2006 IEEE/NLM Life Science Systems and Applications Workshop最新文献_第5页

Detection of gene copy number change in array CGH data 阵列CGH数据中基因拷贝数变化的检测

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250402

Jingke Hu, Jianbo Gao, Yinhe Cao, Weijia Zhang

{"title":"Detection of gene copy number change in array CGH data","authors":"Jingke Hu, Jianbo Gao, Yinhe Cao, Weijia Zhang","doi":"10.1109/LSSA.2006.250402","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250402","url":null,"abstract":"Developing effective methods for analyzing array-CGH data to detect chromosomal aberrations is very important for the diagnosis of pathogenesis of cancer and other diseases. Current analysis methods, being largely based on smoothing and/or segmentation, are not quite capable of detecting both the aberration regions and the boundary break points very accurately. This is undesirable, since each point in the array represents a gene. Furthermore, when evaluating the accuracy of an algorithm for analyzing array-CGH data, it is commonly assumed that noise in the data follows normal distribution. A fundamental question is whether noise in array-CGH is indeed Gaussian, and if not, can one exploit the characteristics of noise to develop novel analysis methods that are capable of detecting accurately the aberration regions as well as the boundary break points simultaneously? By analyzing bacterial artificial chromosomes (BACs) arrays, oligo-nucleotide arrays, and high density NimbleGen data, we show that when there are aberrations, noise in all three types of arrays is highly non-Gaussian and possesses long-range spatial correlations, and that such noise leads to worse performance of existing methods for detecting aberrations in array-CGH than the Gaussian noise case. We further develop a novel method, which has optimally exploited the characteristics of the noise, and is capable of identifying both aberration regions as well as the boundary break points very accurately","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"146 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115630954","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

Diffuse Optical Tomography for Mapping Human Brain Function 漫射光学断层成像成像人脑功能

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250436

J. P. Culver, B. Schlaggar, H. Dehghani, B. Zeff

引用次数: 9

Simulating Transillumination in Organic Material with Near Infrared Light 近红外光模拟有机材料的透照

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250415

R. Sharp, J. Adams, R. Machiraju, R. Lee, R. Crane

引用次数: 0

In situ Biomolecule Assembly and Activity within Completely Packaged Microfluidic Devices 完全封装的微流体装置中的原位生物分子组装和活性

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250370

J. Park, Xiaolong Luo, H. Yi, R. Ghodssi, G. Rubloff

引用次数: 1

A Linear Analysis on Robustness in Biochemical Networks 生物化学网络鲁棒性的线性分析

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250421

Ruiqi Wang, Luonan Chen, K. Aihara

引用次数: 0

Effects of Light Waveforms on a Circadian Oscillation of Clock Genes 光波形对时钟基因昼夜节律振荡的影响

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250395

K. Tsumoto, G. Kurosawa, K. Aihara

引用次数: 0

Nanoscale Biomarkers for Cancer Genomics and Protemics 癌症基因组学和蛋白质学的纳米级生物标志物

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250422

Jie Zeng, Jie Chen, Xiaoping Wang, J. Hou, S. Wong

引用次数: 1

Applying Reduction Mappings in Designing Genomic Regulatory Networks 约简映射在基因组调控网络设计中的应用

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250381

I. Ivanov, R. Pal, E. Dougherty

{"title":"Applying Reduction Mappings in Designing Genomic Regulatory Networks","authors":"I. Ivanov, R. Pal, E. Dougherty","doi":"10.1109/LSSA.2006.250381","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250381","url":null,"abstract":"Probabilistic Boolean networks (PBNs) represent a class of nonlinear models of genetic regulatory networks incorporating the indeterminacy owing to latent variables external to the model that have biological interaction with genes in the model. Besides being used to model biological phenomena, such as cellular state dynamics and the switch-like behavior of certain genes, PBNs have served as the main model for the application of intervention methods, including optimal control strategies, to favorably effect system dynamics. An obstacle in applying PBNs to large-scale networks is the computational complexity of the model. It is sometimes necessary to construct computationally tractable sub-networks while still carrying sufficient structure for the application at hand. Hence, there is a need for size reducing mappings. Such mappings can be used not only to render computationally manageable sub-networks but they can also play an important role in the process of designing PBNs from microarray data. The process of inferring PBNs from data is known to be a one-to-many mapping, and one needs a biologically sound constraints when selecting the PBN that is optimal with respect the given data. This paper proposes such a constraint based on the recently introduced DIRE reduction algorithm","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"2010 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123921384","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

RF/microwave Sensed Cantilevers, Diaphragms, and Tactile Sensors for Passive and Active Sensor Systems 用于被动和主动传感器系统的射频/微波传感悬臂，隔膜和触觉传感器

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250385

R. Weber

引用次数: 3

Stem cell patterning in the single cell microchip platform 单细胞微芯片平台上的干细胞图谱

2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250383

Ching-Hsing Luo, T. Hsieh, Ji-Fu Lin, I-Chung Chun, Mao-Tsun Lin, Ching-Ting Lee

引用次数: 0