2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)最新文献_第6页

Clustering DNA methylation expressions using nonparametric beta mixture model 使用非参数β混合模型聚类DNA甲基化表达

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 2011-12-01 DOI: 10.1109/GENSiPS.2011.6169472

Lin Zhang, Jia Meng, Hui Liu, Yufei Huang

引用次数: 4

Assessing the efficacy of molecularly targeted agents by using Kalman filter 用卡尔曼滤波评价分子靶向药物的疗效

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 2011-12-01 DOI: 10.1109/GENSiPS.2011.6169439

Xiangfang Li, Lijun Qian, M. Bittner, E. Dougherty

引用次数: 2

Steady state probability approximation applied to stochastic model of biological network 稳态概率逼近在生物网络随机模型中的应用

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 2011-12-01 DOI: 10.1109/GENSiPS.2011.6169442

Md. Shahriar Karim, David M. Umulis, G. Buzzard

引用次数: 1

Effects of slice thickness filter in filtered backprojection reconstruction with the parallel breast tomosynthesis imaging configuration 层厚滤波器对平行乳腺层析成像结构滤波后反投影重建的影响

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 2011-12-01 DOI: 10.1109/GENSiPS.2011.6169478

L. Cong, Ying Chen, Weihua Zhou

引用次数: 5

Chromatin signature analysis and prediction of genome-wide novel promoters using finite mixture model 基于有限混合模型的全基因组新型启动子染色质特征分析与预测

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 2011-12-01 DOI: 10.1109/GENSiPS.2011.6169429

C. Taslim, Shili Lin, Kun Huang, T. Huang

{"title":"Chromatin signature analysis and prediction of genome-wide novel promoters using finite mixture model","authors":"C. Taslim, Shili Lin, Kun Huang, T. Huang","doi":"10.1109/GENSiPS.2011.6169429","DOIUrl":"https://doi.org/10.1109/GENSiPS.2011.6169429","url":null,"abstract":"Regulation of gene expression has been shown to involve not only binding of transcription factor in target gene promoters but also characterization of histone around which DNA is wrapped around. Some histone modification, for example di-methylated histone H3 at lysine 4 (H3K4me2), has been shown to be associated with gene activation. However, no clear pattern has been shown to predict human promoters. This paper proposed a novel quantitative approach to characterize chromatin signature and patterns of promoters, which are then used to predict novel (alternative) promoters. In this paper, chromatin immunoprecipitation methods followed by massive parallel sequencing (ChIP-seq) data against RNA Polymerase II (Pol II) and H3K4me2 are used to identify common patterns of promoter regions. These patterns were then used to search for similar patterns over the entire genome to find novel promoters. Common patterns of promoter regions are modeled using a mixture model involving double-exponential and uniform distributions. Regions with high correlations with the common patterns are identified as putative novel promoters. We used this proposed algorithm and RNA-seq data to identify novel promoters in the MCF7 cell line. We found 4,392 high-confidence regions that display the identified promoter patterns (referred to as putative novel promoters). Of these, 875 regions (20%) overlap with RNA transcripts. Around 70% of these putative novel promoters have overlapped with RNA transcripts, EST and/or non-coding RNA suggesting that these putative novel promoters might be promoters which are currently undiscovered.","PeriodicalId":181666,"journal":{"name":"2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125498527","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

A novel approach for tumor sensitivity prediction and combination therapy design for targeted drugs 肿瘤敏感性预测和靶向药物联合治疗设计的新方法

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 2011-12-01 DOI: 10.1109/GENSiPS.2011.6169435

Noah E. Berlow, R. Pal

引用次数: 0

A method for finding novel associations between genome-wide copy number and dna methylation patterns 一种发现全基因组拷贝数和dna甲基化模式之间新关联的方法

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 2011-11-01 DOI: 10.1109/GENSiPS.2011.6169448

Man-Hung Eric Tang, V. Varadan, S. Kamalakaran, Michael Q. Zhang, N. Dimitrova, J. Hicks

引用次数: 0

Comparative copy number variation from whole genome sequencing 全基因组测序比较拷贝数变异

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 2011-10-05 DOI: 10.1109/GENSiPS.2011.6169460

A. Janevski, V. Varadan, S. Kamalakaran, N. Banerjee, N. Dimitrova

引用次数: 1

Multisource biological pathway consolidation 多源生物通路巩固

2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) Pub Date : 1900-01-01 DOI: 10.1109/GENSiPS.2011.6169447

Mark Doderer, Zachry Anguiano, U. Suresh, Ravi Dashnamoorthy, A. Bishop, Yidong Chen

引用次数: 1