Week 45, 2025 · Nov 3 – Nov 9

Top 40

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Systems biology

Assumption-sensitive calibration of epidemic and phylodynamic models

ML / AI methods

Databases annotate TE-initiated transcripts in cancer and enhancer perturbations

Proteomics

Spatial statistics and dimension reduction resolve molecular patterns in omics data

Systems biology

Topological and geometric tests of higher-order structure in fMRI and functional data

Structural bio & protein design

AI structure models extended to protein conformational dynamics and ensemble sampling

6 Deep generative and contrastive models integrate heterogeneous omics and text dataML / AI methods

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

8 Specificity-aware tools for microbial probe design, signature discovery and annotationTools & infrastructure

9 Causal evaluation and graph learning for gene regulatory and disease networksML / AI methods

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

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

12 Machine learning links resistance phenotypes and genotypes in bacterial AMRML / AI methods

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

14 Allele reconstruction from Nanopore amplicon reads without target inputGenomics

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

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

17 Deep learning models predict regulatory states from DNA sequence and chromatin contextEpigenomics

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

19 Sequence models predict viral evolution, RNA structure and protein mutational effectsML / AI methods

20 Computational protein localization and secretory pathway inference from proteomic dataProteomics

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21 Biologically informed tokenization and patching reshape DNA language model inputsML / AI methods

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

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

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

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

26 Assumption-light variant and repeat inference from long and short sequencing readsGenomics

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

28 Context-conditioned generators design molecules, peptides, and cell morphology profilesStructural bio & protein design

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

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

31 Spatial, connectivity, and harmonization constraints in brain imaging statisticsTools & infrastructure

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

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

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

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

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

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

38 Linking neuronal metabolism, callosal genetics, and imaging pipelines to brain diseaseTools & infrastructure

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

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

Week 45, 2025 · Nov 3 – Nov 9

Top 40

Assumption-sensitive calibration of epidemic and phylodynamic models

Databases annotate TE-initiated transcripts in cancer and enhancer perturbations

Spatial statistics and dimension reduction resolve molecular patterns in omics data

Topological and geometric tests of higher-order structure in fMRI and functional data

AI structure models extended to protein conformational dynamics and ensemble sampling

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