Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
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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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, …
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 …
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 …
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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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 …
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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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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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Biphasic responses in cell signalling: A unified approach Biphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signalling and post-translational modification systems and represent safeguards against over-activation …
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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Multilevel Omics-Readouts of in vitro Perturbation Studies are Determined by Memory Effects from Subculture Mass spectrometry-based omics technologies are of increasing relevance for drug discovery. The identification of significant molecular events is a prerequisite in order to map treatments …
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Higher-order co-mutation interactions in mitochondrial genomes Studies of pair-wise co-mutation of mitochondrial genome have already provided ample evidences about roles of genetic interactions in manifestation of phenotype under altered environmental conditions. High-altitude is one such condition which causes mitochondrial …
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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Phosphoproteomics of cellular mechanosensing reveals NFATC4 as a regulator of myofibroblast activity Feedback connections between tissue stiffness and cellular contractile forces can instruct cell identity and activity via a process referred to as mechanosensing. Specific phosphoproteome changes during mechanosensing …
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Coupling allows robust redox circadian rhythms despite heterogeneity and noise Circadian clocks are endogenous oscillators present in almost all cells that drive daily rhythms in physiology and behavior. There are two mechanisms that have been proposed to explain how …
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BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" CRISPR interference screens reveal tradeoffs between growth rate and robustness in Synechocystis sp. PCC 6803 across trophic conditions Barcoded mutant libraries are a powerful tool for elucidating gene function in microbes, particularly when screened in multiple growth conditions. Here, …
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Utilizing high resolution ribosome profiling for the global investigation of gene expression in Chlamydomonas reinhardtii Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression in plant cells. Here, …
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" The balance of acidic and hydrophobic residues predicts acidic transcriptional activation domains from protein sequence Transcription factors activate gene expression in development, homeostasis, and stress with DNA binding domains and activation domains. Although there exist excellent computational models for …
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Logistics of Bone Mineralization in the Chick Embryo Studied by 3D Cryo FIB-SEM Imaging During skeletal development, bone growth and mineralization require transport of substantial amounts of calcium, while maintaining very low concentration. How an organism overcomes this major …
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells Pluripotency can be induced in somatic cells by the expression of the four Yamanaka factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually …
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Pumping Iron: A Multi-omics Analysis of Two Extremophilic Algae Reveals Mechanisms of Iron Economy Marine algae are responsible for half of the world’s primary productivity, but this critical carbon sink is often constrained by insufficient iron. One species of …
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" The impossible challenge of estimating non-existent moments of the Chemical Master Equation Motivation: The Chemical Master Equation is a set of linear differential equations that describes the evolution of the probability distribution on all possible configurations of a (bio-)chemical …