ArticleGenome biology2020
Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- Deciphering enzymatic potential in metagenomic reads through DNA language models.Nucleic acids research · 2025Article
- RFW captures species-level metagenomic functions by integrating genome annotation information.Cell reports methods · 2024Article
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- Current Trends and Challenges of Microbiome Research in Prostate Cancer.Current oncology reports · 2024Review
- Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.Nature biotechnology · 2023Article
- Trait-Based Method of Quantitative Assessment of Ecological Functional Groups in the Human Intestinal Microbiome.Biology · 2023Article
- Strain level microbial detection and quantification with applications to single cell metagenomics.Nature communications · 2022Article
- Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter.Nature communications · 2022Article
- Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.Cell systems · 2021Article
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- RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing.Microorganisms · 2020Article
- Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.Microbial genomics · 2020Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited in their ability to directly compare microbial metabolic function across samples and studies. We introduce Carnelian, an end-to-end pipeline for metabolic functional profiling uniquely suited to finding functional trends across diverse datasets. Carnelian is able to find shared metabolic pathways, concordant functional dysbioses, and distinguish Enzyme Commission (EC) terms missed by existing methodologies. We demonstrate Carnelian's effectiveness on type 2 diabetes, Crohn's disease, Parkinson's disease, and industrialized and non-industrialized gut microbiome cohorts.
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Registered trials
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