scholarly journals Multicellular Systems Biology: Quantifying Cellular Patterning and Function in Plant Organs Using Network Science

2019 ◽  
Vol 12 (6) ◽  
pp. 731-742 ◽  
Author(s):  
George W. Bassel
Keyword(s):  
Systems Biology ◽  
Network Science ◽  
Plant Organs ◽  
Cellular Patterning ◽  
And Function

A Systems Biology Approach for Understanding Granuloma Formation and Function in Tuberculosis

2012 ◽  
pp. 127-155 ◽  
Author(s):  
Mohammad Fallahi-Sichani ◽  
Simeone Marino ◽  
JoAnne L. Flynn ◽  
Jennifer J. Linderman ◽  
Denise E. Kirschner
Keyword(s):  
Systems Biology ◽  
Granuloma Formation ◽  
And Function

scholarly journals Cognitive Network Neuroscience

2015 ◽  
Vol 27 (8) ◽  
pp. 1471-1491 ◽  
Author(s):  
John D. Medaglia ◽  
Mary-Ellen Lynall ◽  
Danielle S. Bassett
Keyword(s):  
Cognitive Neuroscience ◽  
Network Science ◽  
Structural Connectivity ◽  
Cognitive Network ◽  
Network Characteristics ◽  
Time Dynamics ◽  
Neuroimaging Data ◽  
Control Learning ◽  
And Function ◽  
Network Neuroscience

Network science provides theoretical, computational, and empirical tools that can be used to understand the structure and function of the human brain in novel ways using simple concepts and mathematical representations. Network neuroscience is a rapidly growing field that is providing considerable insight into human structural connectivity, functional connectivity while at rest, changes in functional networks over time (dynamics), and how these properties differ in clinical populations. In addition, a number of studies have begun to quantify network characteristics in a variety of cognitive processes and provide a context for understanding cognition from a network perspective. In this review, we outline the contributions of network science to cognitive neuroscience. We describe the methodology of network science as applied to the particular case of neuroimaging data and review its uses in investigating a range of cognitive functions including sensory processing, language, emotion, attention, cognitive control, learning, and memory. In conclusion, we discuss current frontiers and the specific challenges that must be overcome to integrate these complementary disciplines of network science and cognitive neuroscience. Increased communication between cognitive neuroscientists and network scientists could lead to significant discoveries under an emerging scientific intersection known as cognitive network neuroscience.

scholarly journals NetFACS: Using network science to understand facial communication systems

2021 ◽  
Author(s):  
Alexander Mielke ◽  
Bridget M. Waller ◽  
Claire Pérez ◽  
Alan V. Rincon ◽  
Julie Duboscq ◽  
...  
Keyword(s):  
Network Analysis ◽  
Communication Systems ◽  
Network Science ◽  
Coding System ◽  
Communication Tool ◽  
Resampling Methods ◽  
Facial Movements ◽  
The Face ◽  
Analyse Data ◽  
And Function

AbstractUnderstanding facial signals in humans and other species is crucial for understanding the evolution, complexity, and function of the face as a communication tool. The Facial Action Coding System (FACS) enables researchers to measure facial movements accurately, but we currently lack tools to reliably analyse data and efficiently communicate results. Network analysis can provide a way to use the information encoded in FACS datasets: by treating individual AUs (the smallest units of facial movements) as nodes in a network and their co-occurrence as connections, we can analyse and visualise differences in the use of combinations of AUs in different conditions. Here, we present ‘NetFACS’, a statistical package that uses occurrence probabilities and resampling methods to answer questions about the use of AUs, AU combinations, and the facial communication system as a whole in humans and non-human animals. Using highly stereotyped facial signals as an example, we illustrate some of the current functionalities of NetFACS. We show that very few AUs are specific to certain stereotypical contexts; that AUs are not used independently from each other; that graph-level properties of stereotypical signals differ; and that clusters of AUs allow us to reconstruct facial signals, even when blind to the underlying conditions. The flexibility and widespread use of network analysis allows us to move away from studying facial signals as stereotyped expressions, and towards a dynamic and differentiated approach to facial communication.

scholarly journals Systems biology analysis of omeprazole therapy in cirrhosis demonstrates significant shifts in gut microbiota composition and function

2014 ◽  
Vol 307 (10) ◽  
pp. G951-G957 ◽  
Author(s):  
Jasmohan S. Bajaj ◽  
I. Jane Cox ◽  
Naga S. Betrapally ◽  
Douglas M. Heuman ◽  
Mitchell L. Schubert ◽  
...  
Keyword(s):  
Systems Biology ◽  
Gut Microbiota ◽  
Serum Gastrin ◽  
Bacterial Overgrowth ◽  
Infectious Complications ◽  
Functional Change ◽  
Microbiota Composition ◽  
And Function ◽  
Stool Microbiota ◽  
Gut Microbiota Composition

Proton pump inhibitors (PPI) have been associated with infectious complications in cirrhosis, but their impact on distal gut microbiota composition and function is unclear. We aimed to evaluate changes in stool microbiota composition and function in patients with cirrhosis and healthy controls after omeprazole therapy. Both 15 compensated cirrhotic patients and 15 age-matched controls underwent serum gastrin measurement, stool microbiota profiling with multitagged pyrosequencing, and urinary metabolic profiling with NMR spectroscopy to assess microbial cometabolites before/after a 14-day course of 40 mg/day omeprazole under constant diet conditions. Results before (pre) and after PPI were compared in both groups, compared with baseline by systems biology techniques. Adherence was >95% without changes in diet or MELD (model for end-stage liver disease) score during the study. Serum gastrin concentrations significantly increased after PPI in cirrhosis (pre 38.3 ± 35.8 vs. 115.6 ± 79.3 pg/ml P < 0.0001) and controls (pre 29.9 ± 14.5 vs. 116.0 ± 74.0 pg/ml, P = 0.001). A significant microbiota change was seen in both controls and cirrhosis after omeprazole (QIIME P < 0.0001). Relative Streptococcaceae abundance, normally abundant in saliva, significantly increased postomeprazole in controls (1 vs. 5%) and cirrhosis (0 vs. 9%) and was correlated with serum gastrin levels ( r = 0.4, P = 0.005). We found significantly reduced hippurate in cirrhosis vs. controls both pre- and postomeprazole and increased lactate in both groups post vs. preomeprazole, whereas dimethylamine (DMA) decreased in cirrhosis only. On correlation network analysis, significant changes in linkages of bacteria with metabolites (hippurate/DMA/lactate) were found postomeprazole, compared with pre-PPI in cirrhosis patients. In conclusion, omeprazole is associated with a microbiota shift and functional change in the distal gut in patients with compensated cirrhosis that could set the stage for bacterial overgrowth.

Complex systems in pulmonary medicine: a systems biology approach to lung disease

2011 ◽  
Vol 110 (6) ◽  
pp. 1716-1722 ◽  
Author(s):  
David A. Kaminsky ◽  
Charles G. Irvin ◽  
Peter J. Sterk
Keyword(s):  
Systems Biology ◽  
Lung Disease ◽  
Clinical Medicine ◽  
Molecular Genetic ◽  
Whole Body ◽  
Pulmonary Medicine ◽  
Pulmonary Physiology ◽  
The Many ◽  
And Function ◽  
Work Done

The lung is a highly complex organ that can only be understood by integrating the many aspects of its structure and function into a comprehensive view. Such a view is provided by a systems biology approach, whereby the many layers of complexity, from the molecular genetic, to the cellular, to the tissue, to the whole organ, and finally to the whole body, are synthesized into a working model of understanding. The systems biology approach therefore relies on the expertise of many disciplines, including genomics, proteomics, metabolomics, physiomics, and, ultimately, clinical medicine. The overall structure and functioning of the lung cannot be predicted from studying any one of these systems in isolation, and so this approach highlights the importance of emergence as the fundamental feature of systems biology. In this paper, we will provide an overview of a systems biology approach to lung disease by briefly reviewing the advances made at many of these levels, with special emphasis on recent work done in the realm of pulmonary physiology and the analysis of clinical phenotypes.

scholarly journals Opportunities at the Interface of Network Science and Metabolic Modeling

2021 ◽  
Vol 8 ◽  
Author(s):  
Varshit Dusad ◽  
Denise Thiel ◽  
Mauricio Barahona ◽  
Hector C. Keun ◽  
Diego A. Oyarzún
Keyword(s):  
Metabolic Flux ◽  
Network Science ◽  
Emergent Properties ◽  
Cell Physiology ◽  
Industrial Biotechnology ◽  
Metabolic Systems ◽  
Balance Analysis ◽  
Metabolic Connectivity ◽  
And Function ◽  
Genome Scale

Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key to understand how cells respond to genetic, environmental, or therapeutic perturbations. Here we discuss the roles of two complementary strategies for the analysis of genome-scale metabolic models: Flux Balance Analysis (FBA) and network science. While FBA estimates metabolic flux on the basis of an optimization principle, network approaches reveal emergent properties of the global metabolic connectivity. We highlight how the integration of both approaches promises to deliver insights on the structure and function of metabolic systems with wide-ranging implications in discovery science, precision medicine and industrial biotechnology.

Aquamoleculomics: A Thermodynamic Cornerstone of Systems Biology

2021 ◽  
Author(s):  
Zilin Nie ◽  
Yanming Nie
Keyword(s):  
Systems Biology ◽  
Thermodynamic Characteristics ◽  
Living System ◽  
Structure And Function ◽  
Biological Processes ◽  
Modern Biology ◽  
Cell Tissue ◽  
Novel Concept ◽  
And Function ◽  
Current Systems

Systems biology has been established for more than a decade in the post-genomic era. With the help of the computational and mathematical tools, systems biology reconstitutes the entire scenario of the cell, tissue and even organism from the pieces data generated in the past decades. However, the modern biology is mainly focusing on the structure and function of the biomolecule, cell, tissue or organ, which are far from the essence of the life because of missing thermodynamic information. It is doubtable that the current systems biology-based omics is no-how to fully understand the dynamic courses of the structure, function and information in life. For this reason, we promote a novel concept of aquamoleculomics, in which the biological structure and function as well as thermodynamic characteristics and bioinformation of the aquamolecule complexes are included in this theoretical model of systems biology. Water is mother of life, matter and matrix of organism. Indeed, the fundamental roles of H2O molecules in biological processes might be dramatically underestimated. Extremely speaking, H2O networks in the living system might be engaged in all the biological processes including building all the biological structures, the residential places of the motherhood molecules as the honeycombs of honeybees.

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