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Omics: a Journal of Integrative Biology

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...
July 13, 2018: Omics: a Journal of Integrative Biology
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
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
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
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
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
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
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
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
Savita Jayaram, Lavanya Balakrishnan, Manika Singh, Azin Zabihi, Raksha A Ganesh, Kiran K Mangalaparthi, Pranali Sonpatki, Manoj Kumar Gupta, Chaitra B Amaresha, Komal Prasad, Kiran Mariswamappa, Shibu Pillai, Akhila Lakshmikantha, Nameeta Shah, Ravi Sirdeshmukh
Splice variants are known to be important in the pathophysiology of tumors, including the brain cancers. We applied a proteogenomics pipeline to identify splice variants in glioblastoma (GBM, grade IV glioma), a highly malignant brain tumor, using in-house generated mass spectrometric proteomic data and public domain RNASeq dataset. Our analysis led to the identification of a novel exon that maps to the long isoform of Neural cell adhesion molecule 1 (NCAM1), expressed on the surface of glial cells and neurons, important for cell adhesion and cell signaling...
June 2018: Omics: a Journal of Integrative Biology
Nicholas Ekow Thomford, Kevin Dzobo, Emile Chimusa, Kerstin Andrae-Marobela, Shadreck Chirikure, Ambroise Wonkam, Collet Dandara
While drugs remain the cornerstone of medicine, herbal medicine is an important comedication worldwide. Thus, precision medicine ought to face this clinical reality and develop "companion diagnostics" for drugs as well as herbal medicines. Yet, many are in denial with respect to the extent of use of traditional/herbal medicines, overlooking that a considerable number of contemporary therapeutic drugs trace their discovery from herbal medicines. This expert review underscores that absent such appropriate attention on both classical drug therapy and herbal medicines, precision medicine biomarkers will likely not stand the full test of clinical practice while patients continue to use both drugs and herbal medicines and, yet the biomarker research and applications focus only (or mostly) on drug therapy...
June 2018: Omics: a Journal of Integrative Biology
Ilona Kickbusch, Mustafa Bayram, Özgür Bayram, Nezih Hekim, Bülent Kayalı, Vural Özdemir
No abstract text is available yet for this article.
June 2018: Omics: a Journal of Integrative Biology
Vita Rozman, Tanja Kunej
Harnessing the genomics big data requires innovation in how we extract and interpret biologically relevant variants. Currently, there is no established catalog of prioritized missense variants associated with deleterious protein function phenotypes. We report in this study, to the best of our knowledge, the first genome-wide prioritization of sequence variants with the most deleterious effect on protein function (potentially deleterious variants [pDelVars]) in nine vertebrate species: human, cattle, horse, sheep, pig, dog, rat, mouse, and zebrafish...
June 2018: Omics: a Journal of Integrative Biology
Nina Pirih, Tanja Kunej
The volume of publications and the type of research approaches used in omics system sciences are vast and continue to expand rapidly. This increased complexity and heterogeneity of omics data are challenging data extraction, sensemaking, analyses, knowledge translation, and interpretation. An extended and dynamic taxonomy for the classification and summary of omics studies are essential. We present an updated taxonomy for classification of omics research studies based on four criteria: (1) type and number of genomic loci in a research study, (2) number of species and biological samples, (3) the type of omics technology (e...
May 2018: Omics: a Journal of Integrative Biology
Nicholas Ekow Thomford, Kevin Dzobo, Nana Akyaa Yao, Emile Chimusa, Jonathan Evans, Emmanuel Okai, Paul Kruszka, Maximilian Muenke, Gordon Awandare, Ambroise Wonkam, Collet Dandara
Congenital heart defects (CHD) are structural malformations found at birth with a prevalence of 1%. The clinical trajectory of CHD is highly variable and thus in need of robust diagnostics and therapeutics. Major surgical interventions are often required for most CHDs. In Africa, despite advances in life sciences infrastructure and improving education of medical scholars, the limited clinical data suggest that CHD detection and correction are still not at par with the rest of the world. But the toll and genetics of CHDs in Africa has seldom been systematically investigated...
May 2018: Omics: a Journal of Integrative Biology
Eren Ozcagli, Aydan Biri, Bedia Dinc, Semra Sardas
Human papillomavirus (HPV) infection is one of the most common sexually transmitted diseases worldwide and a prime cause of cervical cancer. The HPV DNA is detected in approximately 80-90% of all cervical cancers, with HPV 16 and 18 being the high risk conferring human carcinogens. DNA damage and diminished DNA repair mechanisms are potential biological surrogates of HPV infection that warrant further research in different tissues and populations. Notably, we do not know the extent to which the high risk HPV 16 and 18 differentially affect cervical cells versus other systems such as peripheral blood lymphocytes (PBLs)...
May 2018: Omics: a Journal of Integrative Biology
Hongli Peng, Panlin Zhao, Jiaonan Liu, Jinxia Zhang, Jie Zhang, Youxin Wang, Lijuan Wu, Manshu Song, Wei Wang
Male infertility is an important global health burden that can benefit from novel biomarkers and diagnostics innovation. Aberrant methylation of the imprinted genes H19 and SNRPN (small nuclear ribonucleoprotein polypeptide N) in sperm DNA has been implicated in abnormal sperm parameters and male infertility. However, whether certain methylation patterns of one or multiple CpG sites within an imprinted gene are pathological for multiple sperm defects remains poorly understood. To examine the diagnostic potential of certain methylation patterns of CpG sites for multiphenotype defects in human sperm, the sperm DNA methylation patterns of individual CpG sites within imprinting control regions (ICRs) of imprinted genes H19 and SNRPN were measured by bisulfite pyrosequencing in a Han Chinese population sample: 39 oligoasthenozoospermia (OA) patients, 36 asthenoteratozoospermia (AT) patients, and 50 normozoospermia (N) controls...
May 2018: Omics: a Journal of Integrative Biology
Erik Fisher
No abstract text is available yet for this article.
May 2018: Omics: a Journal of Integrative Biology
Nikolaos Evangelatos, Kapaettu Satyamourthy, Georgia Levidou, Helmut Brand, Pia Bauer, Christina Kouskouti, Angela Brand
"-Omics" systems sciences are at the epicenter of personalized medicine and public health, and drivers of knowledge-based biotechnology innovation. Bioinformatics, a core component of omics research, is one of the disciplines that first employed Free/Libre Open Source Software (FLOSS), and thus provided a fertile ground for its further development. Understanding the use and characteristics of FLOSS deployed in the omics field is valuable for future innovation strategies, policy and funding priorities...
May 2018: Omics: a Journal of Integrative Biology
Keli Hočevar, Aleš Maver, Tanja Kunej, Borut Peterlin
Sarcoidosis is a multifactorial systemic disease characterized by granulomatous inflammation and greatly impacting on global public health. The etiology and mechanisms of sarcoidosis are not fully understood. Recent high-throughput biological research has generated vast amounts of multi-omics big data on sarcoidosis, but their significance remains to be determined. We sought to identify novel candidate regions, and genes consistently altered in heterogeneous omics studies so as to reveal the underlying molecular mechanisms...
May 2018: Omics: a Journal of Integrative Biology
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