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Genomics & Informatics

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https://www.readbyqxmd.com/read/29307145/ivag-an-integrative-visualization-application-for-various-types-of-genomic-data-based-on-r-shiny-and-the-docker-platform
#1
Tae-Rim Lee, Jin Mo Ahn, Gyuhee Kim, Sangsoo Kim
Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307144/hotair-long-non-coding-rna-characterizing-the-locus-features-by-the-in-silico-approaches
#2
Mohammadreza Hajjari, Saghar Rahnama
HOTAIR is an lncRNA that has been known to have an oncogenic role in different cancers. There is limited knowledge of genetic and epigenetic elements and their interactions for the gene encoding HOTAIR. Therefore, understanding the molecular mechanism and its regulation remains to be challenging. We used different in silico analyses to find genetic and epigenetic elements of HOTAIR gene to gain insight into its regulation. We reported different regulatory elements including canonical promoters, transcription start sites, CpGIs as well as epigenetic marks that are potentially involved in the regulation of HOTAIR gene expression...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307143/prediction-of-metal-ion-binding-sites-in-proteins-from-amino-acid-sequences-by-using-simplified-amino-acid-alphabets-and-random-forest-model
#3
Suresh Kumar
Metal binding proteins or metallo-proteins are important for the stability of the protein and also serve as co-factors in various functions like controlling metabolism, regulating signal transport, and metal homeostasis. In structural genomics, prediction of metal binding proteins help in the selection of suitable growth medium for overexpression's studies and also help in obtaining the functional protein. Computational prediction using machine learning approach has been widely used in various fields of bioinformatics based on the fact all the information contains in amino acid sequence...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307142/classification-of-genes-based-on-age-related-differential-expression-in-breast-cancer
#4
Gunhee Lee, Minho Lee
Transcriptome analysis has been widely used to make biomarker panels to diagnose cancers. In breast cancer, the age of the patient has been known to be associated with clinical features. As clinical transcriptome data have accumulated significantly, we classified all human genes based on age-specific differential expression between normal and breast cancer cells using public data. We retrieved the values for gene expression levels in breast cancer and matched normal cells from The Cancer Genome Atlas. We divided genes into two classes by paired t test without considering age in the first classification...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307141/identification-of-new-potential-ape1-inhibitors-by-pharmacophore-modeling-and-molecular-docking
#5
In Won Lee, Jonghwan Yoon, Gunhee Lee, Minho Lee
Apurinic/apyrimidinic endonuclease 1 (APE1) is an enzyme responsible for the initial step in the base excision repair pathway and is known to be a potential drug target for treating cancers, because its expression is associated with resistance to DNA-damaging anticancer agents. Although several inhibitors already have been identified, the identification of novel kinds of potential inhibitors of APE1 could provide a seed for the development of improved anticancer drugs. For this purpose, we first classified known inhibitors of APE1...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307140/structural-analysis-of-recombinant-human-preproinsulins-by-structure-prediction-molecular-dynamics-and-protein-protein-docking
#6
Sung Hun Jung, Chang-Kyu Kim, Gunhee Lee, Jonghwan Yoon, Minho Lee
More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307139/validation-of-customized-cancer-panel-for-detecting-somatic-mutations-and-copy-number-alterations
#7
Su-Hye Choi, Seung-Hyun Jung, Yeun-Jun Chung
Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307138/mismm-an-integrated-pipeline-for-misassembly-detection-using-genotyping-by-sequencing-and-its-validation-with-bac-end-library-sequences-and-gene-synteny
#8
Young-Joon Ko, Jung Sun Kim, Sangsoo Kim
As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307137/synonymous-codon-usage-controls-various-molecular-aspects
#9
REVIEW
Eu-Hyun Im, Sun Shim Choi
Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307136/ctcf-cohesin-and-chromatin-in-human-cancer
#10
REVIEW
Sang-Hyun Song, Tae-You Kim
It is becoming increasingly clear that eukaryotic genomes are subjected to higher-order chromatin organization by the CCCTC-binding factor/cohesin complex. Their dynamic interactions in three dimensions within the nucleus regulate gene transcription by changing the chromatin architecture. Such spatial genomic organization is functionally important for the spatial disposition of chromosomes to control cell fate during development and differentiation. Thus, the dysregulation of proper long-range chromatin interactions may influence the development of tumorigenesis and cancer progression...
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29307135/editor-s-introduction-to-this-issue-g-i-15-4-2017
#11
Yeun-Jun Chung
No abstract text is available yet for this article.
December 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29020726/mergereference-a-tool-for-merging-reference-panels-for-hla-imputation
#12
Seungho Cook, Buhm Han
Recently developed computational methods allow the imputation of human leukocyte antigen (HLA) genes using intergenic single nucleotide polymorphism markers. To improve the imputation accuracy in HLA imputation, it is essential to increase the sample size and the diversity of alleles in the reference panel. Our software, MergeReference, helps achieve this goal by providing a streamlined pipeline for combining multiple reference panels into one.
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29020725/genomic-analysis-of-mir-21-3p-and-expression-pattern-with-target-gene-in-olive-flounder
#13
Ara Jo, Hee-Eun Lee, Heui-Soo Kim
MicroRNAs (miRNAs) act as regulators of gene expression by binding to the 3' untranslated region (UTR) of target genes. They perform important biological functions in the various species. Among many miRNAs, miR-21-3p is known to serve vital functions in development and apoptosis in olive flounder. Using genomic and bioinformatic tools, evolutionary conservation of miR-21-3p was examined in various species, and expression pattern was analyzed in olive flounder. Conserved sequences (5'-CAGUCG-3') in numerous species were detected through the stem-loop structure of miR-21-3p...
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29020724/chromothripsis-in-treatment-resistance-in-multiple-myeloma
#14
Kyoung Joo Lee, Ki Hong Lee, Kyong-Ah Yoon, Ji Yeon Sohn, Eunyoung Lee, Hyewon Lee, Hyeon-Seok Eom, Sun-Young Kong
Multiple myeloma (MM) is a malignant disease caused by an abnormal proliferation of plasma cells, of which the prognostic factors include chromosomal abnormality, β-2 microglobulin, and albumin. Recently, the term chromothripsis has emerged, which is the massive but highly localized chromosomal rearrangement in response to a one-step catastrophic event. Many studies have shown an association of chromothripsis with the prognosis in several cancers; however, few studies have investigated it in MM. Here, we studied the association between chromothripsis-like patterns and treatment resistance or prognosis...
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29020723/chromosomal-microarray-testing-in-42-korean-patients-with-unexplained-developmental-delay-intellectual-disability-autism-spectrum-disorders-and-multiple-congenital-anomalies
#15
Sun Ho Lee, Wung Joo Song
Chromosomal microarray (CMA) is a high-resolution, high-throughput method of identifying submicroscopic genomic copy number variations (CNVs). CMA has been established as the first-line diagnostic test for individuals with developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), and multiple congenital anomalies (MCAs). CMA analysis was performed in 42 Korean patients who had been diagnosed with unexplained DD, ID, ASDs, and MCAs. Clinically relevant CNVs were discovered in 28 patients...
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29020722/editor-s-introduction-to-this-issue-g-i-15-3-2017
#16
Yeun-Jun Chung
No abstract text is available yet for this article.
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28638312/in-silico-signature-prediction-modeling-in-cytolethal-distending-toxin-producing-escherichia-coli-strains
#17
Maryam Javadi, Mana Oloomi, Saeid Bouzari
In this study, cytolethal distending toxin (CDT) producer isolates genome were compared with genome of pathogenic and commensal Escherichia coli strains. Conserved genomic signatures among different types of CDT producer E. coli strains were assessed. It was shown that they could be used as biomarkers for research purposes and clinical diagnosis by polymerase chain reaction, or in vaccine development. cdt genes and several other genetic biomarkers were identified as signature sequences in CDT producer strains...
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28638311/a-variant-in-runx3-is-associated-with-the-risk-of-ankylosing-spondylitis-in-koreans
#18
Sung-Min Cho, Seung-Hyun Jung, Yeun-Jun Chung
Ankylosing spondylitis (AS) is a chronic autoinflammatory disease that affects the spine and sacroiliac joints. Regarding its etiology, although HLA-B27 is known to be the strongest genetic factor of AS, much evidence suggests the potential contribution of non-MHC genes to the susceptibility to AS. Most of these non-MHC genes have been discovered in non-Asian populations; however, just some of them have been validated in Koreans. In this study, we aimed to identify additional AS-associated single-nucleotide polymorphism (SNP) candidates by replicating the candidate SNPs in Korean AS patients and healthy controls...
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28638310/analysis-of-gene-expression-in-human-dermal-fibroblasts-treated-with-senescence-modulating-cox-inhibitors
#19
Jeong A Han, Jong-Il Kim
We have previously reported that NS-398, a cyclooxygenase-2 (COX-2)-selective inhibitor, inhibited replicative cellular senescence in human dermal fibroblasts and skin aging in hairless mice. In contrast, celecoxib, another COX-2-selective inhibitor, and aspirin, a non-selective COX inhibitor, accelerated the senescence and aging. To figure out causal factors for the senescence-modulating effect of the inhibitors, we here performed cDNA microarray experiment and subsequent Gene Set Enrichment Analysis. The data showed that several senescence-related gene sets were regulated by the inhibitor treatment...
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28638309/editor-s-introduction-to-this-issue-g-i-15-2-2017
#20
EDITORIAL
Yeun-Jun Chung
No abstract text is available yet for this article.
June 2017: Genomics & Informatics
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