ArticleGenome biology2019
MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 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
28 citing papers in PubMed, 46 citations in OpenAlex.
- DCVBin: a novel binning method for single-sample metagenomes based on DNA language model and variational autoencoder.Briefings in bioinformatics · 2026Article
- Ecological and evolutionary dynamics of the oral microbiome across childhood.bioRxiv : the preprint server for biology · 2026Article
- AR-CDT NET: a deep deformable convolutional network for gut microbiome-based disease classification.BMC bioinformatics · 2025Article
- A data-driven modeling framework for mapping genotypes to synthetic microbial community functions.bioRxiv : the preprint server for biology · 2025Article
- Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges.Frontiers in microbiology · 2025Review
- A permutable MLP-like architecture for disease prediction from gut metagenomic data.BMC bioinformatics · 2024Article
- Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing.Communications biology · 2024Article
- VirGrapher: a graph-based viral identifier for long sequences from metagenomes.Briefings in bioinformatics · 2024Article
- Metabolites: a converging node of host and microbe to explain meta-organism.Frontiers in microbiology · 2024Review
- GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data.Bioinformatics (Oxford, England) · 2023Article
- Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies.PLoS computational biology · 2023Article
- Early Gut Microbiota Profile in Healthy Neonates: Microbiome Analysis of the First-Pass Meconium Using Next-Generation Sequencing Technology.Children (Basel, Switzerland) · 2023Article
- In-silico computational approaches to study microbiota impacts on diseases and pharmacotherapy.Gut pathogens · 2023Review
- MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities.Genome biology · 2023Article
- DETIRE: a hybrid deep learning model for identifying viral sequences from metagenomes.Frontiers in microbiology · 2023Article
- MLR-OOD: A Markov Chain Based Likelihood Ratio Method for Out-Of-Distribution Detection of Genomic Sequences.Journal of molecular biology · 2022Article
- Article
- Human disease prediction from microbiome data by multiple feature fusion and deep learning.iScience · 2022Article
- Increasing prediction performance of colorectal cancer disease status using random forests classification based on metagenomic shotgun sequencing data.Synthetic and systems biotechnology · 2022Article
- Computational Viromics: Applications of the Computational Biology in Viromics Studies.Virologica Sinica · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show that including reads from unknown organisms significantly increases the prediction accuracy of the disease status for three of the four datasets. We identify new microbial organisms associated with these diseases and show viruses play important prediction roles in colorectal cancer and liver cirrhosis, but not in type 2 diabetes. MicroPro is freely available at https://github.com/zifanzhu/MicroPro .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.