Transplantation

PHbinder and PSGM: A Cascaded Framework for Epitope Prediction and HLA-I Allele Identification

The presentation of antigens by Human Leukocyte Antigen class I (HLA-I) molecules is a cornerstone of adaptive immunity. Although existing prediction tools such as NetMHCpan and MHCflurry exhibit high accuracy in predicting binding affinity between peptides and specific HLA-I alleles, they are constrained to a preset set of alleles. Consequently, they can neither directly determine whether a pepti...

LeGO-Teknik reveals that the neurogenesis pathway is a clone-specific hallmark of brain metastasis in breast cancer

Breast cancer exhibits substantial inter- and intra-patient heterogeneity. Yet the molecular features underlying this diversity and their roles in tumour progression are not yet fully elucidated. Within a primary tumour, certain clones possess a unique capacity to metastasize to distant organs, such as the brain, and this propensity may be associated with specific gene expression profiles. To inve...

New Synapse Detection in the Whole-Brain Connectome of Drosophila

The FlyWire Drosophila brain connectome1 is a graph of roughly 140K neurons and >50 million synaptic connections2,3 reconstructed from the FAFB EM dat...

Computational Tracking of Cell Origins Using CellSexID from Single-Cell Transcriptomes

Cell tracking in chimeric models is essential yet challenging, particularly in developmental biology, regenerative medicine, and transplantation resea...

Transcriptomic profiling and machine learning uncover gene signatures of psoriasis endotypes and disease severity

Despite increased understanding of psoriasis pathogenesis, molecular classification of clinical phenotypes and disease severity is poorly defined. Kno...

CIAdex: Single-Cell FTIR Spectral Fingerprinting for Cell Identity Verification and Aging Quantification in Therapeutic Cell Manufacturing

Ensuring the identity and optimal aging state of cell products is critical for the efficacy and safety of cell therapies. Despite rapid iterations, th...

Quantum Convolutional HLA Immunogenic Peptide Prediction (Q-CHIPP): Next-Generation Neoantigen Prediction with Quantum Neural Networks

The immune system is an intricately evolved series of cellular and protein-protein interactions, which defend the body against pathogens and abnormal ...

DeepPROTECTNeo: A Deep learning-based Personalized and RV-guided Optimization tool leveraging TCR Epitope interaction using Context-aware Transformers

The development of personalized cancer vaccines relies heavily on accurately identifying neoepitopes capable of eliciting strong immune responses. T c...

Compatibility of a competition model for explaining eye fixation durations during free viewing

Intersaccadic times or eye fixation durations (EFD) are relatively stable at around 250ms, equivalent to 4 saccades by second. However, the mean and s...

Cytoplasmic dynamics are overlooked in single nuclei RNA-seq but can be rescued by CytoRescue, a generative AI model to recover cytoplasm enriched gene

Single-nucleus RNA sequencing (snRNA-seq) generates single cell data from nuclei. It provides valuable compatibility with frozen or difficult-to-disso...

Reengineering the antigen optimization process for superior neoantigen vaccine design

Identifying effective neoantigen sequences is essential for enhancing anti-tumor immunity. However, the vast sequence space (>109 possible peptides) a...

Three-dimensional spatial transcriptomics at isotropic resolution enabled by generative deep learning

Mapping the complete three-dimensional (3D), transcriptome-wide spatial architecture of tissues and organs remains a fundamental challenge in biology....

Artificial Intelligence-driven Whole-brain Cell Mapping with Highly Multiplexed In Situ Hybridization

Recent advances in three-dimensional single-cell-resolution imaging have begun to link organ-wide and cellular level research in development and disea...

Imagined Speech Reconstruction with 3D Neural Metabolism and Large Language Model Integration

Cognitive linguistics posits that language underpins human thought, and this principle has influenced the study and development of large language mode...

Acetylcholine demixes heterogeneous dopamine signals for learning and moving

Midbrain dopamine neurons promote both reinforcement learning and movement vigour1–12. A major outstanding question is how dopamine-recipient neurons ...

Deep learning-based image quantification of epithelial cell shapes and its application to polycystic kidney disease

Cell shape is a fundamental determinant of tissue architecture and organ function. In epithelial tissues, cytoskeletal organization and tight junction...

Large vision model framework for automated C. elegans analysis: From static morphometry to dynamic neural activity

Quantitative phenotyping of Caenorhabditis elegans is essential across numerous fields, yet data extraction remains a significant analytical bottlenec...

The Brain/MINDS 3D Digital Marmoset Brain Atlas Version 2.0: Population-based Cortical Region Parcellations with Multi-Modal Standard Templates

We present the Brain/MINDS population-based 3D digital brain atlas version 2.0 (BMA2.0), a population-based 3D digital brain atlas of the common marmo...

Predicting emergent phenotypes from single cell populations using CELLECTION

Biological systems exhibit emergent phenotypes that arise from the collective behavior of individual components, such as whole-organ functions that ar...

Single-cell neural network classifiers reveal that PM21 NK cell expansion is dependent on B cell signaling

In the field drug development ML/AI methods are being applied to improve drug production speed, costs, and reliability. In allogenic NK cell therapy p...