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 …
Author Archives: Kermit Murray
Logistics of Bone Mineralization in the Chick Embryo Studied by 3D Cryo FIB-SEM Imaging
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 …
[ASAP] Sensitive Analysis of Recombinant Human Erythropoietin Glycopeptides by On-Line Phenylboronic Acid Solid-Phase Extraction Capillary Electrophoresis Mass Spectrometry
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Sensitive Analysis of Recombinant Human Erythropoietin Glycopeptides by On-Line Phenylboronic Acid Solid-Phase Extraction Capillary Electrophoresis Mass Spectrometry Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00569 Montserrat Mancera-Arteu, Fernando Benavente, Victoria Sanz-Nebot, and Estela Giménez February 10, …
[ASAP] Mass Spectrometry-Based Atlas of Extracellular Matrix Proteins across 25 Mouse Organs
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Mass Spectrometry-Based Atlas of Extracellular Matrix Proteins across 25 Mouse Organs Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00526 Maxwell C. McCabe, Anthony J. Saviola, and Kirk C. Hansen February 10, 2023 http://dx.doi.org/10.1021/acs.jproteome.2c00526
Pumping Iron: A Multi-omics Analysis of Two Extremophilic Algae Reveals Mechanisms of Iron Economy
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 …
A Structured Evaluation of Genome-Scale Constraint-Based Modeling Tools for Microbial Consortia
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A Structured Evaluation of Genome-Scale Constraint-Based Modeling Tools for Microbial Consortia Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is …
Sensory diversity and precise adaptation enable independent bet-hedging strategies for multiple signals at the same time
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Sensory diversity and precise adaptation enable independent bet-hedging strategies for multiple signals at the same time While navigating their environments, cells encounter many different signals at once. In the face of uncertain conditions, diversifying the sensitivity to different signals …
The impossible challenge of estimating non-existent moments of the Chemical Master Equation
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 …
Integrated transcriptome and proteome analysis provides insights into the mechanism of cytoplasmic male sterility (CMS) in tobacco (Nicotiana tabacum L.)
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Integrated transcriptome and proteome analysis provides insights into the mechanism of cytoplasmic male sterility (CMS) in tobacco (Nicotiana tabacum L.) Publication date: 20 March 2023 Source: Journal of Proteomics, Volume 275 Author(s): Zejun Mo, Yuzhou Ke, Ying Huang, Lili Duan, Pingsong Wang, Wen Luo, Yuanhui …
Reconstructing cellular differentiation networks and identifying cell fate-determining features with CIBER
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Reconstructing cellular differentiation networks and identifying cell fate-determining features with CIBER Most existing trajectory inference methods are similarity-based and lack an understanding of the latent causality among differentiation processes. Here, we present CIBER, a Causal Inference-Based framework for the …
RxRx3: Phenomics Map of Biology
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" RxRx3: Phenomics Map of Biology The combination of modern genetic perturbation techniques with high content screening has enabled genome-scale cell microscopy experiments that can be leveraged to construct maps of biology. These are built by processing microscopy images to …
Pgc-1α is an exercise-responsive regulator of myosteatosis in older individuals
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Pgc-1α is an exercise-responsive regulator of myosteatosis in older individuals Accumulated fat in skeletal muscle, common in sedentary older individuals, compromises skeletal muscle health and function. Mechanistic understanding of how physical activity levels dictate fat accumulation represents a critical …
Continue reading “Pgc-1α is an exercise-responsive regulator of myosteatosis in older individuals”
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF Abstract A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation …
Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses Male subjects in animal and human studies are disproportionately used for toxicological testing. This discrepancy is evidenced in clinical medicine where females are more likely than males …
Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation of Microbial Metabolic Switching
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation of Microbial Metabolic Switching Integration of genome-scale metabolic networks with reactive transport models (RTMs) is an advanced simulation technique that enables predicting the …
Unraveling codon usage of Escherichia coli using machine learning
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Unraveling codon usage of Escherichia coli using machine learning Machine learning is used to investigate the codon usage of protein-encoding genes, which is one of the fundamental questions of molecular biology. The presentation, parameter learning, and decoding of the …
Continue reading “Unraveling codon usage of Escherichia coli using machine learning”
[ASAP] Online Alkaline-pH Reverse Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Conventional Low-pH Method for Global Proteomic Analysis
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Online Alkaline-pH Reverse Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Conventional Low-pH Method for Global Proteomic Analysis Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00765 Jing Gao, Yuqiu Wang, Shu Zhang, Zhicheng Yang, Hongwen Zhu, Xuanyang Luo, Dayun …
[ASAP] NeuroPpred-SVM: A New Model for Predicting Neuropeptides Based on Embeddings of BERT
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] NeuroPpred-SVM: A New Model for Predicting Neuropeptides Based on Embeddings of BERT Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00363 Yufeng Liu, Shuyu Wang, Xiang Li, Yinbo Liu, and Xiaolei Zhu February 7, 2023 http://dx.doi.org/10.1021/acs.jproteome.2c00363
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 …
Continue reading “The isotope distribution: A rose with thorns”
From autopoiesis to self-optimization: Toward an enactive model of biological regulation
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" From autopoiesis to self-optimization: Toward an enactive model of biological regulation The theory of autopoiesis has been influential in many areas of theoretical biology, especially in the fields of artificial life and origins of life. However, it has not …