Bioinformatics & computational biology
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- A framework for designing splice-junction experiments in deep 3' single-cell RNA sequencing
- Senescence-associated KRAS upregulation in peripheral T cells links to premature coronary artery disease
- Physiological Aging and Cardiovascular Disease Distinctly Remodel the Human Cardiac Lymphatic Endothelium
- A first order approximation of a joint Potts and phylogenetic model
- sRNAMap: a lightweight, browser-based web application for small RNA mapping, analysis and visualisation
- Predicting single mutation effects on binding affinity at protein-protein interfaces based on MMPBSA calculations
- TopoFlow: Evolutionarily Conditioned Flow Matching for Protein Conformational Ensemble Generation
- π-MNovo improves de novo peptide sequencing through microbial-domain adaptation and evidence-guided candidate selection
- A Taxonomy-Informed Sparse DNA Foundation Model for Microbial Genomics
- Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions
- Coevolutionary mining of prokaryotic non-coding elements with a genome language model
- RootQuantV2: Adapting a Vision Foundation Model for Root-Trait Regression from Minirhizotron Imagery
- BixBench3: Benchmarking AI agents on research-study-scale computational biology tasks
- Flow Matching for Count Data
- BioHackrXiv: Creating a federated publishing platform
- BiomiX 3.0: A user-friendly platform for democratized multi-omics integration with graph-based learning
- OT-knn: A neighborhood-aware optimal transport framework for aligning spatial transcriptomics data
- All-atom molecular dynamics simulation of Cyclophilin A in complex with Sanglifehrin A
- A Metacell Model of Single Cell RNA-seq Counts Yields a Gaussian Mixture Model in PCA Space
- AF3 Inspector: In-Browser 3D Model Visualization and Confidence Analytics for AlphaFold 3
- Targeted finetuning enables co-folding models to learn ligand-induced protein conformational states
- CryoMV: Structure-Prior-Guided Modeling and Real-Particle Validation of Continuous Conformational Transitions in Cryo-EM
- Benchmarking single-cell foundation models for aging biology
- UniWave-2: A Hybrid Model for Nucleic Acid Waveform Feature Extraction Enhanced by Fourier and Wavelet Transforms
- A meta-interaction basis for cell-cell communication in tissues