A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes
Abstract
Metagenomics holds great promises for deepening our knowledge of key bacterial driven processes, but metagenome assembly remains problematic, typically resulting in representation biases and discarding significant amounts of non-redundant sequence information. In order to alleviate constraints assembly can impose on downstream analyses, and/or to increase the fraction of raw reads assembled via targeted assemblies relying on pre-assembly binning steps, we developed a set of binning modules and evaluated their combination in a new “assembly-free” binning protocol.
Type
Publication
BMC Bioinformatics 17(1):311, August 2016, Aug 19;17(1):311
Authors
Senior AI/ML and genomics practitioner
Senior AI/ML and genomics practitioner with ~15 years building open-source, production-grade tools for large-scale biological data. Maintainer of multiple Bioconductor packages (fastreeR, metabinR, jvecfor), and author of agentic, LLM-driven tooling that runs reproducible bioinformatics workflows from natural-language requests.
Broad multi-omics background spanning genome assembly and annotation, population genomics, large-scale NGS and functional-genomics analysis, and metagenomics, backed by reproducible HPC software and end-to-end program leadership. Currently focused on bringing modern AI — embeddings, deep learning, and LLM-based agents — to making complex omics datasets faster and easier to interrogate.