BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Exploring the onset and progression of prostate cancer through a multicellular agent-based model Over ten percent of men will be diagnosed with prostate cancer (PCa) during their lifetime. Arising from luminal cells of the prostatic acinus, PCa is influenced …
Author Archives: Kermit Murray
Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, …
Enhanced protein secretion in reduced genome strains of Streptomyces lividans
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Enhanced protein secretion in reduced genome strains of Streptomyces lividans S. lividans TK24 is a popular host for the production of small molecules and for the secretion of heterologous proteins. TK24 has a large genome with at least 29 …
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Spectral methods for prediction uncertainty quantification in Systems Biology
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Spectral methods for prediction uncertainty quantification in Systems Biology Uncertainty is ubiquitous in biological systems. These uncertainties can be the result of lack of knowledge or due to a lack of appropriate data. Additionally, the natural variability of biological …
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Out-of-equilibrium gene expression fluctuations in presence of extrinsic noise
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Out-of-equilibrium gene expression fluctuations in presence of extrinsic noise Cell-to-cell variability in protein concentrations is strongly affected by extrinsic noise, especially for highly expressed genes. Extrinsic noise can be due to fluctuations of several possible cellular factors connected to …
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Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants This work presents a methodology to evaluate the bioenergetic feasibility of alternative metabolic pathways for a given microbial conversion, optimising their energy yield and driving forces …
Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA) Spatial transcriptomics (ST) techniques are able to chart the distribution and localization of cell types and RNA molecules across a tissue. Sequencing-based methods allow unbiased capturing of RNA molecules at …
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Insights into the sulfur metabolism of Chlorobaculum tepidum by label‐free quantitative proteomics
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Insights into the sulfur metabolism of Chlorobaculum tepidum by label‐free quantitative proteomics Abstract Chlorobaculum tepidum is an anaerobic green sulfur bacterium which oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. It can …
Agricultural pesticides do not suppress infection of Biomphalaria (Gastropoda) by Schistosoma mansoni (Trematoda)
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Agricultural pesticides do not suppress infection of Biomphalaria (Gastropoda) by Schistosoma mansoni (Trematoda) Background Schistosomiasis is a neglected tropical disease caused by trematodes of the genus Schistosoma. The pathogen is transmitted via freshwater snails. These snails indirectly benefit from …
[ASAP] Proteomes of Micro- and Nanosized Carriers Engineered from Red Blood Cells
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Proteomes of Micro- and Nanosized Carriers Engineered from Red Blood Cells Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00695 Chi-Hua Lee, Jack C. Tang, Nathan G. Hendricks, and Bahman Anvari February 16, 2023 http://dx.doi.org/10.1021/acs.jproteome.2c00695
Automated desorption electrospray ionization two-dimensional tandem mass spectrometry: Instrumentation and software for high throughput analysis
International Journal of Mass Spectrometry ScienceDirect Publication: International Journal of Mass Spectrometry ScienceDirect RSS Automated desorption electrospray ionization two-dimensional tandem mass spectrometry: Instrumentation and software for high throughput analysis Publication date: April 2023 Source: International Journal of Mass Spectrometry, Volume 486 Author(s): Eric T. Dziekonski, Thomas C. Sams, Lucas J. Szalwinski, L. Edwin Gonzalez, R. …
Study of emerging chicken meat quality defects using OMICs: What do we know?
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Study of emerging chicken meat quality defects using OMICs: What do we know? Publication date: 30 March 2023 Source: Journal of Proteomics, Volume 276 Author(s): Xue Zhang, Sawyer Wyatt Smith, Lizzie R. Zaldivar, Dylan J. Lesak, M. Wes Schilling February 15, 2023 https://www.sciencedirect.com/science/article/pii/S187439192300026X?dgcid=rss_sd_all
Mass spectrometry analysis of phosphotyrosine‐containing proteins
Mass Spectrometry Reviews Wiley: Mass Spectrometry Reviews: Table of Contents Table of Contents for Mass Spectrometry Reviews. List of articles from both the latest and EarlyView issues. Mass spectrometry analysis of phosphotyrosine‐containing proteins Abstract Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in …
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Recent developments and applications of selected ion flow tube mass spectrometry (SIFT‐MS)
Mass Spectrometry Reviews Wiley: Mass Spectrometry Reviews: Table of Contents Table of Contents for Mass Spectrometry Reviews. List of articles from both the latest and EarlyView issues. Recent developments and applications of selected ion flow tube mass spectrometry (SIFT‐MS) Abstract Selected ion flow tube mass spectrometry (SIFT-MS) is now recognized as the most versatile analytical technique for …
The isotope distribution: A rose with thorns
Mass Spectrometry Reviews Wiley: Mass Spectrometry Reviews: Table of Contents Table of Contents for Mass Spectrometry Reviews. List of articles from both the latest and EarlyView issues. The isotope distribution: A rose with thorns Abstract The isotope distribution, which reflects the number and probabilities of occurrence of different isotopologues of a molecule, can be theoretically …
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Characterization of the degradation products of lignocellulosic biomass by using tandem mass spectrometry experiments, model compounds, and quantum chemical calculations
Mass Spectrometry Reviews Wiley: Mass Spectrometry Reviews: Table of Contents Table of Contents for Mass Spectrometry Reviews. List of articles from both the latest and EarlyView issues. Characterization of the degradation products of lignocellulosic biomass by using tandem mass spectrometry experiments, model compounds, and quantum chemical calculations Abstract Biomass-derived degraded lignin and cellulose serve as …
Probing gas phase catalysis by atomic metal cations with flow tube mass spectrometry
Mass Spectrometry Reviews Wiley: Mass Spectrometry Reviews: Table of Contents Table of Contents for Mass Spectrometry Reviews. List of articles from both the latest and EarlyView issues. Probing gas phase catalysis by atomic metal cations with flow tube mass spectrometry Abstract The evolution and applications of flow tube mass spectrometry in the study of catalysis …
The mechanism of Pseudomonas aeruginosa outer membrane vesicle biogenesis determines their protein composition
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. The mechanism of Pseudomonas aeruginosa outer membrane vesicle biogenesis determines their protein composition Abstract Gram-negative bacteria produce outer membrane vesicles (OMVs) and contain bacterial cargo including nucleic acids and proteins. The proteome of …
Genetic and epigenetic control of the plant metabolome
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Genetic and epigenetic control of the plant metabolome Abstract Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter …
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Proteomic identification of intracellular vesicle trafficking and protein glycosylation requirements for lumen inflation in Ciona notochord
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Proteomic identification of intracellular vesicle trafficking and protein glycosylation requirements for lumen inflation in Ciona notochord Abstract Lumen formation and inflation are crucial steps for tubular organ morphogenesis, yet the underling mechanism remains …