Journal of Data Mining in Genomics & Proteomics最新文献_第7页

Genome Mining and Comparative Genomic Analysis of Five Coagulase- Negative Staphylococci (CNS) Isolated from Human Colon and Gall Bladder 从人结肠和胆囊分离的5种凝固酶阴性葡萄球菌(CNS)的基因组挖掘和比较基因组分析

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-02-28 DOI: 10.4172/2153-0602.1000192

R. G. Nair, G. Kaur, Indu Khatri, N. Singh, S. K. Maurya, Srikrishna Subramanian, A. Behera, D. Dahiya, J. Agrewala, S. Mayilraj

{"title":"Genome Mining and Comparative Genomic Analysis of Five Coagulase- Negative Staphylococci (CNS) Isolated from Human Colon and Gall Bladder","authors":"R. G. Nair, G. Kaur, Indu Khatri, N. Singh, S. K. Maurya, Srikrishna Subramanian, A. Behera, D. Dahiya, J. Agrewala, S. Mayilraj","doi":"10.4172/2153-0602.1000192","DOIUrl":"https://doi.org/10.4172/2153-0602.1000192","url":null,"abstract":"Coagulase-negative Staphylococci (CNS) are known to cause distinct types of infections in humans like endocarditis and urinary tract infections (UTI). Surprisingly, there is a lack of genome analysis data in literature against CNS particularly of human origin. In light of this, we performed genome mining and comparative genomic analysis of CNS strains Staphylococcus cohnii subsp. cohnii strain GM22B2, Staphylococcus equorum subsp. strain equorum G8HB1, Staphylococcus pasteuri strain BAB3 isolated from gall bladder and Staphylococcus haemolyticus strain 1HT3, Staphylococcus warneri strain 1DB1 isolated from colon. We identified 29% of shared virulence determinants in the CNS strains which involved resistance to antibiotics and toxic compounds, bacteriocins and ribosomally synthesized peptides, adhesion, invasion, intracellular resistance, prophage regions, pathogenicity islands. 10 unique virulence factors involved in adhesion, negative transcriptional regulation, resistance to copper and cadmium, phage maturation were also present in our strains. Apart from comparing the genome homology, size and G + C content, we also showed the presence 10 different CRISPR-cas genes in the CNS strains. Further, KAAS based annotation revealed the presence of CNS genes in different pathways involved in human diseases. In conclusion, this study is a first attempt to unveil the pathogenomics of CNS isolated from two distinct body organs and highlights the importance of CNS as emerging pathogens of health care sector.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"37 1","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2016-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75397581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Learning Machine Implementation for Big Data Analytics, Challenges and Solutions 学习机器实现大数据分析，挑战和解决方案

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-02-22 DOI: 10.4172/2153-0602.1000190

A. N. Al-Masri, Manal M. Nasir

引用次数: 1

Physicochemical Properties of Proteomic Ionic Liquids Matrices for MALDI-MS MALDI-MS中蛋白质组离子液体基质的理化性质研究

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-02-17 DOI: 10.4172/2153-0602.1000189

H. Abdelhamid

引用次数: 11

Conceptual Aspects of Causal Networks in an Applied Context 应用环境中因果网络的概念方面

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-02-17 DOI: 10.4172/2153-0602.1000188

A. Yazdani, A. Yazdani, E. Boerwinkle

引用次数: 7

Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus 基于Imex的黄病毒基因组重复序列分析，包括登革病毒

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-02-06 DOI: 10.4172/2153-0602.1000187

Chaudhary Mashhood Alam, A. Iqbal, Babita Thadari, Safdar Ali

{"title":"Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus","authors":"Chaudhary Mashhood Alam, A. Iqbal, Babita Thadari, Safdar Ali","doi":"10.4172/2153-0602.1000187","DOIUrl":"https://doi.org/10.4172/2153-0602.1000187","url":null,"abstract":"Simple sequence repeats (SSRs), also known as microsatellites, are 1-6 nucleotides repeat motif, present in varying number of iterations, across coding and non-coding regions of prokaryotes, eukaryotes and viruses. Present study focuses on simple sequence repeats (SSRs) in 27 Flavivirus genomes, which includes dengue virus. The comparative viral genomics in the light of SSRs would help us understand the diversity and adaptability to new hosts. A total of 1164 SSRs and 53 cSSRs were uncovered from the 27studied genomes. Mononucleotide A was the most prevalent repeat motif with an average distribution of around 6. This was followed by G (average distribution of 2). Amongst the dinucleotides AG/GA repeat motif was the most prevalent with an average distribution of 14 across studied genomes. The Flavivirus genomes lacked two essential features responsible for genome evolution, dinucleotide repeat motif AT/TA (least represented with average distribution of ~0.5) and cSSR in non-coding regions, suggesting a stable genome or evolution by hitherto unexplained mechanisms. The unveiling of conserved sequences in the isolates of Dengue virus suggests a basis for biomarker development for viral diagnostics.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"6 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2016-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77044016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Family history, genetics services, and cancer risk perception at Brazilian unified health system 巴西统一卫生系统的家族史、遗传服务和癌症风险认知

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-02-04 DOI: 10.4172/2153-0602.S1.004

Milena FloriaSantos

引用次数: 0

Pharmacogenomics of AML: A road towards personalized medicine

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-02-04 DOI: 10.4172/2153-0602.S1.002

J. Lamba

{"title":"Pharmacogenomics of AML: A road towards personalized medicine","authors":"J. Lamba","doi":"10.4172/2153-0602.S1.002","DOIUrl":"https://doi.org/10.4172/2153-0602.S1.002","url":null,"abstract":"Acute myeloid leukemia (AML) is the second most common form of childhood leukemia and has the worst prognosis of all major childhood cancers. Improving the treatment outcome for patients with AML remains a major clinical challenge. The nucleoside analog, cytarabine (ara-C), has been the mainstay of AML chemotherapy for more than 40 years. However, wide inter-patient variation in treatment response, development of resistance, and severe toxicity remain as major hurdles to effective ara-C chemotherapy. Ara-C is a prodrug that requires activation to ara-CTP by multiple phosphorylation steps. Incorporation of ara-CTP in place of dCTP results in chain termination, thereby blocking DNA and RNA synthesis and causing leukemic cell death. Thus, cellular pathways involved in ara-CTP formation and metabolism as well as in ara-CTP mediated cell death are likely to be significant determinants of ara-C treatment response. Inter-patient variation in relevant pharmacokinetic (PK) and pharmacodynamic (PD) genes may impact the clinical response and toxicity among patients receiving ara-C. We have evaluated genes of importance in ara-C chemotherapy and have found that genetic variation in the ara-C pathway genes had similar prognostic relevance as the well-established factors listed above. We will share our results on ara-C pharmcogenomics and its impact on clinical outcome in AM. Overall our results indicate that understanding of genetic variation in key ara-C metabolic pathway genes might be clinically relevant by providing additional explanation of the variability in clinical response beyond known prognostic factors and might have the potential of being additional prognostic markers of clinical outcome.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"136 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72692418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Comparative genomics: From genome sequences to genome biology 比较基因组学:从基因组序列到基因组生物学

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-02-04 DOI: 10.4172/2153-0602.C1.003

Michael Y. Galperin

{"title":"Comparative genomics: From genome sequences to genome biology","authors":"Michael Y. Galperin","doi":"10.4172/2153-0602.C1.003","DOIUrl":"https://doi.org/10.4172/2153-0602.C1.003","url":null,"abstract":"We have developed an invitro model system that consists of 300 human lymphoblastoid cell lines (LCLs) with extensive highthrough genomic data including genome wide SNPs, basal expression array, CpG methylation and microRNA data, together with drug cytotoxicity data to help identify candidate genes that might contribute to chemoresistance and response to targeted therapy and at the same time, to help understand the mechanisms involved in the variation in drug response. We have used this system to identify genes such as NT5C3 and FKBP5 that are important for response to cytidine analogues, gemcitabine and AraC, drugs that are commonly used to treat pancreatic, breast and hematological tumors. In addition, this system also allows us to validate biologically any signals identified during our clinical pharmacogenomic GWA studies. We have performed a GWAS using DNA samples from the largest breast cancer prevention trials, the NSABP P-1 and P-2 SERM (selective estrogen receptor modulator) prevention to identify markers that are associated with breast cancer risk after exposure to SERMs, tamoxifen and raloxifene. During the course of that study, we identified SNP signals in two genes, ZNF423 and CTSO showing that the risk alleles of these two SNP signals associated with Odds Ratio of 5.71 for breast cancer risk. Functional genomic studies further found a SNP dependent, estrogen or SERM dependent regulation of ZNF423 and CTSO expression, which is in parallel with the regulation of BRCA1 expression. These approaches using the LCL model let us to identify not only the potential candidate genes that could funciton as biomarkers for response to therapy but also help reveal novel biology underlying these genes and their involvement in regulation of important pathways in tumor growth and response to therapy.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"311 2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72966226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Identification of Host-Specific Genetic Markers within 16S rDNA Intervening Sequences of 73 Genera of Fecal Bacteria 73属粪便细菌16S rDNA介入序列中宿主特异性遗传标记的鉴定

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-01-31 DOI: 10.4172/2153-0602.1000186

Zhenyu Shen, Ning Zhang, A. Mustapha, Mengshi Lin, Dong Xu, Daiyong Deng, M. Reed, Guolu Zheng

{"title":"Identification of Host-Specific Genetic Markers within 16S rDNA Intervening Sequences of 73 Genera of Fecal Bacteria","authors":"Zhenyu Shen, Ning Zhang, A. Mustapha, Mengshi Lin, Dong Xu, Daiyong Deng, M. Reed, Guolu Zheng","doi":"10.4172/2153-0602.1000186","DOIUrl":"https://doi.org/10.4172/2153-0602.1000186","url":null,"abstract":"Ribosomal intervening sequences (IVSs) were recently proposed as genetic markers for microbial source tracking (MST). This study comprehensively investigated host specificities of IVSs within the 16S rDNA of 73 genera of dominant fecal bacteria using the approaches of bioinformatics and next generation sequencing (NGS). Thirteen types of IVSs were identified in silico to be associated with particular host species; they were found within bacteria of the genera Anaerovibrio, Bacteroides, Faecalibacterium, Mitsuokella, Peptostreptococcus, Phascolarctobacterium, and Subdoligranulum. Based on the DNA sequences of the thirteen types of IVSs, polymerase chain reaction (PCR) assays were developed. PCR amplifications using fecal DNA samples of target and non-target host species demonstrated that eight out of the 13 IVSs were highly associated with human, chicken/turkey, beef cattle/pig, or horse/pig/human feces. Based on the IVS polymorphisms, NGS was applied to search for single-host-associated IVSs from those linked to multiple host species. Consequently, a new type of IVS specific to beef cattle was found and confirmed by PCR amplification using cattle and non-cattle fecal samples. The results suggest that some IVSs may be used as the genetic markers for MST and that NGS may be useful in identifying novel host-specific genetic markers.","PeriodicalId":15630,"journal":{"name":"Journal of Data Mining in Genomics & Proteomics","volume":"60 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2016-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90589872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Mining Datasets for Molecular Subtyping in Cancer 癌症分子分型的数据挖掘

Journal of Data Mining in Genomics & Proteomics Pub Date : 2016-01-20 DOI: 10.4172/2153-0602.1000185

Sally Yepes, M. M. Torres

引用次数: 3