2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)最新文献

Autonomicity - an antidote for complexity? 自主性——复杂性的解药?

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.28

Roy Sterritt, M. Hinchey

引用次数: 12

DockingShop: a tool for interactive protein docking DockingShop:一个交互式蛋白质对接工具

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.54

Ting-Cheng Lu, Jinhui Ding, S. Crivelli

引用次数: 9

Discovering functional transcription factor binding from superimposed gene networks 从重叠基因网络中发现功能性转录因子结合

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.53

M. Weirauch, Joshua M. Stuart

引用次数: 0

Engineering multi-signal systems for complex pattern formation 用于复杂图案形成的工程多信号系统

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.63

D. Karig, Jerome Ku, Ron Weiss

{"title":"Engineering multi-signal systems for complex pattern formation","authors":"D. Karig, Jerome Ku, Ron Weiss","doi":"10.1109/CSBW.2005.63","DOIUrl":"https://doi.org/10.1109/CSBW.2005.63","url":null,"abstract":"Biological pattern formation networks orchestrate complex processes of constituent cells, often through the use of multiple intercellular signals. The forward engineering of such multi-signal systems in synthetic biology has a number of important applications including biosensing, tissue engineering, and biomaterial fabrication. In addition, such synthetic systems provide a testing ground for quantitatively studying the fundamental principles governing similar natural genetic networks. However, an initial requirement for engineering multi-signal networks is the characterization and tuning of various properties of the signaling systems, including crosstalk, receiver response strength, and sensitivity. We characterize crosstalk interactions for synthetic receivers built from components of the Las and Rhl quorum sensing systems from Pseudomonas aeruginosa. Next, we present results from genetic constructs designed to amplify weak transcriptional responses to signaling molecules. We then discuss results from directed evolution of receptor proteins to optimize receiver sensitivity. These methods of engineering synthetic constructs with desired response strengths and sensitivities to external signals have a number of important applications in their own right, such as the development of biosensors for detection of trace amounts of toxins. In addition to the experimental results that show how signaling constructs can be optimized for such applications, we present simulations for two example pattern formation systems that can be constructed from these tuned components.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128510865","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 symbolic approach to the simulation of biochemical models: application to circadian rhythms 生化模型模拟的符号方法:在昼夜节律中的应用

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.17

F. Fontana, L. Bianco, V. Manca

引用次数: 4

Image data mining of fruitfly gene expression patterns 果蝇基因表达模式的图像数据挖掘

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.74

Hanchuan Peng

{"title":"Image data mining of fruitfly gene expression patterns","authors":"Hanchuan Peng","doi":"10.1109/CSBW.2005.74","DOIUrl":"https://doi.org/10.1109/CSBW.2005.74","url":null,"abstract":"Understanding the spatio-temporal gene expression patterns is critical in studying genes roles and their complicated relationships. With the availability of high-resolution digital images of in situ mRNA hybridization expression pattern of Drosophila embryos collected through both the Berkeley Drosophila Transcriptional Network Project (BDTNP) and the Berkeley Drosophila Genome Project (BDGP), we will be able to answer a series of interesting questions, e.g., what are the variations of gene expression patterns, what are the patterning process of gene expression, etc. To achieve these goals at a large scale, it is extremely important to automate the image mining and informatics processes of embryogenesis expression patterns. We developed computer programs to register, compare and analyze these spatio-temporal pattern images. In this talk, I will review four projects on image mining of fruitfly embryo gene expression patterns: (a) Gaussian mixture model based embryonic expression pattern extraction and comparison, (b) Gene expression pattern clustering using novel MSTCUT and probabilistic ensemble clustering techniques, (c) Surface/volume models for 3D modeling and registration of early embryos, and (d) A manifold learning method for spatio-temporal registration of 3D gene expression patterns and reconstruction of the embryonic developmental time series.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129295330","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

Towards interactive exploration of images, meta-data, and analytic results in the open microscopy environment 在开放的显微镜环境中对图像、元数据和分析结果进行交互式探索

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.135

H. Hochheiser, I. Goldberg

引用次数: 0

PET imaging of tumor integrin expression 肿瘤整合素表达的PET显像

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.105

W. Cai, Xiaoyuan Chen

引用次数: 0

The synthetic gene designer: a flexible Web platform to explore sequence space of synthetic genes for heterologous expression 合成基因设计器:一个灵活的Web平台，用于探索合成基因的序列空间以进行异源表达

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.133

Gang Wu, Nabila Bashir-Bello, S. Freeland

引用次数: 3

iSimBioSys: an 'in silico' discrete event simulation framework for modeling biological systems iSimBioSys:一个用于建模生物系统的“在硅”离散事件模拟框架

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.80

Samik Ghosh, P. Ghosh, K. Basu, Sajal K. Das

引用次数: 9