Week 52, 2025 · Dec 22 – Dec 28

Top 40

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Systems biology

Tissue-wide planar cell polarity emerges from local signals in cellular Potts models

Tools & infrastructure

Expert curation anchors scalable annotation of biomedical literature and omics metadata

Tools & infrastructure

Automated pipelines convert raw sequence data into queryable, reusable genomic resources

Systems biology

Inferring kinetics and time labels from nascent, untimed, and mistimed transcriptomic data

Metabolomics

Spectral libraries and origin-aware annotation advance LC-MS metabolomics

6 Deep models for single-cell perturbation, annotation, and foundation-model interpretationML / AI methods

7 Protein language models encode nativeness, taxonomy, and memorization beyond trainingML / AI methods

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

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

10 Selection and phage-bacteria dynamics shape bacterial and phage genetic variationGenomics

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

12 Somatic variants joined to dependency and single-cell context for target nominationML / AI methods

13 Browser and agent-driven tools standardize EV, transcriptomic and omics plotting workflowsTools & infrastructure

14 Curated enzyme databases with HMM pipelines expand halogenase and PET-degrader discoveryTools & infrastructure

15 DFT reference data refines torsion parameters and hybrid ML/MM simulation setupStructural bio & protein design

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

17 Tissue-resolved metabolic models, spatial lipidomics, and curated MASH transcriptomicsMetabolomics

18 Learned models expand protein conformational sampling and sequence-energy fittingStructural bio & protein design

19 Stochastic variability and network structure set cellular timing and sizeSystems biology

20 Curated databases pair bioactivity records with structural and mechanistic annotationTools & infrastructure

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21 Language and graph foundation models target drug repurposing and molecule generationML / AI methods

22 Curated databases structure microbial habitat, antigen, lysin and biosynthetic gene dataML / AI methods

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

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

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

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

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

28 Optimal control and phage dynamics shape bacterial eradication strategiesSystems biology

29 Learned multi-omics integration spans single-cell clustering and patient survivalSingle-cell

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

31 Modeling choices alter conclusions drawn from gene regulatory network analysesSystems biology

32 Path-integral and graph models infer treatment and fitness dynamics from limited dataSystems biology

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

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

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

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

37 Repeats and chromatin context shape genome architecture and regulatory variationEpigenomics

38 Knowledgebases now map regulatory elements and GWAS variants onto genes and traitsGenomics

39 Inferring temporal cell-state dynamics from snapshot single-cell and spatial dataSingle-cell

40 Computational methods sharpen spatial positioning and clone tracing in imaging assaysTranscriptomics

Week 52, 2025 · Dec 22 – Dec 28

Top 40

Tissue-wide planar cell polarity emerges from local signals in cellular Potts models

Expert curation anchors scalable annotation of biomedical literature and omics metadata

Automated pipelines convert raw sequence data into queryable, reusable genomic resources

Inferring kinetics and time labels from nascent, untimed, and mistimed transcriptomic data

Spectral libraries and origin-aware annotation advance LC-MS metabolomics

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