Top 40
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BACKFILLED Code and industry signals are partial for backfilled days.
Rank 1
ML / AI methods
Deep and boosting models predict RNA, chromatin and gene regulatory features from omics
Recent preprints and publications apply supervised deep and boosting models to sequence, signal and expression inputs for biomolecular annotation.
2 preprints · 4 published · ↑ 1.9× vs 4-wk avg
Rank 2 Epigenomics
Sequence-to-function models decode regulatory grammar and 3D chromatin organization
Sequence-to-function models now yield interpretable regulatory rules and 3D genome predictions, extending from enhancers to cross-species Hi-C comparison.
3 preprints · 3 published · ↑ 1.9× vs 4-wk avg
Rank 3 Transcriptomics
Benchmarking ambient RNA removal and deconvolution across single-cell and spatial data
Systematic benchmarks now evaluate ambient RNA removal, deconvolution, and spatial platforms using simulations and paired donor-matched data.
8 preprints · 4 published · ↑ 1.7× vs 4-wk avg
Rank 4 Genomics
Tools for simulating and inferring population variation from haplotypes and mitogenomes
Recent preprints and one publication extend simulation, mitochondrial frequency and ancestry inference to real haplotype and reference-panel data.
4 preprints · 1 published · ↑ 1.8× vs 4-wk avg
Rank 5 ML / AI methods
Computational resources map regulatory elements and transcripts across cancer datasets
Large cancer transcriptomic and single-cell datasets now enable systematic regulatory readouts across enhancers, transposable elements, and miRNAs.
1 preprint · 4 published · ↑ 1.6× vs 4-wk avg
Rank 6 Curated resources encode microbial metabolism and nutrient exchange for computationTools & infrastructureRank 7 Deep learning models predict biomolecular binding, stability, and kinetic endpointsML / AI methodsRank 8 Coarse-grained RNA models add sugar puckering, ion and temperature dependence to foldingStructural bio & protein designRank 9 Transport-theoretic generative models for unbalanced dynamics and 3D molecules↑ 1.6×ML / AI methodsRank 10 Nucleosome simulations and ML models link histone marks to gene expression controlGenomicsRank 11 Boltz-2 benchmarked for virtual screening hit ranking against in vitro binding assaysStructural bio & protein designRank 12 LLM agents grounded in curated biomedical databases, knowledge graphs, and literatureML / AI methodsRank 13 Automated pipelines and databases are consolidating viral and microbial genome analysisTools & infrastructureRank 14 Fine-mapping and functional assays are narrowing causal variants in complex traitsGenomicsRank 15 Compact and scalable representations for genomic sequence comparison and modelingGenomicsRank 16 Graph and histology priors couple expression denoising with spatial inferenceTranscriptomicsRank 17 Deep learning scores interfaces and contacts in cryo-EM and disordered proteinsStructural bio & protein designRank 18 Ionizable residue charge states gate conformational transitions in channels and complex IML / AI methodsRank 19 Biological networks and knowledge graphs guide drug repurposing and toxicity predictionTools & infrastructureRank 20 Large immune omics resources map circulating and infection-linked immune statesSingle-cell
Show 18 more
Rank 21 Pipelines integrate 3D segmentation and atlas registration for spatial transcriptomicsML / AI methodsRank 22 Probabilistic models of nuisance structure sharpen expression-data inferenceProteomicsRank 23 Plasma proteome classifiers for 23 diseases and standardized proteomic reference dataProteomicsRank 24 Models parametrized from monoculture and community data predict microbial interactionsSystems biologyRank 25 Curated genome databases for magnetotactic, endophytic and methanogenic microbesTools & infrastructureRank 26 Formal models link spike statistics, correlated noise, and plasticity to neural codingSystems biologyRank 27 Computational methods resolve hard-to-call variants in duplicated and coding sequenceGenomicsRank 28 Queryable platforms make million-cell and spatial transcriptomic atlases explorableTools & infrastructureRank 29 R tools separate shared and individual variation across multi-omics dataTools & infrastructureRank 30 Curated knowledgebases extend evidence-linked annotation across omics and literatureTools & infrastructureRank 31 Linking DNA sequence to function through variant isolation and high-throughput screensTools & infrastructureRank 32 Machine learning predicts molecular properties with explicit baselines and uncertaintyML / AI methodsRank 33 ML rescoring and offset search refine peptide and PTM identification from MS2 spectraProteomicsRank 34 Computed protein-ligand complexes as substrates for affinity scoring and benchmarkingStructural bio & protein designRank 35 Models convert brain-scan and methylation data into individual aging and risk estimatesEpigenomicsRank 36 Convex coding theory and neural decoding models relate circuit structure to functionSystems biologyRank 37 MD and binding free energy reveal CARF domain open-to-closed transitionStructural bio & protein designRank 38 Bayesian and maximum-entropy inference of cellular dynamics from noisy measurementsSystems biology