Category Archives: Bioinformatics

Bioinformatics, neuroinformatics, immunoinformatics, health informatics, healthcare informatics, medical informatics, computational biology

Whole Grain Cereal, Obesity, and the PI3K/Akt Pathway

Whole grain cereal contains fibers, minerals, vitamins, and phytochemicals. Whole grain cereal has been found to inhibit body weight gain and non-alcoholic fatty liver (Lee et al., 2017). Whole grain cereal could decrease the atrophy-associated factors, fat pad mass, and … Continue reading

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Psychoneuroimmunology Database

The Database of Psychoneuroimmunology (DPNI) The Psychoneuroimmunology (PNI) Portal and Knowledge Base Potential Biomarkers for Anxiety The Database of Biomarkers: Depression Mind-Body Medicine About Meditation: The Portal and Knowledge Base The Nervous System Neuroinformatics The Database of Cytokines Chronobiology The … Continue reading

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The Database of Biological Rhythms (DBBR)

The Database of Biological Rhythms (DBBR) The Chronobiology Portal: Chronobiology, Chronotherapy, Circadian Rhythms, and More Journals about Biological Rhythms and Chronobiology   Biological Rhythm Research Chronobiology International Journal of Biological Rhythms Journal of Chronotherapy and Drug Delivery Journal of Circadian … 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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Microglia, Polydendrocytes, Ependymal cells, and the Embryonic Neural Tube

Microglia are macrophages in the brain. Macrophages are the immune cells in the blood and other parts of the body. Microglia can be activated upon neuronal damages or infections, to destroy foreign stuff or pathogens, as well as necrotic tissues. … Continue reading

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Glia, Astrocytes, Oligodendrocytes, and Schwann Cells

Glia have a close relationship with neurons but this relationship has not been fully understood. Glia are essential partners to neurons and may influence many functions including neuronal and metabolic activities, neurotransmitter kinetics, as well as the blood flow. Glial … Continue reading

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Synapses, Gap Junctions, and Glia: Their Structures, Functions, and Features

Synapses are the regions between the terminal of an axon and the receptors on other cells. Neurotransmitters can bring the messages across the synapses. Synapses can be open or enclosed, large or small. Synaptic inputs can affect the neuron activities. … Continue reading

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Neurotransmitters and Their Functions

There are different types of neurotransmitters. For example, glutamate (glu) is involved in the excitation of the central nervous system (CNS). Aspartate (asp) is involved in the excitation of the brain and spinal cord. Gama-aminobutyric acid (GABA) is involved in … Continue reading

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Structure of the Neurons: Dendrites, Axons, and Membrane Potentials

Types of cells in the nervous system There are two types of cells in the nervous system. One type of cells are called neurons, the other type of cells are called glia. Studies have found that there are about 86 … Continue reading

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Neuroscience Data and Neuroinformatics

Neuroscience Data and Neuroinformatics   Neuroscience Data   At least 50% genes of the mammalian genome are expressed by the nervous system (Sutcliffe et al., 1991). To understand brain-related diseases, it is necessary to map and study the expression patterns … Continue reading

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The Applications and Combination of Bioinformatics, Medical informatics, and Neuroinformatics

The Applications and Combination of Bioinformatics, Medical informatics, and Neuroinformatics   Mental disorders and other brain disorders such as anxiety, depression, schizophrenia, and visual impairments may account for at least one third of the worldwide burden of diseases (Wittchen et … Continue reading

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Neuroinformatics Software and Ontology Tools

Neuroinformatics Software and Ontology Tools     Category Source Name Purposes/Features/Methods Contents Applications URL References Neuroimaging Informatics Tools BrainVisa (BV) For high resolution MR images To quantify global and regional variances About cortical anatomy A plug-in application for structural analysis … Continue reading

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Neuroinformatics Databases about the Brain: Different Species

Neuroinformatics Databases about the Brain: Different Species   Species Source Name Purposes/Features/Methods Contents Applications URL References Mouse 3D digital atlas database of the mouse brain Lower spatial resolution images were utilized to enhance time efficiency for morphological phenotyping The in … Continue reading

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