Top 40
View all ›BACKFILLED Code and industry signals are partial for backfilled days.
Rank 1
Single-cell
Computational reconstruction of tissue gene expression from single-cell and spatial data
Single-cell and spatial atlases now span more species, modalities and histology, demanding methods that correct each measurement's limits.
12 preprints · 4 published · ↑ 4.8× vs 4-wk avg
Rank 2 Single-cell
Context-aware models infer tumor gene expression, mutations and regulatory networks
Noninvasive and single-cell measurements are now paired with models encoding chromatin, cell-state, and mutational context.
14 preprints · 3 published · ↑ 3.6× vs 4-wk avg
Rank 3 ML / AI methods
Learned models link sequence, contact, and epigenomic features to gene regulation
Recent preprints show longer input sequences can hurt expression prediction, shifting attention to integrating proximal multimodal epigenomic data.
5 preprints · 1 published · ↑ 2.3× vs 4-wk avg
Rank 4 Structural bio & protein design
Knowledge graphs and deep models predict drug-target and drug-indication links
Recent preprints extend biomedical knowledge graphs with single-cell expression, literature-mined target-disease links, and agentic discovery workflows.
7 preprints · 2 published · ↑ 2.0× vs 4-wk avg
Rank 5 ML / AI methods
Machine learning and Bayesian models for microbiome and multi-omics inference
Heterogeneous, small-sample, and simulated omics data demand inference methods that handle batch effects, missing data, and phylogenetic structure.
5 preprints · 2 published · ↑ 2.0× vs 4-wk avg
Rank 6 Mechanistic models tie interaction structure and perturbations to population outcomes↑ 1.9×Systems biologyRank 7 Reference-free pipelines recover sequences from complex and mixed natural samples↑ 1.8×GenomicsRank 8 Reference and experimental data constrain and validate structural models↑ 1.8×Structural bio & protein designRank 9 Limits of protein models for variant effects, conformations and backbone geometry↑ 1.7×Structural bio & protein designRank 10 Generative diffusion and autoencoder models are applied to single-cell and spatial omics↑ 1.6×Single-cellRank 11 STR variation and haplotype-resolved assemblies refine population structure inference↑ 1.6×GenomicsRank 12 Learned models infer splicing context and long-range regulatory structure from sequence↑ 1.7×GenomicsRank 13 Per-event quantification of single molecules across microscopy and nanopore readouts↑ 1.5×ProteomicsRank 14 Pangenomes and long-read assemblies link structural variants to crop traitsGenomicsRank 15 Simulation and structure-aware learning for immune receptor and pathogen sequencesML / AI methodsRank 16 Single-cell transformer attention tracks co-expression rather than regulatory contentML / AI methodsRank 17 Methods profiling DNA methylation, chromatin and radiation-induced genomic instabilityEpigenomicsRank 18 Learned models predict molecular binding and activity from sequence and graph inputsML / AI methodsRank 19 Learned models predict enzyme function, RNA structure, and natural product biosynthesisML / AI methodsRank 20 Reproducible benchmarking of genomic, chemical, and single-cell AI modelsML / AI methods
Show 18 more
Rank 21 Protein language models and deep learning are used to predict and design bioactive…ML / AI methodsRank 22 MD simulations link binding and subdomain structure to membrane and pore transportStructural bio & protein designRank 23 Faster alignment and k-mer placement tools for sequencing reads and phylogeniesTools & infrastructureRank 24 Tractable physics-based and generative prediction of protein-ligand bindingStructural bio & protein designRank 25 Sequencing and computational methods map tRNA structure, modifications and RBP bindingEpigenomicsRank 26 Nonsense constraint and deletion predictors refine gene-level variant prioritizationGenomicsRank 27 Force transmission across scales links junctions, nuclei and multicellular tissue…Systems biologyRank 28 Computational recovery of peptide and glycopeptide IDs from existing MS dataProteomicsRank 29 Reusable tools span regulatory modelling, platform conversion and biomarker analysisTools & infrastructureRank 30 Recovering neural dynamics and synaptic structure from network activity modelsSystems biologyRank 31 Neural models link genotypes and imaging to heritable loci and shared genetic liabilityGenomicsRank 32 Criticality, attractor dynamics and decoding probe large-scale brain dynamicsSystems biologyRank 33 Sequence-based models resolve SARS-CoV-2 variant evolution and abundanceGenomicsRank 34 Quantifying spatial dependence in disease spread, immune niches and grapevine geneticsGenomicsRank 35 Scored homology and structure frameworks map protein motifs, complexes and secretomesTools & infrastructureRank 36 Omics and flux models prioritize liver disease genes and dasatinib resistance targetsSystems biologyRank 37 New methods map 3D chromatin organization, enhancer condensates and chromosome mixingEpigenomicsRank 38 Single-cell profiling resolves tumor, cortical and atopic skin cell identitiesSingle-cell