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 …
Author Archives: Kermit Murray
Identifying a urinary peptidomics profile for hypertension in young adults:The African‐PREDICT study
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Identifying a urinary peptidomics profile for hypertension in young adults:The African‐PREDICT study Abstract Hypertension is one of the most important and complex risk factors for cardiovascular diseases. By using urinary peptidomics analyses, we …
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, …
Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources While many heterologous molecules can be produced at trace concentrations via microbial bioconversion processes, maximizing their titers, rates, and yields from lignin-derived …
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 …
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Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation T-cells are critical components of the adaptive immune system. Upon activation, they acquire effector functions through a complex interplay between mRNA transcripts and proteins, the …
MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes Background: The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or omes, measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding …
[ASAP] prolfqua: A Comprehensive R‑Package for Proteomics Differential Expression Analysis
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] prolfqua: A Comprehensive R‑Package for Proteomics Differential Expression Analysis Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00441 Witold E. Wolski, Paolo Nanni, Jonas Grossmann, Maria d’Errico, Ralph Schlapbach, and Christian Panse March 20, 2023 http://dx.doi.org/10.1021/acs.jproteome.2c00441
[ASAP] Evolution of Mass Spectrometry Instruments and Techniques for Blood Proteomics
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Evolution of Mass Spectrometry Instruments and Techniques for Blood Proteomics Journal of Proteome Research DOI: 10.1021/acs.jproteome.3c00102 Yang Zhao, Qian Xue, Man Wang, Bo Meng, You Jiang, Rui Zhai, Yong Zhang, Xinhua Dai, and Xiang …
Innovations in Applications of Mass Spectrometry Impact Many Fields of Science.
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. Innovations in Applications of Mass Spectrometry Impact Many Fields of Science. Abstract I am pleased and honored that Dan Fabris has organized this special issue of reviews that …
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Editorial from Dominic M. Desiderio
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. Editorial from Dominic M. Desiderio Abstract I retired as an Editor of Mass Spectrometry Reviews. I signed my contract on November 1, 1993, and published my first editorial …
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 (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep …
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 …
Exploring the noncanonical translatome using massively integrated coexpression analysis
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Exploring the noncanonical translatome using massively integrated coexpression analysis Cells transcribe and translate thousands of noncanonical open reading frames (nORFs) whose impacts on cellular phenotypes are unknown. Here, we investigated nORF transcription, evolution, and potential cellular roles using a …
[ASAP] Using an In-Sample Addition of Medronic Acid for the Analysis of Purine- and Pyrimidine-Related Derivatives and Its Application in the Study of Lung Adenocarcinoma A549 Cell Lines by LC–MS/MS
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Using an In-Sample Addition of Medronic Acid for the Analysis of Purine- and Pyrimidine-Related Derivatives and Its Application in the Study of Lung Adenocarcinoma A549 Cell Lines by LC–MS/MS Journal of Proteome Research DOI: …
[ASAP] Spatial Proteome Reorganization of a Photosynthetic Model Cyanobacterium in Response to Abiotic Stresses
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Spatial Proteome Reorganization of a Photosynthetic Model Cyanobacterium in Response to Abiotic Stresses Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00759 Yan Wang, Haitao Ge, Zhen Xiao, Chengcheng Huang, Gaojie Wang, Xiaoxiao Duan, Limin Zheng, Jinghui …
A fast, accurate and comprehensive LC-MS/MS method validation for the sensitive quantification of water-soluble vitamins in walnut, almond, hazelnut and pistachio fruits
International Journal of Mass Spectrometry ScienceDirect Publication: International Journal of Mass Spectrometry ScienceDirect RSS A fast, accurate and comprehensive LC-MS/MS method validation for the sensitive quantification of water-soluble vitamins in walnut, almond, hazelnut and pistachio fruits Publication date: June 2023 Source: International Journal of Mass Spectrometry, Volume 488 Author(s): Mustafa Abdullah Yilmaz, Oguz Cakir, Ismail …
Proteomic analysis reveals the non-coding small RNA Qrr5 influences autoaggregation and growth competition in Vibrio parahaemolyticus
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Proteomic analysis reveals the non-coding small RNA Qrr5 influences autoaggregation and growth competition in Vibrio parahaemolyticus Publication date: 15 May 2023 Source: Journal of Proteomics, Volume 279 Author(s): Fei Zha, Rui Pang, Shixuan Huang, Jumei Zhang, Juan Wang, Moutong Chen, Liang Xue, Qinghua Ye, Shi …
Measurement and utilization of the proteomic reactivity by 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. Measurement and utilization of the proteomic reactivity by mass spectrometry Abstract Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to …
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Guide-specific loss of efficiency and off-target reduction with Cas9 variants
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Guide-specific loss of efficiency and off-target reduction with Cas9 variants High-fidelity Cas9 variants have been developed to reduce the off-target effects of CRISPR systems at a cost of efficiency loss. To systematically evaluate the efficiency and off-target tolerance of …
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