Tag Archives: BioRxiv

BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Data-Driven Screening to Infer Metabolic Modulators of the Cancer Epigenome Metabolites such as acetyl-CoA and citrate play an important moonlighting role by influencing the levels of histone post-translational modifications (PTMs) and regulating gene expression. This cross talk between metabolism …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" PrePPI: A structure informed proteome-wide database of protein-protein interactions We present an updated version of the Predicting Protein-Protein Interactions (PrePPI) webserver which predicts PPIs on a proteome-wide scale. PrePPI combines structural and non-structural clues within a Bayesian framework to …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Methodology for inference of intercellular gene interactions To govern organ size, shape, and function, cell-secreted diffusible molecules called morphogens spatially pattern cell differentiation, gene expression, and proliferation. Local morphogen concentration governs cell differentiation through gene regulatory networks (GRN). Previous …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Multiscale networks in multiple sclerosis Complex diseases such as Multiple Sclerosis (MS) cover a wide range of biological scales, from genes and proteins to cells and tissues, up to the full organism. We conducted a multilayer network analysis and …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A compact model for cold tolerance entrainment based on the ICE1-CBF-COR pathway in plants Most temperate plants can tolerate both chilling and freezing temperatures. Plants have developed self-defense mechanisms to perceive cold signal, trigger the cold tolerance for the …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Exploring tumor-normal cross-talk with TranNet: role of the environment in tumor progression There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Multi-view learning to unravel the different levels underlying hepatitis B vaccine response Background: The high complexity of biological systems arises from the large number of spatially and functionally overlapping interconnected components constituting them. The immune system, which is built …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Transkingdom Network Analysis (TkNA): a systems approach inferring causal factors underlying host-microbiota interactions. Technological advances have generated tremendous amounts of high-throughput omics data. Integrating data from multiple cohorts and/or several omics types from new and previously published studies can …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Comparative gene regulatory network analysis in Alzheimer’s disease and major depressive disorder Major depressive disorder and Alzheimer’s disease are two prevalent and devastating disorders that still lack effective treatment. Despite distinct disease phenotypes, these two disorders are characterized by …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease Single-cell atlases across conditions are essential in the characterization of human disease. In these complex experimental designs, patient samples are profiled across distinct cell-types and clinical conditions …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites The medium composition was crucial for achieving the best performance of synthetic construction. What and how medium components determined the production of …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states Large omics datasets are nowadays routinely generated to provide insights into cellular processes. Nevertheless, making sense of omics data and determining intracellular metabolic states remains challenging. Kinetic …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Oxygen intrusions sustain aerobic nitrite oxidation in anoxic marine zones Anoxic marine zones (AMZs) are host to anaerobic metabolisms that drive losses of bioavailable nitrogen from the ocean. The discovery of active nitrite-oxidising bacteria (NOB), long thought to be …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Ongoing HIV replication in lymph node sanctuary sites in treated patients contributes to the total latent HIV at a very slow rate. Lymph nodes (LNs) may serve as a sanctuary site for HIV viruses due to the heterogeneous distribution …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes Motivation: Biological tissues are dynamic and highly organized. Multi-scale models are helpful tools to analyze and understand the processes determining tissue dynamics. These models usually depend on parameters …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches Natural communities are incredibly diverse, and explaining how this biodiversity is even possible remains a central question in ecology. Resource competition is thought to play …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the microbiome influences its host have been identified, …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Discovery of multi-state gene cluster switches determining the adaptive mitochondrial and metabolic landscape of breast cancer Adaptive metabolic switches are proposed to underlie conversions between cellular states during normal development as well as in cancer evolution, where they represent …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting …

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