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 …
Author Archives: Kermit Murray
Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut.
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 …
Bounds on the Ultrasensitivity of Biochemical ReactionCascades
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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Efficient and scalable prediction of spatio-temporal stochastic gene expression in cells and tissues using graph neural networks
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 …
Standard abbreviations
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Standard abbreviations PROTEOMICS, Volume 23, Issue 5, March 2023. March 2, 2023 https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202370034?af=R
Proteomic and phosphoproteomic landscape of salivary extracellular vesicles to assess OSCC therapeutical outcomes
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Proteomic and phosphoproteomic landscape of salivary extracellular vesicles to assess OSCC therapeutical outcomes Abstract Circulating extracellular vesicles (EVs) have emerged as an appealing source for surrogates to evaluate the disease status. Herein, we …
Proteomicsābased scoring of cellular response to stimuli for improved characterization of signaling pathway activity
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Proteomicsābased scoring of cellular response to stimuli for improved characterization of signaling pathway activity Abstract Omics technologies focus on uncovering the complex nature of molecular mechanisms in cells and organisms, including biomarkers and …
Bioprospecting the American Alligator Peptidome for antiviral peptides against Venezuelan equine encephalitis virus
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Bioprospecting the American Alligator Peptidome for antiviral peptides against Venezuelan equine encephalitis virus Abstract The innate immune protection provided by cationic antimicrobial peptides (CAMPs) has been shown to extend to antiviral activity, with …
Isobaric labelingābased quantitative proteomics of FACSāpurified immune cells and epithelial cells from the intestine of Crohn’s disease patients reveals proteome changes of potential importance in disease pathogenesis
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Isobaric labelingābased quantitative proteomics of FACSāpurified immune cells and epithelial cells from the intestine of Crohn’s disease patients reveals proteome changes of potential importance in disease pathogenesis Abstract Crohn’s disease (CD) is a …
Metabolomics investigation of post-mortem human pericardial fluid
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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Systematic Identification of Post-Transcriptional Regulatory Modules
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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[ASAP] Quantitative Proteomics Reveal the Inherent Antibiotic Resistance Mechanism against Norfloxacin Resistance in Aeromonas hydrophila
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Quantitative Proteomics Reveal the Inherent Antibiotic Resistance Mechanism against Norfloxacin Resistance in Aeromonas hydrophila Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00663 Ziqiu Liu, Lishan Zhang, Qingli Song, Huanhuan Song, Yunqi Xu, Jinlian Lu, Qiaozhen Xu, …
Identifying dynamical persistent biomarker structures for rare events using modern integrative machine learning approach
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Identifying dynamical persistent biomarker structures for rare events using modern integrative machine learning approach Abstract The evolution of omics and computational competency has accelerated discoveries of the underlying biological processes in an unprecedented …
Data-Driven Screening to Infer Metabolic Modulators of the Cancer Epigenome
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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PrePPI: A structure informed proteome-wide database of protein-protein interactions
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 …
[ASAP] Human Mitochondrial Protein HSPD1 Binds to and Regulates the Repair of Deoxyinosine in DNA
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Human Mitochondrial Protein HSPD1 Binds to and Regulates the Repair of Deoxyinosine in DNA Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00854 Xiaofang Zheng, Sijia Chang, Yini Liu, Xiaoxia Dai, and Changjun You February 28, 2023 …
Methodology for inference of intercellular gene interactions
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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Multiscale networks in multiple sclerosis
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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Solventāinduced proteome profiling for proteomic quantitation and target discovery of small molecular drugs
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Solventāinduced proteome profiling for proteomic quantitation and target discovery of small molecular drugs Abstract Target identification by modification-free proteomic approaches can potentially reveal the pharmacological mechanism of small molecular compounds. By combining the …
Applying singleācell highly multiplexed secretome proteomics to characterize immunotherapeutic products and predict clinical responses
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Applying singleācell highly multiplexed secretome proteomics to characterize immunotherapeutic products and predict clinical responses Abstract Genetically and phenotypically identical immune cell populations can be highly heterogenous in terms of their immune functions and …