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1. Amato F, Bansal M, Cosentino C, Curatola W, Di Bernardo D Identification of genetic networks by a quadratic systems approach Meeting: BITS 2005 - Year: 2005 Full text in a new tab Topic: Comparative and functional genomics Abstract: The aim of the present work is to identify a connection network describing the expression profiles of the genes involved in the cellular cycle of the yeast. In order to derive such connections from the microarray data, a mathematical model is needed, whose states represent the expression levels of the genes. However, since the cellular dynamics exhibit a limit cycle behavior [1] (i.e. roughly speaking, a periodic response, which is robust to small perturbations), it is not possible to describe the whole phenomenon by means of only linear models. Therefore, we investigate the suitability of quadratic systems [2], for the description of the genetic network dynamics. A quadratic system is made up of a set of first order differential equations, with linear terms plus quadratic terms (i.e. multiplications between two state variables or between a state and an input variable). |
2. Finocchiaro G, Mancuso FM, Muller H Mining published lists of cancer related microarray experiments: Identification of a gene signature having a critical role in cell-cycle control Meeting: BITS 2005 - Year: 2005 Full text in a new tab Topic: Comparative and functional genomics Abstract: The increasing availability and maturity of DNA microarray technology has led to an explosion of cancer related studies. In order to evaluate, integrate, and cross-validate the accumulating amount of publicly available microarray data, new methods are needed. Statistical methods have been applied to raw microarray data to identify intersections of multiple gene expression signatures from a diverse collection of data sets. However, this analysis is very stringent and time consuming. Here we propose a fast method to detect common patterns in gene expression data by mining published lists of microarray experiments |
3. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJM, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans Meeting: BITS 2005 - Year: 2005 Full text in a new tab Topic: Comparative and functional genomics Abstract: Cryptococcus neoformans is an opportunistic human pathogen of global importance. The two strains of C. neoformans serotype D JEC21 and B-3501A are highly related but markedly different in their pathogenicity. We report their genome sequences as an important step in the elucidation of the molecular basis for Cryptococcus virulence and for its difference with other fungal pathogens. |