ArticleMicrobiome2015
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data.
Article in Microbiome, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers.
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118 citing papers in PubMed.
- Metagenomic insights into the taxonomic and metabolic diversity of the microbiome of Lake Karum in the Danakil Depression, Ethiopia.Environmental microbiome · 2026Article
- Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.World journal of microbiology & biotechnology · 2026Article
- Tracking putativemSystems · 2025Article
- Elevated heterotrophic activity in Guaymas Basin hydrothermal plumes influences deep-sea carbon cycling.Nature communications · 2025Article
- A review of neural networks for metagenomic binning.Briefings in bioinformatics · 2025Review
- Effect of dietary zinc supplementation on the gastrointestinal microbiome and host gene expression in theFrontiers in microbiology · 2025Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Targeted protein evolution in the gut microbiome by diversity-generating retroelements.bioRxiv : the preprint server for biology · 2024Article
- Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes.mSphere · 2024Article
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
- Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes.Microbiome · 2024Article
- Genome-resolved metagenomics identifies novel active microbes in biogeochemical cycling within methanol-enriched soil.Environmental microbiology reports · 2024Article
- Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryoticMicrobial genomics · 2024Article
- Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi.Communications biology · 2023Article
- BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes.Microbiome · 2023Article
- Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes.The ISME journal · 2023Article
- Expression ofApplied and environmental microbiology · 2023Article
- Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi.Genome biology and evolution · 2023Article
- Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits.Microbiome · 2022Article
- binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.Briefings in bioinformatics · 2022Article
58 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge.
resultsWe present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented.
conclusionsVizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux.
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