QPath: a method for querying pathways in a protein-protein interaction network

BACKGROUND: Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks. RESULTS: We present a comprehensive framework for protein network searches using pathway queries. Given a linear query pathway and a network of interest, our algorithm, QPath, efficiently searches the network for homologous pathways, allowing both insertions and deletions of proteins in the identified pathways. Matched pathways are automatically scored according to their variation from the query pathway in terms of the protein insertions and deletions they employ, the sequence similarity of their constituent proteins to the query proteins, and the reliability of their constituent interactions. We applied QPath to systematically infer protein pathways in fly using an extensive collection of 271 putative pathways from yeast. QPath identified 69 conserved pathways whose members were both functionally enriched and coherently expressed. The resulting pathways tended to preserve the function of the original query pathways, allowing us to derive a first annotated map of conserved protein pathways in fly. CONCLUSION: Pathway homology searches using QPath provide a powerful approach for identifying biologically significant pathways and inferring their function. The growing amounts of protein interactions in public databases underscore the importance of our network querying framework for mining protein network data

Des Robots Sourds-Muets Bien Bavards

International audienceDans cet article, nous nous intéressons au problème de la diffusion de messages au sein d'une cohorte de robots sourds- muets et nous introduisons l'utilisation de mouvements comme vecteur de transmission des messages. Deux protocoles sont présentés, respectivement en environnement synchrone et asynchrone

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

Advances in sequencing technology are resulting in the rapid emergence of large numbers of complete genome sequences. High throughput annotation and metabolic modeling of these genomes is now a reality. The high throughput reconstruction and analysis of genome-scale transcriptional regulatory networks represents the next frontier in microbial bioinformatics. The fruition of this next frontier will depend upon the integration of numerous data sources relating to mechanisms, components, and behavior of the transcriptional regulatory machinery, as well as the integration of the regulatory machinery into genome-scale cellular models. Here we review existing repositories for different types of transcriptional regulatory data, including expression data, transcription factor data, and binding site locations, and we explore how these data are being used for the reconstruction of new regulatory networks. From template network based methods to de novo reverse engineering from expression data, we discuss how regulatory networks can be reconstructed and integrated with metabolic models to improve model predictions and performance. Finally, we explore the impact these integrated models can have in simulating phenotypes, optimizing the production of compounds of interest or paving the way to a whole-cell model.J.P.F. acknowledges funding from [SFRH/BD/70824/2010] of the FCT (Portuguese Foundation for Science and Technology) PhD program. The work was supported in part by the ERDF—European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness), National Funds through the FCT within projects [FCOMP-01-0124-FEDER015079] (ToMEGIM—Computational Tools for Metabolic Engineering using Genome-scale Integrated Models) and FCOMP-01-0124-FEDER009707 (HeliSysBio—molecular Systems Biology in Helicobacter pylori), the U.S. Department of Energy under contract [DE-ACO2-06CH11357] and the National Science Foundation under [0850546]

Disease Gene Interaction Pathways: A Potential Framework for How Disease Genes Associate by Disease-Risk Modules

BACKGROUND: Disease genes that interact cooperatively play crucial roles in the process of complex diseases, yet how to analyze and represent their associations is still an open problem. Traditional methods have failed to represent direct biological evidences that disease genes associate with each other in the pathogenesis of complex diseases. Molecular networks, assumed as 'a form of biological systems', consist of a set of interacting biological modules (functional modules or pathways) and this notion could provide a promising insight into deciphering this topic. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we hypothesized that disease genes might associate by virtue of the associations between biological modules in molecular networks. Then we introduced a novel disease gene interaction pathway representation and analysis paradigm, and managed to identify the disease gene interaction pathway for 61 known disease genes of coronary artery disease (CAD), which contained 46 disease-risk modules and 182 interaction relationships. As demonstrated, disease genes associate through prescribed communication protocols of common biological functions and pathways. CONCLUSIONS/SIGNIFICANCE: Our analysis was proved to be coincident with our primary hypothesis that disease genes of complex diseases interact with their neighbors in a cooperative manner, associate with each other through shared biological functions and pathways of disease-risk modules, and finally cause dysfunctions of a series of biological processes in molecular networks. We hope our paradigm could be a promising method to identify disease gene interaction pathways for other types of complex diseases, affording additional clues in the pathogenesis of complex diseases

Explicit Communication Among Stigmergic Robots

International audienceIn this paper, we investigate avenues for the exchange of information (explicit communication) among deaf and mute mobile robots scattered in the plane. We introduce the use of movement-signals (analogously to flight signals and bees waggle) as a mean to transfer messages, enabling the use of distributed algorithms among robots. We propose one-to-one deterministic movement protocols that implement explicit communication among semi-synchronous robots. We first show how the movements of robots can provide implicit acknowledgment in semi-synchronous systems. We use this result to design one-to-one communication among a pair of robots. Then, we propose two one-to-one communication protocols for any system of n≥2robots. The former works for robots equipped with observable IDs that agree on a common direction (sense of direction). The latter enables one-to-one communication assuming robots devoid of any observable IDs or sense of direction. All protocols (for either two or any number of robots) assume that no robot remains inactive forever. However, they cannot avoid that the robots move either away or closer to each others, by the way requiring robots with an infinite visibility. In this paper, we also present how to overcome these two disadvantages (some activity of every robot and infinite visibility).Our protocols enable the use of distributing algorithms based on message exchanges among swarms of stigmergic robots. They also allow robots to be equipped with the means of communication to tolerate faults in their communication devices

Deaf, Dumb, and Chatting Robots, Enabling Distributed Computation and Fault-Tolerance Among Stigmergic Robot

We investigate ways for the exchange of information (explicit communication) among deaf and dumb mobile robots scattered in the plane. We introduce the use of movement-signals (analogously to flight signals and bees waggle) as a mean to transfer messages, enabling the use of distributed algorithms among the robots. We propose one-to-one deterministic movement protocols that implement explicit communication. We first present protocols for synchronous robots. We begin with a very simple coding protocol for two robots. Based on on this protocol, we provide one-to-one communication for any system of n ≥ 2 robots equipped with observable IDs that agree on a common direction (sense of direction). We then propose two solutions enabling one-to-one communication among anonymous robots. Since the robots are devoid of observable IDs, both protocols build recognition mechanisms using the (weak) capabilities offered to the robots. The first protocol assumes that the robots agree on a common direction and a common handedness (chirality), while the second protocol assumes chirality only. Next, we show how the movements of robots can provide implicit acknowledgments in asynchronous systems. We use this result to design asynchronous one-to-one communication with two robots only. Finally, we combine this solution with the schemes developed in synchronous settings to fit the general case of asynchronous one-to-one communication among any number of robots. Our protocols enable the use of distributing algorithms based on message exchanges among swarms of Stigmergic robots. Furthermore, they provides robots equipped with means of communication to overcome faults of their communication device

Brief announcement: deaf, dumb, and chatting robots

International audienceNo abstract