Category Archives: Systems Biology

Reviews of Systems Biology

Lipidomics, Circadian Rhythms, and Chronobiology

Lipids are essential for biological mechanisms, from serving as signaling molecules to maintaining cellular processes. They are fundamental elements that compose cellular membranes. They are also the basis of energy storage. In addition to all of these functions, lipids are … Continue reading

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Glucocorticoids, Shift Work, and the Central and Peripheral Clocks

The circadian system can be influenced by both the environment and human activities. For example, shift work can cause a de-synchronization between the circadian timing system in the human body and the external environment (Cuesta et al, 2014). Such disruption … Continue reading

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Negative Impacts of Electronic Devices on Sleep

The decrease of sleep time and quality in recent decades has led to unhealthy lifestyle and negative impacts on health and performances. A recent survey of more than 1,500 adults in the U.S. showed that about ninety percent of them … Continue reading

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The Effects of Artificial Morning Light on Cognition

Chronic sleep restriction (SR) has detrimental influences on cognitive functions. Although such effects can be reduced by light exposure, it is necessary to find out if naturalistic light conditions such as dawn simulating light can promote daytime cognitive functions continuously … Continue reading

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The Effects of Melatonin on Sleep Disorders and Pediatric Problems

Melatonin is a hormone produced by the pineal gland. It is chronobiotic and crucial in the regulation of the circadian clock. As an antioxidant and free radical scavenger, it has many important functions such as anti-inflammation (Bruni et al., 2014). … Continue reading

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The Database of Biomarkers: Depression – fMRI Biomarkers

The Database of Biomarkers: Depression – fMRI Biomarkers •    Potential Biomarkers: Activation patterns: “greater and more sustained signals in three regions: BA24 (dorsal anterior cingulate), BA31 (posterior cingulate), and BA6 (prefrontal cortex)” Potential Applications: Diagnostic biomarkers in late-life anxious depression … Continue reading

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The Database of Biomarkers: Depression – EEG Biomarkers

The Database of Biomarkers: Depression – EEG Biomarkers •    Potential Biomarkers: “Midline and right frontal (MRF) cortical area,  early decreases in theta-band cordance” Potential Applications: Predictive biomarker of remission in major depressive disorder (MDD) References: Cook IA, Hunter AM, Abrams … Continue reading

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The Database of Biomarkers: Depression – Proteomic and Pathway Biomarkers

The Database of Biomarkers: Depression – Proteomic and Pathway Biomarkers •    Potential Biomarkers: The tryptophan-kynurenine pathway Detections: Increased indoleamine 2,3-dioxygenase activity Potential Applications: Diagnostic biomarkers References: Christmas DM, Potokar J, Davies SJ. A biological pathway linking inflammation and depression: activation … Continue reading

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The Database of Biomarkers: Depression – Epigenetic Biomarkers

The Database of Biomarkers: Depression – Epigenetic Biomarkers •    Potential Biomarkers: “DNA methylation profiles of CpG I at the promoters of the brain-derived neurotrophic factor (BDNF)” Potential Applications: Diagnostic biomarker References: Fuchikami M, Morinobu S, Segawa M, Okamoto Y, Yamawaki … Continue reading

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The Database of Biomarkers: Depression – MicroRNA Biomarkers

The Database of Biomarkers: Depression – MicroRNA Biomarkers •    Potential Biomarkers: miR-30e, the polymorphism ss178077483 Potential Applications: Diagnostic biomarker for major depressive disorder (MDD) risks References: Xu Y, Liu H, Li F, Sun N, Ren Y, Liu Z, Cao X, … Continue reading

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The Database of Biomarkers: MicroRNA Biomarkers

The Database of Biomarkers: MicroRNA Biomarkers •    Associated diseases/conditions: Obesity and type 2 diabetes Potential Biomarkers: Serum miR-138, miR-15b, miR-376a (obesity); combination of miR-503 and miR-138 (diabetes) Potential Applications: Predictive biomarkers References: Pescador N, Pérez-Barba M, Ibarra JM, Corbatón A, … Continue reading

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The Database of Biomarkers: MicroRNA Biomarkers – Psychiatric Disorders

The Database of Biomarkers: MicroRNA Biomarkers – Psychiatric Disorders •    Associated diseases/conditions: Mild Cognitive Impairment (MCI), age-related brain changes Potential Biomarkers: Brain-enriched plasma the “miR-132 family” (miR-128/miR-491-5p, miR-132/miR-491-5p and mir-874/miR-491-5p) and the “miR-134 family” (miR-134/miR-370, miR-323-3p/miR-370 and miR-382/miR-370) Potential Applications: … Continue reading

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The Database of Biomarkers: MicroRNA Biomarkers – Cardiovascular Diseases

The Database of Biomarkers: MicroRNA Biomarkers – Cardiovascular Diseases •    Associated diseases/conditions: Atherosclerosis and stroke Potential Biomarkers: Serum miR-21 and miR-221 Potential Applications: Predictive biomarkers References: Tsai PC, Liao YC, Wang YS, Lin HF, Lin RT, Juo SH. Serum microRNA-21 … Continue reading

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The Database of Biomarkers: MicroRNA Biomarkers – Cancers

Associated diseases/conditions: Breast cancer in the Mexican population   Potential Biomarkers: Serum circulating miR-145, miR-155 and miR-382   Potential Applications: Diagnostic biomarkers   References: Mar-Aguilar F, Mendoza-Ramírez JA, Malagón-Santiago I, Espino-Silva PK, Santuario-Facio SK, Ruiz-Flores P, Rodríguez-Padilla C, Reséndez-Pérez D. … Continue reading

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The Database of Biomarkers: Proteomic and Pathway Biomarkers

Associated diseases/conditions: Depression   Potential Biomarkers: “Tumor Necrosis Factor (TNF) and its targets in the inflammatory cytokine pathway”   Detections: Protein expressions   Potential Applications: “Predictive biomarkers for treatment response (to the selective serotonin reuptake inhibitor (SSRI) antidepressant escitalopram)”   … Continue reading

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The Database of Biomarkers: Proteomic and Pathway Biomarkers – Cancers

Associated diseases/conditions: Non-small cell lung cancer (NSCLC)   Potential Biomarkers: Insulin-like growth factor (IGF) pathway   Detections: Protein expressions, serum levels   Potential Applications: Predictive biomarkers (tumor progression and patient outcomes)   References: Shersher DD, Vercillo MS, Fhied C, Basu … Continue reading

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Bioinformatics Databases and Tools for the Discovery of Proteomic and Pathway Biomarkers

BioLayout (http://www.biolayout.org/) Feature: “For the visualization and analysis of network graphs” Cytoscape (http://www.cytoscape.org/) Feature: “Network visualization” E-Cell (http://www.e-cell.org/) Feature: Computational models GelBank (http://gelbank.anl.gov/) Feature: “comparison of 2DE patterns in the context of proteome sequence queries” Gene Ontology (http://www.geneontology.org/) Feature: “Standardizing … Continue reading

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Bioinformatics Resources for MicroRNA (miRNA) Studies and Biomarker Discovery

CircuitsDB (http://biocluster.di.unito.it/circuits/) Feature: “MicroRNA / Transcription Factor Regulatory Circuits in Human and Mouse” deepBase (http://deepbase.sysu.edu.cn/) Feature: “For annotating and discovering small and long ncRNAs” Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) Feature: “The miRNA expression profile” HOCTARdb (http://hoctar.tigem.it/) Feature: “microRNA target prediction” … Continue reading

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The integration of various “omics” technologies in systems biology for better diagnosis and treatment

With the advancements in the “omics” technologies and the information technology, systems biology has become an important approach for biomarker discovery. These technologies allow faster and cheaper analyses of gene expression, protein interactions, signaling pathways, and metabolic mechanisms. In this … Continue reading

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Systems biology approaches for the pharmacokinetic/pharmacodynamic (PK/PD) modeling in drug discovery and development

Systems biology-enabled computational modeling can be useful in almost every step of drug discovery and development, including drug target identification and clinical outcome analysis. Various modeling strategies can be used at different stages. For example, during the basic scientific research … Continue reading

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Systems biology strategies are useful for biomarker identification in traumatic brain injury (TBI)

The identification of biomarkers may have a significant influence on patient care. Biomarkers may be used for better diagnosis, disease profiling, research design, and drug target discovery. For instance, biomarkers have been considered to be critical in the management of … Continue reading

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Systems biology and “omics” technologies for better drug discovery and outcome studies in cancer treatment

The multiple platforms using the “omics” technologies and the integration of systems biology approaches including both experimental and computational methods would support both drug target discovery and clinical outcome studies, especially in cancer treatment. For instance, immunotherapies have become an … Continue reading

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Systems medicine, P4 medicine, and an integrative “Human Model”

Conventional practice in Western medicine focuses on doctors’ “reactive” interventions in response to the occurrence of diseases. With the advancement of genomics, proteomics, and various high efficient “omics” technologies, the multidimensional networks of the human body can be investigated for … Continue reading

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Review of Systems Biology Approaches: Detecting Signaling Pathways in Neurons

Temporal dynamics and spatial features are important factors in cell responses including synaptic plasticity. The complex network and interactions among neuronal signaling pathways result in emergent dynamical behaviors associated with synaptic plasticity. Signaling pathways can be activated by transmembrane receptors … Continue reading

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