Top 40
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Single-cell
Deep learning infers cell states and regulatory logic from single-cell and cfDNA data
Preprints and published studies now pair deep models with single-cell, spatial, and cell-free DNA data for regulatory inference, deconvolution, and…
Transcriptomics
New statistical and long-read methods refine RNA-seq quantification and calibration
Recent preprints and papers pair RNA-seq methods with orthogonal validation such as RT-PCR calibration and long-read sequencing.
Transcriptomics
Higher-order and topological models recover disease structure from multi-omic data
Recent work adds higher-order, topological, and latent-space descriptions of disease states to transcriptomic and multi-omic analysis.
Structural bio & protein design
Web servers now predict peptide structure, protein binding sites, and phosphosites
Recent tools package AlphaFold2, ESMFold, ESM-2, and graph networks into accessible web and CLI platforms for structural and functional prediction.
ML / AI methods
Encoder-plus-context models predict drug response and perturbation outcomes
Context-coupled encoders now link transcriptomic, imaging and graph data to drug response in cancer and single-cell settings.