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Genomics review

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https://www.readbyqxmd.com/read/29679643/classification-and-experimental-identification-of-plant-long-non-coding-rnas
#1
Muneeza I Rai, Maheen Alam, David A Lightfoot, Priyatansh Gurha, Ahmed J Afzal
Our understanding of gene regulation is constantly evolving. It is now clear that the majority of cellular transcripts are non-coding RNAs. The spectrum of non-coding RNAs is diverse and includes short (<200 nt) and long non-coding RNAs (lncRNAs) (>200 nt). LncRNAs regulate gene expression through diverse mechanisms. In this review, we describe the emerging roles of lncRNA mediated plant gene regulation. We discuss the current classification of lncRNAs and their role in genome organization and gene regulation...
April 18, 2018: Genomics
https://www.readbyqxmd.com/read/29679469/influence-of-transporter-polymorphisms-on-drug-disposition-and-response-a-perspective-from-the-international-transporter-consortium
#2
Sook Wah Yee, Deanna J Brackman, Elizabeth A Ennis, Yuichi Sugiyama, Landry K Kamdem, Rebecca Blanchard, Aleksandra Galetin, Lei Zhang, Kathleen M Giacomini
Advances in genomic technologies have led to a wealth of information identifying genetic polymorphisms in membrane transporters, specifically how these polymorphisms affect drug disposition and response. This review describes the current perspective of the International Transporter Consortium (ITC) on clinically important polymorphisms in membrane transporters. ITC suggests that in addition to previously recommended polymorphisms in ABCG2 (BCRP) and SLCO1B1 (OATP1B1), polymorphisms in the emerging transporter, SLC22A1 (OCT1), be considered during drug development...
April 21, 2018: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/29679021/systematic-evaluation-of-rna-quality-microarray-data-reliability-and-pathway-analysis-in-fresh-fresh-frozen-and-formalin-fixed-paraffin-embedded-tissue-samples
#3
Isabella Wimmer, Anna R Tröscher, Florian Brunner, Stephen J Rubino, Christian G Bien, Howard L Weiner, Hans Lassmann, Jan Bauer
Formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources commonly used in pathology. However, formalin fixation modifies nucleic acids challenging the isolation of high-quality RNA for genetic profiling. Here, we assessed feasibility and reliability of microarray studies analysing transcriptome data from fresh, fresh-frozen (FF) and FFPE tissues. We show that reproducible microarray data can be generated from only 2 ng FFPE-derived RNA. For RNA quality assessment, fragment size distribution (DV200) and qPCR proved most suitable...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678955/studying-x-chromosome-inactivation-in-the-single-cell-genomic-era
#4
REVIEW
Andrew Keniry, Marnie E Blewitt
Single-cell genomics is set to revolutionise our understanding of how epigenetic silencing works; by studying specific epigenetic marks or chromatin conformations in single cells, it is possible to ask whether they cause transcriptional silencing or are instead a consequence of the silent state. Here, we review what single-cell genomics has revealed about X chromosome inactivation, perhaps the best characterised mammalian epigenetic process, highlighting the novel findings and important differences between mouse and human X inactivation uncovered through these studies...
April 20, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29678388/leveraging-algal-omics-to-reveal-potential-targets-for-augmenting-tag-accumulation
#5
REVIEW
Neha Arora, Philip T Pienkos, Vikas Pruthi, Krishna Mohan Poluri, Michael T Guarnieri
Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae...
April 17, 2018: Biotechnology Advances
https://www.readbyqxmd.com/read/29678218/developing-inclusivity-and-exclusivity-panels-for-testing-diagnostic-and-detection-tools-targeting-burkholderia-pseudomallei-the-causative-agent-of-melioidosis
#6
Charles H D Williamson, David M Wagner, Paul Keim, Jason W Sahl
Background: Diagnostic tools designed to target Burkholderia pseudomallei , the causative agent of melioidosis that was classified as a Tier 1 Select Agent by the U.S. Centers for Disease Control and Prevention, have typically suffered from false-positive and false-negative results because of a lack of understanding of the genomic diversity of B. pseudomallei and its genetic near neighbors. Objective: In this review, we discuss a strategy for using comparative genomics to guide the design of inclusivity and exclusivity panels for the validation of assays as defined by the Standard Method Performance Requirement (SMPR®)...
April 20, 2018: Journal of AOAC International
https://www.readbyqxmd.com/read/29678194/the-perfect-personalized-cancer-therapy-cancer-vaccines-against-neoantigens
#7
REVIEW
Luigi Aurisicchio, Matteo Pallocca, Gennaro Ciliberto, Fabio Palombo
In the advent of Immune Checkpoint inhibitors (ICI) and of CAR-T adoptive T-cells, the new frontier in Oncology is Cancer Immunotherapy because of its ability to provide long term clinical benefit in metastatic disease in several solid and liquid tumor types. It is now clear that ICI acts by unmasking preexisting immune responses as well as by inducing de novo responses against tumor neoantigens. Thanks to theprogress made in genomics technologies and the evolution of bioinformatics, neoantigens represent ideal targets, due to their specific expression in cancer tissue and the potential lack of side effects...
April 20, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29678078/challenges-in-design-and-creation-of-genetic-openehr-archetype
#8
Priscila A Maranhão, Gustavo Bacelar-Silva, Duarte Gonçalves-Ferreira, Pedro Vieira-Marques, Ricardo Cruz-Correia
Since the Human Genomic Project discovered the sequencing of human genome, the interest about genome content in clinical practice has increased. Genetic information has become a key point to understand diseases or improve treatments, for example, the nutrigenomic and nutrigenetics. However, the huge amount of data generated raises the need for Electronic Health Record (EHR) improvements as it becomes increasingly necessary that it includes more specific genetic information. Thus, we aim to propose standard genetic archetypes (in openEHR) and describe our main challenges in this context...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29677564/-omic-technologies-as-a-helpful-tool-in-radioecological-research
#9
REVIEW
Polina Yu Volkova, Stanislav A Geras'kin
This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.
April 17, 2018: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/29677478/unfinished-business-evolution-of-the-mhc-and-the-adaptive-immune-system-of-jawed-vertebrates
#10
Jim Kaufman
The major histocompatibility complex (MHC) is a large genetic region with many genes, including the highly polymorphic classical class I and II genes that play crucial roles in adaptive as well as innate immune responses. The organization of the MHC varies enormously among jawed vertebrates, but class I and II genes have not been found in other animals. How did the MHC arise, and are there underlying principles that can help us to understand the evolution of the MHC? This review considers what it means to be an MHC and the potential importance of genome-wide duplication, gene linkage, and gene coevolution for the emergence and evolution of an adaptive immune system...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29677463/a-role-for-collagen-iv-in-cardiovascular-disease
#11
Lasse Bach Steffensen, Lars M Rasmussen
Over the past decade, studies have repeatedly found single nucleotide polymorphisms located in the COL4A1 and COL4A2 genes to be associated with cardiovascular disease (CVD), and the 13q34 locus harboring these genes is one of approximately 160 genome-wide significant risk loci for coronary artery disease. COL4A1 and COL4A2 encode the ⍺1- and ⍺2-chains of collagen IV, a major component of basement membranes in various tissues including arteries. In spite of the growing body of evidence indicating a role for collagen IV in CVD, remarkably few studies aim at directly investigating such a role...
April 20, 2018: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/29677173/what-does-this-mutation-mean-the-tools-and-pitfalls-of-variant-interpretation-in-lymphoid-malignancies
#12
REVIEW
Guillermin Yann, Lopez Jonathan, Chabane Kaddour, Hayette Sandrine, Bardel Claire, Salles Gilles, Sujobert Pierre, Huet Sarah
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role in lymphoid malignancies, few guidelines exist to guide biologists and routine laboratories through this constantly evolving field. In this article, we review the challenges of interpreting HTS in lymphoid malignancies and provide a toolkit to interpret single nucleotide variants obtained from HTS...
April 20, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29676688/ophthalmic-manifestations-of-heimler-syndrome-due-to-pex6-mutations
#13
Nutsuchar Wangtiraumnuay, Waleed Abed Alnabi, Mai Tsukikawa, Avrey Thau, Jenina Capasso, Reuven Sharony, Chris F Inglehearn, Alex V Levin
BACKGROUND/AIMS: Pigmentary retinal dystrophy and macular dystrophy have been previously reported in Heimler syndrome due to mutations in PEX1. Here we reported the ocular manifestations in Heimler syndrome due to mutations in PEX6. MATERIALS AND METHODS: Medical records were reviewed to identify patient demographics, ophthalmic and systemic findings, and results of diagnostic testing including whole genome sequencing. RESULTS: Patient 1 is 12-year-old boy with a novel mutation c...
June 2018: Ophthalmic Genetics
https://www.readbyqxmd.com/read/29676245/structure-and-interaction-prediction-in-prokaryotic-rna-biology
#14
Patrick R Wright, Martin Mann, Rolf Backofen
Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in "wet" laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present...
April 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29675992/genetic-counselors-as-social-and-behavioral-scientists-in-the-era-of-precision-medicine
#15
Barbara B Biesecker
In the era of precision medicine, translating genomics into clinical care will involve answering key questions in social and behavioral research. The scope of this research addresses assessing how clients perceive and use genomic information, and how effectively genetic counseling is meeting clients' needs. Outcomes are central to enhancing practice effectiveness, improving patient outcomes, and informing cost effective services to address workforce challenges. While genetic counseling is generally thought of as a clinical practice, genetic counselors contribute to research in several ways...
March 2018: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
https://www.readbyqxmd.com/read/29675939/markers-in-time-and-space-a-review-of-the-last-decade-of-plant-phylogeographic-approaches
#16
Ashley B Morris, Joey Shaw
Plant studies comprise a relatively small proportion of the phylogeographic literature, likely as a consequence of the fundamental challenges posed by the complex genomic structures and life history strategies of these organisms. Comparative plastomics (i.e., comparisons of mutation rates within and among regions of the chloroplast genome) across plant lineages has led to an increased understanding of which markers are likely to provide the most information at low taxonomic levels. However, the extent to which the results of such work have influenced the literature have not been fully assessed, nor has the extent to which plant phylogeographers explicitly analyze markers in time and space, both of which are integral components of the field...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29675864/molecular-based-identification-and-detection-of-salmonella-in-food-production-systems-current-perspectives
#17
REVIEW
Steven C Ricke, Sun Ae Kim, Zhaohao Shi, Si Hong Park
Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies has greatly improved the resolution for differentiating strains within a particular serovar...
April 19, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29675836/complex-multicellularity-in-fungi-evolutionary-convergence-single-origin-or-both
#18
László G Nagy, Gábor M Kovács, Krisztina Krizsán
Complex multicellularity represents the most advanced level of biological organization and it has evolved only a few times: in metazoans, green plants, brown and red algae and fungi. Compared to other lineages, the evolution of multicellularity in fungi follows different principles; both simple and complex multicellularity evolved via unique mechanisms not found in other lineages. Herein we review ecological, palaeontological, developmental and genomic aspects of complex multicellularity in fungi and discuss general principles of the evolution of complex multicellularity in light of its fungal manifestations...
April 19, 2018: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29675039/the-role-of-cell-adhesion-molecule-genes-regulating-neuroplasticity-in-addiction
#19
REVIEW
Dawn E Muskiewicz, George R Uhl, F Scott Hall
A variety of genetic approaches, including twin studies, linkage studies, and candidate gene studies, has established a firm genetic basis for addiction. However, there has been difficulty identifying the precise genes that underlie addiction liability using these approaches. This situation became especially clear in genome-wide association studies (GWAS) of addiction. Moreover, the results of GWAS brought into clarity many of the shortcomings of those early genetic approaches. GWAS studies stripped away those preconceived notions, examining genes that would not previously have been considered in the study of addiction, consequently creating a shift in our understanding...
2018: Neural Plasticity
https://www.readbyqxmd.com/read/29674722/implications-of-publicly-available-genomic-data-resources-in-searching-for-therapeutic-targets-of-obesity-and-type-2-diabetes
#20
REVIEW
Sungwon Jung
Obesity and type 2 diabetes (T2D) are two major conditions that are related to metabolic disorders and affect a large population. Although there have been significant efforts to identify their therapeutic targets, few benefits have come from comprehensive molecular profiling. This limited availability of comprehensive molecular profiling of obesity and T2D may be due to multiple challenges, as these conditions involve multiple organs and collecting tissue samples from subjects is more difficult in obesity and T2D than in other diseases, where surgical treatments are popular choices...
April 20, 2018: Experimental & Molecular Medicine
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