School of Mathematics and Statistics - Research Publications

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    Bioconductor: open software development for computational biology and bioinformatics
    Gentleman, RC ; Carey, VJ ; Bates, DM ; Bolstad, B ; Dettling, M ; Dudoit, S ; Ellis, B ; Gautier, L ; Ge, YC ; Gentry, J ; Hornik, K ; Hothorn, T ; Huber, W ; Iacus, S ; Irizarry, R ; Leisch, F ; Li, C ; Maechler, M ; Rossini, AJ ; Sawitzki, G ; Smith, C ; Smyth, G ; Tierney, L ; Yang, JYH ; Zhang, JH (BMC, 2004)
    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.
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    A new rodent model to assess blood stage immunity to the Plasmodium falciparum antigen merozoite surface protein 119 reveals a protective role for invasion inhibitory antibodies
    de Koning-Ward, TF ; O'Donnell, RA ; Drew, DR ; Thomson, R ; Speed, TP ; Crabb, BS (ROCKEFELLER UNIV PRESS, 2003-09-15)
    Antibodies capable of inhibiting the invasion of Plasmodium merozoites into erythrocytes are present in individuals that are clinically immune to the malaria parasite. Those targeting the 19-kD COOH-terminal domain of the major merozoite surface protein (MSP)-119 are a major component of this inhibitory activity. However, it has been difficult to assess the overall relevance of such antibodies to antiparasite immunity. Here we use an allelic replacement approach to generate a rodent malaria parasite (Plasmodium berghei) that expresses a human malaria (Plasmodium falciparum) form of MSP-119. We show that mice made semi-immune to this parasite line generate high levels of merozoite inhibitory antibodies that are specific for P. falciparum MSP-119. Importantly, protection from homologous blood stage challenge in these mice correlated with levels of P. falciparum MSP-119-specific inhibitory antibodies, but not with titres of total MSP-119-specific immunoglobulins. We conclude that merozoite inhibitory antibodies generated in response to infection can play a significant role in suppressing parasitemia in vivo. This study provides a strong impetus for the development of blood stage vaccines designed to generate invasion inhibitory antibodies and offers a new animal model to trial P. falciparum MSP-119 vaccines.
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    Asymmetrically gauged WZNW models
    Quella, T ; Schomerus, V (WILEY-V C H VERLAG GMBH, 2003)
    Abstract Many interesting exactly solvable backgrounds can be obtained by gauging WZNW models asymmetrically. These include the base of the conifold and the time dependent Nappi‐Witten background in which a 3‐dimensional universe passes through a series of big‐bang big‐crunch singularities. In this short note we review recent results on the conformal field theory description of asymmetric cosets. In particular, we present formulas for their bulk modular invariant partition functions and for a large number of D‐brane boundary states.
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    An algorithm for twisted fusion rules
    Quella, T ; Runkel, I ; Schweigert, C (International Press of Boston, 2002-01-01)
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    Branching rules of semi-simple Lie algebras using affine extensions
    Quella, T (IOP PUBLISHING LTD, 2002-04-26)
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    Asymmetric cosets
    Quella, T ; Schomerus, V (SPRINGER, 2003-02)
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    Non-commutative gauge theory of twisted D-branes
    Alekseev, AY ; Fredenhagen, S ; Quella, T ; Schomerus, V (ELSEVIER SCIENCE BV, 2002-12-09)
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    Symmetry breaking boundary states and defect lines
    Quella, T ; Schomerus, V (SPRINGER, 2002-06)