Top 40
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ML / AI methods
Pretrained biomolecular language model embeddings reused for task-specific prediction
Foundation models for DNA, RNA, protein, and single-cell data are now being reused across regulatory, siRNA, and PTM prediction tasks.
Single-cell
Single-cell methods infer copy number, clonal expansion and rare cell populations
Recent preprints and publications apply deep learning and benchmarking to infer tumor copy number, T cell expansion and rare cell types from single-cell data.
Single-cell
H&E histology predicts spatial gene expression across cell and tissue scales
Multiple 2026 preprints and two published studies pair H&E images with single-cell or spatial expression references to infer in situ transcriptomes.
Transcriptomics
Benchmarked computational frameworks for transcriptomic and proteomic omics data analysis
Omics method papers now validate against simulations, titration references, and metabolic labeling instead of assumed performance.
Tools & infrastructure
Tools for microbial profiling, plasmid assembly and contamination detection
Recent preprints and papers benchmark and release workflows for amplicon, metagenomic, ancient DNA and viral genomic data.