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We propose a mathematical formulation for the notion of optimal projective cluster, starting from natural requirements on the density of points in subspaces. This allows us to develop a Monte Carlo algorithm for iteratively computing projective clusters. We prove that the computed clusters are good with high probability. We implemented a modified version of… (More)

We propose a representation for gene expression data called conserved gene expression motifs or XMOTIFs. A gene's expression level is conserved across a set of samples if the gene is expressed with the same abundance in all the samples. A conserved gene expression motif is a subset of genes that is simultaneously conserved across a subset of samples. We… (More)

RankGene is a program for analyzing gene expression data and computing diagnostic genes based on their predictive power in distinguishing between different types of samples. The program integrates into one system a variety of popular ranking criteria, ranging from the traditional t-statistic to one-dimensional support vector machines. This flexibility makes… (More)

- Matthew D Dyer, T. M Murali, Bruno W Sobral
- PLoS pathogens
- 2008

Infectious diseases result in millions of deaths each year. Mechanisms of infection have been studied in detail for many pathogens. However, many questions are relatively unexplored. What are the properties of human proteins that interact with pathogens? Do pathogens interact with certain functional classes of human proteins? Which infection mechanisms and… (More)

HIV Dependency Factors (HDFs) are a class of human proteins that are essential for HIV replication, but are not lethal to the host cell when silenced. Three previous genome-wide RNAi experiments identified HDF sets with little overlap. We combine data from these three studies with a human protein interaction network to predict new HDFs, using an intuitive… (More)

MOTIVATION
Infectious diseases such as malaria result in millions of deaths each year. An important aspect of any host-pathogen system is the mechanism by which a pathogen can infect its host. One method of infection is via protein-protein interactions (PPIs) where pathogen proteins target host proteins. Developing computational methods that identify which… (More)

- Matthew D. Dyer, Chris Neff, Max Dufford, Corban G. Rivera, Donna Shattuck, Josep Bassaganya-Riera +2 others
- PloS one
- 2010

BACKGROUND
Bacillus anthracis, Francisella tularensis, and Yersinia pestis are bacterial pathogens that can cause anthrax, lethal acute pneumonic disease, and bubonic plague, respectively, and are listed as NIAID Category A priority pathogens for possible use as biological weapons. However, the interactions between human proteins and proteins in these… (More)

We introduce two new related metrics, the geodesic width and the link width, for measuring the " distance " between two nonintersecting polylines in the plane. If the two polylines have n vertices in total, we present algorithms to compute the geodesic width of the two polylines in O(n 2 log n) time using O(n 2) space and the link width in O(n 3 log n) time… (More)

Consistent representations of the boundary and interior of three-dimensional solid objects are required by applications ranging from interactive visualization to nite element analysis. However, most commonly available models of solid objects contain errors and inconsistencies. We describe an algorithm that automatically constructs consistent representations… (More)

We consider the problem of locating a moving target using a group of guards cooperatively moving inside a simple polygon. Our guards always form a simple polygonal chain within the polygon such that consecutive guards along the chain are mutually visible. We develop algorithms that sweep such a chain of guards through a polygon to locate the target. Our two… (More)