Research Areas
Giant Viruses
We study giant viruses recovered from environmental sequence data and laboratory systems to characterize their diversity, genome content, and evolutionary relationships.
Microbial Symbiosis
We investigate symbiotic associations to understand partner specificity, genome evolution, and metabolic exchange.
Microbial Census
We use metagenomics and single-cell genomics to recover genomes from uncultivated lineages and place them in phylogenetic context.
Biothreat Detection
We develop laboratory and computational workflows for rapid identification of pathogens and other agents of concern in environmental and clinical samples.
Extremophile Microbes
We study microorganisms from extreme environments to identify the cellular and genomic features associated with survival under heat, salinity, pressure, and other stressors.
Biological Data & AI
We develop computational methods that use machine learning to support classification, annotation, and comparative analysis of biological sequence data.
Software
- 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 ScientistRuns research agents and checks their declared deliverables against recorded evidence.
- 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 memory CLI for notes, task history, and research records shared by agents.
- 13ViroSyncIdentifies candidate endogenous viral elements in eukaryotic genomes using viral markers, gene taxonomy, and host sequence signals.
- 14CSAGSchema, validator, and command-line tools for linking scientific claims to evidence and context.
- 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.