Current Issue : January - March Volume : 2013 Issue Number : 1 Articles : 6 Articles
Background. Recent advances in computational and biological methods in last two decades have remarkably changed the scale\r\nof biomedical research and with it began the unprecedented growth in both the production of biomedical data and amount of\r\npublished literature discussing it. An automated extraction system coupled with a cognitive search and navigation service over\r\nthese document collections would not only save time and effort, but also pave the way to discover hitherto unknown information\r\nimplicitly conveyed in the texts. Results. We developed a novel framework (named ââ?¬Å?BioEveââ?¬Â) that seamlessly integrates Faceted\r\nSearch (Information Retrieval) with Information Extraction module to provide an interactive search experience for the researchers\r\nin life sciences. It enables guided step-by-step search query refinement, by suggesting concepts and entities (like genes, drugs, and\r\ndiseases) to quickly filter and modify search direction, and thereby facilitating an enriched paradigm where user can discover\r\nrelated concepts and keywords to search while information seeking. Conclusions. The BioEve Search framework makes it easier\r\nto enable scalable interactive search over large collection of textual articles and to discover knowledge hidden in thousands of\r\nbiomedical literature articles with ease....
The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for\r\nannotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available\r\nfor comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences,\r\nand multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO that offers\r\ntools for evaluating such software tools on real and synthetic datasets....
Technological advancements in the field of genetics have led not only to an abundance of experimental data, but also caused an\r\nexponential increase of the number of published biomolecular studies. Text mining is widely accepted as a promising technique\r\nto help researchers in the life sciences deal with the amount of available literature. This paper presents a freely available web\r\napplication built on top of 21.3 million detailed biomolecular events extracted from all PubMed abstracts. These text mining\r\nresults were generated by a state-of-the-art event extraction system and enriched with gene family associations and abstract\r\ngeneralizations, accounting for lexical variants and synonymy. The EVEX resource locates relevant literature on phosphorylation,\r\nregulation targets, binding partners, and several other biomolecular events and assigns confidence values to these events. The\r\nsearch function accepts official gene/protein symbols as well as common names from all species. Finally, the web application is a\r\npowerful tool for generating homology-based hypotheses as well as novel, indirect associations between genes and proteins such\r\nas coregulators....
The world has widely changed in terms of communicating, acquiring, and storing information. Hundreds of millions of people\r\nare involved in information retrieval tasks on a daily basis, in particular while using a Web search engine or searching their\r\ne-mail, making such field the dominant form of information access, overtaking traditional database-style searching. How to\r\nhandle this huge amount of information has now become a challenging issue. In this paper, after recalling the main topics\r\nconcerning information retrieval, we present a survey on the main works on literature retrieval and mining in bioinformatics.\r\nWhile claiming that information retrieval approaches are useful in bioinformatics tasks, we discuss some challenges aimed at\r\nshowing the effectiveness of these approaches applied therein....
Stimulation of human epithelial cells with IL-1 (10 ng/ml) + UVB radiation results in sustained NFB activation\r\ncaused by continuous IKKb phosphorylation. We have recently published a strictly reduced ordinary differential\r\nequation model elucidating the involved mechanisms. Here, we compare model extensions for low IL-1 doses (0.5\r\nng/ml), where delayed IKKb phosphorylation is observed. The extended model including a positive regulatory\r\nelement, most likely auto-ubiquitination of TRAF6, reproduces the observed experimental data most convincingly.\r\nThe extension is shown to be consistent with the original model and contains very sensitive processes which may\r\nserve as potential intervention targets....
Elucidating the structure and/or dynamics of gene regulatory networks from experimental data is a major goal of\r\nsystems biology. Stochastic models have the potential to absorb noise, account for un-certainty, and help avoid\r\ndata overfitting. Within the frame work of probabilistic polynomial dynamical systems, we present an algorithm for\r\nthe reverse engineering of any gene regulatory network as a discrete, probabilistic polynomial dynamical system.\r\nThe resulting stochastic model is assembled from all minimal models in the model space and the probability\r\nassignment is based on partitioning the model space according to the likeliness with which a minimal model\r\nexplains the observed data. We used this method to identify stochastic models for two published synthetic\r\nnetwork models. In both cases, the generated model retains the key features of the original model and compares\r\nfavorably to the resulting models from other algorithms....
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