Bioinformatics & computational biology
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2,115 studies
- ASPIRE: the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems
- Integrating metagenome-scale metabolic models and metabolomics to explore candidate biochemical interactions in cultivated Microcystis phycospheres
- Reference-free and robust copy number inference in single-cell tumor transcriptomes
- De novo transformer modeling improves recovery of genetic cell types from sparse single-cell RNA sequencing
- AI semantics for biomedical data integration
- Pangenome Graph Node-Phenotype Association shows GWAS-like quality results with only few individuals
- ASTRAL-X: Scaling Coalescent-Based Species Tree Inference to 300,000 Taxa
- Benchmarking Twist Genotyping-by-Sequencing Against Whole-Genome Sequencing in Nuclear Families
- Pervasive Backdoor Vulnerabilities in Genomic Foundation Models
- Homology-Based Variant-Effect Predictors Break Down on Cytochrome P450 Pharmacogenes
- OpenAntigens: a structure-aware database for antigen construct design across the human cell-surface and secreted proteome
- MAXWELL: Calibrating the probabilistic outputs of protein language models to the mutation-induced stability change landscape
- AgentBasedModeling.jl: A tool for stochastic simulation of structured population dynamics
- Classical baselines outperform released deep-learning ITS classifiers, which collapse on ITS2 where predictions follow the flanking regions
- Optimized Multiple Circular Sequence Alignment for Cyclic Peptide Motif Discovery
- seqproc: An efficient, flexible, and concise tool for sequence geometry description and transformation
- RKMR: A Rapid Kernel Machine Regression Framework for Optimal Marker Detection in Spatial Omics Data
- The Metabarcoding Analysis Pipeline (MAP): Simple, accurate, and flexible metabarcoding
- MetaClaw: an auditable AI agent for end-to-end, multi-directional metagenomic and multi-omics analysis
- MGM2 as a Multimodal Foundation Model for Microbial Community States and Responses
- Petimot: A Novel Framework for Inferring Protein Motions from Sparse Data Using SE(3)-Equivariant Graph Neural Networks
- Integrative structure determination of a human mitochondrial contact site and cristae organizing system (MICOS) sub-assembly
- Post-transcriptional Regulation of Stochastic Gene Expression Conditioned on Large Deviations
- A Standardized Methodology for FAIRness Assessment and Multi-Dimensional Scoring in Agrosystem Research Data Infrastructures
- seqsizzle: decoding complex barcode and adapter architectures in long-read sequencing data