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...
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)
A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees (2004)
Michael Hu, Paul Kearney, Jonathan Badger
As the amount of sequencing e#orts 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 (2003)
Paul Kearney, J. Ian Munro, Derek Phillips, Caprion Pharmaceuticals
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...
Methods for Reconstructing the History of Tandem Repeats and (2003)
Deep Jaitly, Paul Kearney, Guo-hui Lin, Bin Ma
This paper explores the computational problem of reconstructing the duplication history of a tandem repeat. Speci cally, the problem of reconstructing the minimum-cost duplication history is proved...
A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees (2003)
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 (2003)
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...
Integrating Economics and Genetics Models in Information Ecosystems (2002)
R. E. Smith, Claudio Bonacina, Paul Kearney, Torsten Eymann
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 adaptation...
Embodiment of Evolutionary Computation in General Agents (2002)
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...
A Collapsing Method for Efficient Recovery of Best Supported Edges in Phylogenetic Trees (2002)
Contents ii 3.2.4 Constructing Best xy (m; W ) 53 3.2.5 Constructing Best(m; W k ) iii iv The study of phylogenetic inference is fundamental to the understanding of biological evolution at the...
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...
Agent Oriented Analysis using MESSAGE/UML (2001)
Giovanni Caire, Telecom Italia Lab, Francisco Garijo Jorge, Gomez Juan Pavon, Emilio Vargas, 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...
A Case Study: Using Workflow And Ai Planners (2000)
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....
Recovering Branches on the Tree of Life: An Approximation Algorithm (2000)
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...
Picking Fruit from the Tree of Life - Comments on Taxonomic Sampling and Quartet Methods (2000)
Jonathan H. Badger, Paul Kearney
A topic of recent interest and controversy in the field of systematic biology is the value of "taxonomic sampling", the practice of adding additional sequences (taxa) to an analysis to improve the...
Integrating Economics and Genetics Models in Information Ecosystems (2000)
R. E. Smith, Claudio Bonacina, Paul Kearney, Martlesham Heath, Torsten Eymann
: 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 adaptation...
Whole Mitochondrial, Genome Phylogeny, Ming Li, Jonathan H. Badger, Xin Chen, Sam Kwong, ...
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...
Quartet Cleaning: Improved Algorithms and Simulations (2000)
Vincent Berry, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham
A critical step in many quartet{based phylogeny reconstruction algorithms is the inference of the topology for each set of four species (i.e. quartet). It is a well{known fact that all quartet...
Computing the Quartet Distance Between Evolutionary Trees (1999)
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...
Orchestrating Quartets: Approximation and Data Correction (1999)
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...
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...
Recovering Branches on the Tree of Life: An Approximation Algorithm (1998)
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...
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...