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

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AudioGene: Computer-based prediction of genetic factors involved in non-syndromic hearing impairment

AudioGene: Computer-based prediction of genetic factors invo...

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ACS/ieee International conference on Computer systems and Applications

作者： Kyle R. Taylor Adam P. DeLuca Corey W. Goodman Bruce W. Tompkins Todd E. Scheetz Michael S. Hildebrand Patrick L. M. Huygen Richard J. H. Smith Terry A. Braun Thomas L. Casavant Center for Bioinformatics and Computational Biology University of Iowa Iowa City IA USA Department of Otolaryngology Head and Neck Surgery University of Iowa Iowa City IA USA Department of Otorhinolaryngology University Hospital Nijmegen The Netherlands

AudioGene is a software system developed at the University of Iowa to classify and predict gene mutations that indicate causal or increased risk factors of disease. We focus on a concise example - the most likely genetic causes of a particular form of inherited hearing loss - ADNSHL. Whereas the cost and throughput involved in the collection of genomic data have advanced dramatically during the past decade, gathering and interpreting clinical information regarding disease diagnosis remains slow, costly and error-prone. AudioGene employs machine-learning techniques in an iterative procedure to prioritize probable genetic risk factors of disease, which are then verified with a molecular (wet lab) assay. In our current implementation AudioGene achieves 67% first-choice accuracy (versus 23% using a majority classifier). When the top three choices are considered, accuracy increases to 83%. This has numerous implications for reducing the cost of genetic screening as well as increasing the power of novel gene discovery efforts. While AudioGene is focused on hearing loss, the design and underlying mechanisms are generalizable to many other diseases including heart disease, cancer and mental illness.

关键词： Auditory system Genetics Accuracy Training Support vector machines Diseases Educational institutions

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computational systems-Biology and bioinformatics - First International conference, CSBio 2010, Proceedings

Computational Systems-Biology and Bioinformatics - First Int...

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1st International conference on computational systems Biology and bioinformatics, CSBio 2010

ISBN: (纸本)3642167497

The proceedings contain 19 papers. The topics discussed include: a formal model for gene regulatory networks with time delays;modelling fim expression in escherichia coli K12;study of the structural pathology caused by CYP2C9 polymorphisms towards flurbiprofen metabolism using molecular dynamics simulation;3D structure modeling of a transmembrane protein, fatty acid elongase;sequential application of feature selection and extraction for predicting breast cancer aggressiveness;on assigning individuals from cryptic population structures to optimal predicted subpopulations: an empirical evaluation of non-parametric population structure analysis techniques;extended constraint-based Boolean analysis: a computational method in genetic network inference;mining LINE-1 characteristics that mediate gene expression;and mining regulatory elements in non-coding regions of arabidopsis.

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A Cloud-unaware Programming Model for Easy Development of Composite Services

A Cloud-unaware Programming Model for Easy Development of Co...

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

作者： Enric Tejedor Jorge Ejarque Francesc Lordan Roger Rafanell Javier Alvarez Daniele Lezzi Raul Sirvent Rosa M. Badia Universitat Poliltècnica de Catalunya Barcelona Spain Barcelona Supercomputing Center Barcelona Spain Artificial Intelligence Research Institute (IIIA) Spanish National Research Council Spain

Cloud computing is inherently service-oriented: cloud applications are delivered to consumers as services via the Internet. Therefore, these applications can potentially benefit from the Service-Oriented Architecture (SOA) principles: they can be programmed as added-value services composed by pre-existing ones, thus favouring code reuse. However, new programming models are required to simplify their development, along with systems that are capable of orchestrating the execution of the resulting SaaS in the Cloud. In that regard, this paper presents Service Super scalar (Servicess), an alternative to existing PaaS which provides a programming model and execution runtime to ease the development and execution of service-based applications in clouds. Servicess is a task-based model: the user is only required to select the tasks, which can be services or regular methods, to be spawned asynchronously. The application, a composite service, is programmed in a totally sequential way and no API call must be included in the code. The runtime is in charge of automatically orchestrating the execution of the tasks in the Cloud, as well as of elastically deploying new virtual resources depending on the load. After describing the main characteristics of the programming model and the runtime, we evaluate the productivity of Servicess and show how it offers a good trade-off between programmability and runtime performance.

关键词： Runtime Programming Java Cloud computing computational modeling bioinformatics Service oriented architecture

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An identification and prediction methods for feature-subsets of CpG islands methylation based on human peripheral blood leukocytes of chromosome 21q

An identification and prediction methods for feature-subsets...

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Annual International conference of the ieee Engineering in Medicine and Biology Society

作者： Isse Ali Hussein Sheikh ali Mohamoud Bio-Health Informatics Research Group within the Centre for Computational Intelligence De Montfort University South West Thames Regional Genetics Service St Georges Hospital Cranmer Terrace

ISBN: (纸本)9781424441211

The pace of technology has allowed classification of feature-subset of methylated and unmethylated of CpG islands of DNA sequence properties. As methylation of CpG islands is involved in various biological phenomena and function of the DNA methylation is correlated to various human diseases such as cancer, analysis of the CpG islands has become important and useful in characterizing and modelling biological phenomena and understanding mechanism of such diseases. However, analysis of the data associated with the CpG islands is a quite new and challenging subject in bioinformatics, systems biology and epigenetics. In this paper, the problems associated with prediction of methylated and unmethylated CpG islands on human chromosome 21q are addressed. In order to carry out the prediction, a data set of 132 samples of the CpG islands from human peripheral blood leukocytes of chromosomes 21q and 4 different feature sub-sets totalling 44 attributes that characterise the methylated and unmethylated groups is extracted for each sample. Due to the nature of this unbalanced data set, in order to avoid disadvantages of traditional leave-one-out (LOO) and m-fold cross validation methods, the LOO method is modified by incorporating the m-fold cross validation approach. In addition, K-nearest neighbour classifier is then adapted for the prediction. The results gained through 440 different comprehensive analyses shows that the methylated CpG islands can be distinguished from the unmethylated CpG islands by a predictive accuracy of between 75% and 80%. More importantly, the modified LOO identifies more clearly and reliably when the feature sub-sets are combined. Another interesting observation is that the modified-LOO-based analysis reveals that the CpGI-specific feature-set achieve the highest predictive accuracy when combined with the other feature sets, which is not the case in the traditional LOO. This also further supports the robustness of the modified-LOO cross validation appr

关键词： DNA Humans Accuracy bioinformatics Feature extraction Biological cells Genomics

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Predicting non-classical secretory proteins by using Gene Ontology terms and physicochemical properties

Predicting non-classical secretory proteins by using Gene On...

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ieee International conference on Computer Science and Automation Engineering (CSAE)

作者： Wen-Lin Huang Chyn Liaw Shinn-Ying Ho Department of Management Information System Asia-Pacific Institute of Creativity Miaoli Taiwan Institute of Bioinformatics and Systems Biology National Chiao Tung University Hsinchu Taiwan

Eukaryotic secretory proteins that traverse classical ER-Golgi pathway are usually characterized by short N-terminal signal peptides. However, several secretory proteins lacking the signal peptides are found to be exported by a non-classical secretion pathway. Therefore, predicting non-classical secretory proteins regardless of the N-terminal signal peptides is necessary for developing a critical computational approach. Several prediction methods have been proposed by using various types of features to predict secretory proteins. However, prediction performance seems not acceptable. This study proposes an SVM-based prediction method, namely ProSec-iGOX, which uses a major set of informative Gene Ontology (GO) terms and a minor set of assistance features. Physicochemical properties as the assistance features are useful when a query protein sequence without homologous protein with annotated GO terms. Two data sets, S25 and S40, having the identity 25% and 40%, respectively, are adopted for performance comparisons. The ProSec-iGOX yields test accuracies of 95.1% and 96.8% when adopting on the data sets S25 and S40 respectively. The latter accuracy (96.8%) is significantly higher than that of SPRED (82.2%), which uses frequency of tri-peptides and short peptides, secondary structure, physicochemical properties as input features to a random forest classifier. The experimental results show that GO terms are effective features for predicting non-classical secretory proteins.

关键词： Proteins Accuracy Peptides Ontologies Databases Training Feature extraction

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Predicting non-classical secretory proteins by using Gene Ontology terms and physicochemical properties

Predicting non-classical secretory proteins by using Gene On...

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2011 ieee International conference on Computer Science and Automation Engineering(CSAE 2011)

作者： Chyn Liaw Shinn-Ying Ho Institute of Bioinformatics and Systems Biology National Chiao Tung University

Eukaryotic secretory proteins that traverse classical ER-Golgi pathway are usually characterized by short Nterminal signal ***,several secretory proteins lacking the signal peptides are found to be exported by a nonclassical secretion ***,predicting nonclassical secretory proteins regardless of the N-terminal signal peptides is necessary for developing a critical computational *** prediction methods have been proposed by using various types of features to predict secretory ***,prediction performance seems not *** study proposes an SVM-based prediction method,namely ProSec-iGOX,which uses a major set of informative Gene Ontology(GO) terms and a minor set of assistance *** properties as the assistance features are useful when a query protein sequence without homologous protein with annotated GO *** data sets,S25and S40,having the identity 25% and 40%,respectively,are adopted for performance *** ProSec-iGOX yields test accuracies of 95.1% and 96.8% when adopting on the data sets S25 and S40 *** latter accuracy(96.8%) is significantly higher than that of SPRED(82.2%),which uses frequency of tri-peptides and short peptides,secondary structure,physicochemical properties as input features to a random forest *** experimental results show that GO terms are effective features for predicting non-classical secretory proteins.

关键词： Gene Ontology secretory physicochemical properties non-classical secretion signal peptides

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2010 ieee World Congress on computational Intelligence

作者： Fober, Thomas Huellermeier, Eyke Univ Marburg Dept Math & Comp Sci D-35041 Marburg Germany

ISBN: (纸本)9781424469208

We propose a method for comparing protein structures or, more specifically, protein binding sites in terms of histogram-based representations. These representation are intended to capture important geometrical and physico-chemical properties. In comparison to hitherto existing approaches in structural bioinformatics, especially graph-based methods and methods from computational geometry, our approach is computationally much more efficient. Moreover, despite its simplicity, first experimental studies suggest that it is able to produce useful measures of similarity.

关键词： bioinformatics computational geometry computational geometry fuzzy histogram comparison fuzzy set theory geometrical properties graph based methods graph theory histogram based representations physico chemical properties protein binding sites protein structures proteins similarity measures structural bioinformatics

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Insect navigation and communication in flight and migration: A potential model for joining and collision avoidance in MAVs and mobile robots fleet control

Insect navigation and communication in flight and migration:...

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ieee conference on Aerospace

作者： Zhanshan Ma Axel W. Krings Richard Millar Feng Wang Jun Chao Computational Biology & Bioinformatics Lab KIZ Chinese Academy of Sciences PRC & Computer Science Department & iBE University of Idaho USA Computer Science Department University of Idaho Moscow ID USA Department of Systems Engineering Naval Postgraduate School MD USA Computer Science Department Kunming University of Science and Technology Kunming China Kunming Institute of Zoology KIZ Chinese Academy and Sciences Kunming China

The human being should be awarded the championship of navigation on the planet, on the virtues that they not only have invented and manufactured the compass, GPS, aircraft, vessel, spacecraft, but also have demonstrated exceptional non-instrumental navigation skills. The Austronesian expansion from the Asian mainland into the Pacific performed by the Pacific navigators, who eventually populated the most remote islands of the Pacific about 4000 years ago, is a vivid example (Wehner 1998). However, animals, especially flying birds and insects are strong contenders. Monarch butterflies can migrate up to 2000 miles from their reproductive sites in the eastern US and Canada to their over-wintering sites in the forests of Mexico, and it is postulated that they may possess a biological equivalent of a low-resolution GPS system that is based on the magnetic field of the earth. In fact, even the long-legged ants (Cataglyphis fortis) in the Saharan desert use the dead-reckoning navigation strategy, which is attributed to the Polynesians, but the ants apparently have acquired the capability much earlier, given the relative short evolutionary history of humans. In this article, we briefly review the state-of-the-art research on insect navigation and communication used in flight and communication, with the objective to inspire cross-disciplinary studies in aerospace engineering, biology and computer science. After a brief review, we overview and identify seven cross-disciplinary research topics that may draw on inspirations from insect navigation and communication in flight and migration. These topics include: ants colony inspired swarm intelligence, honeybee inspired group decision-making, insect sociobiology, MAV/mobile robot flight control and remote control of insect flights, optimal migration strategy, Quorum sensing, and joining and collision avoidance for MAV fleet control. An interesting question one may pose is: given the rich and advanced navigation and communication t

关键词： Insects Navigation Visualization Birds Sun

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A Fuzzy Set Framework for Ontological Similarity Measures

A Fuzzy Set Framework for Ontological Similarity Measures

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2010 ieee World Congress on computational Intelligence

作者： Cross, Valerie V. Yu, Xinran Miami Univ Oxford OH 45056 USA

ISBN: (纸本)9781424469208

Advances in biotechnology have given rise to rapid production of biomedical data and the creation of a wide variety of biomedical and bioinformatics ontologies which serve as a primary impetus for the creation of new ontological similarity measures. A new IC ontological similarity measure, a variation of a standard fuzzy set similarity measure, is presented. This new IC ontological similarity measure has never been used in bioinformatics studies. It is compared with two standard IC ontological similarity measures, Resnik and Lin, and also an existing modification of Lin's measure by analyzing the results when used on a set of concepts pairs selected from the cellular component sub-ontology of the Gene Ontology. As part of this experiment, several different methods of calculating IC for an ontological concept are also investigated. These results for the cellular component sub-ontology confirm the results of a previous study on WordNet showing that ontology-based IC measures corresponded closely with corpus-based IC measures.

关键词： IC ontological similarity measure Lin measure Resnik measure WordNet bioinformatics bioinformatics ontology biomedical data biotechnology cellular component fuzzy set fuzzy set theory gene ontology ontologies (artificial intelligence)

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A Vaccine Strategy for Plant Allergy by RNA Interference - An in Silico Approach

A Vaccine Strategy for Plant Allergy by RNA Interference - A...

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1st International conference on computational systems Biology and bioinformatics

作者： Ramadoss, Ramya Kwoh, Chee Keong Nanyang Technol Univ Sch Comp Engn Singapore 639798 Singapore

ISBN: (纸本)9783642167492

Worldwide population affected by allergic rhinitis and asthma are estimated to 400 million and 300 million respectively, and the medical costs for treatment are estimated to exceed that of tuberculosis and AIDS allied. The main objective of this research is to propose a vaccine design strategy for the management of allergy through siRNA vaccination in silencing IgE VH region. The allergen Che a 3 was chosen to demonstrate our approach. Docking interactions between Che a 3 and modeled structures of heavy chain variable region of 31 Immunoglobulin E clones were analyzed in Auto Dock. Concurrently, small interference RNA sequences targeting the Immunoglobulin E clone with least binding energy were designed in siDRM.

关键词： Allergy Asthma Immunoglobulin E Vaccine Immunotherapy Small interference RNA Auto Dock bioinformatics Docking In silico

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