Top 40
View all ›BACKFILLED Code and industry signals are partial for backfilled days.
Rank 1
Systems biology
Inferring signaling and interaction networks from phosphoproteomic and proteomic data
Recent benchmarking and time-resolved differential network models test whether inferred protein and kinase networks recover true structure.
2 preprints · 4 published · ↑ 3.0× vs 4-wk avg
Rank 2 Single-cell
Fusing histology and spatial transcriptomics to refine single-cell tissue measurements
Computational fusion of histology, spatial and single-cell data now corrects what each modality captures alone.
5 preprints · 5 published · ↑ 2.7× vs 4-wk avg
Rank 3 Tools & infrastructure
Reusable software for multi-omics, spatial, single-cell and regulatory data analysis
Recent tools package specialised omics analyses as interactive or scriptable software, lowering barriers to reuse across datasets.
1 preprint · 13 published · ↑ 2.4× vs 4-wk avg
Rank 4 ML / AI methods
Learned representations tested for cross-setting transfer in biological prediction
Cross-cohort and cross-modality generalization, rather than in-sample accuracy, is becoming the test for learned biological representations.
6 preprints · 4 published · ↑ 2.2× vs 4-wk avg
Rank 5 Tools & infrastructure
Tools map RNA-protein binding, transcript quantification, and translational control
Recent benchmarks and pipelines assess RNA-binding, transcript quantification, and translation methods on real and simulated data across species.
1 preprint · 6 published · ↑ 2.1× vs 4-wk avg
Rank 6 Single-cell models encode lineage, barcode, and temporal structure to infer regulation↑ 2.0×Single-cellRank 7 Pangenome graphs resolve structural and transposable element variation across species↑ 1.9×GenomicsRank 8 Mechanistic models link feedback structure to cross-scale biological dynamics↑ 2.0×Systems biologyRank 9 Long-read and targeted methods resolve DNA methylation and radiation-induced genomic…↑ 1.7×GenomicsRank 10 Benchmarks test whether computed conformational ensembles match experimental SAXS data↑ 1.7×Structural bio & protein designRank 11 Generative and latent-variable models for single-cell and spatial omics data↑ 1.7×Single-cellRank 12 Pipelines recover sequence, taxa and transcripts from long-read and amplicon data↑ 1.6×Tools & infrastructureRank 13 Bayesian and hierarchical inference methods for stochastic biological models and assays↑ 1.6×Tools & infrastructureRank 14 Computational models map sequence and chemistry into spaces for design and scoring↑ 1.8×Structural bio & protein designRank 15 Language model and sequence-structure learning predict and design bioactive peptides↑ 1.6×ML / AI methodsRank 16 Benchmarks and structure-aware models for omics and molecular property predictionML / AI methodsRank 17 Neural surrogates and diffusion models for molecular simulation and generationML / AI methodsRank 18 Constraint and dual-coding regions extend variant prioritization beyond missense callsTranscriptomicsRank 19 Software tools for selection scans, admixture, and read simulation in genomicsGenomicsRank 20 Multimodal and graph inputs address generalization limits in gene and RNA predictionML / AI methods
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Rank 21 Sequence models predict enzyme function under limited labels and for unseen EC classesML / AI methodsRank 22 Synaptic tuning and connection type bound decodable and collective neural information↑ 1.5×Systems biologyRank 23 Graph and language models predict immune receptor-peptide recognition from structure and…ML / AI methodsRank 24 Generative and deep learning models prioritize molecules for experimental validationStructural bio & protein designRank 25 Model-based methods extend genetic association inference beyond single-locus frameworksGenomicsRank 26 Repository-scale spectra and benchmarked pipelines widen peptide identification coverageTools & infrastructureRank 27 Reaction network and surrogate models predict and steer gene expression behaviorSystems biologyRank 28 Protein language model embeddings guide mutant screening and CAR-T activity predictionStructural bio & protein designRank 29 Graph and foundation models predict drug responses and cancer subtypes from omics dataML / AI methodsRank 30 Learned models of protein binding face scrutiny under perturbation and ligand classStructural bio & protein designRank 31 Experimental observables benchmark RNA structure predictors and potentialsStructural bio & protein designRank 32 Comparative genomics maps complex, fold and accessory-genome architecture across lineagesGenomicsRank 33 Read-level tools assign taxa and resolve tandem repeat structure from sequencing dataGenomicsRank 34 Coarse-grained and geometric methods extended to absolute binding free energiesStructural bio & protein designRank 35 Quantitative modeling links biomolecular structure to FRET readouts and dye propertiesStructural bio & protein designRank 36 Graph-based methods are advancing spatial and single-cell omics analysisSingle-cellRank 37 Spatial omics methods link tumor protein and gene patterns to patient-level outcomesProteomicsRank 38 Reduced equations and agent-based rules govern multicellular population dynamicsSystems biologyRank 39 Network models rank drug repurposing and microbiome-modulated therapy candidatesSystems biologyRank 40 Models infer chromatin contacts and states from protein binding and epigenetic dataEpigenomics