Global protein function prediction in protein-protein interaction networks

The determination of protein functions is one of the most challenging problems of the post-genomic era. The sequencing of entire genomes and the possibility to access gene's co-expression patterns has moved the attention from the study of single proteins or small complexes to that of the entire proteome. In this context, the search for reliable methods for proteins' function assignment is of uttermost importance. Previous approaches to deduce the unknown function of a class of proteins have exploited sequence similarities or clustering of co-regulated genes, phylogenetic profiles, protein-protein interactions, and protein complexes. We propose to assign functional classes to proteins from their network of physical interactions, by minimizing the number of interacting proteins with different categories. The function assignment is made on a global scale and depends on the entire connectivity pattern of the protein network. Multiple functional assignments are made possible as a consequence of the existence of multiple equivalent solutions. The method is applied to the yeast Saccharomices Cerevisiae protein-protein interaction network. Robustness is tested in presence of a high percentage of unclassified proteins and under deletion/insertion of interactions.Comment: 5 pages, 2 figures, 2 supplementary table

Species lifetime distribution for simple models of ecologies

Interpretation of empirical results based on a taxa's lifetime distribution shows apparently conflicting results. Species' lifetime is reported to be exponentially distributed, whereas higher order taxa, such as families or genera, follow a broader distribution, compatible with power law decay. We show that both these evidences are consistent with a simple evolutionary model that does not require specific assumptions on species interaction. The model provides a zero-order description of the dynamics of ecological communities and its species lifetime distribution can be computed exactly. Different behaviors are found: an initial $t^{-3/2}$ power law, emerging from a random walk type of dynamics, which crosses over to a steeper $t^{-2}$ branching process-like regime and finally is cutoff by an exponential decay which becomes weaker and weaker as the total population increases. Sampling effects can also be taken into account and shown to be relevant: if species in the fossil record were sampled according to the Fisher log-series distribution, lifetime should be distributed according to a $t^{-1}$ power law. Such variability of behaviors in a simple model, combined with the scarcity of data available, cast serious doubts on the possibility to validate theories of evolution on the basis of species lifetime data.Comment: 19 pages, 2 figure

Geometry of compact tubes and protein structures

Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures the well-known characteristics of polymers and their phases but also provides a natural explanation for many of the key features of protein behavior. There are two natural length scales associated with a tube subject to compaction -- the thickness of the tube and the range of the attractive interactions. For short tubes, when these length scales become comparable, one obtains marginally compact structures, which are relatively few in number compared to those in the generic compact phase of polymers. The motifs associated with the structures in this new phase include helices, hairpins and sheets. We suggest that Nature has selected this phase for the structures of proteins because of its many advantages including the few candidate strucures, the ability to squeeze the water out from the hydrophobic core and the flexibility and versatility associated with being marginally compact. Our results provide a framework for understanding the common features of all proteins.Comment: 15 pages, 3 eps figure

Flexible and Low-cost Interface Circuit for Electrochemical and Resistive Gas Sensors

n/

Online Human-Bot Interactions: Detection, Estimation, and Characterization

Increasing evidence suggests that a growing amount of social media content is generated by autonomous entities known as social bots. In this work we present a framework to detect such entities on Twitter. We leverage more than a thousand features extracted from public data and meta-data about users: friends, tweet content and sentiment, network patterns, and activity time series. We benchmark the classification framework by using a publicly available dataset of Twitter bots. This training data is enriched by a manually annotated collection of active Twitter users that include both humans and bots of varying sophistication. Our models yield high accuracy and agreement with each other and can detect bots of different nature. Our estimates suggest that between 9% and 15% of active Twitter accounts are bots. Characterizing ties among accounts, we observe that simple bots tend to interact with bots that exhibit more human-like behaviors. Analysis of content flows reveals retweet and mention strategies adopted by bots to interact with different target groups. Using clustering analysis, we characterize several subclasses of accounts, including spammers, self promoters, and accounts that post content from connected applications.Comment: Accepted paper for ICWSM'17, 10 pages, 8 figures, 1 tabl

An exactly solvable model for a beta-hairpin with random interactions

I investigate a disordered version of a simplified model of protein folding, with binary degrees of freedom, applied to an ideal beta-hairpin structure. Disorder is introduced by assuming that the contact energies are independent and identically distributed random variables. The equilibrium free-energy of the model is studied, performing the exact calculation of its quenched value and proving the self-averaging feature.Comment: 9 page

Wireless ATM layouts for chain networks

In this paper we consider the problem of constructing ATM layouts for wireless networks in which mobile users can move along a chain of base stations. We first show that deciding the existence of a layout with maximum hop count h, load l and channel distance d is NP-complete for every fixed value of d greater or equal to 1. We then provide optimal layout constructions for the case d less than or equal to 2. Finally, optimal layout constructions are obtained also for any d within the class of the so-called canonic layouts, that so far have always been shown to be the optimal ones

Automatic instantiation of abstract tests to specific configurations for large critical control systems

Computer-based control systems have grown in size, complexity, distribution and criticality. In this paper a methodology is presented to perform an ‘abstract testing’ of such large control systems in an efficient way: an abstract test is specified directly from system functional requirements and has to be instantiated in more test runs to cover a specific configuration, comprising any number of control entities (sensors, actuators and logic processes). Such a process is usually performed by hand for each installation of the control system, requiring a considerable time effort and being an error-prone verification activity. To automate a safe passage from abstract tests, related to the so-called generic software application, to any specific installation, an algorithm is provided, starting from a reference architecture and a statebased behavioural model of the control software. The presented approach has been applied to a railway interlocking system, demonstrating its feasibility and effectiveness in several years of testing experience

The egalitarian effect of search engines

Search engines have become key media for our scientific, economic, and social activities by enabling people to access information on the Web in spite of its size and complexity. On the down side, search engines bias the traffic of users according to their page-ranking strategies, and some have argued that they create a vicious cycle that amplifies the dominance of established and already popular sites. We show that, contrary to these prior claims and our own intuition, the use of search engines actually has an egalitarian effect. We reconcile theoretical arguments with empirical evidence showing that the combination of retrieval by search engines and search behavior by users mitigates the attraction of popular pages, directing more traffic toward less popular sites, even in comparison to what would be expected from users randomly surfing the Web.Comment: 9 pages, 8 figures, 2 appendices. The final version of this e-print has been published on the Proc. Natl. Acad. Sci. USA 103(34), 12684-12689 (2006), http://www.pnas.org/cgi/content/abstract/103/34/1268