Week 51, 2025 · Dec 15 – Dec 21

Top 40

Metabolomics

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

Metabolomics

Tissue-resolved metabolic models, spatial lipidomics, and curated MASH transcriptomics

ML / AI methods

Agents chain target discovery, pocket design, and PK simulation for therapeutic design

Systems biology

Quantitative classification and atlases place biological structure on shared spatial axes

Proteomics

Spatial statistics and dimension reduction resolve molecular patterns in omics data

6 Structure-aware statistical methods for single-cell and spatial transcriptomics inferenceML / AI methods

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

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

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

10 Software tools for batch correction, cfDNA fragment analysis and proteomics QCTools & infrastructure

11 Distinguishing intrinsic criticality from latent drive in spiking and EEG modelsSystems biology

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

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

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

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

16 Genome-scale constraint maps proto-gene precursors and duplicate-gene divergenceGenomics

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

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

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

20 Deep learning decodes EEG markers of consciousness, language coherence and predictionML / AI methods

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

22 Hi-C-based 3D models resolve ecDNA, nuclear organization and replication timingEpigenomics

23 Fusing sequence, structure and graph features for multimodal interaction predictionML / AI methods

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

25 Expert curation anchors scalable annotation of biomedical literature and omics metadataTools & infrastructure

26 Optimal control and phage dynamics shape bacterial eradication strategiesSystems biology

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

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

29 Gap-free assemblies and pangenomes expose structural variation across crop lineagesGenomics

30 Inferring kinetics and time labels from nascent, untimed, and mistimed transcriptomic dataSystems biology

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

32 Automated pipelines convert raw sequence data into queryable, reusable genomic resourcesTools & infrastructure

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

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

35 Causal and non-additive models resolve plasma protein genetic effectsGenomics

36 Inhibitory integration, burst-driven weight attractors, and Φ in spiking networksSystems biology

37 Host diversion and spillover risk shape arbovirus and pandemic transmission modelingSystems biology

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

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

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

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