Bioinformatics & computational biology
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- Pocket contrastive learning and conformation fusion for robust structure-conditioned 3D molecular generation under receptor conformational variation.
- Informed forecasting: Leveraging auxiliary knowledge to boost large language model performance on time series forecasting
- Position-wise Fold-Switch Prediction in Metamorphic Proteins: A Comparison of Handcrafted and Language Model Features
- CryoCodex: learning discrete structural representations for cryo-EM map post-processing
- Additive-input encoding fails operator-level target-held-out prediction on current Perturb-seq screens
- msengine: Adaptive Open-Source Signal Extraction for HDX MS
- HyperCom: a hypergraph-based method to infer cell-resolved cell-cell communication
- Transfer Matrix and Tensor Approaches to Nucleic Acid Secondary Structure Thermodynamics
- PaleoRigor: a bounded research agent with a reproducible evidence trail for paleomicrobiome data processing
- Flock: A Negative-Enriched Protein-Protein Interaction Dataset
- pre-miRBench: a multispecies benchmark and reference model for animal precursor microRNA prediction
- ASTRA enables zero-shot super-resolution of spatial transcriptomics across capture geometries
- Tractable and Thermodynamically Consistent pKa Prediction via First-Dissociation Aggregation
- Refining Protein Co-Membership in Reactome: A Weighted Scoring Approach Based on Hierarchy and Sequences of Patwhays
- Cross-Dataset Reanalysis of Mouse Alzheimer Disease Single-Cell RNA-Sequencing Data Reveals a Reproducible Innate Immune Activation Signature
- From Benchmark to Bench: Can Agents Survive Real-World Drug Discovery?
- Slide-level batch structure limits histology-guided supervision of transcriptomic foundation models
- Reconstructing donor genotypes from scRNA-seq for downstream eQTL and HLA-TCR analysis
- MerKurio: sequence extraction and annotation based on matching k-mers
- BlockFormer : Transformer-based inference from genomic contact maps
- Inference on paths of yeast transcription pre-initiation complex assembly by model-based analysis of altered occupancy profiles
- SCITRAM: a Single-cell Integrated transcription regulation modeler for predicting master transcription factors
- The recoverable resolution of cellular perturbation-response prediction
- Deep Learning-Meets-Active Surfaces: A Unified Framework for Multi-Object Segmentation and Shape Analysis in 3D Fluorescence Microscopy
- Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species