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Omics: a Journal of Integrative Biology

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https://www.readbyqxmd.com/read/28402209/culturomics-a-new-kid-on-the-block-of-omics-to-enable-personalized-medicine
#1
Manousos E Kambouris, Cristiana Pavlidis, Efthymios Skoufas, Michael Arabatzis, Maria Kantzanou, Aristea Velegraki, George P Patrinos
This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine...
April 12, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28375712/ovarian-cancer-differential-interactome-and-network-entropy-analysis-reveal-new-candidate-biomarkers
#2
Dilara Ayyildiz, Esra Gov, Raghu Sinha, Kazim Yalcin Arga
Ovarian cancer is one of the most common cancers and has a high mortality rate due to insidious symptoms and lack of robust diagnostics. A hitherto understudied concept in cancer pathogenesis may offer new avenues for innovation in ovarian cancer biomarker development. Cancer cells are characterized by an increase in network entropy, and several studies have exploited this concept to identify disease-associated gene and protein modules. We report in this study the changes in protein-protein interactions (PPIs) in ovarian cancer within a differential network (interactome) analysis framework utilizing the entropy concept and gene expression data...
April 4, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28282257/human-microbiome-and-learning-healthcare-systems-integrating-research-and-precision-medicine-for-inflammatory-bowel-disease
#3
Kim H Chuong, David R Mack, Alain Stintzi, Kieran C O'Doherty
Healthcare institutions face widespread challenges of delivering high-quality and cost-effective care, while keeping up with rapid advances in biomedical knowledge and technologies. Moreover, there is increased emphasis on developing personalized or precision medicine targeted to individuals or groups of patients who share a certain biomarker signature. Learning healthcare systems (LHS) have been proposed for integration of research and clinical practice to fill major knowledge gaps, improve care, reduce healthcare costs, and provide precision care...
March 10, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388302/genome-wide-association-and-replication-study-of-hepatotoxicity-induced-by-antiretrovirals-alone-or-with-concomitant-anti-tuberculosis-drugs
#4
Zelalem Petros, Ming Ta Michael Lee, Atsushi Takahashi, Yanfei Zhang, Getnet Yimer, Abiy Habtewold, Ina Schuppe-Koistinen, Taisei Mushiroda, Eyasu Makonnen, Michiaki Kubo, Eleni Aklillu
Drug-induced hepatotoxicity (DIH) is a common adverse event that is associated with both antiretroviral (ARV) and anti-tuberculosis drugs (ATD). Moreover, the genetic variations predisposing ARV- and ARV-ATD-induced liver toxicity in African populations are not well investigated, despite the two diseases being the major global health problems in sub-Saharan Africa. We performed a genome-wide association study (GWAS) and replication study to identify the genetic variants linked to the risk of developing DIH due to ARV drugs alone, and ARV-ATD co-treatment in Ethiopian HIV-positive patients...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388301/procalcitonin-biomarker-algorithm-reduces-antibiotic-prescriptions-duration-of-therapy-and-costs-in-chronic-obstructive-pulmonary-disease-a-comparison-in-the-netherlands-germany-and-the-united-kingdom
#5
Marloes E van der Maas, Gertjan Mantjes, Lotte M G Steuten
Antibiotics are often recommended as treatment for patients with chronic obstructive pulmonary disease (COPD) exacerbations. However, not all COPD exacerbations are caused by bacterial infections and there is consequently considerable misuse and overuse of antibiotics among patients with COPD. This poses a severe burden on healthcare resources such as increased risk of developing antibiotic resistance. The biomarker procalcitonin (PCT) displays specificity to distinguish bacterial inflammations from nonbacterial inflammations and may therefore help to rationalize antibiotic prescriptions...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388300/minimal-standards-for-reporting-microrna-target-interactions
#6
Klara Piletič, Tanja Kunej
Epigenomics is one of the leading frontiers of postgenomics medicine. The challenges and prospects ahead in epigenomics are related not merely to technology innovation and clinical implementation but also to science communication. In this context, microRNAs (miRNAs) are an important part of the epigenomic regulatory machinery. As the number of publications reporting miRNA-target interactions (MTIs) is growing rapidly, there is an urgent need to standardize reporting. This study reports (1) an analysis of the published literature and databases reporting validated MTIs, and for the first time to the best of our knowledge (2) suggests a solution as a way forward, the minimum information required for MTI standard reporting...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388299/innovation-analysis-on-postgenomic-biomarkers-glycomics-for-chronic-diseases
#7
Eric Adua, Alyce Russell, Peter Roberts, Youxin Wang, Manshu Song, Wei Wang
Despite decades of investment in biomarker research, we still do not have robust and field-tested biomarkers for many chronic diseases so as to anticipate clinical outcomes and thus move toward personalized medicine. Biomarker innovations have tended to focus on genomics, but next-generation biomarkers from the nascent field of glycomics now offer fresh vistas for innovation in chronic disease biomarkers and systems diagnostics. Glycosylation, regarded as a complex enzymatic process where sugars (glycans) bind to proteins and lipids, affects many human biological functions, including cell signaling, adhesion, and motility...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388298/nf-%C3%AE%C2%BAb-is-a-potential-molecular-drug-target-in-triple-negative-breast-cancers
#8
Paola Poma, Manuela Labbozzetta, Natale D'Alessandro, Monica Notarbartolo
Breast cancer continues to cause significant burden in global health morbidity and mortality. Triple-negative breast cancers (TNBCs) are highly aggressive with poor prognosis and are characterized by lack of expression of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor (Her-2). TNBCs are often resistant to cytotoxic chemotherapy and pose major difficulty in achieving personalized medicine due to their molecular heterogeneity. There is increasing evidence that the aberrant activation of nuclear factor (NF)-κB signaling is a frequent characteristic of TNBCs...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388297/cancer-transcriptome-dataset-analysis-comparing-methods-of-pathway-and-gene-regulatory-network-based-cluster-identification
#9
Seungyoon Nam
Cancer transcriptome analysis is one of the leading areas of Big Data science, biomarker, and pharmaceutical discovery, not to forget personalized medicine. Yet, cancer transcriptomics and postgenomic medicine require innovation in bioinformatics as well as comparison of the performance of available algorithms. In this data analytics context, the value of network generation and algorithms has been widely underscored for addressing the salient questions in cancer pathogenesis. Analysis of cancer trancriptome often results in complicated networks where identification of network modularity remains critical, for example, in delineating the "druggable" molecular targets...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253088/association-between-telomere-length-chronic-kidney-disease-and-renal-traits-a-systematic-review
#10
Oluwatoyin I Ameh, Ikechi G Okpechi, Collet Dandara, André-Pascal Kengne
Telomere length (TL) is an important biological variable that can influence a variety of disease-related complex traits as well as host-environment interactions such as drug and nutritional responses. Chronic kidney disease (CKD) is a common global health challenge especially with the currently aging world population. We conducted a PubMed database search according to the preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines for systematic reviews. Studies in adults (18 years and above) in which TL was determined and correlated with CKD, renal traits, and function were included, while animal model studies were excluded...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253087/genome-wide-association-studies-for-idiosyncratic-drug-induced-hepatotoxicity-looking-back-looking-forward-to-next-generation-innovation
#11
Zelalem Petros, Eyasu Makonnen, Eleni Aklillu
Idiosyncratic drug-induced hepatotoxicity is a formidable challenge for rational drug discovery and development, as well as the science of personalized medicine. There is evidence that hereditary factors, in part, contribute to drug toxicity. This expert analysis and review offer the insights gained, and the challenges ahead, for genome-wide association studies (GWASs) of idiosyncratic drug-induced hepatotoxicity. Published articles on genome-wide and subsequent replication studies were systematically searched in the PubMed electronic database...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253086/oocyte-developmental-competence-insights-from-cross-species-differential-gene-expression-and-human-oocyte-specific-functional-gene-networks
#12
Fernando H Biase
Understanding oocyte developmental competence remains a key challenge for reproductive biology and systems sciences. The transcriptome of oocytes in eutherians is highly complex and is associated with the success of embryo development. Due to sample limitations from humans, animal models are used for investigation of the oocyte transcriptome. Nonetheless, little is known about the diversity of the oocyte transcriptome across eutherians. In this report, comprehensive investigation of 7 public data sets in 4 species, human, macaque, mice, and cattle, shows that 16,572 genes are expressed in oocytes...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253085/water-pipe-shisha-hookah-arghile-smoking-and-secondhand-tobacco-smoke-effects-on-cyp1a2-and-cyp2a6-phenotypes-as-measured-by-caffeine-urine-test
#13
Şenay Görücü Yılmaz, Adrián Llerena, Fernando De Andrés, Ümit Karakaş, Hasan Gündoğar, Kamile Erciyas, Sabit Kimyon, Alper Mete, Kıvanç Güngör, Vural Özdemir
Public policies to stop or reduce cigarette smoking and exposure to secondhand smoke and associated diseases have yielded successful results over the past decade. Yet, the growing worldwide popularity of another form of tobacco consumption, water pipe smoking, has received relatively less attention. To the best of our knowledge, no study to date has evaluated the effects of water pipe smoking on cytochrome P450 (CYP450) activities and drug interaction potential in humans, whereas only limited information is available on the impact of secondhand smoke on drug metabolism...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253084/organic-cation-transporter-2-oct2-slc22a2-gene-variation-in-the-south-african-bantu-speaking-population-and-functional-promoter-variants
#14
Nina C Wilson, Ananyo Choudhury, Nadia Carstens, Demetra Mavri-Damelin
SLC22A2 facilitates the transport of endogenous and exogenous cationic compounds. Many pharmacologically significant compounds are transported by SLC22A2, including the antidiabetic drug metformin, anticancer agent cisplatin, and antiretroviral lamivudine. Genetic polymorphisms in SLC22A2 can modify the pharmacokinetic profiles of such important medicines and could therefore prove useful as precision medicine biomarkers. Since the frequency of SLC22A2 polymorphisms varies among different ethnic populations, we evaluated these in South African Bantu speakers, a majority group in the South African population, who exhibit unique genetic diversity, and we subsequently functionally characterized promoter polymorphisms...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28157411/novel-lipidomic-biomarkers-in-hyperlipidemia-and-cardiovascular-diseases-an-integrative-biology-analysis
#15
Sneha Rai, Sonika Bhatnagar
Lipidomics is a new frontier of omics research and offers much promise for new-generation biomarkers for common complex phenotypes such as hyperlipidemia (HL) and cardiovascular diseases (CVDs). HL is a disorder characterized by increased levels of blood lipids and is a well-established risk factor for CVD. Traditional clinical markers for prognosis of hyperlipidemic individuals are inadequate to forecast or diagnose cardiac events. In this expert review, lipidomic profiles from recent HL and CVD studies were compared with the normolipidemic profile prepared from the Standard Reference Material...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28186866/toward-postgenomics-ophthalmology-a-proteomic-map-of-the-human-choroid-retinal-pigment-epithelium-tissue
#16
Manjunath Dammalli, Krishna R Murthy, Sneha M Pinto, Kalpana Babu Murthy, Raja Sekhar Nirujogi, Anil K Madugundu, Gourav Dey, Bipin Nair, Harsha Gowda, Thottethodi Subrahmanya Keshava Prasad
Ophthalmology and visual health research have received relatively limited attention from the personalized medicine community, but this trend is rapidly changing. Postgenomics technologies such as proteomics are being utilized to establish a baseline biological variation map of the human eye and related tissues. In this context, the choroid is the vascular layer situated between the outer sclera and the inner retina. The choroidal circulation serves the photoreceptors and retinal pigment epithelium (RPE). The RPE is a layer of cuboidal epithelial cells adjacent to the neurosensory retina and maintains the outer limit of the blood-retina barrier...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28186865/preventing-electromagnetic-pulse-irradiation-damage-on-testis-using-selenium-rich-cordyceps-fungi-a-preclinical-study-in-young-male-mice
#17
Xia Miao, Yafeng Wang, Haiyang Lang, Yanyun Lin, Qiyan Guo, Mingjuan Yang, Juan Guo, Yanjun Zhang, Jie Zhang, Junye Liu, Yaning Liu, Lihua Zeng, Guozhen Guo
Networked 21st century society, globalization, and communications technologies are paralleled by the rise of electromagnetic energy intensity in our environments and the growing pressure of the environtome on human biology and health. The latter is the entire complement of environmental factors, including the electromagnetic energy and the technologies that generate them, enacting on the digital citizen in the new century. Electromagnetic pulse (EMP) irradiation might have serious damaging effects not only on electronic equipment but also in the whole organism and reproductive health, through nonthermal effects and oxidative stress...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28186864/within-day-baseline-variation-in-salivary-biomarkers-in-healthy-men
#18
Firman Prathama Idris, Yunxia Wan, Xi Zhang, Chamindie Punyadeera
Saliva is an easily accessible sample and offers practical and noninvasive biomarker solutions as an alternative to blood and urine-based diagnostics. Saliva contains a plethora of biomolecules such as nucleic acids, hormones, proteins, and electrolytes. On the other hand, little is known on the extent to which the biomolecules in saliva vary over time within a given person. This baseline information is crucial for future development of robust saliva-based diagnostics. We have collected unstimulated whole mouth saliva from 20 healthy young men at four times during the day, including before and after a meal...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28118098/performance-ratio-based-resource-allocation-decision-making-in-genomic-medicine
#19
Vasilios Fragoulakis, Christina Mitropoulou, Daphne Katelidou, Ron H van Schaik, Nikolaos Maniadakis, George P Patrinos
In modern healthcare systems, the available resources may influence the morbidity, mortality, and-consequently-the level of healthcare provided in every country. This is of particular interest in developing countries where the resources are limited and must be spent wisely to address social justice and the right for equal access in healthcare services by all the citizens in economically viable terms. In this light, the current allocation is, in practice, inefficient and rests mostly on each country's individual political and historical context and, thus, does not always incorporate decision-making enabled by economic models...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28118095/multiomics-approach-to-novel-therapeutic-targets-for-cancer-and-aging-related-diseases-role-of-sld7-in-yeast-aging-network
#20
Irem E Dayan, Kazim Yalcin Arga, Kutlu O Ulgen
Genome instability has long been implicated as a salient causal factor in aging and age-related diseases such as cancer and neurodegeneration. However, the molecular mechanisms associated with genome instability remain unclear. Recent studies suggest growth signaling in the organism Saccharomyces cerevisiae and in higher eukaryotes might affect oxidative stress and aging/age-related diseases by activating DNA replication stress that causes DNA damage. In this broader integrative biology and clinical context, MDM two binding protein (MTBP) is a binding protein that has a role in activation of the tumor suppressor protein p53...
February 2017: Omics: a Journal of Integrative Biology
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