Category Archives: Systems Medicine

Reviews of methods in systems medicine.

Translational Medicine and Drug Discovery

Recent development in translational medicine provides a connection between basic scientific studies and clinical practice. Such an initiative may support the patient-centered objectives in both research and clinical environments. It may also improve the drug discovery procedure by allowing for … Continue reading

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Challenges in Biomarker Discovery

Although biomarkers have been considered more and more important, it is still very difficult to identify and validate effective and useful biomarkers. The obstacles in the biomarker identification include both technical and theoretical reasons. For example, methods for identifying pathology-type … Continue reading

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Biomarkers of Seasonal Allergic Rhinitis (SAR)

Seasonal allergic rhinitis (SAR) is not just a commonly seen health problem in certain seasons. It is also a risk factor that can lead to asthma among many people. Nasal allergies can promote bone-marrow eosinophil generation through cytokines such as … Continue reading

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Systems Biology and Biomarkers in Neuropsychiatry

Neuropsychiatric (NP) disorders such as autism spectrum disorders (ASD) are the leading causes of disability around the world. However, because of their complexity, the etiology and pathophysiology of NP diseases are still mostly unknown. Such complexity may be caused by … Continue reading

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Biomarkers, Oncology, and Precision Medicine

The identification of biomarkers is becoming more and more important in biomedicine, especially for the clinical practice. This is because biomarkers often contain valuable information about the pathology of the diseases such as cancers. Such information is useful for better … Continue reading

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Cytomegalovirus (CMV) Infections, Psychological Stress, and Mood Disorders

Cytomegalovirus (CMV) is a beta-herpes virus that may be associated with aging and many health problems. The infection of CMV can be asymptomatic. However, higher levels of serum cytokines including TNF-alpha and IL-6 have been observed in CMV infections, which … Continue reading

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Stress, Skin Disorders, and Psychoneuroimmunology

With a history of about 30 years, psychoneuroimmunology (PNI) studies the interactions among psychological activities, the nervous system, and the immune system. In the area of dermatology, many dermatologic diseases have been found to be related to mental and psychological … 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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Journals Focusing on Biomarkers

Biomarker Insights Biomarker Research Biomarkers Biomarkers and Genomic Medicine Biomarkers in Cancer Biomarkers in Medicine Cancer Biomarkers Cancer Epidemiology, Biomarkers & Prevention Current Biomarker Findings Genetic Testing and Molecular Biomarkers Journal of Biomarkers Journal of Biomarkers in Drug Development Journal … 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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