Top 40
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Tools & infrastructure
Open-source tools standardize omics, peptide sequencing, and benchmarking workflows
Deep learning models and multi-omics pipelines are now distributed as containerized, reproducible, GUI-accessible software for routine use.
Systems biology
Computational methods extend omics analysis across networks, spatial scales, and cohorts
Recent preprints apply network, spatial, and conformal methods to omics data across radiation, sepsis, PAH, and histology settings.
Genomics
Cross-species genomics links lineage history to mutation, regulation, and selection
Large genome panels combined with alignment, network, and mediation methods now resolve evolutionary rates, selection, and regulatory divergence.
Systems biology
Phylogeny-aware and structure-aware tools link microbial genes to phenotypes
Recent preprints and publications introduce phylogeny-, graph- and structure-aware methods for gene-level inference from metagenomes and genomes.
Transcriptomics
Deep learning and graph methods map spatial molecular architecture in tissue
Recent preprints and papers pair graph and deep learning models with spatial transcriptomic, metabolomic, and histological data at single-cell resolution.