Week 49, 2025 · Dec 1 – Dec 7

Top 40

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Genomics

Assumption-light variant and repeat inference from long and short sequencing reads

Single-cell

Learned multi-omics integration spans single-cell clustering and patient survival

ML / AI methods

Deep learning links routine histology and multi-omics to cancer biomarkers

Systems biology

Whole-brain and neural mass models tested against brain criticality and oscillations

ML / AI methods

Deep generative and contrastive models integrate heterogeneous omics and text data

6 Constrained optimization for marker selection, deconvolution and cell identitySingle-cell

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

26 Spectral libraries and origin-aware annotation advance LC-MS metabolomicsMetabolomics

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

28 Simulation and screening method choices are being framed as reportable design decisionsStructural bio & protein design

29 Repeats and chromatin context shape genome architecture and regulatory variationEpigenomics

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

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

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

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

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

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

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

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

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

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

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

Week 49, 2025 · Dec 1 – Dec 7

Top 40

Assumption-light variant and repeat inference from long and short sequencing reads

Learned multi-omics integration spans single-cell clustering and patient survival

Deep learning links routine histology and multi-omics to cancer biomarkers

Whole-brain and neural mass models tested against brain criticality and oscillations

Deep generative and contrastive models integrate heterogeneous omics and text data

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