MOTIVATION: Identification of functionally conserved regulatory elements in sequence data from closely related organisms is becoming feasible, due to the rapid growth of public sequence databases. Closely related organisms are most likely to have common regulatory motifs; however, the recent speciation of such organisms results in the high degree of correlation in their genome sequences, confounding the detection of functional elements. Additionally, alignment algorithms that use optimization techniques are limited to the detection of a single alignment that may not be representative. Comparative-genomics studies must be able to address the phylogenetic correlation in the data and efficiently explore the alignment space, in order to make specific and biologically relevant predictions. RESULTS: We describe here a Gibbs sampler that employs a full phylogenetic model and reports an ensemble centroid solution. We describe regulatory motif detection using both simulated and real data, and demonstrate that this approach achieves improved specificity, sensitivity, and positive predictive value over non-phylogenetic algorithms, and over phylogenetic algorithms that report a maximum likelihood solution. AVAILABILITY: The software is freely available at http://bayesweb.wadsworth.org/gibbs/gibbs.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A significant problem with telephone communication is that callers do not have enough awareness about the Personal Presence of people they want to call. The result can be unwanted, interrupting calls. Thelive addressbookis an application that helps users make more informed telephone calls and teleconferences, from anywhere, via their wireless PDA or desktop browser. Unlike other network-based address books, which maintain static information, the live addressbook can display dynamic information about where the recipient currently is (i.e., reach number), and how available he/she currently is for calls. The system accomplishes this by applying to telephony the "Buddy List" concepts made popular in Instant Messaging applications. User trials assess the applicability of Personal Presence information in a telephone context.

With the growing use of electronic mail come challenges in how to aid users in handling ever-increasing volumes of email.Firsthand experience as well as the systematic study of users' email patterns suggest that a large fraction of messages are parts of larger transactions.We have implemented an approach toward structuring messages that is intended to help users carry out some of these transactions.Our approach has been to make message structure both general-purpose and optional.Two studies support the applicability and the acceptance of the messaging model.The system, which provides capabilities that are largely absent from conventional email systems, has been deployed in an internal trial.

The effect of coherence is examined using an exponential-power-law model for the signal wavefront correlation. Detection performance is quantified by the small-signal deflection criterion, which is first reviewed in the general setting of quadratic detectors and then applied to matched-field and optimal quadratic beamformers. It is shown that the detection performance of matched-field beamforming is substantially degraded for large arrays and typical coherence lengths. The optimal quadratic processor reduces this coherence loss, but at a cost of greatly increased processor complexity. Several suboptimal beamformers with reduced computational load are also developed, and their detection performance is compared to that of the matched-field and optimal beamformers. One suboptimal processor, the subarray beamformer, has proved outstanding for this application in three respects: it can realize within 1 dB of optimal performance; it is robust over a class of correlation functions; and it entails a computational burden no greater than that of full-array matched-field beamforming.>