BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Temporal perturbation of STAT1/2 activity reveals dynamic ligand discrimination of type I interferon signaling Type-I interferon (IFN-I) subtypes signal through the same IFNalpha receptor (IFNAR), and initiate temporal STAT1/2 activation to orchestrate innate and adaptive immunity. It remains unknown …
Tag Archives: BioRxiv
Predicting phenotype to mechanotype relationships in cells based on intra-cellular signaling network
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Predicting phenotype to mechanotype relationships in cells based on intra-cellular signaling network Cells originating from the same tissue can respond differently to external signals depending on the genotypic and phenotypic state of the cell and its local environment. We …
A multi-omics strategy for the study of microbial metabolism: application to the human skin’s microbiome
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A multi-omics strategy for the study of microbial metabolism: application to the human skin’s microbiome The revolution of omics technologies highlighted that associated microorganisms (also called microbiota) are integrated into the metabolic functions of their hosts. Yet when performing …
Genetic and dietary modulators of the inflammatory response in the gastro-intestinal tract of the BXD mouse genetic reference population
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Genetic and dietary modulators of the inflammatory response in the gastro-intestinal tract of the BXD mouse genetic reference population Inflammatory gut disorders, including inflammatory bowel disease (IBD), can be impacted by dietary, environmental and genetic factors. While the incidence …
High versatility to meet conservation targets for biodiversity and hydrological services at the Riviera Maya, Quintana Roo, Mexico
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" High versatility to meet conservation targets for biodiversity and hydrological services at the Riviera Maya, Quintana Roo, Mexico The ecosystem services (ES) framework has been proposed as an alternative to face the multiple challenges presented by biodiversity conservation, but …
Mathematical models disentangle the role of IL-10 feedbacks in human monocytes upon proinflammatory activation
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Mathematical models disentangle the role of IL-10 feedbacks in human monocytes upon proinflammatory activation Inflammation is one of the vital mechanisms through which the immune system responds to harmful stimuli. During inflammation, pro and anti-inflammatory cytokines interplay to orchestrate …
Clonal differences underlie variable responses to sequential and prolonged treatment
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Clonal differences underlie variable responses to sequential and prolonged treatment Cancer cells exhibit dramatic differences in gene expression at the single-cell level which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity …
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models Likelihood ratios are frequently utilized as basis for statistical tests, for model selection criteria and for assessing parameter and prediction uncertainties, e.g. using the profile likelihood. …
An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells Detecting oscillations in time series datasets remains a challenging problem even after decades of research. Development of improved statistical algorithms, therefore, remains an …
Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results Studies combining metabolomics and genetics, known as metabolite genome-wide association studies (mGWAS), have provided valuable insights into our understanding of the genetic control of metabolite levels. However, …
DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes Most, if not all, proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing the majority of cellular processes in health and disease. …
Learning Perturbation-specific Cell Representations for Prediction of Transcriptional Response across Cellular Contexts
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Learning Perturbation-specific Cell Representations for Prediction of Transcriptional Response across Cellular Contexts Pre-clinical and clinical scientific endeavours provide complementary perspectives on fundamental biological processes of translational value. Harnessing the information value on the totality of such knowledge requires novel …
Compromised beta-cell identity in type 2 diabetes
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Compromised beta-cell identity in type 2 diabetes Compromised beta-cell identity is emerging as an important contributor of beta-cell dysfunction in type 2 diabetes (T2D). Several studies suggest that hyperglycemia induces the inactivation of transcription factors involved in mature beta-cell …
Continue reading “Compromised beta-cell identity in type 2 diabetes”
Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach Quantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory …
standard-GEM: standardization of open-source genome-scale metabolic models
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" standard-GEM: standardization of open-source genome-scale metabolic models The field of metabolic modelling at the genome-scale continues to grow with more models being created and curated. This comes with an increasing demand for adopting common principles regarding transparency and versioning, …
Continue reading “standard-GEM: standardization of open-source genome-scale metabolic models”
Using interactive platforms to encode, manage and explore immune-related adverse outcome pathways
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Using interactive platforms to encode, manage and explore immune-related adverse outcome pathways We address the need for modelling and predicting adverse outcomes in immunotoxicology to improve non-clinical assessments of immunomodulatory therapy safety and efficacy. The integrated approach includes, first, …
Emergence of power-law distributions in protein-protein interaction networks through study bias
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Emergence of power-law distributions in protein-protein interaction networks through study bias Protein-protein interaction (PPI) networks have been found to be power-law-distributed, ie, in observed PPI networks, the fraction of nodes with degree k often follows a power-law (PL) distribution …
The intensities of canonical senescence biomarkers integrate the duration of cell-cycle withdrawal
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" The intensities of canonical senescence biomarkers integrate the duration of cell-cycle withdrawal Senescence, a state of permanent cell-cycle withdrawal, is difficult to distinguish from quiescence, a transient state of cell-cycle withdrawal. This difficulty arises because quiescent and senescent cells …
How total mRNA influences cell growth
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" How total mRNA influences cell growth While the conventional wisdom is that growth rate is prominently set by ribosome amounts, in many biologically relevant situations the levels of mRNA and RNA polymerase can become a bottleneck for growth. Here, …
Modelling the dynamics of senescence spread
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Modelling the dynamics of senescence spread Cellular senescence is a cell surveillance mechanism that arrests the cell cycle in damaged cells. The senescent phenotype can spread from cell to cell through paracrine and juxtacrine signalling, but the dynamics of …
Continue reading “Modelling the dynamics of senescence spread”