Top 40
View all ›BACKFILLED Code and industry signals are partial for backfilled days.
Rank 1
Single-cell
Benchmarking and new frameworks for single-cell and multi-omics biomarker analysis
Recent benchmarks report low overlap among scRNA-seq feature selectors, while new tools extend multi-omics biomarker and survival modeling.
6 preprints · 6 published · ↑ 3.3× vs 4-wk avg
Rank 2 Systems biology
Network models of brain dynamics are judged against empirical neural recordings
Fresh whole-brain and neural mass models are being confronted with HCP, mouse spike and EEG data to test network-level accounts.
5 preprints · 1 published · ↑ 2.4× vs 4-wk avg
Rank 3 Genomics
Algorithms resolving haplotypes, repeats, and variants from sequencing reads
Recent preprints and publications introduce scalable algorithms that convert raw reads into haplotype, repeat, and variant estimates.
4 preprints · 6 published · ↑ 2.3× vs 4-wk avg
Rank 4 Systems biology
Computational models reconstruct cell-cycle and tumor-immune population dynamics
Physics-informed and mechanistic models now link single-cell and spatial data to proliferation, cell-cycle and treatment dynamics across tissues.
4 preprints · 2 published · ↑ 2.3× vs 4-wk avg
Rank 5 ML / AI methods
Structured biological inputs in transformer and LLM models for perturbation and design
Perturbation prediction and molecular design are moving toward models that encode structured biological context as tokens, graphs, or LLM reasoning.
7 preprints · 1 published · ↑ 2.2× vs 4-wk avg
Rank 6 Spatial omics frameworks tackle alignment, phenotyping, and cross-platform integration↑ 2.1×TranscriptomicsRank 7 Structure-conditioned models span protein design, docking, and function prediction↑ 2.0×ML / AI methodsRank 8 Latent models reconcile unpaired, sparse, and spatial single-cell modalities↑ 1.8×Single-cellRank 9 Parallel software accelerates sequencing read processing and gene network inference↑ 1.6×Tools & infrastructureRank 10 Simulation mechanisms and free-energy workflows inform ligand optimization↑ 1.5×Structural bio & protein designRank 11 Pretrained embeddings and new benchmarks reshape deep learning for molecular predictionML / AI methodsRank 12 Scalable genomic tools for k-mer hashing, interval operations and viral element discovery↑ 1.6×Tools & infrastructureRank 13 Compositional and robust models recover protein-level information from mixed dataProteomicsRank 14 Mechanistic and data-driven models predict bioprocess, microbial and plant phenotypesSystems biologyRank 15 Interoperable software frameworks are standardizing omics and flux analysis workflowsTools & infrastructureRank 16 Benchmarked method choices guide protein flexibility, stability and library analysisStructural bio & protein designRank 17 Generative and interpretability methods for genomic and protein deep learning modelsML / AI methodsRank 18 Graph-based models infer drug, microbe and miRNA associations from heterogeneous dataML / AI methodsRank 19 Reference-anchored workflows for metagenomic taxonomy and amplicon analysisTools & infrastructureRank 20 Deep learning links tumor omics and imaging to mutations, survival, and therapy responseML / AI methods
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Rank 21 Generative and energy-based models scaffold enzyme sites into de novo proteinsStructural bio & protein designRank 22 Latent-factor methods for multi-omics grouping, biomarker panels and target nominationTools & infrastructureRank 23 Microbial community models: identifiability limits and Lotka-Volterra coupling errorsSystems biologyRank 24 Benchmarking and adapting omics methods for structural variants, editing, and long readsGenomicsRank 25 Local lipid, ligand and glycan environments reshape protein energy landscapesStructural bio & protein designRank 26 Latent and manifold models recast neuroimaging as low-dimensional brain structureML / AI methodsRank 27 Methods sharpen calibration of genetic association discovery and fine-mappingGenomicsRank 28 Deep learning models predict TCR-pMHC and MHC-peptide binding across benchmark designsML / AI methodsRank 29 Generative models sample protein conformations, energies, and transition pathwaysStructural bio & protein designRank 30 Constrained optimization for marker selection, deconvolution and cell identitySingle-cellRank 31 Tunable control of gene circuit patterns, perceptrons, and protein neural networksSystems biologyRank 32 Modelling selection on weakly deleterious mutations across genomes and virusesGenomicsRank 33 Single-cell tracking is now converted into lineage atlases and model inputsSingle-cellRank 34 Reduced stochastic models connect cell-level noise to population and kinetic behaviorSystems biologyRank 35 Computational frameworks map cell states, ion channels and regulatory networksSystems biologyRank 36 Telomere-to-telomere assemblies and language models refine genome annotation resolutionGenomicsRank 37 Motifs and duplication shape human replication origins and regulatory elementsGenomicsRank 38 Multi-omics and long-read genomics map regulatory genes, triplexes, and disease lociSystems biologyRank 39 Computational scoring of proteoform, spectral variant, and fold-switch statesMetabolomicsRank 40 Stochastic simulation and inference of local rules driving population-level dynamicsEpigenomics