Tag Archives: BioRxiv

BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" 2′-Fucosyllactose helps butyrate producers outgrow competitors in the infant gut A reduced capacity for butyrate production by the early infant gut microbiota is associated with negative health effects, such as inflammation and the development of allergies. Here we develop …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer Colorectal cancer (CRC) shows high incidence and mortality, partly due to the tumor microenvironment, which is viewed as an active promoter of disease progression. Macrophages are among …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" The ability to sense the environment is heterogeneously distributed in cell populations Channel capacity of signaling networks quantifies their fidelity in sensing extracellular inputs. Low estimates of channel capacities for several mammalian signaling networks suggest that cells can barely …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity Inferring accurate models describing the relationship between genotype and phenotype is necessary in order to understand and predict how mutations …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" ENKIE: A package for predicting enzyme kinetic parameter values and their uncertainties Relating metabolite and enzyme abundances to metabolic fluxes requires reaction kinetics, core elements of dynamic and enzyme cost models. However, kinetic parameters have been measured only for …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology A major goal of cancer biology is to understand the mechanisms underlying tumorigenesis driven by somatically acquired mutations. Existing computational approaches focus on either …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function. Objective: Bowel movement frequency (BMF) variation has been linked to changes in the composition of the human gut microbiome and to …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Beyond the Genetic Code: A Tissue Code? The genetic code determines how the precise amino acid sequence of proteins is specified by genomic information in cells. But what specifies the precise histologic organization of cells in plant and animal …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Transcription factor interactions explain the context-dependent activity of CRX binding sites The effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory element (CRE) depend on the local sequence context. In rod photoreceptors, binding sites for …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Inferring gene regulatory networks using transcriptional profiles as dynamical attractors Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance Systems genetics has begun to tackle the complexity of insulin resistance by capitalising on computational advances to study high-diversity populations. "Diversity Outbred in Australia (DOz)" …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" An integrated workflow for quantitative analysis of the newly synthesized proteome The analysis of proteins that are newly synthesized upon a cellular perturbation can provide detailed insight in the proteomic response that is elicited by specific cues. This can …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" The ups and downs of biological oscillators: A comparison of time-delayed negative feedback mechanisms Many biochemical oscillators are driven by the periodic rise and fall of protein concentrations or activities. A negative feedback loop underlies such oscillations. The feedback …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Logic-based mechanistic machine learning on high-content images reveals how drugs differentially regulate cardiac fibroblasts Fibroblasts are essential regulators of extracellular matrix deposition following cardiac injury. These cells exhibit highly plastic responses in phenotype during fibrosis in response to environmental …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut. Microbially-derived short-chain fatty acids (SCFAs) in the human gut are tightly coupled to host metabolism, immune regulation, and integrity of the intestinal epithelium. However, the production …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Bounds on the Ultrasensitivity of Biochemical ReactionCascades The ultrasensitivity of a dose response function can be quantifiably defined using the generalized Hill coefficient of the function. Our group examined an upper bound for the Hill coefficient of the composition …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Systematic Identification of Post-Transcriptional Regulatory Modules In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Efficient and scalable prediction of spatio-temporal stochastic gene expression in cells and tissues using graph neural networks The simulation of spatial stochastic models is highly computationally expensive, an issue that has severely limited our understanding of the spatial nature …

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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Metabolomics investigation of post-mortem human pericardial fluid Introduction. Due to its peculiar anatomy and physiology, the pericardial fluid is a biological matrix of particular interest in the forensic field. Despite this, the available literature has mainly focused on post-mortem …

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