We study giant viruses recovered from environmental sequence data and laboratory systems to characterize their diversity, genome content, and evolutionary relationships.
We investigate symbiotic associations to understand partner specificity, genome evolution, and metabolic exchange.
We use metagenomics and single-cell genomics to recover genomes from uncultivated lineages and place them in phylogenetic context.
We develop laboratory and computational workflows for rapid identification of pathogens and other agents of concern in environmental and clinical samples.
We study microorganisms from extreme environments to identify the cellular and genomic features associated with survival under heat, salinity, pressure, and other stressors.
We develop computational methods that use machine learning to support classification, annotation, and comparative analysis of biological sequence data.
- 01GVClassClassifies giant-virus contigs and metagenome-assembled genomes and reports completeness and contamination estimates.
- 02SymclatronPredicts symbiotic potential across the symbiosis continuum from genome-derived features.
- 03SGTreeBuilds phylogenetic trees from built-in or custom HMM marker sets and selects markers by gene-tree to species-tree reconciliation.
- 04NNGeneTreeBuilds gene trees from protein sequences and identifies nearest neighbors in evolutionary context.
- 05SSUEXTRACTExtracts SSU rRNA sequences from contigs with covariance models and annotates hits against SILVA and PR2.
- 06PDMClustClusters sequences or genomes from phylogenetic distance matrices, with optional taxonomy-aware consistency checks.
- 07ModuCompCalculates metabolic module completeness and metabolic complementarity across genomes and microbiomes.
- 08gvmagDBDuckDB and Parquet-backed database of giant-virus and microbial genomes with integrated search and a dashboard.
- 09NeLLi AI ScientistBenchmark-first harness for OpenAI-compatible research agents and local tool use.
- 10Omics SkillsAgent and skill collection for bioinformatics, scientific writing, and data visualization.
- 11Scientific Illustrations SkillGenerates publication-ready scientific illustrations through a planner, stylist, visualizer, and critic workflow.
- 12memdLocal MCP memory server for searchable notes, task history, and review artifacts across agents.
- 01NeLLi Symposium 2025The 6th NeLLi Symposium covered the tree of life, cellular complexity, and microbial symbiosis, with invited talks and posters over two days.
- 02VEGA Symposium 2024Methods for recovering uncultivated viruses, characterizing their roles in natural ecosystems, and studying viral genetic diversity.
- 03NeLLi Symposium 2023The 5th NeLLi Symposium covered metagenomics, single-cell genomics, and microbial ecology, with methods for characterizing undescribed lineages.