bioRxiv

Showing 4581 to 4590 of 5021 articles

Unraveling miRNA-Driven DNA Damage Response Networks in Pancreatic Adenocarcinoma: A Multi-Omics and Machine Learning Approach

bioRxiv Jan 1, 2025
Due to the late detection, aggressive nature, and paucity of treatment options, pancreatic adenocarcinoma (PAAD) remains one of the most lethal cancers worldwide. MicroRNAs (miRNAs) are small non-coding RNAs that function as oncogenes or tumor suppre...
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A Multi-modal LLM for Dynamic Protein-Ligand Interactions and Generative Molecular Design

bioRxiv Jan 1, 2025
BioDynaGen (Biological Dynamics and Generation) is a novel multi-modal framework unifying protein sequences, dynamic binding site conformations, small molecule ligand SMILES, and natural language text into a single discrete token representation. Buil...
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A Multi-Modal Transfer Learning Framework to Reduce Health Disparities in Prostate Adenocarcinoma

bioRxiv Jan 1, 2025
Prostate cancer is the second most common cancer in men across the United States, of which prostate adenocarcinoma (PRAD) is the most common subtype. Despite remarkable progress has been made in PRAD diagnosis and prognosis, Black American men have b...
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Improved Estimation of Correlation Accuracy for Machine Learning Brain-Phenotype Associations

bioRxiv Jan 1, 2025
Machine learning is used in neuroscience to examine brain-phenotype associations and facilitate individual prediction from high-dimensional brain imaging. For continuous phenotypes, Pearson’s correlation between the observed and predicted phenotype i...
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Dorsolateral striatal acetylcholine reorganizes neural ensembles to anticipate threat

bioRxiv Jan 1, 2025
Adaptive behavior requires flexible encoding of emotional valence. Although striatal acetylcholine (ACh) signaling is critical for reinforcement learning, its contribution to aversive learning has remained poorly defined. Here, we demonstrate that AC...
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Predicting and Designing Red Fluorescent Protein Variants Using Sequence-to-Function Machine Learning Models

bioRxiv Jan 1, 2025
Fluorescent proteins (FPs) are widely used reporters for visualizing cellular structures and processes. Traditional wet-lab strategies for FP engineering (rational design and directed evolution) have enabled substantial improvements in photophysical ...
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Scoring gene importance by interpreting single-cell foundation models

bioRxiv Jan 1, 2025
Determining a gene’s functional significance within a cellular context has long been a challenge, as absolute expression level is an unreliable indicator. We introduce SIGnature, a framework for scoring gene importance by leveraging attributions deri...
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Gaze reinstatement during working memory for natural scenes

bioRxiv Jan 1, 2025
The information we hold in mind with working memory (WM) may propagate beyond the cortex and out to the peripheral motor system. For instance, directionally biased hand and eye movements can express simple visuo-spatial features during WM maintenance...
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Disentangling Superpositions: Interpretable Brain Encoding Model with Sparse Concept Atoms

bioRxiv Jan 1, 2025
Encoding models based on word embeddings or artificial neural network (ANN) features reliably predict brain responses to naturalistic stimuli but remain difficult to interpret. A central limitation is superposition—the entanglement of distinct semant...
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Microcompartments in archaeal ancestors of eukaryotes: a bioenergetic engine that could have fuelled eukaryogenesis

bioRxiv Jan 1, 2025
Eukaryotic intracellular compartmentalization is a key innovation in the evolution of complex cellular life. While microcompartments enable metabolic specialization in many bacteria, to our knowledge, no analogous systems have been identified in Arch...
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