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检索条件"任意字段=IEEE Computational Systems Bioinformatics Conference"

共 881 条记录，以下是391-400 订阅

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Qualitative Analysis of Gene Regulatory Networks by Satisfiability Checking of Linear Temporal Logic

Qualitative Analysis of Gene Regulatory Networks by Satisfia...

引用

ieee Symposium on bioinformatics and Bioengineering (BIBE)

作者： Sohei Ito Naoko Izumi Shigeki Hagihara Naoki Yonezaki Department of Computer Science Graduate School of Information Science and Engineering Tokyo Institute of Technology Meguro Tokyo Japan The Department of Social and Information Sciences Jumonji University Saitama Japan

We developed a method for analyzing the dynamics of gene regulatory networks in purely qualitative fashion. In our method, constraints for possible behaviors of a network and a biological property of interest are described as Linear Temporal Logic formulas, being automatically analyzed by satisfiability checking. In this way, we can investigate whether there exists some behavior which satisfies a specified property or whether all the behaviors satisfy a specified property, which are difficult in quantitative analysis.

关键词： Biological system modeling Biological systems Information analysis computational modeling Automatic logic units Differential equations Numerical simulation Gene expression bioinformatics Biomedical engineering

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An Intelligent Multi-Agents Method for Study on Membrane Protein Interaction Network

An Intelligent Multi-Agents Method for Study on Membrane Pro...

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The 4th International conference on bioinformatics and Biomedical Engineering(第四届ieee生物信息与生物医学工程国际会议 iCBBE 2010)

作者： Yi-Zhen Shen Yong-Sheng Ding College of Information Sciences and Technology Donghua University Shanghai 201620 P.R.China College of Information Sciences and Technology Donghua University Engineering Research Center of D

Membrane protein and its interaction network has become a novel research direction in bioinformatics. Multiple researches on these interactions can improve our understanding of diseases and provide the basis to revolutionize therapeutic treatments. In this paper, a novel membrane protein interaction network simulator is proposed for system biology studies by intelligent multi-agents method. We consider biological system as a set of active computational components interacting with each other and with an external environment. Then we can use the network simulator to construct membrane protein interaction networks. Interactions among small membrane protein interaction networks can emerge a large membrane protein interaction network which has its remarkable ability to accomplish a complex function or task. Based on the proposed approach, we find out that the membrane protein interaction network almost has the some dynamic and collective characters, such as small-world network, topological character, and hierarchical module structure. These characters of the membrane protein interaction network will be valuable for its relatively biological and medical studies.

关键词： Intelligent networks Biomembranes Proteins Biological system modeling computational modeling bioinformatics Diseases systems biology computational intelligence Biological systems

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Exploring Architecture Options for a Federated, Cloud-Based System Biology Knowledgebase

Exploring Architecture Options for a Federated, Cloud-Based ...

引用

ieee International conference on Cloud Computing Technology and Science (CloudCom)

作者： Ian Gorton Yan Liu Jian Yin Pacific Northwest National Laboratory Richland WA USA

systems biology is characterized by a large community of scientists who use a wide variety of fragmented and competing data sets and computational tools of all scales to support their research. In order to provide a more coherent computational environment for systems biology, we are working as part of the Department of Energy systems Biology Knowledgebase (Kbase) project to define a federated cloud-based system architecture. The Kbase will eventually host massive amounts of biological data, provide high performance and scalable computational resources, and support a large user community with tools and services to enable them to utilize the Kbase resources. In this paper, we describe the results of our investigations into the design of a workflow infrastructure suitable for use in the Kbase. The approach utilizes standards-based workflow description and open source integration technologies, and incorporates a data aware workflow execution layer for exploiting data locality in the federated architecture. We describe a use case and the initial prototype implementation we have built that demonstrates the feasibility of our approach.

关键词： Computer architecture bioinformatics Genomics systems biology Prototypes Peptides

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TRAC: A Platform for Structure-Function Studies of NSS-Proteins Integrates Information from bioinformatics and Biomedical Literature

TRAC: A Platform for Structure-Function Studies of NSS-Prote...

引用

ieee Symposium on bioinformatics and Bioengineering (BIBE)

作者： Lei Shi Marko Srdanovic Thijs Beuming Lucy Skrabanek Jonathan A. Javitch Harel Weinstein The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine Weill Medical College of Cornell University New York NY USA Department of Physiology and Biophysics Weill Medical College of Cornell University New York NY USA Cornell University Joan and Sanford I Weill Medical College New York NY US Departments of Psychiatry and Pharmacology Center of Molecular Recognition College of Physicians and Surgeons Columbia University New York NY USA

To enable rigorous and reliable modeling of functional mechanisms of membrane proteins, the computational modeling and simulation approaches must take advantage, to the fullest extent possible, of the wealth of data obtained experimentally. This type of information makes it possible not only to construct rigorous molecular models and quantitative representations of function, but also to test, verify and refine them continuously. Among the proteins in the cell membrane, the family of Neurotransmitter: Sodium Symporter (NSS) exhibits highly complex mechanisms that involve multiple molecular states in the substrate and ion transport cycle. Due to their high biological and medical importance, experimental data for these systems is abundant, and efficient management of information from the literature and other relevant data sources promises to be very rewarding. We have developed an information management system (IMS) for data concerning the NSS proteins to enable retrieval, structured organization, and query of information available in the literature. The IMS supports the interplay between computational approaches and experimental studies of structure, function and physiological mechanisms of the NSS, and is of special utility in the integration of data of different types and various sources, and of the mechanistic understanding emerging from separate functional studies of individual members of the family.

关键词： bioinformatics Biomembranes Proteins computational modeling Biological system modeling Testing Cells (biology) Neurotransmitters Information management Health information management

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A distributed system for fast alignment of next-generation sequencing data

A distributed system for fast alignment of next-generation s...

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ieee International conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Jaydeep K. Srimani Po-Yen Wu John H. Phan May D. Wang Department of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA USA The Wallace H. Coulter Biomedical Engineering Department Georgia Institute of Technology and Emory University Atlanta GA USA

We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.

关键词： Databases bioinformatics computational modeling Software Biological system modeling Genomics

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Improving security in ID tokens through HW/SW co-design

Improving security in ID tokens through HW/SW co-design

引用

International Carnahan conference on Security Technology

作者： Judith Liu-Jimenez Raul Sanchez-Reillo Oscar Miguel-Hurtado Universidad Carlos III de Madrid Madrid Spain

Nowadays, more biometric systems are used. These systems used for identification or verification purposes have shown a more secure solution than conventional identification systems; however the consequences of a successful attack in these systems are worst than in previous one. A successful attack can compromise personal data, such the biometric template, attempt against user's privacy and furthermore, requires changes in the system infrastructure. In this paper, the authors examine these attacks to make a new biometric ID token proposal. The new approach made tries to reduce these attacks by an effective combination on hardware and software implementations. This proposal covers several aspects which these systems are subjected to, taking advantages of the two platforms they use for reducing computational time or hardware area, but also to increase security or minimize misidentification errors.

关键词： Biometrics Security Hardware Software bioinformatics Microprogramming Random access memory

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computational inference of transcription factor cooperation by fuzzy frequent itemset mining

Computational inference of transcription factor cooperation ...

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ieee International conference on Fuzzy systems (FUZZ-ieee)

作者： F. Javier Lopez Carlos Cano Fernando Garcia Armando Blanco Department of Computer Science and Artificial Intelligence University of Granada Granada Spain

Eucaryotic gene control regions consist of a promoter plus regulatory DNA sequences which may appear distant from the gene promoter. Regulatory proteins (called transcription factors, TFs), coordinately bind to these regions (TF binding sites, TFBSs) and produce the correct gene expression patterns. We present a novel fuzzy approach to study significant co-occurences of closely located TFBSs in the yeast whole-genome. Our approach takes advantage of the ability of fuzzy techniques to handle imprecision, inherent to regulatory-regions location data. The methodology is based on a fuzzy frequent itemset mining algorithm and overcomes some of the limitations of previous approaches. The results obtained from the yeast genome allow us to propose the application of the procedure over more complex genomes in future works.

关键词： Itemsets Genomics bioinformatics Data mining DNA Proteins

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Protein Structure Modeling in Two-Level Topology Strings for Structure Comparison

Protein Structure Modeling in Two-Level Topology Strings for...

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International ieee conference on Signal-Image Technologies and Internet-Based System

作者： Jafar Razmara Safaai B. Deris Sepideh Parvizpour Faculty of Computer Science and Information Systems Universiti Teknologi Malaysia Johor Bahru Malaysia Faculty of Bioscience and Bioengineering Universiti Teknologi Malaysia Johor Bahru Malaysia

Biological data representation in textual sequences has opened a new hybrid research area in protein structure analysis. The paper presents a novel method for structural comparison and alignment of proteins based on text modeling techniques. The method firstly models the geometry of protein secondary and tertiary structure in two-level topology strings and then, employs n-gram modeling and cross-entropy concept from computational linguistics approach to compare strings and align structures. The results of the experiments confirm the validity and efficiency of the proposed method. Moreover, conceptual simplicity of the method indicates applicability and preference of the method in comparison to the other related techniques.

关键词： Proteins Topology Hidden Markov models computational modeling Entropy Geometry bioinformatics

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Prediction of secondary structure of RNAs with pseudoknots using matched filter

Prediction of secondary structure of RNAs with pseudoknots u...

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Annual ieee Northeast Workshop on Circuits and systems (NEWCAS)

作者： Rajasekhar Kakumani M. Omair Ahmad Vijay Devabhaktuni Department of Electrical and Computer Engineering Concordia University Montreal QUE Canada Department of Electrical Engineering and Computer Science University of Tolctlo and Eötvös Lárand University Toledo OH USA

Prediction of RNA secondary structure is one of the pivotal tasks in bioinformatics. Several computational methods based on dynamic programming, statistical models, have been proposed with considerable success. A typical substructure that occurs in several classes of RNAs, called pseudoknot, plays vital role in many biological processes. Prediction of the pseudoknots in RNA secondary structure is still an open research problem. In this paper, we employ matched filtering approach to determine the secondary structure of a target RNA. The central idea is to match the stem patterns in the base-pairing matrix of RNA with unknown secondary structure. The proposed approach predicts number of stems, loops and also the presence of pseudoknot in the secondary structure of RNA. Illustrative examples on real RNA sequences illustrate the effectiveness and accuracy of our proposed method.

关键词： RNA Symmetric matrices Prediction algorithms Databases bioinformatics Algorithm design and analysis

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An ontological fuzzy Smith-Waterman with applications to patient retrieval in Electronic Medical Records

An ontological fuzzy Smith-Waterman with applications to pat...

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ieee International conference on Fuzzy systems (FUZZ-ieee)

作者： Mihail Popescu Informatics Institute University of Missouri Columbia MO USA

With the introduction of Electronic Medical Records (EMR) systems in health care institutions, a huge data repository has been created. By employing computational intelligence (CI) techniques, this data repository can be used to address important health care issues such as improving quality and reducing medical errors. In this paper, we introduce a general word sequence alignment method based on a fuzzy version of the Smith-Waterman (SW) dynamic programming algorithm. The word similarity matrix used in computing the sequence alignment is calculated based on a domain ontology (taxonomy). The fuzzy version of the SW algorithm is designed to accommodate words not present in the initial dictionary used to precompute the similarity matrix, hence avoiding its recalculation. We apply the developed algorithm for patient retrieval in an EMR. Each patient is described by an ordered sequence of ICD9 diagnoses. We analyze various properties of the proposed algorithm on a patient dataset that contains 107 patients described by ICD9 diagnose sequences.

关键词： Medical diagnostic imaging Ontologies Neodymium bioinformatics Algorithm design and analysis Drugs

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