Week 44, 2025 · Oct 27 – Nov 2

Top 40

ML / AI methods

Databases annotate TE-initiated transcripts in cancer and enhancer perturbations

ML / AI methods

Causal evaluation and graph learning for gene regulatory and disease networks

ML / AI methods

Sequence models predict viral evolution, RNA structure and protein mutational effects

ML / AI methods

Pretrained genomic language models are repurposed for expression and variant prediction

Single-cell

Systematic evaluation of analytical choices in single-cell RNA-seq analysis

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

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

8 Allele reconstruction from Nanopore amplicon reads without target inputGenomics

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

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

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

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

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

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

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

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

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

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

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

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

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21 Computational checks expose DNA off-targeting artifacts and novel intronic polyadenylationEpigenomics

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

23 Computational protein localization and secretory pathway inference from proteomic dataProteomics

24 Assumption-sensitive calibration of epidemic and phylodynamic modelsSystems biology

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

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

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

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