Bioinformatics & computational biology
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- A compact motif vocabulary is differentially interpreted across human cell types
- Recurrence in Sequence Space: How Epistasis Mimics Shared Ancestry
- Enhancing cell type deconvolution in spatial transcriptomics through incorporating multiple reference panels
- BlastPhyMe: A toolkit for rapid generation and analysis of protein-coding sequence datasets
- Spatial transcriptomic mapping of anti-MDA5 dermatomyositis reveals perivascular enrichment of type I interferon responses and immune activation
- Computational Analysis of Antioxidant Effects on Stress Response Mechanisms in Candida albicans
- SPaRTA: Spatial Reasoning in Text-to-SQL for Omics Analysis
- 2D U-NET Deep Learning Architecture for Atherosclerotic Lesion Segmentation and Quantification
- Decision benchmarking of cryo-EM re-refinement
- Reference-Guided De Novo Retrieval of 3D Chromatin Organizational Features with Representation Learning
- FedEpitope: Parameter-Efficient Federated Protein Language Models for Linear B-Cell Epitope Prediction
- Parameter-Efficient Adaptation of Protein Language Models for Dual-Target Antimicrobial Peptide Discovery Under Strict Homology Constraints
- NEPTUNE: a neuronal cell death pathway prediction tool used to decipher neurodegeneration using single cell RNA-seq datasets
- Consensus methods for trees of blobs and level-1 phylogenetic networks
- Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions
- Prefrontal cortex transcriptomes distinguish Alzheimers disease from asymptomatic amyloid pathology, neuropeptide loss, immune-complement activation and glial remodelling
- SENgEAR: an interactive visualization platform for comparative analysis of senescence signatures and cellular communication
- DirectClean: artifact-aware preprocessing and read rescue for Oxford Nanopore direct-cDNA transcriptome sequencing
- Deducing splicing events from transcript sets with splicelogic
- Classifying tumors from broad category to hierarchical molecular subtype: an interpretable hierarchical framework for precision oncology
- A comparative transcriptomic framework across kidney organoid, assembloid, and transplantation models
- A trustworthy semantic knowledge network linking data-driven cell phenotypes to diseases and drugs
- HYphlow: bringing end-to-end flow to HyPhy selection analyses, from taxon reconciliation to trait-based foreground assignment
- GSET: Gene Signals from Embedding Trajectories select compact contexts for mechanistic GRN inference
- The Reasoning Paradox in Scientific Sandboxes: Why Extended Reasoning Fails in Autonomous Bioinformatics and How to Fix It.