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Genomics & Informatics

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https://www.readbyqxmd.com/read/27729842/sequence-analysis-of-hypothetical-proteins-from-helicobacter-pylori-26695-to-identify-potential-virulence-factors
#1
Ahmad Abu Turab Naqvi, Farah Anjum, Faez Iqbal Khan, Asimul Islam, Faizan Ahmad, Md Imtaiyaz Hassan
Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP). This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729841/in-silico-study-of-mirna-based-gene-regulation-involved-in-solid-cancer-by-the-assistance-of-argonaute-protein
#2
Surya Narayan Rath, Debasrita Das, V Badireenath Konkimalla, Sukanta Kumar Pradhan
Solid tumor is generally observed in tissues of epithelial or endothelial cells of lung, breast, prostate, pancreases, colorectal, stomach, and bladder, where several genes transcription is regulated by the microRNAs (miRNAs). Argonaute (AGO) protein is a family of protein which assists in miRNAs to bind with mRNAs of the target genes. Hence, study of the binding mechanism between AGO protein and miRNAs, and also with miRNAs-mRNAs duplex is crucial for understanding the RNA silencing mechanism. In the current work, 64 genes and 23 miRNAs have been selected from literatures, whose deregulation is well established in seven types of solid cancer like lung, breast, prostate, pancreases, colorectal, stomach, and bladder cancer...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729840/virtual-screening-for-potential-inhibitors-of-ns3-protein-of-zika-virus
#3
Maheswata Sahoo, Lingaraja Jena, Sangeeta Daf, Satish Kumar
Zika virus (ZIKV) is a mosquito borne pathogen, belongs to Flaviviridae family having a positive-sense single-stranded RNA genome, currently known for causing large epidemics in Brazil. Its infection can cause microcephaly, a serious birth defect during pregnancy. The recent outbreak of ZIKV in February 2016 in Brazil realized it as a major health risk, demands an enhanced surveillance and a need to develop novel drugs against ZIKV. Amodiaquine, prochlorperazine, quinacrine, and berberine are few promising drugs approved by Food and Drug Administration against dengue virus which also belong to Flaviviridae family...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729839/identification-of-suitable-natural-inhibitor-against-influenza-a-h1n1-neuraminidase-protein-by-molecular-docking
#4
Maheswata Sahoo, Lingaraja Jena, Surya Narayan Rath, Satish Kumar
The influenza A (H1N1) virus, also known as swine flu is a leading cause of morbidity and mortality since 2009. There is a need to explore novel anti-viral drugs for overcoming the epidemics. Traditionally, different plant extracts of garlic, ginger, kalmegh, ajwain, green tea, turmeric, menthe, tulsi, etc. have been used as hopeful source of prevention and treatment of human influenza. The H1N1 virus contains an important glycoprotein, known as neuraminidase (NA) that is mainly responsible for initiation of viral infection and is essential for the life cycle of H1N1...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729838/analysis-of-nuclear-mitochondrial-dna-segments-of-nine-plant-species-size-distribution-and-insertion-loci
#5
Young-Joon Ko, Sangsoo Kim
Nuclear mitochondrial DNA segment (Numt) insertion describes a well-known phenomenon of mitochondrial DNA transfer into a eukaryotic nuclear genome. However, it has not been well understood, especially in plants. Numt insertion patterns vary from species to species in different kingdoms. In this study, the patterns were surveyed in nine plant species, and we found some tip-offs. First, when the mitochondrial genome size is relatively large, the portion of the longer Numt is also larger than the short one. Second, the whole genome duplication event increases the ratio of the shorter Numt portion in the size distribution...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729837/recapitulation-of-candidate-systemic-lupus-erythematosus-associated-variants-in-koreans
#6
Ki-Sung Kwon, Hye-Young Cho, Yeun-Jun Chung
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that affects multiple organ systems. Although the etiology of SLE remains unclear, it is widely accepted that genetic factors could be involved in its pathogenesis. A number of genome-wide association studies (GWASs) have identified novel single-nucleotide polymorphisms (SNPs) associated with the risk of SLE in diverse populations. However, not all the SNP candidates identified from non-Asian populations have been validated in Koreans. In this study, we aimed to replicate the SNPs that were recently discovered in the GWAS; these SNPs have not been validated in Koreans or have only been replicated in Koreans with an insufficient sample size to conclude any association...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729836/mutational-analysis-of-extranodal-nk-t-cell-lymphoma-using-targeted-sequencing-with-a-comprehensive-cancer-panel
#7
Seungkyu Choi, Jai Hyang Go, Eun Kyung Kim, Hojung Lee, Won Mi Lee, Chun-Sung Cho, Kyudong Han
Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729835/structural-variation-of-alu-element-and-human-disease
#8
Songmi Kim, Chun-Sung Cho, Kyudong Han, Jungnam Lee
Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery...
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729834/editor-s-introduction-to-this-issue
#9
Yeun-Jun Chung
No abstract text is available yet for this article.
September 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27445649/genome-wide-association-study-of-bone-mineral-density-in-korean-men
#10
Ye Seul Bae, Sun-Wha Im, Mi So Kang, Jin Hee Kim, Soon Hang Lee, Be Long Cho, Jin Ho Park, You-Seon Nam, Ho-Young Son, San Deok Yang, Joohon Sung, Kwang Ho Oh, Jae Moon Yun, Jong Il Kim
Osteoporosis is a medical condition of global concern, with increasing incidence in both sexes. Bone mineral density (BMD), a highly heritable trait, has been proven a useful diagnostic factor in predicting fracture. Because medical information is lacking about male osteoporotic genetics, we conducted a genome-wide association study of BMD in Korean men. With 1,176 participants, we analyzed 4,414,664 single nucleotide polymorphisms (SNPs) after genomic imputation, and identified five SNPs and three loci correlated with bone density and strength...
June 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27445648/multilevel-precision-based-rational-design-of-chemical-inhibitors-targeting-the-hydrophobic-cleft-of-toxoplasma-gondii-apical-membrane-antigen-1-ama1
#11
Umashankar Vetrivel, Shalini Muralikumar, B Mahalakshmi, K Lily Therese, H N Madhavan, Mohamed Alameen, Indhuja Thirumudi
Toxoplasma gondii is an intracellular Apicomplexan parasite and a causative agent of toxoplasmosis in human. It causes encephalitis, uveitis, chorioretinitis, and congenital infection. T. gondii invades the host cell by forming a moving junction (MJ) complex. This complex formation is initiated by intermolecular interactions between the two secretory parasitic proteins-namely, apical membrane antigen 1 (AMA1) and rhoptry neck protein 2 (RON2) and is critically essential for the host invasion process. By this study, we propose two potential leads, NSC95522 and NSC179676 that can efficiently target the AMA1 hydrophobic cleft, which is a hotspot for targeting MJ complex formation...
June 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27445647/classification-of-colon-cancer-patients-based-on-the-methylation-patterns-of-promoters
#12
Wonyoung Choi, Jungwoo Lee, Jin-Young Lee, Sun-Min Lee, Da-Won Kim, Young-Joon Kim
Diverse somatic mutations have been reported to serve as cancer drivers. Recently, it has also been reported that epigenetic regulation is closely related to cancer development. However, the effect of epigenetic changes on cancer is still elusive. In this study, we analyzed DNA methylation data on colon cancer taken from The Caner Genome Atlas. We found that several promoters were significantly hypermethylated in colon cancer patients. Through clustering analysis of differentially methylated DNA regions, we were able to define subgroups of patients and observed clinical features associated with each subgroup...
June 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27445646/ultra-rare-disease-and-genomics-driven-precision-medicine
#13
REVIEW
Sangmoon Lee, Murim Choi
Since next-generation sequencing (NGS) technique was adopted into clinical practices, revolutionary advances in diagnosing rare genetic diseases have been achieved through translating genomic medicine into precision or personalized management. Indeed, several successful cases of molecular diagnosis and treatment with personalized or targeted therapies of rare genetic diseases have been reported. Still, there are several obstacles to be overcome for wider application of NGS-based precision medicine, including high sequencing cost, incomplete variant sensitivity and accuracy, practical complexities, and a shortage of available treatment options...
June 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27445645/editor-s-introduction-to-this-issue
#14
Yeun-Jun Chung
No abstract text is available yet for this article.
June 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27103889/non-negligible-occurrence-of-errors-in-gender-description-in-public-data-sets
#15
Jong Hwan Kim, Jong-Luyl Park, Seon-Young Kim
Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described...
March 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27103888/compiling-multicopy-single-stranded-dna-sequences-from-bacterial-genome-sequences
#16
Wonseok Yoo, Dongbin Lim, Sangsoo Kim
A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences...
March 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27103887/the-oauth-2-0-web-authorization-protocol-for-the-internet-addiction-bioinformatics-iabio-database
#17
REVIEW
Jeongseok Choi, Jaekwon Kim, Dong Kyun Lee, Kwang Soo Jang, Dai-Jin Kim, In Young Choi
Internet addiction (IA) has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet...
March 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27103886/neuropeptidomics-mass-spectrometry-based-identification-and-quantitation-of-neuropeptides
#18
REVIEW
Ji Eun Lee
Neuropeptides produced from prohormones by selective action of endopeptidases are vital signaling molecules, playing a critical role in a variety of physiological processes, such as addiction, depression, pain, and circadian rhythms. Neuropeptides bind to post-synaptic receptors and elicit cellular effects like classical neurotransmitters. While each neuropeptide could have its own biological function, mass spectrometry (MS) allows for the identification of the precise molecular forms of each peptide without a priori knowledge of the peptide identity and for the quantitation of neuropeptides in different conditions of the samples...
March 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27103885/network-based-protein-biomarker-discovery-platforms
#19
REVIEW
Minhyung Kim, Daehee Hwang
The advances in mass spectrometry-based proteomics technologies have enabled the generation of global proteome data from tissue or body fluid samples collected from a broad spectrum of human diseases. Comparative proteomic analysis of global proteome data identifies and prioritizes the proteins showing altered abundances, called differentially expressed proteins (DEPs), in disease samples, compared to control samples. Protein biomarker candidates that can serve as indicators of disease states are then selected as key molecules among these proteins...
March 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27103884/editor-s-introduction-to-this-issue
#20
Yeun-Jun Chung
No abstract text is available yet for this article.
March 2016: Genomics & Informatics
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