Top 40
View all ›BACKFILLED Code and industry signals are partial for backfilled days.
Rank 1
Tools & infrastructure
Nanopore and short-read tools for bacterial typing, methylation and mobile elements
Nanopore-native and short-read pipelines now address raw-signal correction, outbreak analysis, methyltransferase detection and typing in prokaryotic genomes.
6 preprints · 3 published · ↑ 2.4× vs 4-wk avg
Rank 2 Single-cell
Computational models forecasting drug and perturbation responses from multi-omic data
Recent preprints and a published study extend virtual-cell and signaling-network models to predict perturbation effects and zero-shot drug responses.
9 preprints · 1 published · ↑ 2.5× vs 4-wk avg
Rank 3 Single-cell
Computational tools correcting, normalizing and accelerating sequencing data analysis
Recent releases address normalization, sex checking, integration, and GPU-accelerated annotation across bulk and single-cell sequencing workflows.
8 preprints · 3 published · ↑ 2.3× vs 4-wk avg
Rank 4 ML / AI methods
Latent embeddings unify heterogeneous biological inputs for molecular prediction
Foundation-model embeddings now feed compact, uncertainty-aware predictors across genomics, single-cell, and drug-discovery tasks.
6 preprints · 6 published · ↑ 2.1× vs 4-wk avg
Rank 5 ML / AI methods
Pretrained sequence models extend to RNA, protein, and peptide prediction tasks
Recent preprints pair pretrained sequence model embeddings with new targets, while CHANRG shows limited generalization under fair splits.
10 preprints · 2 published · ↑ 2.1× vs 4-wk avg
Rank 6 Pretrained protein language model embeddings paired with graph and structural context↑ 2.0×ML / AI methodsRank 7 Pangenome and gene-annotation advances link genome architecture to function in eukaryotes↑ 2.0×GenomicsRank 8 Coupling image and expression latent spaces for spatial and single-cell transcriptomics↑ 1.9×Single-cellRank 9 Metagenomes reveal CRISPR-Cas records of bacterial mobile element interactions↑ 1.9×GenomicsRank 10 Implementation-aware benchmarks test genotype-to-phenotype inference methods↑ 1.8×GenomicsRank 11 Computational tools link chromatin architecture and accessibility to expression readouts↑ 1.8×EpigenomicsRank 12 Simulations map allosteric conformational control in mTORC1, GPCR, PP2A and Hsp70Structural bio & protein designRank 13 Context-specific metabolic models integrate flux, topology, and transcriptomic dataSystems biologyRank 14 Inferring temporal cell-state dynamics from snapshot single-cell and spatial dataSingle-cellRank 15 Sequence models infer viral hosts, strains, reassortment and pathogenicityML / AI methodsRank 16 Mapping genetic variation to cell-type gene regulation in human brainGenomicsRank 17 Haplotype-resolved genomics spans transposon arms races and rearranged cancer karyotypesGenomicsRank 18 Open software tools are packaging spatial and whole-slide image analysis steps for reuseTranscriptomicsRank 19 Transformer and language models extend sequence design to mRNA nucleotide spaceML / AI methodsRank 20 Coarse-grained and refined force-field models extend nucleic acid simulationsStructural bio & protein design
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Rank 21 Computational modeling of protein stability, oxidation and non-canonical residuesStructural bio & protein designRank 22 Structure-based pipelines are benchmarked for RNA ligands and PDE5 selectivityStructural bio & protein designRank 23 Learned latent spaces reformulate protein and molecular sampling bottlenecksML / AI methodsRank 24 Multiobjective generative models steer protein and biosequence design across criteriaStructural bio & protein designRank 25 Learned models prioritize drug and synthetic lethality candidates under scarce labelsML / AI methodsRank 26 Constant-space minimizers and sub-3-bit subset rank cut k-mer index memoryTools & infrastructureRank 27 Interpretable models rank causal genes from QTL, perturbation, and fitness dataSystems biologyRank 28 Engineering advances in omics data parsing, structure viewing, and workflow toolingTools & infrastructureRank 29 Computational methods resolve cell states and niches from spatial and single-cell dataSingle-cellRank 30 Reduced-resolution models probe force- and ion-dependent RNA-protein bindingStructural bio & protein designRank 31 Proteome and tri-omics profiling resolve functional gene modules and drug responsesML / AI methodsRank 32 Long-read data quantify somatic repeat instability and resolve haplotype-phased genomesTools & infrastructureRank 33 Simulations couple molecular binding to emergent cell and tissue architectureStructural bio & protein designRank 34 Formal graph-level treatments of pangenome diversity, homology, and haplotype blocksGenomicsRank 35 ODE and power-law models dissect glycolytic oscillations and plant circadian networksSystems biologyRank 36 Electrostatic and simulation checks gauge fidelity of membrane and peptide modelsStructural bio & protein designRank 37 Neurodegeneration studies nominate cell-type and protein-level molecular signaturesProteomicsRank 38 Recurrent CA3 models unify time and place cell formation in hippocampal networksSystems biologyRank 39 Coupling models link myelin, electric fields, and neural states across scalesSystems biologyRank 40 Software tools for glycan 3D modeling and site-specific glycoproteomics analysisProteomics