snapshot

KEGG for integration and interpretation of large-scale molecular data sets

inferredcites →https://doi.org/10.1093/nar/gks251openalex-snapshot

Grinder: a versatile amplicon and shotgun sequence simulator

inferredcites →https://doi.org/10.1093/nar/gkx935openalex-snapshot

The MetaCyc database of metabolic pathways and enzymes

inferredcites →https://doi.org/10.1093/nar/gky1033openalex-snapshot

PubChem 2019 update: improved access to chemical data

inferredcites →https://doi.org/10.1093/nar/gkz310openalex-snapshot

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

inferredcites →https://doi.org/10.1093/nar/gkz654openalex-snapshot

A deep learning genome-mining strategy for biosynthetic gene cluster prediction

inferredcites →https://doi.org/10.1101/2020.06.07.138974openalex-snapshot

Decomposing metabolite set activity levels with PALS

inferredcites →https://doi.org/10.1111/imr.12567openalex-snapshot

Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease

inferredcites →https://doi.org/10.1126/science.1203980openalex-snapshot

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

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Small molecules from the human microbiota

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Pervasive human-driven decline of life on Earth points to the need for transformative change

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A metagenomic strategy for harnessing the chemical repertoire of the human microbiome

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The Human Oral Microbiome

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Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease

inferredcites →https://doi.org/10.1128/mbio.01256-18openalex-snapshot

Energy Conservation via Hydrogen Cycling in the Methanogenic Archaeon Methanosarcina barkeri

inferredcites →https://doi.org/10.1128/mbio.01947-17openalex-snapshot

Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source

inferredcites →https://doi.org/10.1128/mbio.02579-19openalex-snapshot

Drug-Resistant Epimutants Exhibit Organ-Specific Stability and Induction during Murine Infections Caused by the Human Fungal Pathogen Mucor circinelloides

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Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules

inferredcites →https://doi.org/10.1128/msystems.00129-17openalex-snapshot

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

inferredcites →https://doi.org/10.1177/0022034517698096openalex-snapshot

Targeting of Streptococcus mutans Biofilms by a Novel Small Molecule Prevents Dental Caries and Preserves the Oral Microbiome

inferredcites →https://doi.org/10.1177/0022034518805739openalex-snapshot

The Oral Microbiota Is Modified by Systemic Diseases

inferredcites →https://doi.org/10.1186/1471-2105-6-225openalex-snapshot

Pathway level analysis of gene expression using singular value decomposition

inferredcites →https://doi.org/10.1186/1753-6561-5-s2-s9openalex-snapshot

MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets

inferredcites →https://doi.org/10.1186/2047-217x-1-1openalex-snapshot

Large and linked in scientific publishing

inferredcites →https://doi.org/10.1186/2047-217x-1-7openalex-snapshot

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

inferredcites →https://doi.org/10.1186/s12859-015-0844-1openalex-snapshot

Weakly supervised learning of biomedical information extraction from curated data

inferredcites →https://doi.org/10.1186/s12859-016-1278-0openalex-snapshot

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

inferredcites →https://doi.org/10.1186/s13059-015-0866-zopenalex-snapshot

Ancient DNA and the rewriting of human history: be sparing with Occam’s razor

inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot

Mash: fast genome and metagenome distance estimation using MinHash

inferredcites →https://doi.org/10.4103/jomfp.jomfp_304_18openalex-snapshot

Oral microbiome: Unveiling the fundamentals

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Plasmid Library Construction From Genomic DNA

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Metagenomic Approaches for the Discovery of Pollutant-Remediating Enzymes: Recent Trends and Challenges

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Comparing microbial communities in mucilage and seawater samples: Metagenomic insights into mucilage formation in the Marmara Sea

inferred← citeshttps://doi.org/10.1038/s41576-021-00363-7openalex-snapshot

Mining genomes to illuminate the specialized chemistry of life

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A roadmap for metagenomic enzyme discovery

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A systematic analysis of metabolic pathways in the human gut microbiota

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Identifying rhizosphere bacteria and potential mechanisms linked to compost suppressiveness towards Fusarium oxysporum

inferred← citeshttps://doi.org/10.18174/543999openalex-snapshot

Mapping natural product diversity through genomics

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