Metagenomic microbial community profiling using unique clade-specific marker genes

Segata, Nicola, Waldron, Levi, Ballarini, Annalisa, Narasimhan, Vagheesh, Jousson, Olivier, Huttenhower, Curtis·2012·Nature Methods
DOI 10.1038/nmeth.2066

Cited by (1,002)

Items 201–300 of 1,002

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  2. Large-scale comparative metagenomics of <i>Blastocystis</i>, a common member of the human gut microbiome
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  3. Scalable metagenomic taxonomy classification using a reference genome database
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  4. Emerging Technologies for Gut Microbiome Research
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  5. Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids
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  7. SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
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  8. Emerging Priorities for Microbiome Research
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  9. Kingdom-Agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities
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  10. Novel Fecal Biomarkers That Precede Clinical Diagnosis of Ulcerative Colitis
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  11. DESMAN: a new tool for de novo extraction of strains from metagenomes
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  12. Evidence of natural Wolbachia infections in field populations of Anopheles gambiae
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  13. Antibiotic Resistance Genes and Correlations with Microbial Community and Metal Resistance Genes in Full-Scale Biogas Reactors As Revealed by Metagenomic Analysis
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  14. DeepMicrobes: taxonomic classification for metagenomics with deep learning
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  15. Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
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  16. Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups
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  17. Orione, a web-based framework for NGS analysis in microbiology
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  18. CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
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  19. Antibiotic resistome in a large‐scale healthy human gut microbiota deciphered by metagenomic and network analyses
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  20. Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data
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  24. Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage
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  26. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
    Tracey Allen K. Freitas, Po‐E Li, Matthew B. Scholz, Patrick Chain · 2015 · Nucleic Acids Research
  27. Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project
    Sean Conlan, Heidi H. Kong, Julia A. Segre · 2012 · PLoS ONE
  28. Diet influences the functions of the human intestinal microbiome
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    Tiffany R. Simms-Waldrip, Gauri Sunkersett, Laura A. Coughlin, Milan R. Savani, Carlos Arana, Jiwoong Kim, Minsoo Kim, Xiaowei Zhan, David E. Greenberg, Yang Xie et al. · 2017 · Transplantation and Cellular Therapy
  30. Gut microbiota density influences host physiology and is shaped by host and microbial factors
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  32. Effects of Fecal Microbiome Transfer in Adolescents With Obesity
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    Alexander Dilthey, Chirag Jain, Sergey Koren, Adam M. Phillippy · 2019 · Nature Communications
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    Wei Lan Zhou, Michelle Spoto, Rachel Hardy, Changhui Guan, Elizabeth S. Fleming, Peter J. Larson, Joseph S. Brown, Julia Oh · 2020 · Cell
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    Panagiotis Tsapekos, Panagiotis Kougias, Laura Treu, Stefano Campanaro, İrini Angelidaki · 2016 · Applied Energy
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    Jun Shen, Lianjun Yang, Ke You, Tao Chen, Zhihai Su, Zhifei Cui, Min Wang, Weicong Zhang, Bin Liu, Kai Zhou et al. · 2022 · Frontiers in Immunology
  41. Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
    Karcher, Nicolai, Nigro, Eleonora, Punčochář, Michal, Blanco-Míguez, Aitor, Ciciani, Matteo, Manghi, Paolo, Zolfo, Moreno, Cumbo, Fabio, Manara, Serena, Golzato, Davide et al. · 2021 · Genome Biology
  42. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
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  43. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money
    Antony T. Vincent, Nicolas Derôme, Brian Boyle, Alexander I. Culley, Steve J. Charette · 2016 · Journal of Microbiological Methods
  44. Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions
    Z. Weinberg, Christina E. Lünse, Keith A. Corbino, T. Ames, James W. Nelson, Adam Roth, Kevin R. Perkins, M. Sherlock, R. Breaker · 2017 · Nucleic Acids Research
  45. Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants
    Lauren C. Beck, Andrea C. Masi, Gregory R. Young, Tommi Vatanen, Christopher Andrew Lamb, Rachel Smith, Jonathan Coxhead, Alana Butler, Benjamin J. Marsland, Nicholas David Embleton et al. · 2022 · Nature Microbiology
  46. One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification
    Samuel S. Minot, Niklas Krumm, Nicholas B. Greenfield · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
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  48. Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
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  49. Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut
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  50. Nutrient-Controlled Niche Differentiation of Western Lake Erie Cyanobacterial Populations Revealed via Metatranscriptomic Surveys
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  51. Low number of fixed somatic mutations in a long-lived oak tree
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  52. GMrepo: a database of curated and consistently annotated human gut metagenomes
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  53. Human microbiome signatures of differential colorectal cancer drug metabolism
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  54. SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial
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  55. Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome– a pilot study
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  56. Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods
    Johannes Dröge, Ivan Gregor, Alice Carolyn McHardy · 2014 · Bioinformatics
  57. Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling
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  67. Optimized DNA extraction and metagenomic sequencing of airborne microbial communities
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  81. MG-RAST version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis
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