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Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2007-09
Abstract: 

The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

Document type: 
Article
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Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2007-07
Abstract: 

The (asymptotic) degree distributions of the best-known “scale-free” network models are all similar and are independent of the seed graph used; hence, it has been tempting to assume that networks generated by these models are generally similar. In this paper, we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the “right” seed graph (typically a dense subgraph of the protein–protein interaction network analyzed), the duplication model captures many topological features of publicly available protein–protein interaction networks very well

Document type: 
Article
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Ambient Data Collection with Wireless Sensor Networks

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

One of the most important applications for wireless sensor networks (WSNs) is Data Collection, where sensing data arecollected at sensor nodes and forwarded to a central base station for further processing. Since using battery powers and wirelesscommunications, sensor nodes can be very small and easily attached at specified locations without disturbing surroundingenvironments. This makes WSN a competitive approach for data collection comparing with its wired counterpart. In this paper,we review recent advances in this research area. We first highlight the special features of data collection WSNs, by comparingwith wired data collection network and other WSN applications. With these features in mind, we then discuss issues and priorsolutions on the data gathering protocol design. Our discussion also covers different approaches for message dissemination, whichis a critical component for network control and management and greatly affects the overall performance of a data collectionWSNsystem.

Document type: 
Article

Cooperative Coding and Caching for Streaming Data in Multihop Wireless Networks

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

This paper studies the distributed caching managements for the current flourish of the streaming applications inmultihop wirelessnetworks. Many caching managements to date use randomized network coding approach, which provides an elegant solution forubiquitous data accesses in such systems. However, the encoding, essentially a combination operation, makes the coded datadifficult to be changed. In particular, to accommodate new data, the system may have to first decode all the combined datasegments, remove some unimportant ones, and then reencode the data segments again. This procedure is clearly expensivefor continuously evolving data storage. As such, we introduce a novel Cooperative Coding and Caching (C3) scheme, whichallows decoding-free data removal through a triangle-like codeword organization. Its decoding performance is very close to theconventional network coding with only a sublinear overhead. Our scheme offers a promising solution to the caching managementfor streaming data.

Document type: 
Article

A Replica Exchange Monte Carlo Algorithm for Protein Folding in the HP Model

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2007
Abstract: 

Background: The ab initio protein folding problem consists of predicting protein tertiary structurefrom a given amino acid sequence by minimizing an energy function; it is one of the most importantand challenging problems in biochemistry, molecular biology and biophysics. The ab initio proteinfolding problem is computationally challenging and has been shown to be -hard even whenconformations are restricted to a lattice. In this work, we implement and evaluate the replicaexchange Monte Carlo (REMC) method, which has already been applied very successfully to morecomplex protein models and other optimization problems with complex energy landscapes, incombination with the highly effective pull move neighbourhood in two widely studied HydrophobicPolar (HP) lattice models.Results: We demonstrate that REMC is highly effective for solving instances of the square (2D)and cubic (3D) HP protein folding problem. When using the pull move neighbourhood, REMCoutperforms current state-of-the-art algorithms for most benchmark instances. Additionally, weshow that this new algorithm provides a larger ensemble of ground-state structures than theexisting state-of-the-art methods. Furthermore, it scales well with sequence length, and it findssignificantly better conformations on long biological sequences and sequences with a provablyunique ground-state structure, which is believed to be a characteristic of real proteins. We alsopresent evidence that our REMC algorithm can fold sequences which exhibit significant interactionbetween termini in the hydrophobic core relatively easily.Conclusion: We demonstrate that REMC utilizing the pull move neighbourhood significantlyoutperforms current state-of-the-art methods for protein structure prediction in the HP model on2D and 3D lattices. This is particularly noteworthy, since so far, the state-of-the-art methods for2D and 3D HP protein folding – in particular, the pruned-enriched Rosenbluth method (PERM) and,to some extent, Ant Colony Optimisation (ACO) – were based on chain growth mechanisms. Tothe best of our knowledge, this is the first application of REMC to HP protein folding on the cubiclattice, and the first extension of the pull move neighbourhood to a 3D lattice.

Document type: 
Article

Trombone Synthesis by Model and Measurement

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2011
Abstract: 

A physics-based synthesis model of a trombone is developed using filter elements that are both theoretically-based and estimatedfrom measurement. The model consists of two trombone instrument transfer functions: one at the position of the mouthpieceenabling coupling to a lip-valve model and one at the outside of the bell for sound production. The focus of this work is onextending a previously presented measurement technique used to obtain acoustic characterizations of waveguide elements forcylindrical and conical elements, with further development allowing for the estimation of the flared trombone bell reflection andtransmission functions for which no one-parameter traveling wave solution exists. A one-dimensional bell model is developedproviding an approximate theoretical expectation to which estimation results may be compared. Dynamic trombone modelelements, such as those dependent on the bore length, are theoretically and parametrically modeled. As a result, the trombonemodel focuses on accuracy, interactivity, and efficiency, making it suitable for a number of real-time computer music applications.

Document type: 
Article

Generating Test Cases for Marine Safety and Security Scenarios: A Composition Framework

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2012
Abstract: 

In this paper we address the problem of testing complex computer models forinfrastructure protection and emergency response based on detailed and realisticapplication scenarios using advanced computational methods and tools. Specifically,we focus here on testing situation analysis decision support models for marine safety& security operations as a sample application domain. Arguably, methodicalapproaches for analyzing and validating situation analysis methods, decision supportmodels, and information fusion algorithms require realistic vignettes that describe ingreat detail how a situation unfolds over time depending on initial configurations,dynamic environmental conditions and uncertain operational aspects. Meaningfulresults from simulation runs require appropriate test cases, the production of whichis in itself a complex activity. To simplify this task, we introduce here the conceptualdesign of a Vignette Generator that has been developed and tested in an industrialresearch project. We also propose a framework for composing vignettes fromreusable vignette elements together with a formal representation for vignettes usingthe Abstract State Machine method and illustrate the approach by means of variouspractical examples.

Document type: 
Article

A Web-Based Graphical User Interface for Evidence-Based Decision Making for Health Care Allocations in Rural Areas

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2008
Abstract: 

Background: The creation of successful health policy and location of resources increasingly relieson evidence-based decision-making. The development of intuitive, accessible tools to analyse,display and disseminate spatial data potentially provides the basis for sound policy and resourceallocation decisions. As health services are rationalized, the development of tools such graphicaluser interfaces (GUIs) is especially valuable at they assist decision makers in allocating resourcessuch that the maximum number of people are served. GIS can used to develop GUIs that enablespatial decision making.Results: We have created a Web-based GUI (wGUI) to assist health policy makers andadministrators in the Canadian province of British Columbia make well-informed decisions aboutthe location and allocation of time-sensitive service capacities in rural regions of the province. Thistool integrates datasets for existing hospitals and services, regional populations and road networksto allow users to ascertain the percentage of population in any given service catchment who areserved by a specific health service, or baskets of linked services. The wGUI allows policy makersto map trauma and obstetric services against rural populations within pre-specified travel distances,illustrating service capacity by region.Conclusion: The wGUI can be used by health policy makers and administrators with little or noformal GIS training to visualize multiple health resource allocation scenarios. The GUI is poised tobecome a critical decision-making tool especially as evidence is increasingly required fordistribution of health services.

Document type: 
Article

Fast Prediction of RNA-RNA Interaction

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

Background: Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting thetranslation of an mRNA by establishing stable interactions with a target sequence. There is great demand forefficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s).There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunatelyat a very high computational cost. Although some existing target prediction approaches are much faster, they arespecialized for interactions with a single binding site.Methods: In this paper we present a novel algorithm to accurately predict the minimum free energy structure ofRNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introducea fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs.Results: We verify the performance of our algorithms for joint structure and binding site prediction on a set ofknown interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform allcompetitive approaches.

Document type: 
Article