Related references
Note: Only part of the references are listed.A unified catalog of 204,938 reference genomes from the human gut microbiome
Alexandre Almeida et al.
NATURE BIOTECHNOLOGY (2021)
Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle
David K. Jacobson et al.
SCIENTIFIC REPORTS (2021)
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
Ivica Letunic et al.
NUCLEIC ACIDS RESEARCH (2021)
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Francesco Beghini et al.
ELIFE (2021)
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Pierre-Alain Chaumeil et al.
BIOINFORMATICS (2020)
Struo: a pipeline for building custom databases for common metagenome profilers
Jacobo de la Cuesta-Zuluaga et al.
BIOINFORMATICS (2020)
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
Eli L. Moss et al.
NATURE BIOTECHNOLOGY (2020)
Impact of commonly used drugs on the composition and metabolic function of the gut microbiota
Arnau Vich Vila et al.
NATURE COMMUNICATIONS (2020)
Accurate and complete genomes from metagenomes
Lin-Xing Chen et al.
GENOME RESEARCH (2020)
The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography
Tayte P. Campbell et al.
ISME JOURNAL (2020)
A complete domain-to-species taxonomy for Bacteria and Archaea
Donovan H. Parks et al.
NATURE BIOTECHNOLOGY (2020)
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
Kristopher Kieft et al.
MICROBIOME (2020)
SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes
Jennifer Lu et al.
PLOS COMPUTATIONAL BIOLOGY (2020)
High-depth African genomes inform human migration and health
Ananyo Choudhury et al.
NATURE (2020)
A new genomic blueprint of the human gut microbiota
Alexandre Almeida et al.
NATURE (2019)
New insights from uncultivated genomes of the global human gut microbiome
Stephen Nayfach et al.
NATURE (2019)
The microbiome, cancer, and cancer therapy
Beth A. Helmink et al.
NATURE MEDICINE (2019)
Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels
Ana Lokmer et al.
PLOS ONE (2019)
Transmission of human-associated microbiota along family and social networks
Ilana L. Brito et al.
NATURE MICROBIOLOGY (2019)
The ancestral and industrialized gut microbiota and implications for human health
Erica D. Sonnenburg et al.
NATURE REVIEWS MICROBIOLOGY (2019)
Evolution of the gut microbiome following acute HIV-1 infection
Muntsa Rocafort et al.
MICROBIOME (2019)
Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes
Mitsuhiko P. Sato et al.
DNA RESEARCH (2019)
Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation
Ryan Brewster et al.
TRENDS IN MICROBIOLOGY (2019)
Role of the Microbiota in the Modulation of Vaccine Immune Responses
Annalisa Ciabattini et al.
FRONTIERS IN MICROBIOLOGY (2019)
Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health
Kaitlyn Oliphant et al.
MICROBIOME (2019)
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Robert A. Edwards et al.
NATURE MICROBIOLOGY (2019)
Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans
Thomas Hagan et al.
CELL (2019)
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
Robert D. Stewart et al.
NATURE BIOTECHNOLOGY (2019)
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations
Adrian Tett et al.
CELL HOST & MICROBE (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)
Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses
Claude Kwe Yinda et al.
MSPHERE (2019)
Links between environment, diet, and the hunter-gatherer microbiome
Gabriela K. Fragiadakis et al.
GUT MICROBES (2019)
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Matthew E. B. Hansen et al.
GENOME BIOLOGY (2019)
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
BIOINFORMATICS (2018)
Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens
Jacqueline M. Leung et al.
FRONTIERS IN MICROBIOLOGY (2018)
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
Christian M. K. Sieber et al.
NATURE MICROBIOLOGY (2018)
Environment dominates over host genetics in shaping human gut microbiota
Daphna Rothschild 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)
Evaluation of Oxford Nanopore's MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
Andrea D. Tyler et al.
SCIENTIFIC REPORTS (2018)
Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization
Jacobo de la Cuesta-Zuluaga et al.
SCIENTIFIC REPORTS (2018)
US Immigration Westernizes the Human Gut Microbiome
Pajau Vangay et al.
CELL (2018)
Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut
Emma Guerin et al.
CELL HOST & MICROBE (2018)
A Microbiota Assimilation
Justin Sonnenburg et al.
CELL METABOLISM (2018)
Emerging evidence linking the gut microbiome to neurologic disorders
Jessica A. Griffiths et al.
GENOME MEDICINE (2018)
Gut microbiome transition across a lifestyle gradient in Himalaya
Aashish R. Jha et al.
PLOS BIOLOGY (2018)
Streptomyces, shared microbiome member of soil and gut, as 'old friends' against colon cancer
Alireza Bolourian et al.
FEMS MICROBIOLOGY ECOLOGY (2018)
Fast and accurate de novo genome assembly from long uncorrected reads
Robert Vaser et al.
GENOME RESEARCH (2017)
Trends in obesity and diabetes across Africa from 1980 to 2014: an analysis of pooled population-based studies
Andre Pascal Kengne et al.
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY (2017)
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
Matthew R. Olm et al.
ISME JOURNAL (2017)
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M. Bowers et al.
NATURE BIOTECHNOLOGY (2017)
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Samuel A. Smits et al.
SCIENCE (2017)
Geography, Ethnicity or Subsistence-SpecificVariations in Human Microbiome Composition and Diversity
Vinod K. Gupta et al.
FRONTIERS IN MICROBIOLOGY (2017)
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks et al.
NATURE MICROBIOLOGY (2017)
Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients
Maria Laura Santoru et al.
SCIENTIFIC REPORTS (2017)
Systematically investigating the impact of medication on the gut microbiome
Lisa Maier et al.
CURRENT OPINION IN MICROBIOLOGY (2017)
Progression of the epidemiological transition in a rural South African setting: findings from population surveillance in Agincourt, 1993-2013
Chodziwadziwa W. Kabudula et al.
BMC PUBLIC HEALTH (2017)
Bracken: estimating species abundance in metagenomics data
Jennifer Lu et al.
PEERJ COMPUTER SCIENCE (2017)
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
Yu-Wei Wu et al.
BIOINFORMATICS (2016)
Urban-rural and geographic differences in overweight and obesity in four sub-Saharan African adult populations: a multi-country cross-sectional study
IkeOluwapo O. Ajayi et al.
BMC PUBLIC HEALTH (2016)
Assembly of long error-prone reads using de Bruijn graphs
Yu Lin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle
Anastassia Gorvitovskaia et al.
MICROBIOME (2016)
MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
David Koslicki et al.
MSYSTEMS (2016)
Diverse Empirical Evidence on Epidemiological Transition in Low- and Middle-Income Countries: Population-Based Findings from INDEPTH Network Data
Ailiana Santosa et al.
PLOS ONE (2016)
The Evolving Demographic and Health Transition in Four Low- and Middle-Income Countries: Evidence from Four Sites in the INDEPTH Network of Longitudinal Health and Demographic Surveillance Systems
Ayaga Bawah et al.
PLOS ONE (2016)
H3Africa AWI-Gen Collaborative Centre: a resource to study the interplay between genomic and environmental risk factors for cardiometabolic diseases in four sub-Saharan African countries
M. Ramsay et al.
GLOBAL HEALTH EPIDEMIOLOGY AND GENOMICS (2016)
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Fredrik Backhed et al.
CELL HOST & MICROBE (2015)
Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota
Simone Rampelli et al.
CURRENT BIOLOGY (2015)
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Donovan H. Parks et al.
GENOME RESEARCH (2015)
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
Kristoffer Forslund et al.
NATURE (2015)
Subsistence strategies in traditional societies distinguish gut microbiomes
Alexandra J. Obregon-Tito et al.
NATURE COMMUNICATIONS (2015)
The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes
Ines Martinez et al.
CELL REPORTS (2015)
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
James Kaminski et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
Dongwan D. Kang et al.
PEERJ (2015)
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
Molly K. Gibson et al.
ISME JOURNAL (2015)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
An Expanded Genomic Representation of the Phylum Cyanobacteria
Rochelle M. Soo et al.
GENOME BIOLOGY AND EVOLUTION (2014)
Binning metagenomic contigs by coverage and composition
Johannes Alneberg et al.
NATURE METHODS (2014)
Ribosomal Database Project: data and tools for high throughput rRNA analysis
James R. Cole et al.
NUCLEIC ACIDS RESEARCH (2014)
The Unfolding Counter-Transition in Rural South Africa: Mortality and Cause of Death, 1994-2009
Brian Houle et al.
PLOS ONE (2014)
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker et al.
PLOS ONE (2014)
Gut microbiome of the Hadza hunter-gatherers
Stephanie L. Schnorr et al.
NATURE COMMUNICATIONS (2014)
Migration and the epidemiological transition: insights from the Agincourt sub-district of northeast South Africa
Mark A. Collinson et al.
GLOBAL HEALTH ACTION (2014)
Kraken: ultrafast metagenomic sequence classification using exact alignments
Derrick E. Wood et al.
GENOME BIOLOGY (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans
Junhai Ou et al.
AMERICAN JOURNAL OF CLINICAL NUTRITION (2013)
The Comprehensive Antibiotic Resistance Database
Andrew G. McArthur et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)
QUAST: quality assessment tool for genome assemblies
Alexey Gurevich et al.
BIOINFORMATICS (2013)
Differential abundance analysis for microbial marker-gene surveys
Joseph N. Paulson et al.
NATURE METHODS (2013)
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
Sara C. Di Rienzi et al.
ELIFE (2013)
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
Jose U. Scher et al.
ELIFE (2013)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2012)
A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010
Stephen S. Lim et al.
LANCET (2012)
Structure, function and diversity of the healthy human microbiome
Curtis Huttenhower et al.
NATURE (2012)
Human gut microbiome viewed across age and geography
Tanya Yatsunenko et al.
NATURE (2012)
Carbohydrate metabolism in Bifidobacteria
Karina Pokusaeva et al.
GENES AND NUTRITION (2011)
Complete genome sequence of Treponema succinifaciens type strain (6091(T))
Cliff Han et al.
STANDARDS IN GENOMIC SCIENCES (2011)
A human gut microbial gene catalogue established by metagenomic sequencing
Junjie Qin et al.
NATURE (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
Carlotta De Filippo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Household-based prevalence of helminths and parasitic protozoa in rural KwaZulu-Natal, South Africa, assessed from faecal vault sampling
Linda Tronnberg et al.
TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE (2010)
DNAPlotter: circular and linear interactive genome visualization
Tim Carver et al.
BIOINFORMATICS (2009)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh et al.
NATURE (2009)
Cohort profile: Mandela's children: The 1990 birth to twenty study in South Africa
Linda Richter et al.
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY (2007)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
D Laslett et al.
NUCLEIC ACIDS RESEARCH (2004)