Bioinformatics & computational biology
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- Hidden assumptions in nascent RNA sequencing pipelines define reproducibility states
- CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo
- GBZ-base and GAF-base: Indexed pangenome file formats
- FUSED: A Functional Representation for Joint Structural and Elemental Analysis of Protein Ligand Binding Sites
- Panorama: A robust pangenome-based method for predicting and comparing biological systems across species
- Spatial mitochondrial lineage tracing uncovers a premetastatic niche and microenvironment programmed fate switching in osteosarcoma
- Exploring the Comedone Switch through Single-Cell Resolution of Human Acne Lesions
- PKProbDesign: RNA inverse folding including pseudoknots by optimizing thermodynamic folding probability
- Ribosomal RNA cleavage by the previously unidentified RelS–RelI toxin–antitoxin system controls growth of Mycobacterium tuberculosis
- Advancing Tier-1 environmental risk assessment with time-resolved estimates of x% lethal effect concentrations
- Effect of cellular nutrient economy on the evolution of genome size in phytoplankton
- SPARC Reveals Distinct Osteoclastogenesis-Associated Malignant States in Metastatic Osteosarcoma
- Metagenomic contextualization of proteins with state space models
- Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data
- FORGE audits residue-level information encoded in RNA tertiary structure geometry
- A historical journey of metabolite–protein interaction discovery: from data harmonization to AI-driven prediction
- PredHLM: quantitative and interpretable prediction of metabolic half-life in human liver microsomes
- MetaboCensoR: A Shiny Application for Data Filtering in Untargeted LC-MS Metabolomics to Enhance Interpretability
- DELPHAI predicts heterogeneous perturbation responses with learned single-cell fitness
- Reconstruction of ancestral plant genomes for inter-crop translational research
- Estimation of splicing metrics for NMD-sensitive transcripts
- False discovery rate control enables trustworthy deep-learning-based de novo peptide sequencing
- Homology-aware cross-validation strategies for generalization assessment in RNA secondary structure prediction
- Active-learning-guided optimization of cell-free systems for genome-wide transcriptomic profiling reveals progressive layers of regulation