Top 40
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Tools & infrastructure
Open computational frameworks infer molecular states from sequencing data
Recent preprints and publications package harmonization, benchmarking, and QC into open tools for multimodal and single-cell sequencing data.
Transcriptomics
Computational methods resolve RNA regulation and artifacts across transcriptomic datasets
Context-aware models and artifact-aware assemblers now resolve RNA regulation across bulk, single-cell, and long-read transcriptomic data.
Single-cell
Learned encoders recover spatial tissue structure from transcriptomic and histology data
Learned representations now extend from histology-based expression prediction to in silico perturbation across spatial and single-cell transcriptomics.
Structural bio & protein design
Protein language models applied to stability, cysteine states, and genome annotation
Mega-scale stability data, ESM-2 and Evo2 embeddings, and influenza fitness estimates now enable residue-level predictions across divergent proteomes.
Single-cell
Inferring cell-state dynamics from static single-cell snapshots via generative models
Recent preprints and publications apply optimal transport, Neural ODEs, and Gaussian processes to reconstruct trajectories from destructive snapshot data.