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Genomics & Informatics

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https://www.readbyqxmd.com/read/28154519/mining-the-proteome-of-fusobacterium-nucleatum-subsp-nucleatum-atcc-25586-for-potential-therapeutics-discovery-an-in-silico-approach
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/28154516/demographic-trends-in-korean-native-cattle-explained-using-bovine-snp50-beadchip
#4
Aditi Sharma, Dajeong Lim, Han-Ha Chai, Bong-Hwan Choi, Yongmin Cho
Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154515/metabolic-pathways-associated-with-kimchi-a-traditional-korean-food-based-on-in-silico-modeling-of-published-data
#5
Ga Hee Shin, Byeong-Chul Kang, Dai Ja Jang
Kimchi is a traditional Korean food prepared by fermenting vegetables, such as Chinese cabbage and radishes, which are seasoned with various ingredients, including red pepper powder, garlic, ginger, green onion, fermented seafood (Jeotgal), and salt. The various unique microorganisms and bioactive components in kimchi show antioxidant activity and have been associated with an enhanced immune response, as well as anti-cancer and anti-diabetic effects. Red pepper inhibits decay due to microorganisms and prevents food from spoiling...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154514/identification-of-a-copy-number-variation-on-chromosome-20q13-12-associated-with-osteoporotic-fractures-in-the-korean-population
#6
Tae-Joon Park, Mi Yeong Hwang, Sanghoon Moon, Joo-Yeon Hwang, Min Jin Go, Bong-Jo Kim
Osteoporotic fractures (OFs) are critical hard outcomes of osteoporosis and are characterized by decreased bone strength induced by low bone density and microarchitectural deterioration in bone tissue. Most OFs cause acute pain, hospitalization, immobilization, and slow recovery in patients and are associated with increased mortality. A variety of genetic studies have suggested associations of genetic variants with the risk of OF. Genome-wide association studies have reported various single-nucleotide polymorphisms and copy number variations (CNVs) in European and Asian populations...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154513/investigation-of-splicing-quantitative-trait-loci-in-arabidopsis-thaliana
#7
Wonseok Yoo, Sungkyu Kyung, Seonggyun Han, Sangsoo Kim
The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs)...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154512/interleukin-10-polymorphisms-in-association-with-prognosis-in-patients-with-b-cell-lymphoma-treated-by-r-chop
#8
Min Kyeong Kim, Kyong-Ah Yoon, Eun Young Park, Jungnam Joo, Eun Young Lee, Hyeon-Seok Eom, Sun-Young Kong
Interleukin-10 (IL10) plays an important role in initiating and maintaining an appropriate immune response to non-Hodgkin lymphoma (NHL). Previous studies have revealed that the transcription of IL10 mRNA and its protein expression may be infl uenced by several single-nucleotide polymorphisms in the promoter and intron regions, including rs1800896, rs1800871, and rs1800872. However, the impact of polymorphisms of the IL10 gene on NHL prognosis has not been fully elucidated. Here, we investigated the association between IL10 polymorphisms and NHL prognosis...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154511/effects-of-single-nucleotide-polymorphism-marker-density-on-haplotype-block-partition
#9
Sun Ah Kim, Yun Joo Yoo
Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154510/multiple-group-testing-procedures-for-analysis-of-high-dimensional-genomic-data
#10
Hyoseok Ko, Kipoong Kim, Hokeun Sun
In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154509/genetic-association-analysis-of-fasting-and-1-and-2-hour-glucose-tolerance-test-data-using-a-generalized-index-of-dissimilarity-measure-for-the-korean-population
#11
Jaeyong Yee, Yongkang Kim, Taesung Park, Mira Park
Glucose tolerance tests have been devised to determine the speed of blood glucose clearance. Diabetes is often tested with the standard oral glucose tolerance test (OGTT), along with fasting glucose level. However, no single test may be sufficient for the diagnosis, and the World Health Organization (WHO)/International Diabetes Federation (IDF) has suggested composite criteria. Accordingly, a single multi-class trait was constructed with three of the fasting phenotypes and 1- and 2-hour OGTT phenotypes from the Korean Association Resource (KARE) project, and the genetic association was investigated...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154508/comparison-of-two-meta-analysis-methods-inverse-variance-weighted-average-and-weighted-sum-of-z-scores
#12
Cue Hyunkyu Lee, Seungho Cook, Ji Sung Lee, Buhm Han
The meta-analysis has become a widely used tool for many applications in bioinformatics, including genome-wide association studies. A commonly used approach for meta-analysis is the fixed effects model approach, for which there are two popular methods: the inverse variance-weighted average method and weighted sum of z-scores method. Although previous studies have shown that the two methods perform similarly, their characteristics and their relationship have not been thoroughly investigated. In this paper, we investigate the optimal characteristics of the two methods and show the connection between the two methods...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154507/gene-gene-interaction-analysis-for-the-accelerated-failure-time-model-using-a-unified-model-based-multifactor-dimensionality-reduction-method
#13
Seungyeoun Lee, Donghee Son, Wenbao Yu, Taesung Park
Although a large number of genetic variants have been identified to be associated with common diseases through genome-wide association studies, there still exits limitations in explaining the missing heritability. One approach to solving this missing heritability problem is to investigate gene-gene interactions, rather than a single-locus approach. For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely applied, since the constructive induction algorithm of MDR efficiently reduces high-order dimensions into one dimension by classifying multi-level genotypes into high- and low-risk groups...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154506/efficient-strategy-to-identify-gene-gene-interactions-and-its-application-to-type-2-diabetes
#14
Donghe Li, Sungho Won
Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide polymorphisms. However, such tests are computationally demanding and methodologically challenging. Recently, a simple but powerful method, named "BOolean Operation-based Screening and Testing" (BOOST), was proposed for genome-wide gene-gene interaction analyses...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154505/prediction-of-quantitative-traits-using-common-genetic-variants-application-to-body-mass-index
#15
Sunghwan Bae, Sungkyoung Choi, Sung Min Kim, Taesung Park
With the success of the genome-wide association studies (GWASs), many candidate loci for complex human diseases have been reported in the GWAS catalog. Recently, many disease prediction models based on penalized regression or statistical learning methods were proposed using candidate causal variants from significant single-nucleotide polymorphisms of GWASs. However, there have been only a few systematic studies comparing existing methods. In this study, we first constructed risk prediction models, such as stepwise linear regression (SLR), least absolute shrinkage and selection operator (LASSO), and Elastic-Net (EN), using a GWAS chip and GWAS catalog...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154504/risk-prediction-using-genome-wide-association-studies-on-type-2-diabetes
#16
Sungkyoung Choi, Sunghwan Bae, Taesung Park
The success of genome-wide association studies (GWASs) has enabled us to improve risk assessment and provide novel genetic variants for diagnosis, prevention, and treatment. However, most variants discovered by GWASs have been reported to have very small effect sizes on complex human diseases, which has been a big hurdle in building risk prediction models. Recently, many statistical approaches based on penalized regression have been developed to solve the "large p and small n" problem. In this report, we evaluated the performance of several statistical methods for predicting a binary trait: stepwise logistic regression (SLR), least absolute shrinkage and selection operator (LASSO), and Elastic-Net (EN)...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28154503/editor-s-introduction-to-this-issue
#17
EDITORIAL
Taesung Park
No abstract text is available yet for this article.
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/27729842/sequence-analysis-of-hypothetical-proteins-from-helicobacter-pylori-26695-to-identify-potential-virulence-factors
#18
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
#19
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
#20
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
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