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Current Genomics

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https://www.readbyqxmd.com/read/30386174/a-network-biology-approach-for-assessing-the-role-of-pathologic-adipose-tissues-in-insulin-resistance-using-meta-analysis-of-microarray-datasets
#1
Aditya Saxena, Kumar Sachin
Background: The role of adipose tissue in Insulin resistance (IR) and Type 2 Diabetes (T2D) has well been received in the biomedical community; being a precursor of T2D, identification of the molecular basis of IR is therefore, vital to elucidate T2D- pathogenesis and meta-analysis of previously conducted microarray studies provides an inexpensive approach to achieve this end. Methods: In this study, we have carried out a statistical meta-analysis of 157 microarray datasets from five independent studies and identified a meta-signature of 1,511 genes; their functional meaning was elucidated by integrated pathways-analysis...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386173/interplay-between-micrornas-and-targeted-genes-in-cellular-homeostasis-of-adult-zebrafish-danio-rerio
#2
Ludivine Renaud, Willian A da Silveira, William B Glen, Edward S Hazard, Gary Hardiman
Background: Cellular homeostasis is regulated by the intricate interplay between a plethora of signaling pathways and "energetic sensors" in organs. In order to maintain energy balance, induction or repression of metabolic pathways must be regulated and act in concert with the energetic demands of the cell at a given point in time. A new class of small noncoding RNAs, the microRNAs (miRNAs), has added yet further complexity to the control of metabolic homeostasis. Objective: Understanding the damages induced by toxins in the liver and the intestine as well as the interplay between the miRNome and transcriptome first requires baseline characterization in these tissues in healthy animals under cellular homeostasis...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386172/parallel-algorithms-for-inferring-gene-regulatory-networks-a-review
#3
REVIEW
Omid Abbaszadeh, Ali Reza Khanteymoori, Ali Azarpeyvand
System biology problems such as whole-genome network construction from large-scale gene expression data are sophisticated and time-consuming. Therefore, using sequential algorithms are not feasible to obtain a solution in an acceptable amount of time. Today, by using massively parallel computing, it is possible to infer large-scale gene regulatory networks. Recently, establishing gene regulatory networks from large-scale datasets have drawn the noticeable attention of researchers in the field of parallel computing and system biology...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386171/early-life-stress-and-epigenetics-in-late-onset-alzheimer-s-dementia-a-systematic-review
#4
REVIEW
Erwin Lemche
Involvement of life stress in Late-Onset Alzheimer's Disease (LOAD) has been evinced in longitudinal cohort epidemiological studies, and endocrinologic evidence suggests involvements of catecholamine and corticosteroid systems in LOAD. Early Life Stress (ELS) rodent models have successfully demonstrated sequelae of maternal separation resulting in LOAD-analogous pathology, thereby supporting a role of insulin receptor signalling pertaining to GSK-3beta facilitated tau hyper-phosphorylation and amyloidogenic processing...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386170/preterm-birth-and-the-risk-of-neurodevelopmental-disorders-is-there-a-role-for-epigenetic-dysregulation
#5
REVIEW
Eamon Fitzgerald, James P Boardman, Amanda J Drake
Preterm Birth (PTB) accounts for approximately 11% of all births worldwide each year and is a profound physiological stressor in early life. The burden of neuropsychiatric and developmental impairment is high, with severity and prevalence correlated with gestational age at delivery. PTB is a major risk factor for the development of cerebral palsy, lower educational attainment and deficits in cognitive functioning, and individuals born preterm have higher rates of schizophrenia, autistic spectrum disorder and attention deficit/hyperactivity disorder...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386169/editorial-a-genomic-and-epigenomic-approach-for-studying-neuropsychiatric-disorders-associated-to-early-life-stress-part-i
#6
EDITORIAL
Xena Giada Pappalardo, Sebastiano Cavallaro
No abstract text is available yet for this article.
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30258280/neuroarray-a-custom-cgh-microarray-to-decipher-copy-number-variants-in-alzheimer-s-disease
#7
Denis Cuccaro, Maria Guarnaccia, Rosario Iemmolo, Velia D'Agata, Sebastiano Cavallaro
Background: Copy Number Variants (CNVs) represent a prevailing type of structural variation (deletions or duplications) in the human genome. In the last few years, several studies have demonstrated that CNVs represent significant mutations in Alzheimer's Disease (AD) hereditability. Currently, innovative high-throughput platforms and bioinformatics algorithms are spreading to screening CNVs involved in different neurological diseases. In particular, the use of custom arrays, based on libraries of probes that can detect significant genomic regions, have greatly improved the resolution of targeted regions and the identification of chromosomal aberrations...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258279/an-effective-pipeline-based-on-relative-coverage-for-the-genome-assembly-of-phytoplasmas-and-other-fastidious-prokaryotes
#8
Cesare Polano, Giuseppe Firrao
Background: For the plant pathogenic phytoplasmas, as well as for several fastidious prokaryotes, axenic cultivation is extremely difficult or not possible yet; therefore, even with second generation sequencing methods, obtaining the sequence of their genomes is challenging due to host sequence contamination. Objective: With the Phytoassembly pipeline here presented, we aim to provide a method to obtain high quality genome drafts for the phytoplasmas and other uncultivable plant pathogens, by exploiting the coverage differential in the ILLUMINA sequences from the pathogen and the host, and using the sequencing of a healthy, isogenic plant as a filter...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258278/artificial-neural-network-as-a-classifier-for-the-identification-of-hepatocellular-carcinoma-through-prognosticgene-signatures
#9
Satya Eswari Jujjavarapu, Saurabh Deshmukh
Background: Artificial Neural Networks (ANNs) can be used to classify tumor of Hepatocellular carcinoma based on their gene expression signatures. The neural network is trained with gene expression profiles of genes that were predictive of recurrence in liver cancer, the ANNs became capable of correctly classifying all samples and distinguishing the genes most suitable for the organization. The ability of the trained ANN models in recognizing the Cancer Genes was tested as we analyzed additional samples that were not used beforehand for the training procedure, and got the correctly classified result in the validation set...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258277/regulation-of-age-related-decline-by-transcription-factors-and-their-crosstalk-with-the-epigenome
#10
REVIEW
Xin Zhou, Ilke Sen, Xin-Xuan Lin, Christian G Riedel
Aging is a complex phenomenon, where damage accumulation, increasing deregulation of biological pathways, and loss of cellular homeostasis lead to the decline of organismal functions over time. Interestingly, aging is not entirely a stochastic process and progressing at a constant rate, but it is subject to extensive regulation, in the hands of an elaborate and highly interconnected signaling network. This network can integrate a variety of aging-regulatory stimuli, i.e. fertility, nutrient availability, or diverse stresses, and relay them via signaling cascades into gene regulatory events - mostly of genes that confer stress resistance and thus help protect from damage accumulation and homeostasis loss...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258276/genetic-alterations-of-periampullary-and-pancreatic-ductal-adenocarcinoma-an-overview
#11
REVIEW
Nilabja Sikdar, Gourab Saha, Ashmita Dutta, Shibajyoti Ghosh, Shailesh V Shrikhande, Sudeep Banerjee
Pancreatic Ductal AdenoCarcinoma (PDAC) is one of the most lethal malignancies of all solid cancers. Precancerous lesions for PDAC include PanIN, IPMNs and MCNs. PDAC has a poor prognosis with a 5-year survival of approximately 6%. Whereas Periampulary AdenoCarcinoma (PAC) having four anatomic subtypes, pancreatic, Common Bile Duct (CBD), ampullary and duodenum shows relative better prognosis. The highest incidence of PDAC has been reported with black with respect to white population. Similarly, incidence rate of PAC also differs with different ethnic populations...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258275/-neuroarray-a-customized-acgh-for-the-analysis-of-copy-number-variations-in-neurological-disorders
#12
Valentina La Cognata, Giovanna Morello, Giulia Gentile, Francesca Cavalcanti, Rita Cittadella, Francesca Luisa Conforti, Elvira Valeria De Marco, Angela Magariello, Maria Muglia, Alessandra Patitucci, Patrizia Spadafora, Velia D'Agata, Martino Ruggieri, Sebastiano Cavallaro
Background: Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258274/copy-number-variations-in-adult-onset-neuropsychiatric-diseases
#13
REVIEW
Alexandra R Lew, Timot R Kellermayer, Balint P Sule, Kinga Szigeti
Adult-onset neuropsychiatric diseases are one of the most challenging areas of medicine. While symptomatic treatments are available, for most of these diseases the exact pathomechanism is not known, thus, disease-modifying therapies are difficult to conceptualize and find. The two most common and best studied neuropsychiatric diseases affecting higher cortical functions in humans are schizophrenia and Alzheimer's disease; both diseases have high heritability, however, the genetic architecture is not fully elucidated...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258273/a-review-of-copy-number-variants-in-inherited-neuropathies
#14
REVIEW
Vincenzo Salpietro, Andreea Manole, Stephanie Efthymiou, Henry Houlden
The rapid development in the last 10-15 years of microarray technologies, such as oligonucleotide array Comparative Genomic Hybridization (CGH) and Single Nucleotide Polymorphisms (SNP) genotyping array, has improved the identification of fine chromosomal structural variants, ranging in length from kilobases (kb) to megabases (Mb), as an important cause of genetic differences among healthy individuals and also as disease-susceptibility and/or disease-causing factors. Structural genomic variations due to unbalanced chromosomal rearrangements are known as Copy-Number Variants (CNVs) and these include variably sized deletions, duplications, triplications and translocations...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258272/editorial-copy-number-variants-in-neurological-disorder
#15
EDITORIAL
Giulia Gentile, Sebastiano Cavallaro
No abstract text is available yet for this article.
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30065615/impact-of-p53-arg72pro-snp-on-breast-cancer-risk-in-north-indian-population
#16
Naseem Akhter, Sajad A Dar, Shilpi Chattopadhyay, Shafiul Haque, Razique Anwer, Mohd Wahid, Arshad Jawed, Mohtashim Lohani, Raju K Mandal, N K Shukla, Yasir Abdul, Syed Akhtar Husain
Background: Genetic changes in p53 gene contribute to breast cancer susceptibility. Objective and Methods: A case-control study and a meta-analysis were performed to investigate the role of p53 codon72 SNP with breast cancer susceptibility in Indian women. Results: p53 heterozygous arginine variant was associated with decreased risk of breast cancer in total cohort. In meta-analysis, Allelic and GG vs. CC genetic comparison model were found to be associated with breast cancer risk...
August 2018: Current Genomics
https://www.readbyqxmd.com/read/30065614/an-ultrahigh-dimensional-mapping-model-of-high-order-epistatic-networks-for-complex-traits
#17
Kirk Gosik, Lidan Sun, Vernon M Chinchilli, Rongling Wu
Background: Genetic interactions involving more than two loci have been thought to affect quantitatively inherited traits and diseases more pervasively than previously appreciated. However, the detection of such high-order interactions to chart a complete portrait of genetic architecture has not been well explored. Methods: We present an ultrahigh-dimensional model to systematically characterize genetic main effects and interaction effects of various orders among all possible markers in a genetic mapping or association study...
August 2018: Current Genomics
https://www.readbyqxmd.com/read/30065613/functional-polymorphism-in-the-msi1-gene-promoter-confers-a-decreased-risk-of-lung-cancer-in-chinese-by-reducing-msi1-expression
#18
Lin Liu, Fuman Qiu, Jiansong Chen, Di Wu, Qingqing Nong, Yifeng Zhou, Jiachun Lu
Background: Musashi1 (MSI1) is a characteristic stem cell marker that regulates the balance between cell self-renewal and differentiation. Evidence has identified MSI1 as a pivotal oncogenic regulator in diverse malignancies. However, little evidence uncovers the role of genetic variations of MSI1 gene in cancer etiology. Objective: The aim of this study was to investigate the association between genetic variants in the MSI1 gene and lung cancer risk. Methods: Based on a two-stage retrospective study with a total of 1559 patients with lung cancer and 1667 healthy controls, we evaluated the relevance between three putative functional SNPs in the MSI1 promoter (i...
August 2018: Current Genomics
https://www.readbyqxmd.com/read/30065612/an-otof-frameshift-variant-associated-with-auditory-neuropathy-spectrum-disorder
#19
Hong Xia, Xiangjun Huang, Hongbo Xu, Yi Guo, Pengzhi Hu, Xiong Deng, Zhijian Yang, An Liu, Hao Deng
Background: Auditory Neuropathy Spectrum Disorder (ANSD) is manifested as impairment of auditory nerve activity but preservation of the outer hair cell function. Objective: This study was to detect the disease-causing gene and variant(s) in a Chinese ANSD family. Methods: A four-generation consanguineous Chinese ANSD family and 200 unrelated healthy controls were enrolled. Exome sequencing and Sanger sequencing were applied to identify the genetic basis for ANSD in this family...
August 2018: Current Genomics
https://www.readbyqxmd.com/read/30065611/molecular-insights-into-muscle-homeostasis-atrophy-and-wasting
#20
REVIEW
Bianca Maria Scicchitano, Gabriella Dobrowolny, Gigliola Sica, Antonio MusarĂ²
Muscle homeostasis is guaranteed by a delicate balance between synthesis and degradation of cell proteins and its alteration leads to muscle wasting and diseases. In this review, we describe the major anabolic pathways that are involved in muscle growth and homeostasis and the proteolytic systems that are over-activated in muscle pathologies. Modulation of these pathways comprises an attractive target for drug intervention.
August 2018: Current Genomics
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