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Omics: a Journal of Integrative Biology

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https://www.readbyqxmd.com/read/30207826/rise-of-clinical-microbial-proteogenomics-a-multiomics-approach-to-nontuberculous-mycobacterium-the-case-of-mycobacterium-abscessus-uc22
#1
Jayshree Advani, Renu Verma, Oishi Chatterjee, Rex Devasahayam Arokia Balaya, Mohd Altaf Najar, Namitha Ravishankara, Sneha Suresh, Praveen Kumar Pachori, Umesh D Gupta, Sneha M Pinto, Devendra S Chauhan, Srikanth Prasad Tripathy, Harsha Gowda, T S Keshava Prasad
Nontuberculous mycobacterial (NTM) species present a major challenge for global health with serious clinical manifestations ranging from pulmonary to skin infections. Multiomics research and its applications toward clinical microbial proteogenomics offer veritable potentials in this context. For example, the Mycobacterium abscessus, a highly pathogenic NTM, causes bronchopulmonary infection and chronic pulmonary disease. The rough variant of the M. abscessus UC22 strain is extremely virulent and causes lung upper lobe fibrocavitary disease...
September 12, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30183544/interethnic-variability-in-cyp2d6-cyp2c9-and-cyp2c19-genes-and-predicted-drug-metabolism-phenotypes-among-6060-ibero-and-native-americans-ribef-ceiba-consortium-report-on-population-pharmacogenomics
#2
María-Eugenia G Naranjo, Fernanda Rodrigues-Soares, Eva M Peñas-Lledó, Eduardo Tarazona-Santos, Humberto Fariñas, Idania Rodeiro, Enrique Terán, Manuela Grazina, Graciela E Moya, Marisol López-López, Alba P Sarmiento, Luis R Calzadilla, Ronald Ramírez-Roa, Rocío Ortiz-López, Francisco E Estévez-Carrizo, Martha Sosa-Macías, Ramiro Barrantes, Adrián LLerena
Pharmacogenetic variation in Latin Americans is understudied, which sets a barrier for the goal of global precision medicine. The RIBEF-CEIBA Network Consortium was established to characterize interindividual and between population variations in CYP2D6, CYP2C9, and CYP2C19 drug metabolizing enzyme genotypes, which were subsequently utilized to catalog their "predicted drug metabolism phenotypes" across Native American and Ibero American populations. Importantly, we report in this study, a total of 6060 healthy individuals from Ibero-America who were classified according to their self-reported ancestry: 1395 Native Americans, 2571 Admixed Latin Americans, 96 Afro-Latin Americans, 287 white Latin Americans (from Cuba), 1537 Iberians, and 174 Argentinean Ashkenazi Jews...
September 11, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30124362/asthma-microrna-regulome-development-using-validated-mirna-target-interaction-visualization
#3
Simon Fekonja, Peter Korošec, Matija Rijavec, Taja Jeseničnik, Tanja Kunej
Asthma is a common multifactorial complex disease caused by an interaction of genetic and environmental factors. There are no robust biomarkers or molecular diagnostics for asthma or its detailed phenotypic stratification in the clinic. Regulatory and epigenomic factors are priority candidates for asthma biomarker discovery and translational research because this common disease emerges in association with host/environment interactions. In this context, epigenomic molecular events such as microRNA (miRNA) silencing affect asthma susceptibility and severity...
August 20, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30124358/rise-of-deep-learning-for-genomic-proteomic-and-metabolomic-data-integration-in-precision-medicine
#4
Dmitry Grapov, Johannes Fahrmann, Kwanjeera Wanichthanarak, Sakda Khoomrung
Machine learning (ML) is being ubiquitously incorporated into everyday products such as Internet search, email spam filters, product recommendations, image classification, and speech recognition. New approaches for highly integrated manufacturing and automation such as the Industry 4.0 and the Internet of things are also converging with ML methodologies. Many approaches incorporate complex artificial neural network architectures and are collectively referred to as deep learning (DL) applications. These methods have been shown capable of representing and learning predictable relationships in many diverse forms of data and hold promise for transforming the future of omics research and applications in precision medicine...
August 20, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30106669/exciting-history-of-tip60-and-its-companions-in-carcinogenesis-across-the-heterochromatin-landscapes
#5
Mouhamed Idrissou, Khaldoun Rifaï, Marine Daures, Frédérique Penault-Llorca, Yves-Jean Bignon, Dominique Bernard-Gallon
No abstract text is available yet for this article.
August 14, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30106667/do-perineuronal-net-elements-contribute-to-pathophysiology-of-spinal-muscular-atrophy-in-vitro-and-transcriptomics-insights
#6
Didem Dayangac-Erden, Bala Gur-Dedeoglu, Fatma Nazli Eskici, Yasemin Oztemur-Islakoglu, Sevim Erdem-Ozdamar
Spinal muscular atrophy (SMA) is one of the most common childhood onset neurodegenerative disorders in global health whereby novel biomarkers and therapeutic targets are sorely needed. SMA is an autosomal recessive genetic disorder resulting in degeneration of α-motor neurons in the brain stem and spinal cord that leads to mortality in infants worldwide. In majority of the patients, SMA is caused by homozygous deletion of the SMN1 gene. The clinical spectrum of the SMA displays, however, large person-to-person variations where the underlying mechanisms are poorly understood...
August 14, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30106354/the-nile-river-microbiome-reveals-a-remarkably-stable-community-between-wet-and-dry-seasons-and-sampling-sites-in-a-large-urban-metropolis-cairo-egypt
#7
Walaa A Eraqi, Marwa T ElRakaiby, Salwa A Megahed, Noha H Yousef, Mostafa S Elshahed, Aymen S Yassin
World freshwater supplies are in need of microbiome diversity analyses as a first step to future ecological studies, and to monitor water safety and quality. The Nile is a major north-flowing river in Africa that displays both spatial and temporal variations in its water quality. Here, we present the first microbiome analysis of the Nile River water in two seasons: (1) summer representing the wet season, and (2) winter representing the dry season, as sampled around Cairo, the capital of Egypt. Surface river water samples were collected from selected locations along the path of river, and the microbial composition was analyzed by next-generation sequencing of the 16S rRNA gene...
August 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30106353/dissecting-candida-pathobiology-post-translational-modifications-on-the-candida-tropicalis-proteome
#8
Arun H Patil, Keshava K Datta, Santosh Kumar Behera, Sandeep Kasaragod, Sneha M Pinto, Shashanka G Koyangana, Premendu P Mathur, Harsha Gowda, Akhilesh Pandey, Thottethodi Subrahmanya Keshava Prasad
Candida tropicalis belongs to the non-albicans group of Candida, and causes epidermal, mucosal, or systemic candidiasis in immunocompromised individuals. Although the prevalence of candidiasis has increased worldwide and non-albicans Candida (NAC) are becoming more significant, there are very few studies that focus on the NAC biology. Proteins and their post-translational modifications (PTMs) are an integral aspect in the pathobiology of such medically important fungi. Previously, we had reported the largest proteomic catalog of C...
August 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30106352/a-next-generation-sequencing-based-molecular-approach-to-characterize-a-tick-vector-in-lyme-disease
#9
Anil K Madugundu, Babylakshmi Muthusamy, Sreelakshmi K Sreenivasamurthy, Chandra Bhavani, Jyoti Sharma, Bankatesh Kumar, Krishna R Murthy, Raju Ravikumar, Akhilesh Pandey
Next-generation sequencing approaches have revolutionized genomic medicine and enabled rapid diagnosis for several diseases. These approaches are widely used for pathogen detection in several infectious diseases. Lyme disease is a tick-borne infectious disease, which affects multiple organs. The causative organism is a spirochete, Borrelia burgdorferi, which is transmitted by ticks. Lyme disease can be treated easily if detected early, but its diagnosis is often delayed or is incorrect leading to a chronic debilitating condition...
August 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30036157/to-genotype-or-phenotype-for-drug-and-food-safety-exiting-the-technology-echo-chambers
#10
Vural Özdemir, Laszlo Endrenyi, Nezih Hekim, Tanja Kunej, Lotte M Steuten, Simon Springer, Semra Şardaş, Erol Ergüler, Mustafa Bayram
No abstract text is available yet for this article.
August 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30036141/humanome-versus-microbiome-games-of-dominance-and-pan-biosurveillance-in-the-omics-universe
#11
Manousos E Kambouris, Georgios Gaitanis, Yiannis Manoussopoulos, Michael Arabatzis, Maria Kantzanou, George D Kostis, Aristea Velegraki, George P Patrinos
Global governance of pathogens such as Ebola virus and infectious diseases is central to global health, and to innovation in systems medicine. Worrisomely, the gaps in human immunity and healthcare services combined with novel pathogens emerging by travel, biotechnological advances, or the rupture of the host-species barrier challenge infectious diseases' global governance. Such biorisks and biothreats may scale up to global catastrophic biological risks (GCBRs) spatiotemporally, either as individual or as collective risks...
August 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30004300/precision-medicine-goes-global-how-to-get-it-right-four-ways-to-mobilize-scientific-knowledge
#12
Vural Özdemir
Globalization and knowledge mobilization (KM) are twin challenges impacting precision medicine currently. Previous KM models have been largely limited to an implementation framework whereby knowledge is imagined as a billiard ball to be simply rolled over from the laboratory to society and from developed to developing countries. This narrow and sanitized understanding of KM and science as being detached from social forces, human values, politics, and power inequities does not help to achieve robust and responsible emergence of precision medicine, not least because tailored medicines are not simple products ready to use off-the-shelf without customization in each country, local context and society...
August 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30004846/new-targets-for-parkinson-s-disease-adhesion-g-protein-coupled-receptor-b1-is-downregulated-by-amp-activated-protein-kinase-activation
#13
Jae-Sun Choi, Woom-Yee Bae, Seungyoon Nam, Joo-Won Jeong
While progressive dopaminergic neurodegeneration is responsible for the cardinal motor defects in Parkinson's disease (PD), new diagnostics and therapeutic targets are necessary to effectively address this major global health burden. We evaluated whether the adhesion G protein-coupled receptor B1 (ADGRB1, formerly BAI1, brain-specific angiogenesis inhibitor 1) might contribute to dopaminergic neuronal loss. We used bioinformatic analyses, as well as in vitro and in vivo PD models. We report in this study that ADGRB1 is decreased in PD and that the ADGRB1 level is specifically decreased in dopaminergic neurons in the substantia nigra of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-intoxicated mice...
July 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30004845/a-systems-biology-approach-to-understanding-the-pathophysiology-of-high-grade-serous-ovarian-cancer-focus-on-iron-and-fatty-acid-metabolism
#14
Anna Konstorum, Miranda L Lynch, Suzy V Torti, Frank M Torti, Reinhard C Laubenbacher
Ovarian cancer (OVC) is the most lethal of the gynecological malignancies, with diagnosis often occurring during advanced stages of the disease. Moreover, a majority of cases become refractory to chemotherapeutic approaches. Therefore, it is important to improve our understanding of the molecular dependencies underlying the disease to identify novel diagnostic and precision therapeutics for OVC. Cancer cells are known to sequester iron, which can potentiate cancer progression through mechanisms that have not yet been completely elucidated...
July 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30004844/genetic-susceptibility-for-cervical-cancer-in-african-populations-what-are-the-host-genetic-drivers
#15
Oppah Kuguyo, Nomsa Tsikai, Nicholas E Thomford, Thulani Magwali, Mugove G Madziyire, Charles F B Nhachi, Alice Matimba, Collet Dandara
Human papillomavirus (HPV) is an essential but not a sufficient cervical cancer etiological factor. Cancer promoters, such as host genetic mutations, significantly modulate therapeutic responses and susceptibility. In cervical cancer, of interest have been viral clearing genes and HPV oncoprotein targets, for which conflicting data have been reported among different populations. This expert analysis evaluates cervical cancer genetic susceptibility biomarkers studied in African populations. Notably, the past decade has seen Africa as a hotbed of biomarker and precision medicine innovations, thus potentially informing worldwide biomarker development strategies...
July 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30004843/type-2-diabetes-mellitus-integrative-analysis-of-multiomics-data-for-biomarker-discovery
#16
Siqi Ge, Youxin Wang, Manshu Song, Xingang Li, Xinwei Yu, Hao Wang, Jing Wang, Qiang Zeng, Wei Wang
Increased fasting plasma glucose (FPG) is an independent risk factor for type 2 diabetes mellitus (T2DM). The development of systems biology technologies for integration of multiomics data is crucial for predicting increased FPG levels. In this case-control study, immunoglobulin (Ig) G glycosylation profiling and genome-wide association analyses were performed on 511 participants, and among them 76 had increased FPG (aged 47.6 ± 6.14 years), and 435 had decreased or fluctuant FPG (aged 47.9 ± 6.08 years)...
July 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30004842/toward-precision-nutrition-commercial-infant-formulas-and-human-milk-compared-for-stereospecific-distribution-of-fatty-acids-using-metabolomics
#17
Thiago I B Lopes, Mayara C Cañedo, Fernanda M P Oliveira, Glaucia B Alcantara
Precision nutrition and nutrimetabolomics are emerging omics technology applications in public health. In this context, the infant formula (IF) is a manufactured foodstuff that aims to match the composition of human milk (HM), especially the lipid profile. The IF manufacturers have achieved relative success in matching the predominant fatty acid (FAs) profiles, but the stereospecific structures of the triacylglycerides in HM require deeper analyses with system sciences. We employed NMR-based metabolomics to compare the lipid profiles of 12 commercial IF samples and 10 HM samples...
July 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30004841/unlocking-human-brain-metabolism-by-genome-scale-and-multiomics-metabolic-models-relevance-for-neurology-research-health-and-disease
#18
Mustafa Sertbas, Kutlu O Ulgen
Neurology research and clinical practice are transforming toward postgenomics integrative biology. One such example is the study of human brain metabolism that is highly sophisticated due to reactions occurring in and between the astrocytes and neurons. Because of the inherent difficulty of performing experimental studies in human brain, metabolic network modeling has grown in importance to decipher the contribution of brain metabolite kinetics to human health and disease. Multiomics system science-driven metabolic models, using genome-scale and transcriptomics Big Data, offer the promise of new insights on metabolic networks in human brain...
July 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29927718/multiomics-data-triangulation-for-asthma-candidate-biomarkers-and-precision-medicine
#19
Matija Pecak, Peter Korošec, Tanja Kunej
Asthma is a common complex disorder and has been subject to intensive omics research for disease susceptibility and therapeutic innovation. Candidate biomarkers of asthma and its precision treatment demand that they stand the test of multiomics data triangulation before they can be prioritized for clinical applications. We classified the biomarkers of asthma after a search of the literature and based on whether or not a given biomarker candidate is reported in multiple omics platforms and methodologies, using PubMed and Web of Science, we identified omics studies of asthma conducted on diverse platforms using keywords, such as asthma, genomics, metabolomics, and epigenomics...
June 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29927717/drug-targeting-and-biomarkers-in-head-and-neck-cancers-insights-from-systems-biology-analyses
#20
Tania Islam, Rezanur Rahman, Esra Gov, Beste Turanli, Gizem Gulfidan, Anwarul Haque, Kazım Yalçın Arga, Nurul Haque Mollah
The head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in the world, but robust biomarkers and diagnostics are still not available. This study provides in-depth insights from systems biology analyses to identify molecular biomarker signatures to inform systematic drug targeting in HNSCC. Gene expression profiles from tumors and normal tissues of 22 patients with histological confirmation of nonmetastatic HNSCC were subjected to integrative analyses with genome-scale biomolecular networks (i...
June 2018: Omics: a Journal of Integrative Biology
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