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The study of severe cutaneous drug hypersensitivity reactions from a systems biology perspective.

PURPOSE OF REVIEW: Stevens-Johnson syndrome and toxic epidermal necrolysis are severe hypersensitivity reactions, the majority of which are … these diseases and suggest ways in which the data can be combined and reanalyzed using integrative systems biology techniques. We also suggest future lines of research using recent technology that could shed further light on their underlying mechanisms.

The silicon trypanosome: a test case of iterative model extension in systems biology.

The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and an…

A systems biology perspective on rational design of peptide vaccine against virus infections.

With the recent onset of influenza A (H1N1) pandemic, the need for improved vaccines against virus infections has become an international pr … in an interaction network. Therefore, single viral peptide alone fails to provide optimal immunity. Systems biology offers a systems-level perspective of how the various arms of the immune response are integrated to give immune response, as well as how host and virus interact, thereby providing an integrated approach to select the most promising candidates for pe …

The heat shock response: systems biology of proteotoxic stress in aging and disease.

All organisms sense and respond to environmental and physiological stress by inducing cell stress responses that protect core biosynthetic processes such as DNA repair, protein folding, and clearance of damaged proteins. Of these, the heat shock response (HSR) protects the proteome against acute exposure to elevated temperatures, oxidants, and heavy metals, for example, and to the chronic expression of metastable, aggregation-prone proteins associated with aging and diseases of protein conformation. Induction of the HSR leads to the rapid and robust expression of molecular chaperones and other

Quality and safety of Chinese herbal medicines guided by a systems biology perspective.

Chinese herbal medicines, often referred as Chinese materia medica (CMM), are comprised of a complex multicomponent nature. The activities are aimed at the system level via interactions with a multitude of targets in the human body. This review aims at the toxicity aspects of CMM and its preparations at the different steps of production; harvesting, processing and the final formulation. The historic perspective and today's issues of the safety of CMM are introduced briefly, followed by the descriptions of the toxic CMM in the current Chinese Pharmacopoeia (2005). Subsequently, several aspects

Empirically Informed Blood Vessel Network Reconstruction for Multimodality Image-Based Vascular Systems Biology.

OBJECTIVE: Reconstruction of vascular topology from imperfect 3D imaging data is essential for accurate hemodynamic simulations. Therefore, we developed a "gap-filling" method predicated on vascular biology and empirical patterns to restore incomplete vessels, independent of the imaging modality and spatial resolution employed. METHODS: Our gap-filling algorithm reconstructs a vascular network based on distributions of its extant morphological features and employs different rules for healthy and tumor tissue. Algorithm performance was evaluated on (i) incomplete synthetic vascular trees with

Systems biology of Alzheimer's Disease: a scoping review of key pathways and mechanisms.

Alzheimer’s Disease (AD) is a progressive and ultimately fatal neurodegenerative disorder, representing the most common form of dementia and … iomarkers for early detection, prediction of progression, and for evaluating response to treatment. Systems biology provides a powerful framework for this effort, leveraging multi-omics for biomarker discovery and elucidation of critical Disease pathways. The purpose of this scoping review is to identify and inform the field on key pathways being intensively inve …

Determining parameter impact in systems biology models via sensitivity analysis: a comparative approach.

Mathematical modeling is a powerful tool to understand biological phenomena, predict behavior, and guide experiments. Model parameters represent experimentally derived rates, and it can be challenging to understand how parameters affect the system's output(s). Global sensitivity analysis (GSA) can help determine how uncertainty in model outcomes can be attributed to parameters. Methods like Sobol' indices provide detailed analysis but at a high computational cost. Thus, it may be necessary to precede it by another method to reduce the parameter space. Morris Method Screening (MMS) is a qualita

Sea buckthorn for future foods: bioactive mechanisms, synthetic biology, and precision delivery systems.

Sea buckthorn (Hippophae rhamnoides) is a multifunctional plant rich in bioactive compounds, exhibiting antioxidant, anti-inflammatory, cardioprotective, and metabolic regulatory properties. With increasing interests in natural health-promoting ingredients, sea buckthorn has emerged as a promising candidate for functional and personalized foods. This review provides a comprehensive synthesis of recent advances in the identification and understanding of mechanisms of sea buckthorn's bioactive constituents, including flavonoids, carotenoids, fatty acids, vitamins, and polysaccharides, along with

Deciphering Membrane Protein Complexes in Plasmodium falciparum Gametocytes via Integrative Structural Systems Biology.

Malaria is caused by protozoan parasites of the genus Plasmodium that proliferate asexually in human erythrocytes. During each replication cycle, a small fraction of the parasites differentiates into gametocytes. These sexual gametocytes are the only stages of the parasite that can infect the mosquito vector and transmit malaria. Their progression and maturation depend on a profound remodeling of the erythrocyte. This is achieved by the export of parasite proteins into the erythrocyte, leading to structural and mechanistic changes in the cytoskeleton and membrane of the host cell, crucial for

Circulating Tumor Function: A Systems Biology Framework for Liquid Biopsy in Genitourinary Cancers.

Liquid biopsy enables minimally invasive detection and longitudinal monitoring of tumor-derived material in blood and urine. In genitourinar … that determine progression and treatment response. We propose circulating tumor function (CTF) as a systems biology framework for integrating tumor-derived and host-derived genomic, regulatory, metabolic, redox, and immune signals obtained through serial liquid biopsy. CTF is not a single analyte or assay; rather, it is an inference model intended to generate int …

Longitudinal Meta-cohort study protocol using systems biology to identify vaccine safety biomarkers.

The International Network of Special Immunization Services (INSIS) was established to investigate the causes and risk factors of rare adverse events following immunizations (AEFIs) and develop immunization strategies for mitigating or preventing risk for individuals with prior AEFIs or at risk of AEFIs. INSIS integrates clinical data with multi-omic technologies (e.g., transcriptomics, proteomics, metabolomics) through a global consortium of clinical networks, leading immunology, pharmacogenomics teams to uncover the molecular mechanisms behind AEFIs. The network ensures accurate and standardi

Systems biology approaches investigating mitochondrial dysfunction in cyanotic heart disease: a systematic review.

BACKGROUND: Cyanotic congenital heart disease (CCHD) affects over 3 million individuals globally and can progress to heart failure. Mitochondrial dysfunction is well established in adult heart failure and is also a central feature of CCHD. CCHD cyanosis itself contributes to further mitochondrial dysfunction. Systems biology methods detail the epigenomic, transcriptomic, and metabolomic profile of biological samples. This systematic review highlights CCHD systems biology literature related to mitochondrial dysfunction. METHODS: OVID/Medline was searched between January 2010 and June 2025. Stu…

Systems biology approach uncovers candidates for kidney-heart interorgan crosstalk after myocardial infarction.

Myocardial infarction (MI) and subsequent heart failure are frequently accompanied by chronic kidney disease, further impairing outcomes and complicating treatment. To better understand heart-kidney crosstalk, we used RNA sequencing data to infer interorgan signalling after experimentally induced MI in mice, focusing on secreted biomolecules and interorgan cross talk that may drive cardiorenal syndrome (CRS). To assess acute and chronic effects, we examined kidneys at 5d and 28d post-MI, evaluating changes in renal gene expression and fibrosis. During the acute phase 5d post-MI, several genes

Тип перегонки 1 диабет через ось эндоканнабиноидома-микробиота: системная биологическая перспектива.

Тип 1 диабет (T1D) давно признан аутоиммунным заболеванием на основе Т. Вместе с тем все больше фактов свидетельствует об участии в его развитии факторов, связанных с метаболизмом, подстрекательством и кишечной микробиотой. Эндоканнабиноидная система (ЭКС), являющаяся одним из ключевых регуляторов иммунного и метаболического гомеостаза, все чаще привлекается к аутоиммунной патофизиологии, в частности благодаря ее взаимодействию с кишечными метаболитами. В этой гипотетической статье подчеркивается необходимость пересмотра патофизиологии Т1D путем интеграции дисфункции ЭКС, кишечного дисбиоза и

Совпадение в аннотации оригинала
Type 1 diabetes (T1D) has long been recognized as a T-cell-driven autoimmune disease. However, growing evidence highlights the involvement o … T1D pathophysiology by integrating ECS dysfunction, gut dysbiosis, and metabolic imbalances into a systems biology framework. The proposed Endocannabinoidome-Microbiota (ECBoM) model highlights a shared hallmark of autoimmunity-SCFA depletion, increased intestinal permeability, and ECS dysregulation-as key drivers of chronic inflammation and immune dysfunction. …

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

INTRODUCTION: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. METHODS: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue-…

Neutrophil biology in injuries and diseases of the central and peripheral nervous systems.

The role of inflammation in nervous system injury and disease is attracting increased attention. Much of that research has focused on microglia in the central nervous system (CNS) and macrophages in the peripheral nervous system (PNS). Much less attention has been paid to the roles played by neutrophils. Neutrophils are part of the granulocyte subtype of myeloid cells. These cells, like macrophages, originate and differentiate in the bone marrow from which they enter the circulation. After tissue damage or infection, neutrophils are the first immune cells to infiltrate into tissues and are dir

Integrative systems biology characterizes immune-mediated neurodevelopmental changes in murine Zika virus microcephaly.

Characterizing perturbation of molecular pathways in congenital Zika virus (ZIKV) infection is critical for improved therapeutic approaches. Leveraging integrative systems biology, proteomics, and RNA-seq, we analyzed embryonic brain tissues from an immunocompetent, wild-type congenital ZIKV infection mouse model. ZIKV induced a robust immune response accompanied by the downregulation of critical neurodevelopmental gene programs. We identified a negative correlation between ZIKV polyprotein abundance and host cell cycle-inducing proteins. We further captured the downregulation of genes/protein…

Identifying novel mechanisms of abdominal aortic aneurysm via unbiased proteomics and systems biology.

BACKGROUND: Abdominal aortic aneurysm (AAA), characterized by a continued expansion of the aorta, leads to rupture if not surgically repaired. Mice aid the study of disease progression and its underlying mechanisms since sequential studies of aneurysm development are not feasible in humans. The present study used unbiased proteomics and systems biology to understand the molecular relationship between the mouse models of AAA and the human disease. METHODS AND RESULTS: Aortic tissues of developing and established aneurysms produced by either angiotensin II (AngII) infusion in Apoe -/- and Ldlr …

Potential Candidates for Biomarkers in Bipolar Disorder: A Proteomic Approach through Systems Biology.

Bipolar disorder (BD) is one of the most disabling diseases characterized by severe humor fluctuation. It is accompanied by cognitive and functional impairment in addiction to high suicide rates. BD is often underdiagnosed and treated incorrectly because many of the reported symptoms are not exclusive to the disorder. Once the diagnosis is exclusively clinical, it is not possible to state precisely. From that, proteomic approaches were used to identify, in a large scale, all proteins involved in cellular or tissue processes. This review aggregate data from blood proteomes, by using protein ass