bioRxiv

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Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences

bioRxiv Jan 1, 2025
Microbiomes influence diverse ecosystems, and viruses increasingly appear to impose key constraints. While viromics has expanded genomic catalogs, host identification for these viruses remains challenging due to the limitations in scaling cultivation...
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Evaluating the contribution of genome 3D folding to variation in human height using machine learning

bioRxiv Jan 1, 2025
Genome-wide association studies (GWAS) have identified thousands of variants associated with complex traits, yet the majority lie in noncoding regions, making it difficult to determine their functional impact. Alterations to the three-dimensional (3D...
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Mitosis Detection in the Wild Using Detection Transformers

bioRxiv Jan 1, 2025
Identification of mitotic cells and its down-stream analysis, is an important parameter in understanding the pathology of cancer, predicting response to chemotherapy and overall survival. However, their reliable detection remains challenging due to m...
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Fusing Sequence Motifs and Pan-Genomic Features: Antimicrobial Resistance Prediction using an Explainable Lightweight 1D CNN - XGBoost Ensemble

bioRxiv Jan 1, 2025
Antimicrobial Resistance (AMR) is a rapidly escalating global health crisis. While genomic sequencing enables rapid prediction of resistance phenotypes, current computational methods have limitations. Standard machine learning models treat the genome...
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A Novel MiRNA Detection System Combining TWJ-SDA, Multistep L-TEAM, and CRISPR-Cas3

bioRxiv Jan 1, 2025
MicroRNAs (miRNAs) serve critical regulatory roles in gene expression and are valuable biomarkers for early disease detection. However, their inherent low concentration in biological fluids poses significant detection challenges. Although traditional...
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Graph Autoencoder and StrNN based Causal Analysis of Mortality in Heart Failure Patients

bioRxiv Jan 1, 2025
Though analyzed for decades, dissecting and finding mechanisms of cardiovascular diseases, especially heart failures, are still an on-going task for many researchers. However, through recent floods of machine learning and deep learning algorithms to ...
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Spinal Circuit Mechanisms Constrain Therapeutic Windows for ALS Intervention

bioRxiv Jan 1, 2025
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive breakdown of neural circuits which leads to motoneuron death. Earlier work from our lab showed that dysregulation of inhibitory V1 interneurons prec...
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Uncovering genetic architecture of the heart via genetic association studies of unsupervised deep learning derived endophenotypes

bioRxiv Jan 1, 2025
Recent genome-wide association studies (GWAS) have effectively linked genetic variants to quantitative traits derived from time-series cardiac magnetic resonance imaging, revealing insights into cardiac morphology and function. Deep learning approach...
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Iron Deficiency Impairs Mitochondrial Energetics and Early Axonal Growth and Branching in Developing Hippocampal Neurons

bioRxiv Jan 1, 2025
Each stage of neuronal development (i.e., proliferation, differentiation, migration, neurite outgrowth and synapse formation) requires functional and highly coordinated metabolic activity to ultimately ensure proper sculpting of complex neural networ...
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Neural Underpinnings of Olfactory Dysfunction across Parkinson’s and Alzheimer’s Spectra

bioRxiv Jan 1, 2025
Olfactory dysfunction is a frequent yet understudied feature of neurodegenerative spectrum disorders, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). To disentangle the neural substrates of hyposmia across disease spectra, we examine...
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