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BACKGROUND: Publication records and citation indices often are used to evaluate academic performance. For this reason, obtaining or computing them accurately is important. This can be difficult, largely due to a lack of complete knowledge of an individual's publication list and/or lack of time available to manually obtain or construct the publication-citation record. While online publication search engines have somewhat addressed these problems, using raw search results can yield inaccurate estimates of publication-citation records and citation indices. METHODOLOGY: In this paper, we present a new, automated method that produces estimates of an individual's publication-citation record from an individual's name and a set of domain-specific vocabulary that may occur in the individual's publication titles. Because this vocabulary can be harvested directly from a research web page or online (partial) publication list, our method delivers an easy way to obtain estimates of a publication-citation record and the relevant citation indices. Our method works by applying a series of stringent name and content filters to the raw publication search results returned by an online publication search engine. In this paper, our method is run using Google Scholar, but the underlying filters can be easily applied to any existing publication search engine. When compared against a manually constructed data set of individuals and their publication-citation records, our method provides significant improvements over raw search results. The estimated publication-citation records returned by our method have an average sensitivity of 98% and specificity of 72% (in contrast to raw search result specificity of less than 10%). When citation indices are computed using these records, the estimated indices are within of the true value 10%, compared to raw search results which have overestimates of, on average, 75%. CONCLUSIONS: These results confirm that our method provides significantly improved estimates over raw search results, and these can either be used directly for large-scale (departmental or university) analysis or further refined manually to quickly give accurate publication-citation records.

Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods. Several researchers have observed that the connectivity of a network alone can provide significant insights into its dynamics. Motivated by this fundamental observation, we present the signaling Petri net, a non-parametric model of cellular signaling networks, and the signaling Petri net-based simulator, a Petri net execution strategy for characterizing the dynamics of signal flow through a signaling network using token distribution and sampling. The result is a very fast method, which can analyze large-scale networks, and provide insights into the trends of molecules' activity-levels in response to an external stimulus, based solely on the network's connectivity. We have implemented the signaling Petri net-based simulator in the PathwayOracle toolkit, which is publicly available at http://bioinfo.cs.rice.edu/pathwayoracle. Using this method, we studied a MAPK1,2 and AKT signaling network downstream from EGFR in two breast tumor cell lines. We analyzed, both experimentally and computationally, the activity level of several molecules in response to a targeted manipulation of TSC2 and mTOR-Raptor. The results from our method agreed with experimental results in greater than 90% of the cases considered, and in those where they did not agree, our approach provided valuable insights into discrepancies between known network connectivities and experimental observations.