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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...
May 10, 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)...
April 30, 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...
April 30, 2018: Omics: a Journal of Integrative Biology
Erik Fisher
No abstract text is available yet for this article.
April 26, 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...
April 26, 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...
April 24, 2018: Omics: a Journal of Integrative Biology
Federica Fusi, Daniele Manzella, Selim Louafi, Eric Welch
This genomics global governance research study presents the dynamics and the evolving nature of salient challenges that global genomics initiatives encounter in designing new models for data management, exchange, and collaboration across disciplines, sectors, and countries. Using a multiple case study approach, we assessed and compared organizational responses across diverse genomics initiatives. The richness of a comparative qualitative analysis clearly shows the complexity addressed by genomics initiatives and, importantly, expands current studies by moving beyond an open versus property regime dichotomy...
March 27, 2018: Omics: a Journal of Integrative Biology
Jae-Eun Lee, Young-Youl Kim
Biobanks are infrastructures for large-scale biology innovation. Governance of biobanks can be usefully informed by studies of publication trends, for example, on the types of biosamples employed in scientific publications. We examined trends in each of the serum, plasma, peripheral blood mononuclear cell (PBMC), buffy coat, tissue, and gut microbiome biosample-related scientific publications over the past 40 years, using data between 1977 and 2016 from the Scopus database. We found that the number of tissue-related publications was the highest in each year of our analysis than other biosamples, but was generally less than the sum of serum- and plasma-related publications...
March 27, 2018: Omics: a Journal of Integrative Biology
Giuseppa Augello, Daniele Balasus, Caterina Fusilli, Tommaso Mazza, Maria Rita Emma, Lydia Giannitrapani, Rosalia Agliastro, Melchiorre Cervello, Giuseppe Montalto
There are currently no biomarkers that predict hepatocellular carcinoma (HCC) risk in patients with hepatitis C virus (HCV)-related cirrhosis. We investigated the relationships among major histocompatibility complex (MHC) class I chain-related gene A (MICA) polymorphisms, plasma levels of soluble MICA (sMICA), and HCC risk in patients with HCV-related HCC. One hundred fifty-four HCV-related HCC patients, 93 HCV-related liver cirrhosis (LC) cases, and 244 healthy controls, all sampled from the native Sicilian population, were genotyped using the KASP™ single-nucleotide polymorphism genotyping method...
March 27, 2018: Omics: a Journal of Integrative Biology
Khaldoun Rifaï, Mouhamed Idrissou, Marine Daures, Yves-Jean Bignon, Frédérique Penault-Llorca, Dominique Bernard-Gallon
No abstract text is available yet for this article.
March 27, 2018: Omics: a Journal of Integrative Biology
Manousos E Kambouris, Yiannis Manoussopoulos, Stavroula Kritikou, Aphroditi Milioni, Spyridon Mantzoukas, Aristea Velegraki
Agrigenomics is one of the emerging focus areas for omics sciences. Yet, agrigenomics differs from medical omics applications such as pharmacogenomics and precision medicine, by virtue of vastly distributed geography of applications at the intersection of agriculture, nutrition, and genomics research streams. Crucially, agrigenomics can address diagnostics and safety surveillance needs in remote and rural farming communities or decentralized food, crop, and environmental monitoring programs for prompt, selective, and differential identification of pathogens...
March 27, 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
Maja Zadel, Aleš Maver, Anja Kovanda, Borut Peterlin
Huntington's disease (HD) is a severe neurodegenerative disorder manifesting as progressive impairment of motor function, cognitive decline, psychiatric symptoms, and immunological and endocrine dysfunction. We explored the consistency of blood transcriptomic biomarkers in HD based on a novel Slovene patient cohort and expert review of previous studies. HumanHT-12 v4 BeadChip microarrays were performed on the whole blood samples of a cohort of 23 HD mutation carriers and 23 controls to identify differentially expressed (DE) transcripts...
April 2018: Omics: a Journal of Integrative Biology
Ilaria Laudadio, Valerio Fulci, Francesca Palone, Laura Stronati, Salvatore Cucchiara, Claudia Carissimi
The analysis of microbiota composition in humans, animals, and built environments is important because of emerging roles and applications in a broad range of disease and ecological phenotypes. Next Generation Sequencing is the current method of choice to characterize microbial community composition. The taxonomic profile of a microbial community can be obtained either by shotgun analysis of random DNA fragments or through 16S ribosomal RNA gene (rDNA) amplicon sequencing. It has been previously shown that the 16S rDNA amplicon sequencing approach yields quantitatively and qualitatively different results compared to shotgun metagenomics when the two techniques are used to assess microbial community composition on the same samples...
April 2018: Omics: a Journal of Integrative Biology
Ramy K Aziz
No abstract text is available yet for this article.
April 2018: Omics: a Journal of Integrative Biology
Busra Aydin, Tugba Ozer, Ebru Toksoy Oner, Kazim Yalcin Arga
Metabolic systems engineering is being used to redirect microbial metabolism for the overproduction of chemicals of interest with the aim of transforming microbial hosts into cellular factories. In this study, a genome-based metabolic systems engineering approach was designed and performed to improve biopolymer biosynthesis capability of a moderately halophilic bacterium Halomonas smyrnensis AAD6T producing levan, which is a fructose homopolymer with many potential uses in various industries and medicine. For this purpose, the genome-scale metabolic model for AAD6T was used to characterize the metabolic resource allocation, specifically to design metabolic engineering strategies for engineered bacteria with enhanced levan production capability...
March 2018: Omics: a Journal of Integrative Biology
Nikolaos Evangelatos, Kapaettu Satyamoorthy, Georgia Levidou, Pia Bauer, Helmut Brand, Christina Kouskouti, Hans Lehrach, Angela Brand
"-Omics" research is in transition with the recent rise of multi-omics technology platforms. Integration of "-omics" and multi-omics research is of high priority in sepsis, a heterogeneous syndrome that is widely recognized as a global health burden and a priority biomedical funding field. We report here an original study on bibliometric trends in the use of "-omics" technologies, and multi-omics approaches in particular, in sepsis research in three (supra)national settings, the United States, the European Union 28 Member States (EU-28), and China...
March 2018: Omics: a Journal of Integrative Biology
(no author information available yet)
No abstract text is available yet for this article.
March 2018: Omics: a Journal of Integrative Biology
Khoudia Diop, Awa Diop, Anthony Levasseur, Oleg Mediannikov, Catherine Robert, Nicholas Armstrong, Carine Couderc, Florence Bretelle, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar
Microbial culturomics is a new subfield of postgenomic medicine and omics biotechnology application that has broadened our awareness on bacterial diversity of the human microbiome, including the human vaginal flora bacterial diversity. Using culturomics, a new obligate anaerobic Gram-stain-negative rod-shaped bacterium designated strain khD1T was isolated in the vagina of a patient with bacterial vaginosis and characterized using taxonogenomics. The most abundant cellular fatty acids were C15:0 anteiso (36%), C16:0 (19%), and C15:0 iso (10%)...
March 2018: Omics: a Journal of Integrative Biology
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