Bioinformatics & computational biology
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- VenusGenome: Genome-Aware Masked Autoencoding for Microbial Genome Representation Learning
- Can Folding Models Tell Binders from Bluffers? Evidence from POISK: The Patent-Derived Antibody Dataset
- Expanding gmx_MMPBSA capabilities for end-state binding free energy calculations with GROMACS and AMBER
- Alignment-free discovery of conserved RNA structures in the human genome
- Digital twins forecast individual immune trajectories
- Automated screening of Parkinson's Disease using Smooth Pursuit Eye Movements
- Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D
- IG-28 enables identification and quantification of high-confidence isoforms from large bulk and single-cell full-length cDNA datasets
- CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers
- Multi-resolution humanness scoring of antibodies via a region-isolated language model
- NK-RCPP: a receptor-conditioned computational workflow for prioritizing neurokinin-receptor peptide candidates
- 'PhyTaxR', a set of phytoplankton taxonomic curation tools in R
- Building virtual cell dynamics that evolve with biological measurements
- Phenologs at knowledge-graph scale: a mouse-to-slime-mold catalog of candidate genes for thousands of human diseases
- Perturbation-based propagation of bacterial composition uncertainty improves robustness and reproducibility of microbiome differential abundance analysis.
- AltereGO: Prediction of Protein Function by Multimodal Fusion of Protein Language Models.
- Integrative Single-Cell Transcriptomics and Explainable AI for Disease Mechanism and Biomarker Discovery in Triple-Negative Breast Cancer
- Influenza A virus H5Nx genotypes assigned by genetic similarity are incongruent with global phylogenies
- Viral host assignment across the tree of life with VHAMSTeR
- Sequence architecture of RNA reveals key molecular signatures driving RNA phase separation
- Probabilistic uncertainty in virtual spatial transcriptomics from histology is largely redundant with the predicted mean
- Oak gall wasps lack conserved microbial symbionts
- Dual activities of lysis and capsule degradation enable the bacteriophage protein Lys33795 to effectively disrupt Streptococcus suis biofilms
- Behavioral Mapping of Hierarchical Dynamical Models Accelerates Bayesian Parameter Inference
- Reference normalizations of Effort-To-Compress across length, alphabet size, and composition