The Experts below are selected from a list of 312 Experts worldwide ranked by ideXlab platform

Hiroyuki Ohshima - One of the best experts on this subject based on the ideXlab platform.

Nidhi Mathur - One of the best experts on this subject based on the ideXlab platform.

Sara C Madeira - One of the best experts on this subject based on the ideXlab platform.

  • a polynomial time biclustering algorithm for finding Approximate Expression patterns in gene Expression time series
    Algorithms for Molecular Biology, 2009
    Co-Authors: Sara C Madeira, Arlindo L Oliveira
    Abstract:

    The ability to monitor the change in Expression patterns over time, and to observe the emergence of coherent temporal responses using gene Expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local Expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series Expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters. In this work, we propose e-CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with Approximate Expression patterns in time polynomial in the size of the time series gene Expression matrix. This polynomial time complexity is achieved by manipulating a discretized version of the original matrix using efficient string processing techniques. We also propose extensions to deal with missing values, discover anticorrelated and scaled Expression patterns, and different ways to compute the errors allowed in the Expression patterns. We propose a scoring criterion combining the statistical significance of Expression patterns with a similarity measure between overlapping biclusters. We present results in real data showing the effectiveness of e-CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic Expression patterns occurring in Saccharomyces cerevisiae in response to heat stress. In particular, the results show the advantage of considering Approximate patterns when compared to state of the art methods that require exact matching of gene Expression time series. The identification of co-regulated genes, involved in specific biological processes, remains one of the main avenues open to researchers studying gene regulatory networks. The ability of the proposed methodology to efficiently identify sets of genes with similar Expression patterns is shown to be instrumental in the discovery of relevant biological phenomena, leading to more convincing evidence of specific regulatory mechanisms. A prototype implementation of the algorithm coded in Java together with the dataset and examples used in the paper is available in http://kdbio.inesc-id.pt/software/e-ccc-biclustering .

  • a polynomial time biclustering algorithm for finding Approximate Expression patterns in gene Expression time series
    Algorithms for Molecular Biology, 2009
    Co-Authors: Sara C Madeira, Arlindo L Oliveira
    Abstract:

    Background The ability to monitor the change in Expression patterns over time, and to observe the emergence of coherent temporal responses using gene Expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local Expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series Expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters.

Noguchi Yasutaka - One of the best experts on this subject based on the ideXlab platform.

  • method of estimating temperature of rotor of eddy current system speed reducer and brake controller and eddy current system speed reducer
    2004
    Co-Authors: Yamaguchi Hiroyuki, Tasaka Masahira, Noguchi Yasutaka
    Abstract:

    PROBLEM TO BE SOLVED: To estimate the temperature of a rotor with accuracy by detecting the actually-measured temperature of an eddy current system of speed reducer or its vicinity thereby computing the initial temperature of the rotor, and further, using an Approximate Expression. SOLUTION: This is a method of estimating the temperature of the rotor of the eddy current system speed reducer, which switches off the braking just before the rotor reaches the tolerable upper limit value. The actually measured temperature of the eddy current system speed reducer at switching or its vicinity is detected. The initial temperature of the rotor at brake ON switching is computed based on the correlative relation between this actually measured temperature and the rotor temperature. The rate of change of the initial temperature and the first temperature change rate Approximate Expression are decided from this rotor's initial temperature, and the estimated temperature of the rotor from the time of brake ON switching to the time of switching off the braking is computed, using the above rotor initial temperature, the first temperature change rate Approximate Expression, and the second temperature change rate Approximate Expression decided beforehand. This way, the rotor temperature can be estimated with accuracy by appropriately correcting the rate of temperature change, considering the influence of the temperature at brake switching or the influence of the number of revolutions. COPYRIGHT: (C)2004,JPO

  • method of estimating temperature of rotor of eddy current system speed reducer and brake controller and eddy current system speed reducer
    2004
    Co-Authors: Yamaguchi Hiroyuki, Tasaka Masahira, Noguchi Yasutaka
    Abstract:

    PROBLEM TO BE SOLVED: To estimate the temperature of a rotor with accuracy by detecting the actually-measured temperature of an eddy current system of speed reducer or its vicinity thereby computing the initial temperature of the rotor, and further, using an Approximate Expression. SOLUTION: This is a method of estimating the temperature of the rotor of the eddy current system speed reducer, which switches off the braking just before the rotor reaches the tolerable upper limit value. The actually measured temperature of the eddy current system speed reducer at switching or its vicinity is detected. The initial temperature of the rotor at brake ON switching is computed based on the correlative relation between this actually measured temperature and the rotor temperature. The rate of change of the initial temperature and the first temperature change rate Approximate Expression are decided from this rotor's initial temperature, and the estimated temperature of the rotor from the time of brake ON switching to the time of switching off the braking is computed, using the above rotor initial temperature, the first temperature change rate Approximate Expression, and the second temperature change rate Approximate Expression decided beforehand. This way, the rotor temperature can be estimated with accuracy by appropriately correcting the rate of temperature change, considering the influence of the temperature at brake switching or the influence of the number of revolutions. COPYRIGHT: (C)2004,JPO

Ergun Simsek - One of the best experts on this subject based on the ideXlab platform.

  • A closed-form Approximate Expression for the optical conductivity of graphene.
    Optics letters, 2013
    Co-Authors: Ergun Simsek
    Abstract:

    A closed-form Approximate Expression for the optical conductivity of graphene is developed, which generates results with less than 0.8% maximum absolute error for λ>250  nm. The Expression takes wavelength, temperature, chemical potential, and hopping parameter into account and provides a fast, easy, and reliable alternative to well-known methods that include singular integrals. Numerical results confirm that the effective complex electrical permittivity derived from the optical conductivity successfully represents this one atom thick material in three-dimensional electromagnetic simulations and analyses.