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5th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011

作者： Tsai, Zing Tsung-Yeh Huang, Grace Tzu-Wei Tsai, Huai-Kuang Institute of Information Science Academia Sinica Taipei 115 Taiwan Bioinformatics Program Taiwan International Graduate Program Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh PA United States Research Center for Information Technology Innovation Taipei 115 Taiwan Computer Science and Engineering National Taiwan Ocean University Keelung 202 Taiwan

ISBN: (纸本)9780769543734

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. © 2011 IEEE.

关键词： Yeast

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Simultaneous Identification for Synergistic Transcription Factors and their Transcription Factor Binding Sites

Simultaneous Identification for Synergistic Transcription Fa...

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International Conference on Complex, Intelligent and Software Intensive Systems, CISIS

作者： Zing Tsung-Yeh Tsai Grace Tzu-Wei Huang Huai-Kuang Tsai Institute of Information Science Academia Sinica Taipei Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh USA Computer Science and Engineering National Taiwan Ocean University Keelung Taiwan

关键词： Bioinformatics Analysis of variance DNA Databases Gene expression Proteins Stress

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An incremental approach for niching and building block detection via clustering

An incremental approach for niching and building block detec...

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7th International Conference on Intelligent Systems Design and Applications, ISDA'07

作者： Emmendorfer, Leonardo Ramos Pozo, Aurora Trinidad Ramirez Numerical Methods in Engineering PhD Program Federal University of Paraná Brazil Department of Computer Science Federal University of Paraná Brazil

ISBN: (纸本)0769529763

Diversity preservation has already been established as an important concern for evolutionary computation. Clustering techniques were, among others, successfully applied to this purpose. Another important aspect of the research on evolutionary computation is related to linkage learning - the detection of the problem structure avoiding disruption of building blocks when new individuals are generated. This paper presents a novel approach which is a new estimation of distribution algorithm (EDA) where clustering plays two roles: diversity preservation and linkage learning. Initial empirical investigations illustrate the behavior of the algorithm when solving two benchmark optimization problems. © 2007 IEEE.

关键词： Evolutionary algorithms

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Assessing English-as-a-second-language middle school students' ability to learn engineering concepts

Assessing English-as-a-second-language middle school student...

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114th Annual ASEE Conference and Exposition, 2007

作者： Klenk, Paul Dreher, Frank Condon, Emilie Ybarra, Gary Oliver, Lara Kelly, Glenda Shaw, Nancy Duke University United States Sigma Xi United States Scientific Research Society United States TeachEngineeirng Digital Library Project Duke United States Githens Middle School Sherwood Githens Middle School Durham NC United States Department of Electrical and Computer Engineering Duke University United States Engineering K-PhD Program Duke United States Pratt School of Engineering Duke University United States

This paper presents evidence that English as a second language (ESL) middle school students can effectively learn engineering concepts through a sequence of one hour, hands-on activities. Electrical and mechanical engineering concepts are introduced through an integrated sequence of one hour modules. These cross-disciplinary modular activities include exploring mechanical potential through flowing water, building electric circuits, and using this knowledge to build a model electric car. These engineering-based activities provide a rich source for enhancing academic language skills through speaking and writing in English. Methods for training undergraduate and graduate engineering Teaching Fellows to work effectively with ESL students are provided. The process of creating K-12 engineering-based lessons and activities for publication in the Teachengineering Digital Library, part of the National Science Digital Library, is outlined using the engineering-based curricular unit created in this project. This project was completed by a senior undergraduate student in the Department of Biomedical engineering at Duke University in partial fulfillment of the requirements for the Bachelor of Science in engineering Degree. © American Society for engineering Education, 2007.

关键词： Students

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A weighted k-nearest neighbor method for gene ontology based protein function prediction

A weighted k-nearest neighbor method for gene ontology based...

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2nd International Multi-Symposiums on computer and Computational Sciences 2007, IMSCCS'07

作者： Kharsikar, Saket Mugler, Dale Sheffer, Daniel Moore, Francisco Duan, Zhong-Hui Department of Biomedical Engineering University of Akron Akron OH 44236 United States Department of Theoretical and Applied Mathematics University of Akron Akron OH 44236 United States Integrated Bioscience PhD Program University of Akron Akron OH 44236 United States Department of Biology University of Akron Akron OH 44236 United States Department of Computer Science University of Akron Akron OH 44236 United States

ISBN: (纸本)0769530397

Numerous genome projects have produced a large and ever increasing amount of genomic sequence data. However, the biological functions of many proteins encoded by the sequences remain unknown. Protein function annotation and prediction become an essential and challenging task of post-genomic research. In this paper, we present an automated protein function prediction system based on a set of proteins of known biological functions. The functions of the proteins are characterized with gene ontology (GO) annotations. The prediction system uses a novel measure to calculate the pair-wise overall similarity between protein sequences. The protein function prediction is performed based on the GO annotations of similar sequences using a weighted k-nearest neighbor method. We show the prediction accuracies obtained using the model organism yeast (Sacchyromyces cerevisiae). The results indicate that the weighted k-nearest neighbor method significantly outperforms the regular k-nearest neighbor method for protein molecular function prediction. © 2007 IEEE.

关键词： Proteins

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Applying fuzzy functions and sequential coordination to optimization of machinery arrangement and pipe routing

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NAVAL ENGINEERS JOURNAL 1998年第6期110卷 43-54页

作者： Wu, BC Young, GS Schmidt, W Choppella, K Dr. Bi-Chu Wu:received a PhD in Mechanical Engineering from the University of Maryland College Park in 1991. She has worked on projects involving naval architecture design optimization solid mechanics and database development. Presently a senwr engineer with Angle Incorporated Dr Wu's research interests are in design optimization and fuzzy logic applications. Dr. Gin-Shu Young: a senior engineer with Angle Incorporated holds a PhD in Mechanical Engineering from the University of Maryland College Park. As a guest researcher with National Institute of Standards and Technologies from 1990 to 1993 he worked on vision-based navigation for autonomous vehicles. His experience also includes applications of optimization fuzzy logic neural network and genetic algorithm methods to engineering system design Mr. William Schmidt:co-founded Angle Incorporated in 1990 and has served as Vice PresidentlChiefScientist during this tame. He holds a B.Sc. in Applied Science from the Naval Acadt?my and an M.Sc. in Physics from the Naval Post Graduate School. He has cner 20 years experience in technical leadership material and personnel management. He has led the application of computer aided design (CAD) and Product Model Information Exchange to the shipbuilding industry. His experience also includes leading the amlication of model based operational analysis to support the Live Fire Test Program for DDG 51 Class Destroyers. Mr. Krishna M. Choppella:is a Sofware Engineer at Eidea Laboratories Incotporated where he works on componentbased distributed enterpvise frameworks. He has been involved in creating data analysis tools for the US Nay by integrating CAD modeis databases and graphical front ends. His work in the Masters degree program in Mechanical Engineering at the University of Texas at Austin was in di0ddase.r spectroscopy of combustion products in porous-matri burners. He received his Bachelors degree in Electrical Engineering in India. He was a Research Associate at the Centre for Laser Technology and Project Engi

Ship design is often multidisciplinary involving several design elements with various types of objectives and constraints (O/C) some easily described as mathematical formulas, others better modeled as descriptive assertions. This paper describes a method based on fuzzy functions and an integrated performance index to model O/C using descriptive assertions to be used with mathematical formulas in optimization. Another issue addressed in this paper concerns the coordination of design elements when sequentially coupled, that is, when one leads the other and the performance of the follower depends greatly on the design of the leader. Based on neuro-fuzzy techniques, the method described here coordinates and optimizes sequentially coupled elements. The two methods are applied to machinery arrangement (MA) and pipe routing (PR). Preliminary models for optimization of MA and PR are described considering convenience, producibility: engine room size, interference and location as factors in the O/C set. Some test results from MA/PR applications are presented and discussed. The methods are generic and can be extended to other elements in ship design. They are mutually independent and may be used separately Two advantages of their use are an improvement in overall performance and a reduction in the need for redesign of elements.

关键词： Optimization

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Windows computer laboratory as a tutorial for undergraduate electromagnetics

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computer Applications in engineering Education 1995年第3期3卷 183-183页

作者： McCulloch, J. Keddy, W.A. Stuchly, M.A. University of Victoria Department of Electrical and Computer Engineering University of Victoria Victoria British Columbia Canada Janet McCulloch:is a native of Toronto Canada where she briefly attended both York University and the University of Toronto before she set off on a year-long adventure through the Middle East and North Africa. When she returned to Canada she relocated to California. She spent a number of years living both in Los Angeles and coastal Northern California interspersed with several extended trips through the United States Mexico and Central America. Ms. McCulloch moved to Victoria British Columbia in 1989 and a year later registered in the cooperative education program in Electrical Engineering at the University of Victoria. She is presently in the fifth and final year of the program and has her sights set on graduate school. Besides the work described in this article she has been very much involved in the use of technology to assist in the delivery of curriculum at the senior secondary level. She lives on a country property a half-hour from the University with her husband her horse and three cats. W. Alfred Keddy:is an applications programmer/analyst for the Department of Electrical and Computer Engineering at the University of Victoria. He received a BEng (1988) in Electrical Engineering and an MASc (1994) from the University of Victoria. His research interests include distributed systems image processing local area networks VLSI and DSP system design for computation and communication and human–computer interface design. Maria A. Stuchly:received an MSc in Electrical Engineering in 1962 from Warsaw Technical University and a PhD in Electrical Engineering from the Polish Academy of Sciences in 1970. Between the years of 1962 and 1970 she was with the Warsaw Technical University an Institute of the Polish Academy of Sciences. After immigrating to Canada during 1970 her first position was with the University of Manitoba. In 1976 she became employed by the Bureau of Radi

Contents and implementation of a computer laboratory for undergraduate electromagnetics are described. The laboratory consists of four 3-hour sessions covering vector calculus, Maxwell's equations (integral and differential forms), wave propagation in materials, and wave behavior at planar interfaces. Each session contains theory (in the Help file), animations (where relevant) and a quiz. The program runs on IBM compatible 486-based PCs in a Windows environment and uses the Borland C ++ 4.0 compiler.

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Development and integration of an equation-solving program for engineering thermodynamics courses

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computer Applications in engineering Education 1993年第3期1卷 265-265页

作者： Klein, S.A. Mechanical Engineering Department University of Wisconsin-Madison 53706 Dr. S. A. Klein:is a professor of Mechanical Engineering at University of Wisconsin-Madison. His engineering degrees (BS University of Illinois-Chicago MS PhD University of Wisconsin-Madison) were obtained in Chemical Engineering. Professor Klein is a member of the Solar Energy Laboratory at Wisconsin. He is the developer of the F-Chart method for sizing solar heating systems and the TRNSYS simulation program which is widely used in simulations of solar processes. Currently Professor Klein is involved in research on solar energy system performance absorption power cycles finite-time thermodynamics applications adsorption processes for air conditioning and air quality control and alternative refrigerants and systems for refrigeration and air conditioning applications. Professor Klein is also involved in the development of engineering computer tools for both instruction and research. In addition to the EES program described in this paper he is the primary author of the thermodynamics instructional program CP/Thermo and the finite element program FEHT.

Thermodynamics problems can be separated into conceptual and mathematical parts. The conceptual part consists of the problem formulation and analysis. The mathematical part seeks to obtain an answer to a problem by solving the equations identified in the analysis. The mathematical part can be complex and time-consuming and often directs the students' focus away from the concepts. An equation solving program called engineering Equation Solver (EES) was developed to reduce the time and effort required by students to solve the mathematical part of thermodynamics problems. EES differs from existing equation solving programs in that it is designed for use by students and it includes an extensive library of built-in functions for thermodynamic and transport properties of fluids. Thermodynamic and transport property data needed for solving engineering problems (eg, steam tables, refrigerant properties, psychrometric and combustion gas data) are built into the program. By eliminating table lookups and algebra, EES allows students to concentrate on engineering fundamentals, as well as to do more complex design problems.

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Educational use of a microwave electromagnetic analysis of 3-D planar structures

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computer Applications in engineering Education 1993年第3期1卷 243-243页

作者： Rautio, J.C. Sonnet Software Inc. Suite 203 135 Old Cove Road Liverpool NY 13090 Dr. James C. Rautio:founded Sonnet Software a developer of 3-D planar electromagnetic microwave software in 1983 with support from the David Sarnoff Research Center Hewlett Packard General Electric and Syracuse University. He has served as a visiting member of the faculty at Syracuse University and as an adjunct faculty member at Cornell University teaching microwave and computer courses as well as pursuing research in electromagnetics. Dr. Rautio previously worked in General Electric's Space Division and Electronics Laboratory. He designed microwave circuits including filters for a Landsat receiver and various GaAs microwave integrated circuits. He also developed microwave and millimeter wave automated measurement equipment and wrote a large microwave circuit analysis program. Dr. Rautio holds a BS in Electrical Engineering from Cornell University an MS in Systems Engineering from the University of Pennsylvania and a PhD in Electrical Engineering from Syracuse University

The use of an electromagnetic analysis of 3-D planar structures is described with respect to the educational requirements of students from the college freshman level through the graduate level. The analysis is intended primarily for microwave use; however, there is also significant potential interest from the student of high speed digital design. The analysis is used for passive planar circuits with any number of layers. The third dimension is represented by vias. A mature graphical user interface is provided allowing rapid capture of structure geometry, color visualization, and animation of the resulting current distributions. The software is also explicitly designed to work in conjunction with popular circuit theory based microwave software and with SPICE.

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Interactive tools for signal processing education. The signal processing instructional facility (SPIF lab) at Washington State University

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computer Applications in engineering Education 1993年第6期1卷 517-517页

作者： Bamberger, R.H. Signal Processing Instructional Facility School of Electrical Engineering and Computer Science Washington State University Pullman WA 99164-2752 Dr. Roberto H. Bamberger:was born on January 30 1965 in Buenos Aires Argentina. He received his B.E.E and PhD from the Georgia Institute of Technology in 1986 and 1990 respectively. Currently Dr. Bamberger is an assistant professor in the School of Electrical Engineering and Computer Science at Washington State University. Dr. Bamberger's research program is focused on the design implementation and application of multidimensional multirate filter banks subband image and video compression analysis of nonstationary data and application of digital signal processing techniques in the design of analog and mixed-mode integrated circuits. Dr. Bamberger is the founder and director of the Signal Processing Instructional Facility (SPIF Lab) at Washington State University. The SPIF Lab features interactive multimedia-based tools for teaching concepts related to linear systems theory. Dr. Bamberger is active in developing multimedia-based instructional laboratories for a variety of other topics as well. In addition to his teaching and research programs Dr. Bamberger is an associate editor for theIEEE Transactions on Signal Processingand a member of the editorial board forComputer Applications in Engineering Education. Dr. Bamberger is also advisor to the WSU Student Branch of the IEEE and assistant director of the WSU Cougar Marching Band. Dr. Bamberger is a member of Phi Eta Sigma Eta Kappa Nu Tau Beta Pi and Kappa Kappa Psi.

The Signal Processing Instructional Facility (SPIF Lab) is an experiment in using in interactive multimedia for teaching concepts related to linear systems theory and signal processing. The goals of the SPIF lab are to augment, enhance, and interconnect sophomore, junior, and senior level courses with the common thread of linear systems and transforms by unifying the experimentation medium. In this fashion, physical phenomenon is returned to the forefront of engineering education. The laboratory features powerful Mathematica Notebooks (a form of hypertext) and interactive applications that use dedicated DSP microprocessors.

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