BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG In individuals with Down syndrome (DS), cardiovascular and pulmonary diseases are the most common health problem and result in increased mortality and morbidity. …
Author Archives: Kermit Murray
Distilling identifiable and interpretable dynamic models from biological data
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Distilling identifiable and interpretable dynamic models from biological data Mechanistic dynamical models allow us to study the behavior of complex biological systems. They can provide an objective and quantitative understanding that would be difficult to achieve through other means. …
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Post-mortem muscle proteome of crossbred bulls and steers: Relationships with carcass and meat quality
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Post-mortem muscle proteome of crossbred bulls and steers: Relationships with carcass and meat quality Publication date: 30 April 2023 Source: Journal of Proteomics, Volume 278 Author(s): Bismarck Santiago, Welder Baldassini, Otávio Machado Neto, Luis Artur Chardulo, Rodrigo Torres, Guilherme Pereira, Rogério Curi, Marcos Roberto Chiaratti, …
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics Abstract Accurate retention time prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning …
Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Leveraging spatial molecular information to construct a phylogeographic map of tumor evolution can …
A systematic search for RNA structural switches across the human transcriptome
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A systematic search for RNA structural switches across the human transcriptome RNA structural switches are key regulators of gene expression in bacteria, yet their characterization in Metazoa remains limited. Here we present SwitchSeeker, a comprehensive computational and experimental approach …
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Multidimensional proteomics identifies molecular trajectories of cellular aging and rejuvenation
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Multidimensional proteomics identifies molecular trajectories of cellular aging and rejuvenation The declining capacity of cells to maintain a functional proteome is a major driver of cellular dysfunction and decreased fitness in aging. Here we assess the impact of aging …
A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreatic beta-Cell
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreatic beta-Cell The pancreas plays a critical role in maintaining glucose homeostasis through the secretion of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by the pancreatic beta-cell …
OptEnvelope: a target point guided method for growth-coupled production using knockouts
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" OptEnvelope: a target point guided method for growth-coupled production using knockouts Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a metabolic model is a challenge in biotechnology. In this research, a …
A sensitive on-tissue chemical derivatization-mass spectrometry imaging method for the quantitative visualization of helicid in mice
International Journal of Mass Spectrometry ScienceDirect Publication: International Journal of Mass Spectrometry ScienceDirect RSS A sensitive on-tissue chemical derivatization-mass spectrometry imaging method for the quantitative visualization of helicid in mice Publication date: June 2023 Source: International Journal of Mass Spectrometry, Volume 488 Author(s): Yanhua Liu, Yuxin Cai, Xueying Bai, Xinyu Zhao, Xianyue Meng, Xin Zhang, …
2′-Fucosyllactose helps butyrate producers outgrow competitors in the infant gut
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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Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer
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 …
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 …
iTRAQ‐based proteomic analysis reveals proteins associated with cold stress response in two different populations of Manila clam (Ruditapes philippinarum)
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. iTRAQ‐based proteomic analysis reveals proteins associated with cold stress response in two different populations of Manila clam (Ruditapes philippinarum) Abstract Water temperature is one of the key environmental factors for marine ectotherms and …
transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks
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 …
The ability to sense the environment is heterogeneously distributed in cell populations
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 …
Biochemical network analysis of protein-protein interactions to follow-up T1 bladder cancer patients
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Biochemical network analysis of protein-protein interactions to follow-up T1 bladder cancer patients Publication date: 30 April 2023 Source: Journal of Proteomics, Volume 278 Author(s): Luís B. Carvalho, José Luis Capelo Martínez, Carlos Lodeiro, Rafael Bento, Rajiv Dhir, Jeremiah J. Morrissey, Luis Campos Pinheiro, Mariana Medeiros, …
[ASAP] Comparison of Database Searching Programs for the Analysis of Single-Cell Proteomics Data
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Comparison of Database Searching Programs for the Analysis of Single-Cell Proteomics Data Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00821 Jiaxi Peng, Calvin Chan, Fei Meng, Yechen Hu, Lingfan Chen, Ge Lin, Shen Zhang, and Aaron …
Towards the discovery of goat meat quality biomarkers using label-free proteomics
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Towards the discovery of goat meat quality biomarkers using label-free proteomics Publication date: 30 April 2023 Source: Journal of Proteomics, Volume 278 Author(s): Melisa Lamri, Antonella della Malva, Djamel Djenane, María López-Pedrouso, Daniel Franco, Marzia Albenzio, José M. Lorenzo, Mohammed Gagaoua March 9, 2023 https://www.sciencedirect.com/science/article/pii/S187439192300057X?dgcid=rss_sd_all
An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity
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 …