The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. Being a reference expression database with user-friendly tools, Genevestigator V3 facilitates discovery research and hypothesis validation.

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In this paper we study the problem of gathering in the same location of the plane a collection of identical oblivious mobile robots. Previous investigations have focused mostly on the unlimited visibility setting, where each robot can always see all the other ones, regardless of their distance.In the more difficult and realistic setting where the robots have limited visibility, the existing algorithmic results are only for convergence (towards a common point, without ever reaching it) and only for synchronous environments, where robots' movements are assumed to be performed instantaneously.In contrast, we study this problem in a totally asynchronous setting, where robots' actions, computations, and movements require a finite but otherwise unpredictable amount of time. We present a protocol that allows anonymous oblivious robots with limited visibility to gather in the same location in finite time, provided they have orientation (i.e., agreement on a coordinate system).Our result indicates that, with respect to gathering, orientation is at least as powerful as instantaneous movements.

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De novo sequencing of peptides poses one of the most challenging tasks in data analysis for proteome research. In this paper, a generative hidden Markov model (HMM) of mass spectra for de novo peptide sequencing which constitutes a novel view on how to solve this problem in a Bayesian framework is proposed. Further extensions of the model structure to a graphical model and a factorial HMM to substantially improve the peptide identification results are demonstrated. Inference with the graphical model for de novo peptide sequencing estimates posterior probabilities for amino acids rather than scores for single symbols in the sequence. Our model outperforms state-of-the-art methods for de novo peptide sequencing on a large test set of spectra.