2016 International Conference on Bioinformatics and Systems Biology (BSB)最新文献_第5页

Count-based transcriptome analysis to identify differentially expressed genes for breast cancer 基于计数的转录组分析鉴定乳腺癌差异表达基因

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552147

R. Tripathi, Pawan Sharma, P. Chakraborty, P. Varadwaj

{"title":"Count-based transcriptome analysis to identify differentially expressed genes for breast cancer","authors":"R. Tripathi, Pawan Sharma, P. Chakraborty, P. Varadwaj","doi":"10.1109/BSB.2016.7552147","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552147","url":null,"abstract":"Sequencing the coding regions or the whole cancer transcriptome can provide valuable information about the differential expression patterns of the genes. Previous researches centered on ~2% of coding human genome, assuming that the non-coding sequences were “junk” lacking significant functional information. Recent medical research show that a major percentage of the human genome (~70-90%) are non-coding, stored in the cell in the form of non-coding RNA (ncRNA) which overshadows the coding information limited only to a small percentage. These ncRNAs are composed of mostly ultraconserved elements, lacking protein-coding potential and regulating gene expression acting as enhancers whose aberrant expression may be involved in pathological process such as cancer. Here, we have described RNA-seq data analysis for the profiling of transcriptome of Breast cells and provided a generic outline of the whole pipeline from next-generation sequencing (NGS) output for quantification of differential gene expression across different conditions (e.g., control vs test). We have used tool Cufflinks-Cuffdiff to estimate transcript-level expression for gene discovery extracted from high-throughput RNA-seq data across distinct conditions that represent candidate biomarkers for future research. This study provides the survey of coding transcripts associated genes expression within a cancer system.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"454 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122938079","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: 1

In-silico structure prediction and domain characterization of inter alpha trypsin inhibitor heavy chain 4 胰蛋白酶抑制剂重链4的硅结构预测及结构域表征

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552125

Ankita Sharma, R. Malhotra, P. Kumari, S. Biswas, G. Soundhara Rajan

引用次数: 1

Meta-analysis of potential miRNA in Triticum astivum reveals their genome biased association with different metabolisms EST based potential miRNA identification in wheat 基于EST的小麦潜在miRNA鉴定表明，小麦潜在miRNA的基因组偏倚与不同代谢相关

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552126

D. Nigam, Puneet Kumar Kadimi, Sanjeev Kumar, D. Mishra, P. Pandey, Manoj Kumar singh, A. Rai, Subodh Kumar Sinha

{"title":"Meta-analysis of potential miRNA in Triticum astivum reveals their genome biased association with different metabolisms EST based potential miRNA identification in wheat","authors":"D. Nigam, Puneet Kumar Kadimi, Sanjeev Kumar, D. Mishra, P. Pandey, Manoj Kumar singh, A. Rai, Subodh Kumar Sinha","doi":"10.1109/BSB.2016.7552126","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552126","url":null,"abstract":"MicroRNAs (miRNAs) are the key modulators implicated in the regulation of virtually every biological process found in multicellular eukaryotes. Wheat (Triticum aestivum) is one of the most important cereal crops worldwide. To date, only a few conserved miRNAs have been reported in wheat and their association with different metabolic process is still in dark. Therefore, the present study we attempt to predict miRNA and their association with metabolic pathways in wheat. Total 39 potential mature miRNA's were predicted using 1287279 ESTs of wheat and 8496 known mature miRNA's, along with their precursor sequences, of Viridiplantae. Overall, 11380 genome wise target genes across 21 chromosomes were identified and functionally characterized via meta-analysis. As a result, genome wise miRNA-targets signatures under different conditions and their regulatory pathways along with network structures were examined. Here, a concept of “miRNA community” was proposed and a miRNA community linked with nitrogen metabolism was identified. Top two potential miRNA's from this community were verified by stem loop pulsed RT-PCR for their expression in root and leaf tissue under nitrogen starvation. Exploration of such type of miRNAs communities will provide in depth understanding of metabolic processes that may leads to improved genotypes.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"53 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114786886","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: 0

Stilbene analogues as inhibitors of breast cancer Stem cells through P-glycoprotein efflux; A 3D quantitative structure-activity relationship study (Inhibitory activity of stilbenes analogues on breast cancer stem cells) 二苯乙烯类似物通过p -糖蛋白外排抑制乳腺癌干细胞二苯乙烯类似物对乳腺癌干细胞抑制活性的三维定量构效关系研究

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552134

A. Tripathi, K. Misra

引用次数: 4

Embryo and endosperm specific comparative transcriptome analysis of triticum aestivum in response to ABA and H2O2 stress ABA和H2O2胁迫下小麦胚和胚乳特异性比较转录组分析

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552157

Saurabh Gupta, Utkarsh Raj, Himansu Kumar, Pritish Kumar Varadwaj, Adhyana Gupta

{"title":"Embryo and endosperm specific comparative transcriptome analysis of triticum aestivum in response to ABA and H2O2 stress","authors":"Saurabh Gupta, Utkarsh Raj, Himansu Kumar, Pritish Kumar Varadwaj, Adhyana Gupta","doi":"10.1109/BSB.2016.7552157","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552157","url":null,"abstract":"Wheat seed germination directly affects wheat yield and quality. Embryo and endosperm are two main parts of wheat seed and plays crucial role in seed germination and subsequent plant growth and other development. In the process of seed germination a systematic bi-directional molecular interactions are major component and that got affected by the means of abiotic stresses. A variety of proteomic and transcriptomic approaches have been used so far to investigate seed germination process in response to abiotic stresses. In this study, we have investigated deferentially expressed genes/transcripts (DEGs) of embryo and endosperm in response to ABA and H2O2 stress by the means of stress systems biology approaches using microarray data. Further, role of DEGs in response to each stress was explored, which identify biological and molecular functions of genes during seed germination embryo and endosperm. Our results provide the insight into comparative transcriptomic mechanism of the embryo and endosperm in response to ABA and H2O2 treatment during seed germination process.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131139908","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

A bioinformatics study of miRNAs and their regulating targets in Curcuma longa (turmeric) 姜黄mirna及其调控靶点的生物信息学研究

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552160

Noopur Singh, S. Srivastava, Ashok Sharma

{"title":"A bioinformatics study of miRNAs and their regulating targets in Curcuma longa (turmeric)","authors":"Noopur Singh, S. Srivastava, Ashok Sharma","doi":"10.1109/BSB.2016.7552160","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552160","url":null,"abstract":"microRNAs are small, endogenous, noncoding RNA, work at post-transcriptional level and control the gene regulation in animals and plants. Turmeric is an Asian medicinal plant known for its medicinal properties. The present work focused on identification of the miRNAs take part in the developmental process of turmeric. Eight miRNA families (miR156, miR157, miR159, miR170, miR171, miR319, miR396 and miR5015) were identified by using bioinformatics approach. Phylogenetic analysis of selective miRNAs was performed. Six miRNA families were observed to regulate eighty-six target transcripts. Our results further indicated their role in binding, reproduction, stress and other developmental process. Gene annotation and pathway analysis illustrate the biological function of the targets regulated by the putative miRNAs. Involvement of miR156 and miR5015 in the regulation of rhizome development was also observed. Other miRNAs were found to be involved in the growth and developmental process of turmeric. To the best of our knowledge, this is the first report on miRNA prediction and regulation in turmeric.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"115 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133795873","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: 1

Modeling and simulation analysis of Salmonella typhimurium inside human epithelial cells: Host-pathogen relationship analysis by system biology 人上皮细胞内鼠伤寒沙门菌的建模和模拟分析:系统生物学的宿主-病原体关系分析

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552121

D. Arora, V. Singh, Ajeet Singh

引用次数: 1

Copy number variation detection workflow using next generation sequencing data 使用下一代测序数据的拷贝数变异检测工作流程

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552117

Prashanthi Dharanipragada, N. Parekh

引用次数: 1

Glycolysis as a determinant of genome and proteome composition of different extremophilic archaea species 糖酵解是不同嗜极古菌基因组和蛋白质组组成的决定因素

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552130

Ayon Pal, A. K. Bothra, Subhasis Mukhopadhyay

引用次数: 0

A neural network based model of M and P LGN cells 基于神经网络的M和P LGN细胞模型

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-01 DOI: 10.1109/BSB.2016.7552165

Kuntal Ghosh

引用次数: 2