Week 48, 2025 · Nov 24 – Nov 30

Top 40

Single-cell

Constrained optimization for marker selection, deconvolution and cell identity

Single-cell

Explicit objectives now guide single-cell lineage inference and clustering resolution

ML / AI methods

Deep generative and contrastive models integrate heterogeneous omics and text data

Genomics

Causal and non-additive models resolve plasma protein genetic effects

Transcriptomics

Computational methods sharpen spatial positioning and clone tracing in imaging assays

6 Pretrained genomic language models are repurposed for expression and variant predictionML / AI methods

7 Scalable algorithms for viral discovery, read alignment, and amplicon and genome analysisGenomics

8 Mechanistic and latent models infer treatment response dynamics from sparse dataML / AI methods

9 Learned and sparse models infer nonlinear fitness landscapes and population dynamicsGenomics

10 Repeats and chromatin context shape genome architecture and regulatory variationEpigenomics

11 Modelling selection on weakly deleterious mutations across genomes and virusesGenomics

12 Simulation-based inference tackles intractable likelihoods in epidemic and phylodynamic…ML / AI methods

13 Systematic evaluation of analytical choices in single-cell RNA-seq analysisSingle-cell

14 Transformer and foundation models are learning microbial traits from genomes and…ML / AI methods

15 Sequence language models probed for genome generation, ancestry, and chromatin loopsML / AI methods

16 Assay-aware preprocessing and annotation tools for long-read and genomic interval dataTools & infrastructure

17 New callers resolve CNVs, structural variants, uniparental disomy and aneuploidy from NGSGenomics

18 Stochastic models link reproductive timing, replication asymmetry, and repeat evolutionSystems biology

19 LLMs grounded in curated biomedical databases for gene and literature reasoningML / AI methods

20 Quantifying topology, calibration, and model uncertainty in phylogenetic inferenceSystems biology

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21 Benchmarks expose setting-dependent limits of learned protein-ligand binding and dockingTools & infrastructure

22 Computational protein localization and secretory pathway inference from proteomic dataProteomics

23 Sequence patterning governs peptide condensation and membrane translocationStructural bio & protein design

24 Databases annotate TE-initiated transcripts in cancer and enhancer perturbationsML / AI methods

25 Physical polymer models connect 3D genome organization to regulatory outputEpigenomics

26 Automated curation and standardization of small-molecule data for predictive modelingTools & infrastructure

27 Spatial statistics and dimension reduction resolve molecular patterns in omics dataProteomics

28 Whole-brain and neural mass models tested against brain criticality and oscillationsSystems biology

29 ML and simulations reveal GPCR activation pathways and lipid allosteric bindingStructural bio & protein design

30 Combinatorial path and block alignment formalized for pangenomes, genealogies, syntenyGenomics

31 Explicit mechanistic models of promoter, stress-response and allosteric dynamicsSystems biology

32 AI structure models extended to protein conformational dynamics and ensemble samplingStructural bio & protein design

33 Inferring cell trajectories and tissue heterogeneity from single-cell transcriptomesSingle-cell

34 Deep learning extracts molecular structure from single-molecule and cryo-EM imagesStructural bio & protein design

35 Assumption-sensitive calibration of epidemic and phylodynamic modelsSystems biology

36 Computational tools map Plasmodium population genomics and recurrence inferenceTools & infrastructure

37 Protonation and ion handling shape membrane transport and penetration in MD simulationsStructural bio & protein design

38 Network and generative models of AML treatment response and drug designSystems biology

39 Atlases and tools link GWAS loci and QTLs to cell types, pathways, and mechanismsGenomics

40 Computational methods track atom provenance and assign metabolite stereoisomer identityMetabolomics

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