Bioinformatics & computational biology
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- Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation
- GENOAR: Global Engine for Navigating the Omnicell space via Agent-based Research
- CnidoSite: A Multi-Omics Database for Cnidarians
- A computable probability landscape for T cell receptor repertoire sampling and comparison
- Going beyond labels: Semi-supervised learning for enzyme kinetic parameter prediction
- DEEP: Extracting Latent Energetic Landscapes from Protein Structure Predictors
- The Role of Environmental Information and the Limitations of Predictability with Transformer-based Time-Series Models for complex Astrocyte Trajectories
- LoCoFlow: Local-Context Flow Matching for Single-Cell Dynamics and Fate Inference
- GEO-BERT: A Retrieval augmented LLM Framework for Intelligent Dataset Retrieval from the Gene Expression Omnibus
- Combining RNA-seq and proteomics boosts sensitivity to detect differentially expressed genes by rpMeta
- BiNVaST: niche boundary-preserving and synthetic data-guided variational autoencoders for concordant inference across high-resolution spatial transcriptomic platforms
- Optimal transport reveals unresolved cells in single cell multi-omics
- In Other Words: Learning When to Trust Generated Protein Function Descriptions
- Single-nucleus chromatin accessibility time course of excisional wound repair in rat skin
- RiboBridge couples RNA backbone generation to sequence design through a learned interaction topology
- Scalable Enzyme Reaction Retrieval Enables Metagenomic Biocatalyst Discovery
- LigRNA: High-accuracy prediction of RNA-ligand binding sites via dynamic chemical complementarity and language model encoding
- Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing
- Capturing domain-level detail of molecular interactions in the IMEx Consortium binding domain data set
- Dual-graph deconvolution of enzyme fitness: an interpretable framework to identify and explain catalytic modulators
- Pre-binning correction of chimeric contigs reduces reference-discordant gene annotations in near-complete metagenome-assembled genomes
- PanRes: a database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search
- UniProt data pruning and the growing invisibility of the dark proteome
- Bioinformatic and experimental analyses revealed pathogen-derived pathoPEPs candidates predicted to control plant miRNAs expression and infection
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