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Genomics & Informatics

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https://www.readbyqxmd.com/read/29020726/mergereference-a-tool-for-merging-reference-panels-for-hla-imputation
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
EDITORIAL
Yeun-Jun Chung
No abstract text is available yet for this article.
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416950/trapr-r-package-for-statistical-analysis-and-visualization-of-rna-seq-data
#10
Jae Hyun Lim, Soo Youn Lee, Ju Han Kim
High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416949/circulating-tumor-dna-in-a-breast-cancer-patient-s-plasma-represents-driver-alterations-in-the-tumor-tissue
#11
Jieun Lee, Sung-Min Cho, Min Sung Kim, Sug Hyung Lee, Yeun-Jun Chung, Seung-Hyun Jung
Tumor tissues from biopsies or surgery are major sources for the next generation sequencing (NGS) study, but these procedures are invasive and have limitation to overcome intratumor heterogeneity. Recent studies have shown that driver alterations in tumor tissues can be detected by liquid biopsy which is a less invasive technique capable of both capturing the tumor heterogeneity and overcoming the difficulty in tissue sampling. However, it is still unclear whether the driver alterations in liquid biopsy can be detected by targeted NGS and how those related to the tissue biopsy...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416948/comparative-analysis-of-predicted-gene-expression-among-crenarchaeal-genomes
#12
Shibsankar Das, Brajadulal Chottopadhyay, Satyabrata Sahoo
Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416947/dna-methylation-profiles-of-blood-cells-are-distinct-between-early-onset-obese-and-control-individuals
#13
Je-Keun Rhee, Jin-Hee Lee, Hae Kyung Yang, Tae-Min Kim, Kun-Ho Yoon
Obesity is a highly prevalent, chronic disorder that has been increasing in incidence in young patients. Both epigenetic and genetic aberrations may play a role in the pathogenesis of obesity. Therefore, in-depth epigenomic and genomic analyses will advance our understanding of the detailed molecular mechanisms underlying obesity and aid in the selection of potential biomarkers for obesity in youth. Here, we performed microarray-based DNA methylation and gene expression profiling of peripheral white blood cells obtained from six young, obese individuals and six healthy controls...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416946/use-of-graph-database-for-the-integration-of-heterogeneous-biological-data
#14
Byoung-Ha Yoon, Seon-Kyu Kim, Seon-Young Kim
Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416945/a-chip-seq-data-analysis-pipeline-based-on-bioconductor-packages
#15
Seung-Jin Park, Jong-Hwan Kim, Byung-Ha Yoon, Seon-Young Kim
Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416944/evaluation-of-digital-pcr-as-a-technique-for-monitoring-acute-rejection-in-kidney-transplantation
#16
Hyeseon Lee, Young-Mi Park, Yu-Mee We, Duck Jong Han, Jung-Woo Seo, Haena Moon, Yu-Ho Lee, Yang-Gyun Kim, Ju-Young Moon, Sang-Ho Lee, Jong-Keuk Lee
Early detection and proper management of kidney rejection are crucial for the long-term health of a transplant recipient. Recipients are normally monitored by serum creatinine measurement and sometimes with graft biopsies. Donor-derived cell-free deoxyribonucleic acid (cfDNA) in the recipient's plasma and/or urine may be a better indicator of acute rejection. We evaluated digital PCR (dPCR) as a system for monitoring graft status using single nucleotide polymorphism (SNP)-based detection of donor DNA in plasma or urine...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416943/editor-s-introduction-to-this-issue-g-i-15-1-2017
#17
EDITORIAL
Yeun-Jun Chung
No abstract text is available yet for this article.
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28154519/mining-the-proteome-of-fusobacterium-nucleatum-subsp-nucleatum-atcc-25586-for-potential-therapeutics-discovery-an-in-silico-approach
#18
Abdul Musaweer Habib, Md Saiful Islam, Md Sohel, Md Habibul Hasan Mazumder, Mohd Omar Faruk Sikder, Shah Md Shahik
The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154518/drug-target-identification-and-elucidation-of-natural-inhibitors-for-bordetella-petrii-an-in-silico-study
#19
Surya Narayan Rath, Manisha Ray, Animesh Pattnaik, Sukanta Kumar Pradhan
Environmental microbes like Bordetella petrii has been established as a causative agent for various infectious diseases in human. Again, development of drug resistance in B. petrii challenged to combat against the infection. Identification of potential drug target and proposing a novel lead compound against the pathogen has a great aid and value. In this study, bioinformatics tools and technology have been applied to suggest a potential drug target by screening the proteome information of B. petrii DSM 12804 (accession No...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154517/tissue-specific-expression-levels-of-apoptosis-involved-genes-have-correlations-with-codon-and-amino-acid-usage
#20
Mohammadreza Hajjari, Iman Sadeghi, Abbas Salavaty, Habib Nasiri, Maryam Tahmasebi Birgani
Different mechanisms, including transcriptional and post transcriptional processes, regulate tissue specific expression of genes. In this study, we report differences in gene/protein compositional features between apoptosis involved genes selectively expressed in human tissues. We found some correlations between codon/amino acid usage and tissue specific expression level of genes. The findings can be significant for understanding the translational selection on these features. The selection may play an important role in the differentiation of human tissues and can be considered for future studies in diagnosis of some diseases such as cancer...
December 2016: Genomics & Informatics
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