bioRxiv

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A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model

bioRxiv Jan 1, 2025
Single-cell transcriptomics has revolutionized our understanding of cellular diversity, yet our understanding of the transcriptional programs across the tree of life remains limited. Here we present TranscriptFormer, a family of generative foundation...
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A novel attention mechanism for noise-adaptive and robust segmentation of microtubules in microscopy images

bioRxiv Jan 1, 2025
Segmenting cytoskeletal filaments in microscopy images is essential for understanding their cellular roles but remains challenging, especially in dense, complex networks and under noisy or low-contrast image conditions. While deep learning has advanc...
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A structure and function-based complete mutational map of Human Hemoglobin using AI

bioRxiv Jan 1, 2025
Hemoglobin (Hb), a well-characterized protein central to oxygen transport and molecular medicine, serves as a model for studying how sequence variations influence protein structure and function. Its precise activity depends on tightly regulated struc...
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Towards a universal foundation model for biobank-scale human genome variation

bioRxiv Jan 1, 2025
Millions of human genomes have been genotyped by national biobanks worldwide. Training large language models (LLM) with this data may lead to a universal model of human genome with tremendous potential. Yet the quadrillions (1015) of nucleotides— res...
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From Signal to Symphony: Exploring 2D Sequence Representations for Protein Function Prediction

bioRxiv Jan 1, 2025
Predicting protein function from its primary sequence is a fundamental challenge in computational biology. While deep learning has excelled, the optimal representation of sequence data remains an open question. This study explores protein sonificatio...
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Computing the effects of excitatory-inhibitory balance on neuronal input-output properties

bioRxiv Jan 1, 2025
In sensory systems, stimuli are represented through the diverse firing responses and receptive fields of neurons. These features emerge from the interaction between excitatory (E) and inhibitory (I) neuron populations within the network. Changes in s...
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MRI-based classifier to identify close-to-onset cases in C9orf72 genetic frontotemporal dementia

bioRxiv Jan 1, 2025
Predicting symptom onset in genetic frontotemporal dementia (FTD) is crucial for advancing targeted interventions and clinical trial design. Brain changes begin years before clinical symptoms emerge, making neuroimaging a strong candidate for onset p...
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SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation

bioRxiv Jan 1, 2025
Integrating transcriptome-wide single-cell gene expression data with spatial context significantly enhances our understanding of tissue biology, cellular interactions, and disease progression. Although single-cell RNA sequencing (scRNA-seq) provides ...
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Nephrobase Cell+: Multimodal Single-Cell Foundation Model for Decoding Kidney Biology

bioRxiv Jan 1, 2025
Large foundation models have revolutionized single-cell analysis, yet no kidney-specific model currently exists, and it remains unclear whether organ-focused models can outperform generalized models. The kidney’s complex cellular architecture and dyn...
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Multi-scale structural similarity embedding search across entire proteomes

bioRxiv Jan 1, 2025
The rapid expansion of three-dimensional (3D) biomolecular structure information, driven by breakthroughs in artificial intelligence/deep learning (AI/DL)-based structure predictions, has created an urgent need for scalable and efficient structure si...
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