1 THE USE OF FUNCTIONAL DOMAINS TO IMPROVE TRANSMEMBRANE PROTEIN TOPOLOGY PREDICTION (2009)
Emily W. Xu, Ab Tn N, Daniel G. Brown, Paul Kearney
Transmembrane proteins affect vital cellular functions and diseases, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure....
A COLLAPSING METHOD FOR THE EFFICIENT RECOVERY OF OPTIMAL EDGES IN PHYLOGENETIC TREES (2009)
Michael Hu, Paul Kearney, Jonathan Badger
As the amount of sequencing efforts and genomic data volume continue to increase at an accelerated rate, phylogenetic analysis provides an evolutionary context for understanding and interpreting this...
Some Open Problems in Computational Molecular Biology (2008)
Samir Khuller, Tao Jiang, Paul Kearney, Ming Li
This column will carry problems arising in the design of algorithms for discrete optimization problems. Problems are solicited in all areas of algorithm design that are covered by the Journal of...
There is a variety of applications that can benefit from the ability to find optimal or good solutions to a proposed problem automatically. The Artificial Intelligent (AI) community has been actively...
MSMS Peak Identification and its Applications (2008)
Deep Jaitly, Denis Faubert, Pierre Thibault, Paul Kearney
A peak detection algorithm for Tandem Mass Spectra is presented that scores a fragment using intensity and isotopic distribution. It classifies each fragment in a spectrum as noise or signal based on...
A case study: using Workflow and AI planners (2008)
Md R-moreno, Paul Kearney, Daniel Meziat
This paper argues that the use of AI planning techniques with existing Workflow Management Systems can improve overall system functionality and help to automate the definition of business processes....
ABSTRACT Teaching Technology to the (2008)
Of The Naccq, Playstation Generation, Paul Kearney, Stephen Skelton
Today's computing students arrive in our classroom familiar with a wide range of technology. They are used to rapid change and fast paced, interactive environments that this brings. This is the...
Paul Kearney, Nathan L. Currier, Daniel Chelsky, Clarissa Desjardins
Disease and drugs can modulate the concentrations of hundreds of proteins in the blood which can be accurately measured using contemporary proteomic methods. Nevertheless, it is common practice to...
A Collapsing Method for the Ecient Recovery of Optimal Edges in Phylogenetic Trees (2007)
Mike Hu, Paul Kearney, Jonathan Badger
As the amount of sequencing eorts and genomic data volume continue to increase at an accelerated rate, phylogenetic analysis provides an evolutionary context for understanding and interpreting this...
Email: robert.smithuwe.ac.uk c2-bonacinauwe.ac.uk (2007)
R. E. Smith, Claudio Bonacina, Paul Kearney, Torsten Eymann
Abstract: Multi-agent software systems can be modeled as complex, dynamic systems in which agent adaptation and interaction occur continuously and concurrently. A genetics inspired view has agent...
British Telecom Laboratories (2007)
Robert E. Smith, Ph. D, Claudio Bonacina, Paul Kearney, Walter Merlat, Martlesham Heath Ipswich
Holland’s Adaptation in Natural and Artificial Systems largely dealt with how systems, comprised of many self-interested entities, can and should adapt as a whole. This seminal book led to the last...
Paul Kearney, Ming Li, John Tsang, Tao Jiang
Many fundamental questions in evolution remain unresolved despite the abundance of genetic sequence data that is now available to answer these questions. This state of affairs is largely due to the...
A CASE STUDY: USING WORKFLOW AND AI PLANNERS MD R-Moreno 1 (2007)
This paper argues that the use of AI planning techniques with existing Workflow Management Systems can improve overall system functionality and help to automate the definition of business processes....
A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees (2007)
Mike Hu, Paul Kearney, Jonathan Badger
As the amount of sequencing efforts and genomic data volume continue to increase at an accelerated rate, phylogenetic analysis provides an evolutionary context for understanding and interpreting this...
A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees (2007)
Michael Hu, Paul Kearney, Jonathan Badger
As the amount of sequencing efforts and genomic data volume continue to increase at an accelerated rate, phylogenetic analysis provides an evolutionary context for understanding and interpreting this...
Efficient Generation of Uniform Samples from Phylogenetic Trees (2007)
Paul Kearney, J. Ian Munro, Derek Phillips
In this paper, we introduce new algorithms for selecting taxon (leaf) samples from large phylogenetic trees, uniformly at random, under certain biologically relevant constraints on the taxa. All the...
Deep Jaitly, Paul Kearney, Guo-hui Lin, Bin Ma
The genomes of many species are dominated by short sequences repeated consecutively called tandem repeats. An understanding of the biological mechanisms that create and extend tandem repeats would be...
D: The Use of Functional Domains to Improve Transmembrane Protein Topology Prediction (2006)
Emily W. Xu, Daniel G. Brown, Paul Kearney
Transmembrane proteins affect vital cellular functions and diseases, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure....
Cognitive Callisthenics: Do FPS computer games enhance the player’s cognitive abilities? (2005)
Presented at the International DiGRA Conference, June 16th - 20th, 2005, Vancouver, British Columbia, Canada (http://www.gamesconference.org/digra2005/overview.php)
Playing in the Sandbox: Developing games for children with disabilities. (2005)
Presented at the International DiGRA Conference, June 16th - 20th, 2005, Vancouver, British Columbia, Canada (http://www.gamesconference.org/digra2005/overview.php)
Towards a Trust and Contract Management Framework for Dynamic Virtual Organisations (2004)
Theo Dimitrakos, David Golby, Paul Kearney
Abstract: TrustCom is a new European integrated project that aims to develop a framework for trust, security and contract management in dynamic Virtual Organisations. The framework will enable the...
Probabilistic analysis indicates discordant gene trees in chloroplast evolution (2003)
Claus Vogl, Jonathan Badger, Paul Kearney, Ming Li, Michael Clegg, Tao Jiang
Abstract. Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny estimated for the entire genome. We present a probabilistic...
A Collapsing Method for Efficient Recovery of Best Supported Edges in Phylogenetic Trees (2002)
We present a new algorithm, HyperCleaning* for effectively...
Agent Oriented Analysis using MESSAGE/UML (2001)
Giovanni Caire, Wim Coulier, Francisco Garijo, Jorge Gomez, Juan Pavon, Francisco Leal, ...
This paper presents the MESSAGE/UML agent oriented software engineering methodology and illustrates it on an analysis case study. The methodology covers MAS analysis and design and is intended for...
Ruth Aylett, Susanne Biundo, Malik Ghallab, Simon De Givry, Paul Kearney, Lee Mccluskey
Planning and Scheduling is the field of Artificial Intelligence that is concerned with all aspects of the system-supported or fully automated synthesis, execution, and monitoring of courses of...
Ruth Aylett, Susanne Biundo, Malik Ghallab, Simon De Givry, Paul Kearney, Lee Mccluskey
Planning and Scheduling is the field of Artificial Intelligence that is concerned with all aspects of the system-supported or fully automated synthesis, execution, and monitoring of courses of...
Li, Ming, Badger, Jonathan H., Chen, Xin, Kwong, Sam, Kearney, Paul, Zhang, Haoyong
Motivation: Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length...
Analysis of Codon Usage Patterns of Bacterial Genomes Using the Self-Organizing Map (2001)
Wang, Huai-Chun, Badger, Jonathan, Kearney, Paul, Li, Ming
Codon usage varies both between organisms and between different genes in the same organism. This observation has been used as a basis for earlier work in identifying highly expressed and horizontally...
Computing the quartet distance between evolutionary trees (2000)
David Bryant, John Tsang, Paul Kearney, Ming Li
The comparison of evolutionary trees is a fundamental problem in evolutionary biology. Di erent evolutionary hypotheses (or con icting phylogenies) arise
Computing the quartet distance between evolutionary trees (2000)
David Bryant, John Tsang, Paul Kearney, Ming Li
The comparison of evolutionary trees is a fundamen-tal problem in evolutionary biology. Different evolu-tionary hypotheses (or conflicting phylogenies) arise
A practical algorithm for recovering the best supported edges of an evolutionary tree (2000)
Vincent Berry, David Bryant, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham, ...
It is now routine for biologists to conduct evolutionary analyses of large DNA and protein sequence datasets. A computational bottleneck in these analyses is the recovery of the topology of the...
Computing the Quartet Distance Between Evolutionary Trees (2000)
David Bryant, John Tsang, Paul Kearney, Ming Li
this paper, we study the quartet metric, which is based on common subtrees induced by four leaves. This metric has several attractive properties, though its use has been limited by the time required...
Tao Jiang, Paul Kearney, Ming Li
. Inferring evolutionary trees has long been a challenging problem both for biologists and computer scientists. In recent years research has concentrated on the quartet method paradigm for inferring...
Vincent Berry, David Bryant, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham, ...
) Vincent Berry David Bryant y Tao Jiang z Paul Kearney x Ming Li -- Todd Wareham k Haoyong Zhang Abstract It is now routine for biologists to conduct evolutionary analyses of large DNA and protein...
Quartet Cleaning: Improved Algorithms and Simulations (1999)
Vincent Berry, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham
A critical step in all quartet methods for constructing evolutionary trees is the inference of the topology for each set of four species (i.e. quartet). It is a well-known fact that all quartet...
Quartet Cleaning: Improved Algorithms and Simulations (1999)
Vincent Berry, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham, Département De Mathématiques, ...
A critical step in all quartet methods for constructing evolutionary trees is the inference of the topology for each set of four sequences (i.e. quartet). It is a well--known fact that all quartet...
Orchestrating quartets: approximation and data correction (1998)
Tao Jiang, Paul Kearney, Ming Li
Inferring evolutionary trees has long been a challenging problem both for biologists and computer scientists. In recent years research has concentrated on the quartet method paradigm for inferring...
Orchestrating Quartets: Approximation and Data Correction (1998)
Tao Jiang, Paul Kearney, Ming Li
Inferring evolutionary trees has long been a challenging problem both for biologists and computer scientists. In recent years research has concentrated on the quartet method paradigm for inferring...