bioRxiv

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Deciphering the 3D genome organization across species from Hi-C data

bioRxiv Jan 1, 2025
Three-dimensional genome organization is essential for gene regulation, yet in various species it is driven by different biological mechanisms. Species-specific factors and DNA sequences influence chromatin folding, complicating cross-species compari...
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Scaling Large Language Models for Next-Generation Single-Cell Analysis

bioRxiv Jan 1, 2025
Single-cell RNA sequencing has transformed our understanding of cellular diversity, yet current singlecell foundation models (scFMs) remain limited in their scalability, flexibility across diverse tasks, and ability to natively integrate textual info...
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Integrating Mutation and Stop Signals for Improved RNA Structure Analysis and Insight Discovery

bioRxiv Jan 1, 2025
Understanding RNA structures is essential for exploring its diverse cellular roles. Chemical modification-based RNA structure probing remains a key approach to revealing RNA structures in complex in vivo conditions. Practically, chemical modification...
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Integrated analysis implicates novel insights of NMB into lactate metabolism and immune response prediction in primary glioblastoma

bioRxiv Jan 1, 2025
Glioblastoma (GBM), the most aggressive primary brain tumor in adults, exhibits profound treatment resistance and poor prognosis. Despite advances in immunotherapy for other cancers, GBM remains refractory, potentially due to its lactate-rich, immuno...
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Machine Learning Guided Video Analysis Identifies Sound-Evoked Pain Behaviors from Facial Grimace and Body Cues in Mice

bioRxiv Jan 1, 2025
Humans can experience auditory pain in response to sound, either from extremely loud noise or in cases of pain hyperacusis, where typically tolerable sounds become painful. However, the mechanisms underlying auditory pain remain poorly understood. De...
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Episodic memories enable powerful algorithms for goal-directed decision making that are context-aware and explainable

bioRxiv Jan 1, 2025
Current AI tools are often criticized for their lack of content-awareness and explainability. This make their planning and action selection sometimes undesirable for a given context, or even unsafe. In contrast, our brains can adjust planning and act...
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Cholinergic-dependent dopamine signals in mouse dorsal striatum are regulated by frontal but not sensory cortices

bioRxiv Jan 1, 2025
Everyday decisions depend on linking sensory stimuli with actions and outcomes. The striatum supports these sensorimotor associations through dopamine-dependent plasticity. Thus, the timing and magnitude of dopamine release is critical for learning. ...
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Deep multiplexed 50-marker imaging of circulating tumor cells expands actionable biomarker profiling for precision oncology

bioRxiv Jan 1, 2025
Liquid biopsy-derived circulating tumor cells (CTCs) offer a minimally invasive avenue for precision oncology by enabling longitudinal monitoring of actionable molecular and cell-phenotypic biomarkers. However, conventional immunofluorescence imaging...
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Generative design of antibody Fc-variants with synthetic and programmable functional profiles

bioRxiv Jan 1, 2025
Beyond antigen recognition, antibodies direct diverse immune effector functions through their constant (Fc) domain. While the Fc domain is central to antibody biology and therapeutic efficacy, our understanding of how Fc sequence encodes function rem...
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Screening of Oyster Peptides for Anti-Muscle Atrophy Based on Machine Learning and Computer Simulation: Guided by Antioxidant Pathways

bioRxiv Jan 1, 2025
Muscle atrophy poses a serious threat to human health, with its primary pathogenic mechanisms closely linked to oxidative stress. This study focuses on the potential of oyster peptides in alleviating dexamethasone (DEX)-induced skeletal muscle atroph...
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