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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)
The advent of high-throughput biology has catalyzed a remarkable improvement in our ability to identify new genes. A large fraction of newly discovered genes have an unknown functional role, particularly when they are specific to a particular lineage or organism. These genes, currently labeled "hypothetical," might support important biological cell(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)
Free Air [CO2] Enrichment (FACE) allows for plant growth under fully open-air conditions of elevated [CO2] at concentrations expected to be reached by mid-century. We used Arabidopsis thaliana ecotypes Col-0, Cvi-0, and WS to analyze changes in gene expression and metabolite profiles of plants grown in “SoyFACE” (http://www.soyface.uiuc.edu/), a system of(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)
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)
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)
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)
BACKGROUND Infectious diseases result in millions of deaths each year. Physical interactions between pathogen and host proteins often form the basis of such infections. While a number of methods have been proposed for predicting protein-protein interactions (PPIs), they have primarily focused on intra-species protein-protein interactions. METHODOLOGY We(More)
We introduce two new related metrics, the geodesic width and the link width, for measuring the " distance " between two non-intersecting 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)(More)