Bioinformatics & computational biology
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- ContrasTED: contrastive domain embeddings for scalable remote homology classification
- The human metabolite - protein interactome reveals a global layer of cellular coordination
- Cell-type separability predicts annotation accuracy and outweighs algorithm choice: a factorial benchmark across seven scRNA paradigms
- Towards Sparse Causal Features for Zero-shot Mutation Effect Prediction in a Protein Language Model
- From neuropeptide and receptor annotation to ligand-receptor pairing: a sequence- and structure-based framework for mapping the neuropeptide-receptor interactome in Gryllus bimaculatus
- Beyond benchmark accuracy: machine-learning turnover-number predictors require system-level validation
- Macrophage signature-based prediction of cancer treatment response using MIL-attention
- Transcriptomic profile of a rat jaw opener (anterior digastric) and a jaw closer (superficial masseter).
- Calibration-free compression brings Evo 2 to its full million-token context on a single GPU
- GNMCADS: Sampling For Protein Conformation Diversity With Gaussian Network Model Guided Condition Annealed Diffusion Sampler
- CyChat: a conversational Cytoscape app for no-code, reproducible network analysis
- Spatial Transcriptomics Reveals Compartment-Specific Immune Activation Signatures in Ileal and Lymph Node Tissue in Treated HIV Infection
- CryoAnomaly: Few-Shot Cryo-EM Particle Picking via Anomaly-Guided Hard Negative Suppression
- FoldKit: A Python library for efficient storage and retrieval of co-folding predictions
- Neuromorphic architectures as numerical solvers for computational neuroscience
- Quantifying the Rearrangement Complexity of Pangenomes
- Coarse composition suffices: tabular in-context learning for multi-activity antimicrobial peptide profiling
- Probing the transcriptome response to shivering in skeletal muscle using a multilayered bioinformatics approach
- An Information Geometry approach to model topological trajectories and Gene Expression Radius from UMAP geometry.
- spatialMET: an open and scalable framework for spatial metabolomics analysis
- Interactive downstream proteomics analysis with MiraProt using Mueller cell proteomes from equine recurrent uveitis
- High-Resolution Subtyping of Pediatric Low-Grade Glioma Using an Integrated Meta-Clustering Framework
- EXTRARNAS: A Framework for Extracting RNA Structures with Multiple Tools
- dnoise: Fast Native Data Reduction for Bruker timsTOF
- XpBrew and PanXpresso - automatic RNA-seq processing workflow and comprehensive collection of gene expression data