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Omics: a Journal of Integrative Biology

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https://www.readbyqxmd.com/read/30388053/meta-microrna-biomarker-signatures-to-classify-breast-cancer-subtypes
#1
Yasemin Oztemur Islakoglu, Senem Noyan, Alp Aydos, Bala Gur Dedeoglu
Breast cancer is one of the leading causes of morbidity and mortality that is in need of novel diagnostics and therapeutics. Meta-analysis of microarray data offers promise to combine studies and provide more robust results. We report here a molecular classification of pathological subtypes (estrogen receptor [ER], progesterone receptor [PR], and Human Epidermal Growth Factor Receptor 2 [HER2]) of breast cancers with microRNA (miRNA)-dependent signatures. A ranking-based meta-analysis approach was applied to eight independent microarray data sets and meta-miRNA lists were obtained that are specific to each breast cancer subtype...
November 2, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30362880/is-space-the-new-frontier-for-omics-mars-omics-planetary-science-and-the-next-generation-technology-futurists
#2
Mustafa Bayram, Remziye Aşar, Vural Özdemir
Omics technologies are key to research and innovation in human health, food and nutrition, drugs, agriculture, and ecology research. Yet, the actual scope of applications is much broader. One emerging possibility is planetary science driven in part by current debates on and possibilities for travel to Mars. In July 2018, radar evidence has suggested the presence of subglacial liquid water in a 20-km-wide zone, likely a saltwater lake, in the Planum Australe region in the south pole of Mars. If confirmed, this will be a promising place to search for microbial life on the red planet...
October 26, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30207826/rise-of-clinical-microbial-proteogenomics-a-multiomics-approach-to-nontuberculous-mycobacterium-the-case-of-mycobacterium-abscessus-uc22
#3
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/30346884/drug-target-prioritization-for-alzheimer-s-disease-using-protein-interaction-network-analysis
#4
Avijit Podder, Mansi Pandit, Latha Narayanan
Alzheimer's disease (AD) is an age-related neurodegenerative disorder that accounts for numerous deaths worldwide. AD is the most common cause of dementia, characterized by accumulation of fibrous amyloid beta protein in the brain with clinical symptoms, such as loss of intellectual and social skills, gradually leading to the death of brain cells. The genetic complexity of AD during disease progression requires a systems-level understanding to design viable therapeutics. We present an integrative computational analysis to prioritize AD-associated genes outlined through a protein-protein interaction network...
October 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30346883/human-optic-nerve-an-enhanced-proteomic-expression-profile
#5
Gayathree Karthikkeyan, Yashwanth Subbannayya, Mohd Altaf Najar, Varshasnata Mohanty, Sneha M Pinto, Cynthia Arunachalam, Thottethodi Subrahmanya Keshava Prasad, Krishna R Murthy
Ophthalmology and visual health are new frontiers for postgenomic research and technologies such as proteomics. In this context, the optic nerve and retina extend as the outgrowth of the brain, wherein the latter receives the optical input and the former relays the information for processing. While efforts to understand the optic nerve proteome have been made earlier, there exists a lacuna in its biochemical composition and molecular functions. We report, in this study, a high-resolution mass spectrometry-based approach using an Orbitrap Fusion Tribrid mass spectrometer to elucidate the human optic nerve proteomic profile...
October 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30281399/a-call-for-articles-internet-of-things-artificial-intelligence-sensors-and-omics-convergence
#6
Vural Özdemir
No abstract text is available yet for this article.
October 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30260743/differential-expression-profile-of-micrornas-during-prolonged-storage-of-platelet-concentrates-as-a-quality-measurement-tool-in-blood-banks
#7
Jersey Heitor da Silva Maués, Caroline de Fátima Aquino Moreira-Nunes, Thaís Brilhante Pontes, Priscilla Cristina Moura Vieira, Raquel Carvalho Montenegro, Letícia Martins Lamarão, Eleonidas Moura Lima, Rommel Mário Rodriguez Burbano
Platelet concentrate (PC) is a key blood component, which even in good storage conditions, susceptible to cellular damage over time. Hence, blood banks discard unused PC bags after 5 days of storage. Biomarkers of PC quality are therefore highly sought after in blood bank governance. We used the data (Gene Expression Omnibus: GSE61856) generated with next-generation sequencing to examine the expression profiles of microRNAs (miRNAs) from PCs that were stored for 6 days in a blood bank, that is, 1 day longer than is normally stored PC...
October 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30260734/the-dark-side-of-the-moon-the-internet-of-things-industry-4-0-and-the-quantified-planet
#8
Vural Özdemir
Industry 4.0 is an innovation framework launched initially at the 2011 Hanover Fair in Germany. It is premised on extreme digital connectivity to build smart factories and deliver extreme automation in science and society. Industry 4.0 has recently scaled up worldwide beyond Germany and Europe. Industry 4.0 employs the Internet of Things (IoT) to connect, communicate, and collect big data from embedded sensors in living and inanimate objects. When we add artificial intelligence (AI) powered real-time data analyses to the IoT, a state of worldwide extreme connectivity, or "The Quantified Planet," is created...
October 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
#9
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...
October 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30235109/pharmacogenetics-of-antiretroviral-drug-response-and-pharmacokinetic-variations-in-indigenous-south-african-populations
#10
Kevin S O'Connell, Marelize Swart, Nathaniel W McGregor, Collet Dandara, Louise Warnich
Interindividual and interethnic differences in response to antiretroviral drugs (ARVs) are influenced by genetic variation. The few genomic studies conducted among African-Americans and African ethnic groups do not reflect the extensive genetic diversity within African populations. ARVs are widely used in Africa. Therefore, genomic characterization of African populations is required before genotype-guided dosing becomes possible. The aim of this study was to determine and report on the frequency of genetic variants in genes implicated in metabolism and transport of ARVs in South African populations...
September 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30235108/is-procalcitonin-biomarker-guided-antibiotic-therapy-a-cost-effective-approach-to-reduce-antibiotic-resistant-and-clostridium-difficile-infections-in-hospitalized-patients
#11
Lotte Steuten, Janne Mewes, Isabelle Lepage-Nefkens, Hubertus Vrijhoef
Antibiotics (AB) can reduce morbidity and mortality in the treatment of patients with sepsis and chronic obstructive pulmonary disease (COPD) exacerbations. Yet, AB overuse or misuse increases antibiotic resistance (ABR) and Clostridium difficile infections (CDI). This study projected the expected impact of a procalcitonin (PCT) biomarker testing strategy on incremental ABR cases and CDI, and costs of care in a population of patients hospitalized with suspected sepsis or a COPD exacerbation, in three European countries: the United Kingdom, Germany, and the Netherlands...
September 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
#12
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 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/30124362/asthma-microrna-regulome-development-using-validated-mirna-target-interaction-visualization
#13
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...
September 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
#14
Mouhamed Idrissou, Khaldoun Rifaï, Marine Daures, Frédérique Penault-Llorca, Yves-Jean Bignon, Dominique Bernard-Gallon
No abstract text is available yet for this article.
September 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
#15
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...
September 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
#16
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
#17
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
#18
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
#19
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
#20
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
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